bluuebunny/crossref_metadata_2025 huggingface dataset:
Surface energy balance and melt thresholds over 11 years at Taylor Glacier, Antarctica
Authors: Hoffman Matthew J. , Fountain Andrew G. , Liston Glen E.
Published: December 2008

In the McMurdo Dry Valleys, Victoria Land, Antarctica, melting of glacial ice is the primary source of water to streams, lakes, and associated ecosystems. To understand geochemical fluxes and ecological responses to past and future climates requires a physically based energy balance model. We applied a one‐dimensional model to one site on Taylor Glacier using 11 years of daily meteorological data and seasonal ablation measurements. Inclusion of transmission of solar radiation into the ice was necessary to accurately model summer ablation and ice temperatures. Results showed good correspondence between calculated and measured ablation and ice temperatures over the 11 years. Ablation (∼18 cm a−1) was dominated by sublimation with very few occurrences of melt (42 days during 11 years). Results also indicated that above freezing air temperatures did not necessarily result in melt and, in turn, melt occurred during subfreezing air temperatures under some conditions. For air temperatures near freezing, low wind speed was critically important for melt initiation. According to the model, subsurface melt, away from rocks and sediment in the ice, occurred three times more frequently than surface melt; occurs no deeper than 50 cm below the glacier surface; and was small, never exceeding 8% by mass. The magnitude of subsurface melting and the energy balance indicate that Taylor Glacier ice is intermediate in optical properties between snow and blue ice.
Expansion of subarctic water masses in the North Atlantic and Pacific oceans and implications for mid‐Pleistocene ice sheet growth
Authors: McClymont Erin L. , Rosell‐Melé Antoni , Haug Gerald H. , Lloyd Jerry M.
Published: December 2008

Past surface ocean circulation changes associated with the mid‐Pleistocene transition, 0.9–0.6 Ma, were reconstructed in the northern North Atlantic (ODP 983) and the northwest Pacific (ODP 882), using proxies for subarctic/subpolar water mass distributions (%C37:4alkenone) and sea surface temperature (U37K). Both sites experienced a secular expansion of subarctic waters from ∼1.15 Ma, spanning both glacial and interglacial intervals. After 0.9 Ma, low %C37:4at Site 983 records a northward retreat of subarctic waters during interglacials in the Atlantic, while continued high glacial %C37:4indicate extensive subarctic waters during glacial maxima associated with the development of the larger late Pleistocene ice sheets. In contrast, a secular decline in %C37:4occurred at Site 882 from 0.9 to 0.5 Ma, marking a more gradual retreat of subarctic conditions in the Pacific. It is proposed that the expansion of subarctic waters between 1.15 and 0.9 Ma exerted negative feedbacks to the moisture supply to the ice sheet source regions and may account for the apparent delayed ice sheet response to atmosphere‐ocean circulation changes associated with the mid‐Pleistocene transition that began as early as 1.2 Ma.
Scaling hyporheic exchange and its influence on biogeochemical reactions in aquatic ecosystems
Authors: O'Connor Ben L. , Harvey Judson W.
Published: December 2008

Hyporheic exchange and biogeochemical reactions are difficult to quantify because of the range in fluid‐flow and sediment conditions inherent to streams, wetlands, and nearshore marine ecosystems. Field measurements of biogeochemical reactions in aquatic systems are impeded by the difficulty of measuring hyporheic flow simultaneously with chemical gradients in sediments. Simplified models of hyporheic exchange have been developed using Darcy's law generated by flow and bed topography at the sediment‐water interface. However, many modes of transport are potentially involved (molecular diffusion, bioturbation, advection, shear, bed mobility, and turbulence) with even simple models being difficult to apply in complex natural systems characterized by variable sediment sizes and irregular bed geometries. In this study, we synthesize information from published hyporheic exchange investigations to develop a scaling relationship for estimating mass transfer in near‐surface sediments across a range in fluid‐flow and sediment conditions. Net hyporheic exchange was quantified using an effective diffusion coefficient (De) that integrates all of the various transport processes that occur simultaneously in sediments, and dimensional analysis was used to scaleDeto shear stress velocity, roughness height, and permeability that describe fluid‐flow and sediment characteristics. We demonstrated the value of the derived scaling relationship by using it to quantify dissolved oxygen (DO) uptake rates on the basis of DO profiles in sediments and compared them to independent flux measurements. The results support a broad application of theDescaling relationship for quantifying coupled hyporheic exchange and biogeochemical reaction rates in streams and other aquatic ecosystems characterized by complex fluid‐flow and sediment conditions.
Biodiesel: Freedom from Dependence on Fossil Fuels?
Authors: Prusty B. Anjan Kumar , Chandra Rachna , Azeez P. A.
Published: December 2008

In view of the depleting oil reserves and exponential rise in petroleum prices, the search for alternative sources of fuel is very timely and important. The present paper addresses the underlying issues in biodiesel production from biomaterials and sustainable production and supply of first-generation biofuels, especially the one from jatropha. The agencies and research institutions involved in the production of biofuels and the national and international efforts made in this regard are discussed here. There is also a dire need of a step towards large-scale production and supply of second-generation biofuels, although in infant stage, to strengthen the world economy in general and Indian economy in particular. However, the production of biofuels are likely to have serious socio-economic implications especially to the lesser developed societies. This needs serious attention from policy makers and public at large.
Phosphorylation of Ewing's sarcoma protein (EWS) and EWS-Fli1 in response to DNA damage
Authors: Klevernic Iva V. , Morton Simon , Davis Roger J. , Cohen Philip
Published: December 2008

