bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of BfrH, a Putative Siderophore Receptor of
Bordetella bronchiseptica
, Is Regulated by Iron, Fur1, and the Extracellular Function Sigma Factor EcfI
Authors: Burgos Jonathan M. , King-Lyons Natalie D. , Connell Terry D. 
Published: December 2009

ABSTRACT

Iron (Fe) in soluble elemental form is found in the tissues and fluids of animals at concentrations insufficient for sustaining growth of bacteria. Consequently, to promote colonization and persistence, pathogenic bacteria evolved a myriad of scavenging mechanisms to acquire Fe from the host.
Bordetella bronchiseptica
, the etiologic agent of upper respiratory infections in a wide range of mammalian hosts, expresses a number of proteins for acquisition of Fe. Using proteomic and genomic approaches, three Fe-regulated genes were identified in the bordetellae:
bfrH
, a gene encoding a putative siderophore receptor;
ecfI
, a gene encoding a putative extracellular function (ECF) sigma factor; and
ecfR
, a gene encoding a putative EcfI modulator. All three genes are highly conserved in
B. pertussis
,
B. parapertussis
, and
B. avium
. Genetic analysis revealed that transcription of
bfrH
was coregulated by
ecfI
,
ecfR
, and
fur1
, one of two
fur
homologues carried by
B. bronchiseptica
. Overexpression of
ecfI
decoupled
bfrH
from Fe-dependent regulation. In contrast, expression of
bfrH
was significantly reduced in an
ecfI
deletion mutant. Deletion of
ecfR
, however, was correlated with a significant increase in expression of
bfrH
, due in part to a
cis
-acting nucleotide sequence within
ecfR
which likely reduces the frequency of readthrough transcription of
bfrH
from the Fe-dependent
ecfIR
promoter. Using a murine competition infection model,
bfrH
was shown to be required for optimal virulence of
B. bronchiseptica
. These experiments revealed
ecfIR
-
bfrH
as a locus encoding a new member of the growing family of Fe and ECF sigma factor-modulated regulons in the bordetellae.
Paleomagnetic and geochemical evidence for a pre-Triassic age for the Lower Amaranth Member of the Williston Basin of Manitoba (Canada)
Authors: Szabó Erika , Cioppa Maria T. , Al-Aasm Ihsan S. 
Published: December 2009

Paleomagnetic and geochemical data obtained from six wells in southwestern Manitoba indicate that the Lower Amaranth redbeds were deposited earlier than Jurassic or Triassic, the most commonly cited depositional ages for this formation in the Williston Basin. The magnetization is carried primarily by detrital specular and pigmentary hematite and occasionally magnetite. Inclination-only analysis of paleomagnetic data (83 specimens from 60 plugs) indicates two possible depositional magnetization ages: Devonian–Pennsylvanian (D, found in very few samples) or Carboniferous to Permian, as suggested by the inclination and the polarity of the most predominant magnetization (B). An isolated magnetization (C) could be a mid-Jurassic to Neogene localized fluid flow remagnetization event. The oxygen and carbon isotope values of dolomite (–6.45‰ to 0.30‰ Vienna PeeDee Belemnite (VPDB) δ18O, –1.57‰ to 5.44‰ VPDB δ13C; n = 18) indicate that dolomitization could have occurred anytime between Carboniferous and Jurassic. However, the distribution of these values is a function of the three types of dolomite present in the Lower Amaranth strata: detrital, cement, and matrix replacive and reflects both the primary values and diagenetic overprints. Detrital and cement dolomite show depleted values in both oxygen and carbon isotopes, most likely inherited from the original values of the detrital dolomite, with superimposed effects of recrystallization. The matrix replacive dolomite has no detrital content, and its oxygen isotope values are similar to the expected values for primary or early diagenetic dolomite from Carboniferous to Jurassic times. Mixtures of detrital and replacive matrix dolomite give intermediate oxygen and carbon isotope values.
Factors affecting the growth and condition of lake whitefish (Coregonus clupeaformis)
Authors: Rennie Michael D. , Sprules W. Gary , Johnson Timothy B. 
Published: December 2009

