bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced collective focusing of intense neutralized ion beam pulses in the presence of weak solenoidal magnetic fields
Authors: Dorf Mikhail A. , Davidson Ronald C. , Kaganovich Igor D. , Startsev Edward A.
Published: June 2012

The design of ion drivers for warm dense matter and high energy density physics applications and heavy ion fusion involves transverse focusing and longitudinal compression of intense ion beams to a small spot size on the target. To facilitate the process, the compression occurs in a long drift section filled with a dense background plasma, which neutralizes the intense beam self-fields. Typically, the ion bunch charge is better neutralized than its current, and as a result a net self-pinching (magnetic) force is produced. The self-pinching effect is of particular practical importance, and is used in various ion driver designs in order to control the transverse beam envelope. In the present work we demonstrate that this radial self-focusing force can be significantly enhanced if a weak (B ∼ 100 G) solenoidal magnetic field is applied inside the neutralized drift section, thus allowing for substantially improved transport. It is shown that in contrast to magnetic self-pinching, the enhanced collective self-focusing has a radial electric field component and occurs as a result of the overcompensation of the beam charge by plasma electrons, whereas the beam current becomes well-neutralized. As the beam leaves the neutralizing drift section, additional transverse focusing can be applied. For instance, in the neutralized drift compression experiments (NDCX) a strong (several Tesla) final focus solenoid is used for this purpose. In the present analysis we propose that the tight final focus in the NDCX experiments may possibly be achieved by using a much weaker (few hundred Gauss) magnetic lens, provided the ion beam carries an equal amount of co-moving neutralizing electrons from the preceding drift section into the lens. In this case the enhanced focusing is provided by the collective electron dynamics strongly affected by a weak applied magnetic field.
Optical reflectivity of GaAs nanowire arrays: Experiment and model
Authors: Convertino Annalisa , Cuscunà Massimo , Rubini Silvia , Martelli Faustino
Published: June 2012

In this work, we present a systematic study of the optical reflectivity of GaAs nanowire arrays as a function of nanowire size, morphology, and arrangement on the substrate. To analyze the results, we extend a recently proposed model, which describes the nanowire mat as an ensemble of diffuse optical reflectors, by including the effective medium description and the low or zero-absorption regime. The modified model is very general and well accounts for the behavior of all the samples analyzed in this work, which covers a wide range of common situations: from the array of disordered parallel oriented and small nanowires (1.5–2 μm long and 30–50 nm large) to the randomly oriented wire array with non-uniform distribution of the sizes. The results that we report here for GaAs nanowires can be applied to any other type of semiconductor nanowires and provide useful insights to design more efficient solar cells.
Emission from a dipole-forbidden energy state in a ZnO quantum dot induced by a near-field interaction with a fiber probe
Authors: Yatsui T. , Tsuji M. , Liu Y. , Kawazoe T. , Ohtsu M.
Published: June 2012

The emission intensity from the dipole-forbidden state in a spherical quantum dot (QD) was enhanced by introducing an aperture fiber probe close to the ZnO QD to induce a near-field interaction between the probe tip and the QD. The cross-sectional profiles of the photoluminescence intensities of the ground exciton state and the excited exciton states varied spatially in an anti-correlated manner.
Momentum dependence of the excitons in pentacene
Authors: Roth Friedrich , Schuster Roman , König Andreas , Knupfer Martin , Berger Helmuth
Published: June 2012

We have carried out electron energy-loss investigations of the lowest singlet excitons in pentacene at 20 K. Our studies allow to determine the full exciton band structure in the a*, b* reciprocal lattice plane. The lowest singlet exciton can move coherently within this plane, and the resulting exciton dispersion is highly anisotropic. The analysis of the energetically following (satellite) features indicates a strong admixture of charge transfer excitations to the exciton wave function.
Note: Emittance measurements of intense pulsed proton beam for different pulse length and repetition rate
Authors: Miracoli R. , Gammino S. , Celona L. , Castro G. , Mascali D. , Gobin R. , Delferrière O. , Adroit G. , Senèe F. , Ciavola G.
Published: June 2012

The high intensity ion source (SILHI), in operation at CEA-Saclay, has been used to produce a 90 mA pulsed proton beam with pulse length and repetition rates suitable for the European Spallation Source (ESS) linac. Typical r-r′ rms normalized emittance values smaller than 0.2π mm mrad have been measured for operation in pulsed mode (0.01 < duty cycle < 0.15 and 1 ms < pulse duration < 10 ms) that are relevant for the design update of the Linac to be used at the ESS in Lund.
Noniterative algorithm for improving the accuracy of a multicolor-light-emitting-diode-based colorimeter
Authors: Yang Pao-Keng
Published: June 2012

We present a noniterative algorithm to reliably reconstruct the spectral reflectance from discrete reflectance values measured by using multicolor light emitting diodes (LEDs) as probing light sources. The proposed algorithm estimates the spectral reflectance by a linear combination of product functions of the detector's responsivity function and the LEDs’ line-shape functions. After introducing suitable correction, the resulting spectral reflectance was found to be free from the spectral-broadening effect due to the finite bandwidth of LED. We analyzed the data for a real sample and found that spectral reflectance with enhanced resolution gives a more accurate prediction in the color measurement.
Performance characteristics of nanocrystalline diamond vacuum field emission transistor array
Authors: Hsu S. H. , Kang W. P. , Davidson J. L. , Huang J. H. , Kerns D. V.
Published: June 2012