In Ewing's sarcomas, chromosomal translocations cause the N-terminal domain of the EWS (Ewing's sarcoma protein) to fuse with the DNA-binding domains of the Ets (E26 transformation-specific) family of transcription factors. Here we show that EWS and EWS-Fli1 (Friend leukaemia virus integration 1), the fusion most frequently found in Ewing's sarcomas, become phosphorylated at Thr79 in response to either mitogens or DNA-damaging agents. The much weaker mitogen-induced phosphorylation of EWS is catalysed by the MAPKs (mitogen-activated protein kinases) ERK1 (extracellular signal-regulated kinase 1) and ERK2, whereas the much stronger phosphorylation of EWS induced by the DNA alkylating agent MMS (methyl methanesulphonate) can be catalysed by JNK (c-Jun N-terminal kinase) and at least one other protein kinase distinct from ERK1/ERK2. In contrast, the phosphorylation of EWS-Fli1 induced by MMS was largely mediated by p38α/p38β MAPKs. MMS induced a much stronger phosphorylation of EWS-Fli1 than EWS in heterodimers comprising both proteins.
Structural and photoluminescence properties of ZnO thin films prepared by sol-gel process
Authors: Petersen J. , Brimont C. , Gallart M. , Crégut O. , Schmerber G. , Gilliot P. , Hönerlage B. , Ulhaq-Bouillet C. , Rehspringer J. L. , Leuvrey C. , Colis S. , Aubriet H. , Becker C. , Ruch D. , Slaoui A. , Dinia A.
Published: December 2008

The present study focuses on the structural and optical properties of ZnO thin films fabricated by sol-gel process and spin coated onto Si (100) and quartz substrates. The ZnO films have a hexagonal wurtzite structure with a grain size of about 50 nm. The x-ray photoelectron spectroscopy measurements reveal the presence of Zn2+ and of zinc hydroxyl groups at the film. Optical properties were studied by photoluminescence (PL) and absorption spectroscopy at low and room temperatures. The absorption spectrum is dominated by a sharp excitonic peak at room and low temperatures. At room temperature, PL observations show two transitions: one near the absorption edge in the ultraviolet (UV) region and the second centered at 640 nm, characteristic of the deep electronic levels in the bandgap. The spectrum at 6 K is dominated by donor bound exciton lines and donor-acceptor pair transitions. LO-phonon replica and two-electron satellite transitions are also observed. These optical characteristics are a signature of good structural quality of the films.
A kinetic model for liquids: Relaxation in liquids, origin of the Vogel–Tammann–Fulcher equation, and the essence of fragility
Authors: Wang L. W. , Fecht H.-J.
Published: December 2008

On the basis of the kinetic model for liquids, which gave a quantitative description of liquid substructures, atomic relaxations in a model liquid were calculated. A crossover temperature Tcoop was recognized: relaxations were noncooperative at temperatures above Tcoop while cooperative below Tcoop. The cooperation in relaxation was responsible for the very slow dynamics near glass transition, departing significantly from the Arrhenius relation. This found supports in a large variety of glass forming liquids. The degree of cooperation in relaxation was straightforwardly determined by the number of atoms, N, in the liquid substructure and was responsible for the fragility of liquids: the larger the N was, the more fragile a liquid was.
The influence of the droplet composition on the vapor-liquid-solid growth of InAs nanowires on GaAs (1¯1¯1¯)B by metal-organic vapor phase epitaxy
Authors: Bauer Jens , Gottschalch Volker , Wagner Gerald
Published: December 2008

The heteroepitaxial growth of InAs nanowires (NWs) on GaAs (1¯1¯1¯)B substrate was investigated by metal-organic vapor phase epitaxy. The vapor-liquid-solid (VLS) growth mechanism was applied with gold as seed material. InAs NW with two types of morphology were observed. The first morphology type exhibited a tapered NW shape. In a distinct region below the alloy particle the shape was influenced by the precursor surface diffusion. The NW growth was attributed to Au-rich liquid alloy particles containing gallium as a result of the initial Au–GaAs interaction. Differential scanning calorimetry measurements revealed the lowest eutectic temperature of the Au–Ga–In liquid alloy for different compositions. For a considerable amount of gallium inside the ternary alloy, the eutectic temperature was found to be below the InAs NW growth temperature window. A second type of morphology with a more columnlike shape was related to a very high indium fraction inside the liquid alloy particle during VLS growth. These NW exhibited a change in the side facet orientation from {2¯11} to {1¯10} below the droplet. Additionally, the sample structure was studied by transmission electron microscopy. A change in the InAs NW crystal structure from sphalerite-type to mainly wurtzite-type was observed with an increase in the growth temperature.
Charge dissociation in polymer:fullerene bulk heterojunction solar cells with enhanced permittivity
Authors: Lenes M. , Kooistra F. B. , Hummelen J. C. , Van Severen I. , Lutsen L. , Vanderzande D. , Cleij T. J. , Blom P. W. M.
Published: December 2008

