bluuebunny/crossref_metadata_2025 huggingface dataset:
The lowest energy states of the group-IIIA–group-VA heteronuclear diatomics: BN, BP, AlN, and AlP from full configuration interaction calculations
Authors: Gan Zhengting , Grant Daniel J. , Harrison Robert J. , Dixon David A.
Published: September 2006

Full configuration interaction (CI) calculations on the group-IIIA–group-VA diatomic molecules BN, BP, AlN, and AlP have been performed with the cc-pVTZ correlation-consistent basis set and compared to CCSD(T) calculations with the same basis set. The CCSD(T) calculations are good to better than 1kcal∕mol in comparison with the full CI results if the T1 diagnostic is small and to within about 2kcal∕mol if the T1 diagnostic is large. Inspection of the T2 amplitudes shows that the simple T1 diagnostic is providing useful insight into the quality of the starting wave function. The ground state of BN, BP, and AlN is predicted to be the Π3 and, for AlP, the ground state is predicted to be Σ−3. For all molecules except BP, there is an excited state within 1.1kcal∕mol of the ground state. The ordering of the state energies can be explained in terms of simple orbital and bonding models. The results provide little evidence for placing the π orbital below the σ orbital for the ground state of these heteronuclear diatomic molecules.
The effects of Au aggregate morphology on surface-enhanced Raman scattering enhancement
Authors: Sztainbuch Isaac W.
Published: September 2006

We have identified empirically a relationship between the surface morphology of small individual aggregates (<100 Au nanoparticles) and surface-enhanced Raman scattering (SERS) enhancement. We have found that multilayer aggregates generated greater SERS enhancement than aggregates limited to two-dimensional (2D) or one-dimensional structures, independent of the number of particles. SERS intensity was measured using the 730cm−1 vibrational mode of the adsorbed adenine molecule on 75nm Au particles, at an excitation wavelength of 632.8nm. To gain insight into these relationships and its mechanism, we developed a qualitative model that considers the collections of interacting Au nanoparticles of an individual aggregate as a continuous single entity that retains its salient features. We found the dimensions of the modeled surface features to be comparable with those found in rough metal surfaces, known to sustain surface plasmon resonance and generate strong SERS enhancement. Among the aggregates that we have characterized, a three 75nm nanoparticle system was the smallest to generate strong SERS enhancement. However, we also identified single individual Au nanoparticles as SERS active at the same wavelength, but with a diameter twice in size. For example, we observed a symmetric SERS-active particle of 180nm in diameter. Such individual nanoparticles generated SERS enhancement on the same order of magnitude as the small monolayer Au aggregates, an intensity value significantly stronger than predicted in recent theoretical studies. We also found that an aspect of our model that relates the dimensions of its features to SERS enhancement is also applicable to single individual Au particles. We conclude that the size of the nanoparticle itself, or the size of a protrusion of an irregularly shaped single Au particle, will contribute to SERS enhancement provided that its dimensions satisfy the conditions for plasmon resonance. In addition, by considering the ratio of the generated intensities of typical 2D Au aggregates to the enhancement of individual SERS-active particles, a value of approximately 2 is determined. Its moderate value suggests that it is not the aggregation effect that is responsible for much of the observed SERS enhancement but the surface region associated with the SERS-active site.
High-precision anemometer with thermal wave
Authors: Rachalski Andrzej
Published: September 2006

A new, highly accurate method of measurement of the gas flow velocity has been developed. The method employs the phenomenon of propagation of thermal waves in flowing gas. The probe consists of three thin wires. One of these is a hot wire and it is used to generate a thermal wave while the two remaining wires are used for wave detection. Since the phase shift of the wave between two points is proportional to the wave frequency, the flow velocity can be derived from the slope of the regression line. Signals from the wave detectors are sent via an analog to digital converter to the computer and processed. We report measurements of the laminar flow with the velocity between 30 and 200cm∕s. The accuracy of the velocity measurements is about 0.2cm∕s.
Thermal analysis of the vortex tube based thermocycler for fast DNA amplification: Experimental and two-dimensional numerical results
Authors: Raghavan V. , Whitney Scott E. , Ebmeier Ryan J. , Padhye Nisha V. , Nelson Michael , Viljoen Hendrik J. , Gogos George
Published: September 2006

In this article, experimental and numerical analyses to investigate the thermal control of an innovative vortex tube based polymerase chain reaction (VT-PCR) thermocycler are described. VT-PCR is capable of rapid DNA amplification and real-time optical detection. The device rapidly cycles six 20μl 96bp λ-DNA samples between the PCR stages (denaturation, annealing, and elongation) for 30cycles in approximately 6min. Two-dimensional numerical simulations have been carried out using computational fluid dynamics (CFD) software FLUENT v.6.2.16. Experiments and CFD simulations have been carried out to measure/predict the temperature variation between the samples and within each sample. Heat transfer rate (primarily dictated by the temperature differences between the samples and the external air heating or cooling them) governs the temperature distribution between and within the samples. Temperature variation between and within the samples during the denaturation stage has been quite uniform (maximum variation around ±0.5 and 1.6°C, respectively). During cooling, by adjusting the cold release valves in the VT-PCR during some stage of cooling, the heat transfer rate has been controlled. Improved thermal control, which increases the efficiency of the PCR process, has been obtained both experimentally and numerically by slightly decreasing the rate of cooling. Thus, almost uniform temperature distribution between and within the samples (within 1°C) has been attained for the annealing stage as well. It is shown that the VT-PCR is a fully functional PCR machine capable of amplifying specific DNA target sequences in less time than conventional PCR devices.
Single-crystal CdSe nanoribbon field-effect transistors and photoelectric applications
Authors: Jie J. S. , Zhang W. J. , Jiang Y. , Lee S. T.
Published: September 2006

