bluuebunny/crossref_metadata_2025 huggingface dataset:
Remote sensing of particle depletion by coastal suspension-feeders
Authors: Grant Jon , Bugden Gary , Horne Edward , Archambault Marie-Claude , Carreau Michel
Published: May 2007

Marine bivalves have been designated ecosystem engineers owing to their capacity to control estuarine water quality, particle dynamics, and primary production. Globally, bivalves have higher production than any other cultured animal. Large populations of natural, invasive, and cultured bivalves are suggested to cause changes in coastal ecosystem function through suspension-feeding of particles and biodeposition of waste materials. Association of bivalves with particle depletion is a trophic tenet of coastal ecosystems, but there are no previous observations of this process except at small scales. Using airborne hyperspectral remote sensing, we show direct evidence of aquaculture impacts at the ecosystem scale (kilometres), documenting significant depletion of phytoplankton through a blue mussel (Mytilus edulis) farm in eastern Canada, compared with dispersion in circulation model results without mussels. Understanding of factors controlling primary production and ecosystem processes in the coastal zone is critical in light of growing reliance on this region for development and resource extraction worldwide.
Spatial and temporal patterns in the food web structure of a large floodplain river assessed using stable isotopes
Authors: Herwig Brian R , Wahl David H , Dettmers John M , Soluk Daniel A
Published: May 2007

We assessed naturally occurring stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) for available food resources and consumers in the mainstream channel of the Mississippi River. Isotopic ratios were assessed for organic sources and organisms at two different sites during a fall, spring, and two summer seasons. Terrestrial C4 plants did not appear to be an important carbon source for consumers in the mainstream channel. A mixing model, IsoSource, indicated that terrestrial C3 vegetation, suspended algae, and epixylon were at times important food resources for large river consumers. Many consumer signatures fell outside the mixing polygon defined by these sources, indicating that there was a 13C-depleted food resource for which we did not account. We could not distinguish precisely whether downstream allochthonous and autochthonous carbon, or in situ production, was the dominant food resource supporting consumers in these systems. However, our data suggest that in situ organic matter sources can be important. Consumer δ13C and δ15N signatures intermediate between several sources indicated widespread omnivory in the river reaches that we studied. To fully understand food web structure and energy sources in complex large river ecosystems, an integrative approach that combines related empirical data sets is needed.
Individual variability in activity patterns of juvenile Atlantic salmon (Salmo salar) in Catamaran Brook, New Brunswick
Authors: Breau Cindy , Weir Laura K , Grant James WA
Published: May 2007

The activity of juvenile salmonids in streams varies between seasons, age classes, and times of day, but few studies have quantified the magnitude of individual variation in the behaviour of wild individuals. We monitored the activity patterns of 35 young-of-the-year (YOY) (fork length: 25.6–34.6 mm) and eight 1+ (fork length: 68.2–78.7 mm) Atlantic salmon (Salmo salar) over an 8-week summer field season. Age 1+ salmon were more active at night than during the day, whereas YOY fish were almost exclusively active during the day. However, daytime activity did not peak at 16–20 °C, the optimal water temperature range for growth determined in laboratory studies. Rather, the activity of 1+ fish peaked at 21 °C, whereas the activity of YOY fish continued to increase until 23 °C and then leveled off between 23 and 27 °C. There was also considerable individual variability within an age class in how fish responded to environmental variables that was often obscured by the average patterns. In a multiple logistic regression analysis for the activity of the 35 YOY, 18 responded significantly to time of day, 17 to water temperature, and 16 to day of the year. The causes of this individual variability and the consequences for growth and mortality deserve further study.
The influence of spawning habitat restoration on juvenile brown trout (Salmo trutta) density
Authors: Palm Daniel , Brännäs Eva , Lepori Fabio , Nilsson Kjell , Stridsman Stefan
Published: May 2007

Between 1992 and 2003, we assessed the density of age-0+ brown trout (Salmo trutta) in a channelized stream in northern Sweden, which was restored using two different schemes. One section of the stream was restored by the addition of boulders and reconstruction of gravel beds (boulder + gravel section), whereas another section was restored through addition of boulders only (boulder-only section). In addition, we compared the substrate size composition of gravel beds and the egg-to-fry survival between the two stream sections, and we related the density of age-0+ brown trout to the area of reconstructed gravel beds. After the restoration, the density of age-0+ brown trout increased significantly in the boulder + gravel section and was positively correlated with the area of reconstructed gravel beds. By contrast, the density of age-0+ brown trout did not change in the boulder-only treatment. Egg-to-fry survival was significantly higher in the boulder + gravel section compared with the boulder-only section, probably because of the higher content of sand and fines in the gravel beds of the latter treatment. This study shows that the density of age-0+ brown trout was limited by the availability and quality of spawning substrate rather than by the structural habitat complexity.
Rate of species introductions in the Great Lakes via ships' ballast water and sediments
Authors: Drake John M , Lodge David M
Published: May 2007