The dissociation efficiency of bound electron-hole pairs at the donor-acceptor interface in bulk heterojunction solar cells is partly limited due to the low dielectric constant of the polymer:fullerene blend. We investigate the photocurrent generation in blends consisting of a fullerene derivative and an oligo(oxyethylene) substituted poly(p-phenylene vinylene) (PPV) derivative with an enhanced relative permittivity of 4. It is demonstrated that in spite of the relatively low hole mobility of the glycol substituted PPV the increase in the spatially averaged permittivity leads to an enhanced charge dissociation of 72% for these polymer:fullerene blends.
An extended model for upconversion in solar cells
Authors: Badescu Viorel
Published: December 2008

Here we analyze the system proposed by Trupke et al. (J. Appl. Phys. 92, 4117 (2002)) to increase solar cell efficiency. The system consists in adding to the cell a so-called upconverter, which is a device able to convert the low-energy (subband-gap) incident solar photons into photons of higher energy. The model takes account of (i) the nonradiative recombination in both solar cell and converter and (ii) the refractive index of both cell and converter. Two configurations are studied: cell and rear converter (C-RC) and front converter and cell. The main conclusions are as follows. (1) When nonradiative recombination is neglected for both cell and converter, the energy conversion efficiency of a C-RC system slightly exceeds the efficiency of a solar cell operating alone (under 1 sun illumination). (2) When similar realistic values for the radiative recombination efficiency are considered for both cell and converter, the energy conversion efficiency of a C-RC system is lower than the efficiency of a solar cell operating alone (under 1 sun illumination). (3) Adding a rear upconverter to the solar cell is beneficial in the case of present-day quality solar cells under concentrated solar radiation. (4) At small values of the cell refractive index (roughly less than 2), the conversion efficiency does not depend on the converter refractive index. (5) At higher values of the cell refractive index, the conversion efficiency decreases by increasing the converter refractive index. (6) The energy conversion efficiency does not increase by adding a front upconverter to the cell, whatever the values of the radiative recombination efficiency and solar radiation concentration ratio are.
Stabilization of tetragonal and cubic phases of ZrO2 in pulsed sputter deposited ZrO2/Al2O3 and ZrO2/Y2O3 nanolayered thin films
Authors: Barshilia Harish C. , Deepthi B. , Rajam K. S.
Published: December 2008

We have prepared nanolayered thin films of ZrO2/Al2O3 and ZrO2/Y2O3 using pulsed sputtering to study the feasibility of stabilization of various polymorphs of ZrO2. These films have been deposited at various substrate temperatures (350–700 °C), individual layer thicknesses (1.9–25.2 nm), and modulation wavelengths (Λ, 9.6–32.7 nm). The cross section of ZrO2 and Y2O3 films consisted of microcolumns, whereas the ZrO2/Al2O3 and ZrO2/Y2O3 multilayer systems exhibited a less columnar microstructure. X-ray diffraction (XRD) data showed monoclinic, cubic, and amorphous structures for ZrO2, Y2O3, and Al2O3 thin films, respectively. The tetragonal phase of ZrO2 (t-ZrO2) was stabilized for ZrO2/Al2O3 nanolayered thin films prepared at Λ≤13.8 nm. Our studies demonstrated that a critical ZrO2 thickness (≤10.5 nm at a substrate temperature of 700 °C) is required in order to stabilize the t-ZrO2 phase, which was in agreement with thermodynamically derived critical radius for the stabilization of the tetragonal phase. In the case of ZrO2/Y2O3 nanolayered thin films, the cubic phase of ZrO2 was stabilized for films prepared at 24.4 nm≥Λ≥9.9 nm. The nanolayered thin films prepared at Λ=9.9 nm exhibited satellite reflections of third order, suggesting the formation of superlattice structure. The formation of various polymorphs of ZrO2 was also confirmed by micro-Raman spectroscopy. XRD studies of nanolayered thin films heat treated in air demonstrated the stability of the tetragonal and the cubic phases of ZrO2 in the ZrO2/Al2O3 and ZrO2/Y2O3 multilayers, respectively, up to 1100 °C. ZrO2/Al2O3 and ZrO2/Y2O3 nanolayered thin films exhibited maximum nanoindentation hardness values of 30.5 and 28 GPa, respectively, which were very high as compared to the rule-of-mixture values. Detailed studies on elastic/plastic behavior of the multilayers indicated highest resistance to plastic deformation for the ZrO2/Al2O3 multilayers.
Thermal properties of heat storage composites containing multiwalled carbon nanotubes
Authors: Wang Jifen , Xie Huaqing , Xin Zhong
Published: December 2008

Thermal performance enhanced heat storage nanocomposites consisting of palmitic acid (PA) and multiwalled carbon nanotubes (CNTs) were prepared by dispersing chemically treated CNTs into melting PA. The PA/CNT composites remain stable after repeating energy storage and release 80 times. The melting point and latent heat capacity decrease with an increase in the mass fraction of CNTs. PA/CNT composites have enhanced thermal conductivities compared to pure PA, with the enhancement ratios increasing with the mass fraction of CNTs. For PA/CNT composite containing CNTs with a mass fraction of 5.0%, the thermal conductivity enhancement ratios amount up to 36% and 56% in solid and liquid states, respectively.
Tuning the sensing responses of polymer-coated fiber Bragg gratings
Authors: Lu Ping , Men Liqiu , Chen Qiying
Published: December 2008

