bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple valley couplings in nanometer Si metal–oxide–semiconductor field-effect transistors
Authors: Deng Hui-Xiong , Jiang Xiang-Wei , Luo Jun-Wei , Li Shu-Shen , Xia Jian-Bai , Wang Lin-Wang
Published: June 2008

We investigate the couplings between different energy band valleys in a metal–oxide–semiconductor field-effect transistor (MOSFET) device using self-consistent calculations of million-atom Schrödinger–Poisson equations. Atomistic empirical pseudopotentials are used to describe the device Hamiltonian and the underlying bulk band structure. The MOSFET device is under nonequilibrium condition with a source-drain bias up to 2 V and a gate potential close to the threshold potential. We find that all the intervalley couplings are small, with the coupling constants less than 3 meV. As a result, the system eigenstates derived from different bulk valleys can be calculated separately. This will significantly reduce the simulation time because the diagonalization of the Hamiltonian matrix scales as the third power of the total number of basis functions.
Analysis of barrier height at crystalline domain boundary and in-domain mobility in pentacene polycrystalline films on SiO2
Authors: Matsubara Ryousuke , Ohashi Noboru , Sakai Masatoshi , Kudo Kazuhiro , Nakamura Masakazu
Published: June 2008

Crystalline domain size and temperature dependences of the carrier mobility of commonly used pentacene polycrystalline films on SiO2 have been studied by four-point-probe field-effect transistor measurements. The mobility is found to be proportional to the crystalline domain size and thermally activated. This behavior is well explained by a polycrystalline model with the diffusion theory, and thereby the barrier height at boundary and the mobility in domain are calculated to be 150meV and 1.0cm2∕Vs, respectively. The in-domain mobility is lower than those expected in single crystals, which suggests that there exist some other limiting factors of carrier transport than the domain boundaries.
Reduction in threshold voltages in GaN-based metal oxide semiconductor field effect transistors
Authors: Fujishima Tatsuya , Otake Hirotaka , Ohta Hiroaki
Published: June 2008

The dc characteristics, such as on-resistances (Ron) and threshold voltages (Vth), of gallium nitride-based metal oxide semiconductor field effect transistors with vertical trench gates have been theoretically derived. The optimized acceptor density and the thickness of p-type layers for n channels (channel length) were estimated to be 3×1017cm−3 and 0.5μm, respectively, in order to realize Ron in the sub-mΩcm2 range. On the other hand, this resulted in a high Vth of 18V due to the wide bandgap. To achieve low Ron and moderate Vth less than 10V simultaneously, the insertion of an additional p−-type or n-type layer with finite thickness between the gate insulator and the p-type layer was suggested.
Multibands of negative refractive indexes in the left-handed metamaterials with multiple dendritic structures
Authors: Zhu Weiren , Zhao Xiaopeng , Guo Jiquan
Published: June 2008

We demonstrate that the multibands of negative refraction indexes in the left-handed metamaterials may be appeared based on multiple dendritic structures cells. Employing microwave transmission experiment, the medium exhibits simultaneous negative refraction at the frequencies of 9.50, 10.24, and 10.78GHz for the electromagnetic wave parallel incidence, and at the frequencies of 9.24, 9.98, and 10.78GHz for normal incidence. The multiple dendritic metamaterials here open a way to prepare the cloak suitable for multifrequencies, especially for the cloak of infrared or visible frequency.
Does dam parity affect the performance of ewe progeny born to 2-year-old ewes?
Authors: Kenyon P. R. , Morris S. T. , Blair H. T. , Stafford K. J.
Published: June 2008

An increasing number of ewe lambs are being presented for breeding in New Zealand, resulting in more two-tooth ewes of second parity compared with the more normal first parity. The effect of this on the resulting ewe progeny is unknown but is of interest as they are potential replacement ewes. This study was designed to determine if parity of Romney two-tooth ewes had any effect on their ewe lamb progeny to 20 months of age. Two-hundred and fifty female progeny born to two-tooth dams, which had lambed as a ewe lamb (n = 97), failed to conceive at ewe lamb breeding (n = 79), or had not been presented for breeding as a ewe lamb (n = 74), were weighed at regular intervals. The progeny also had onset of puberty and two-tooth breeding and pregnancy scanning performance measured. There were no effects of dam group on liveweight, condition score, 18-month breeding performance or pregnancy diagnosis. However, ewe lambs born to dams which failed to conceive as ewe lambs themselves were less likely (P < 0.05) to achieve puberty. In comparison with single-born lambs, twin-born ewes were lighter (P < 0.05) during their first year of age only. Birth rank had no effect on puberty onset or 18-month breeding performance. These findings indicate that ewe progeny born to second parity two-tooths or two-tooths, which were not presented for breeding as a ewe lamb, do not differ in their productive performance and that either group are suitable as replacement ewes. However, progeny born to two-tooth dams, which failed to conceive as a ewe lamb, would be less suitable as replacement ewes in production systems where ewe lamb breeding is an integral component of the system. Further studies are required to determine if similar relationships would be observed under differing environmental conditions and with different breeds.
Ruminal protein degradability of a range of tropical pastures
Authors: Bowen M. K. , Poppi D. P. , McLennan S. R.
Published: June 2008