We report results from a study of species in ballast tanks of ships entering the Great Lakes between 2000 and 2002. We collected 1349 individuals from at least 93 unique taxonomic groups, of which approximately half were identified to species. We estimated that the zooplankton assemblage in ballast water destined for the Great Lakes comprised from 200 to 1000 unique taxa consisting of both freshwater and marine species. Between 14 and 39 of these taxa have not yet been recorded from the Great Lakes. Further, 13.9% of individual specimens identified to the species level were from species not previously collected from the Great Lakes. We collected seven nonindigenous freshwater species not currently found in the Great Lakes: Brachionus plicatilis, Cyclocypria kinkaidia, Maraenobiotus insignipes, Microcyclops rubellus, Microcyclops varicans, Neomysis awatchensis, and Paracyclops chiltoni. We found no evidence that ship age, seasonal timing, or age of ballast water affected the abundance of individuals or species in the ballast tanks. To our knowledge, these are the first extrapolations of data from ballast water collections to estimate the rate of species introduction to any ecosystem.
Characterization of stage-classified biological processes using multinomial models: a case study of anchovy (Engraulis encrasicolus) eggs in the Bay of Biscay
Authors: Ibaibarriaga Leire , Bernal Miguel , Motos Lorenzo , Uriarte Andrés , Borchers David L , Lonergan Mike E , Wood Simon N
Published: May 2007

This paper describes how multinomial models can be used to study developmental rates of biological processes and how these are affected by different factors such as temperature or parental effects. First, the most common multinomial models for ordinal categorical data (namely, proportional odds, continuation-ratio, and extended continuation-ratio models) are described within the particular framework of developmental rates for discrete and ordered stage classified biological processes. Then, the extraction from the fitted models of a series of biologically meaningful parameters is proposed. In particular, maximum probable age and several alternative definitions for stage duration are presented and pros and cons of each of them are discussed. As an example, the methodology is applied to analyze the temperature dependent development of anchovy (Engraulis encrasicolus) eggs in the Bay of Biscay.
Density, climate, and the processes of prespawning mortality and egg retention in Pacific salmon (Oncorhynchusspp.)
Authors: Quinn T P , Eggers D M , Clark J H , Rich, Jr. H B
Published: May 2007

In 2004 and 2005, exceptionally large runs of sockeye salmon (Oncorhynchus nerka) to the Alagnak River system in Bristol Bay, Alaska, coincided with weak runs to the nearby Kvichak River system. Restricted fishing to protect the Kvichak populations resulted in densities on the Alagnak River system's spawning grounds that were 11.5-fold (in 2004) and 9.0-fold (in 2005) above the long-term (1956–2003) average. Carcass sampling indicated that 23% (2004) and 44% (2005) of the potential egg deposition was lost to prespawning mortality or incomplete spawning in the Alagnak populations. Much lower levels of egg retentions were observed in spawning populations in the Kvichak River and Wood River systems, where the runs did not appreciably exceed the escapement goals, indicating that density-dependent spawning failure may have occurred. However, in 2005, significantly higher egg retention rates were observed in the Alagnak River system despite slightly lower densities than in 2004, indicating that environmental processes (probably low river levels and high temperatures) influenced prespawning mortality as well. More limited sampling in 2006 revealed only 3% egg retention in one of the Alagnak populations, but the combination of lower density and cooler conditions did not allow us to determine the relative contributions of these two factors to spawning failure.
A proposed all-solid-state transportable narrow-band sodium lidar for mesopause region temperature and horizontal wind measurements
Authors: She Chial -Yao , Vance J D , Kawahara Takuya D , Williams Bifford P , Wu Qian
Published: May 2007

An all-solid-state narrowband sodium lidar transmitter based on proven technologies is proposed. These proven technologies include: (i) the sum frequency generation of 589 nm coherent radiation with pulsed solid-state Nd:YAG lasers at 1064 and 1319 nm, developed for laser-guided star research and used in lidar measurements of mesopause-region temperatures by Shinshu University, (ii) the Doppler-free spectroscopic seed control developed by the Colorado State University and employed in a lidar system with hybrid solid-state and dye technologies for mesopause-region temperature and horizontal wind measurements, and (iii) the low-power continuous wave, tunable light around 589 nm via sum frequency generation developed by the University of Nevada. The proper combination of these mature technologies, deployed along with sodium-vapor Faraday filters, also developed by Colorado State University, will lead to a new all-solid-state sodium fluorescence lidar, capable of measuring mesopause-region temperatures and horizontal winds on a 24 h continuous basis, weather permitting. The integration of these proven solid-state technologies will make this proposed lidar transportable and suitable for remote operation in harsh environments. PACS Nos.: 42.68.Wt, 42.79.Qx, 92.60.–e, 07.20.Dt, 42.79.Qx
Microchamp sur un traceur
Authors: Poquérusse A
Published: May 2007

Mixtures of two ionic species are simulated by classical molecular dynamics, where a screened potential accounts for the high frequency electric field from free electrons. With an absolute precision of 1% of the maximum, the resulting probability distribution of the quasi static microfield at ions or neutrals is characterized by a simple rational fraction involving only three parameters, which are given for a wide variety of charges and concentrations.
O2 Atmospheric band and OH(6–2) airglow and temperature variability over Spain using SATI observations: Planetary-scale oscillations during autumn
Authors: López-González MJ , Rodríguez E , Shepherd G G , Shepherd M G , Sargoytchev S , Aushev V M , García-Comas M , Brown S , Wiens R H
Published: May 2007