We demonstrate the application of polyimide-coated fiber Bragg grating (FBG) as a substance sensor and reveal the dependences of the sensitivity and time response on the coating thickness as well as factors influencing these properties. As an example of polyimide-coated sensor for detecting soluble substances, the use of the grating for salinity measurement shows that a judicious selection of coating thickness is needed in order to achieve suitable sensitivity and time response for specific application. The experimental results indicated that the salinity sensitivities of the polyimide-coated FBGs with coating thicknesses of 11, 17, 20, and 24 μm were 1.45, 2.45, 2.95, and 3.70 pm/% (blueshifted), respectively. In addition, the response time is another signature for discriminating different parameters.
Nanoscale surface electrical properties of aluminum zinc oxide thin films investigated by scanning probe microscopy
Authors: Chen Sy-Hann , Yu Chang-Feng , Lin Yung-Shao , Xie Wen-Jia , Hsu Ting-Wei , Tsai Din Ping
Published: December 2008

Conducting atomic force microscopy and scanning surface potential microscopy were adopted to study the nanoscale surface electrical properties of aluminum zinc oxide (AZO) films that were prepared by pulsed laser deposition (PLD) at various substrate temperatures for use as anode materials in polymer light-emitting diodes (PLEDs). Experimental results indicate that when substrate temperatures exceed 100°C, the local conductivity and work function are positively correlated with the concentrations of Al dopant and O2− on AZO surface. When the substrate temperature is approximately 150°C, the percentage coverage of conducting regions of the AZO surface and the mean work function are 90.20% and 4.85eV, respectively. Additionally, both microcosmic uniformities meet the standard applied to PLEDs. This low-temperature condition for PLD significantly reduces the yield rate of impurities when AZO vacuum evaporation is performed on a plastic substrate, supporting various applications of AZO films.
Changes in immunity to rabbit haemorrhagic disease virus, and in abundance and rates of increase of wild rabbits in Mackenzie Basin, New Zealand
Authors: Parkes John P. , Glentworth Brent , Sullivan Graham
Published: December 2008

The evolutionary race between diseases and their hosts may lead to attenuation of the disease agent, increasing resistance in the host, or both. This is an undesirable outcome when the disease is being used as a biocontrol agent but a desired outcome when the host is valued by people. Introduced wild rabbits Oryctolagus cuniculus are a pest to agriculture and biodiversity values in New Zealand’s grasslands, particularly on the drier eastern sides of both islands. The costs to manage them using conventional control could not be sustained by landowners who since the 1980s have proposed the introduction of the viral biocontrol agents myxomatosis and then rabbit haemorrhagic disease virus (RHDV). Myxomatosis failed to establish but RHDV did establish and spread following its illegal introduction in 1997. However, since 1997, rabbit haemorrhagic disease (RHD) has become less effective for biocontrol of rabbits in New Zealand. Three lines of evidence from our four study sites in the Mackenzie Basin support this claim. First, the proportion of rabbits of all ages with antibodies to RHDV has increased in samples of rabbits shot each year since 1997. Taken alone this may simply reflect an accumulation in cross-sectional samples of seropositive older rabbits that have been exposed to infection but survived successive epizootics. Second, the proportion of young rabbits, sampled at an age when they have been exposed to a single epizootic event, that have antibodies to RHDV has also increased since 1997. This is strong evidence that something has changed in the rabbit–virus interaction. The cause of this effect remains unknown but is reflected in the third line of evidence, that the abundance of rabbits as indexed by standardised spotlight counts has increased since 1997. The rate of increase has, however, been much slower than that seen in the same populations as they recovered from conventional control before the arrival of RHD. Thus, we conclude that RHD is still an effective biocontrol but its efficacy is waning.
Distribution of a recolonising species may not reflect habitat suitability alone: the case of the Eurasian otter (Lutra lutra) in southern Italy
Authors: Remonti Luigi , Prigioni Claudio , Balestrieri Alessandro , Sgrosso Silvia , Priore Giuseppe
Published: December 2008

Management of recolonising species needs precise knowledge concerning those environmental parameters that can influence the species current distribution at the margins of their range and their potential for further expansion. The otter (Lutra lutra) is one of the most endangered species of the Italian fauna. After a sharp decline, it has gradually recovered and, at present, it is confined to southern Italy. At the southern boundaries of the Italian otter range, the influence of two geographic and 15 habitat variables on otter distribution (estimated by 1-year monitoring of 18 spraint-sampling stations) was assessed, to improve management efficacy. Latitude represented the main source of variation in the spraint-collection data. The species was in fact well established in central and northern areas, whereas the southern and western sampling stations showed an unstable river occupancy (the average percentage of positive surveys being 94.5 and 35.8%, respectively; U = 0, P = 0.0014). Secondarily, otter relative abundance was positively associated with the degree of cover of aquatic macrophytes. Our results suggest that the whole analysed hydrographic network offers a suitable habitat for otters. Thus we argue that the discontinuous distribution observed in our study area could be a consequence of the sharp decline suffered by the Italian otter populations during the 1970s and 1980s. The positive trend of the last decades has resulted in the progressive recolonisation of empty habitat patches, a process that is still hindered by the lack of connectivity to extant populations. Our findings have implications for landscape restoration projects, suggesting that provision of suitable habitat alone may not be sufficient to effect recolonisation by some species.
Effects of site, time, weather and light on urban bat activity and richness: considerations for survey effort
Authors: Scanlon Annette T. , Petit Sophie
Published: December 2008