Field-effect transistors made of individual CdSe nanoribbons were fabricated and characterized. The CdSe nanoribbon showed n-type semiconducting characteristics, while the transistors revealed a threshold voltage of 20.9V, an on-off ratio >104, and an electron mobility of 9.6cm2∕Vs in the dark. CdSe nanoribbons showed high sensitivity to above-band-gap irradiation with four-orders-of-magnitude increase in conductance and millisecond response speed. The increase of electron mobility due to light irradiation was demonstrated to contribute to increased photoconductance.
Quantum control of internal conversion in 24-vibrational-mode pyrazine
Authors: Christopher P. S. , Shapiro M. , Brumer P.
Published: September 2006

Quantum control of the S2→S1 internal conversion in a complete 24-mode dimensionality model of pyrazine is demonstrated. The fully quantum mechanical study makes use of the recently developed “QP algorithm” for performing accurate computations of projected quantum dynamics and the role of overlapping resonances in control. The results are extremely encouraging, demonstrating active control over internal conversion so as to almost completely suppress the process over time scales of ∼50–100fs [well in excess of the natural internal conversion times (∼20fs)] or to accelerate it to complete internal conversion in less than 5fs. A number of new diagnostics are introduced to demonstrate the significance of overlapping-resonance contributions to control. Control is far better than for a reduced dimensionality model of pyrazine, presumably because of the increased degree of overlap between bound state resonances existing in the full dimensionality case.
Kinetic Vlasov simulations of collisionless magnetic reconnection
Authors: Schmitz H. , Grauer R.
Published: September 2006

A fully kinetic Vlasov simulation of the Geospace Environment Modeling Magnetic Reconnection Challenge is presented. Good agreement is found with previous kinetic simulations using particle in cell (PIC) codes, confirming both the PIC and the Vlasov code. In the latter the complete distribution functions fk (k=i,e) are discretized on a numerical grid in phase space. In contrast to PIC simulations, the Vlasov code does not suffer from numerical noise and allows a more detailed investigation of the distribution functions. The role of the different contributions of Ohm’s law are compared by calculating each of the terms from the moments of the fk. The important role of the off-diagonal elements of the electron pressure tensor could be confirmed. The inductive electric field at the X line is found to be dominated by the nongyrotropic electron pressure, while the bulk electron inertia is of minor importance. Detailed analysis of the electron distribution function within the diffusion region reveals the kinetic origin of the nongyrotropic terms.
Extremal covariant measurements
Authors: Chiribella Giulio , Mauro D’Ariano Giacomo
Published: September 2006

We characterize the extremal points of the convex set of quantum measurements that are covariant under a finite-dimensional projective representation of a compact group, with action of the group on the measurement probability space which is generally nontransitive. In this case the POVM density is made of multiple orbits of positive operators, and, in the case of extremal measurements, we provide a bound for the number of orbits and for the rank of POVM elements. Two relevant applications are considered, concerning state discrimination with mutually unbiased bases and the maximization of the mutual information.
Plasmon hybridization in nanoshells with a nonconcentric core
Authors: Wu Yanpeng , Nordlander Peter
Published: September 2006

We apply the plasmon hybridization method to a nanoshell with a nonconcentric (offset) core and investigate how the energy and excitation cross section of the plasmon modes depend on the offset distance D of the inner core from the nanoshell center. A two-center spherical coordinate system is used for mathematical convenience. It is shown that the presence of an offset core shifts the plasmon energies and makes higher multipolar nanoshell plasmons dipole active and visible in the optical spectrum. The dependence of the plasmon shifts on D is weak for small offsets but strong for large offsets. The polarization dependence of the optical absorption spectra is found to be relatively weak. The electromagnetic field enhancements are shown to be much larger than on a concentric nanoshell. The results agree very well with results from finite difference time domain simulations.
Dielectric properties of Bi1.5Zn1.0Nb1.5O7∕Mn-doped Ba0.6Sr0.4TiO3 heterolayered films grown by pulsed laser deposition
Authors: Fu Wangyang , Cao Lingzhu , Wang Shufang , Sun Zhihui , Cheng Bolin , Wang Qian , Wang Hong
Published: September 2006

Bi 1.5 Zn 1.0 Nb 1.5 O 7 ∕ Mn -doped Ba0.6Sr0.4TiO3 heterolayered films have been deposited on (111) Nb:SrTiO3 substrate by pulsed laser deposition. The heterolayered films were found to possess a medium permittivity around 200, a low loss tangent of 0.0025, and a relatively high tunability up to 25% measured with dc bias field of 850kV∕cm. The authors analyzed the bias field dependent permittivity of the heterolayered films using layer model. Based on the analysis, a structure with the tunability as high as 40% under a bias field of 420kV∕cm was suggested after optimizing the thickness of the component layers.
Are electrical switching and rectification inherent properties of carbon nanotube Y junctions?
Authors: Andriotis Antonis N. , Menon Madhu
Published: September 2006