Long-term ground-based airglow observations with a spectral airglow temperature imager (SATI) installed at Sierra Nevada Observatory (37.06°N, 3.38°W) at 2900~m height are used to investigate the main features of the quasi planetary waves in the period range of 3–20 days during autumn at this latitude in the mesosphere and lower thermosphere region. The modulations of periods 5 day, (6–7) day, and 10 day have been clearly detected during autumn at this location, being the most prominent waves detected at this location during the autumn. They have a strong persistence during the autumn period and relative amplitudes are generally constant during the period although a slight tendency to increase seems to be detected towards winter.PACS Nos.: 92.60.hw, 92.60.hb, 92.60.hc, 92.60.hh, 92.60.hv
Artificial neural network forecasting of nonlinear Markov processes
Authors: Fleming Sean W
Published: May 2007

I assessed the performance characteristics of the feed-forward artificial neural network (ANN) as a first-order nonlinear Markov modelling technique. The ability to recover the underlying structure of five synthetic random time series was first tested. The method was then applied to an observed geophysical time series, and the results were compared against external empirical constraints and a simple representation of the underlying physics. The Monte Carlo experiments suggested that the ANN–Markov technique: (i) yields good prediction skill; (ii) in general, accurately retrieves the form of the iterative mapping, even for extremely noisy data; (iii) accomplishes the foregoing without any need to consider or adjust for the distributional characteristics of the data or driving noise; and (iv) accurately estimates the distribution of the strictly stochastic signal component. Application to a historical river-flow record again showed good forecast skill. Moreover, the robustness, flexibility, and simplicity of the method permitted easy identification of the fundamental nonlinear physical dynamics of this environmental system directly from the time series data, perhaps belying the common perception of ANNs as a strictly black-box prediction technique. The ANN–Markov technique may thus serve as a valuable data-driven tool for guiding the development of both process-based and parameteric statistical models. The lack of specific distributional assumptions and requirements notwithstanding, it was also found that manual distributional transformations may permit the method to be tuned to particular applications by emphasizing or de-emphasizing certain features of the data. Drawbacks to the method include substantial data-set length requirements, a general limitation of ANNs, as well as an inconsistent but potentially troubling tendency to partially imprint the form of the ANN activation function upon the estimated recursion relationship.

PACS Nos.: 02.50.Ga, 05.10.–a, 05.45.Tp, 07.05.Mh, 02.50.Ey, 92.40.Fb
Height-dependent meteor temperatures and comparisons with lidar and OH measurements
Authors: Hocking W K , Argall P S , Lowe R P , Sica R J , Ellinor H
Published: May 2007

A new method is introduced that allows meteor radars to potentially produce height-dependent temperatures, rather than simply averages over the meteor region. The method is applied to data from the Clovar radar, near London, Ontario, and then a three-way comparison between Rayleigh lidar temperatures, hydroxyl temperatures, and meteor temperatures is undertaken. The three methods prove to be complementary. The OH measurements have good accuracy, but suffer slightly from lack of precise knowledge about their height and the fact that they are effectively integrated over the depth of the OH layer. The lidar temperatures are measured at well-defined altitudes and have better accuracy than the meteor method. The meteor temperatures have the largest errors, but still provide sufficient accuracy for many types of atmospheric studies, and have the advantage that these measurements can be made 24 h a day and in all sky conditions (including during cloud and strong sunlight and moonlight). The measurements from these instruments are complementary in that they are useful for studying the temperature on different time and altitude scales. PACS No.: 94.10.Dy
Modern topics in theoretical nuclear physics
Authors: Jennings B K , Schwenk A
Published: May 2007

Over the past five years there have been profound advances in nuclear physics based on effective field theory and the renormalization group. In this review, we summarize these advances and discuss how they impact our understanding of nuclear systems and experiments that seek to unravel their unknowns. We discuss future opportunities and focus on modern topics in low-energy nuclear physics, with special attention on the strong connections to many-body atomic and condensed-matter physics, as well as to astrophysics. This makes it an exciting era for nuclear physics.

PACS Nos.: 21.60.–n, 21.30.Fe
Motion of a particle with extrinsic curvature in an electromagnetic field
Authors: Gryb S B , McKeon D GC
Published: May 2007

The equations of motion for a particle whose free Lagrangian involves not only the arc length of its trajectory, but also its extrinsic curvature, is known to imply that the particle follows a helical path. We examine the parameters associated with this path to see if it can provide a realistic classical model for an electron. The radiation emitted by this point particle while following its helical trajectory is considered, and found to be well below the rest energy of the electron when the helical velocity of the electron is chosen to be 10–4c.

PACS No.: 11:15Kc
Expression ofNocardia brasiliensissuperoxide dismutase during the early infection of murine peritoneal macrophages
Authors: Revol Agnès , Espinoza-Ruiz Marisol , Medina-Villanueva Igor , Salinas-Carmona Mario Cesar
Published: May 2007

Nocardia brasiliensis is the main agent of actinomycetoma in Mexico, but little is known about its virulence and molecular pathogenic pathways. These facultative intracellular bacteria are able to survive and divide within the host phagocytic cells, in part by neutralizing the reactive oxygen intermediates. Superoxide dismutase (SOD) participates in the intracellular survival of several bacterial species and, in particular, constitutes one of Nocardia asteroides virulence factors. To clarify SOD participation in the N. brasiliensis early infective process, we report its isolation and the consequent comparison of its transcript level. A 630 bp polymerase chain reaction fragment that included most of the coding sequence of N. brasiliensis sodA was cloned. A competitive assay was developed, allowing comparison of bacterial sod expression in exponential culture and 1 h after infecting peritoneal macrophages from BALB/c mice. At that time, there were viable bacteria in the macrophages. The intracellular bacteria presented a clear decrease in their sod transcript amount, although their 16S rRNA (used as an internal control) and hsp levels were maintained or slightly increased, respectively. These results indicate that sodA transcription is not maintained within the SOS bacterial response induced by phagosomal conditions. Further kinetics will be necessary to precisely define sod transcriptional regulation during N. brasiliensis intra-macrophage growth.Key words: Nocardia brasiliensis, superoxide dismutase, macrophage infection, differential gene expression.
Chitinolytic bacteria in the intestinal tract of Japanese coastal fishes
Authors: Itoi Shiro , Okamura Toshihiro , Koyama Yuki , Sugita Haruo
Published: May 2007

