bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen sorption by the bundles of single-wall carbon nanotubes, irradiated in various gas media
Authors: Dolbin A. V. , Esel'son V. B. , Gavrilko V. G. , Manzhelii V. G. , Vinnikov N. A. , Yaskovets I. I. , Uvarova I. Yu. , Tripachko N. A. , Danilchenko B. A.
Published: August 2013

The effect of radioactive irradiation on H2 sorption by bundles of single-wall carbon nanotubes (SWNTs) has been investigated in various gas media. The samples were irradiated with γ-quanta (1.2 MeV) of 60Co ((1.5–1.7) × 107 rad) radiation at room temperature in deuterium, nitrogen, and oxygen atmosphere (P = 1 atm), and in a vacuum. The processes of H2 sorption and desorption in the SWNT bundles were investigated before and after irradiation in the temperature interval 12–1270 K. It is found that irradiation in a gas environment has a significant effect both on the low-temperature H2 sorption induced by the weak physical interaction, and the chemical H2 sorption by the SWNT bundles. A phenomenological model has been proposed to explain the defect generation in carbon nanotubes irradiated in gas media.
On multiple manifestations of the second response branch in streamwise vortex-induced vibrations
Authors: Cagney N. , Balabani S.
Published: August 2013

The structural motion and velocity field in the wake of a cylinder exhibiting vortex-induced vibration (VIV) in the streamwise direction were measured using Particle-Image Velocimetry. The effect of hysteresis on the amplitude response of the cylinder and the existence of multiple wake modes in the region of the second response branch were examined. As the reduced velocity was decreased, there was a reduction in the lock-in range; outside this range the amplitude response was found to be negligible and the A-II mode (which is similar to the von Kármán vortex street) was observed in the wake. When the reduced velocity was increased the second branch could be manifested in two forms, depending on whether the wake exhibited the SA or the A-IV mode (in which two and four vortices are shed per wake cycle, respectively). The A-IV mode has been observed in studies in which a cylinder was forced to oscillate in the streamwise direction; however, this represents the first time that it has been recorded in the wake of a freely oscillating body, and it was not previously known that the A-IV mode was capable of exciting self-sustaining vibrations. Both the SA and A-IV modes were stable and no intermittent mode-switching was observed; however, it was found to be unpredictable which mode would dominate as the reduced velocity was varied and the cylinder entered the second response branch. Analysis of the cylinder displacement signals measured while each mode was dominant indicated that the SA mode excited larger amplitude vibrations than the A-IV mode. A reduced velocity near the second response branch was identified at which the wake could exhibit either the SA, A-IV, or A-II modes, with the latter occurring as the reduced velocity was decreased. Although bi-modal behaviour is well established in VIV studies, as far as the authors are aware, this represents the first time that a point has been observed in the response regime of a freely oscillating structure in which three stable states have been observed, each corresponding to a different wake mode and vibration amplitude, for the same structural parameters, reduced velocity, and Reynolds number. This suggests that the mechanism determining which wake mode dominates and the fluid-structure interaction in the case of streamwise VIV may be more complex than has previously been thought. Finally, the vortex-formation and shedding processes associated with the A-II, SA, and A-IV modes were described using phase-averaged vorticity fields, and the differences between the SA and A-IV modes were discussed.
Ge0.97Sn0.03 p-channel metal-oxide-semiconductor field-effect transistors: Impact of Si surface passivation layer thickness and post metal annealing
Authors: Guo Pengfei , Han Genquan , Gong Xiao , Liu Bin , Yang Yue , Wang Wei , Zhou Qian , Pan Jisheng , Zhang Zheng , Soon Tok Eng , Yeo Yee-Chia
Published: August 2013

A low-temperature (∼370 °C) Si2H6 treatment was used to form an ultrathin Si layer on a Ge0.97Sn0.03 channel layer on Ge substrate in the fabrication of Ge0.97Sn0.03 channel pMOSFETs. The impact of the Si passivation layer thickness on the electrical characteristics of Ge0.97Sn0.03 pMOSFETs was investigated. By increasing the thickness of Si passivation layer from 4 to 7 monolayers (ML), the effective hole mobility μeff at an inversion carrier density Ninv of 1 × 1013 cm−2 was improved by ∼19% ± 4%. This is attributed to reduced carrier scattering by charges found at the interface between the Si layer and the gate dielectric. In addition, the effects of post metal annealing (PMA) were investigated. It was observed that the mid-gap interface trap density Dit was reduced in devices with PMA. Ge0.97Sn0.03 pMOSFETs with PMA have improved intrinsic transconductance Gm,int, subthreshold swing S, and μeff as compared to the control devices without PMA.
Dendritic brushes under theta and poor solvent conditions
Authors: Gergidis Leonidas N. , Kalogirou Andreas , Charalambopoulos Antonios , Vlahos Costas
Published: August 2013