To maximise bat retention in urban environments, efficient bat monitoring is needed, but the factors that influence survey results for urban bats are unclear. We used echolocation call detectors (n = 378 detector-nights from November 2005 to October 2006) to assess bat activity among different sites in the Adelaide City parklands, temporal variations in activity (hourly, nightly, monthly), and responses to weather and light (artificial and moon). Bat species did not occur evenly in urban conditions; dark parks were more important for bat diversity and activity (six species groups in the darkest park) than were artificially lit parkland areas (three species groups in the flood-lit park). Gould’s wattled bat (Chalinolobus gouldii) and Mormopterus species 4 (94% of calls) were advantaged in urban parklands, being the only species recorded when lights were on at sports parks, whereas five species groups occurred when the lights were off. Minimal bat activity was recorded in the first 2 h after civil twilight, suggesting that bats may roost outside the city and commute nightly into parklands. Bat activity increased with temperature, with a burst in activity occurring after 7°C. Rainfall (>1 mm/24 h) and moon illumination at midnight did not influence activity. Urban environments should provide diversity to attract a diverse assemblage of bat species. Activity fluctuated among sites, nights, and across the year, indicating that large sample sizes over long periods of time are required to monitor and survey bats reliably with detectors.
Visible Implant Alphanumeric tags as an alternative to toe-clipping for marking amphibians - a case study
Authors: Heard Geoffrey W. , Scroggie Michael P. , Malone Brian
Published: December 2008

The removal of toes in unique combinations (‘toe-clipping’) has historically been the most popular technique for individually marking amphibians. However, recent studies have questioned the utility and ethics of this technique, and provided impetus for research on the efficacy of alternative methods. In this study, the efficacy of Visible Implant Alphanumeric (VIA) tags for marking juvenile growling grass frogs (Litoria raniformis) was assessed with reference to the fundamental assumptions of the mark–recapture approach. Three questions were investigated: (1) What is the probability of tag loss? (2) What is the probability of tag misidentification, and does it vary between frogs or observers, or with observer experience? and (3) To what extent does tagging influence survival or growth? Laboratory and field trials demonstrated that the probability of tag loss for juvenile L. raniformis was ~0.07 (95% CI: 0.03–0.13) when tags where implanted on the dorsolateral region of the thorax, eight times lower than that estimated for tags implanted on the thigh (mean 0.59; 95% CI: 0.29–0.86). Tags were rarely misidentified by naïve observers (mean probability of tag misidentification <0.01), but tag read accuracy varied amongst observers. In the laboratory, tagging did not adversely influence survival or growth of L. raniformis during the 12-week study period. Given that modification of the techniques used here may eliminate tag loss, and that variation in tag read accuracy between observers may be easily avoided, it is concluded that VIA tags represent a promising alternative to toe-clipping for marking L. raniformis and other amphibians.
Rationalizing translation attenuation in the network architecture of the unfolded protein response
Authors: Trusina Ala , Papa Feroz R. , Tang Chao
Published: December 2008

Increased levels of unfolded proteins in the endoplasmic reticulum (ER) of all eukaryotes trigger the unfolded protein response (UPR). Lower eukaryotes solely use an ancient UPR mechanism, whereby they up-regulate ER-resident chaperones and other enzymatic activities to augment protein folding and enhance degradation of misfolded proteins. Metazoans have evolved an additional mechanism through which they attenuate translation of secretory pathway proteins by activating the ER protein kinase PERK. In mammalian professional secretory cells such as insulin-producing pancreatic β-cells, PERK is highly abundant and crucial for proper functioning of the secretory pathway. Through a modeling approach, we propose explanations for why a translation attenuation (TA) mechanism may be critical for β-cells, but is less important in nonsecretory cells and unnecessary in lower eukaryotes such as yeast. We compared the performance of a model UPR, both with and without a TA mechanism, by monitoring 2 variables: (
i
) the maximal increase in ER unfolded proteins during a response, and (
ii
) the accumulation of chaperones between 2 consecutive pulses of stress. We found that a TA mechanism is important for minimizing these 2 variables when the ER is repeatedly subjected to transient unfolded protein stresses and when it sustains a large flux of secretory pathway proteins which are both conditions encountered physiologically by pancreatic β-cells. Low expression of PERK in nonsecretory cells, and its absence in yeast, can be rationalized by lower trafficking of secretory proteins through their ERs.
Increasing corn for biofuel production reduces biocontrol services in agricultural landscapes
Authors: Landis Douglas A. , Gardiner Mary M. , van der Werf Wopke , Swinton Scott M.
Published: December 2008

