bluuebunny/crossref_metadata_2025 huggingface dataset:
Fruit and vegetables are similarly categorised by 8–13-year-old children
Authors: Sepulveda Karina Knight , Beltran Alicia , Watson Kathy , Baranowski Tom , Baranowski Janice , Islam Noemi , Missaghian Mariam
Published: June 2008

Objective

This exploratory study assessed how 8–13-year-old children categorised and labelled fruit and vegetables (FaV), and how these were influenced by child characteristics, to specify second-level categories in a hierarchical food search system for a computerised 24 h dietary recall (hdr).

Design

Two sets of food cards, sixty-seven for fruit (F) and sixty-four for vegetables (V), with pictures and names of FaV from ten professionally defined food categories were sorted, separately, by each child into piles of similar foods. Demographic data, BMI and 6-n-propylthiouracil (PROP) taster status were obtained.

Setting

Participants attended the Children’s Nutrition Research Center in the summer of 2006.

Subjects

In all, 152 8–13-year-old children, predominantly English-speaking, of whom sixteen were predominantly Spanish-speaking.

Results

Children created an average of 8·5 (5·3) piles with 7·9 (11·4) cards per pile for the F, and an average of 10·1 (4·8) piles with 6·2 (7·9) cards per pile for the V. No substantial differences in Robinson clustering were detected across subcategories for each of the demographic characteristics, BMI or PROP sensitivity. Children provided clusters names that were mostly ‘Taxonomic – Professional’ labels, such as salads, berries, peppers, for both F (51·8 %) and V (52·1 %).

Conclusions

These categories should be tested to assess their ability to facilitate search of FaV items in a computerised 24 hdr for children in this age group.
Dynamics of Mount Etna before, during, and after the July–August 2001 eruption inferred from GPS and differential synthetic aperture radar interferometry data
Authors: Puglisi Giuseppe , Bonforte Alessandro , Ferretti Alessandro , Guglielmino Francesco , Palano Mimmo , Prati Claudio
Published: June 2008

Ground deformation data from GPS and differential synthetic aperture radar interferometry (DInSAR) techniques are analyzed to study the July–August 2001 Mount Etna eruption as well as the dynamics preceding and following this event. Five GPS surveys were carried out on the entire Mount Etna network or on its southeastern part, from July 2000 to October 2001. Five ERS‐2 ascending passes and three descending ones are used to form five interferograms spanning periods from a month to 1 year, before and encompassing the eruption. Numerical and analytical inversions of the GPS and DInSAR data were performed to obtain analytical models for preeruptive, syneruptive and posteruptive periods. The deformation sources obtained were from the Mogi model: (1) pressure sources located beneath the upper western flank of the volcano, inflating before the eruption onset and deflating afterward; (2) tensile dislocations to model the intrusion of a N‐S dike in the central part of the volcano; and (3) two sliding and two normal dislocations to model the eastern and southern flank dynamics. This study confirms that the lower vents of the eruption were fed by a magma stored at depth ranging from 9 to 4 km below sea level, as proposed from petrochemical and geophysical researches. The rising of the magma through the shallow crust started months before the eruption onset but accelerated on the last day; this study suggests that in the volcanic pile the path of the rising magma was driven by the volcano topography. The eastern sliding plane and the interaction between dike intrusion and flank instability have been better defined with respect to previous studies. The sliding motion abruptly accelerated with the dike intrusion, and this continued after the end of the eruption. The acceleration was accompanied by the propagation of the strain field toward the eastern periphery of the volcano.
Global N removal by freshwater aquatic systems using a spatially distributed, within‐basin approach
Authors: Wollheim Wilfred M. , Vörösmarty Charles J. , Bouwman A. F. , Green Pamela , Harrison John , Linder Ernst , Peterson Bruce J. , Seitzinger Sybil P. , Syvitski James P. M.
Published: June 2008

We explored the role of aquatic systems in the global N cycle using a spatially distributed, within‐basin, aquatic nitrogen (N) removal model, implemented within the Framework for Aquatic Modeling in the Earth System (FrAMES‐N). The model predicts mean annual total N (TN) removal by small rivers (with drainage areas from 2.6–1000 km2), large rivers, lakes, and reservoirs, using a 30′ latitude × longitude river network to route and process material from continental source areas to the coastal zone. Mean annual aquatic TN removal (for the mid‐1990s time period) is determined by the distributions of aquatic TN inputs, mean annual hydrological characteristics, and biological activity. Model‐predicted TN concentrations at basin mouths corresponded well with observations (median relative error = −12%, interquartile range of relative error = 85%), an improvement over assumptions of uniform aquatic removal across basins. Removal by aquatic systems globally accounted for 14% of total N inputs to continental surfaces, but represented 53% of inputs to aquatic systems. Integrated aquatic removal was similar in small rivers (16.5% of inputs), large rivers (13.6%), and lakes (15.2%), while large reservoirs were less important (5.2%). Bias related to runoff suggests improvements are needed in nonpoint N input estimates and/or aquatic biological activity. The within‐basin approach represented by FrAMES‐N will improve understanding of the freshwater nutrient flux response to anthropogenic change at global scales.
Revisiting the parameterization of potential evaporation as a driver of long‐term water balance trends
Authors: Hobbins Michael T. , Dai Aiguo , Roderick Michael L. , Farquhar Graham D.
Published: June 2008