The effects of solvent quality on the internal stratification of polymer brushes formed by dendron polymers up to third generation were studied by means of molecular dynamics simulations with Langevin thermostat. The distributions of polymer units, of the free ends, the radii of gyration, and the back folding probabilities of the dendritic spacers were studied at the macroscopic states of theta and poor solvent. For high grafting densities we observed a small decrease in the height of the brush as the solvent quality decreases. The internal stratification in theta solvent was similar to the one we found in good solvent, with two and in some cases three kinds of populations containing short dendrons with weakly extended spacers, intermediate-height dendrons, and tall dendrons with highly stretched spacers. The differences increase as the grafting density decreases and single dendron populations were evident in theta and poor solvent. In poor solvent at low grafting densities, solvent micelles, polymeric pinned lamellae, spherical and single chain collapsed micelles were observed. The scaling dependence of the height of the dendritic brush at high density brushes for both solvents was found to be in agreement with existing analytical results.
Band gap energies of solar micro/meso-porous composites of zinc (hydr)oxide with graphite oxides
Authors: Islam SM Z. , Gayen Taposh , Seredych Mykola , Mabayoje Oluwaniyi , Shi Lingyan , Bandosz Teresa J. , Alfano Robert R.
Published: August 2013

The band gap energies of micro/meso-porous zinc (hydr)oxide and its composites with 2 wt. % and 5 wt. % graphite oxides are reported using three optical characterization techniques. The obtained energy gaps (from 2.84 eV to 2.95 eV) of the composites are smaller than that for zinc oxide (∼3.2 eV) and zinc (hydr)oxide (∼3.06 eV). The band gap narrowing of the composite materials is due to the presence of defects, larger particle size, and weaker confinement. The bonds between zinc (hydr)oxide lattice and the carbon of graphene phase also contribute to this phenomenon. The structural properties of these materials are presented using Transmission Electron Microscopy, Scanning Tunneling Electron Microscopy, X-Ray analysis, and Two-Photon Fluorescence imaging Microscopy.
Influence of a MoOx interlayer on the open-circuit voltage in organic photovoltaic cells
Authors: Zou Yunlong , Holmes Russell J.
Published: August 2013

Metal-oxides have been used as interlayers at the anode-organic interface in organic photovoltaic cells (OPVs) to increase the open-circuit voltage (VOC). We examine the role of MoOx in determining the maximum VOC in a planar heterojunction OPV and find that the interlayer strongly affects the temperature dependence of VOC. Boron subphthalocyanine chloride (SubPc)-C60 OPVs that contain no interlayer show a maximum VOC of 1.2 V at low temperature, while those with MoOx show no saturation, reaching VOC > 1.4 V. We propose that the MoOx-SubPc interface forms a Schottky junction that provides an additional contribution to VOC at low temperature.
Acoustic band gaps of three-dimensional periodic polymer cellular solids with cubic symmetry
Authors: Chen Yanyu , Yao Haimin , Wang Lifeng
Published: August 2013

The band structure and sound attenuation of the triply periodic co-continuous composite materials with simple cubic lattice, body-centered cubic lattice, and face-centered cubic lattice consisting of PMMA and air are investigated using finite element method. Complete band gaps are found in these structures and the width of band gaps is depending on volume fraction. It is shown that the width of band gaps along different directions in the first irreducible Brillouin zone enlarges as the volume fraction increases from 0.2 to 0.7. The largest complete band gap widths of the three types of co-continuous structures are 0.29, 0.54, and 0.55, respectively. As the complete band gaps appear in audible range of frequencies, these triply periodic co-continuous composite materials can be utilized to control noise.
A symplectic geometry-based method for nonlinear time series decomposition and prediction
Authors: Xie Hong-Bo , Dokos Socrates
Published: August 2013

We present a technique to decompose a time series into the sum of a small number of independent and interpretable components based on symplectic geometry theory. The proposed symplectic geometry spectrum analysis technique consists of embedding, symplectic QR decomposition of the matrix into an orthogonal matrix and a triangular matrix, grouping, and diagonal averaging steps. As an example application, the noisy Lorenz series demonstrate the effectiveness of this technique in nonlinear prediction.
High sensitivity gravimetric sensor made of carbon fiber epoxy composite on Pb(Mg1/3Nb2/3)O3-PbTiO3 single crystal substrate
Authors: Huang Naixing , Lü Tianquan , Zhang Rui , Cao Wenwu
Published: August 2013

We have derived a general formula for sensitivity optimization of gravimetric sensors and use it to design a high sensitivity gravimetric sensor using unidirectional carbon fiber epoxy composite (CFEC) guiding layer on (1-x)Pb(Mg1/3Nb2/3)O3-xPbTiO3 (PMN-xPT) single crystal substrate. The normalized maximum sensitivity (|Smf|λ)max exhibits an increasing tendency with the decrease of (h/λ)opt. For the CFEC/[011]c poled PMN-0.29PT sensor configuration with λ = 24 μm, the maximum sensitivity |Smf|max can reach as high as 1230 cm2/g, which is about 3 times that of a traditional SiO2/ST quartz configuration gravimetric sensor.
Full-field convection flow visualization in pendant droplets by tilt-angle imaging
Authors: He Bin , Duan Fei
Published: August 2013

The flow field in a droplet can be distorted as the light passes through a convex liquid-vapor interface in the measurement of Particle Image Velocimetry. We have developed a solution from ray tracing to recover the distortion flow in the droplet. A three-dimensional surface model has been applied to a self developed ray tracer to recover the distorted images. By tilting the camera upwards between 10° and 20° in angle, about 95% of the full internal flow vectors of a pendant droplet, especially near the interface, can be recovered to the real positions for further analysis.
Nb2O5 nanofiber memristor
Authors: Grishin A. M. , Velichko A. A. , Jalalian A.
Published: August 2013