Recent experimental results on carbon nanotube Y junctions have indicated ballistic rectification and switching, making them promising candidates for molecular device applications. The question still persists, however, whether this switching is the result of inherent nanotube properties or caused by the remnants of catalyst particles in the junction region of the nanotubes. In the present work, through a detailed theoretical calculation of quantum conductance of Y junctions with and without the presence of catalyst particles blocking the junction region the authors show that rectification and switching properties can be attributable entirely to the inherent nanotube properties and not to the catalysts.
Dielectric and piezoelectric properties of hydroxyapatite-BaTiO3 composites
Authors: Bowen C. R. , Gittings J. , Turner I. G. , Baxter F. , Chaudhuri J. B.
Published: September 2006

This letter describes the relationships between the composition and the dielectric and piezoelectric properties of hydroxyapatite-barium titanate composites for polarized bone substitutes. The ac conductivity and permittivity were characterized from 0.1Hzto1MHz, along with measurements of the d33 piezoelectric charge coefficient. The addition of BaTiO3 led to an increase in permittivity and ac conductivity of the material. The increase in both properties was attributed to the presence of the high permittivity ferroelectric phase. The d33 and g33 coefficients decreased rapidly as hydroxyapatite was introduced into BaTiO3 material. Composites below 80% by volume of BaTiO3 exhibited no net piezoelectric effect.
Matching-pursuit/split-operator-Fourier-transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine
Authors: Chen Xin , Batista Victor S.
Published: September 2006

A simple approach for numerically exact simulations of nonadiabatic quantum dynamics in multidimensional systems is introduced and applied to the description of the photoabsorption spectroscopy of pyrazine. The propagation scheme generalizes the recently developed matching-pursuit/split-operator-Fourier-transform (MP/SOFT) method [Y. Wu and V. S. Batista, J. Chem. Phys. 121, 1676 (2004)] to simulations of nonadiabatic quantum dynamics. The time-evolution operator is applied, as defined by the Trotter expansion to second order accuracy, in dynamically adaptive coherent-state expansions. These representations are obtained by combining the matching-pursuit algorithm with a gradient-based optimization method. The accuracy and efficiency of the resulting computational approach are demonstrated in calculations of time-dependent survival amplitudes and photoabsorption cross sections, using a model Hamiltonian that allows for direct comparisons with benchmark calculations. Simulations in full-dimensional potential energy surfaces involve the propagation of a 24-dimensional wave packet to describe the S1∕S2 interconversion of pyrazine after S0→S2 photoexcitation. The reported results show that the generalized MP/SOFT method is a practical and accurate approach to model nonadiabatic reaction dynamics in polyatomic systems.
Dissociation processes of singlet and triplet excitons in organic photovoltaic cells
Authors: Xu Zhihua , Wu Yue , Hu Bin
Published: September 2006

The dissociation processes of singlet and triplet excitons are studied based on fluorescent aluminum (III) 8-hydroxyquinoline (Alq3) and phosphorescent fac-tris-(2-phenylpyridine) iridium [Ir(ppy)3] molecules. We find that phosphorescent Ir(ppy)3 shows a more efficient photovoltaic response as compared to fluorescent Alq3. The short-circuit photocurrent action spectra and magnetic-field-dependent photocurrents reveal that the triplet excitons dissociate directly into free charge carriers at the metal-electrode interface while the singlet excitons experience bulk dissociation through polaron-pair states. This interface dissociation of triplet excitons forms a mechanism for phosphorescent organic materials to yield efficient photovoltaic responses.
Ultrasonic generation by exciting electric arc: A tool for grain refinement in welding process
Authors: He Longbiao , Wu Minsheng , Li Luming , Hao Hongwei
Published: September 2006

Traditional ultrasonic generation ways can not be applied in welding process effectively. This letter introduced a way of ultrasonic generation by exciting electric arc. When electric arc is excited by high frequency current, it generates ultrasonic. Experiments showed that welding arc had broad band response characteristic and the main factor of ultrasonic intensity was the exciting current. With the ultrasonic treatment generated by exciting arc, effect of grain refinement was found in the Ti–6Al–4V welding joint. This method of ultrasonic generation is believed to have an extensive use in material processing.
Enhanced tetragonality in (x)PbTiO3–(1−x)Bi(B′B″)O3 systems: Bi(Zn3∕4W1∕4)O3
Authors: Stein David M. , Suchomel Matthew R. , Davies Peter K.
Published: September 2006

Solid solutions in the (x)PbTiO3–(1−x)Bi(Zn3∕4W1∕4)O3 system have been examined by x-ray diffraction, dielectric measurements, and thermal analysis. Bi(Zn3∕4W1∕4)O3 increases the tetragonality and Curie temperature of PbTiO3 which reach a value of 1.08 and 530°C, respectively, at the limit of the single-phase perovskite forming region (x∼0.8). The observation of a sustained increase in the tetragonality in this system is similar to the behavior of the (x)PbTiO3–(1−x)Bi(Zn1∕2Ti1∕2)O3 system and highlights the unique properties of Bi-based systems when the B sites contain high concentrations of highly polarizable cations.
Real-time detection of probe loss in atomic force microscopy
Authors: De Tathagata , Agarwal Pranav , Sahoo Deepak R. , Salapaka Murti V.
Published: September 2006