Intestinal bacteria from several coastal fish species were screened on 1/20 PYBG medium containing 0.2% colloidal chitin, and 361 bacteria capable of decomposing colloidal chitin were isolated. These isolates were subsequently screened on media containing either 0.5% α-chitin or 0.5% β-chitin resulting in the identification of 31 α-chitinolytic and 275 β-chitinolytic bacterial isolates. Partial 16S rRNA gene sequencing was carried out and homology searches of the resultant sequences against the DDBJ, EMBL, and GenBank databases revealed that the majority (99%) of the chitinolytic bacteria isolated belonged to the Vibrionaceae. Phylogenetic analysis using a Bayesian approach showed that the α-chitinolytic bacteria belonging to the Vibrionaceae formed a separate cluster from the non-α-chitinolytic bacteria in the Vibrionaceae.Key words: chitinolytic bacteria, 16S rRNA, α-chitin, coastal fish, intestinal bacteria.
Adaptive changes of chemolithoautotrophic acidophilic sulfur-oxidizing bacteria during growth in sewage sludge
Authors: Matlakowska Renata , Sklodowska Aleksandra
Published: May 2007

A chemolithoauthotrophic, acidophilic, sulfur-oxidizing strain was isolated from sewage sludge and identified as Acidithiobacillus thiooxidans. The morphology and physiology of the isolate grown in mineral medium or sterilized sewage sludge were investigated. Morphological and ultrastructural differences between cells grown in mineral medium and sewage sludge were clearly visible. Sodium dodecyl sulfate polyacrylamide gel electrophoresis revealed some changes in the protein expression profiles in the periplasmic fraction as well as a lower level of cytochromes. Adaptation of A. thiooxidans to sewage sludge was not only a physiological process but also included genetic changes. Restriction fragment length polymorphism analysis using pulsed field gel electrophoresis showed structural changes in chromosomal DNA of such bacteria. Most of the restriction fragments were highly conserved and shared by strains grown under different conditions. Cultivation in mineral medium did, however, lead to the appearance of an additional restriction fragment. In combination, the obtained results provide evidence of adaptive responses by A. thioxidans during growth in sewage sludge and confirm that this bacteria can be useful in biotechnologies of heavy metal bioleaching from different environments polluted with hazardous compounds.Key words: Acidithiobacillus thiooxidans, sewage sludge, adaptation, SDS-PAGE, PFGE.
Effect of hydrogen peroxide on antibacterial activities of Canadian honeys
Authors: Brudzynski Katrina
Published: May 2007

Honey is recognized as an efficacious topical antimicrobial agent in the treatment of burns and wounds. The antimicrobial activity in some honeys depends on the endogenous hydrogen peroxide content. This study was aimed to determine whether honey's hydrogen peroxide level could serve as a honey-specific, activity-associated biomarker that would allow predicting and assessing the therapeutic effects of honey. Using a broth microdilution assay, I analyzed antibacterial activities of 42 Canadian honeys against two bacterial strains: Escherichia coli (ATCC 14948) and Bacillus subtilis (ATCC 6633). The MIC90 and MIC50 were established from the dose-response relationship between antibacterial activities and honey concentrations. The impact of H2O2 on antibacterial activity was determined (i) by measuring the levels of H2O2 before and after its removal by catalase and (ii) by correlating the results with levels of antibacterial activities. Canadian honeys demonstrated moderate to high antibacterial activity against both bacterial species. Both MIC90 and MIC50 revealed that the honeys exhibited a selective growth inhibitory activity against E. coli, and this activity was strongly influenced by endogenous H2O2 concentrations. Bacillus subtilis activity was marginally significantly correlated with H2O2 content. The removal of H2O2 by catalase reduced the honeys' antibacterial activity, but the enzyme was unable to completely decompose endogenous H2O2. The 25%-30% H2O2 "leftover" was significantly correlated with the honeys' residual antibacterial activity against E. coli. These data indicate that all Canadian honeys exhibited antibacterial activity, with higher selectivity against E. coli than B. subtilis, and that these antibacterial activities were correlated with hydrogen peroxide production in honeys. Hydrogen peroxide levels in honey, therefore, is a strong predictor of the honey's antibacterial activity.Key words: honey, antibacterial activity, hydrogen peroxide, catalase, Escherichia coli, Bacillus subtilis.
Differentially expressed genes reveal adaptations between free-living and symbiotic niches of Vibrio fischeri in a fully established mutualism
Authors: Jones B W , Nishiguchi M K
Published: May 2007