Nitrogen-incorporated nanocrystalline diamond (ND) vacuum field emission transistor (VFET) with self-aligned gate is fabricated by mold transfer microfabrication technique in conjunction with chemical vapor deposition (CVD) of nanocrystalline diamond on emitter cavity patterned on silicon-on-insulator (SOI) substrate. The fabricated ND-VFET demonstrates gate-controlled emission current with good signal amplification characteristics. The dc characteristics of the ND-VFET show well-defined cutoff, linear, and saturation regions with low gate turn-on voltage, high anode current, negligible gate intercepted current, and large dc voltage gain. The ac performance of the ND-VFET is measured, and the experimental data are analyzed using a modified small signal circuit model. The experimental results obtained for the ac voltage gain are found to agree with the theoretical model. A higher ac voltage gain is attainable by using a better test setup to eliminate the associated parasitic capacitances. The paper reveals the amplifier characteristics of the ND-VFET for potential applications in vacuum microelectronics.
Development of piezoelectric microcantilever flow sensor with wind-driven energy harvesting capability
Authors: Liu Huicong , Zhang Songsong , Kathiresan Ramprakash , Kobayashi Takeshi , Lee Chengkuo
Published: June 2012

We have developed a piezoelectric (PZT) microcantilever as an air flow sensor and a wind-driven energy harvester for a self-sustained flow-sensing microsystem. A flow sensing sensitivity of 0.9 mV/(m/s) is obtained. The output voltage and optimized power regarding to the load resistance of 100 kΩ are measured as 18.1 mV and 3.3 nW at flow velocity of 15.6 m/s, respectively. The corresponding power density is as large as 0.36 mW/cm3. The experimental results have elucidated the smart function of using PZT microcantilevers as flow-sensors and wind-driven energy harvesters simultaneously.
The glass transition and the distribution of voids in room-temperature ionic liquids: A molecular dynamics study
Authors: Forero-Martinez N. C. , Cortes-Huerto R. , Ballone P.
Published: June 2012

The glass transition in prototypical room temperature ionic liquids has been investigated by molecular dynamics simulations based on an Amber-like empirical force field. Samples of [C4mim][PF6], [C4mim][Tf2N], and [C3mim][Tf2N] have been quenched from the liquid phase at T = 500 to a glassy state at T ∼ 0 K in discontinuous steps of 20 K every 1.2 ns. The glass temperature estimated by simulation (Tg = 209 K for [C4mim][PF6], Tg = 204 K for [C4mim][Tf2N], and Tg = 196 K for [C3mim][Tf2N]) agrees semi-quantitatively with the experimental values (Tg = 193÷196 K for [C4mim][PF6], Tg = 186÷189 K for [C4mim][Tf2N], and Tg = 183 K for [C3mim][Tf2N]). A model electron density is introduced to identify voids in the system. The temperature dependence of the size distribution of voids provided by simulation reproduce well the experimental results of positron annihilation lifetime spectroscopy reported in G. Dlubek, Y. Yu, R. Krause-Rehberg, W. Beichel, S. Bulut, N. Pogodina, I. Krossing, and Ch. Friedrich, J. Chem. Phys. 133, 124502 (2010), with only one free parameter needed to fit the experimental data.
Photonic crystal tunable slow light device integrated with multi-heaters
Authors: Ishikura Norihiro , Hosoi Ryo , Hayakawa Ryo , Tamanuki Takemasa , Shinkawa Mizuki , Baba Toshihiko
Published: June 2012

We fabricated photonic crystal slow light waveguides integrated with multi-heaters, using CMOS-compatible process. By optimizing heating powers and adjusting the index distribution, a clear delay peak was observed, which suggests that the fabrication errors were compensated for completely. When a linear index chirp was added to this condition, the delay was tuned by 54 ps. When a quadratic chirp was added, arbitrary group delay dispersion was generated at wavelengths around 1550 nm within a 3 nm bandwidth. The continuously tunable range was from −32 to 54 ps/nm/mm. Using this as a dispersion compensator, we compressed pre-chirped pico-second pulses.
Effect of Alfvén resonance on low-frequency fast wave current drive
Authors: Wang C. Y. , Batchelor D. B. , Carter M. D. , Jaeger E. F. , Stallings D. C.
Published: June 2012

The Alfvén resonances may occur on the low- and high-field sides for a low-frequency fast wave current drive scenario proposed for the International Thermonuclear Experimental Reactor (ITER) [Nucl. Fusion 31, 1135 (1991)]. At the resonance on the low-field side, the fast wave may be mode converted into a short-wavelength slow wave, which can be absorbed by electrons at the plasma edge, before the fast wave propagates into the core area of the plasma. Such absorption may cause a significant parasitic power loss.
Evidence for Majorana fermions in a nanowire
Authors: Wilson R. Mark
Published: June 2012

Electrical conductance measurements reveal what may be massless, chargeless, and spinless quasiparticles of zero energy.
Carbon dioxide drove the ending of the last glacial epoch
Authors: Schwarzschild Bertram M.
Published: June 2012

A worldwide assemby of proxy paleothermometers has addressed the disputed role of greenhouse gases in periodic deglaciations.
Teaching general relativity to undergraduates
Authors: Christensen Nelson , Moore Thomas
Published: June 2012

Inspired by new results in cosmology and astrophysics, undergraduates are increasingly eager to learn about general relativity. A number of innovative textbooks make it easier than ever before to satisfy that demand.
AMS Applications in Nuclear Astrophysics: New Results for 13C(n,γ) 14C and 14N(n,p) 14C
Authors: Wallner A. , Buczak K. , Dillmann I. , Feige J. , Käppeler F. , Korschinek G. , Lederer C. , Mengoni A. , Ott U. , Paul M. , Schätzel G. , Steier P. , Trautvetter H. P.
Published: June 2012