In this letter, a real-time methodology is developed to determine regions of dynamic atomic force microscopy based image where the cantilever fails to be an effective probe of the sample. Conventional imaging signals such as the amplitude signal and the vertical piezoactuation signal cannot identify the areas of probe loss. It is experimentally demonstrated that probe-loss affected portion of the image can be unambiguously identified by a real-time signal called reliability index. Reliability index, apart from indicating the probe-loss affected regions, can be used to minimize probe-loss affected regions of the image, thus aiding high speed AFM applications.
Observation of carbon-containing nanostructured mixed titania phases for visible-light photocatalysts
Authors: Chou P.-W. , Treschev S. , Chung P.-H. , Cheng C.-L. , Tseng Y.-H. , Chen Y.-J. , Wong M. S.
Published: September 2006

This research analyzed a visible-light-responsive carbon-containing titania photocatalysts prepared by sol-gel method using confocal Raman spectral mapping, transmission electron microscopy, and UV/visible spectroscopy. The incorporation of carbons in the initial titania powder of anatase and amorphous phases was found to facilitate the formation of rutile or brookite phases from the amorphous phase in the 150–250°C temperature range, resulting in nanostructured mixed titania phases which create interface states and effectively shift the band gap to ∼2.7eV. The further shift in the absorption tails up to 800nm was attributed to carbon species-covered and/or defected titania powders.
In situ reaction mechanism studies of plasma-assisted atomic layer deposition of Al2O3
Authors: Heil S. B. S. , Kudlacek P. , Langereis E. , Engeln R. , van de Sanden M. C. M. , Kessels W. M. M.
Published: September 2006

Reaction mechanisms during plasma-assisted atomic layer deposition (ALD) of Al2O3 from Al(CH3)3 and O2 plasma were studied by time-resolved quartz crystal microbalance measurements, mass spectrometry, and optical emission spectroscopy. Al(CH3)3 chemisorption on the oxide surface after the plasma pulse releases CH4 products while from the detection of CO, CO2, and H2O in the O2 plasma it is established that surface –CH3 groups are predominantly removed by O radical-driven combustionlike reactions. Also a second pathway exists for –CH3 removal driven by H2O generated in this plasma step. These reaction pathways are expected to be generic for plasma-assisted ALD of oxides from metal organic precursors.
Electrical conductivity and dielectric properties of multiwalled carbon nanotube and alumina composites
Authors: Ahmad Kaleem , Pan Wei , Shi Sui-Lin
Published: September 2006

Alumina/multiwalled carbon nanotube (MWNT) composites with different MWNT contents ranging from 0.5to10vol% were prepared by spark plasma sintering technique. The dc electrical conductivity and dielectric properties of the composites were investigated and percolation theory was applied to demonstrate the electrical property transition from insulator to conductor. The experimental results have shown that the electrical conductivity increased sharply as the content of MWNTs was close to percolation threshold of 0.79vol%. In the low frequency range, the dielectric constant reached as high as 5000 when the content of MWNTs was at 1.74vol% and nearly frequency independent.
Surface potential imaging of nanoscale LiNbO3 domains investigated by electrostatic force microscopy
Authors: Liu Xiaoyan , Kitamura Kenji , Terabe Kazuya
Published: September 2006

The surface potential imaging of nanoscale domains engineered on near-stoichiometric LiNbO3 (SLN) crystals was investigated using Kelvin probe-based, electrostatic force microscopy. The surface potential image reflected in the domain structure was clearly obtained using heat treatment in vacuum due to the decreases in spontaneous polarization and screening charge adsorption. In-vacuum observation revealed that the surface potential contrast and polarity of nanoscale engineered domains can be repeatedly changed by switching the temperature between 298 and 393K, demonstrating the controllability of the spontaneous polarization distribution in SLN crystals.
Separate encoding of identity and similarity of complex familiar odors in piriform cortex
Authors: Kadohisa Mikiko , Wilson Donald A.
Published: September 2006

Piriform cortical circuits are hypothesized to form perceptions from responses to specific odorant features, but the anterior piriform cortex (aPCX) and posterior piriform cortex (pPCX) differ markedly in their anatomical organization, differences that could lead to distinct roles in odor encoding. Here, we tested whether experience with a complex odorant mixture would modify encoding of the mixture and its components in aPCX and pPCX. Rats were exposed to an odorant mixture and its components in a go/no-go rewarded odor discrimination task. After reaching behavioral performance criterion, single-unit recordings were made from the aPCX and pPCX in these rats and in odor-naïve, control, urethane-anesthetized rats. After odor experience, aPCX neurons were more narrowly tuned to the test odorants, and there was a decorrelation in aPCX population responses to the mixture and its components, suggesting a more distinct encoding of the familiar mixture from its components. In contrast, pPCX neurons were more broadly tuned to the familiar odorants, and pPCX population responses to the mixture and its components became more highly correlated, suggesting a pPCX encoding of similarity between familiar stimuli. The results suggest aPCX and pPCX play different roles in the processing of familiar odors and are consistent with an experience-dependent encoding (perceptual learning) of synthetic odorant identity in aPCX and an experience-dependent encoding of odor similarity or odor quality in pPCX.
Midgut bacteria required for
Bacillus thuringiensis
insecticidal activity
Authors: Broderick Nichole A. , Raffa Kenneth F. , Handelsman Jo
Published: September 2006