A major force driving in the innovation of mutualistic symbioses is the number of adaptations that both organisms must acquire to provide overall increased fitness for a successful partnership. Many of these symbioses are relatively dependent on the ability of the symbiont to locate a host (specificity), as well as provide some novel capability upon colonization. The mutualism between sepiolid squids and members of the Vibrionaceae is a unique system in which development of the symbiotic partnership has been studied in detail, but much remains unknown about the genetics of symbiont colonization and persistence within the host. Using a method that captures exclusively expressed transcripts in either free-living or host-associated strains of Vibrio fischeri, we identified and verified expression of genes differentially expressed in both states from two symbiotic strains of V. fischeri. These genes provide a glimpse into the microhabitat V. fischeri encounters in both free-living seawater and symbiotic host light organ-associated habitats, providing insight into the elements necessary for local adaptation and the evolution of host specificity in this unique mutualism.Key words: Vibrionaceae, gene expression, Sepiolidae, Euprymna, SCOTS.
Purification and characterization of an extracellular protease produced by psychrotolerant Clostridium sp. LP3 from lake sediment of Leh, India
Authors: Alam Syed Imteyaz , Dube Smita , Agarwal Mukesh Kumar , Singh Lokendra
Published: May 2007

An anaerobic, proteolytic bacterium isolated from lake sediments of Leh, India, was characterized with respect to morphology, biochemical characteristics, and 16S rRNA sequence and was identified as Clostridium species, with closest similarity to Clostridium subterminale. Isolate LP3 was psychrophilic, forming maximum cell mass between 10 and 20 °C, and produced extracellular protease. Growth was observed in the pH range of 7.0–8.5, with optimum at pH 7.5. Protease was purified 62.4-fold with a total yield of 17.5%. The effects of temperature, pH, and salt concentration on enzyme activity were studied. Protease was found to be a serine-type metallo-enzyme, active in a broad range of pHs. It was thermolabile and resistant to sodium dodecyl sulfate. Enzyme kinetics showed a tendency to increase Km with an increase in temperature for casein substrate.Key words: Clostridium sp., psychrotolerant, protease, anaerobe.
Role of burning season on initial understory vegetation response to prescribed fire in a mixed conifer forest
Authors: Knapp Eric E , Schwilk Dylan W , Kane Jeffrey M , Keeley Jon E
Published: May 2007

Although the majority of fires in the western United States historically occurred during the late summer or early fall when fuels were dry and plants were dormant or nearly so, early-season prescribed burns are often ignited when fuels are still moist and plants are actively growing. The purpose of this study was to determine if burn season influences postfire vegetation recovery. Replicated early-season burn, late-season burn, and unburned control units were established in a mixed conifer forest, and understory vegetation was evaluated before and after treatment. Vegetation generally recovered rapidly after prescribed burning. However, late-season burns resulted in a temporary but significant drop in cover and a decline in species richness at the 1 m2 scale in the following year. For two of the several taxa that were negatively affected by burning, the reduction in frequency was greater after late-season than early-season burns. Early-season burns may have moderated the effect of fire by consuming less fuel and lessening the amount of soil heating. Our results suggest that, when burned under high fuel loading conditions, many plant species respond more strongly to differences in fire intensity and severity than to timing of the burn relative to stage of plant growth.
Modelling and forecasting Finnish pine sawlog stumpage prices using alternative time-series methods
Authors: Malaty Ramses , Toppinen Anne , Viitanen Jari
Published: May 2007

This study analyzes the Nordic pine (Pinus sylvestris L.) sawlog markets in four main regions in Finland by using monthly real stumpage prices over the period January 1995 to June 2005. The special emphasis is on the short-run forecasting of different time-series models up to April 2006. As a benchmark case, we compare the models performance in terms of root mean square forecasting errors (RMSE) of standard autoregressive moving average (ARIMA) and vector autoregressive (VAR) models to those of Harvey's (1989) structural time series model (STSM), which, unlike the standard methods, decomposes the time series into unobservable components, such as deterministic and stochastic trend and seasonal and cyclical behaviour. The results indicate that, in most cases, the STSM together with Kalman filter estimation outperform ARIMA and VAR estimation. With hindsight, stumpage markets experienced a price decrease during July–December 2005 and a turning point up in early 2006 that none of these models were able to accurately predict. Based on these results, it seems to be that, in real-life forecasting situations, it is quite difficult to get precise estimates for the stumpage prices solely using the time-series approach, irrespective of how flexible the models may be with respect to structural changes.
Biomass partitioning in red pine (Pinus resinosa) along a chronosequence in the Upper Peninsula of Michigan
Authors: King J S , Giardina C P , Pregitzer K S , Friend A L
Published: May 2007

Carbon (C) allocation to the perennial coarse-root system of trees contributes to ecosystem C sequestration through formation of long-lived live wood biomass and, following senescence, by providing a large source of nutrient-poor detrital C. Our understanding of the controls on C allocation to coarse-root growth is rudimentary, but it has important implications for projecting belowground net primary production responses to global change. Age-related changes in C allocation to coarse roots represent a critical uncertainty for modeling landscape-scale C storage and cycling. We used a 55 year chronosequence approach with complete above- and below-ground harvests to assess the effects of stand development on biomass partitioning in red pine (Pinus resinosa Ait.), a commercially important pine species. Averaged within site, individual-tree root/shoot ratios were dynamic across stand development, changing from 0.17 at 2-, 3-, and 5-year-old sites, to 0.80 at the 8-year-old site, to 0.29 at the 55-year-old site. The results of our study suggest that a current research challenge is to determine the generality of patterns of root-shoot biomass partitioning through stand development for both coniferous and hardwood forest types, and to document how these patterns change as a function of stand age, tree size, environment, and management.
Characteristics and development of improved Pinus sylvestris in northern Sweden
Authors: Andersson Bengt , Elfving Björn , Persson Torgny , Ericsson Tore , Kroon Johan
Published: May 2007