We examine the effects of two different parameterizations of potential evaporation on long‐term trends in soil moisture, evaporative flux and runoff simulated by the water balance model underlying the Palmer Drought Severity Index. The first, traditional parameterization is based on air temperature alone. The second parameterization is derived from observations of evaporation from class‐A pans. Trends in potential evaporation from the two parameterizations are opposite in sign (±) at almost half the stations tested over Australia and New Zealand. The sign of trends in the modelled soil moisture, evaporative flux and runoff depends on the parameterization used and on the prevailing climatic regime: trends in water‐limited regions are driven by precipitation trends, but the choice of parameterization for potential evaporation is shown to be critical in energy‐limited regions.
Has fire suppression increased the amount of carbon stored in western U.S. forests?
Authors: Fellows Aaron W. , Goulden Michael L.
Published: June 2008

Active 20th century fire suppression in western US forests, and a resulting increase in stem density, is thought to account for a significant fraction of the North American carbon sink. We compared California forest inventories from the 1930s with inventories from the 1990s to quantify changes in aboveground biomass. Stem density in mid‐montane conifer forests increased by 34%, while live aboveground carbon stocks decreased by 26%. Increased stem density reflected an increase in the number of small trees and a net loss of large trees. Large trees contain a disproportionate amount of carbon, and the loss of large trees accounts for the decline in biomass between surveys. 20th century fire suppression and increasing stand density may have decreased, rather than increased, the amount of aboveground carbon in western US forests.
First observations of non‐volcanic, long‐period seismicity in the central Apennines, Italy
Authors: Piccinini Davide , Saccorotti Gilberto
Published: June 2008

We report unprecedented observations of long‐period (LP) seismicity in non‐volcanic setting. Our data are from the Central‐Northern sector of the Apennine chain, Italy. For this area, intense CO2 circulation of mantle origin has been documented by either groundwater composition and borehole measurements. We perform waveform correlation and stacking to obtain reliable epicenter estimates. Following Chouet's crack model, we find that both the quality factor and dominant frequency of LP oscillations are consistent with the sustained resonance of a wet crack filled by a water‐CO2 mixture.
Impact of cross‐equatorial flow on intra‐seasonal variability of Indian summer monsoon rainfall
Authors: Kakade S. B. , Dugam S. S.
Published: June 2008

850‐hPa zonal wind gradient anomaly between the region‐1 [Equation‐25°N; 30°E–75°E] and region‐2 [Equation‐10°S; 30°E–75°E] is used to represent the cross‐equatorial flow. Long‐term daily mean of 1st June to 30th September, for the period 1951–2000, of gradient time series is correlated with Indian summer monsoon daily mean rainfall, for the same period. The correlation coefficient is 0.92, which is statistically significant at 1% level. In order to understand the impact of 850‐hPa zonal wind gradient on daily rainfall activity over India during monsoon season, the composite analysis of daily rainfall activity over India during extreme positive and negative 850‐hPa zonal wind gradient anomaly is performed. This analysis reveals that when 850‐hPa zonal wind gradient anomaly in last 20 days of May is extremely positive then almost all days in June show above‐normal rainfall activity and vice versa. The correlation coefficients between 20‐day mean of rainfall departure and previous 20‐day mean of 850‐hPa zonal wind gradient anomaly, for the period 1951–2003, are computed. This correlation analysis suggests that statistically significant (at 5% level) relationship is seen only up to the 30th June rainfall and from this point onward the relationship becomes insignificant. The result also indicates that 850‐hPa zonal wind gradient anomaly, in last 20‐days of May, is important for daily rainfall activity over India during onset phase of monsoon but, when the monsoon season sets in then it loses its significance.
Stalling of near‐inertial waves in a cyclone
Authors: Oey L.‐Y. , Inoue M. , Lai R. , Lin X.‐H. , Welsh S. E. , Rouse L. J.
Published: June 2008

Observations at the edge of the Loop Current after hurricane Katrina show inertial energy amplified at a depth of approximately 600∼700 m. Ray‐analysis using the eddy field obtained from a numerical simulation with data assimilation suggests that the amplification is due to inertial motions stalled in a deep cyclone.
On the generation of narrow‐banded ULF/ELF pulsations in the lower ionospheric conducting layer
Authors: Sorokin V. M. , Hayakawa M.
Published: June 2008

The coupling between the atmosphere and lower ionosphere (due to either the DC electric field or atmospheric gravity waves) may lead to the formation of horizontal irregularities of ionospheric conductivity over an earthquake preparation region. Such interaction of these irregularities with the background electromagnetic noise leads to occurrence of periodic polarization electric currents. These currents are considered to be a coherent source of gyrotropic waves propagating in the ionospheric conducting layer with finite thickness. The theoretical estimation has been performed on the generation of those ionospheric micropulsations in the frequency range of ULF to ELF in the equatorial latitude with horizontal Earth's magnetic field. Then it is found that those waves appear as a narrow‐banded line spectrum in the frequency range from 1 to 30 Hz, and these waves are expected to be observed on Earth's surface.
Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures
Authors: Jehmlich Nico , Schmidt Frank , von Bergen Martin , Richnow Hans-Hermann , Vogt Carsten
Published: June 2008