Bacillus thuringiensis
is the most widely applied biological insecticide and is used to manage insects that affect forestry and agriculture and transmit human and animal pathogens. This ubiquitous spore-forming bacterium kills insect larvae largely through the action of insecticidal crystal proteins and is commonly deployed as a direct bacterial spray. Moreover, plants engineered with the
cry
genes encoding the
B. thuringiensis
crystal proteins are the most widely cultivated transgenic crops. For decades, the mechanism of insect killing has been assumed to be toxin-mediated lysis of the gut epithelial cells, which leads to starvation, or
B. thuringiensis
septicemia. Here, we report that
B. thuringiensis
does not kill larvae of the gypsy moth in the absence of indigenous midgut bacteria. Elimination of the gut microbial community by oral administration of antibiotics abolished
B. thuringiensis
insecticidal activity, and reestablishment of an
Enterobacter
sp. that normally resides in the midgut microbial community restored
B. thuringiensis
-mediated killing.
Escherichia coli
engineered to produce the
B. thuringiensis
insecticidal toxin killed gypsy moth larvae irrespective of the presence of other bacteria in the midgut. However, when the engineered
E. coli
was heat-killed and then fed to the larvae, the larvae did not die in the absence of the indigenous midgut bacteria.
E. coli
and the
Enterobacter
sp. achieved high populations in hemolymph, in contrast to
B. thuringiensis
, which appeared to die in hemolymph. Our results demonstrate that
B. thuringiensis
-induced mortality depends on enteric bacteria.
Casein kinase 2 (CK2) increases survivin expression via enhanced β-catenin–T cell factor/lymphoid enhancer binding factor-dependent transcription
Authors: Tapia J. C. , Torres V. A. , Rodriguez D. A. , Leyton L. , Quest A. F. G.
Published: September 2006

Increased expression of casein kinase 2 (CK2) is associated with hyperproliferation and suppression of apoptosis in cancer. Mutations in the tumor suppressor APC (adenomatous polyposis coli) are frequent in colon cancer and often augment β-catenin–T cell factor (Tcf)/lymphoid enhancer binding factor (Lef)-dependent transcription of genes such as
c-myc
and
cyclin-D1
. CK2 has also been implicated recently in the regulation of β-catenin stability. To identify mechanisms by which CK2 promotes survival, effects of the specific CK2 inhibitors 4,5,6,7-tetrabromobenzotriazole (TBB) and 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole were assessed. TBB and 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole significantly decreased proliferation and increased apoptosis of HT29(US) colon cancer cells. RT-PCR and immunoblot analysis revealed that both inhibitors decreased survivin mRNA and protein levels in HT29(US) cells. Similar effects were observed with TBB in human DLD-1 and SW-480 colorectal cells as well as ZR-75 breast cancer cells and HEK-293T embryonic kidney cells. Expression of GFP–CK2α in HEK-293T cells resulted in β-catenin–Tcf/Lef-dependent up-regulation of survivin and increased resistance to anticancer drugs. Augmented β-catenin–Tcf/Lef-dependent transcription and resistance to apoptosis observed upon GFP–CK2α expression were abolished by TBB. Alternatively, HEK-293T cells expressing GFP–survivin were resistant to TBB-induced apoptosis. Finally, siRNA-mediated down-regulation of CK2α in HEK-293T cells coincided with reduced β-catenin and survivin levels. Taken together, these results suggest that CK2 kinase activity promotes survival by increasing survivin expression via β-catenin–Tcf/Lef-mediated transcription. Hence, selective CK2 inhibition or down-regulation in tumors may provide an attractive opportunity for the development of novel cancer therapies.
piggyBac
is a flexible and highly active transposon as compared to
Sleeping Beauty
,
Tol2
, and
Mos1
in mammalian cells
Authors: Wu Sareina Chiung-Yuan , Meir Yaa-Jyuhn James , Coates Craig J. , Handler Alfred M. , Pelczar Pawel , Moisyadi Stefan , Kaminski Joseph M.
Published: September 2006

A nonviral vector for highly efficient site-specific integration would be desirable for many applications in transgenesis, including gene therapy. In this study we directly compared the genomic integration efficiencies of
piggyBac
, hyperactive
Sleeping Beauty
(
SB11
),
Tol2
, and
Mos1
in four mammalian cell lines.
piggyBac
demonstrated significantly higher transposition activity in all cell lines whereas
Mos1
had no activity. Furthermore,
piggyBac
transposase coupled to the GAL4 DNA-binding domain retains transposition activity whereas similarly manipulated gene products of
Tol2
and
SB11
were inactive. The high transposition activity of
piggyBac
and the flexibility for molecular modification of its transposase suggest the possibility of using it routinely for mammalian transgenesis.
A purified
Bacillus thuringiensis
crystal protein with therapeutic activity against the hookworm parasite
Ancylostoma ceylanicum
Authors: Cappello Michael , Bungiro Richard D. , Harrison Lisa M. , Bischof Larry J. , Griffitts Joel S. , Barrows Brad D. , Aroian Raffi V.
Published: September 2006