Increased demand for corn grain as an ethanol feedstock is altering U.S. agricultural landscapes and the ecosystem services they provide. From 2006 to 2007, corn acreage increased 19% nationally, resulting in reduced crop diversity in many areas. Biological control of insects is an ecosystem service that is strongly influenced by local landscape structure. Here, we estimate the value of natural biological control of the soybean aphid, a major pest in agricultural landscapes, and the economic impacts of reduced biocontrol caused by increased corn production in 4 U.S. states (Iowa, Michigan, Minnesota, and Wisconsin). For producers who use an integrated pest management strategy including insecticides as needed, natural suppression of soybean aphid in soybean is worth an average of $33 ha−1. At 2007–2008 prices these services are worth at least $239 million y−1in these 4 states. Recent biofuel-driven growth in corn planting results in lower landscape diversity, altering the supply of aphid natural enemies to soybean fields and reducing biocontrol services by 24%. This loss of biocontrol services cost soybean producers in these states an estimated $58 million y−1in reduced yield and increased pesticide use. For producers who rely solely on biological control, the value of lost services is much greater. These findings from a single pest in 1 crop suggest that the value of biocontrol services to the U.S. economy may be underestimated. Furthermore, we suggest that development of cellulosic ethanol production processes that use a variety of feedstocks could foster increased diversity in agricultural landscapes and enhance arthropod-mediated ecosystem services.
Regulation of bone formation by osteoclasts involves Wnt/BMP signaling and the chemokine sphingosine-1-phosphate
Authors: Pederson Larry , Ruan Ming , Westendorf Jennifer J. , Khosla Sundeep , Oursler Merry Jo
Published: December 2008

Under most conditions, resorbed bone is nearly precisely replaced in location and amount by new bone. Thus, it has long been recognized that bone loss through osteoclast-mediated bone resorption and bone replacement through osteoblast-mediated bone formation are tightly coupled processes. Abundant data conclusively demonstrate that osteoblasts direct osteoclast differentiation. Key questions remain, however, as to how osteoblasts are recruited to the resorption site and how the amount of bone produced is so precisely controlled. We hypothesized that osteoclasts play a crucial role in the promotion of bone formation. We found that osteoclast conditioned medium stimulates human mesenchymal stem (hMS) cell migration and differentiation toward the osteoblast lineage as measured by mineralized nodule formation in vitro. We identified candidate osteoclast-derived coupling factors using the Affymetrix microarray. We observed significant induction of sphingosine kinase 1 (SPHK1), which catalyzes the phosphorylation of sphingosine to form sphingosine 1-phosphate (S1P), in mature multinucleated osteoclasts as compared with preosteoclasts. S1P induces osteoblast precursor recruitment and promotes mature cell survival. Wnt10b and BMP6 also were significantly increased in mature osteoclasts, whereas sclerostin levels decreased during differentiation. Stimulation of hMS cell nodule formation by osteoclast conditioned media was attenuated by the Wnt antagonist Dkk1, a BMP6-neutralizing antibody, and by a S1P antagonist. BMP6 antibodies and the S1P antagonist, but not Dkk1, reduced osteoclast conditioned media-induced hMS chemokinesis. In summary, our findings indicate that osteoclasts may recruit osteoprogenitors to the site of bone remodeling through SIP and BMP6 and stimulate bone formation through increased activation of Wnt/BMP pathways.
Correlation between the conformational states of F
1
-ATPase as determined from its crystal structure and single-molecule rotation
Authors: Okuno Daichi , Fujisawa Ryo , Iino Ryota , Hirono-Hara Yoko , Imamura Hiromi , Noji Hiroyuki
Published: December 2008

F
1
-ATPase is a rotary molecular motor driven by ATP hydrolysis that rotates the γ-subunit against the α
3
β
3
ring. The crystal structures of F
1
, which provide the structural basis for the catalysis mechanism, have shown essentially 1 stable conformational state. In contrast, single-molecule studies have revealed that F
1
has 2 stable conformational states: ATP-binding dwell state and catalytic dwell state. Although structural and single-molecule studies are crucial for the understanding of the molecular mechanism of F
1
, it remains unclear as to which catalytic state the crystal structure represents. To address this issue, we introduced cysteine residues at βE391 and γR84 of F
1
from thermophilic
Bacillus
PS3. In the crystal structures of the mitochondrial F
1
, the corresponding residues in the ADP-bound β (β
DP
) and γ were in direct contact. The βE190D mutation was additionally introduced into the β to slow ATP hydrolysis. By incorporating a single copy of the mutant β-subunit, the chimera F
1
, α
3
β
2
β(E190D/E391C)γ(R84C), was prepared. In single-molecule rotation assay, chimera F
1
showed a catalytic dwell pause in every turn because of the slowed ATP hydrolysis of β(E190D/E391C). When the mutant β and γ were cross-linked through a disulfide bond between βE391C and γR84C, F
1
paused the rotation at the catalytic dwell angle of β(E190D/E391C), indicating that the crystal structure represents the catalytic dwell state and that β
DP
is the catalytically active form. The former point was again confirmed in experiments where F
1
rotation was inhibited by adenosine-5′-(β,γ-imino)-triphosphate and/or azide, the most commonly used inhibitors for the crystallization of F
1
.
A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution
Authors: Gifford Robert J. , Katzourakis Aris , Tristem Michael , Pybus Oliver G. , Winters Mark , Shafer Robert W.
Published: December 2008