Non-woven bead-free 100 μm long and 80–200 nm in diameter highly crystalline orthorhombic T-Nb2O5 nanofibers were sintered by sol-gel assisted electrospinning technique. Electrical and dielectric spectroscopy tests of individual fibers clamped onto Pt coated Si substrate were performed using a spreading resistance mode of atomic force microscope. Reproducible resistive switching with ON-OFF resistance ratio as high as 2 × 104 has a bipolar character, starts with a threshold voltage of 0.8–1.7 V, and follows by continuous growth of conductivity. Resistive memory effect is associated with a voltage-driven accumulation/depletion of oxygen vacancies at Nb2O5/Pt cathode interface. Poole-Frenkel emission from the electronic states trapped at reduced NbOx complexes determines a shape of Nb2O5/Pt diode I-V characteristics. Simple thermodynamic model explains a threshold character of switching, relates experimentally observed characteristics in low and high resistive states, and gives a reasonable estimate of the concentration of oxygen vacancies.
BiFeO3 nanodots prepared via dip-pen lithography on Nb-doped SrTiO3 and highly ordered pyrolytic graphite substrates
Authors: Kim Woo-Hee , Yeog Son Jong
Published: August 2013

Ferroelectric BiFeO3 (BFO) nanodots were prepared on two substrate types, a Nb-doped SrTiO3 (Nb:STO) and a highly ordered pyrolytic graphite (HOPG), using elaborately controllable dip-pen nanolithography (DPN) technology. The lateral dimension and thickness of the formed BFO nanodots exhibited the substrate dependency, resulting in higher aspect ratio with smaller lateral dimension and higher thickness on the hydrophobic HOPG substrate than that of the Nb:STO substrate. Based on piezoelectric force microscope (PFM) measurements, superior ferroelectricity in d33 hysteresis loop of the BFO nanodots on the HOPG was demonstrated by significant reduction in the substrate clamping effect, compared to that on the Nb:STO.
Evidence for adsorbate-enhanced field emission from carbon nanotube fibers
Authors: Murray P. T. , Back T. C. , Cahay M. M. , Fairchild S. B. , Maruyama B. , Lockwood N. P. , Pasquali M.
Published: August 2013

We used residual gas analysis (RGA) to identify the species desorbed during field emission (FE) from a carbon nanotube (CNT) fiber. The RGA data show a sharp threshold for H2 desorption at an external field strength that coincides with a breakpoint in the FE data. A comprehensive model for the gradual transition of FE from adsorbate-enhanced CNTs at low bias to FE from CNTs with reduced H2 adsorbate coverage at high bias is developed which accounts for the gradual desorption of the H2 adsorbates, alignment of the CNTs at the fiber tip, and importance of self-heating effects with applied bias.
Optical spectroscopy goes subnanometer
Authors: Wilson R. Mark
Published: August 2013

A scanning probe technique simultaneously maps the topographic structure and vibrational spectra inside a single molecule.
Obama climate plan will hit coal hard
Authors: Kramer David
Published: August 2013

New loan guarantees for spurring development of technologies to control carbon emissions are not likely to help utilities cut their CO2 output in the short term.
Things your adviser never told you: Entrepreneurship’s role in physics education
Authors: Arion Douglas N.
Published: August 2013

Programs that augment the core physics curriculum with real-world business skills could hold the key to the discipline’s future growth.
Which Policy First? A Network-Centric Approach for the Analysis and Ranking of Policy Measures
Authors: Taeihagh Araz , Givoni Moshe , Bañares-Alcántara René
Published: August 2013

In addressing various policy problems, deciding which policy measure to start with given the range of measures available is challenging and essentially involves a process of ranking the alternatives, commonly done using multicriteria decision analysis (MCDA) techniques. In this paper a new methodology for analysis and ranking of policy measures is introduced which combines network analysis and MCDA tools. This methodology not only considers the internal properties of the measures but also their interactions with other potential measures. Consideration of such interactions provides additional insights into the process of policy formulation and can help domain experts and policy makers to better assess the policy measures and to understand the complexities involved. This new methodology is applied in this paper to the formulation of a policy to increase walking and cycling.
The Travel—Obesity Connection: Discerning the Impacts of Commuting Trips with the Perspective of Individual Energy Expenditure and Time Use
Authors: Yang Jiawen , French Steven
Published: August 2013

It has been widely reported that individual travel has significant implications for obesity. In this research we try to clarify the connection between travel and obesity from an individual energy-expenditure perspective. It is hypothesized here that individual travel affects the likelihood of becoming obese not only directly through a reliance on automobile-based travel that requires low amounts of individual energy expenditure, but also indirectly through the fatigue and stress stemming from driving, which reduces time available for physical activities and exercise. We use the American Time Use Survey ( http://www.bls.gov/tus/ ) for 2003–08 and its Eating and Health Module for 2006 and 2007 to examine individual travel, energy expenditure, and obesity. Empirical analysis illustrates how individual body mass index (BMI) and individual travel are correlated and how this correlation can be explained from the perspective of individual energy expenditure. In addition, a distinction is drawn between commuting and noncommuting trips: Commuting trips have a relatively larger impact on individual BMI. Analysis results point to a potential to reduce obesity rates through planning efforts at the regional level.
Chemical screening identifies filastatin, a small molecule inhibitor of
Candida albicans
adhesion, morphogenesis, and pathogenesis
Authors: Fazly Ahmed , Jain Charu , Dehner Amie C. , Issi Luca , Lilly Elizabeth A. , Ali Akbar , Cao Hong , Fidel Paul L. , P. Rao Reeta , Kaufman Paul D.
Published: August 2013