Crystal (Cry) proteins produced by the soil bacterium
Bacillus thuringiensis
(Bt) are harmless to vertebrates, but they are highly toxic to insects and nematodes. Their value in controlling insects that destroy crops and transmit human diseases is well established. Although it has recently been demonstrated that a few individual Bt Cry proteins, such as Cry5B, are toxic to a wide range of free-living nematodes, the potential activity of purified Cry proteins against parasitic nematodes remains largely unknown. We report here studies aimed at characterizing
in vitro
and
in vivo
anthelminthic activities of purified recombinant Cry5B against the hookworm parasite
Ancylostoma ceylanicum
, a bloodfeeding gastrointestinal nematode for which humans are permissive hosts. By using
in vitro
larval development assays, Cry5B was found to be highly toxic to early stage hookworm larvae. Exposure of adult
A. ceylanicum
to Cry5B was also associated with significant toxicity, including a substantial reduction in egg excretion by adult female worms. To demonstrate therapeutic efficacy
in vivo
, hamsters infected with
A. ceylanicum
were treated with three daily oral doses of purified Cry5B, the benzimidazole anthelminthic mebendazole, or buffer. Compared with control (buffer-treated) animals, infected hamsters that received Cry5B showed statistically significant improvements in growth and blood hemoglobin levels as well as reduced worm burdens that were comparable to the mebendazole-treated animals. These data demonstrate that Cry5B is highly active
in vitro
and
in vivo
against a globally significant nematode parasite and that Cry5B warrants further clinical development for human and veterinary use.
Protein kinase A regulates RNA polymerase III transcription through the nuclear localization of Maf1
Authors: Moir Robyn D. , Lee JaeHoon , Haeusler Rebecca A. , Desai Neelam , Engelke David R. , Willis Ian M.
Published: September 2006

Maf1 is an essential and specific mediator of transcriptional repression in the RNA polymerase (pol) III system. Maf1-dependent repression occurs in response to a wide range of conditions, suggesting that the protein itself is targeted by the major nutritional and stress-signaling pathways. We show that Maf1 is a substrate for cAMP-dependent PKA
in vitro
and is differentially phosphorylated on PKA sites
in vivo
under normal versus repressing conditions. PKA activity negatively regulates Maf1 function because strains with unregulated high PKA activity block repression of pol III transcription
in vivo
, and strains lacking all PKA activity are hyperrepressible. Nuclear accumulation of Maf1 is required for transcriptional repression and is regulated by two nuclear localization sequences in the protein. An analysis of PKA phosphosite mutants shows that the localization of Maf1 is affected via the N-terminal nuclear localization sequence. In particular, mutations that prevent phosphorylation at PKA consensus sites promote nuclear accumulation of Maf1 without inducing repression. These results indicate that negative regulation of Maf1 by PKA is achieved by inhibiting its nuclear import and suggest that a PKA-independent activation step is required for nuclear Maf1 to function in the repression of pol III transcription. Finally, we report a previously undescribed phenotype for Maf1 in tRNA gene-mediated silencing of nearby RNA pol II transcription.
Synaptically released zinc gates long-term potentiation in fear conditioning pathways
Authors: Kodirov Sodikdjon A. , Takizawa Shuichi , Joseph Jamie , Kandel Eric R. , Shumyatsky Gleb P. , Bolshakov Vadim Y.
Published: September 2006

The functional role of releasable Zn
2+
in the central nervous system remains unknown. Here we show that zinc transporter 3 (ZnT-3), which maintains a high concentration of Zn
2+
in synaptic vesicles and serves as a marker for zinc-containing neurons, is enriched in the lateral nucleus of the amygdala and in the temporal area 3 of the auditory cortex, an area that conveys information about the auditory conditioned stimulus to the lateral nucleus of the amygdala, but not in other conditioned stimulus areas located in the auditory thalamus. Using whole-cell recordings from amygdala slices, we demonstrated that activity-dependent release of chelatable Zn
2+
is required for the induction of spike timing-dependent long-term potentiation in cortical input to the amygdala implicated in fear learning. Our data indicate that synaptically released Zn
2+
enables long-term potentiation at the cortico-amygdala synapses by depressing feed-forward GABAergic inhibition of principal neurons. This regulatory mechanism, implicating pathway-dependent release of Zn
2+
, may serve an essential control function in assuring spatial specificity of long-lasting synaptic modifications in the neural circuit of a learned behavior.
The Yeast Tumor Suppressor Homologue Sro7p Is Required for Targeting of the Sodium Pumping ATPase to the Cell Surface
Authors: Wadskog Ingrid , Forsmark Annabelle , Rossi Guendalina , Konopka Catherine , Öyen Mattias , Goksör Mattias , Ronne Hans , Brennwald Patrick , Adler Lennart
Published: September 2006

The SRO7/SOP1 encoded tumor suppressor homologue of Saccharomyces cerevisiae is required for maintenance of ion homeostasis in cells exposed to NaCl stress. Here we show that the NaCl sensitivity of the sro7Δ mutant is due to defective sorting of Ena1p, the main sodium pump in yeast. On exposure of sro7Δ mutants to NaCl stress, Ena1p fails to be targeted to the cell surface, but is instead routed to the vacuole for degradation via the multivesicular endosome pathway. SRO7-deficient mutants accumulate post-Golgi vesicles at high salinity, in agreement with a previously described role for Sro7p in late exocytosis. However, Ena1p is not sorted into these post-Golgi vesicles, in contrast to what is observed for the vesicles that accumulate when exocytosis is blocked in sec6-4 mutants at high salinity. These observations imply that Sro7p has a previously unrecognized role for sorting of specific proteins into the exocytic pathway. Screening for multicopy suppressors identified RSN1, encoding a transmembrane protein of unknown function. Overexpression of RSN1 restores NaCl tolerance of sro7Δ mutants by retargeting Ena1p to the plasma membrane. We propose a model in which blocked exocytic sorting in sro7Δ mutants, gives rise to quality control-mediated routing of Ena1p to the vacuole.
BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network
Authors: Chen Xiaohui , Chen Ming , Ning Kaida
Published: September 2006

Summary:  BNArray is a systemized tool developed in R. It facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network. Significant sub-modules of regulatory networks with high confidence are reconstructed by using our extended sub-network mining algorithm of directed graphs. BNArray can handle microarray datasets with missing data. To evaluate the statistical features of generated Bayesian networks, re-sampling procedures are utilized to yield collections of candidate 1st-order network sets for mining dense coherent sub-networks.

