bluuebunny/crossref_metadata_2025 huggingface dataset:
Großräumige grenzüberschreitende Verflechtungsräume
Authors: Hartz Andrea , Damm Gerd-Rainer , Köhler Stefan
Published: November 2010

A federal pilot project will explore the role played by economically strong border regions in interaction with European metropolitan and urban regions. Jointly with partners from the Maas-Rhine Euroregion, (SaarLorLux+) Euroregion, Trinational Upper Rhine metropolitan area and Lake Constance region, the regional policy of the federal government is aimed at establishing the particular importance of cross-border metropolitan areas for growth and innovation, as well as for the European target of territorial cohesion, within regional policy discussions in Germany and Europe. Testing the strategic approach of “supra-regional partnerships” in a cross-border context, is one significant aspect. The interests of the partners involved in the project are furthermore focussed on the regions themselves. This means, the project is dedicated to promote a coherent regional development, as well as effective cooperation structures across national borders. The project finally pursues the creation of an initiative in the form of an open alliance of cross-border metropolitan regions, in order to more effectively represent the interests of border regions on a national and European level. The article explores the genesis, objectives and approach of this pilot project against the background provided by current debates on sustainable spatial development in Germany and Europe.
Modulation of innate immunity by African Trypanosomes
Authors: PAULNOCK DONNA M. , FREEMAN BAILEY E. , MANSFIELD JOHN M.
Published: November 2010

The experimental studies ofBruceigroup trypanosomes presented here demonstrate that the balance of host and parasite factors, especially IFN-γGPI-sVSG respectively, and the timing of cellular exposure to them, dictate the predominant MP and DC activation profiles present at any given time during infection and within specific tissues. The timing of changes in innate immune cell functions following infection consistently support the conclusion that the key events controlling host resistance occur within a short time following initial exposure to the parasite GPI substituents. Once the changes in MP and DC activities are initiated, there appears little that the host can do to reverse these changes and alter the final outcome of these regulatory events. Instead, despite the availability of multiple innate and adaptive immune mechanisms that can control parasites, there is an inability to control trypanosome numbers sufficiently to prevent the emergence and establishment of virulent trypanosomes that eventually kill the host. Overall it appears that trypanosomes have carefully orchestrated the host innate and adaptive immune response so that parasite survival and transmission, and alterations of host immunity, are to its ultimate benefit.
An empirical study of the expressiveness of the functional basis
Authors: Caldwell Benjamin W. , Sen Chiradeep , Mocko Gregory M. , Summers Joshua D.
Published: November 2010

Function models are frequently used in engineering design to describe the technical functions that a product performs. This paper investigates the use of the functional basis, a function vocabulary developed to aid in communication and archiving of product function information, in describing consumer products that have been decomposed, analyzed, modeled functionally, and stored in a Web-based design repository. The frequency of use of function terms and phrases in 11 graphical and 110 list-based representations in the repository is examined and used to analyze the organization and expressiveness of the functional basis and function models. Within the context of reverse engineering, we determined that the modeling resolution provided by the hierarchical levels, especially the tertiary level, is inadequate for function modeling; the tertiary terms are inappropriate for capturing sufficient details desired by modelers for archiving and reuse, and there is a need for a more expressive flow terms and flow qualifiers in the vocabulary. A critical comparison is also presented of two representations in the design repository: function structures and function lists. The conclusions are used to identify new research opportunities, including the extension of the vocabulary to incorporate flow qualifiers in addition to more expressive terms.
Making the case for plant diversity
Authors: Smith Paul , Dickie John , Linington Simon , Probert Robin , Way Michael
Published: November 2010

The Millennium Ecosystem Assessment estimates that between 60,000 and 100,000 plant species are threatened with extinction–equivalent to around one-quarter of the total number of known plant species. Why should we care? There are a number of reasons. The first is that these plants may be useful to us in unknown ways. Secondly, ecology has taught us that resilience is found in diversity. Thirdly, we should be saving plant species from extinction because we can–there is no technological reason why any plant species should become extinct. Where we can't protect and manage plant diversity in situ, we should be employing ex situ conservation techniques, ranging from seed banks to habitat restoration. The Millennium Ecosystem Assessment describes such interventions as ‘techno-gardening’. This is not an abstract concept–it is already a reality in the majority of man-managed landscapes. In this context the perception of ex situ conservation as simply a back-up strategy for in situ conservation is mistaken. We are all involved in ex situ conservation to some degree, from cultivating our back gardens, to farming, to management of protected areas. Ex situ conservation should be seen as a complementary approach to in situ conservation and on the same spectrum. Kew's Millennium Seed Bank Partnership, comprising more than 120 plant science institutions in 50 countries, epitomizes this philosophy in action. We work actively on every seed collection we bank, finding out how useful it is and how we can grow it to enable human innovation, adaptation and resilience. Challenges remain at the policy level; for example, the need to factor-in the value of natural capital to development decision making, and better defining a role for public-sector science. At the technical level, also, there is much to do. Perhaps the greatest technical challenges relate to the restoration and management of complex, self-sustaining habitats or species assemblages. If we are to techno-garden effectively, in order to maintain ecosystem services and sustain biodiversity, then a multidisciplinary approach will be required. Many plant science institutions have recognized this and are becoming engaged increasingly in restoration activities and in situ management. Ultimately, humanity's ability to innovate and adapt is dependent on our having access to the full range of plant species and the alleles they contain.
Biogeochemical fluxes through microzooplankton
Authors: Buitenhuis Erik T. , Rivkin Richard B. , Sailley Sévrine , Le Quéré Corinne
Published: November 2010