Infection by pathogenic fungi, such as
Candida albicans
, begins with adhesion to host cells or implanted medical devices followed by biofilm formation. By high-throughput phenotypic screening of small molecules, we identified compounds that inhibit adhesion of
C. albicans
to polystyrene. Our lead candidate compound also inhibits binding of
C. albicans
to cultured human epithelial cells, the yeast-to-hyphal morphological transition, induction of the hyphal-specific
HWP1
promoter, biofilm formation on silicone elastomers, and pathogenesis in a nematode infection model as well as alters fungal morphology in a mouse mucosal infection assay. We term this compound filastatin based on its strong inhibition of filamentation, and we use chemical genetic experiments to show that it acts downstream of multiple signaling pathways. These studies show that high-throughput functional assays targeting fungal adhesion can provide chemical probes for study of multiple aspects of fungal pathogenesis.
Catalytic domain of plasmid pAD1 relaxase TraX defines a group of relaxases related to restriction endonucleases
Authors: Francia María Victoria , Clewell Don B. , de la Cruz Fernando , Moncalián Gabriel
Published: August 2013

Plasmid pAD1 is a 60-kb conjugative element commonly found in clinical isolates of
Enterococcus faecalis.
The relaxase TraX and the primary origin of transfer
oriT2
are located close to each other and have been shown to be essential for conjugation. The
oriT2
site contains a large inverted repeat (where the
nic
site is located) adjacent to a series of short direct repeats. TraX does not show any of the typical relaxase sequence motifs but is the prototype of a unique family of relaxases (MOB
C
). The present study focuses on the genetic, biochemical, and structural analysis of TraX, whose 3D structure could be predicted by protein threading. The structure consists of two domains: (
i
) an N-terminal domain sharing the topology of the DNA binding domain of the MarR family of transcriptional regulators and (
ii
) a C-terminal catalytic domain related to the PD-(D/E)XK family of restriction endonucleases. Alignment of MOB
C
relaxase amino acid sequences pointed to several conserved polar amino acid residues (E28, D152, E170, E172, K176, R180, Y181, and Y203) that were mutated to alanine. Functional analysis of these mutants (in vivo DNA transfer and cleavage assays) revealed the importance of these residues for relaxase activity and suggests Y181 as a potential catalytic residue similarly to His-hydrophobe-His relaxases. We also show that TraX binds specifically to dsDNA containing the
oriT2
direct repeat sequences, confirming their role in transfer specificity. The results provide insights into the catalytic mechanism of MOB
C
relaxases, which differs radically from that of His-hydrophobe-His relaxases.
PRMT5 dimethylates R30 of the p65 subunit to activate NF-κB
Authors: Wei Han , Wang Benlian , Miyagi Masaru , She Yun , Gopalan Banu , Huang De-Bin , Ghosh Gourisankar , Stark George R. , Lu Tao
Published: August 2013

The ubiquitous inducible transcription factor NF-κB plays central roles in immune and inflammatory responses and in tumorigenesis. Complex posttranslational modifications of the p65 subunit (RelA) are a major aspect of the extremely flexible regulation of NF-κB activity. Although phosphorylation, acetylation, ubiquitination, and lysine methylation of NF-κB have been well described, arginine methylation has not yet been found. We now report that, in response to IL-1β, the p65 subunit of NF-κB is dimethylated on arginine 30 (R30) by protein-arginine methyltransferase 5 (PRMT5). Expression of the R30A and R30K mutants of p65 substantially decreased the ability of NF-κB to bind to κB elements and to drive gene expression. A model in which dimethyl R30 is placed into the crystal structure of p65 predicts new van der Waals contacts that stabilize intraprotein interactions and indirectly increase the affinity of p65 for DNA. PRMT5 was the only arginine methyltransferase that coprecipitated with p65, and its overexpression increased NF-κB activity, whereas PRMT5 knockdown had the opposite effect. Microarray analysis revealed that ∼85% of the NF-κB–inducible genes that are down-regulated by the R30A mutation are similarly down-regulated by knocking PRMT5 down. Many cytokine and chemokine genes are among these, and conditioned media from cells expressing the R30A mutant of p65 had much less NF-κB–inducing activity than media from cells expressing the wild-type protein. PRMT5 is overexpressed in many types of cancer, often to a striking degree, indicating that high levels of this enzyme may promote tumorigenesis, at least in part by facilitating NF-κB-induced gene expression.
Electronic excitations and metallization of dense solid hydrogen
Authors: Cohen R. E. , Naumov Ivan I. , Hemley Russell J.
Published: August 2013