Availability: The R package and the supplementary documentation are available at .

Contact:  mchen@zju.edu.cn
A scalable method for integration and functional analysis of multiple microarray datasets
Authors: Huttenhower Curtis , Hibbs Matt , Myers Chad , Troyanskaya Olga G.
Published: September 2006

Motivation: The diverse microarray datasets that have become available over the past several years represent a rich opportunity and challenge for biological data mining. Many supervised and unsupervised methods have been developed for the analysis of individual microarray datasets. However, integrated analysis of multiple datasets can provide a broader insight into genetic regulation of specific biological pathways under a variety of conditions.

Results: To aid in the analysis of such large compendia of microarray experiments, we present Microarray Experiment Functional Integration Technology (MEFIT), a scalable Bayesian framework for predicting functional relationships from integrated microarray datasets. Furthermore, MEFIT predicts these functional relationships within the context of specific biological processes. All results are provided in the context of one or more specific biological functions, which can be provided by a biologist or drawn automatically from catalogs such as the Gene Ontology (GO). Using MEFIT, we integrated 40 Saccharomyces cerevisiae microarray datasets spanning 712 unique conditions. In tests based on 110 biological functions drawn from the GO biological process ontology, MEFIT provided a 5% or greater performance increase for 54 functions, with a 5% or more decrease in performance in only two functions.

Contact:  ogt@cs.princeton.edu

Supplementary information: Supplementary data, a collection of predictions made by MEFIT and software implementing MEFIT are available online at .
Accurate, Automated, Continuously Displayed Pulmonary Artery Pressure Measurement
Authors: Mitchell Mark M. , Meathe Edward A. , Jones Brian R. , Donch Terese E. , Ricks William G. , Benumof Jonathan L. , Saidman Lawrence J.
Published: September 2006

A computerized signal processing technique that removes low-frequency respiratory variation from pulmonary artery pressure and other central vascular pressure measurements, and produces a waveform devoid of respiratory artifact, has been developed. This technique has been integrated into a portable bedside monitor. The authors tested the technique in critically ill patients, and found that, compared to physician readings of conventional strip charts, it proved to be a very convenient and accurate method of determining pulmonary artery pressures continuously, regardless of ventilation.
The Minimum Alveolar Concentration (MAC) of Isoflurane in Preterm Neonates
Authors: LeDez Kenneth M. , Lerman Jerrold
Published: September 2006

Studies in fetal lambs suggested that the minimum alveolar concentration (MAC) in preterm neonates may be less than that in full-term neonates and older infants. To determine the MAC of isoflurane in preterm neonates, 20 patients < 32 weeks gestation at birth and 16 patients 32–37 weeks gestation at birth, all less than 1 month post-natal age, were studied. Following tracheal intubation, the neonates were anesthetized with a predetermined end-tidal concentration of isoflurane in oxygen and air. The move-no move responses to skin incision were recorded, and MAC was determined using the “up-and-down” technique. Heart rate and systolic arterial pressure were recorded awake, before skin incision, and after skin incision. MAC (mean ± SD) of isoflurane in preterm neonates < 32 weeks gestation was 1.28 ± 0.17%, and MAC in neonates 32–37 weeks gestation was 1.41 ± 0.18% (P < 0.05). Although heart rate did not decrease significantly in either group during the study, systolic arterial pressure decreased between 20 and 30% below awake values both before and after skin incision in both age groups (P < 0.01). We conclude that the MAC of isoflurane in preterm neonates < 32 weeks gestation is significantly less than that in pretern neonates 32–37 weeks gestation, and that systolic arterial pressure decreases to a similar extent at ∼1 MAC isoflurane in both age groups.
Effects of Graded Exercise on Leg Exchange of Energy Substrates in Malignant Hyperthermia Susceptible Subjects
Authors: Rutberg Hans , Hakanson Erik , Hall George M. , Jorfeldt Lennart
Published: September 2006

It has been speculated that, in malignant hyperthermia-susceptible (MHS) individuals, an abnormality of sympathetic activity is seen during stressful situations, such as exercise. The authors investigated whether muscle metabolism in eight MHS subjects, at rest and during moderate and heavy short-term exercise, is different then that in normals. Leg exchange of energy substrates (glucose, lactate, and glycerol) was quantified by measuring leg blood flow and arterial-venous concentration differences. Muscle biopsies were also performed, and ATP, glycogen, and lactate were analyzed. Catecholamines and oxygen uptake were also measured. The study was performed at rest with subjects in the supine position and during two periods (40% and 80% of the subjects maximal oxygen uptake, respectively) on a bicycle ergometer. The principal finding of the study was that there was no major difference in oxygen uptake or leg exchange of glucose, lactate, and glycerol between MHS-subjects and previously standard normals during different grades of exercise. Furthermore, muscle metabolites and plasma catecholamines did not differ between the groups. This study indicates a normal sympathetic activity and muscle metabolism in MHS subjects during rest, as well as during moderate and severe exercise. The authors' results do not support the opinion that persons with positive in vitro tests for MH should restrict their physical activity.
Effect of an Intubating Dose of Succinylcholine and Atracurium on the Diaphragm and the Adductor Pollicis Muscle in Humans
Authors: Pansard Jean-Louis , Chauvin Marcel , Lebrault Claude , Gauneau Pascal , Duvaldestin Philippe
Published: September 2006