Microzooplankton ingest a significant fraction of primary production in the ocean and thus remineralize nutrients and stimulate regenerated primary production. We synthesized observations on microzooplankton carbon‐specific grazing rate, partitioning of grazed material, respiration rate, microzooplankton biomass, microzooplankton‐mediated phytoplankton mortality rate, and phytoplankton growth rate. We used these observations to parameterize and evaluate the microzooplankton compartment in a global biogeochemical model that represents five plankton functional types. Microzooplankton biomasses predicted in this simulation are closer to the independently derived evaluation data than in the previous model version. Most rates, including primary production, microzooplankton grazing, and export of sinking detritus are within observational constraints. However, the model underestimates microzooplankton and mesozooplankton biomasses and chlorophyll concentrations. Thus, we propose that sufficient carbon enters the model ecosystem, but insufficient carbon is retained. For microzooplankton, the low retention of carbon could be improved by parameterizing the model with ciliate gross growth efficiency only, indicating that ciliates may contribute more to microzooplankton activity than their biomass contribution suggests. By taking into account the model underestimation of biomass, we estimate that the ocean inventory of microzooplankton biomass is 0.24 Pg C (a range of 0.14–0.33 Pg C), which is similar to the biomass of mesozooplankton.
Spatiotemporal gravity variations to look deep into the southern flank of Etna volcano
Authors: Greco Filippo , Currenti Gilda , Del Negro Ciro , Napoli Rosalba , Budetta Gennaro , Fedi Maurizio , Boschi Enzo
Published: November 2010

A 14‐year‐long microgravity data set (October 1994 to September 2007) collected along a 24‐km east‐west trending profile of 19 stations was analyzed to detect underground mass redistributions related to the volcanic activity involving the southern flank of Mt Etna (Italy). A multiresolution wavelet analysis was applied to separate the volcano‐related anomalies from the unwanted components. The residual image having both spatial extension and temporal duration evidenced two complete gravity increase/decrease cycles mainly affecting the central and eastern stations of the profile. The first gravity increase (early 1995 to the end of 1996) and decrease (end of 1996 to late in 1998) cycle reached a maximum amplitude of approximately 90 μGal. The second gravity increase (mid‐1999 to mid‐2000) and decrease (mid‐2000 to early‐2004) cycle attained an amplitude of about 80 μGal. After about 5 years of a persistent negative gravity anomaly, a new semicycle started at the end of 2006 and continued during the last survey carried out in September 2007. The density changes, modeled over time since 1994 using a Quadratic Programming algorithm, are mainly located at a depth of 2–4 km bsl in a region recognized to be a preferential pathway of magma rising and an intermediate zone of magma storage/withdrawal. The computed positive mass variations of about 105 × 109 kg were interpreted as magma accumulation, while negative mass changes of about −120 × 109 kg were associated with either magma drainage or opening of new voids by tectonic stresses within a source volume, where tensional earthquakes occurred.
A HYCOM modeling study of the Persian Gulf: 1. Model configurations and surface circulation
Authors: Yao Fengchao , Johns William E.
Published: November 2010

The circulation and water mass transformation processes in the Persian Gulf and the water exchange with the Indian Ocean through the Strait of Hormuz are studied using the Hybrid Coordinate Ocean Model (HYCOM). Model results show that the Indian Ocean Surface Water (IOSW) propagates in two branches into the gulf, one along the Iranian coast toward the northern gulf and the other one onto the southern banks driven by the Ekman drift due to the prevailing northwesterly winds. These two branches of inflow form two cyclonic gyres in the northern and in the southern gulf. A salinity front separates the fresher intruding IOSW from the saltier waters in the gulf. Eddies with size of about 100 km are fully developed along the salinity front in summer. The intrusion of the IOSW in the model extends much farther into the gulf in summer than in winter. By analyzing the salt balance in the basin and conducting sensitivity experiments, we show that it is the balance between the advection of IOSW and vertical salt flux induced by mixing that mainly controls the seasonal variation of the surface salinity. Surface wind stress plays a secondary role in modulating the seasonal intrusion of the IOSW. High‐frequency atmospheric forcing produces more realistic surface temperatures than obtained from climatological forcing, as a result of increased heat loss in winter. However, the high‐frequency forcing does not change significantly the general features of the circulation.
Extratropical cyclones, frontal waves, and Mars dust: Modeling and considerations
Authors: Hollingsworth J. L. , Kahre M. A.
Published: November 2010