The technique of accelerator mass spectrometry (AMS) offers a complementary tool for studying long-lived radionuclides in nuclear astrophysics: (1) as a tool for investigating nucleosynthesis in the laboratory; and (2) via a direct search of live long-lived radionuclides in terrestrial archives as signatures of recent nearby supernova-events. A key ingredient to our understanding of nucleosynthesis is accurate cross-section data. AMS was applied for measurements of the neutron-induced cross sections 13C(n,γ) and 14N(n,p), both leading to the long-lived radionuclide 14C. Solid samples were irradiated at Karlsruhe Institute of Technology with neutrons closely resembling a Maxwell–Boltzmann distribution for kT = 25 keV, and with neutrons of energies between 123 and 178 keV. After neutron activation the amount of 14C nuclides in the samples was measured by AMS at the VERA (Vienna Environmental Research Accelerator) facility. Both reactions, 13C(n,γ)14C and 14N(n,p)14C, act as neutron poisons in s-process nucleosynthesis. However, previous experimental data are discordant. The new data for both reactions tend to be slightly lower than previous measurements for the 25 keV Maxwell–Boltzmann energy distribution. For the higher neutron energies no previous data did exist for 13C(n,γ), but model calculations indicated a strong resonance structure between 100 and 300 keV which is confirmed by our results. Very limited information is available for 14N(n,p) at these energies. Our new data at 123 and 178 keV suggest lower cross sections than expected from previous experiments and data evaluations.
Comparative transcriptional profiling of two rice genotypes carrying SUB1A-1 but exhibiting differential tolerance to submergence
Authors: Xiong Huaiyang , Li Yang , Yang Jing , Li Yangsheng
Published: June 2012

Submergence tolerance in rainfed lowland rice (Oryza sativa L.) is determined mainly by SUB1A-1, which confers the tolerance by regulating the ethylene- and gibberellin-mediated gene expression responsible for carbohydrate consumption, cell elongation and ethanolic fermentation. However, two indica rice genotypes, FR13A and Goda Heenati, both carrying this gene, exhibited differential tolerance to submergence. Comparative analysis of transcriptional profiling of the two genotypes revealed that many of antioxidant genes were more highly expressed in FR13A than in Goda Heenati under both submergence and control conditions, or only under submergence, whereas most of genes involved in biosynthesis and signalling of ethylene and GA and in anaerobic carbohydrate metabolism had comparable levels of expression between genotypes under the same conditions. H2O2 and malondialdehyde (MDA) assays demonstrated that Goda Heenati accumulated more H2O2 and had more MDA, a product of lipid peroxidation, than FR13A under submergence. These findings suggest that apart from SUB1A-mediated ‘quiescence strategy’, the detoxification of reactive oxygen species (ROS) is another important trait associated with submergence tolerance. The information obtained from this study helps in further understanding of the mechanism underlying submergence tolerance.
Time of pruning affects fruit abscission, stem carbohydrates and yield of macadamia
Authors: McFadyen Lisa , Robertson David , Sedgley Margaret , Kristiansen Paul , Olesen Trevor
Published: June 2012

Macadamia (Macadamia integrifolia Maiden and Betche, M. tetraphylla Johnson and hybrids) orchards in Australia are typically hedged around anthesis (September). Such hedging reduces yields, largely through competition for carbohydrates between early fruit set and the post-pruning vegetative flush, but also through a reduction in photosynthetic capacity caused by the loss of canopy. We examined whether hedging at other times might mitigate yield losses. Hedging time was found to affect yields across four cultivars: ‘A4’, ‘A38’, ‘344’ and ‘816’. Yield losses were lower for trees hedged in November–December than for trees hedged in September. Yields for trees hedged in June were higher than for trees hedged in September in one experiment, but were similar in a second experiment. Yield losses for September and October hedging were similar. Hedging time changed the pattern of fluctuations in stem water-soluble carbohydrates (WSC). WSC declined shortly after hedging in September, October or November, and the declines preceded increases in fruit abscission relative to unpruned control trees. The increase in fruit abscission was less pronounced for the trees hedged in November, consistent with the idea that fruit become less sensitive to carbon limitation as they mature.
Functional unfold principal component analysis for automatic plant-based stress detection in grapevine
Authors: Baert Annelies , Villez Kris , Steppe Kathy
Published: June 2012

Detection of drought stress is of great importance in grapevines because the plant’s water status strongly affects the quality of the grapes and hence, resulting wine. Measurements of stem diameter variations show promise for detecting drought stress, but they depend strongly on microclimatic changes. Tools for advanced data analysis might be helpful to distinguish drought from microclimate effects. To this end, we explored the possibilities of two data mining techniques: Unfold principal component analysis (UPCA) – an already established tool in several biotechnological domains – and functional unfold principal component analysis (FUPCA) – a newer technique combining functional data analysis with UPCA. With FUPCA, the original, multivariate time series of variables are first approximated by fitting the least-squares optimal linear combination of orthonomal basis functions. The resulting coefficients of these linear combinations are then subjected to UPCA. Both techniques were used to detect when the measured stem diameter variations in grapevine deviated from their normal conditions due to drought stress. Stress was detected with both UPCA and FUPCA days before visible symptoms appeared. However, FUPCA is less complex in the statistical sense and more robust than original UPCA modelling. Moreover, FUPCA can handle days with missing data, which is not possible with UPCA.
The role of SORBITOL DEHYDROGENASE in Arabidopsis thaliana
Authors: Nosarzewski Marta , Downie A. Bruce , Wu Benhong , Archbold Douglas D.
Published: June 2012