Though declines in the growth and condition of Great Lakes lake whitefish ( Coregonus clupeaformis ) have been largely attributed to food web disruptions caused by invasive dreissenid mussels, a comprehensive evaluation of alternative hypotheses is currently lacking. Using various statistical approaches, we evaluated 69 years of data from the inner basin of South Bay, Lake Huron, considering the role of biological variables (food availability as Diporeia abundance and lake whitefish relative abundance as catch per unit effort, CPUE) versus environmental variables (climate change as growing degree days >5 °C and productive habitat capacity as percent epilimnetic volume, EV) on the condition and early growth rates of resident lake whitefish. Consistently, biological variables (Diporeia abundance, CPUE) best explained changes in lake whitefish growth and condition, respectively, in years when Diporeia data were available. In their absence, environmental variables (EV) best explained early growth rates of lake whitefish, whereas CPUE again best explained lake whitefish condition. Our analysis revealed that environmental change contributed significantly but alone was not sufficient to explain declines in lake whitefish growth after dreissenid establishment, whereas biological variables considered here could account for the majority of growth and condition changes observed in this population.
Long-term food web change in Lake Superior
Authors: Schmidt Stephanie N. , Vander Zanden M. Jake , Kitchell James F. 
Published: December 2009

Restoration and rehabilitation of native species in the Laurentian Great Lakes is a priority for fisheries management agencies. Restoration efforts are increasingly incorporating a perspective that considers species within a broader food web context. We used stable isotope analysis and museum-preserved specimens to describe and quantify 100 years of food web changes in the Lake Superior fish community. We validated stable isotope analysis of museum specimens by showing a positive correlation between isotope- and diet-based estimates of trophic position. While introductions have created a more trophically diverse food web than historically found in Lake Superior, two separate metrics revealed little community-wide change in the food web. Our species-specific analysis revealed trophic niche differences between shortjaw ( Coregonus zenithicus ) and shortnose ( Coregonus reighardi ) ciscoes, two species previously argued to be indistinguishable based on morphological characteristics. By providing a historical context, our findings show the ability of the Lake Superior food web to accommodate non-native species introductions over the last century while still supporting native species populations. This long-term information about food web structure can help guide management and restoration goals in Lake Superior. Furthermore, Lake Superior can serve as a basis for comparing food web changes in other, more highly altered Great Lakes.
Mach–Zehnder fiber interferometer test of the anisotropy of the speed of light
Authors: de Haan Victor 
Published: December 2009

Two optical fiber Mach–Zehnder interferometers were constructed in an environment with a temperature stabilization of better than 1 mK per day. One interferometer consisted of a length of 12 m optical fiber in each arm, with the main direction of the arms perpendicular to each other while the other consisted of a length of 2 m optical fiber in each arm, where the main direction of the arms are parallel, and served as a control. In each arm, 1 m of fiber was wound around a ring made of piezo material, enabling the control of the length of the arms by means of an applied voltage. The influence of the temperature on the optical phase difference between the interferometer arms was measured. The temperature change induced a variation of the interaction region of the optical fiber couplers. Further, the influence of rotation of the interferometers at the Earth surface on the observed phase differences was determined. For one interferometer (with the long and perpendicular arms), it was found that the phase difference depends on the azimuth of the interferometer. For the other one (with the short and parallel arms), no relevant dependence on the azimuth has been measured.
Physical and hydraulic characterization of fractured, hydrophobic sulphur within above-ground sulphur blocks
Authors: Bonstrom Kristie , Barbour S. Lee , Hendry M. Jim 
Published: December 2009

Volatility in the price of sulphur has resulted in the temporary storage of sulphur in large, surface blocks at oil sands properties in northern Alberta, Canada, that are subject to oxidation which produces acidic effluent. Characterization of water storage and migration within these blocks is required to assess potential environmental impacts. Investigation of the elemental sulphur (S0) blocks at Syncrude’s Mildred Lake site included fracture mapping and laboratory testing of core samples for density and permeability to air and water. Internal porosity was mapped with X-ray tomography, and water-intrusion porosimetry was used to define saturation–pressure relationships. The blocks have regular polygonal fractures with a porosity of approximately 1.4%. The mean total and water-available porosity of core samples was 9% and 6%, respectively. The water-entry pressure head was 1–2 m for matrix pores, but only 1–2 mm for fractures. Estimated functional relationships for volumetric water content versus water pressure of the fracture and matrix system are used to illustrate how infiltration is likely to occur rapidly along fracture pathways but with insufficient pressure to allow water to penetrate the matrix, suggesting that acid production occurs by flushing of the fracture surface with little influence from the matrix.
Soil processes and microbial community structures in 45- and 135-year-old lodgepole pine stands
Authors: Chatterjee A. , Ingram L.J. , Vance G.F. , Stahl P.D. 
Published: December 2009