The rumen degradability parameters of the diet selected by two to four oesophageal-fistulated Brahman steers grazing a range of tropical pastures were determined by incubation of extrusa in nylon bags suspended in the rumen of rumen-fistulated (RF) Brahman steers. The effective protein degradability (Edg) was determined by measuring the rate of disappearance of neutral detergent insoluble nitrogen (NDIN) less acid detergent insoluble nitrogen (ADIN) in the incubated extrusa. Six to eight RF steers also grazed each of the pastures along with the oesophageal-fistulated steers, to allow determination of key rumen parameters and rumen particulate matter fractional outflow rates (FOR). The seven pastures studied included: native tropical grass (C4) pasture (major species Heteropogon contortus and Bothriochloa bladhii), studied in the early wet (NPEW), the wet/dry transition (NPT) and the dry (NPD) seasons; introduced tropical grass (C4) pasture (Bothriochloa insculpta), studied in the mid wet season (BB); the introduced tropical legumes (C3), Lablab purpureus (LL) and Clitoria ternatea (BP); and the temperate grass (C3) pasture, ryegrass (Lolium multiflorum, RG). Using the measured particle FOR values in calculations, the Edg estimates were very high for both C4 and C3 species: 0.82–0.91 and 0.95–0.98 g/g crude protein (CP), respectively. Substitution of an assumed FOR (kp = 0.02/h) for the measured values for each pasture type did not markedly affect estimates of Edg. However, C4 tropical grasses had much lower effective rumen degradable protein (ERDP) fractions (23–66 g/kg DM) than the C3 pasture species RG and LL (356 and 243 g/kg DM, respectively). This was associated with a lower potential degradability and degradation rate of organic matter (OM) in sacco, lower in vitro organic matter digestibility (IVOMD) and CP concentrations in the extrusa, and lower ammonia-N and branched-chain fatty acid concentrations in rumen fluid for the tropical grasses. As tropical grass pastures senesced, there was a decline in Edg, the ERDP and rumen undegradable protein (UDP) fractions, the potential degradability and degradation rate of OM and the IVOMD. These results provide useful data for estimating protein supply to cattle grazing tropical pastures.
Effect of heifer frame size on their subsequent reproductive performance and preweaning performance of their calves
Authors: Taylor G. J. , Swanepoel F. J. C. , Webb E. C. , Stroebel A.
Published: June 2008

The effects of heifer frame size on subsequent performance and the preweaning growth of calves were evaluated using records collected from the Waterburg Estates at Otjiwarongo, Namibia. Based on hip height at 18 months of age, heifers were assigned to three different frame size groups: small (<124 cm), medium (124 to 135 cm), or large (>135 cm). Calving rate (CR), calving date (CD), postnatal calf survival rate (CSR), reproductive efficiency (Sandex), weaning rate (WR), birthweight (BW), weaning weight (WT) and preweaning average daily gain (ADG) were collected from first (n = 830), second (n = 623) and third and greater parity (n = 571) cows. Frame size of heifers significantly influenced (P < 0.001) CR in second and third and greater parity. The postnatal CSR was similar for all frame size and parity groups. WR of large frame size, second-parity cows was less (P < 0.001) than that of small and medium frame size animals. Birthweights of calves born to large frame size animals were significantly higher (P < 0.05) than the small and medium frame size animals. Small frame size animals, as first parity cows, had calves with lower (P < 0.05) WT than those weaned by medium and larger frame size animals. In first parity cows, calves of large frame size had greater ADG (P < 0.05), but in second parity cows the calves from medium frame size (P < 0.05) out performed those of small and large frame size, while calves from third and greater parity cows of medium and larger frame size had greater (P < 0.05) ADG than cows with a small frame size. Male calves were heavier (P < 0.05) at birth, at weaning and grew faster (ADG) than their female counterparts. Due to the later calving dates (P < 0.05), the reproductive efficiency (Sandex) of large frame size at second and third and greater parity groups was lower (P < 0.001). Therefore, selecting cattle for the extensive hot and dry climatic regions of Southern Africa, the recommended cow frame size should be a medium frame.
Occurrence, home range and movement patterns of juvenile bull (Carcharhinus leucas) and lemon (Negaprion brevirostris) sharks within a Florida estuary
Authors: Yeiser B. G. , Heupel M. R. , Simpfendorfer C. A.
Published: June 2008

The movement patterns of large juveniles are poorly known for many shark species. With increasing pressure on shark populations these data are critical for the management of large coastal species. A series of acoustic receivers were positioned in Pine Island Sound, Florida, USA, to passively track the long-term movements of large juvenile bull (Carcharhinus leucas) and lemon (Negaprion brevirostris) sharks. Nineteen C. leucas and five N. brevirostris were monitored during 2003 and 2004. Individual C. leucas were present for 8 to 89 days, while N. brevirostris were present for 12 to 83 days. Weekly minimum convex polygons and kernel utilisation distributions were calculated to demonstrate the home range and core areas of use of both species. Spectral analysis demonstrated that several N. brevirostris showed repetitive diel north–south movement patterns over periods of up to 28 consecutive days. C. leucas demonstrated regular use of backwater habitats. Long-term use of estuarine areas by these large juvenile sharks suggests that estuarine coastal lagoons provide an important habitat for this portion of their life history and as such, protection of these habitats may assist in shark management and conservation.
Temporal patterns of gastropod egg mass deposition on southeastern Australian shores
Authors: Przeslawski Rachel
Published: June 2008