Theoretical calculations and an assessment of recent experimental results for dense solid hydrogen lead to a unique scenario for the metallization of hydrogen under pressure. The existence of layered structures based on graphene sheets gives rise to an electronic structure related to unique features found in graphene that are well studied in the carbon phase. The honeycombed layered structure for hydrogen at high density, first predicted in molecular calculations, produces a complex optical response. The metallization of hydrogen is very different from that originally proposed via a phase transition to a close-packed monoatomic structure, and different from simple metallization recently used to interpret recent experimental data. These different mechanisms for metallization have very different experimental signatures. We show that the shift of the main visible absorption edge does not constrain the point of band gap closure, in contrast with recent claims. This conclusion is confirmed by measured optical spectra, including spectra obtained to low photon energies in the infrared region for phases III and IV of hydrogen.
Insulin-dependent diabetes induced by pancreatic beta cell expression of IL-15 and IL-15Rα
Authors: Chen Jing , Feigenbaum Lionel , Awasthi Parirokh , Butcher Donna O. , Anver Miriam R. , Golubeva Yelena G. , Bamford Richard , Zhang Xiaojie , St. Claire Mark B. , Thomas Craig J. , Discepolo Valentina , Jabri Bana , Waldmann Thomas A.
Published: August 2013

Increased serum levels of IL-15 are reported in type 1 diabetes (T1D). Here we report elevated serum soluble IL-15Rα levels in human T1D. To investigate the role of IL-15/IL-15Rα in the pathogenesis of T1D, we generated double transgenic mice with pancreatic β-cell expression of IL-15 and IL-15Rα. The mice developed hyperglycemia, marked mononuclear cell infiltration, β-cell destruction, and anti-insulin autoantibodies that mimic early human T1D. The diabetes in this model was reversed by inhibiting IL-15 signaling with anti-IL2/IL15Rβ (anti-CD122), which blocks IL-15 transpresentation. Furthermore, the diabetes could be reversed by administration of the Janus kinase 2/3 inhibitor tofacitinib, which blocks IL-15 signaling. In an alternative diabetes model, nonobese diabetic mice, IL15/IL-15Rα expression was increased in islet cells in the prediabetic stage, and inhibition of IL-15 signaling with anti-CD122 at the prediabetic stage delayed diabetes development. In support of the view that these observations reflect the conditions in humans, we demonstrated pancreatic islet expression of both IL-15 and IL-15Rα in human T1D. Taken together our data suggest that disordered IL-15 and IL-15Rα may be involved in T1D pathogenesis and the IL-15/IL15Rα system and its signaling pathway may be rational therapeutic targets for early T1D.
Individual‐Based Modeling of Delta Smelt Population Dynamics in the Upper San Francisco Estuary: I. Model Description and Baseline Results
Authors: Rose Kenneth A. , Kimmerer Wim J. , Edwards Karen P. , Bennett William A.
Published: August 2013

Many factors have been implicated in the decline of Delta Smelt Hypomesus transpacificus in the upper San Francisco Estuary, and the importance of each factor is difficult to determine using field data alone. We describe a spatially explicit, individual‐based population model of Delta Smelt configured for the upper estuary. The model followed the reproduction, growth, mortality, and movement of individuals over their entire life cycle on the same spatial grid of cells as the Delta Simulation Model (DSM2) hydrodynamics model. Daily values of water temperature, salinity, and densities of six zooplankton prey types were represented on the spatial grid. Reproduction was evaluated daily, and new individuals were introduced into the model as yolk sac larvae. Growth of feeding individuals was based on bioenergetics and zooplankton densities. Mortality sources included natural mortality, starvation, and entrainment in water diversion facilities. Movement of larvae was determined using a particle tracking model, while movement of juveniles and adults was based on salinity. Simulations were performed for 1995–2005. The baseline simulation was generally consistent with the available data. Predicted daily fractions of larvae entrained and annual fractions of adults entrained were similar in magnitude to data‐based estimates but showed less interannual variation. Interannual differences in mean length at age 1 had large effects on maturity and subsequent egg production. Predicted and observed spatial distributions in the fall showed moderately good agreement for extremely low‐ and high‐outflow years. As indicated by the population growth rate, 1998 was the best year and 2001 was the worst year. Water year 1998 (i.e., October 1997–September 1998) was characterized by fast growth in fall 1997, low entrainment, and high stage‐specific survival rates, whereas water year 2001 had opposite conditions. Our analysis further shows how multiple factors can operate simultaneously to result in the decline in abundance of Delta Smelt.
Individual‐Based Modeling of Delta Smelt Population Dynamics in the Upper San Francisco Estuary: II. Alternative Baselines and Good versus Bad Years
Authors: Rose Kenneth A. , Kimmerer Wim J. , Edwards Karen P. , Bennett William A.
Published: August 2013

We used a previously described individual‐based population model to further explore the population dynamics of Delta Smelt Hypomesus transpacificus in the upper San Francisco Estuary. We formulated four alternative baseline configurations of the model and used a factorial design to systematically isolate the effects of factors that determined a good versus bad year. The alternative baseline conditions were obtained by substituting different assumptions about growth, maturity, and mortality into the original baseline configuration. In the simulation experiment, we varied five factors by setting each value to its 1998 (best year) or 2001 (worst year) value: salinity, temperature, zooplankton densities, hydrodynamics, and eggs per age‐1 individual at spawning. Although some of the alternative baselines resulted in lower January abundances, estimated finite population growth rates were very similar for all versions. The simulation experiment showed that juvenile growth in the winter prior to spawning (i.e., eggs per age‐1 individual) was the most important single factor in making 2001 a bad year, although no single factor alone was sufficient to fully account for the poor conditions in 2001 relative to 1998. Temperature played an important secondary role, and hydrodynamics played a more minor role. The results of the simulation experiment were robust, as similar results were obtained under the four alternative baselines. We compare our results with previous modeling and statistical analyses of the long‐term monitoring data; we also discuss some implications of our results for Delta Smelt management and suggest future directions for analyses.
Physical inactivity and muscle oxidative capacity in humans
Authors: Gram Martin , Dahl Rannvá , Dela Flemming
Published: August 2013