Lentiviruses chronically infect a broad range of mammalian species and have been transmitted from primates to humans, giving rise to multiple outbreaks of HIV infection over the past century. Although the circumstances surrounding these recent zoonoses are becoming clearer, the nature and timescale of interaction between lentiviruses and primates remains unknown. Here, we report the discovery of an endogenous lentivirus in the genome of the gray mouse lemur (
Microcebus murinus
), a strepsirrhine primate from Madagascar, demonstrating that lentiviruses are capable of invading the primate germ line. Phylogenetic analysis places gray mouse lemur prosimian immunodeficiency virus (pSIVgml) basal to all known primate lentiviruses and, consistent with this, its genomic organization is intermediate between the nonprimate lentiviruses and their more derived primate counterparts. Thus, pSIVgml represents the first unambiguous example of a viral transitional form, revealing the acquisition and loss of genomic features during lentiviral evolution. Furthermore, because terrestrial mammal populations in Madagascar and Africa are likely to have been isolated from one another for at least 14 million years, the presence of pSIVgml in the gray mouse lemur genome indicates that lentiviruses must have been infecting primates for at least this period of time, or have been transmitted between Malagasy and African primate populations by a vector species capable of traversing the Mozambique channel. The discovery of pSIVgml illustrates the utility of endogenous sequences for the study of contemporary retroviruses and indicates that primate lentiviruses may be considerably older and more broadly distributed than previously thought.
Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface
Authors: Vaishnava Shipra , Behrendt Cassie L. , Ismail Anisa S. , Eckmann Lars , Hooper Lora V.
Published: December 2008

The intestinal epithelium is in direct contact with a vast microbiota, yet little is known about how epithelial cells defend the host against the heavy bacterial load. To address this question we studied Paneth cells, a key small intestinal epithelial lineage. We found that Paneth cells directly sense enteric bacteria through cell-autonomous MyD88-dependent toll-like receptor (TLR) activation, triggering expression of multiple antimicrobial factors. Paneth cells were essential for controlling intestinal barrier penetration by commensal and pathogenic bacteria. Furthermore, Paneth cell-intrinsic MyD88 signaling limited bacterial penetration of host tissues, revealing a role for epithelial MyD88 in maintaining intestinal homeostasis. Our findings establish that gut epithelia actively sense enteric bacteria and play an essential role in maintaining host-microbial homeostasis at the mucosal interface.
The
Candida albicans pescadillo
homolog is required for normal hypha-to-yeast morphogenesis and yeast proliferation
Authors: Shen Junqing , Cowen Leah E. , Griffin April M. , Chan Leon , Köhler Julia R.
Published: December 2008

A single species,
Candida albicans
, causes half of all invasive fungal infections in humans. Unlike other fungal pathogens, this organism switches between growth as budding yeast and as pseudohyphal and hyphal filaments in host organs and
in vitro
. Both cell types play a role in invasive disease: while hyphal and pseudohyphal filaments penetrate host cells and tissues, yeast cells are likely to facilitate dissemination through the bloodstream and establishment of distant foci of infection. Many regulators of the yeast-to-hypha switch have emerged from intensive investigations of this morphogenetic step, but the hypha-to-yeast switch remains poorly understood. Using a forward genetic approach, a novel putative regulator involved in the hypha-to-yeast switch was identified, the
C. albicans pescadillo
homolog,
PES1
. In eukaryotes from yeast to human,
pescadillo
homologs are involved in cell cycle control and ribosome biogenesis, and are essential. We find a
pescadillo
homolog to act in fungal morphogenesis, specifically in lateral yeast growth on filamentous cells. We also find essentiality of
PES1
in
C. albicans
to be dependent on cell type, because hyphal cells, but not yeast cells, tolerate its loss.
PES1
is therefore critical for completion of the
C. albicans
life cycle, in which the fungus switches between filamentous and yeast growth. Consistent with these
in vitro
findings,
PES1
is required for
C. albicans
virulence in an
in vivo
insect model of infection.
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
Authors: Zheng Lianqing , Chen Mengen , Yang Wei
Published: December 2008

In the past few decades, many ingenious efforts have been made in the development of free-energy simulation methods. Because complex systems often undergo nontrivial structural transition during state switching, achieving efficient free-energy calculation can be challenging. As identified earlier, the “Hamiltonian” lagging, which reveals the fact that necessary structural relaxation falls behind the order parameter move, has been a primary problem for generally low free-energy simulation efficiency. Here, we propose an algorithm by achieving a random walk in both the order parameter space and its generalized force space; thereby, the order parameter move and the required conformational relaxation can be efficiently synchronized. As demonstrated in both the alchemical transition and the conformational transition, a leapfrog improvement in free-energy simulation efficiency can be obtained; for instance, (
i
) it allows us to solve a notoriously challenging problem: accurately predicting the

pK
a

value of a buried titratable residue, Asp-66, in the interior of the V66E staphylococcal nuclease mutant, and (
ii
) it allows us to gain superior efficiency over the metadynamics algorithm.
Etifoxine improves peripheral nerve regeneration and functional recovery
Authors: Girard Christelle , Liu Song , Cadepond Françoise , Adams David , Lacroix Catherine , Verleye Marc , Gillardin Jean-Marie , Baulieu Etienne-Emile , Schumacher Michael , Schweizer-Groyer Ghislaine
Published: December 2008

