bluuebunny/crossref_metadata_2025 huggingface dataset:
Human Immunodeficiency Virus Type 1 gp120 and Other Activation Stimuli Are Highly Effective in Triggering Alpha Interferon and CC Chemokine Production in Circulating Plasmacytoid but Not Myeloid Dendritic Cells
Authors: Del Cornò Manuela , Gauzzi Maria Cristina , Penna Giuseppe , Belardelli Filippo , Adorini Luciano , Gessani Sandra
Published: September 2005

Exposure to aldrithiol-2-inactivated human immunodeficiency virus type 1 or gp120, but not gp41, triggered alpha interferon (IFN-α), CC chemokine ligand 2 (CCL2), CCL3, and CCL4 production in human plasmacytoid dendritic cells (DCs) but not in myeloid DCs (M-DCs) or monocyte-derived DCs from the same donors. The nonresponsiveness of M-DCs for IFN-α/β production was a general feature specific to these cells, as they also failed to produce it in response to inactivated influenza virus, poly(I-C), lipopolysaccharide,
Staphylococcus aureus
Cowans I, or CD40L. The different capacities of circulating DC subsets to produce immune mediators in response to most stimuli argue for a different role for these cells in the regulation of innate immunity to pathogens.
Diabetic heart disease
Authors: Marwick T H
Published: September 2005

Diabetes mellitus is responsible for a spectrum of cardiovascular disease. The best known complications arise from endothelial dysfunction, oxidation, inflammation, and vascular remodelling and contribute to atherogenesis. However, the effects on the heart also relate to concurrent hypertensive heart disease, as well as direct effects of diabetes on the myocardium. Diabetic heart disease, defined as myocardial disease in patients with diabetes that cannot be ascribed to hypertension, coronary artery disease, or other known cardiac disease, is reviewed.
Food abundance and fish density alters habitat selection, growth, and habitat suitability curves for juvenile coho salmon (Oncorhynchus kisutch)
Authors: Rosenfeld Jordan S , Leiter Thomas , Lindner Gerhard , Rothman Lorne
Published: September 2005

To understand how fish density and food availability affect habitat selection and growth of juvenile coho salmon (Oncorhynchus kisutch), we manipulated fish density (212 fish·m2) and natural invertebrate drift (0.0470.99 mg·m3) in 12 experimental stream channels constructed in a side-channel of Chapman Creek, British Columbia. Increased food resulted in increased growth of both dominant and subdominant fish and a shift to higher average focal velocities (from 6.5 to 8.4 cm·s1) with maximum growth in the range of 1012 cm·s1. Increased food appears to permit juvenile coho to exploit higher velocity microhabitats that might otherwise be bioenergetically unsuitable at lower food levels. Increased fish density resulted in lower growth of subdominant but not of dominant fish and a general displacement of fish to both higher and lower focal velocities. The shapes of habitat suitability curves were sensitive to food abundance, implying that differences in food availability may affect transferability of habitat suitability curves between streams of different productivity. While habitat suitability curves captured the change in extent of available habitat following prey enrichment, actual increases in growth rate with enrichment (i.e., changes in habitat quality) were poorly represented by habitat suitability values and better represented by bioenergetic model predictions.
Stochastic growth
Authors: Gudmundsson Gudmundur
Published: September 2005

Environmental variations in food and temperature induce substantial irregular variations in the growth of many living organisms. In fisheries research, stochastic growth has been modelled by adding a random term to deterministic growth functions. This entails large fluctuations in individual growth paths, including spells of negative growth. A different approach to modelling stochastic growth is presented where the anomalous short-term behaviour is avoided. The third moment of length distributions contains valuable information for the formulation of growth models. The size distribution of actual stocks is modified by size-dependent mortality. New methods for estimation of growth functions, taking this effect into account, are presented, requiring less specific assumptions about the properties of growth and stochastic variations than previous methods. Actual length distributions are also affected by genetic variability. The effects of this upon the development of second and third moments of length distributions with age differ depending on whether they are associated with maximum length or growth.
Microsatellite analyses of spatial genetic structure in darkblotched rockfish (Sebastes crameri): Is pooling samples safe?
Authors: Gomez-Uchida Daniel , Banks Michael A
Published: September 2005