Physical inactivity is associated with a high prevalence of type 2 diabetes and is an independent predictor of mortality. It is possible that the detrimental effects of physical inactivity are mediated through a lack of adequate muscle oxidative capacity. This short review will cover the present literature on the effects of different models of inactivity on muscle oxidative capacity in humans. Effects of physical inactivity include decreased mitochondrial content, decreased activity of oxidative enzymes, changes in markers of oxidative stress and a decreased expression of genes and contents of proteins related to oxidative phosphorylation. With such a substantial down‐regulation, it is likely that a range of adenosine triphosphate (ATP)‐dependent pathways such as calcium signalling, respiratory capacity and apoptosis are affected by physical inactivity. However, this has not been investigated in humans, and further studies are required to substantiate this hypothesis, which could expand our knowledge of the potential link between lifestyle‐related diseases and muscle oxidative capacity. Furthermore, even though a large body of literature reports the effect of physical training on muscle oxidative capacity, the adaptations that occur with physical inactivity may not always be opposite to that of physical training. Thus, it is concluded that studies on the effect of physical inactivity per se on muscle oxidative capacity in functional human skeletal muscle are warranted.
Geometry and Markoff’s spectrum for ℚ(𝕚), I
Authors: Abe Ryuji , Aitchison Iain
Published: August 2013

We develop a study of the relationship between geometry of geodesics and Markoff’s spectrum for

Q

(
i
)

\mathbb {Q}(i)

. There exists a particular immersed totally geodesic twice punctured torus in the Borromean rings complement, which is a double cover of the once punctured torus having Fricke coordinates

(
2

2

,
2

2

,
4
)

(2\sqrt {2}, 2\sqrt {2}, 4)

. The set of the simple closed geodesics on this once punctured torus is decomposed into two subsets. The discrete part of Markoff’s spectrum for

Q

(
i
)

\mathbb {Q}(i)

(except for one) is given by the maximal Euclidean height of the lifts of the simple closed geodesics composing one of the subsets.
miR-29b represses intestinal mucosal growth by inhibiting translation of cyclin-dependent kinase 2
Authors: Xiao Lan , Rao Jaladanki N. , Zou Tongtong , Liu Lan , Cao Shan , Martindale Jennifer L. , Su Weijie , Chung Hee Kyoung , Gorospe Myriam , Wang Jian-Ying
Published: August 2013

The epithelium of the intestinal mucosa is a rapidly self-renewing tissue in the body, and defects in the renewal process occur commonly in various disorders. microRNAs (miRNAs) posttranscriptionally regulate gene expression and are implicated in many aspects of cellular physiology. Here we investigate the role of miRNA-29b (miR-29b) in the regulation of normal intestinal mucosal growth and further validate its target mRNAs. miRNA expression profiling studies reveal that growth inhibition of the small intestinal mucosa is associated with increased expression of numerous miRNAs, including miR-29b. The simple systemic delivery of locked nucleic acid–modified, anti–miR-29b-reduced endogenous miR-29b levels in the small intestinal mucosa increases cyclin-dependent kinase 2 (CDK2) expression and stimulates mucosal growth. In contrast, overexpression of the miR-29b precursor in intestinal epithelial cells represses CDK2 expression and results in growth arrest in G1 phase. miR-29b represses CDK2 translation through direct interaction with the cdk2 mRNA via its 3′-untranslated region (3′-UTR), whereas point mutation of miR-29b binding site in the cdk2 3′-UTR prevents miR-29b–induced repression of CDK2 translation. These results indicate that miR-29b inhibits intestinal mucosal growth by repressing CDK2 translation.
Graph-based peak alignment algorithms for multiple liquid chromatography-mass spectrometry datasets
Authors: Wang Jijie , Lam Henry
Published: August 2013

Liquid chromatography coupled to mass spectrometry (LC-MS) is the dominant technological platform for proteomics. An LC-MS analysis of a complex biological sample can be visualized as a ‘map’ of which the positional coordinates are the mass-to-charge ratio (m/z) and chromatographic retention time (RT) of the chemical species profiled. Label-free quantitative proteomics requires the alignment and comparison of multiple LC-MS maps to ascertain the reproducibility of experiments or reveal proteome changes under different conditions. The main challenge in this task lies in correcting inevitable RT shifts. Similar, but not identical, LC instruments and settings can cause peptides to elute at very different times and sometimes in a different order, violating the assumptions of many state-of-the-art alignment tools. To meet this challenge, we developed LWBMatch, a new algorithm based on weighted bipartite matching. Unlike existing tools, which search for accurate warping functions to correct RT shifts, we directly seek a peak-to-peak mapping by maximizing a global similarity function between two LC-MS maps. For alignment tasks with large RT shifts (>500 s), an approximate warping function is determined by locally weighted scatterplot smoothing of potential matched features, detected using a novel voting scheme based on co-elution. For validation, we defined the ground truth for alignment success based on tandem mass spectrometry identifications from sequence searching. We showed that our method outperforms several existing tools in terms of precision and recall, and is capable of aligning maps from different instruments and settings.

Availability: Available at https://sourceforge.net/projects/rt-alignment/.