SORBITOL DEHYDROGENASE (SDH, EC 1.1.1.14) catalyses the interconversion of polyols and ketoses (e.g. sorbitol ↔ fructose). Using two independent Arabidopsis thaliana (L.) Heynh. sdh knockout mutants, we show that SDH (At5g51970) plays a primary role in sorbitol metabolism as well as an unexpected role in ribitol metabolism. Sorbitol content increased in both wild-type (WT) and mutant plant leaves during drought stress, but mutants showed a dramatically different phenotype, dying even if rewatered. The lack of functional SDH in mutant plants was accompanied by accumulation of foliar sorbitol and at least 10-fold more ribitol, neither of which decreased in mutant plants after rewatering. In addition, mutant plants were uniquely sensitive to ribitol in a concentration-dependent manner, which either prevented them from completing seed germination or inhibited seedling development, effects not observed with other polyols or with ribitol-treated WT plants. Ribitol catabolism may occur solely through SDH in A. thaliana, though at only 30% the rate of that for sorbitol. The results indicate a role for SDH in metabolism of sorbitol to fructose and in ribitol conversion to ribulose in A. thaliana during recovery from drought stress.
Rootstocks affect pear (Pyrus communis) tree growth through extent of node neoformation and flowering with key differences to apple
Authors: Watson Amy E. , Seleznyova Alla N. , Dayatilake Geegana A. , Tustin D. Stuart
Published: June 2012

Improved knowledge of rootstock effects on pear (Pyrus communis L.) tree development is required before early assessment of rootstock breeding populations can be improved. Two cultivars, ‘Doyenné du Comice’ and ‘Concorde’, were grafted on Pyrus calleryana Decne. (vigorous), Quince BA29 (semi-vigorous) and Quince C (semi-dwarfing) rootstocks. Growth of the compound trees was studied over 2 years after grafting and flowering was recorded in the spring of the third year. Using architectural analysis, annual shoot types common to all treatments and closely connected to the patterns of extension of preformed and neoformed metamers were identified and the differences among rootstock vigour treatments were quantified by proportions of these shoot types. Rootstock affected node neoformation, which was highest in the treatment with P. calleryana. The extent of sylleptic branching varied among the treatments, whereas the budbreak along the primary-axis in the second year of growth was unaffected, hence, the number of proleptic secondary axes was largely determined the primary-axis node number developed in year one. Spring flowering first occurred in the third year of tree growth and its intensity was influenced by rootstock. Quince C, the least vigorous rootstock, produced the highest number of floral buds. Flowering was delayed in young pear trees compared with apple, as shown in previous studies, so we conclude flowering does not play such a pivotal role in secondary axes development and early tree dwarfing by rootstock as has been observed in apple.
Rapidly assessing changes in bone mineral balance using natural stable calcium isotopes
Authors: Morgan Jennifer L. L. , Skulan Joseph L. , Gordon Gwyneth W. , Romaniello Stephen J. , Smith Scott M. , Anbar Ariel D.
Published: June 2012

The ability to rapidly detect changes in bone mineral balance (BMB) would be of great value in the early diagnosis and evaluation of therapies for metabolic bone diseases such as osteoporosis and some cancers. However, measurements of BMB are hampered by difficulties with using biochemical markers to quantify the relative rates of bone resorption and formation and the need to wait months to years for altered BMB to produce changes in bone mineral density large enough to resolve by X-ray densitometry. We show here that, in humans, the natural abundances of Ca isotopes in urine change rapidly in response to changes in BMB. In a bed rest experiment, use of high-precision isotope ratio MS allowed the onset of bone loss to be detected in Ca isotope data after about 1 wk, long before bone mineral density has changed enough to be detectable with densitometry. The physiological basis of the relationship between Ca isotopes and BMB is sufficiently understood to allow quantitative translation of changes in Ca isotope abundances to changes in bone mineral density using a simple model. The rate of change of bone mineral density inferred from Ca isotopes is consistent with the rate observed by densitometry in long-term bed rest studies. Ca isotopic analysis provides a powerful way to monitor bone loss, potentially making it possible to diagnose metabolic bone disease and track the impact of treatments more effectively than is currently possible.
Kinetic and structural studies, origins of selectivity, and interfacial charge transfer in the artificial photosynthesis of CO
Authors: Smieja Jonathan M. , Benson Eric E. , Kumar Bhupendra , Grice Kyle A. , Seu Candace S. , Miller Alexander J. M. , Mayer James M. , Kubiak Clifford P.
Published: June 2012

The effective design of an artificial photosynthetic system entails the optimization of several important interactions. Herein we report stopped-flow UV-visible (UV-vis) spectroscopy, X-ray crystallographic, density functional theory (DFT), and electrochemical kinetic studies of the Re(bipy-
t
Bu)(CO)
3
(L) catalyst for the reduction of CO
2
to CO. A remarkable selectivity for CO
2
over H
+
was observed by stopped-flow UV-vis spectroscopy of [Re(bipy-
t
Bu)(CO)
3
]
-1
. The reaction with CO
2
is about 25 times faster than the reaction with water or methanol at the same concentrations. X-ray crystallography and DFT studies of the doubly reduced anionic species suggest that the highest occupied molecular orbital (HOMO) has mixed metal-ligand character rather than being purely doubly occupied

, which is believed to determine selectivity by favoring CO
2
(
σ
 + 
π
) over H
+
(
σ
only) binding. Electrocatalytic studies performed with the addition of Brönsted acids reveal a primary H/D kinetic isotope effect, indicating that transfer of protons to Re -CO
2
is involved in the rate limiting step. Lastly, the effects of electrode surface modification on interfacial electron transfer between a semiconductor and catalyst were investigated and found to affect the observed current densities for catalysis more than threefold, indicating that the properties of the electrode surface need to be addressed when developing a homogeneous artificial photosynthetic system.
Ultrametric skeletons
Authors: Mendel Manor , Naor Assaf
Published: June 2012