As forests develop, changes in soil organic matter quantity and quality affect both nutrient dynamics and microbial community structure. Litter decomposition and nitrogen mineralization in association with soil microbial communities were compared between 45- and 135-year-old lodgepole pine ( Pinus contorta var. latifolia (Englem.)) stands in southeastern Wyoming, USA. Compared with the 45-year-old stand, the 135-year-old stand was found to have greater live-tree biomass, litter decomposition rates (264 versus 135 mg·(g litter)–1·year–1), soil nitrification rates (0.38 versus 0.19 µg NO3–·(g soil)–1 after 265 days of field incubation), and total phospholipid fatty acid (PLFA) concentrations (25 versus 9.2 nmol·(g soil)–1 at 0–5 cm depth). Canonical correspondence analysis indicated that variation of PLFA profiles within the 45-year-old stand was explained by soil pH and bulk density, whereas soil process rates explained the distributions of PLFA profiles within the 135-year-old stand. The results of these studies indicate that stand age influences live-tree biomass and soil properties that can lead to changes in litter decomposition rates and soil microbial communities in lodgepole pine forests.
Decomposition of Nothofagus wood in vitro and nutrient mobilization by fungi
Authors: Clinton Peter W. , Buchanan P. K. , Wilkie J. P. , Smaill S. J. , Kimberley M. O. 
Published: December 2009

The role of fungi in determining rates of wood decomposition and nutrient release in forest ecosystems is poorly understood. The decomposition of wood from three species of Nothofagus by 12 species of widely occurring New Zealand wood-decay fungi was investigated in vitro under standardized conditions. Wood mass loss varied strongly among fungal species and to a lesser extent with the species of wood. The species of fungi in this study were divided into three groups based on the extent of mass loss after 15 weeks: (1) rapid (>65% reduction in mass, Fomes hemitephrus , Pleurotus purpureoolivaceus , Trametes versicolor , and Ganoderma cf. applanatum), (2) intermediate (15%–30%, Phellinus sp., Schizopora radula , Phellinus nothofagi , and Skeletocutis stramenticus ), and (3) slow (<10%, Armillaria novaezelandiae , Postia pelliculosa , Australoporus tasmanicus , and Laetiporus portentosus ). For several fungal species, the final contents of nitrogen, phosphorus, and calcium in the remaining wood exceeded the initial nutrient contents in the wood, indicating that nutrient sequestration from the supporting soil matrix occurred during decomposition. Nutrient dynamics during decomposition varied with wood species, but the variation among different fungal species was much greater, indicating that fungal diversity is an important factor in determining nutrient flux in decaying wood.
A meta-regression analysis of forest carbon offset costs
Authors: van Kooten G. Cornelis , Laaksonen-Craig Susanna , Wang Yichuan 
Published: December 2009

The main focus of efforts to mitigate climate change is on the avoidance of fossil fuel emissions. However, the Kyoto Protocol rules permit the use of forestry activities that create carbon offset credits. These could obviate the need for lifestyle-changing reductions in fossil fuel use. Therefore, it is necessary for policy purpose to determine the cost effectiveness of creating forest sink carbon credits. In this study, meta-regression analyses with 1047 observations from 68 studies are used to determine factors that affect carbon sequestration costs. Results indicate that forest plantations and use of harvested biomass for energy make forestry activities more attractive. It also turns out that forestry activities are competitive with emissions reduction in tropical regions and, perhaps, boreal regions but certainly not in Europe. Finally, the regression estimates are used to project the potential costs of carbon uptake for various forest management scenarios — costs range from 0 to over 200 US$/t CO2.
On the Origin of Planetary-Scale Extratropical Winter Circulation Regimes
Authors: Hannachi A. 
Published: December 2009