A Mars GCM is utilized to investigate dust lifting and organization associated with extratropical cyclogenesis and frontal waves. The model is applied at high resolution in simulations related to Mars' dust cycle. A single extratropical synoptic weather event is examined to ascertain lifting, transport and convergence/divergence of dust by large‐scale cyclonic/anticyclonic weather systems, and the sub‐synoptic frontal waves that ensue. Low‐ and high‐pressure cores develop, travel eastward and remain mostly confined within the seasonal CO2 polar cap. The bulk of dust lifting occurs in the northern‐hemisphere western highlands associated with nocturnal down‐slope drainage flows, and lifting infrequently occurs near the frontal convergence zone. Dust becomes organized and transported within circulations associated with the synoptic/sub‐synoptic circulations accompanying the frontal waves. Dynamical considerations are invoked regarding frontogenesis revealing correlations with regards to dust lifting, organization and transport. Implications of large‐scale extratropical weather systems on the martian dust cycle are discussed.
Entropy versus APE production: On the buoyancy power input in the oceans energy cycle
Authors: Tailleux R.
Published: November 2010

This letter argues that the current controversy about whether Wbuoyancy, the power input due to the surface buoyancy fluxes, is large or small in the oceans stems from two distinct and incompatible views on how Wbuoyancy relates to the volume‐integrated work of expansion/contraction B. The current prevailing view is that Wbuoyancy should be identified with the net value of B, which current theories estimate to be small. The alternative view, defended here, is that only the positive part of B, i.e., the one converting internal energy into mechanical energy, should enter the definition of Wbuoyancy, since the negative part of B is associated with the non‐viscous dissipation of mechanical energy. Two indirect methods suggest that by contrast, the positive part of B is potentially large.
Electronic spin and valence states of Fe in CaIrO3‐type silicate post‐perovskite in the Earth's lowermost mantle
Authors: Mao Z. , Lin J. F. , Jacobs C. , Watson H. C. , Xiao Y. , Chow P. , Alp E. E. , Prakapenka V. B.
Published: November 2010

The electronic spin and valence states of Fe in post‐perovskite ((Mg0.75Fe0.25)SiO3) have been investigated by synchrotron X‐ray diffraction, Mössbauer and X‐ray emission spectroscopy at 142 GPa and 300 K. Rietveld refinement of the X‐ray diffraction patterns revealed that our sample was dominated by CaIrO3‐type post‐perovskite. Combined Mössbauer and X‐ray emission results show that Fe in post‐perovskite is predominantly Fe2+ (70%) in the intermediate‐spin state with extremely high quadrupole splitting of 3.77(25) mm/s. The remaining 30% Fe can be assigned to two sites. Compared with recent studies, our results indicate that the intermediate‐spin Fe2+ is stabilized in CaIrO3‐type post‐perovskite over a wide range of Fe content, whereas the low‐spin Fe3+ is more dominant in the 2 × 1 kinked post‐perovskite structure. The characterization of these structural and compositional effects on the spin and valence states of Fe in post‐perovskite can help in understanding the geochemical and geophysical behavior of the core‐mantle region.
Importance of location for describing typical and extreme wind speed behavior
Authors: Griffin B. J. , Kohfeld K. E. , Cooper A. B. , Boenisch G.
Published: November 2010

Several recent studies have considered the potential impact of climate change on regional wind intensity. However, previous wind speed studies in the Pacific Northwest (PNW) present conflicting results for wind speed trends in relation to climate drivers. This study analyzes the percentiles (50th, 75th, and 95th) of the strongly positively skewed distributions for PNW maximum daily wind speeds from 92 meteorological stations, and reveals different behaviors for average and extreme wind speeds. Considerably stronger winds are found at coastal locations compared with sites further inland. Extreme wind speeds at these coastal locations appear to follow an eight to nine‐year cyclic pattern, while mainland sites have a small, linear downward wind speed trend. This finding of a behavioral dependence on location helps reconcile previous, apparently contradictory results and has important global implications for wind research and infrastructure planning, such as wind energy feasibility studies and air quality management activities.
Observed relationships between extreme sub‐daily precipitation, surface temperature, and relative humidity
Authors: Hardwick Jones Rhys , Westra Seth , Sharma Ashish
Published: November 2010

Expected changes to future extreme precipitation remain a key uncertainty associated with anthropogenic climate change. Recently, extreme precipitation has been proposed to scale with the precipitable water content in the atmosphere, which assuming relative humidity stays constant, will increase at a rate of ∼6.8%/°C as indicated by the Clausius‐Clapeyron (C‐C) relationship. We examine this scaling empirically using data from 137 long‐record pluviograph and temperature gauges across Australia. We find that scaling rates are consistent with the C‐C relationship for surface temperatures up to between 20°C and 26°C and for precipitation durations up to 30 minutes, implying that such scaling applies only for individual storm systems. At greater temperatures negative scaling is observed. Consideration of relative humidity data shows a pronounced decrease in the maximum relative humidity for land surface temperatures greater than 26°C, indicating that moisture availability becomes the dominant driver of how extreme precipitation scales at higher temperatures.
J2: An evaluation of new estimates from GPS, GRACE, and load models compared to SLR
Authors: Lavallée D. A. , Moore P. , Clarke P. J. , Petrie E. J. , van Dam T. , King M. A.
Published: November 2010