Spawning of marine invertebrates may be affected by environmental factors (e.g. food availability, environmental stress) or intrinsic factors (e.g. phylogenetic constraints, developmental mode); intrinsic factors may obscure environmental effects. Two-year surveys of gastropod egg mass deposition were conducted at two rocky intertidal sites in south-eastern Australia to test the following hypotheses: (1) temporal patterns of spawning are more similar within taxonomic order than across orders; and (2) species with planktotrophic larvae are more likely to spawn in seasons coinciding with maximum food availability. There were no discernible effects of either order or developmental mode on spawning patterns, suggesting that spawning behaviour is unrelated to taxonomic order or larval food availability. Alternatively, low numbers of species in certain groups may have increased the risk of not detecting significant effects (type II error). Comparisons with anecdotal data from other regions suggest that developmental mode may indeed play a role in marine gastropod spawning. Criteria are provided for future comparative studies, including a direct focus on specific families and the inclusion of similar latitudes and habitats to those used here. Such studies will help to determine the roles of developmental mode, food availability and environmental stress in the evolution of egg mass deposition.
Risk Factors for Methicillin-Resistant Staphylococcus aureus (MRSA) Acquisition in Roommate Contacts of Patients Colonized or Infected With MRSA in an Acute-Care Hospital
Authors: Moore Christine , Dhaliwal Jastej , Tong Agnes , Eden Sarah , Wigston Cindi , Willey Barbara ,   Mount Sinai Hospital Infection Control Team, McGeer Allison
Published: June 2008

Objective.

To identify risk factors for acquisition of methicillin-resistant Staphylococcus aureus (MRSA) in patients exposed to an MRSA-colonized roommate.

Design.

Retrospective cohort study.

Setting.

A 472-bed acute-care teaching hospital in Toronto, Canada.

Patients.

Inpatients who shared a room between 1996 and 2004 with a patient who had unrecognized MRSA colonization.

Methods.

Exposed roommates were identified from infection-control logs and from results of screening for MRSA in the microbiology database. Completed follow-up was defined as completion of at least 2 sets of screening cultures (swab samples from the nares, the rectum, and skin lesions), with at least 1 set of samples obtained 7–10 days after the last exposure. Chart reviews were performed to compare those who did and did not become colonized with MRSA.

Results.

Of 326 roommates, 198 (61.7%) had completed follow-up, and 25 (12.6%) acquired MRSA by day 7–10 after exposure was recognized, all with strains indistinguishable by pulsed-field gel electrophoresis from those of their roommate. Two (2%) of 101 patients were not colonized at day 7–10 but, with subsequent testing, were identified as being colonized with the same strain as their roommate (one at day 16 and one at day 18 after exposure). A history of alcohol abuse (odds ratio [OR], 9.8 [95% confidence limits {CLs}, 1.8, 53]), exposure to a patient with nosocomially acquired MRSA (OR, 20 [95% CLs, 2.4,171]), increasing care dependency (OR per activity of daily living, 1.7 [95% CLs, 1.1, 2.7]), and having received levofloxacin (OR, 3.6 [95% CLs, 1.1,12]) were associated with MRSA acquisition.

Conclusions.

Roommates of patients with MRSA are at significant risk for becoming colonized. Further study is needed of the impact of hospital antimicrobial formulary decisions on the risk of acquisition of MRSA.
Theoretical Studies on Electronic Structures and Spectroscopy of Fluorescent Arylamino Fumaronitrile
Authors: Chen Xiao-peng , Ding Yu-qi , Teng Qi-wen
Published: June 2008

A new series of fluorescent arylamino fumarinitrile derivatives was designed and optimized using density function theory at the B3LYP/6-31G* level. Based on the optimized geometries, the electronic, fluorescent and 13C NMR spectra are calculated with INDO/CIS, CIS-ZINDO TD, and B3LYP/6-31G* methods, respectively. Starting with the first of the series, the LUMO-HOMO energy gaps of the derivatives become wider and the fluorescent wavelengths and the main peaks in the electronic spectra are blue-shifted owing to the large steric effect of naphthyl rings. On the contrary, the energy gaps of the derivatives turn narrow, and the fluorescent wavelengths and the main peaks in the electronic spectra are red-shifted since hydroxyl groups improve the symmetry and extend the conjugation system. The chemical shifts of sp2-C on the phenyl rings are moved upfield, while chemical shifts of carbon atoms on the cyano groups and those connected with the cyano groups are changed downfield in the presence of hydroxyl groups.
Aromaticity of Heterofullerenes C18BxNy(x+y= 2) and Their Molecular Ions
Authors: Chen Jia-li , Kerim Ablikim
Published: June 2008

The aromaticity of all possible substituted fullerene isomers of C18N2, C18B2, C18BN, and their molecular ions which originate from the C20 (Ih) cage were studied by the topological resonance energy (TRE) and the percentage topological resonance energy methods. The relationship between the aromaticity of C18BxNy isomers and the sites where the heteroatoms dope at the C20 (Ih) cage is discussed. Calculation results show that at the neutral and cationic states all the isomers are predicted to be antiaromatic with negative TREs, but their polyvalent anions are predicted to be aromatic with positive TREs. The most stable isomer is formed by heteroatom doping at the 1, 11-sites in C18N2, C18B2, and C18BN. Heterofullerenes are more aromatic than C20. The stability order in the neutral states is C18N2 > C18 BN > C18 B2 > C20. The stability order in closed-shell is C18B28 > C206 > C18BN6 > C18N24. This predicts theoretically that their polyvalent anions have high aromaticity.
Ultrasonic Study on JahnTeller Distortions in La1/3Sr2/3CoO3
Authors: Yi Jian-xing , Kong Hui , Zhu Chang-fei
Published: June 2008