We prove that for every
ε
∈(0,1) there exists
C

ε

∈(0,∞) with the following property. If (
X
,
d
) is a compact metric space and
μ
is a Borel probability measure on
X
then there exists a compact subset
S
⊆
X
that embeds into an ultrametric space with distortion
O
(1/
ε
), and a probability measure
ν
supported on
S
satisfying
ν
(
B

d

(
x
,
r
))⩽(
μ
(
B

d

(
x
,
C

ε

r
))

1-
ε

for all
x
∈
X
and
r
∈(0,∞). The dependence of the distortion on
ε
is sharp. We discuss an extension of this statement to multiple measures, as well as how it implies Talagrand’s majorizing measure theorem.
Ideal MHD stability and performance of ITER steady-state scenarios with ITBs
Authors: Poli F.M. , Kessel C.E. , Chance M.S. , Jardin S.C. , Manickam J.
Published: June 2012

Non-inductive steady-state scenarios on ITER will need to operate with internal transport barriers (ITBs) in order to reach adequate fusion gain at typical currents of 9 MA. The large pressure gradients at the location of the internal barrier are conducive to the development of ideal MHD instabilities that may limit the plasma performance and may lead to plasma disruptions. Fully non-inductive scenario simulations with five combinations of heating and current drive sources are presented in this work, with plasma currents in the range 7–10 MA. For each configuration the linear, ideal MHD stability is analysed for variations of the Greenwald fraction and of the pressure peaking factor around the operating point, aiming at defining an operational space for stable, steady-state operations at optimized performance. It is shown that plasmas with lower hybrid heating and current drive maintain the minimum safety factor above 1.5, which is desirable in steady-state operations to avoid neoclassical tearing modes. Operating with moderate ITBs at 2/3 of the minor radius, these plasmas have a minimum safety factor above 2, are ideal MHD stable and reach Q ≳ 5 operating above the ideal no-wall limit.
Astronomy and astrophysics with gravitational waves in the advanced detector era
Authors: Weinstein Alan J ,   for the LIGO Scientific Collaboration and the Virgo Collaboration
Published: June 2012

With the advanced gravitational wave detectors coming on line in the next 5 years, we expect to make the first detections of gravitational waves from astrophysical sources, and study the properties of the waves themselves as tests of general relativity. In addition, these gravitational waves will be powerful tools for the study of their astrophysical sources and source populations. They carry information that is quite complementary to what can be learned from electromagnetic or neutrino observations, probing the central gravitational engines that power the electromagnetic emissions at the outer layers of the source. Preparations are being made to enable near-simultaneous observations of both gravitational wave and electromagnetic observations of transient sources, using low-latency search pipelines and rapid sky localization. We will review the many opportunities for multi-messenger astronomy and astrophysics with gravitational waves enabled by the advanced detectors, and the preparations that are being made to quickly and fully exploit them.
Extremal ergodic measures and the finiteness property of matrix semigroups
Authors: Dai Xiongping , Huang Yu , Xiao MingQing
Published: June 2012

Let

S

=
{

S
1

,
…
,

S
K

}

{\boldsymbol {S}}=\{S_1,\ldots ,S_K\}

be a finite set of complex

d
×
d

d\times d

matrices and

Σ

K

+

\varSigma _{\!K}^+

be the compact space of all one-sided infinite sequences

i

⋅

:

N

→
{
1
,
…
,
K
}

i_{\boldsymbol {\cdot }}\colon \mathbb {N}\rightarrow \{1,\dotsc ,K\}

. An ergodic probability

μ
∗

\mu _*

of the Markov shift

θ
:

Σ

K

+

→

Σ

K

+

;
 

i

⋅

↦

i

⋅
+
1

\theta \colon \varSigma _{\!K}^+\rightarrow \varSigma _{\!K}^+;\ i_{\boldsymbol {\cdot }}\mapsto i_{\boldsymbol {\cdot }+1}

, is called “extremal” for

S

{\boldsymbol {S}}

if
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="rho left-parenthesis bold-italic upper S right-parenthesis equals limit Underscript n right-arrow normal infinity Endscripts RootIndex n StartRoot double-vertical-bar upper S Subscript i 1 Baseline midline-horizontal-ellipsis upper S Subscript i Sub Subscript n Subscript Baseline double-vertical-bar EndRoot">

ρ

(

S

)
=

lim

n
→
∞

‖

S

i
1

⋯

S

i
n

‖

n

{\rho }({\boldsymbol {S}})=\lim _{n\to \infty }\sqrt [n]{\left \|S_{i_1}\cdots S_{i_n}\right \|}

holds for

μ
∗

\mu _*

-a.e.

i

⋅

∈

Σ

K

+

i_{\boldsymbol {\cdot }}\in \varSigma _{\!K}^+

, where

ρ
(

S

)

\rho ({\boldsymbol {S}})

denotes the generalized/joint spectral radius of

S

{\boldsymbol {S}}

. Using the extremal norm and the Kingman subadditive ergodic theorem, it is shown that

S

{\boldsymbol {S}}

has the spectral finiteness property (i.e.
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="rho left-parenthesis bold-italic upper S right-parenthesis equals RootIndex n StartRoot rho left-parenthesis upper S Subscript i 1 Baseline midline-horizontal-ellipsis upper S Subscript i Sub Subscript n Subscript Baseline right-parenthesis EndRoot">