AbstractSectorial and planetary-scale winter circulation regimes are studied and the relationship between them is investigated in order to find how much the simultaneous occurrence of sectorial regimes contributes to the occurrence of hemispheric regimes. The strategy is based on the multivariate Gaussian mixture model. The number of components in the model is estimated using two approaches. The first one is based on arguments from order statistics of the mixture proportions and the second uses a more severe test based on reproducibility. The procedure is applied next to the 500-hPa height field over the North Pacific, the North Atlantic, and the Northern Hemisphere using the empirical orthogonal function state space. Two highly significant regimes are found in each case, namely, the Pacific–North America (pattern) (±PNA)–North Atlantic Oscillation (±NAO) for the hemisphere—±PNA for the Pacific sector and ±NAO for the Atlantic sector. The sectorial regimes reflect mainly blocking and no-blocking flows. The results are tested further by applying a spatial clustering algorithm and are found to be consistent, particularly along the regime axes in the system state space. The relationship between hemispheric and sectorial circulation regimes is investigated. The data in each sector are first classified and then the times of simultaneous occurrence of sectorial regimes are identified. A new hemispheric dataset is then obtained by discarding maps corresponding to those co-occurrence times, and a new regime analysis is conducted. The results show that the hemispheric regime behavior has significantly decreased, suggesting that synchronization between sectorial circulation regimes could play an important role in the occurrence of planetary circulation regimes. The interannual variability of regime events is also discussed.
Relationships between Upper-Level Circulation over South America and Rainfall over Southeastern South America: A Physical Base for Seasonal Predictions
Authors: Zamboni Laura , Mechoso Carlos R. , Kucharski Fred 
Published: December 2009

Abstract
The existence of a significant simultaneous correlation between bimonthly mean precipitation anomalies over southeastern South America (SESA) and either the first or the second (depending on season) leading mode of interannual variability of upper-level wind over South America (SA) is demonstrated during all seasons except winter. The pattern associated with these modes of variability is similar during all seasons and consists of a continental-scale vortex centered over the eastern coast of subtropical SA. The vortex has a quasi-barotropic structure during all seasons, and its variability modifies moisture transport from the South American low-level jet and the western tropical Atlantic to SESA thus creating precipitation anomalies in this region. During spring (October–November) and summer (January–February) the circulation creates a second center of precipitation anomalies over the South Atlantic convergence zone that are of opposite sign to those over SESA, while during fall (April–May) precipitation anomalies are primarily confined to SESA. On the basis of the correlation between upper-level winds and precipitation, an empirical method to produce long-range forecasts of bimonthly mean precipitation over SESA is developed. Method tests in hindcast mode for the period 1959–2001 show a potential for reliable predictions during the southern spring, summer, and fall. The method is further tested in an experimental mode by using Development of a European Multimodel Ensemble System for Seasonal-to-Interannual Prediction (DEMETER) wind hindcasts. Forecasts obtained in this way are skillful during spring only, with highest skill during El Niño–Southern Oscillation years. During summer and fall, the DEMETER forecasts of wind anomalies limit the method’s ability to make reliable real predictions.
The Sensitivity of Latent Heat Flux to Changes in the Radiative Forcing: A Framework for Comparing Models and Observations
Authors: Winter Jonathan M. , Eltahir Elfatih A. B. 
Published: December 2009

Abstract
A climate model must include an accurate surface physics scheme in order to examine the interactions between the land and atmosphere. Given an increase in the surface radiative forcing, the sensitivity of latent heat flux to available energy plays an important role in determining the energy budget and has a significant impact on the response of surface temperature.
The Penman–Monteith equation is used to construct a theoretical framework for evaluating the climatology of evapotranspiration and the sensitivity of latent heat flux to available energy. Regional Climate Model version 3 coupled to Integrated Biosphere Simulator (RegCM3–IBIS); RegCM3 with its native land surface model, Biosphere–Atmosphere Transfer Scheme 1e (RegCM3–BATS1e); and Flux Network (FLUXNET) micrometeorological tower observations are compared and contrasted using the developed methodology.
RegCM3–IBIS and RegCM3–BATS1e simulate the observed sensitivity of latent heat flux to available energy reasonably well during the summer on average; however, there are significant variations in the monthly values. Additional information provided by the physically based Penman–Monteith framework is employed for identifying deficiencies and guiding improvements in models, allowing calibration of both the climatology of evapotranspiration and the sensitivity of latent heat flux to available energy.
Seasonal Variations of the Synoptic-Scale Transient Eddy Activity and Polar Front Jet over East Asia
Authors: Ren Xuejuan , Yang Xiuqun , Chu Cuijiao 
Published: December 2009