Changes in J2, resulting from past and present changes in Earth's climate, are traditionally observed by Satellite Laser ranging (SLR). Assuming an elastic Earth, it is possible to infer changes in J2 from changes in Earth's shape observed by GPS. We compare estimates of non‐secular J2 changes from GPS, SLR, GRACE, and a load model. The GPS and SLR annual signals agree but are different (16%) to the load model. Subtraction of the load model removes the annual variation from GPS, SLR, and GRACE, and the semi‐annual variation in GPS. The GPS and SLR long‐term signals are highly correlated, but GPS is better correlated with the loading model. Subtraction of the load model removes the 1998 anomaly from the GPS J2 series but not completely from the SLR J2 series, suggesting that the SLR anomaly may not be entirely due to mass re‐distribution as has been presumed.
Evolution of an active lava flow field using a multitemporal LIDAR acquisition
Authors: Favalli M. , Fornaciai A. , Mazzarini F. , Harris A. , Neri M. , Behncke B. , Pareschi M. T. , Tarquini S. , Boschi E.
Published: November 2010

Application of light detection and ranging (LIDAR) technology in volcanology has developed rapidly over the past few years, being extremely useful for the generation of high‐spatial‐resolution digital elevation models and for mapping eruption products. However, LIDAR can also be used to yield detailed information about the dynamics of lava movement, emplacement processes occuring across an active lava flow field, and the volumes involved. Here we present the results of a multitemporal airborne LIDAR survey flown to acquire data for an active flow field separated by time intervals ranging from 15 min to 25 h. Overflights were carried out over 2 d during the 2006 eruption of Mt. Etna, Italy, coincident with lava emission from three ephemeral vent zones to feed lava flow in six channels. In total 53 LIDAR images were collected, allowing us to track the volumetric evolution of the entire flow field with temporal resolutions as low as ∼15 min and at a spatial resolution of <1 m. This, together with accurate correction for systematic errors, finely tuned DEM‐to‐DEM coregistration and an accurate residual error assessment, permitted the quantification of the volumetric changes occuring across the flow field. We record a characteristic flow emplacement mode, whereby flow front advance and channel construction is fed by a series of volume pulses from the master vent. Volume pulses have a characteristic morphology represented by a wave that moves down the channel modifying existing channel‐levee constructs across the proximal‐medial zone and building new ones in the distal zone. Our high‐resolution multitemporal LIDAR‐derived DEMs allow calculation of the time‐averaged discharge rates associated with such a pulsed flow emplacement regime, with errors under 1% for daily averaged values.
Constraining ventilation during deepwater formation using deep ocean measurements of the dissolved gas ratios 40Ar/36Ar, N2/Ar, and Kr/Ar
Authors: Nicholson David , Emerson Steven , Caillon Nicolas , Jouzel Jean , Hamme Roberta C.
Published: November 2010

The concentration of inert gases and their isotopes in the deep ocean are useful as tracers of air‐sea gas exchange during deepwater formation. ΔKr/Ar, ΔN2/Ar, and δ40Ar were measured in deep profiles of samples collected in the northwest Pacific, subtropical North Pacific and tropical Atlantic oceans. For the ocean below 2000 m, we determined a mean ΔKr/Ar composition of −0.96% ± 0.16%, a mean ΔN2/Ar of 1.29% ± 0.21% relative to equilibrium saturation, and for δ40Ar a value of 1.188‰ ± 0.055‰ relative to air. These data are used to constrain high‐latitude ventilation processes in the framework of three‐box and seven‐box ocean models. For the three‐box model tracer data, we constrain the appropriate surface area of the high‐latitude region in both models to be 3.6% (+2.5%, −1.7%) of ocean surface area and the bubble air injection rate to be 22.7 (+8.8, −7.3) mol air m−2 yr−1. Results for the seven‐box model were similar, with a high‐latitude area of 3.3% (+2.2%, −1.3%). Our results provide geochemical support for suggestions that the effective area of high‐latitude ventilation is much smaller than the region of elevated preformed nutrients and demonstrate that noble gases strongly constrain the ocean solubility pump. Reducing high‐latitude surface area weakens the CO2 solubility pump in the box models and limits communication between the atmosphere and deep ocean. These tracers should be useful constraints on high‐latitude ventilation and the strength of the solubility pump in more complex ocean general circulation models.
Impact of lightning NO emissions on North American photochemistry as determined using the Global Modeling Initiative (GMI) model
Authors: Allen Dale , Pickering Kenneth , Duncan Bryan , Damon Megan
Published: November 2010