Genetic differences are described between improved and unimproved Scots pine (Pinus sylvestris L.) in 36 northern Swedish field tests, covering wide geographical and climatic gradients (latitude 62.3°–67.8°N). Improved trees were represented by progenies from controlled crosses of first-generation, phenotypically selected plus trees, whereas unimproved trees originated from unselected natural stands. Improved trees were superior in terms of height (9.2%), stem diameter (5.4%), and stem volume (18.9%) at the age of 27.4 years. The height growth of improved trees from ages of 10.5 years to 27.4 years was similar to that of unimproved trees at a site with a higher site index. Improved trees had a 5.5% greater height/diameter ratio (i.e., were more slender) than unimproved trees, whereas differences between the tree categories in terms of survival and frequencies of ramicorns and stem breaks were minor and mostly insignificant. Little or no interaction between tree categories and site conditions for growth characters was found, implying that the results are generally applicable. No difference in response to competition between the improved and unimproved trees was detected. However, differences in their reactions to transfer were found: survival rates increased more and height growth decreased less in improved trees than in unimproved trees when grown at a site south of their geographical origin. The use of competition and height indices based on neighbouring trees to adjust for bias and site variability in single-tree plots significantly improved the estimates.
Tree colonization of sub-Mediterranean grasslands: effects of dispersal limitation and shrub facilitation
Authors: Kunstler Georges , Chaduf Joël , Klein Etienne K , Curt Thomas , Bouchaud Monique , Lepart Jacques
Published: May 2007

Encroachment of trees into low-productivity grasslands is a serious threat to grassland biodiversity throughout Europe. Although the rate of encroachment of trees into grassland is variable and poorly understood, it is thought to result from variation in tree seedling recruitment, which is limited mainly by the availability of safe sites and the dispersal distances of propagules. In this study, we established spatially explicit models of seedling recruitment for two major sub-Mediterranean trees: Quercus pubescens Willd. and Fagus sylvatica L. We quantified the spatial distribution of Q. pubescens and F. sylvatica seedlings up to 20 years old at three grassland sites. We also quantified the spatial distribution and size of mature trees and of the two dominant species of shrubs, Buxus sempervirens L. and Juniperus communis L., at each of the three sites. Ninety-eight percent of the regeneration took place under shrub canopy. Quercus pubescens seedlings showed higher seedling production per unit of canopy area and longer mean effective dispersal distances than did F. sylvatica seedlings. Quercus pubescens seedlings also had a large advantage over F. sylvatica seedlings for establishment in open areas. Juniperus shrubs were better safe sites for the establishment of Q. pubescens and F. sylvatica seedlings than were Buxus shrubs. We calculated indices of seedling dispersal limitation and safe site availability for recruitment for four dates. In the dolomitic Causse grasslands examined in this study, the availability of safe sites for germination and survival was far more important than seedling dispersal limitation for recruitment of both tree species.
The Folate Receptor α Is Frequently Overexpressed in Osteosarcoma Samples and Plays a Role in the Uptake of the Physiologic Substrate 5-Methyltetrahydrofolate
Authors: Yang Rui , Kolb E. Anders , Qin Jing , Chou Alexander , Sowers Rebecca , Hoang Bang , Healey John H. , Huvos Andrew G. , Meyers Paul A. , Gorlick Richard
Published: May 2007

Purpose: Two major systems exist for folate cell entry: the reduced folate carrier (RFC) and the folate receptor (FR). Although defective RFC-mediated transport was frequently identified as a mechanism of methotrexate (MTX) resistance in osteosarcoma, the status of FR and its role in this disease are unknown.

Experimental Design: mRNA for FRα was measured in 107 osteosarcoma specimens using quantitative reverse transcription-PCR and was related to RFC expression. The effect of FRα overexpression on MTX resistance and natural folate uptake was studied using FRα non-expressing osteosarcoma 143B cells transfected with FRα cDNA in comparison with those transfected with sense or antisense RFC in the same genetic background.

Results: Eighty-four samples (78.5%) had detectable FRα mRNA, and 29.9% had higher levels than the ovarian cancer cell line SKOV-3. No correlation was found between mRNA levels of FRα and RFC (r2 = 0.002). FRα overexpression had minor effects on the transport of MTX and sensitivity to this drug. Among the transfected 143B sublines, only the 143B-FRα was able to uptake 5-methyltetrahydrofolate when the extracellular concentration was reduced to 2 nmol/L, which conferred a growth advantage in physiologic folate concentrations compared with vector-only–transfected cells. Importantly, this was not similarly achieved by RFC overexpression.