By pooling or removing samples of small size, we investigated how results from microsatellite analyses of spatial genetic structure in darkblotched rockfish (Sebastes crameri) were affected. Genotypes from six and seven microsatellite loci from 1206 specimens collected offshore from Washington to California were employed in the analyses. Sample sizes varied greatly among locations (n = 11114). When adjacent samples of n < 25 were pooled using an absolute genetic distance (FST≤ 0), the correlation between genetic and geographic distance found in the original data set increased nearly twofold, and overall FST(95% confidence interval) increased from 0.001 (0.0000.002) to 0.002 (0.0010.003). Removing samples where n < 25 gave a similar result, yet the correlation increase was smaller. Another pooling strategy based on similarity tests allowed larger sizes in composite samples (n > 100) and further increased the correlation, although this strategy did not raise overall FST. These results indicate that under genetic isolation by distance, excessive pooling might not enhance the overall genetic differentiation among populations. The regression slope in isolation by distance plots was robust throughout all treatments, and its value suggests limited dispersal distance on this species.
In situ swimming speed and swimming behaviour of fish feeding on the krill Meganyctiphanes norvegica
Authors: Onsrud M SR , Kaartvedt S , Breien M T
Published: September 2005

In situ swimming speed and swimming behaviour of dielly migrating planktivorous fish were studied at a 120-m-deep location. Acoustic target tracking was performed using a hull-mounted transducer and submersible transducers located on the sea bottom and free hanging in the water column. The original data displayed a relationship between distance to transducer and swimming speed. A simplistic smoother applied during post-processing, appeared to break this relationship. Target tracking thus provided robust results on in situ swimming behaviour throughout the water column. Swimming speeds of deep-living fish, mainly Norway pout (Trisopterus esmarkii) and whiting (Merlangius merlangus), were highest during the day (speeds centred around 1416 cm·s1) and decreased somewhat by night (modes around 1011 cm·s1). Fish in the upper 1030 m swam somewhat faster (speeds ranging from 16 to 24 cm·s1). Fish in the upper layer at night were mainly Atlantic herring (Clupea harengus), sprat (Sprattus sprattus), and whiting. We ascribe the reduction of swimming speed in deep-living fish at night to a switch from visual feeding during daytime to nonvisual feeding by night. We suggest that shallow-living fish could forage visually even by night. Most tracks were fairly short, but some long tracks unveiled elaborate swimming paths as well as cyclic swimming behaviour.
Changing patterns in coastal cutthroat trout (Oncorhynchus clarki clarki) diet and prey in a gradient of deciduous canopies
Authors: Romero Nicolas , Gresswell Robert E , Li Judith L
Published: September 2005

We examined the influence of riparian vegetation patterns on coastal cutthroat trout Oncorhynchus clarki clarki diet and prey from the summer of 2001 through the spring of 2002. Benthic and drifting invertebrates, allochthonous prey, and fish diet were collected from deciduous, conifer, and mixed sections of three Oregon coastal watersheds. The nine sites were best characterized as a continuum of deciduous cover, and shrub cover and proportion of deciduous canopy were positively correlated (r = 0.74). Most sources of prey (benthic invertebrate biomass, allochthonous invertebrate inputs, aquatic and total invertebrate drift) and aquatic prey ingested by coastal cutthroat trout were greater where shrub cover was more abundant. Only aquatic drift, total invertebrate drift, and allochthonous invertebrates were positively correlated with deciduous vegetation. Compared with coniferous sites, allochthonous invertebrates under deciduous and mixed canopies were almost 30% more abundant. Stream discharge likely influenced seasonal fluxes of aquatic invertebrate biomass in the benthos and drift. Aquatic insects dominated gut contents during this study; however, terrestrial prey were most common in the diet during the summer and fall. In the Pacific northwest, systematic removal of deciduous riparian vegetation to promote conifers may have unintended consequences on food resources of coastal cutthroat trout and aquatic food web interactions.
Landscape heterogeneity and the biodiversity of Arctic stream communities: a habitat template analysis
Authors: Huryn Alexander D , Slavik Karie A , Lowe Rex L , Parker Stephanie M , Anderson Dennis S , Peterson Bruce J
Published: September 2005