The longitudinal ultrasonic velocity (V1), attenuation (1), magnetization and resistivity of single phase poly crystalline La1/3Sr2/3CoO3 were measured as a function of temperature from 20 K to 300 K. The resistivity shows metallic behavior in the whole temperature range and a kink at 235 K was observed, which coincides with the ferromagnetic transition temperature (Tc). As the temperature cools down from Tc, the V1 softens conspicuously at beginning and reaches a minimum at 120 K. After that the V1 dramatically stiffens below 120 K accompanied by a wide attenuation peak. The analysis of the results suggests that these ultrasonic anomalies may correspond to local lattice distortions via the JahnTeller effect of intermediate spin Co3+.
Effect of Potassium Addition on Coprecipitated Iron Catalysts for Fischer-Tropsch Synthesis Using Bio-oil-syngas
Authors: Wang Zhao-xiang , Dong Ting , Kan Tao , Li Quan-xin
Published: June 2008

The effects of potassium addition and the potassium content on the activity and selectivity of coprecipitated iron catalyst for Fischer-Tropsch synthesis (FTS) were studied in a fixed bed reactor at 1.5 MPa, 300C, and contact time (W/F) of 12.5 gcath/mol using the model bio-oil-syngas of H2/CO/CO2/N2 (62/8/25/5, vol%). It was found that potassium addition increases the catalyst activity for FTS and the reverse water gas shift reaction. Moreover, potassium increases the average molecular weight (chain length) of the hydrocarbon products. With the increase of potassium content, it was found that CH4 selectivity decreases and the selectivity of liquid phase products (C5+) increases. The characteristics of FTS catalysts with different potassium content were also investigated by various characterization measurements including X-ray diffraction, X-ray photoelectron spectroscopy and Brunauer-Emmett-Teller surface area. Based on experimental results, 100Fe/6Cu/16Al/6K (weight ratio) was selected as the optimal catalyst for FTS from bio-oil-syngas. The results indicate that the 100Fe/6Cu/16Al/6K catalyst is one of the most promising candidates to directly synthesize liquid bio-fuel using bio-oil-syngas.
Effects of Calcium Ions on Thermodynamic Properties of Mixed Bilirubin/Cholesterol Monolayers
Authors: Wu Qiong , Tang Yu-feng , Li Ye-min , Xie An-jian , Shen Yu-hua , Zhu Jin-miao , Li Chuan-hao
Published: June 2008

The mixed monolayer behavior of bilirubin/cholesterol was studied through surface pressure-area (-A) isotherms on aqueous solutions containing various concentrations of calcium ions. Based on the data of -A isotherms, the mean area per molecule, collapse pressure, surface compressibility modulus, excess molecular areas, free energy of mixing, and excess free energy of mixing of the monolayers on different subphases were calculated. The results show an expansion in the structure of the mixed monolayer with Ca2+ in subphase, and non-ideal mixing of the components at the air/water interface is observed with positive deviation from the additivity rule in the excess molecular areas. The miscibility between the components is weakened with the increase of concentration of Ca2+ in subphase. The facts indicate the presence of coordination between Ca2+ and the two components. The mixed monolayer, in which the molar ratio of bilirubin to cholesterol is 3:2, is more stable from a thermodynamic point of view on pure water. But the stable 3:2 stoichiometry complex is destroyed with the increase of the concentration of Ca2+ in subphase. Otherwise, the mixed monolayers have more thermodynamic stability at lower surface pressure on Ca2+ subphase.
Spectral Properties and Solubilization Location of 2-Ethylhexyl 4-(N,N-Dimethylamino) benzoate in Micelles
Authors: Ding Ning , Du Xin-zhen , Wang Chun , Lu Xiao-quan
Published: June 2008

Dual fluorescence and UV absorption of 2-ethylhexyl 4-(N,N-dimethylamino)benzoate (EHDMAB) were investigated in cationic, non-ionic and anionic micelles. When EHDMAB was solubilized in different micelles, the UV absorption of EHDMAB was enhanced. Twisted intramolecular charge transfer (TICT) emission with longer wavelength was observed in ionic micelles, whereas TICT emission with shorter wavelength was obtained in non-ionic micelles. In particular, dual fluorescence of EHDMAB was significantly quenched by the positively charged pyridinium ions arranged in the Stern layer of cationic micelles. UV radiation absorbed mainly decays via TICT emission and radiationless deactivation. The dimethylamino group of EHDMAB experiences different polar environments in ionic and non-ionic micelles according to the polarity dependence of TICT emission of EHDMAB in organic solvents. In terms of the molecular structures and sizes of EHDMAB and surfactants, each individual EHDMAB molecule should be buried in micelles with its dimethylamino group toward the polar head groups of different micelles and with its 2-ethylhexyl chain toward the hydrophobic micellar core. Dynamic fluorescence quenching measurements of EHDMAB provide further support for the location of EHDMAB in different micelles.
Effect of Short Chain Alcohols upon Viscosity of TTAB Solution
Authors: Yan Yu-fei , Li Hua-zhen , Yang Hai-yang , Qian Jia-sheng , Zhu Ping-ping , He Ping-sheng
Published: June 2008