The impact of nitric oxide (NO) emissions by lightning on summertime North American nitrogen oxides (NOx) and ozone is studied using the Global Modeling Initiative (GMI) CTM and an improved lightning NO algorithm. The spatial distributions of modeled and National Lightning Detection Network‐based flash rates during the summers of 2004–2006 agree well (R2 = 0.49, 18% low bias). Despite this reasonable agreement, 9–12 km model NOx during the Intercontinental Chemical Transport Experiment (INTEX‐A) campaign is a factor of 2.2–3.6 too low for a simulation that includes a 480 mol per flash midlatitude lightning NO source, the source that provides the best agreement with measurements. Possible causes of this low bias include biases in model convection and/or too rapid NOx chemistry in the upper troposphere. Model tropospheric NO2 columns over the southeastern United States during these summers show a 7% high bias with respect to the OMI DOMINO/GEOS‐Chem tropospheric column NO2 product. Observed changes between 2004 and 2006 in upper tropospheric ozone at southeastern U. S. INTEX Ozonesonde Network Study sites are captured by the model and appear to be caused by a stronger upper tropospheric anticyclone in 2006 that led to an increase from 21 to 30 ppbv between 2004 and 2006 in the amount of ozone with a lightning NO source; lightning NO emissions were 15%–20% larger in 2004. The contribution of lightning NO to monthly average summertime 300 hPa NOx over the eastern United States during 2004–2006 varies from 61%–73% (0.09–0.16 ppbv), while the contribution to ozone varies from 19%–31% (15–24 ppbv).
Thin‐skinned deformation of sedimentary rocks in Valles Marineris, Mars
Authors: Metz Joannah , Grotzinger John , Okubo Chris , Milliken Ralph
Published: November 2010

Deformation of sedimentary rocks is widespread within Valles Marineris, characterized by both plastic and brittle deformation identified in Candor, Melas, and Ius Chasmata. We identified four deformation styles using HiRISE and CTX images: kilometer‐scale convolute folds, detached slabs, folded strata, and pull‐apart structures. Convolute folds are detached rounded slabs of material with alternating dark‐ and light‐toned strata and a fold wavelength of about 1 km. The detached slabs are isolated rounded blocks of material, but they exhibit only highly localized evidence of stratification. Folded strata are composed of continuously folded layers that are not detached. Pull‐apart structures are composed of stratified rock that has broken off into small irregularly shaped pieces showing evidence of brittle deformation. Some areas exhibit multiple styles of deformation and grade from one type of deformation into another. The deformed rocks are observed over thousands of kilometers, are limited to discrete stratigraphic intervals, and occur over a wide range in elevations. All deformation styles appear to be of likely thin‐skinned origin. CRISM reflectance spectra show that some of the deformed sediments contain a component of monohydrated and polyhydrated sulfates. Several mechanisms could be responsible for the deformation of sedimentary rocks in Valles Marineris, such as subaerial or subaqueous gravitational slumping or sliding and soft sediment deformation, where the latter could include impact‐induced or seismically induced liquefaction. These mechanisms are evaluated based on their expected pattern, scale, and areal extent of deformation. Deformation produced from slow subaerial or subaqueous landsliding and liquefaction is consistent with the deformation observed in Valles Marineris.
Bayesian inverse problem and optimization with iterative spatial resampling
Authors: Mariethoz Grégoire , Renard Philippe , Caers Jef
Published: November 2010

Measurements are often unable to uniquely characterize the subsurface at a desired modeling resolution. In particular, inverse problems involving the characterization of hydraulic properties are typically ill‐posed since they generally present more unknowns than data. In a Bayesian context, solutions to such problems consist of a posterior ensemble of models that fit the data (up to a certain precision specified by a likelihood function) and that are a subset of a prior distribution. Two possible approaches for this problem are Markov chain Monte Carlo (McMC) techniques and optimization (calibration) methods. Both frameworks rely on a perturbation mechanism to steer the search for solutions. When the model parameters are spatially dependent variable fields obtained using geostatistical realizations, such as hydraulic conductivity or porosity, it is not trivial to incur perturbations that respect the prior spatial model. To overcome this problem, we propose a general transition kernel (iterative spatial resampling, ISR) that preserves any spatial model produced by conditional simulation. We also present a stochastic stopping criterion for the optimizations inspired from importance sampling. In the studied cases, this yields posterior distributions reasonably close to the ones obtained by a rejection sampler, but with a greatly reduced number of forward model runs. The technique is general in the sense that it can be used with any conditional geostatistical simulation method, whether it generates continuous or discrete variables. Therefore it allows sampling of different priors and conditioning to a variety of data types. Several examples are provided based on either multi‐Gaussian or multiple‐point statistics.
Impact of internal waves on the spatial distribution of Planktothrix rubescens (cyanobacteria) in an alpine lake
Authors: Cuypers Yannis , Vinçon-Leite Brigitte , Groleau Alexis , Tassin Bruno , Humbert Jean-François
Published: November 2010