Abstract
Seasonal variations of the synoptic-scale transient eddy activity (STEA) and the jet streams over East Asia are examined through analysis of the 40-yr European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis (ERA-40) data. Extracted from the 6-hourly upper-level wind fields, the distribution of the jet core numbers exhibits a distinct geographical border for the East Asian subtropical jet (EASJ) and the East Asian polar front jet (EAPJ) at the latitudes of the northern Tibetan Plateau (TP). In the cool seasons, two branches of the STEA and low-level baroclinicity exist over the East Asian landmass, accompanied by the two-jet state of the EASJ and EAPJ. In the warm seasons, a single jet pattern of the EASJ along the north flank of the TP is accompanied by the weakened STEA over the mid- to high latitudes of East Asia. Further analysis shows two distinct features of the seasonal variations of the STEA over East Asia, compared with that over the North Pacific. First, during the transitional period of April–June, the main STEA band over East Asia migrates northward dramatically, in conjunction with the EAPJ shifting in the same direction. Second, both the upper-level STEA and the lower-level baroclinicity poleward of the TP are prosperous in spring. The relationship between the STEA, baroclinicity, vertical wind shear, and static stability in the EAPJ region in different seasons is further investigated. It is found that in addition to the time-mean wind fields, the rapid increase in the sensible heat flux poleward side of the TP region in spring and the associated boundary layer processes are partially responsible for the spring prosperity of the local baroclinicity and the STEA.
Error Propagation of Remote Sensing Rainfall Estimates in Soil Moisture Prediction from a Land Surface Model
Authors: Serpetzoglou Efthymios , Anagnostou Emmanouil N. , Papadopoulos Anastasios , Nikolopoulos Efthymios I. , Maggioni Viviana 
Published: December 2009

Abstract
The study presents an in-depth investigation of the properties of remotely sensed rainfall error propagation in the prediction of near-surface soil moisture from a land surface model (LSM). Specifically, two error sources are compared: rainfall forcing due to estimation error by remote sensing techniques and the representation of land–atmospheric processes due to LSM uncertainty [the Community Land Model, version 3.5 (CLM3.5), was used in this particular study]. CLM3.5 is forced by three remotely sensed precipitation products, namely, two satellite-based estimates—NASA’s Tropical Rainfall Measuring Mission (TRMM) multisatellite precipitation analysis and NOAA’s Climate Prediction Center morphing technique (CMORPH)—and a rain gauge-adjusted radar–rainfall product from the Weather Surveillance Radar-1988 Doppler (WSR-88D) network. The error analysis is performed for the warm seasons of 2004 and 2006 and is facilitated through the use of in situ measurements of soil moisture, rainfall, and other meteorological variables from a network of stations capturing the state of Oklahoma (Oklahoma Mesonet). The study also presents a rigorous benchmarking of the Mesonet network as to its accuracy in deriving area rainfall estimates at the resolution of satellite products (0.25° and 3 h) through comparisons against the most definitive measurements of a smaller-yet-denser network of rain gauges in southwestern Oklahoma (Micronet). The study compares error statistics between modeling and precipitation error sources and between the various remote sensing techniques. Results are contrasted between the relatively moist summer period of 2004 to the drier summer period of 2006, indicating model and error propagation dependencies. An intercomparison between rainfall and modeling error shows that the two error sources are of similar magnitudes in the case of high modeling accuracy (i.e., 2004), whereas the contribution of rainfall forcing error to the uncertainty of soil moisture prediction can be lower when the model’s efficiency skill is relatively low (i.e., 2006).