This study compares the neuromuscular blocking effect of succinylcholine (0.8 mg • kg−1) and atracurium (0.6 mg • kg−1) on the diaphragm (D) and the adductor pollicis (AP) in 20 patients anesthetized with nitrous oxide, oxygen, and fentanyl. The diaphragm was monitored by measuring transdiaphragmatic pressure following bilateral phrenic nerve stimulation. After succinylcholine, the time from injection of succinylcholine to maximum depression of the single twitch response (onset time) was of 50 ± 11 s (±SD) for D compared to 80 ± 24 s for AP (P < 0.001). After succinylcholine, recovery from paralysis was earlier for D than AP. Single twitch height (TH) returned to 25% of its control value (T25) after 5 ± 2 min for D compared to 7 ± 3 min for AP (P < 0.001). Complete recovery of TH (T100) was achieved after 9 ± 4 min for D and 11 ± 5 min for AP (P < 0.01). Recovery index (T25–75) was of 2 ± 1 min for both muscles. After atracurium, the onset time for D was of 137 ± 31 s compared to 181 ± 45 s for AP (P < 0.001). The T25 was achieved after 38 ± 7 min for D compared to 63 ± 13 min for AP (P < 0.001). The TH of D returned to T100 after 60 ± 12 min compared to 87 ± 17 min for AP (P < 0.01). The train-of-four ratio returned to 1 after 64 ± 15 min for D compared to 99 ± 21 min for AP (P < 0.001). After an intubating dose of succinylcholine (0.8 mg • kg−1) or atracurium (0.6 mg • kg−1), D was always completely paralyzed, when the TH of AP was abolished and the TH of D had completely recovered when the TH of the AP had returned to 100%.
Isoflurane When Compared to Enflurane and Halothane Decreases the Frequency of Cerebral Ischemia During Carotid Endarterectomy
Authors: Michenfelder John D. , Sundt Thoralf M. , Fode Nicolee , Sharbrough Frank W.
Published: September 2006

Data from the records of patients who underwent 2223 carotid endarterectomies at the Mayo Clinic between January 1, 1972, and December 31, 1985, were abstracted to compare the effects of isoflurane, enflurane, and halothane on the critical cerebral blood flow (CBF) (i.e., the CBF below which the majority of patients develop EEG ischemic changes within 3 min of carotid occlusion), the incidence of EEG ischemic changes, and the neurologic outcome. In a total of 2196 of these procedures, the patient received one of the three volatile anesthetics and, in 2010 of these, both the EEG and the CBF were monitored. Chronologically, halothane was the primary agent from 1972–1974; enflurane progressively replaced halothane during 1975–1981; and isoflurane was used almost exclusively since 1982. This analysis confirmed a previous study that the critical CBF during isoflurane anesthesia (703 procedures) was approximately 10 ml ± 100 g−1 • min−1, as contrasted to that of approximately 20 ml ± 100 g−1 • min−1 during halothane anesthesia (467 procedures). This analysis also established that the critical CBF during enflurane anesthesia (840 procedures) was approximately 15 ml ± 100 g−1 • min−1. The incidence of EEG ischemic changes was significantly less (P < 0.001) during isoflurane anesthesia (18%) than during either enflurane (26%) or halothane (25%) anesthesia. This difference occurred despite the fact that the preoperative risk status was greater in the patients given isoflurane. There was no difference in neurologic outcome between the three anesthetics, and none was expected, since all patients with EEG changes were immediately shunted, if possible. The authors conclude that relative to halothane and enflurane, isoflurane does offer a degree of cerebral protection for transient incomplete regional cerebral ischemia during carotid endarterectomy.
Closed-loop Feedback Control of Methohexital Anesthesia by Quantitative EEG Analysis in Humans
Authors: Schwilden Helmut , Schüttler Jürgen , Stoeckel Horst
Published: September 2006

A combined pharmacokinetic and pharmacodynamic model of methohexital was used to establish and evaluate feedback control of methohexital anesthesia in 13 volunteers. The median frequency of the EEG power spectrum served as the pharmacodynamic variable constituting feedback. Median frequency values from 2–3 Hz were chosen as the desired EEG level (set-point). In 11 volunteers, the feedback system succeeded in maintaining a satisfactory depth of anesthesia (i.e., unresponsiveness to verbal commands and tactile stimuli). During feedback control, 75% of all measured median frequency values were in the preset range of 2–3 Hz. This distribution of median frequency was obtained by applying random stimulation (six different acoustic and tactile stimuli) to the volunteers approximately every 1.5 min. The decrease of median frequency from baseline to anesthetic values was primarily induced by increasing the fractional power in the frequency band of 0.5–2 Hz from 12.6 ± 4.5% (mean ± SD) to 46.0 ± 2.5%. The median time to recovery (as defined by opening eyes on command) after cessation of the feedback control period was 20.6 min (10.7–44.5 min) when median EEG frequency was 5.2 Hz (4.7–8.4 Hz). The average requirement of methohexital (mean ± SD) during the 2 h was 1.02 ± 0.16 g. It is concluded that pharmacokinetic-pharmacodynamic models of intravenous anesthetics established previously may be used to form a suitable background for model-based feedback control of anesthesia by quantitative EEG analysis. This approach gives a possible solution to the problem of adapting pharmacokinetic and pharmacodynamic data to individuals when using population mean data as starting values for drug therapy.