The effect of ethanol (C2H5OH), propanol (C3H7OH), and butanol (C4H9OH) upon the viscosity of tetradecyltrimethylammonium bromide (TTAB) solution in the presence or absence of KBr at 30 C was investigated, where the surfactant concentration CS is kept constant. In the absence of KBr, the relative viscosity r of TTAB solution increases linearly with the alcohol concentration CA, indicating that the alcohols do not promote micelle formation of TTAB. In the presence of KBr, r linearly decreases with CA for C2H5OH, but it exhibits a maximum with increasing CA for C3H7OH or C4H9OH. The facts reveal that C2H5OH or C4H9OH promotes the micelle formation of TTAB. A possible explanation is that the hydrophobicity of the micellar interior is enhanced by KBr, so that C2H5OH or C4H9OH can dissolve in micelle and promotes micelle formation. In the presence of KCl, which is less efficient in promoting the micelle formation of cationic surfactant, both C3H7OH and C4H9OH have only a slight effect on the micelle formation. In contrast, due to the hydrophilicity, C2H5OH cannot dissolve in micelles in the presence of KBr or KCl.
Preparation and Spectroscopic Study of Different Stoichiometric Solid Supramolecular Inclusion Complexes of -Cyclodextrin with Short Chain Aliphatic Amines
Authors: Song Le-xin , Teng Chuan-feng , Wang Hai-ming , Bai Lei
Published: June 2008

The solid Supramolecular complexes of -cyclodextrin (-CD) with ethylenediamine 1, diethylenetriamine 2 and triethylamine 3 were obtained and characterized using elemental analysis, powder X-ray diffraction, infrared spectroscopy, thermogravimetric analysis, and 1H nuclear magnetic resonance spectroscopy. Based on the results of elemental analysis and 1H NMR, the guest-host stoichiometries of the three solid complexes were determined to be 5:2 for 1- -CD, 1:1 for 2- -CD, and 1:3 for 3- -CD. The yields were relative to the molar volume ratio of guest to -CD cavity, and increased in the order: 1- -CD2- -CD3- -CD. X-ray diffraction patterns of the inclusion complexes gave very good exhibitions not only in location of diffraction peaks but also in shape and diffraction intensity of the peaks due to the intermolecular complexations between -CD and the guests. The formation of host-guest inclusion complexes exhibited obviously enhanced phase change temperatures of the complexed guests such as 1 and 3. The H-5 protons located at the narrower rim inside the CD cavity experienced a higher shift upon inclusion while all other protons experienced lower shifts.
Growth Mechanism and Characterization of Single-crystalline Ga-doped SnO2 Nanowires and Self-organized SnO2/Ga2O3 Heterogeneous Microcomb Structures
Authors: Su Yong , Xu Liang , Liang Xue-mei , Chen Yi-qing
Published: June 2008

Single-crystalline Ga-doped SnO2 nanowires and SnO2:Ga2O3 heterogeneous microcombs were synthesized by a simple one-step thermal evaporation and condensation method. They were characterized by means of X-ray powder diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDS), transmission electron microscopy (TEM) and selected-area electron diffraction (SAED). FE-SEM images showed that the products consisted of nanowires and microcombs that represent a novel morphology. XRD, SAED and EDS indicated that they were single-crystalline tetragonal SnO2. The influence of experimental conditions on the morphologies of the products is discussed. The morphology of the product showed a ribbon-like stem and nanoribbon array aligned evenly along one or both side of the nanoribbon. It was found that many Ga2O3 nanoparticles deposited on the surface of the microcombs. The major core nanoribbon grew mainly along the [110] direction and the self-organized branching nanoribbons grew epitaxially along [110] or [110] orientation from the (110) plane of the stem. A growth process was proposed for interpreting the growth of these remarkable SnO2:Ga2O3 heterogeneous microcombs. Due to the heavy doping of Ga, the emission peak in photoluminescence spectra has red-shifted as well as broadened significantly.
Latrunculin A Delays Anaphase Onset in Fission Yeast by Disrupting an Ase1-independent Pathway Controlling Mitotic Spindle Stability
Authors: Meadows John C. , Millar Jonathan
Published: June 2008

It has been proposed previously that latrunculin A, an inhibitor of actin polymerization, delays the onset of anaphase by causing spindle misorientation in fission yeast. However, we show that Δmto1 cells, which are defective in nucleation of cytoplasmic microtubules, have profoundly misoriented spindles but are not delayed in the timing of sister chromatid separation, providing compelling evidence that fission yeast does not possess a spindle orientation checkpoint. Instead, we show that latrunculin A delays anaphase onset by disrupting interpolar microtubule stability. This effect is abolished in a latrunculin A-insensitive actin mutant and exacerbated in cells lacking Ase1, which cross-links antiparallel interpolar microtubules at the spindle midzone both before and after anaphase. These data indicate that both Ase1 and an intact actin cytoskeleton are required for preanaphase spindle stability. Finally, we show that loss of Ase1 activates a checkpoint that requires only the Mad3, Bub1, and Mph1, but not Mad1, Mad2, or Bub3 checkpoint proteins.
Telomerase Reverse Transcriptase Is Required for the Localization of Telomerase RNA to Cajal Bodies and Telomeres in Human Cancer Cells
Authors: Tomlinson Rebecca L. , Abreu Eladio B. , Ziegler Tania , Ly Hinh , Counter Christopher M. , Terns Rebecca M. , Terns Michael P.
Published: June 2008