It is still a challenge to link specific metabolic activities to certain species in a microbial community because of methodological limitations. We developed a method to analyze the specific metabolic activity of a single bacterial species within a consortium making use of [13C7]-toluene for metabolic labelling of proteins. Labelled proteins were subsequently analyzed by 2D gel electrophoresis (2-DE) and mass spectrometry (MS) to characterize their identity as well as their 13C content as an indicator for function and activity of the host organism. To establish this method, we analyzed the metabolic incorporation of 13C carbon atoms into proteins of Aromatoleum aromaticum strain EbN1. This strain is capable of metabolizing toluene under nitrate-reducing conditions and was grown in either pure culture or in a mixed consortium with a gluconate-consuming enrichment culture. First, strain EbN1 was grown with non-labelled toluene or labelled [13C7]-toluene as carbon sources, respectively, and their proteins were subjected to 2-DE. In total, 60 unique proteins were identified by MALDI-MS/MS. From 38 proteins, the levels of 13C incorporation were determined as 92.3±0.8%. Subsequently, we mixed strain EbN1 and the enrichment culture UFZ-1, which does not grow on toluene but on gluconate, and added non-labelled toluene, [13C7]-toluene and/or non-labelled gluconate as carbon sources. The isotope labelling of proteins was analyzed after 2-DE by MS as a quantitative indicator for metabolic transformation of isotopic-labelled toluene by the active species of the consortium. Incorporation of 13C was exclusively found in proteins from strain EbN1 at a content of 82.6±2.3%, as an average calculated from 19 proteins, demonstrating the suitability of the method used to identify metabolic active species with specific properties within a mixed culture.
Intracellular trafficking of Shiga‐toxin‐B‐subunit‐functionalized spherulites
Authors: Bouter Anthony , Delord Brigitte , Dransart Estelle , Poirier Cécile , Johannes Ludger , van Effenterre Damien
Published: June 2008

Background information. Spherulites are multi‐lamellar lipidic vesicles that can encapsulate biomolecules and may be used as carriers for drug delivery. STxB (Shiga toxin B‐subunit) is known to bind the glycosphingolipid Gb3 (globotriaosyl ceramide), which is overexpressed by various human tumours. After Gb3 binding, the toxin enters the cytoplasm via the retrograde route, bypassing the degrading environment of the late endosomes/lysosomes. STxB is non‐toxic and has been identified as a promising tool for drug delivery. So far, applications have relied on direct coupling with therapeutic agents. In the present study, we have investigated the functionalization of spherulites by STxB and the intracellular trafficking of these structures.

Results. We demonstrate that STxB‐spherulites (ST×B‐functionalized spherulites) are internalized into HeLa cells in a receptor‐dependent manner. The intracellular distribution was studied by confocal microscopy for lipids, ligand and content. We observed an early separation between spherulites and STxB, leading to a late endosomal/lysosomal localization of lipids and content, whereas STxB remained partially at the plasma membrane.

Conclusions. Although recognition of Gb3 is the cause of their specific adhesion to cell membranes, STxB‐spherulites do not follow the retrograde transport route. Our results strongly suggest that STxB‐spherulites are, at least in part, disrupted at the plasma membrane, leading to lipid and content targeting to the classical endocytic pathway. We discuss how these findings influence the development of innovative delivery strategies.
Role of Fyn and PI3K in H2O2-induced inhibition of apical Cl−/OH− exchange activity in human intestinal epithelial cells
Authors: Saksena Seema , Gill Ravinder K. , Tyagi Sangeeta , Alrefai Waddah A. , Ramaswamy Krishnamurthy , Dudeja Pradeep K.
Published: June 2008

H2O2 is a highly reactive oxygen metabolite that has been implicated as an important mediator of inflammation-induced intestinal injury associated with ischaemia/reperfusion, radiation and inflammatory bowel disease. Previous studies have shown that H2O2 inhibits NaCl absorption and activates Cl− secretion in the rat and rabbit colon. To date, however, almost no information is available with respect to its effect on the human intestinal apical anion exchanger Cl−/OH− (HCO3−). The present studies were, therefore, undertaken to examine the direct effects of H2O2 on OH− gradient-driven DIDS (4,4′-di-isothiocyanostilbene-2,2′-disulfonate)-sensitive 36Cl− uptake utilizing a post-confluent transformed human intestinal epithelial cell line, Caco-2. Our results demonstrate that H2O2 (1 mM for 60 min) significantly inhibited (approx. 60%; P<0.05) Cl−/OH− exchange activity in Caco-2 cells. H2O2-mediated inhibition of Cl−/OH− exchange activity involved the Src kinase Fyn and PI3K (phosphoinositide 3-kinase)-dependent pathways. H2O2 also induced phosphorylation of Fyn and p85 (the regulatory subunit of PI3K) in Caco-2 cells. Moreover, an increased association of Fyn and p85 was observed in response to H2O2, resulting in the activation of the downstream target PLCγ1 (phospholipase Cγ1). Elevated intracellular Ca2+ levels and PKCα (protein kinase Cα) functioned as downstream effectors of H2O2-induced PLCγ1 activation. Our results, for the first time, provide evidence for H2O2-induced Src kinase Fyn/PI3K complex association. This complex association resulted in the subsequent activation of PLCγ1 and Ca2+-dependent PKCα, resulting in the inhibition of Cl−/OH− exchange activity. These findings suggest that H2O2-induced inhibition of the Cl−/OH− exchange process may play an important role in the pathophysiology of diarrhoea associated with inflammatory disorders, where the amount of reactive oxygen species is markedly elevated.
Effects of phosphatidylethanolamine glycation on lipid–protein interactions and membrane protein thermal stability
Authors: Levi Valeria , Villamil Giraldo Ana M. , Castello Pablo R. , Rossi Juan P. F. C. , González Flecha F. Luis
Published: June 2008