Peripheral nerves show spontaneous regenerative responses, but recovery after injury or peripheral neuropathies (toxic, diabetic, or chronic inflammatory demyelinating polyneuropathy syndromes) is slow and often incomplete, and at present no efficient treatment is available. Using well-defined peripheral nerve lesion paradigms, we assessed the therapeutic usefulness of etifoxine, recently identified as a ligand of the translocator protein (18 kDa) (TSPO), to promote axonal regeneration, modulate inflammatory responses, and improve functional recovery. We found by histologic analysis that etifoxine therapy promoted the regeneration of axons in and downstream of the lesion after freeze injury and increased axonal growth into a silicone guide tube by a factor of 2 after nerve transection. Etifoxine also stimulated neurite outgrowth in PC12 cells, and the effect was even stronger than for specific TSPO ligands. Etifoxine treatment caused a marked reduction in the number of macrophages after cryolesion within the nerve stumps, which was rapid in the proximal and delayed in the distal nerve stumps. Functional tests revealed accelerated and improved recovery of locomotion, motor coordination, and sensory functions in response to etifoxine. This work demonstrates that etifoxine, a clinically approved drug already used for the treatment of anxiety disorders, is remarkably efficient in promoting acceleration of peripheral nerve regeneration and functional recovery. Its possible mechanism of action is discussed, with reference to the neurosteroid concept. This molecule, which easily enters nerve tissues and regulates multiple functions in a concerted manner, offers promise for the treatment of peripheral nerve injuries and axonal neuropathies.
Fluorodeoxyglucose positron emission tomography (FDG-PET) and PET/computed tomography imaging characteristics of thyroid lymphoma and their potential clinical utility
Authors: Basu S. , Li G. , Bural G. , Alavi A.
Published: December 2008

Background: A relative paucity of data exists in the literature with regard to the utility of fluorodeoxyglucose positron emission tomography (FDG-PET) imaging in the clinical management of patients with primary lymphoma of the thyroid gland (PTL).

Purpose: To explore the FDG-PET imaging characteristics and their potential role in PTL, and to compare the results with anatomical imaging modalities.

Material and Methods: Patients with thyroid lymphoma who had undergone whole-body FDG-PET or PET/computed tomography (CT) during their course of the disease were identified by examination of case records. PET scans were reevaluated, and maximum standardized uptake value (SUVmax) was calculated and used as the semiquantitative measure of FDG uptake for this analysis. CT and/or magnetic resonance imaging (MRI) studies carried out within 1 week of FDG-PET scan and without any therapeutic intervention between the two studies were considered for the purpose of comparison. A total of six patients with 20 studies (14 FDG-PET and six PET/CT examinations) were identified following the criteria. All patients were female (age 16–83 years). Among these, five were proven to have PTL. Two patients had localized PTL (stage IE), two patients had associated regional nodal involvement (IIE), and one patient had associated nodal involvement on both sides of the diaphragm (IIIE) at presentation. Except for one patient with follicular B-cell lymphoma, all others were diffuse large-B-cell lymphoma (DLBCL) subtype.

Results: Avid FDG uptake was observed in both cases of untreated PTL, with SUVmax of 23 and 7.6, respectively. One patient showed focal FDG uptake (SUVmax 6.7) in the thyroid in the setting of a responding abdominal non-Hodgkin lymphoma (NHL) and was subsequently proven as adenomatous nodule with Hurthle cell changes. Following successful therapy, SUVmax declined consistently with improvement in disease status. In one patient, complete response was noted earlier by FDG-PET compared to CT. Disease recurrence was detected earlier by FDG-PET compared to CT in two patients with increased FDG activity in both thyroid lobes without any corresponding CT abnormality.

Conclusion: FDG-PET is a useful and sensitive modality for assessing disease activity in thyroid lymphoma. Its ability to detect disease recurrence was found to be superior compared to CT in two patients.
Dual role for B-1a cells in immunity to influenza virus infection
Authors: Choi Youn Soo , Baumgarth Nicole
Published: December 2008

B-1 cells are known to contribute most of the “natural antibodies” that are secreted in the steady state, antibodies which are crucial for protection against many pathogens including influenza virus. Whether the CD5+ B-1a subset plays a role during an active immune response is incompletely understood. In contrast to recent data suggesting a passive role for B-1a cells, data provided here show strong highly localized activation of B-1 cells in the draining lymph nodes of the respiratory tract after influenza infection. B-1 cells are identified as a major source for both steady state and infection-induced local virus-neutralizing IgM. The CD5+ B-1a subset is the main B-1 cell subset generating this response. B-1a cell responses are generated by their increased local accumulation rather than by antigen-specific expansion. Our study reveals that during infection with influenza, CD5-expressing B-1a cells respond to and contribute to protection, presumably without the need for B cell receptor–mediated antigen-specific signals, which are known to induce the death of B-1a cells rather than activation. With that, our data reveal fundamental differences in the response regulation of B-1 and B-2 cells during an infection.
Perverse Engineering
Authors: Haufe Chris
Published: December 2008

Evolutionary psychologists, among others, have used a method called “reverse engineering” to uncover (a) whether a trait was selected for, and (b) if so, why that trait was selected for. In this paper I argue that reverse engineering cannot deliver on either (a) or (b), and tends to pervert, rather than enhance, our knowledge of natural history. In particular, I expose as false a fundamental assumption of reverse engineering—namely, that all traits selected for a particular function will share some nontrivial properties.
Milne's Argument for the Log-Ratio Measure
Authors: Huber Franz
Published: December 2008

This article shows that a slight variation of the argument in Milne 1996 yields the log-likelihood ratio l rather than the log-ratio measure r as “the one true measure of confirmation.”