The vertical and horizontal distribution of the cyanobacterium, Planktothrix rubescens, was studied in a deep alpine lake (Lac du Bourget) in a 2-year monitoring program with 11 sampling points, and a 24-h survey at one sampling station. This species is known to proliferate in the metalimnic layer of numerous deep mesotrophic lakes in temperate areas, and also to produce hepatotoxins. When looking at the distribution of P. rubescens at the scale of the entire lake, we found large variations (up to 10 m) in the depth of the biomass peak in the water column. These variations were closely correlated to isotherm displacements. We also found significant variations in the distribution of the cyanobacterial biomass in the northern and southern parts of the lake. We used a physical modeling approach to demonstrate that two internal wave modes can explain these variations. Internal waves are generated by wind events, but can still be detected several days after the end of these events. Finally, our 24-h survey at one sampling point demonstrated that the V1H1 sinusoidal motion could evolve into nonlinear fronts. All these findings show that internal waves have a major impact on the distribution of P. rubescens proliferating in the metalimnic layer of a deep lake, and that this process could influence the growth of this species by a direct impact on light availability.
The Human Microbiome and Recurrent Abdominal Pain in Children
Authors: Raza Sabeen , Gibbs Richard , Mandal Debasmita , Qin Xiang , Lynch Susan , Versalovic James , Shulman Robert , Riehle Kevin , Saulnier Delphine , Mistretta Toni-Ann , Petrosino Joseph , Diaz Maria
Published: November 2010

This project explores the nature of the human intestinal microbiome in healthy children and children with recurrent abdominal pain. The overall goal is to obtain a robust knowledge base of the intestinal microbiome in children without evidence of pain or gastrointestinal disease and in those with recurrent abdominal pain (functional abdominal pain (FAP) and FAP associated with changes in bowel habits, i.e., irritable bowel syndrome or IBS). Specific aims include: 1. Characterize the composition of the gut microbiome in healthy children by DNA sequencing. 2. Determine the presence of disease-specific organism signatures of variable gut microbiomes in children with recurrent abdominal pain. 3. Perform functional gut metagenomics by evaluation of whole community gene expression profiles and discovery of disease-specific pathway signatures. Multiple strategies have been deployed to navigate and understand the nature of the intestinal microbiome in childhood. These strategies included 454 pyrosequencing-based strategies to sequence 16S rRNA genes and understand the detailed composition of microbes in healthy and disease groups. Microarray-based hybridization with the PhyloChip and quantitative real-time PCR (qPCR) probes were applied as complementary strategies to gain an understanding of the intestinal microbiome from various perspectives. Data collected and analyzed during the HMP UH2 Demo project, from a set of healthy and IBS children (7-12 yo) may enable the identification of core microbiomes in children, in addition to variable components that may distinguish healthy from diseased pediatric states. Twenty-two children with IBS and twenty-two healthy children were enrolled and analyzed in the UH2 phase of this study. The planned enrollment targets for the UH2/3 phases include 50 healthy children, 50 children with FAP and 50 children with IBS (minimum of 3 time points per child). We are currently analyzing the dataset for the presence of disease-specific signatures in the human microbiome, and correlating these microbial signatures with pediatric health or IBS disease status in addition to IBS subtype (e.g., diarrhea-vs constipation-predominant). In the next phase, whole genome shotgun sequencing and metatranscriptomics will be performed with a subset of children in each group. This study explores the nature of core and variable human microbiome in pre-adolescent healthy children and children with IBS.
Characterisation of dissolved organic matter in water extracts of thermally altered plant species found in box - ironbark forests
Authors: Quill Eben S. , Angove Michael J. , Morton David W. , Johnson Bruce B.
Published: November 2010

This study investigated the chemical structure of extracted dissolved organic matter (DOM) derived from thermally altered plant material found in the box–ironbark environments of central Victoria, namely: Eucalyptus tricarpa, Pinus pinaceae, Isolepsis nodosa, Acacia pycnantha, and Cassinia arcuata. Samples taken from the plants were burnt at 150, 300, and 400°C, under oxidising and reducing conditions in order to represent the variable combustion undergone by plants during bushfire events. The extraction of DOM from the burnt residues into water was conducted over 96 h. During the extraction period, solution concentrations of DOM were measured using HPLC and TOC methods, while the chemistry of the extracted DOM was characterised using ATR-IR. The nature of the extracted DOM depended on the originating species and whether burnt under oxidising or reducing conditions. DOM derived from the residues of the Australian native trees and shrubs (E. tricarpa, A. pycnantha, and C. arcuata) were generally more aromatic and conjugated than the materials extracted from herbaceous I. nodosa and introduced dendrophyte P. pinaceae. When burnt under reducing conditions, fire residues were less polar, indicated by the fact that they were significantly less soluble and ATR-IR spectra spectroscopy showed little OH stretching compared with the extracts obtained under oxidising conditions. Water extracts from the burnt residues sorbed strongly to the mineral goethite, but had less affinity for the kaolinite surface.
Soil carbon sequestration rates and associated economic costs for farming systems of south-eastern Australia
Authors: Grace Peter R. , Antle John , Ogle Stephen , Paustian Keith , Basso Bruno
Published: November 2010