Non-enzymatic glycation of biomolecules has been implicated in the pathophysiology of aging and diabetes. Among the potential targets for glycation are biological membranes, characterized by a complex organization of lipids and proteins interacting and forming domains of different size and stability. In the present study, we analyse the effects of glycation on the interactions between membrane proteins and lipids. The phospholipid affinity for the transmembrane surface of the PMCA (plasma-membrane Ca2+-ATPase) was determined after incubating the protein or the phospholipids with glucose. Results show that the affinity between PMCA and the surrounding phospholipids decreases significantly after phosphospholipid glycation, but remains unmodified after glycation of the protein. Furthermore, phosphatidylethanolamine glycation decreases by ∼30% the stability of PMCA against thermal denaturation, suggesting that glycated aminophospholipids induce a structural rearrangement in the protein that makes it more sensitive to thermal unfolding. We also verified that lipid glycation decreases the affinity of lipids for two other membrane proteins, suggesting that this effect might be common to membrane proteins. Extending these results to the in vivo situation, we can hypothesize that, under hyperglycaemic conditions, glycation of membrane lipids may cause a significant change in the structure and stability of membrane proteins, which may affect the normal functioning of membranes and therefore of cells.
Two-dimensional fifth-order Raman spectroscopy of liquid formamide: Experiment and Theory
Authors: Li Y. L. , Huang L. , Dwayne Miller R. J. , Hasegawa Taisuke , Tanimura Yoshitaka
Published: June 2008

The fifth-order two-dimensional (2D) Raman spectrum of liquid formamide has been obtained. The absolute signal levels, qualitative features, as well as quantitative aspects of the 2D spectrum are found to be in good agreement with recent molecular dynamics calculations. The most important singular feature is the relatively strong rephasing signal observed along the diagonal. This finding illustrates the more structured nature of the hydrogen bond network of liquid formamide in comparison with simple liquids as exemplified by CS2. The theoretical calculations have been extended to include comparisons of different potentials that illustrate the sensitivity of the experiment to the anharmonic motions in the liquid state. The theoretical results point out the key features in the 2D spectrum that probe the essential details in the intermolecular potential. The experiment has been demonstrated to provide new insight into collective effects operating in hydrogen bonded liquids and opens up the exploration of other liquids with this approach.
Parametric two-electron reduced-density-matrix method applied to computing molecular energies and properties at nonequilibrium geometries
Authors: DePrince A. Eugene , Kamarchik Eugene , Mazziotti David A.
Published: June 2008

A parametric approach to the variational calculation of the two-electron reduced density matrix (2-RDM) for many-electron atoms and molecules has recently been developed in which the 2-RDM is parametrized to be both size consistent and nearly N-representable [C. Kollmar, J. Chem. Phys. 125, 084108 (2006); A. E. DePrince and D. A. Mazziotti, Phys. Rev. A 76, 049903 (2007)]. The parametric variational 2-RDM method is applied to computing ground-state molecular energies and properties at nonequilibrium geometries in significantly larger basis sets than previously employed. We study hydrogen abstraction from the hydroxide groups of H2O, NH3OH, and CH3OH. The 2-RDM method, parametrized by single and double excitations, shows significant improvement over coupled-cluster methods with similar excitations in predicting the shape of potential energy curves and bond-dissociation energies. Previous work completes the parametrization of the energy and 2-RDM by a system of n2h2 normalization constraints, where n and h are the number of occupied and unoccupied orbitals, respectively. In the present paper, however, we show that the constraints can be eliminated by incorporating them into the energy and 2-RDM functions and, hence, the constrained optimization of the ground-state energy can be reformulated as an unconstrained optimization. The 2-RDMs from the parametric method are very nearly N-representable, and as measured by an l2 norm, they are more accurate than the 2-RDMs from configuration interaction truncated at single and double excitations by an order of magnitude.
The free energy of the metastable supersaturated vapor via restricted ensemble simulations. II. Effects of constraints and comparison with molecular dynamics simulations
Authors: Nie Chu , Geng Jun , Marlow W. H.
Published: June 2008

Extensive restricted canonical ensemble Monte Carlo simulations [D. S. Corti and P. Debenedetti, Chem. Eng. Sci. 49, 2717 (1994)] were performed. Pressure, excess chemical potential, and excess free energy with respect to ideal gas data were obtained at different densities of the supersaturated Lennard-Jones (LJ) vapor at reduced temperatures from 0.7 to 1.0. Among different constraints imposed on the system studied, the one with the local minimum of the excess free energy was taken to be the approximated equilibrium state of the metastable LJ vapor. Also, a comparison of our results with molecular dynamic simulations [A. Linhart et al., J. Chem. Phys. 122, 144506 (2005)] was made.
A generalized Ablowitz–Ladik hierarchy, multi-Hamiltonian structure and Darboux transformation
Authors: Zhenyun Qin
Published: June 2008

Starting from a discrete spectral problem, we derive a hierarchy of nonlinear discrete equations which includes the Ablowitz–Ladik hierarchy and a new hierarchy as special cases. Especially, we investigate in detail the integrability and resolvability of the new hierarchy. It is shown that the new hierarchy is integrable in Liouville’s sense and possesses multi-Hamiltonian structure. A Darboux transformation is established for a typical discrete system in the new hierarchy with the help of the gauge transformation of its Lax pair. As applications of the Darboux transformation, new exact solutions of the discrete system are explicitly given.
A Peltier cell calorimeter for the direct measurement of the isothermal entropy change in magnetic materials
Authors: Basso Vittorio , Küpferling Michaela , Sasso Carlo P. , Giudici Laura
Published: June 2008