Conclusions: This study suggests that FRα plays a role in the uptake of 5-methyltetrahydrofolate when the concentration gradient is insufficient for RFC-mediated transport. FRα overexpression is unlikely secondary to the decreased RFC expression in osteosarcoma.
Phase I and Pharmacokinetic Study of 7-Hydroxystaurosporine and Carboplatin in Advanced Solid Tumors
Authors: Edelman Martin J. , Bauer Kenneth S. , Wu Suhlan , Smith Ruth , Bisacia Sonia , Dancey Janet
Published: May 2007

Purpose: Based on preclinical data showing synergy between 7-hydroxystaurosporine (UCN-01) and platinum agents, a phase I trial of carboplatin with UCN-01 administered as a 3 h infusion in patients with advanced solid tumors was done. The primary goals of this trial were to evaluate the tolerability of this combination and the pharmacokinetics of UCN-01 when administered over 3 h and to compare the tolerability and pharmacokinetics with previously described schedules.

Patients and Methods: Patients with advanced solid tumors, good performance status, normal organ function, and no potentially curative therapy were eligible for the trial. Carboplatin was escalated from an area under the curve (AUC) of 3 to an AUC of 5. UCN-01 was escalated from 50 to 90 mg/m2.

Results: Twenty-three patients with advanced solid tumors (20 with prior platinum treatment) received a total of 60 cycles of therapy. Full doses of both agents (carboplatin AUC 5, UCN-01 90 mg/m2 in cycle 1, 45 mg/m2 in subsequent cycles) could be administered. The major toxicity noted was hypotension, which could be abrogated with the use of saline prehydration and posthydration. No responses were seen; however, seven patients were able to receive more than two courses of therapy. Of note, two of three patients with refractory, progressive small cell lung cancer were able to receive six cycles of therapy without evidence of progression. One patient experienced resolution of paraneoplastic syndrome of inappropriate antidiuretic hormone. The pharmacokinetic variables Cmax and t1/2 of the 3 h infusion were essentially identical to those previously observed when UCN-01 was administered over 72 h. The average t1/2 for cycle 1 was 506 ± 301 h, and the mean Cmax for all dose levels was >30 μmol/L. The mean AUC over the dosing interval for each dose level ranged from ∼6,000 to 9,000 μmol/L h. Thus, the AUC of UCN-01 after the 3 h infusion was lower than was observed after a 72 h infusion.

Conclusion: The regimen of carboplatin and UCN-01 (administered as a 3 h infusion) was well tolerated. Further development of this combination, particularly in small cell lung cancer, is warranted.
Expression of a Peroxisome Proliferator-Activated Receptor γ1 Splice Variant that Was Identified in Human Lung Cancers Suppresses Cell Death Induced by Cisplatin and Oxidative Stress
Authors: Kim Hyo Jung , Hwang Jin-Yong , Kim Hyun Jun , Choi Wan Sung , Lee Jae Heun , Kim Hye Jung , Chang Ki Churl , Nishinaka Toru , Yabe-Nishimura Chihiro , Seo Han Geuk
Published: May 2007

Purpose: The activation of peroxisome proliferator-activated receptor γ (PPARγ) has been implicated in the inhibition of tumor progression in lung cancers through the induction of differentiation and apoptosis. Recently, we identified a novel splice variant of human PPARγ1 (hPPARγ1) that exhibits dominant-negative activity in human tumor-derived cell lines. This study aimed to examine the expression and pathophysiologic roles of a truncated splice variant of hPPARγ1 (hPPARγ1tr) in primary human lung cancer tissues.

Experimental Design: The expression and localization of hPPARγ1tr was surveyed in human primary lung cancer tissues using immunohistochemistry and Western blot analysis. Using transfectants stably expressing wild-type hPPARγ1 (hPPARγ1wt) and hPPARγ1tr, we also analyzed the pathophysiologic roles of hPPARγ1tr.

Results: We showed that PPARγ is expressed predominantly in the nucleus of nontumorous tissues, whereas it is present in both the nucleus and the cytoplasm of tumorous tissues in squamous cell carcinoma (SCC) of the lung. Western blot analysis confirmed the presence of PPARγ1tr in primary lung SCC tissue but not in nontumorous tissue. Expression of PPARγ1tr in Chinese hamster ovary cells attenuated their susceptibility to cell death induced by oxidative stress or cisplatin, whereas their susceptibility was completely recovered by down-regulation of PPARγ1tr with small interfering RNA.

Conclusions: hPPARγ1tr is expressed strongly in tumorous tissues of primary human lung SCC and its overexpression renders transfected cells more resistant to chemotherapeutic drug- and chemical-induced cell death. These data suggest that the decreased drug sensitivity of PPARγ1tr-expressing cells may be associated with increased tumor aggressiveness and poor clinical prognosis of patients.
Methylation of O6-Methylguanine DNA Methyltransferase and Loss of Heterozygosity on 19q and/or 17p Are Overlapping Features of Secondary Glioblastomas with Prolonged Survival
Authors: Eoli Marica , Menghi Francesca , Bruzzone Maria Grazia , De Simone Tiziana , Valletta Lorella , Pollo Bianca , Bissola Lorena , Silvani Antonio , Bianchessi Donatella , D'Incerti Ludovico , Filippini Graziella , Broggi Giovanni , Boiardi Amerigo , Finocchiaro Gaetano
Published: May 2007

Purpose: Recent data suggest that methylation of the DNA repair gene O6-methylguanine DNA methyltransferase (MGMT), by increasing the chemosensitivity of glioblastoma multiforme, is significantly associated with improved prognosis. Results in contradiction with these findings, however, are present in the literature and the clinical and genetic context framing MGMT methylation is poorly characterized.