Telomere maintenance by telomerase is critical for the unlimited division potential of most human cancer cells. The two essential components of human telomerase, telomerase RNA (hTR) and telomerase reverse transcriptase (hTERT), are recruited from distinct subnuclear sites to telomeres during S phase. Throughout the remainder of the cell cycle hTR is found primarily in Cajal bodies. The localization of hTR to Cajal bodies and telomeres is specific to cancer cells where telomerase is active and is not observed in primary cells. Here we show that the trafficking of hTR to both telomeres and Cajal bodies depends on hTERT. RNA interference–mediated depletion of hTERT in cancer cells leads to loss of hTR from both Cajal bodies and telomeres without affecting hTR levels. In addition, expression of hTERT in telomerase-negative cells (including primary and ALT cancer cell lines) induces hTR to localize to both sites. Factors that did not stimulate hTR localization in our experiments include increased hTR RNA levels and Cajal body numbers, and expression of SV40 large T antigen and oncogenic Ras. Our findings suggest that the trafficking of telomerase to Cajal bodies and telomeres in cancer cells correlates with and depends on the assembly of the enzyme.
Nucleocytoplasmic Trafficking of G2/M Regulators in Yeast
Authors: Keaton Mignon A. , Szkotnicki Lee , Marquitz Aron R. , Harrison Jake , Zyla Trevin R. , Lew Daniel J.
Published: June 2008

Nucleocytoplasmic shuttling is prevalent among many cell cycle regulators controlling the G2/M transition. Shuttling of cyclin/cyclin-dependent kinase (CDK) complexes is thought to provide access to substrates stably located in either compartment. Because cyclin/CDK shuttles between cellular compartments, an upstream regulator that is fixed in one compartment could in principle affect the entire cyclin/CDK pool. Alternatively, the regulators themselves may need to shuttle to effectively regulate their moving target. Here, we identify localization motifs in the budding yeast Swe1p (Wee1) and Mih1p (Cdc25) cell cycle regulators. Replacement of endogenous Swe1p or Mih1p with mutants impaired in nuclear import or export revealed that the nuclear pools of Swe1p and Mih1p were more effective in CDK regulation than were the cytoplasmic pools. Nevertheless, shuttling of cyclin/CDK complexes was sufficiently rapid to coordinate nuclear and cytoplasmic events even when Swe1p or Mih1p were restricted to one compartment. Additionally, we found that Swe1p nuclear export was important for its degradation. Because Swe1p degradation is regulated by cytoskeletal stress, shuttling of Swe1p between nucleus and cytoplasm serves to couple cytoplasmic stress to nuclear cyclin/CDK inhibition.
Predicting sub-Golgi localization of type II membrane proteins
Authors: van Dijk A. D. J. , Bosch D. , ter Braak C. J. F. , van der Krol A. R. , van Ham R. C. H. J.
Published: June 2008

Motivation: Recent research underlines the importance of finegrained knowledge on protein localization. In particular, subcompartmental localization in the Golgi apparatus is important, for example, for the order of reactions performed in glycosylation pathways or the sorting functions of SNAREs, but is currently poorly understood.

Results: We assemble a dataset of type II transmembrane proteins with experimentally determined sub-Golgi localizations and use this information to develop a predictor based on the transmembrane domain of these proteins, making use of a dedicated proteinstructure based kernel in an SVM. Various applications demonstrate the power of our approach. In particular, comparison with a large set of glycan structures illustrates the applicability of our predictions on a ‘glycomic’ scale and demonstrates a significant correlation between sub-Golgi localization and the ordering of different steps in glycan biosynthesis.

Contact:  roeland.vanham@wur.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Predicting functional regulatory polymorphisms
Authors: Torkamani Ali , Schork Nicholas J.
Published: June 2008

Motivation: Limited availability of data has hindered the development of algorithms that can identify functionally meaningful regulatory single nucleotide polymorphisms (rSNPs). Given the large number of common polymorphisms known to reside in the human genome, the identification of functional rSNPs via laboratory assays will be costly and time-consuming. Therefore appropriate bioinformatics strategies for predicting functional rSNPs are necessary. Recent data from the Encyclopedia of DNA Elements (ENCODE) Project has significantly expanded the amount of available functional information relevant to non-coding regions of the genome, and, importantly, led to the conclusion that many functional elements in the human genome are not conserved.

Results: In this article we describe how ENCODE data can be leveraged to probabilistically determine the functional and phenotypic significance of non-coding SNPs (ncSNPs). The method achieves excellent sensitivity (∼80%) and specificity (∼99%) based on a set of known phenotypically relevant and non-functional SNPs. In addition, we show that our method is not overtrained through the use of cross-validation analyses.

Availability: The software platforms used in our analyses are freely available (http://www.cs.waikato.ac.nz/ml/weka/). In addition, we provide the training dataset (Supplementary Table 3), and our predictions (Supplementary Table 6), in the Supplementary Material.