Contact:  kehlam@ust.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Filling the gap: a new class of old star cluster?
Authors: Forbes Duncan A. , Pota Vincenzo , Usher Christopher , Strader Jay , Romanowsky Aaron J. , Brodie Jean P. , Arnold Jacob A. , Spitler Lee R.
Published: August 2013

It is not understood whether long-lived star clusters possess a continuous range of sizes and masses (and hence densities) or if rather, they should be considered as distinct types with different origins. Utilizing the Hubble Space Telescope to measure sizes and long exposures on the Keck 10 m telescope to obtain distances, we have discovered the first confirmed star clusters that lie within a previously claimed size–luminosity gap dubbed the ‘avoidance zone’ by Hwang et al. The existence of these star clusters extends the range of sizes, masses and densities for star clusters, and argues against current formation models that predict well-defined size–mass relationships (such as stripped nuclei, giant globular clusters or merged star clusters). The red colour of these gap objects suggests that they are not a new class of object but are related to faint fuzzies observed in nearby lenticular galaxies. We also report a number of low-luminosity ultracompact dwarfs with sizes of up to 50 pc. Future, statistically complete, studies will be encouraged now that it is known that star clusters possess a continuous range of structural properties.
Incongruity of the unified scheme with a 3CRR-like equatorial strong-source sample
Authors: Singal Ashok K. , Singh Raj Laxmi
Published: August 2013

We examine the consistency of the unified scheme of the powerful extragalactic radio sources with the 408 MHz BRL sample (Best, Röttgering & Lehnert) from the equatorial sky region, selected at the same flux-density level as the 3CRR sample. We find that, unlike in the 3CRR sample, a foreshortening in the observed sizes of quasars, expected from the orientation-based unified scheme model, is not seen in the BRL sample, at least in different redshift bins up to z ∼ 1. Even the quasar fraction in individual redshift bins up to z ∼ 1 does not match with that expected from the unified scheme, where radio galaxies and quasars are supposed to belong to a common parent population at all redshifts. This not only casts strong doubts on the unified scheme, but also throws up an intriguing result that in a sample selected from the equatorial sky region, using almost the same criteria as in the 3CRR sample from the Northern hemisphere, the relative distribution of radio galaxies and quasars differs qualitatively from the 3CRR sample.
A Replicase of Potato virus X Acts as the Resistance-Breaking Determinant for JAX1-Mediated Resistance
Authors: Sugawara Kyoko , Shiraishi Takuya , Yoshida Tetsuya , Fujita Naoko , Netsu Osamu , Yamaji Yasuyuki , Namba Shigetou
Published: August 2013

Lectin-mediated resistance (LMR) has been suggested to comprise an uncharacterized branch of antiviral plant innate immunity. To unveil the feature of resistance conferred by jacalin-type lectin required for potexvirus resistance 1 (JAX1), a recently isolated LMR gene against potexviruses, we analyzed the resistance-breaking variants to find the viral component involved in resistance. We employed grafting-mediated inoculation, a high-pressure virus inoculation method, to obtain Potato virus X (PVX) variants that can overcome JAX1-mediated resistance. Whole-genome sequencing of the variants suggested that a single amino acid in the methyl transferase domain of the replicase encoded by PVX is responsible for this resistance-breaking property. Reintroduction of the amino-acid substitution to avirulent wild-type PVX was sufficient to overcome the JAX1-mediated resistance. These results suggest that viral replicase is involved in JAX1-mediated resistance. The residue that determines the resistance-breaking properties was highly conserved among potexviruses, suggesting a general role of the residue in potexvirus–JAX1 interactions.
Purification of Oligodendrocyte Precursor Cells from Rat Cortices by Immunopanning
Authors: Dugas Jason C. , Emery Ben
Published: August 2013

This protocol describes how to purify oligodendrocyte precursor cells (OPCs) from postnatal rodent brains. The method utilizes an immunopanning technique to first remove unwanted cells by negative selection and then purify OPCs by positive selection and subsequent enzymatic release from the final panning plate. Included are modifications that allow for purification and culturing of OPCs from mouse instead of rat tissue and for use of optic nerves instead of whole brains. The method for isolating OPCs from whole brain can be used for isolating OPCs from any specific region of the brain, provided that the area can be dissected away from the rest of the tissue. Suggested culture media for maintaining proliferating OPCs or inducing oligodendrocyte (OL) differentiation are also described.
Two-Photon Imaging of Blood Flow in the Rat Cortex
Authors: Driscoll Jonathan D. , Shih Andy Y. , Drew Patrick J. , Cauwenberghs Gert , Kleinfeld David
Published: August 2013

Cerebral blood flow plays a central role in maintaining homeostasis in the brain, and its dysfunction leads to pathological conditions such as stroke. Moreover, understanding the dynamics of blood flow is central to the interpretation of data from imaging modalities—such as intrinsic optical signaling and functional magnetic resonance imaging—that rely on changes in cerebral blood flow and oxygen level to infer changes in the underlying neural activity. Recent advances in imaging techniques have allowed detailed studies of blood flow in vivo at high spatial and temporal resolutions. We discuss techniques to accurately measure cerebral blood flow at the level of individual blood vessels using two-photon laser-scanning microscopy. By directing the scanning laser along a user-defined path, it is possible to measure red blood cell (RBC) velocity and vessel diameter across multiple vessels simultaneously. The combination of these measurements permits accurate assessment of total flux with sufficient time resolution to measure fast modulations in flux, such as those caused by heartbeat, as well as slower signals caused by vasomotion and hemodynamic responses to stimulus. Here, we discuss general techniques for animal preparation and measurement of blood flow with two-photon microscopy. We incorporate extensions to existing methods to accurately acquire flux data simultaneously across multiple vessels in a single trial. Central to these measurements is the ability to generate scan paths that smoothly connect user-defined lines of interest while maintaining high accuracy of the scan path.
Immunostaining, Dehydration, and Clearing of Mouse Embryos for Ultramicroscopy
Authors: Becker Klaus , Jährling Nina , Saghafi Saiedeh , Dodt Hans-Ulrich
Published: August 2013