Soil organic carbon (C) sequestration rates based on the Intergovernmental Panel for Climate Change (IPCC) methodology were combined with local economic data to simulate the economic potential for C sequestration in response to conservation tillage in the six agro-ecological zones within the Southern Region of the Australian grains industry. The net C sequestration rate over 20 years for the Southern Region (which includes discounting for associated greenhouse gases) is estimated to be 3.6 or 6.3 Mg C/ha after converting to either minimum or no-tillage practices, respectively, with no-till practices estimated to return 75% more carbon on average than minimum tillage. The highest net gains in C per ha are realised when converting from conventional to no-tillage practices in the high-activity clay soils of the High Rainfall and Wimmera agro-ecological zones. On the basis of total area available for change, the Slopes agro-ecological zone offers the highest net returns, potentially sequestering an additional 7.1 Mt C under no-tillage scenario over 20 years. The economic analysis was summarised as C supply curves for each of the 6 zones expressing the total additional C accumulated over 20 years for a price per t C sequestered ranging from zero to AU$200. For a price of $50/Mg C, a total of 427 000 Mg C would be sequestered over 20 years across the Southern Region, <5% of the simulated C sequestration potential of 9.1 Mt for the region. The Wimmera and Mid-North offer the largest gains in C under minimum tillage over 20 years of all zones for all C prices. For the no-tillage scenario, for a price of $50/Mg C, 1.74 Mt C would be sequestered over 20 years across the Southern Region, <10% of the simulated C sequestration potential of 18.6 Mt for the region over 20 years. The Slopes agro-ecological zone offers the best return in C over 20 years under no-tillage for all C prices. The Mallee offers the least return for both minimum and no-tillage scenarios. At a price of $200/Mg C, the transition from conventional tillage to minimum or no-tillage practices will only realise 19% and 33%, respectively, of the total biogeochemical sequestration potential of crop and pasture systems of the Southern Region over a 20-year period.
Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding
Authors: Romano Keith P. , Ali Akbar , Royer William E. , Schiffer Celia A.
Published: November 2010

Hepatitis C virus infects an estimated 180 million people worldwide, prompting enormous efforts to develop inhibitors targeting the essential NS3/4A protease. Resistance against the most promising protease inhibitors, telaprevir, boceprevir, and ITMN-191, has emerged in clinical trials. In this study, crystal structures of the NS3/4A protease domain reveal that viral substrates bind to the protease active site in a conserved manner defining a consensus volume, or substrate envelope. Mutations that confer the most severe resistance in the clinic occur where the inhibitors protrude from the substrate envelope, as these changes selectively weaken inhibitor binding without compromising the binding of substrates. These findings suggest a general model for predicting the susceptibility of protease inhibitors to resistance: drugs designed to fit within the substrate envelope will be less susceptible to resistance, as mutations affecting inhibitor binding would simultaneously interfere with the recognition of viral substrates.
Sumoylation activates the transcriptional activity of Pax-6, an important transcription factor for eye and brain development
Authors: Yan Qin , Gong Lili , Deng Mi , Zhang Lan , Sun Shuming , Liu Jiao , Ma Haili , Yuan Dan , Chen Pei-Chao , Hu Xiaohui , Liu Jinping , Qin Jichao , Xiao Ling , Huang Xiao-Qin , Zhang Jian , Li David Wan-Cheng
Published: November 2010

Pax-6 is an evolutionarily conserved transcription factor regulating brain and eye development. Four Pax-6 isoforms have been reported previously. Although the longer Pax-6 isoforms (p46 and p48) bear two DNA-binding domains, the paired domain (PD) and the homeodomain (HD), the shorter Pax-6 isoform p32 contains only the HD for DNA binding. Although a third domain, the proline-, serine- and threonine-enriched activation (PST) domain, in the C termini of all Pax-6 isoforms mediates their transcriptional modulation via phosphorylation, how p32 Pax-6 could regulate target genes remains to be elucidated. In the present study, we show that sumoylation at K91 is required for p32 Pax-6 to bind to a HD-specific site and regulate expression of target genes. First, in vitro-synthesized p32 Pax-6 alone cannot bind the P3 sequence, which contains the HD recognition site, unless it is preincubated with nuclear extracts precleared by anti–Pax-6 but not by anti-small ubiquitin-related modifier 1 (anti-SUMO1) antibody. Second, in vitro-synthesized p32 Pax-6 can be sumoylated by SUMO1, and the sumoylated p32 Pax-6 then can bind to the P3 sequence. Third, Pax-6 and SUMO1 are colocalized in the embryonic optic and lens vesicles and can be coimmunoprecipitated. Finally, SUMO1-conjugated p32 Pax-6 exists in both the nucleus and cytoplasm, and sumoylation significantly enhances the DNA-binding ability of p32 Pax-6 and positively regulates gene expression. Together, our results demonstrate that sumoylation activates p32 Pax-6 in both DNA-binding and transcriptional activities. In addition, our studies demonstrate that p32 and p46 Pax-6 possess differential DNA-binding and regulatory activities.
Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening
Authors: Bachovchin Daniel A. , Ji Tianyang , Li Weiwei , Simon Gabriel M. , Blankman Jacqueline L. , Adibekian Alexander , Hoover Heather , Niessen Sherry , Cravatt Benjamin F.
Published: November 2010