ρ
(

S

)
=

ρ
(

S

i
1

⋯

S

i
n

)

n

\rho ({\boldsymbol {S}})=\sqrt [n]{\rho (S_{i_1}\cdots S_{i_n})}

for some finite-length word

(

i
1

,
…
,

i
n

)

(i_1,\ldots ,i_n)

) if and only if for some extremal measure

μ
∗

\mu _*

of

S

{\boldsymbol {S}}

, it has at least one periodic density point

i

⋅

∈

Σ

K

+

i_{\boldsymbol {\cdot }}\in \varSigma _{\!K}^+

.
Distinguished tame supercuspidal representations and odd orthogonal periods
Authors: Hakim Jeffrey , Lansky Joshua
Published: June 2012

We further develop and simplify the general theory of distinguished tame supercuspidal representations of reductive

p
p

-adic groups due to Hakim and Murnaghan, as well as the analogous theory for finite reductive groups due to Lusztig. We apply our results to study the representations of

G
L

n

(
F
)

\mathrm {GL}_n(F)

, with

n
n

odd and

F
F

a nonarchimedean local field, that are distinguished with respect to an orthogonal group in

n
n

variables. In particular, we determine precisely when a supercuspidal representation is distinguished with respect to an orthogonal group and, if so, that the space of distinguishing linear forms has dimension one.
Setup for Functional Cell Ablation with Lasers: Coupling of a Laser to a Microscope
Authors: Sweeney Sean T. , Hidalgo Alicia , de Belle J. Steven , Keshishian Haig
Published: June 2012

The selective removal of cells by ablation is a powerful tool in the study of eukaryotic developmental biology, providing much information about their origin, fate, or function in the developing organism. In Drosophila, three main methods have been used to ablate cells: chemical, genetic, and laser ablation. Each method has its own applicability with regard to developmental stage and the cells to be ablated, and its own limitations. The primary advantage of laser-based ablation is the flexibility provided by the method: The operations can be performed in any cell pattern and at any time in development. Laser-based techniques permit manipulation of structures within cells, even to the molecular level. They can also be used for gene activation. However, laser ablation can be expensive, labor-intensive, and time-consuming. Although live cells can be difficult to image in Drosophila embryos, the use of vital fluorescent imaging methods has made laser-mediated cell manipulation methods more appealing; the methods are relatively straightforward. This article provides the information necessary for setting up and using a laser microscope for lasesr ablation studies.
Photoconversion for Tracking the Dynamics of Cell Movement in Xenopus laevis Embryos
Authors: Chernet Brook T. , Adams Dany S. , Levin Michael
Published: June 2012

Xenopus laevis is an ideal model system for investigating dynamic morphogenetic processes during embryogenesis, regeneration, and homeostasis. Our understanding of these events has been greatly facilitated by lineage labeling, that is, marking a cell or a group of cells and all their descendants using vital dyes, fluorescent molecules, or transplantation techniques. Unfortunately, these strategies are limited in their spatiotemporal resolution: They do not allow long-term dynamic in vivo imaging, are generally invasive, and labeling is restricted to cells on the surface. Genetically encoded fluorescent proteins (FPs), on the other hand, provide excellent alternative methods to traditional lineage labeling, enabling labeling with high spatiotemporal resolution and tracking of cellular and subcellular structures to study patterning events. Over the past decade, FPs have evolved to allow fine control of their spectral properties (in a defined region of interest) for greater labeling specificity. One example is EosFP, which is a protein cloned from the scleractinian coral Lobophyllia hemprichii that can be photoconverted from green to red fluorescence state with near-ultraviolet (UV) light irradiation. Here, we describe EosFP-photoconversion of Xenopus embryos to track cells during developmental and regenerative processes using a metal-halide- or xenon-arc-based fluorescent microscope system, which provides a simpler, less expensive alternative to photoconversion using laser microscopy.
Construction of Flow Chambers for Polarized Total Internal Reflection Fluorescence Microscopy (polTIRFM) Motility Assays
Authors: Beausang John F. , Sun Yujie , Quinlan Margot E. , Forkey Joseph N. , Goldman Yale E.
Published: June 2012

Polarized total internal reflection fluorescence microscopy (polTIRFM) can be used to detect the spatial orientation and rotational dynamics of single molecules. polTIRFM determines the three-dimensional angular orientation and the extent of wobble of a fluorescent probe bound to the macromolecule of interest. This protocol describes how to construct sample chambers (flow chambers) for polTIRFM motility assays. Each chamber can hold ∼20 µL of solution. To flow a solution through the chamber, the solution is added to the chamber with a pipette while wicking out the previous contents with filter paper. Each end of the coverslip should extend beyond the edge of the slide to support the pipette tip and filter paper. The flow rate can be roughly controlled by adjusting the contact area between the filter paper and the solution. The chambers can be used for investigating the motility of myosin V in vitro with the processive motility assay, as well as for assessing the motility of actin using the twirling assay.
The Polarized Total Internal Reflection Fluorescence Microscopy (polTIRFM) Processive Motility Assay for Myosin V
Authors: Beausang John F. , Sun Yujie , Quinlan Margot E. , Forkey Joseph N. , Goldman Yale E.
Published: June 2012