This protocol describes the preparation of mouse embryos for ultramicroscopy (UM), a powerful imaging technique that achieves precise and accurate three-dimensional (3D) reconstructions of intact macroscopic specimens with micrometer resolution. In UM, a specimen in the size range of ∼1–15 mm is illuminated perpendicular to the observation pathway by two thin counterpropagating sheets of laser light. In combination with fluorescein isothiocyanate (FITC) immunostaining, UM allows visualization of somatic motor and sensorial nerve fibers in whole mouse embryos. Even the fine branches of the sensomotoric fibers can be visualized over a distance of up to several millimeters. In this protocol, mouse embryos are fixed and immunostained in preparation for UM. Because UM requires the excitation light sheet to travel throughout the entire horizontal width of the specimen, specimens usually have to be rendered transparent before microscope inspection. Here, the embryos are dehydrated in ethanol and then cleared in a solution of benzyl alcohol and benzyl benzoate.
Local Estimators of Size in Stereological Studies
Authors: West Mark J.
Published: August 2013

There are two general categories of stereological methods, global and local. Global stereological estimators include estimators of total volume, surface, length, and number. Local estimators can be used to estimate the volumes or surfaces of single objects and, thereby, the distribution of object sizes or the mean size of objects within a population. Two local estimators that have proved to be of practical value for measuring the volume of cells in neurobiological studies are the nucleator and the rotator, which are the focus of this article. Variants of the nucleator can be used for estimating object number, object surface, and the spatial distributions of objects.
Ultramicroscopy: Light-Sheet-Based Microscopy for Imaging Centimeter-Sized Objects with Micrometer Resolution
Authors: Becker Klaus , Jährling Nina , Saghafi Saiedeh , Dodt Hans-Ulrich
Published: August 2013

Ultramicroscopy (UM) is a powerful imaging technique that achieves precise and accurate three-dimensional (3D) reconstructions of intact macroscopic specimens with micrometer resolution. It was developed for specimens in the size range of ∼1–15 mm, such as whole mouse brains, mouse embryos, mouse organs, and Drosophila melanogaster. In UM, the specimen is illuminated perpendicular to the observation pathway by two thin counterpropagating sheets of laser light. UM is closely related to a growing family of comparable microscopy approaches based on light sheet illumination developed in recent years. This article presents an overview of light-sheet-based microscopy and describes the underlying physics of light sheet generation. The assembly of an “ultramicroscope” for investigating fixed chemically cleared tissue is described in detail, and the functions of the essential components, such as mechanics, camera, and objectives, are discussed. Finally, practical applications of UM for studying mouse organs, mouse embryos, and Drosophila adults are described.
Fitness costs and benefits of ultraviolet radiation exposure in marine pelagic copepods
Authors: Hylander Samuel , Grenvald Julie Cornelius , Kiørboe Thomas
Published: August 2013

Life‐history theory predicts that organisms should allocate energy throughout their life such that they maximize their fitness. Copepod zooplankton are known to accumulate sunscreens (so‐called mycosporine‐like amino acids, MAAs) and antioxidant carotenoids to mitigate negative effects of ultraviolet radiation (UVR), but it is not well known how this affects their fitness.

We followed cohorts of the marine copepod Acartia tonsa and assessed how fitness was affected by UVR exposure and a diet rich in UVR‐protective sunscreens.

Several fitness components including somatic growth, egg quality and nauplii production (larvae) were negatively affected by UVR, whereas other components such as size at maturity, survival and length of life were not. Nauplii production through low egg quality was the most influential life‐history parameter that changed in response to UVR.

There was interaction between fitness costs and food source. If copepods were fed a diet rich in UVR‐screening MAAs, they were able to maintain and even increase their fitness even though they were exposed to otherwise detrimental radiation. Levels of UVR‐protective carotenoids were low in the studied species and a meta‐analysis revealed that marine copepods in general have much lower – by an order of magnitude – levels of carotenoids than freshwater species, while levels of MAAs are similar between the two habitats.

We conclude that allocation to different fitness components to some extent is plastic although egg quality is by far the most influential factor, and this is an example of how environmental variability affects overall fitness. Fitness costs associated with UVR exposure in the absence of UVR‐screening MAAs were present. Other costs such as costs for accumulating MAAs were not detected, and if present, they were outweighed by a stimulated fitness in combined UVR and MAA treatments challenging the common model that inducible defences (such as accumulation of MAAs) should come with a cost. Low levels of carotenoids in marine systems suggest high predation pressures on pigmented specimens. Accumulation of nonpigmented MAAs could hence be a key adaptation for surface‐dwelling marine zooplankton to maintain or even increase their fitness when exposed to detrimental radiation.