Serine hydrolases (SHs) are one of the largest and most diverse enzyme classes in mammals. They play fundamental roles in virtually all physiological processes and are targeted by drugs to treat diseases such as diabetes, obesity, and neurodegenerative disorders. Despite this, we lack biological understanding for most of the 110+ predicted mammalian metabolic SHs, in large part because of a dearth of assays to assess their biochemical activities and a lack of selective inhibitors to probe their function in living systems. We show here that the vast majority (> 80%) of mammalian metabolic SHs can be labeled in proteomes by a single, active site-directed fluorophosphonate probe. We exploit this universal activity-based assay in a library-versus-library format to screen 70+ SHs against 140+ structurally diverse carbamates. Lead inhibitors were discovered for ∼40% of the screened enzymes, including many poorly characterized SHs. Global profiles identified carbamate inhibitors that discriminate among highly sequence-related SHs and, conversely, enzymes that share inhibitor sensitivity profiles despite lacking sequence homology. These findings indicate that sequence relatedness is not a strong predictor of shared pharmacology within the SH superfamily. Finally, we show that lead carbamate inhibitors can be optimized into pharmacological probes that inactivate individual SHs with high specificity in vivo.
Quorum sensing and a global regulator TsrA control expression of type VI secretion and virulence in
Vibrio cholerae
Authors: Zheng Jun , Shin Ok S. , Cameron D. Ewen , Mekalanos John J.
Published: November 2010

Vibrio cholerae
is a human pathogen that causes the life-threatening diarrheal disease cholera. A type VI secretion system (T6SS) was recently shown to be required for full virulence in the O37 serogroup strain V52, which causes only sporadic human disease, but T6SS is not expressed in seventh pandemic O1 El Tor strains under standard laboratory conditions. In this study, we show that in the O1 El Tor strain C6706, T6SS is repressed by both quorum sensing and the uncharacterized protein VC0070 (TsrA). Disruption of TsrA and the quorum sensing regulator LuxO induces expression and secretion of the T6SS substrate Hcp, and this is dependent on the downstream regulator HapR, which directly binds to the promoter region of the T6SS genes
hcp1
and
hcp2
to induce expression. The activated T6SS in C6706 is functional and can translocate the effector protein VgrG-1 into macrophage cells, and T6SS activation leads to fecal diarrhea and intestinal inflammation in infant rabbits. Using an infant mouse infection model, we show that deletion of
tsrA
results in a 9.3-fold increase in intestinal colonization compared with wild type. TsrA functions as a global regulator to activate expression of hemagglutinin protease and repress cholera toxin and toxin coregulated pilus. Our findings provide significant insight into the molecular mechanism of T6SS and ToxT regulon gene regulation by quorum sensing and TsrA.
Contact
Authors: van der Kooij Els
Published: November 2010

Abstract
In early, simultaneous analyses of signs, [a_contact] is a multivalent feature pertaining to the movement parameter (cf. Friedman 1976). In models that make use of sequential units (Liddell and Johnson 1989, Sandler 1989, Perlmutter 1989, van der Hulst 1993) the valence of [contact] can be reduced to one. In comparing two types of sequential models I will show that one of them - the No-Movement model -is more adequate in accounting for the contact types proposed in Friedman (1976). By examining the consequences of the representation of the contact types in the No-Movement model of van der Hulst (1993) and further developments thereof (Crasborn 1995,1996; van der Hulst 1995, 1996; van der Kooij 1994, 1996; van der Kooij and Crasborn 1996). I will show that contact is a redundant property, predictable from the place specification of the sign. Being phonologically redundant, variation and non-distinctiveness of contact is correctly predicted.
Internationalization of the organic fruit market: The case of Washington State's organic apple exports to the European Union
Authors: Peck Gregory M. , Andrews Preston K. , Richter Cindy , Reganold John P.
Published: November 2010

Production of some organic commodities, such as apples, is heavily concentrated in the United States (US), with Washington State being the leading US producer of organic apples. In 2003, there were 4047 ha of certified organic apple orchards in Washington State, an all-time high and a more than tenfold increase since 1989. But this growth has not occurred without difficulties. Washington State's organic apple growers have encountered international supply and demand pressures forcing them to seek new markets, such as the European Union (EU). In this paper, we explore the complexities of the international marketing of organic fruit, using organic apple production in Washington State and market opportunities for this organic fruit in the EU, as a case study. We find that as a result of the expansion of organic apple plantings in Washington State, there has been a decrease in the price premiums, which traditionally offset the greater costs of organic production and which originally motivated many Washington growers to certify their apple orchards. We also find that increased demand for organic fruits in the EU has been outpacing supply, making EU member states the most important export market for Washington's organic apples. However, despite the unification of US standards by the US Department of Agriculture (USDA) and an overriding EU standard, an entanglement of regulatory bodies from around the world is involved in the certification of organic products. For example, growers and marketers may have to interact with as many as six different regulatory bodies in order to export organic produce from the US to the EU. This study shows that while the EU market remains a promising destination for US organic apples, organic growers and marketers must plan ahead and thoroughly understand the multitude of regulations involved in the international trade of organic fruits.