Contact:  nschork@scripps.edu.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cross-front variations in adult abundance and recruitment of Patagonian scallop (Zygochlamys patagonica) at the SW Atlantic Shelf Break Front
Authors: Mauna A. Cecilia , Franco Bárbara C. , Baldoni Ana , Acha E. Marcelo , Lasta Mario L. , Iribarne Oscar O.
Published: June 2008

Mauna, A. C., Franco, B. C., Baldoni, A., Acha, E. M., Lasta, M. L., and Iribarne, O. O. 2008. Cross-front variations in adult abundance and recruitment of Patagonian scallop (Zygochlamys patagonica) at the SW Atlantic Shelf Break Front. – ICES Journal of Marine Science, 65: 1184–1190. We studied cross-front variations in adult abundance and recruitment of Patagonian scallop (Zygochlamys patagonica) and their relationship with the Shelf Break Front and satellite-derived chlorophyll a in the Southwest Atlantic between 38°S and 39°30′S. Integrated data from commercial fleets (CF, 1996–2005), research cruises (RC, 1998–2005), sea surface temperature (SST; 1985–1997), and satellite-derived chlorophyll a (CSAT; 1998–2004) were included in the analysis. One-way ANOVA was used to assess differences in recruitment and scallop abundance in a cross-front direction. The abundance of scallops was greatest (RC > 200 kg h−1) closer to the onshore side of the front or beneath it, and the East–West extension of scallop beds (∼40 km) matched the seasonal zonal displacement of the front (∼37 km). The highest CSAT gradients were west of or matched the position of the front. The annual mean position of the front correlated with the spatial variability in recruitment within areas where the species recruited successfully (RC > 2000 h−1). The spatial variability in adult abundance and recruitment of scallops is strongly related to the spatial variability in the position of the front and with the high CSAT concentrations associated with it.
The sweet life: diet sugar concentration influences paracellular glucose absorption
Authors: Napier Kathryn R , Purchase Cromwell , McWhorter Todd J , Nicolson Susan W , Fleming Patricia A
Published: June 2008

Small birds and bats face strong selection pressure to digest food rapidly in order to reduce digesta mass carried during flight. One mechanism is rapid absorption of a high proportion of glucose via the paracellular pathway (transfer between epithelial cells, not mediated by transporter proteins). Intestinal paracellular permeability to glucose was assessed for two nectarivorous passerines, the Australian New Holland honeyeater (
Phylidonyris novaehollandiae
) and African white-bellied sunbird (
Cinnyris talatala
) by measuring the bioavailability of radiolabelled, passively absorbed
l
-glucose. Bioavailability was high in both species and increased with diet sugar concentration (honeyeaters, 37 and 81% and sunbirds, 53 and 71% for 250 and 1000 mmol l
−1
sucrose diets, respectively). We conclude that the relative contribution of paracellular to total glucose absorption increases with greater digesta retention time in the intestine, and paracellular absorption may also be modulated by factors such as intestinal lumen osmolality and interaction with mediated glucose uptake. The dynamic state of paracellular absorption should be taken into account in future studies.
Sea lice escape predation on their host
Authors: Connors B.M , Krkošek M , Dill L.M
Published: June 2008

Parasites seldom have predators but often fall victim to those of their hosts. How parasites respond to host predation can have important consequences for both hosts and parasites, though empirical investigations are rare. The exposure of wild juvenile salmon to sea lice (Lepeophtheirus salmonis) from salmon farms allowed us to study a novel ecological interaction: the response of sea lice to predation on their juvenile pink and chum salmon hosts by two salmonid predators—coho smolts and cut-throat trout. In approximately 70% of trials in which a predator consumed a parasitized prey, lice escaped predation by swimming or moving directly onto the predator. This trophic transmission is strongly male biased, probably because behaviour and morphology constrain female movement and transmission. These findings highlight the potential for sea lice to be transmitted up marine food webs in areas of intensive salmon aquaculture, with implications for louse population dynamics and predatory salmonid health.
Formation of magnetite by bacteria and its application
Authors: Arakaki Atsushi , Nakazawa Hidekazu , Nemoto Michiko , Mori Tetsushi , Matsunaga Tadashi
Published: June 2008

Magnetic particles offer high technological potential since they can be conveniently collected with an external magnetic field. Magnetotactic bacteria synthesize bacterial magnetic particles (BacMPs) with well-controlled size and morphology. BacMPs are individually covered with thin organic membrane, which confers high and even dispersion in aqueous solutions compared with artificial magnetites, making them ideal biotechnological materials. Recent molecular studies including genome sequence, mutagenesis, gene expression and proteome analyses indicated a number of genes and proteins which play important roles for BacMP biomineralization. Some of the genes and proteins identified from these studies have allowed us to express functional proteins efficiently onto BacMPs, through genetic engineering, permitting the preservation of the protein activity, leading to a simple preparation of functional protein–magnetic particle complexes. They were applicable to high-sensitivity immunoassay, drug screening and cell separation. Furthermore, fully automated single nucleotide polymorphism discrimination and DNA recovery systems have been developed to use these functionalized BacMPs. The nano-sized fine magnetic particles offer vast potential in new nano-techniques.
On radial crack and half-penny crack induced by Vickers indentation
Authors: Tang Yuye , Yonezu Akio , Ogasawara Nagahisa , Chiba Norimasa , Chen Xi
Published: June 2008

Based on the stress fields formed upon Vickers indentation, the radial crack and half-penny crack systems are analysed separately using finite-element analyses. The crack length is correlated with the stress intensity factor (SIF) at the crack front and material elastoplastic properties via explicit relationships, from which a reverse analysis can be carried out such that the critical SIF (fracture toughness) can be readily derived once the crack length is measured. The proposed technique is validated by comparing with experimental data in the literature as well as parallel experiments of Vickers indentation-induced cracking.
Models and computational strategies linking physiological response to molecular networks from large-scale data
Authors: Ortega Fernando , Sameith Katrin , Turan Nil , Compton Russell , Trevino Victor , Vannucci Marina , Falciani Francesco
Published: June 2008