We developed a calorimetric technique to measure the isothermal magnetocaloric entropy change. The method consists in the use of Peltier cells as heat flow sensor and heat pump at the same time. In this paper, we describe the setup, the constitutive equations of the Peltier cell as sensor and actuator, and the calibration procedure. The Peltier heat is used to keep the sample isothermal when magnetic field is changed. The temperature difference between the sample and the thermal reservoir is kept by a digital control within 5mK for a magnetic field rate of 20mTs−1. The heat flux sensitivity around 1μW. With this method, it is possible to measure the magnetocaloric effect in magnetic materials by tracing the curves of the exchanged entropy Δes as a function of the magnetic field H. The method proves to be, in particular, suitable to reveal the role of the entropy production Δis, which is connected with hysteresis. Measurement examples are shown for Gd, BaFe12O19 ferrite, and Gd–Si–Ge.
Kinematical superalgebras and Lie algebras of order 3
Authors: Campoamor-Stursberg R. , Rausch de Traubenberg M.
Published: June 2008

We study and classify kinematical algebras which appear in the framework of Lie superalgebras or Lie algebras of order 3. All these algebras are related through generalized Inonü–Wigner contractions from either the orthosymplectic superalgebra or the de Sitter Lie algebra of order 3.
Influence of germanium doping on the mechanical strength of Czochralski silicon wafers
Authors: Chen Jiahe , Yang Deren , Ma Xiangyang , Zeng Zhidan , Tian Daxi , Li Liben , Que Duanlin , Gong Longfei
Published: June 2008

The mechanical strength in germanium-doped Czochralski silicon (GCz-Si) wafers has been investigated through the on-line warpage statistics analysis, indentation tests, and fracture structure measurements. It was found that the wafer warpage during manufacturing processes could be statistically suppressed by the germanium doping slightly. The enhancement effect of germanium doping on the mechanical strength in GCz-Si wafers could be shown obviously when the germanium concentration was higher than 1018cm−3. Meanwhile, the fracture strength for both the as-grown and the postannealed GCz-Si wafers might be greater compared to that of the conventional Czochralski (Cz-Si) wafers. Moreover, the generation and mobilization of the dislocations induced by indentation in Cz-Si wafers could be suppressed by the germanium doping. These phenomena are interpreted through a dislocation pinning-up effect associated with the smaller-sized higher-density oxygen precipitates formed in GCz-Si wafers.
Three dimensional photoelasticity with equilibrium constraint
Authors: Oguni Kenji , Wijerathne M. L. L. , Hori Muneo
Published: June 2008

A method for stress field tomography based on three dimensional photoelasticity has been developed. The proper treatment of the nonlinearity and the ill-posedness is the key to the robust tomographic method. In the proposed method, the nonlinearity has been addressed by the load incremental approach which divides the nonlinear solution space into segments with unique solutions. Also, the ill-posedness has been suppressed by introducing constraints from the equilibrium of the stress field. Validating both numerically and experimentally, the proposed method is shown to be robust enough and applicable to experimental stress measurements.
Diet quality and liveweight gain of steers grazing Leucaena - grass pasture estimated with faecal near infrared reflectance spectroscopy (F.NIRS)
Authors: Dixon R. M. , Coates D. B.
Published: June 2008

Three drafts of Bos indicus cross steers (initially 178–216 kg) grazed Leucaena–grass pasture [Leucaena leucocephala subspecies glabrata cv. Cunningham with green panic (Panicum maximum cv. trichoglume)] from late winter through to autumn during three consecutive years in the Burnett region of south-east Queensland. Measured daily weight gain (DWGActual) of the steers was generally 0.7–1.1 kg/day during the summer months. Estimated intakes of metabolisable energy and dry matter (DM) were calculated from feeding standards as the intakes required by the steers to grow at the DWGActual. Diet attributes were predicted from near infrared reflectance spectroscopy spectra of faeces (F.NIRS) using established calibration equations appropriate for northern Australian forages. Inclusion of some additional reference samples from cattle consuming Leucaena diets into F.NIRS calibrations based on grass and herbaceous legume–grass pastures improved prediction of the proportion of Leucaena in the diet. Mahalanobis distance values supported the hypothesis that the F.NIRS predictions of diet crude protein concentration and DM digestibility (DMD) were acceptable. F.NIRS indicated that the percentage of Leucaena in the diet varied widely (10–99%). Diet crude protein concentration and DMD were usually high, averaging 12.4 and 62%, respectively, and were related asymptotically to the percentage of Leucaena in the diet (R2 = 0.48 and 0.33, respectively). F.NIRS calibrations for DWG were not satisfactory to predict this variable from an individual faecal sample since the s.e. of prediction were 0.33–0.40 kg/day. Cumulative steer liveweight (LW) predicted from F.NIRS DWG calibrations, which had been previously developed with tropical grass and grass–herbaceous legume pastures, greatly overestimated the measured steer LW; therefore, these calibrations were not useful. Cumulative steer LW predicted from a modified F.NIRS DWG calibration, which included data from the present study, was strongly correlated (R2 = 0.95) with steer LW but overestimated LW by 19–31 kg after 8 months. Additional reference data are needed to develop robust F.NIRS calibrations to encompass the diversity of Leucaena pastures of northern Australia. In conclusion, the experiment demonstrated that F.NIRS could improve understanding of diet quality and nutrient intake of cattle grazing Leucaena–grass pasture, and the relationships between nutrient supply and cattle growth.
Data assimilation in a coupled physical-biological model for the Bohai Sea and the Northern Yellow Sea
Authors: Xu Qing , Lin Hui , Liu Yuguang , Lv Xianqing , Cheng Yongcun
Published: June 2008