Polarized total internal reflection fluorescence microscopy (polTIRFM) can be used to detect the spatial orientation and rotational dynamics of single molecules. polTIRFM determines the three-dimensional angular orientation and the extent of wobble of a fluorescent probe bound to the macromolecule of interest. This protocol describes the processive motility assay for investigating the motility of myosin V in vitro. Biotin-Alexa actin filaments are fixed to a slide by biotin/streptavidin linkages and aligned with the microscope x-axis by fluid flow. The orientation of a rhodamine–calmodulin (CaM) probe bound to a single myosin V molecule is determined as it moves along an actin filament. Excess wild-type calmodulin (WT-CaM) is present in the buffer solution to replenish lost CaM from the myosin lever arm. The techniques for myosin V should be generally applicable to other single-molecule experiments where angular changes have an important mechanistic role in their biological function.
The Polarized Total Internal Reflection Fluorescence Microscopy (polTIRFM) Twirling Filament Assay
Authors: Beausang John F. , Sun Yujie , Quinlan Margot E. , Forkey Joseph N. , Goldman Yale E.
Published: June 2012

Polarized total internal reflection fluorescence microscopy (polTIRFM) can be used to detect the spatial orientation and rotational dynamics of single molecules. polTIRFM determines the three-dimensional angular orientation and the extent of wobble of a fluorescent probe bound to the macromolecule of interest. This protocol describes the twirling filament assay, so named because actin sometimes twirls about its own axis as it is translocated by myosin. A gliding filament assay is constructed in which a sparsely labeled actin filament (0.3% of the actin monomers contain 6′- iodoacetamidotetramethylrhodamine [IATR]) is translocated by a field of unlabeled myosin V fixed to the surface. The polTIRFM twirling assay differs from a standard gliding filament assay in that full filaments are not visible, but rather individual fluorophores are spaced along each filament. The goal is to investigate possible rotational motions of the actin filament about its axis (i.e., twirling) by measuring the spatial angle of the fluorescent probe as a function of time. Successful assays contain microscopic fields of approximately 50 isolated points of fluorescence that move across the field in the presence of ATP. Actin is usually translocated by more than one myosin molecule, depending on the filament length and the myosin surface density. Sparsely labeled filaments are required because the orientation of only one probe can be resolved at a time.
A Colony-Forming Assay for Determining the Establishment Efficiency of S/MAR-Containing Nonviral Episomal Expression Vectors
Authors: Hagedorn Claudia , Baiker Armin , Postberg Jan , Ehrhardt Anja , Lipps Hans J.
Published: June 2012

As with all eukaryotic replicons, the stable establishment of S/MAR (scaffold/matrix attached region) vectors is a stochastic event that depends on poorly understood epigenetic factors such as chromatin structure and nuclear localization. Establishment efficiency describes the percentage of cells in which a particular S/MAR vector is stably retained as an episome after an initial selection period. Expected establishment efficiency for S/MAR vectors is 1–5%. This article describes a colony-forming assay that may be used either to determine establishment efficiency or to generate single cell clones.
Rescue of S/MAR-Containing Nonviral Episomal Expression Vectors
Authors: Hagedorn Claudia , Baiker Armin , Postberg Jan , Ehrhardt Anja , Lipps Hans J.
Published: June 2012

The episomal status of S/MAR (scaffold/matrix attached region)-based vectors can be confirmed by several methods including Southern blots, fluorescence in situ hybridization (FISH) analysis, or plasmid rescue experiments. In rescue experiments, genomic DNA (gDNA) or DNA from Hirt extracts is isolated from cell clones or mixed populations in which S/MAR plasmids are stably established. Bacteria are transformed with this DNA and if episomal plasmid DNA (pDNA) is present, resistant bacterial colonies will form.
Electroporation and Use of Hepatitis B Virus Envelope L Proteins as Bionanocapsules: Figure 1.
Authors: Yamada Tadanori , Jung Joohee , Seno Masaharu , Kondo Akihiko , Ueda Masakazu , Tanizawa Katsuyuki , Kuroda Shun'ichi
Published: June 2012

Hepatitis B virus (HBV) envelope L proteins, when synthesized in yeast cells, form a hollow bionanocapsule (BNC) in which genes (including large plasmids up to 40 kbp), small interfering RNA (siRNA), drugs, and proteins can be enclosed by electroporation. BNCs made from L proteins have several advantages as a delivery system: Because they display a human liver-specific receptor (the pre-S region of the L protein) on their surface, BNCs can efficiently and specifically deliver their contents to human liver-derived cells and tissues ex vivo (in cell culture) and in vivo (in a mouse xenograft model). Retargeting can be achieved simply by substituting other biorecognition molecules such as antibodies, ligands, receptors, and homing peptides for the pre-S region. In addition, BNCs have already been proven to be safe for use in humans during their development as an immunogen of hepatitis B vaccine. This protocol describes the loading of BNCs and their use in cell culture and in vivo.
Generation of Volume Data by Episcopic Three-Dimensional Imaging of Embryos: Figure 1.
Authors: Mohun Timothy J. , Weninger Wolfgang J.
Published: June 2012

Episcopic fluorescence image capturing (EFIC) and high-resolution episcopic microscopy (HREM) are related techniques that are used to generate digital volume data and create three-dimensional (3D) images. Both techniques require specimens that are embedded in an appropriate medium, and images are captured from successive sections before removal from the embedded tissue block. EFIC detects autofluorescence emitted from the embedded tissue, whereas HREM requires the tissue to be stained with a fluorescent dye such as eosin. Volume data are generated as the successive sections are imaged and removed using a microtome. This protocol describes the procedure for digital data processing, visualization, and archiving for both EFIC and HREM.
Handling S/MAR Vectors
Authors: Hagedorn Claudia , Baiker Armin , Postberg Jan , Ehrhardt Anja , Lipps Hans J.
Published: June 2012