An important area of research in systems biology involves the analysis and integration of genome-wide functional datasets. In this context, a major goal is the identification of a putative molecular network controlling physiological response from experimental data. With very fragmentary mechanistic information, this is a challenging task. A number of methods have been developed, each one with the potential to address an aspect of the problem. Here, we review some of the most widely used methodologies and report new results in support of the usefulness of modularization and other modelling techniques in identifying components of the molecular networks that are predictive of physiological response. We also discuss how system identification in biology could be approached, using a combination of methodologies that aim to reconstruct the relationship between molecular pathways and physiology at different levels of the organizational complexity of the molecular network.
Epidemiology and pathogenesis of Kaposi's sarcoma–associated herpesvirus
Authors: Boshoff Chris , Weiss Robin A.
Published: June 2008

Kaposi's sarcoma (KS) occurs in Europe and the Mediterranean countries (classic KS) and Africa (endemic KS), immunosuppressed patients (iatrogenic or post–transplant KS) and those with acquired immunodeficiency syndrome (AIDS), especially among those who acquired human immunodeficiency virus sexually (AIDS–KS). KS–associated herpesvirus (KSHV or HHV–8) is unusual among herpesviruses in having a restricted geographical distribution. Like KS, which it induces in immunosuppressed or elderly people, the virus is prevalent in Africa, in Mediterranean countries, among Jews and Arabs and certain Amerindians. Distinct KSHV genotypes occur in different parts of the world, but have not been identified as having a differential pathogenesis. KSHV is aetiologically linked to three distinct neoplasms: (i) KS, (ii) primary effusion lymphoma, and (iii) plasmablastic multicentric Castleman's disease. The histogenesis, clonality and pathology of the tumours are described, together with the epidemiology and possible modes of transmission of the virus.
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
Authors: Dinger Marcel E. , Amaral Paulo P. , Mercer Tim R. , Pang Ken C. , Bruce Stephen J. , Gardiner Brooke B. , Askarian-Amiri Marjan E. , Ru Kelin , Soldà Giulia , Simons Cas , Sunkin Susan M. , Crowe Mark L. , Grimmond Sean M. , Perkins Andrew C. , Mattick John S.
Published: June 2008

The transcriptional networks that regulate embryonic stem (ES) cell pluripotency and lineage specification are the subject of considerable attention. To date such studies have focused almost exclusively on protein-coding transcripts. However, recent transcriptome analyses show that the mammalian genome contains thousands of long noncoding RNAs (ncRNAs), many of which appear to be expressed in a developmentally regulated manner. The functions of these remain untested. To identify ncRNAs involved in ES cell biology, we used a custom-designed microarray to examine the expression profiles of mouse ES cells differentiating as embryoid bodies (EBs) over a 16-d time course. We identified 945 ncRNAs expressed during EB differentiation, of which 174 were differentially expressed, many correlating with pluripotency or specific differentiation events. Candidate ncRNAs were identified for further characterization by an integrated examination of expression profiles, genomic context, chromatin state, and promoter analysis. Many ncRNAs showed coordinated expression with genomically associated developmental genes, such as Dlx1, Dlx4, Gata6, and Ecsit. We examined two novel developmentally regulated ncRNAs, Evx1as and Hoxb5/6as, which are derived from homeotic loci and share similar expression patterns and localization in mouse embryos with their associated protein-coding genes. Using chromatin immunoprecipitation, we provide evidence that both ncRNAs are associated with trimethylated H3K4 histones and histone methyltransferase MLL1, suggesting a role in epigenetic regulation of homeotic loci during ES cell differentiation. Taken together, our data indicate that long ncRNAs are likely to be important in processes directing pluripotency and alternative differentiation programs, in some cases through engagement of the epigenetic machinery.
The Molecular Basis of Shoot Responses of Maize Seedlings to Trichoderma harzianum T22 Inoculation of the Root: A Proteomic Approach
Authors: Shoresh Michal , Harman Gary E.
Published: June 2008

Trichoderma spp. are effective biocontrol agents for several soil-borne plant pathogens, and some are also known for their abilities to enhance systemic resistance to plant diseases and overall plant growth. Root colonization with Trichoderma harzianum Rifai strain 22 (T22) induces large changes in the proteome of shoots of maize (Zea mays) seedlings, even though T22 is present only on roots. We chose a proteomic approach to analyze those changes and identify pathways and genes that are involved in these processes. We used two-dimensional gel electrophoresis to identify proteins that are differentially expressed in response to colonization of maize plants with T22. Up- or down-regulated spots were subjected to tryptic digestion followed by identification using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry and nanospray ion-trap tandem mass spectrometry. We identified 91 out of 114 up-regulated and 30 out of 50 down-regulated proteins in the shoots. Classification of these revealed that a large portion of the up-regulated proteins are involved in carbohydrate metabolism and some were photosynthesis or stress related. Increased photosynthesis should have resulted in increased starch accumulation in seedlings and did indeed occur. In addition, numerous proteins induced in response to Trichoderma were those involved in stress and defense responses. Other processes that were up-regulated were amino acid metabolism, cell wall metabolism, and genetic information processing. Conversely, while the proteins involved in the pathways noted above were generally up-regulated, proteins involved in other processes such as secondary metabolism and protein biosynthesis were generally not affected. Up-regulation of carbohydrate metabolism and resistance responses may correspond to the enhanced growth response and induced resistance, respectively, conferred by the Trichoderma inoculation.