One difficulty with coupled physical-biological ocean models is determining optimal values of poorly known model parameters. The variational adjoint assimilation method is a powerful tool for the automatic estimation of parameters. We used this method to incorporate remote-sensed chlorophyll-a data into a coupled physical-biological model developed for the Bohai Sea and the Northern Yellow Sea. A 3-D NPZD model of nutrients (N), phytoplankton (P), zooplankton (Z) and detritus (D) was coupled with a physical model, the Princeton Ocean Model. Sensitivity analysis was carried out to choose suitable control variables from the model parameters. Numerical twin experiments were then conducted to demonstrate whether the spatio-temporal resolutions of the observations were adequate for estimating values of the control variables. Finally, based on the success of the twin experiments, we included remote-sensed chlorophyll-a data in the NPZD model. With the adjoint assimilation of these chlorophyll-a data, the coupled model better describes spring and autumn phytoplankton blooms and the annual cycle of phytoplankton at the surface layer for the study area. The annual cycle of simulated surface nutrient concentrations also agreed well with field observations. The adjoint method greatly improves the modelling capability of coupled ocean models, helping us to better understand and model marine ecosystems.
What the bat's voice tells the bat's brain
Authors: Ulanovsky Nachum , Moss Cynthia F.
Published: June 2008

For over half a century, the echolocating bat has served as a valuable model in neuroscience to elucidate mechanisms of auditory processing and adaptive behavior in biological sonar. Our article emphasizes the importance of the bat's vocal-motor system to spatial orientation by sonar, and we present this view in the context of three problems that the echolocating bat must solve: (
i
) auditory scene analysis, (
ii
) sensorimotor transformations, and (
iii
) spatial memory and navigation. We summarize our research findings from behavioral studies of echolocating bats engaged in natural tasks and from neurophysiological studies of the bat superior colliculus and hippocampus, brain structures implicated in sensorimotor integration, orientation, and spatial memory. Our perspective is that studies of neural activity in freely vocalizing bats engaged in natural behaviors will prove essential to advancing a deeper understanding of the mechanisms underlying perception and memory in mammals.
Ku70
, an essential gene, modulates the frequency of rAAV-mediated gene targeting in human somatic cells
Authors: Fattah Farjana J. , Lichter Natalie F. , Fattah Kazi R. , Oh Sehyun , Hendrickson Eric A.
Published: June 2008

Gene targeting has two important applications. One is the inactivation of genes (“knockouts”), and the second is the correction of a mutated allele back to wild-type (“gene therapy”). Central to these processes is the efficient introduction of the targeting DNA into the cells of interest. In humans, this targeting is often accomplished through the use of recombinant adeno-associated virus (rAAV). rAAV is presumed to use a pathway of DNA double-strand break (DSB) repair termed homologous recombination (HR) to mediate correct targeting; however, the specifics of this mechanism remain unknown. In this work, we attempted to generate
Ku70
-null human somatic cells by using a rAAV-based gene knockout strategy. Ku70 is the heterodimeric partner of Ku86, and together they constitute an end-binding activity that is required for a pathway [nonhomologous end joining (NHEJ)] of DSB repair that is believed to compete with HR. Our data demonstrated that
Ku70
is an essential gene in human somatic cells. More importantly, however, in
Ku70
+/−
cells, the frequency of gene targeting was 5- to 10-fold higher than in wild-type cells. RNA interference and short-hairpinned RNA strategies to deplete Ku70 phenocopied these results in wild-type cells and greatly accentuated them in
Ku70
+/−
cell lines. Thus, Ku70 protein levels significantly influenced the frequency of rAAV-mediated gene targeting in human somatic cells. Our data suggest that gene-targeting frequencies can be significantly improved in human cells by impairing the NHEJ pathway, and we propose that Ku70 depletion can be used to facilitate both knockout and gene therapy approaches.
A polycystin-1 controls postcopulatory reproductive selection in mice
Authors: Sutton Keith A. , Jungnickel Melissa K. , Florman Harvey M.
Published: June 2008

Pkdrej, a member of the polycystin-1 gene family, is expressed only in the male germ line. Male mice that are homozygous for a targeted mutation in thePkdrejallele (Pkdrejtm/tm) are fertile in unrestricted mating trials, but exhibit lower reproductive success when competing with wild-type males in sequential mating trials and in artificial insemination of mixed-sperm populations. Following mating, sperm fromPkdrejtm/tmmice require >2 h longer than those of wild-type males to be detected within the egg/cumulus complex in the oviduct. Sperm from mice of both genotypes are able to capacitatein vitro. However, one of the component processes of capacitation, the ability to undergo a zona pellucida–evoked acrosome reaction, develops more slowly in sperm fromPkdrejtm/tmanimals than in sperm from wild-type males. In contrast, a second component process of capacitation, the transition to hyperactivated flagellar motility, develops with a similar time course in both genotypes. These two behavioral consequences of capacitation, exocytotic competence and altered motility, are therefore differentially regulated. These data suggest thatPkdrejcontrols the timing of fertilizationin vivothrough effects on sperm transport and exocytotic competence and is a factor in postcopulatory sexual selection.
BAG1
plays a critical role in regulating recovery from both manic-like and depression-like behavioral impairments
Authors: Maeng Sungho , Hunsberger Joshua G. , Pearson Brandon , Yuan Peixiong , Wang Yun , Wei Yanling , McCammon Joseph , Schloesser Robert J. , Zhou Rulun , Du Jing , Chen Guang , McEwen Bruce , Reed John C. , Manji Husseini K.
Published: June 2008