Experimental Design: To address these issues, we have investigated the MGMT methylation status, clinical and magnetic resonance imaging characteristics, and relevant genetic features (loss of heterozygosity on 17p and 19q, EGFR amplification, and p53 mutations) in a retrospective study on 86 patients affected by glioblastoma multiforme: 72 patients had a clinical history indicating de novo insurgence of the tumor and the remaining 14 were secondary glioblastoma multiforme.

Results: MGMT methylation was detected by methylation-specific PCR in 41 of 86 cases (47.7%; Meth+). Progression-free survival and overall survival were significantly longer in Meth+ than in Meth− patients [10 versus 7 months (P = 0.003, log-rank test) and 18 versus 14 months (P = 0.0003, log-rank test), respectively]. Mixed-nodular enhancement at magnetic resonance imaging was significantly more frequent in Meth+ and secondary glioblastoma multiforme and ring enhancement in Meth− and primary glioblastoma multiforme (P < 0.005). MGMT methylation was more present in secondary glioblastoma multiforme (P = 0.006) and associated with loss of heterozygosity on 17p and/or 19q (P = 0.005).

Conclusions: These observations suggest that MGMT methylation is part of a genetic signature of glioblastomas that developed from lower-grade gliomas.
Epigenetic Modifications of RASSF1A Gene through Chromatin Remodeling in Prostate Cancer
Authors: Kawamoto Ken , Okino Steven T. , Place Robert F. , Urakami Shinji , Hirata Hiroshi , Kikuno Nobuyuki , Kawakami Toshifumi , Tanaka Yuichiro , Pookot Deepa , Chen Zhong , Majid Shahana , Enokida Hideki , Nakagawa Masayuki , Dahiya Rajvir
Published: May 2007

Purpose: The RAS-association domain family 1, isoform A (RASSF1A) gene is shown to be inactivated in prostate cancers. However, the molecular mechanism of silencing of the RASSFIA gene is not fully understood. The present study was designed to investigate the mechanisms of inactivation of the RASSF1A gene through the analysis of CpG methylation and histone acetylation and H3 methylation associated with the RASSF1A promoter region.

Experimental Design: Methylation status of the RASSF1A gene was analyzed in 131 samples of prostate cancer, 65 samples of benign prostate hypertrophy (BPH), and human prostate cell lines using methylation-specific PCR. Histone acetylation (acetyl-H3, acetyl-H4) and H3 methylation (dimethyl-H3-K4, dimethyl-H3-K9) status associated with the promoter region in prostate cells were analyzed by chromatin immunoprecipitation (ChIP) assay.

Results: Aberrant methylation was detected in 97 (74.0%) prostate cancer samples and 12 (18.5%) BPH samples. The methylation frequency of RASSF1A showed a significant increase with high Gleason sum and high stage. The ChIP assays showed enhancement of histone acetylation and dimethyl-H3-K4 methylation on the unmethylated RASSF1A promoter. TSA alone was unable to alter key components of the histone code. However, after 5-aza-2′-deoxy-cytidine treatment, there was a complete reversal of the histone components in the hypermethylated promoter. Levels of acetyl-H3, acetyl-H4, and dimethyl-H3-K4 became more enriched, whereas H3K9me2 levels were severely depleted.

Conclusions: This is the first report suggesting that reduced histone acetylation or H3K4me2 methylation and increased dimethyl-H3-K9 methylation play a critical role in the maintenance of promoter DNA methylation–associated RASSF1A gene silencing in prostate cancer.
CD4+CD25+ Regulatory T-Cell Frequency in HER-2/neu(HER)-Positive and HER-Negative Advanced-Stage Breast Cancer Patients
Authors: Perez Sonia A. , Karamouzis Michael V. , Skarlos Dimosthenes V. , Ardavanis Alexandros , Sotiriadou Nectaria N. , Iliopoulou Eleni G. , Salagianni Maria L. , Orphanos George , Baxevanis Constantin N. , Rigatos Gerasimos , Papamichail Michael
Published: May 2007

Purpose: CD4+CD25bright regulatory T cells (Tregs) are increased in patients with several malignancies and correlate with disease stage and prognosis. Breast cancer patients represent a heterogeneous population with unpredictable disease progression even at advanced stages. Circulating Tregs in correlation with HER-2/neu (HER) status and treatment with chemotherapy, either alone or in combination with trastuzumab therapy, were monitored in advanced-stage breast cancer patients.

Experimental Design: Circulating Treg frequency and absolute counts of 46 HER+ and 28 HER−, stage III and IV, breast cancer patients before therapy and during trastuzumab therapy and/or chemotherapy have been compared with 24 healthy donors and correlated with plasma HER extracellular domain concentration and clinical outcome.

Results: Treg frequency in HER+ patients was significantly increased compared with both HER− patients and healthy donors. Trastuzumab therapy, with or without combined chemotherapy, resulted in a progressive decrease of circulating Tregs. Percentage change in Tregs statistically correlated with percentage change in plasma HER extracellular domain. Furthermore, decrease in Tregs correlated with either objective clinical response or stable disease, whereas increased Treg frequency during trastuzumab therapy coincided with disease progression. No statistically significant change in Treg frequency following chemotherapy was observed in HER− patients.

Conclusions: Treg cell frequency does not directly correlate with clinical stage in breast cancer, as stage III and IV HER+ and HER− patients exhibit significantly different Treg profiles. Trastuzumab therapy, either alone or combined with chemotherapy, results in decreased Treg frequency in HER+ advanced patients with an objective clinical response.