Nonviral episomal vectors represent attractive alternatives to currently used virus-based expression systems. In the late 1990s, it was shown that a plasmid containing an expression cassette linked to a scaffold/matrix attached region (S/MAR) replicates as a low copy number episome in all cell lines tested, as well as primary cells, and can be used for the genetic modification of higher animals. Once established in the cell, the S/MAR vector replicates early during S-phase and, in the absence of selection, is stably retained in the cells for an unlimited period of time. This vector can therefore be regarded as a minimal model system for studying the epigenetic regulation of replication and functional nuclear architecture. In theory, this construct represents an almost “ideal” expression system for gene therapy. In practice, S/MAR-based vectors stably modify mammalian cells with efficiencies far below those of virus-based constructs. Consequently, they have not yet found application in gene therapy trials. Furthermore, S/MAR vector systems are not trivial to handle and several critical technical issues have to be considered when modifying these vectors for various applications.
Dietary ontogeny and niche shift to piscivory in lacustrine brown trout Salmo trutta revealed by stomach content and stable isotope analyses
Authors: Jensen H. , Kiljunen M. , Amundsen P.‐A.
Published: June 2012

The feeding ecology and ontogeny of a large size range of brown trout Salmo trutta in Lake Fyresvatnet, southern Norway, were examined by stomach content and stable isotope analyses. According to the stomach contents, the S. trutta changed their diet at c. 30 cm total length (LT). The smaller size classes fed on benthic invertebrates and surface insects, whereas larger S. trutta (>30 cm) fed mainly on whitefish Coregonus lavaretus. A similar, but more gradual shift to piscivory in the size range 25–30 cm was found when using the stable isotope mixing model SIAR to reveal dietary ontogeny. The δ13C isotopic signature confirmed that S. trutta independent of size predominantly relied upon benthic energy sources, suggesting that the littoral zone was the primary foraging habitat for both invertebrate and piscivorous feeders. The δ15N values and trophic position increased with predator length, ranging from an average of 3·60 for small‐sized S. trutta (<15 cm) to 4·15 for large‐sized fish (>35 cm). The S. trutta exhibited a relatively slow growth rate during the predominant invertebrate feeding stages up to 7 years of age and 28 cm LT, whereas fish above this size and age displayed a rapid growth rate of 9–11 cm year−1, demonstrating the profitability of piscivorous feeding.
Feeding ecology of indigenous and non‐indigenous fish species within the family Sphyraenidae
Authors: Kalogirou S. , Mittermayer F. , Pihl L. , Wennhage H.
Published: June 2012

The feeding ecology of two common indigenous (Sphyraena viridensis and Sphyraena sphyraena) and one abundant non‐indigenous sphyraenid species, Sphyraena chrysotaenia, of Indo‐Pacific Ocean origin, was investigated in an area of the eastern Mediterranean Sea. The stomach contents of 738 individuals of varying size, collected during the period December 2008 to August 2009, were examined. The dietary analyses revealed that all three species were specialized piscivores with a diet consisting of >90% fish, both by number and mass. Concurrent sampling of the fish assemblage made it possible to calculate selectivity as well as diet breadth and overlap of these strict piscivores. Even though several prey species were found in the stomachs of the three predators examined, selectivity towards Atherina boyeri was highly significant. For all species examined, >70% of the diet by mass was made up by three indigenous species of commercial value: Spicara smaris, Boops boops and A. boyeri. Diet breadth and size of prey increased with increasing body size for all predators. With increased body size, the diet overlap between indigenous and non‐indigenous species decreased. This could be attributed to increased diet breadth and the specific life‐history characteristics of indigenous species developing into larger individuals. During winter, the condition factor of the non‐indigenous species was significantly lower than that of the indigenous, indicating that winter conditions in the Mediterranean Sea may limit its further expansion north and westward. With this study, the gap in knowledge of the feeding preferences of the most abundant piscivorous species found in coastal areas of the study region is filled. Additionally, the results indicate that non‐indigenous species familial affiliation to indigenous ones does not facilitate invasion success.
Identification and expression profiles of grass carp Ctenopharyngodon idella tlr7 in responses to double‐stranded RNA and virus infection
Authors: Yang C. , Su J. , Zhang R. , Peng L. , Li Q.
Published: June 2012

The toll‐like receptor 7 (tlr7) gene was identified and characterized from grass carp Ctenopharyngodon idella (designated as citlr7), and the messenger (m)RNA expression profiles were examined in vivo and in vitro. The citlr7 genomic sequence consists of 4276 nucleotides (nts), including two exons and one intron. The full length of citlr7 complementary (c)DNA sequence is 3354 nts with the longest open reading frame (ORF) of 3156 nts encoding a peptide of 1051 amino acids. citlr7 mRNA expression was high in spleen, skin and heart, and low in hepatopancreas, muscle, head kidney and trunk kidney in healthy fish. The expression of citlr7 was rapidly and significantly up‐regulated at 6 h after grass carp reovirus (GCRV) injection (72·91 fold, P < 0·05), and recovered to the original level at 24 h post‐injection in the spleen. The citlr7 transcript was rapidly and significantly down‐regulated at the 6 h time point (0·32 fold, P < 0·05) and retrieved the normal level at 72 h post‐injection in the hepatopancreas. The citlr7 transcripts were rapidly and significantly inhibited at 2 h post‐GCRV infection in the C. idella kidney (CIK) cell line (0·62 fold, P < 0·05), and were rapidly and significantly elevated by the stimulation of the synthetic double‐stranded RNA polyriboinosinic–polyribocytidylic acid sodium salt [poly(I:C)] in CIK in a dose and time‐dependent manner (P < 0·05). The results imply that citlr7 is involved in the responses to double‐stranded RNA and virus infection.