Recent microarray studies with stringent validating criteria identified Bcl-2-associated athanogene (
BAG1
) as a target for the actions of medications that are mainstays in the treatment of bipolar disorder (BPD).
BAG1
is a Hsp70/Hsc70-regulating cochaperone that also interacts with glucocorticoid receptors (GRs) and attenuates their nuclear trafficking and function. Notably, glucocorticoids are one of the few agents capable of triggering both depressive and manic episodes in patients with BPD. As a nexus for the actions of glucocorticoids and bipolar medications, we hypothesized that the level of
BAG1
expression would play a pivotal role in regulating affective-like behaviors. This hypothesis was investigated in neuron-selective
BAG1
transgenic (TG) mice and
BAG1
heterozygous knockout (+/−) mice. On mania-related tests,
BAG1
TG mice recovered much faster than wild-type (WT) mice in the amphetamine-induced hyperlocomotion test and displayed a clear resistance to cocaine-induced behavioral sensitization. In contrast,
BAG1
+/− mice displayed an enhanced response to cocaine-induced behavioral sensitization. The
BAG1
TG mice showed less anxious-like behavior on the elevated plus maze test and had higher spontaneous recovery rates from helplessness behavior compared with WT mice. In contrast, fewer
BAG1
+/− mice recovered from helplessness behavior compared with their WT controls.
BAG1
TG mice also exhibited specific alterations of hippocampal proteins known to regulate GR function, including Hsp70 and FKBP51. These data suggest that
BAG1
plays a key role in affective resilience and in regulating recovery from both manic-like and depression-like behavioral impairments.
A RECQ5–RNA polymerase II association identified by targeted proteomic analysis of human chromatin
Authors: Aygün Ozan , Svejstrup Jesper , Liu Yilun
Published: June 2008

Although the active forms of factors involved in DNA-related processes such as DNA replication, repair, and transcription are associated with chromatin, proteins are rarely purified from this source. Here, we describe a protocol for the isolation of chromatin-associated factors and use it to identify proteins interacting with human RNA polymerase II (RNAPII). Our data establish RECQ5 helicase as a bona fide RNAPII-associated protein. The RECQ5–RNAPII interaction is direct and is mediated by the RPB1 subunit of RNAPII, and RECQ5 appears to be the only member of the human RECQ family of helicases that associates with RNAPII. These data suggest an unexpected role for RECQ5 helicase at the interface of transcription and genomic stability.
Local Hospital Perspective on a Nationwide Outbreak of Pseudomonas aeruginosa Infection in Norway
Authors: Walberg Mette , Frøslie Kathrine Frey , Røislien Jo
Published: June 2008

Objective.

To implement a system for monitoring of rare events based on statistical process control charts.

Design.

Statistical process control plotting by g chart of clinical microbiology laboratory data.

Setting.

Primary and secondary care Norwegian hospital with a 9-bed intensive care unit.

Results.

During the winter of 2001–2002 in Norway, there was a national monoclonal nosocomial outbreak of Pseudomonas aeruginosa infection mainly affecting patients in intensive care units. In the present work, we demonstrate how the use of SPC at one of the affected hospitals would have detected this outbreak several weeks before the alert from the Norwegian National Public Health Institute (NIPH). By plotting the monthly incidence rate of P. aeruginosa infection (with a c chart), we found that the hospital would have been alerted in February, by plotting the number of days between events (with a g chart), we found that the hospital would have detected a process already out of control in early January 2002. Not until 9 weeks later (ie, mid-March) did the NIPH declare the P. aeruginosa outbreak to be national, and a commercially produced mouth swab contaminated during the manufacturing process was found to be the source.

Conclusion.

The plotting of rare events, such as an outbreak of nosocomial infection, with a g chart may be used for early detection of a process out of control.
Photoinduced Intramolecular Charge Transfer in Donor-acceptor Dyad and Donor-bridge-acceptor Triad
Authors: Ding Yong , Li Yuan-zuo , Ma Feng-cai
Published: June 2008

The ground and excited state properties of the [60]fullerene, diphenylbenzothiadiazole-triphenylamine (PBTDP-TPA) dyad and fullerene-diphenylbenzothiadiazole-triphenylamine (fullerene-PBTDP-TPA) triad were investigated theoretically using density functional theory with B3LYP functional and 3-21G basis set and time-dependent density functional theory with B3LYP functional and STO-3G basis set as well as 2D and 3D real space analysis methods. The 2D site representation reveals the electron-hole coherence on excitation. The 3D transition density shows the orientation and strength of the transition dipole moment, and the 3D charge difference density gives the orientation and result of the intramolecular charge transfer. Also, photoinduced intermolecular charge transfer (ICT) in PBTDP-TPA-fullerene triad are identified with 2D and 3D representations, which reveals the mechanisms of ICT in donor-bridge-acceptor triad on excitation. Besides that we also found that the direct superexchange ICT from donor to acceptor (tunneling through the bridge) strongly promotes the ICT in the donor-bridge-acceptor triad.
Polyubiquitylation of Histone H2B
Authors: Geng Fuqiang , Tansey William P.
Published: June 2008

Covalent modification of histones by ubiquitylation is a prominent epigenetic mark that features in a variety of chromatin-based events such as histone methylation, gene silencing, and repair of DNA damage. The prototypical example of histone ubiquitylation is that of histone H2B in Saccharomyces cerevisiae. In this case, attachment of ubiquitin to lysine 123 (K123) of H2B is important for regulation of both active and transcriptionally silent genes and participates in trans to signal methylation of histone H3. It is generally assumed that H2B is monoubiquitylated at K123 and that it is this single ubiquitin moiety that influences H2B function. To determine whether this assumption is correct, we have re-examined the ubiquitylation status of endogenous H2B in yeast. We find that, contrary to expectations, H2B is extensively polyubiquitylated. Polyubiquitylation of H2B appears to occur within the context of chromatin and is not associated with H2B destruction. There are at least two distinct modes of H2B polyubiquitylation: one that occurs at K123 and depends on the Rad6–Bre1 ubiquitylation machinery and another that occurs on multiple lysine residues and is catalyzed by an uncharacterized ubiquitin ligase(s). Interestingly, these ubiquitylation events are under the influence of different combinations of ubiquitin-specific proteases, suggesting that they have distinct biological functions. These results raise the possibility that some of the biological effects of ubiquitylation of H2B are exerted via ubiquitin chains, rather than a single ubiquitin group.
JunD Represses Transcription and Translation of the Tight Junction Protein Zona Occludens-1 Modulating Intestinal Epithelial Barrier Function
Authors: Chen Jie , Xiao Lan , Rao Jaladanki N. , Zou Tongtong , Liu Lan , Bellavance Emily , Gorospe Myriam , Wang Jian-Ying
Published: June 2008

The AP-1 transcription factor JunD is highly expressed in intestinal epithelial cells, but its exact role in maintaining the integrity of intestinal epithelial barrier remains unknown. The tight junction (TJ) protein zonula occludens (ZO)-1 links the intracellular domain of TJ-transmembrane proteins occludin, claudins, and junctional adhesion molecules to many cytoplasmic proteins and the actin cytoskeleton and is crucial for assembly of the TJ complex. Here, we show that JunD negatively regulates expression of ZO-1 and is implicated in the regulation of intestinal epithelial barrier function. Increased JunD levels by ectopic overexpression of the junD gene or by depleting cellular polyamines repressed ZO-1 expression and increased epithelial paracellular permeability. JunD regulated ZO-1 expression at the levels of transcription and translation. Transcriptional repression of ZO-1 by JunD was mediated through cAMP response element-binding protein-binding site within its proximal region of the ZO-1-promoter, whereas induced JunD inhibited ZO-1 mRNA translation by enhancing the interaction of the ZO-1 3′-untranslated region with RNA-binding protein T cell-restricted intracellular antigen 1-related protein. These results indicate that JunD is a biological suppressor of ZO-1 expression in intestinal epithelial cells and plays a critical role in maintaining epithelial barrier function.
On E-values for tandem MS scoring schemes
Authors: Segal Mark R.
Published: June 2008

Contact:  mark@biostat.ucsf.edu
Tristability of thin orthotropic shells with uniform initial curvature
Authors: Vidoli S , Maurini C
Published: June 2008

Composite shells show a rich multistable behaviour of interest for the design of shape-changing (morphing) structures. Previous studies have investigated how the initial shape determines the shell stability properties. For uniform initial curvatures and orthotropic material behaviour, not more than two stable equilibria have been reported. In this paper, we prove that untwisted, uniformly curved, thin orthotropic shells can have up to three stable equilibrium configurations. Cases of tristability are first documented using a numerical stability analysis of an extensible shallow shell model. Including mid-plane extension shows that the shells must be sufficiently curved in relation to their thickness to be multistable. Thus, an inextensible model allows us to perform an analytical stability analysis. Focusing on untwisted initial configurations, we illustrate with simple analytical results how the material parameters of the shell control the dependence of its multistable behaviour on the initial curvatures. In particular, we show that when the bending stiffness matrix approaches a degeneracy condition, the shell exhibits three stable equilibria for a wide range of initial curvatures.
Social information trumps vegetation structure in breeding-site selection by a migrant songbird
Authors: Betts Matthew G , Hadley Adam S , Rodenhouse Nicholas , Nocera Joseph J
Published: June 2008

To maximize fitness, organisms must assess and select suitable habitat. Early research studying birds suggested that organisms consider primarily vegetation structural cues in their habitat choices. We show that experimental exposure to singing in the post-breeding period provides a social cue that is used for habitat selection the following year by a migrant songbird, the black-throated blue warbler (Dendroica caerulescens). Our experimental social cues coerced individuals to adopt territories in areas of very poor habitat quality where individuals typically do not occur. This indicates that social information can override typical associations with vegetation structure. We demonstrate that a strong settlement response was elicited because post-breeding song at a site is highly correlated with reproductive success. These results constitute a previously undocumented, but highly parsimonious mechanism for the inadvertent transfer of reproductive (public) information from successful breeders to dispersers. We hypothesize that post-breeding song is a pervasive and reliable cue for species that communicate vocally, inhabit temporally autocorrelated environments, produce young asynchronously and/or abandon territories after reproductive failure.