We predicted that substratum freezing and instability are major determinants of the variability of stream community structure in Arctic Alaska. Their effects were conceptualized as a two-dimensional habitat template that was assessed using a natural experiment based on five stream types (mountain-spring, tundra-spring, tundra, mountain, glacier). Detrended correspondence analysis (DCA) indicated distinct macroinvertebrate assemblages for each stream type. The contribution of functional feeding groups to assemblage biomass varied systematically among stream types, indicating that structure and function are linked. Assemblage position within a DCA biplot was used to assess factors controlling its structure. Springs separated from other stream types along a gradient of nutrient concentration and freezing probability. Glacier and mountain streams separated from springs and tundra streams along a gradient of substratum instability and freezing probability. Owing to differences in sources of discharge to streams, the effects of nutrients and substratum stability could not be separated from freezing. Although many factors likely contribute to the variability of Arctic stream communities, the major determinants may be conceptualized as a template structured by gradients in (i) nutrient supply and substratum freezing and (ii) substratum instability and substratum freezing. This template provides a basis for predicting the response of Arctic stream communities to climate change.
Identification and mapping of bottom fish assemblages in Davis Strait and southern Baffin Bay
Authors: Jørgensen O A , Hvingel C , Møller P R , Treble M A
Published: September 2005

The bathymetry of Baffin Bay, with shallow sills both to the north and south, creates a relatively isolated body of deep polar water, unique among the Arctic Seas. During 263 trawl hauls completed during October 1999 and September to November 2001, 116 fish species were collected in Davis Strait and the southern Baffin Bay (61°44.1′ N73°52.8′ N, depths of 1451484 m). The abundance data for the 80 benthic species were used for analyses of the fish fauna diversity and fish assemblages. As a first step, seven assemblages were found by a standard type of cluster analysis. A Bayesian multinomial logit model was then applied to calculate vectors of probabilities defining the likelihood of each haul belonging to each of the seven clusters. The spatial distribution of the conditional probabilities for each cluster (assemblage) was mapped by means of a geostatistical tool. Each assemblage was further defined by indicator species, depth, and temperature. Four of the assemblages were found in Baffin Bay, two in Davis Strait and one mainly in Davis Strait but scattered into Baffin Bay.
Incorporating predation interactions in a statistical catch-at-age model for a predator-prey system in the eastern Bering Sea
Authors: Jurado-Molina Jesús , Livingston Patricia A , Ianelli James N
Published: September 2005

Virtual population analysis and the statistical catch-at-age methods are common stock assessment models used for management advice. The difference between them is the statistical assumptions allowing the fitting of parameters by considering how errors enter into the models and the data sources for the estimation. Fishery managers are being asked to consider multispecies interactions in their decisions. One option to achieve this goal is the multispecies virtual population analysis (MSVPA); however, its lack of statistical assumptions does not allow the use of tools used in single-species stock assessment. We chose to use a two-species system, walleye pollock (Theragra chalcogramma) and Pacific cod (Gadus macrocephalus), to incorporate the predation equations from MSVPA into an age-structured multispecies statistical model (MSM). Results suggest that both models produced similar estimates of suitability coefficients and predation mortalities. The adult population estimates from the single-species stock assessment and MSM were also comparable. MSM provides a measure of parameter uncertainty, which is not available with the MSVPA technologies. MSM is an important advancement in providing advice to fisheries managers because it incorporates the standard tools such as Bayesian methods and decision analysis into a multispecies context, helping to establish useful scenarios for management in the Bering Sea.
A potential model system for studying the genetics of domestication: behavioral variation among wild and domesticated strains of zebra danio (Danio rerio)
Authors: Robison Barrie D , Rowland William
Published: September 2005

The process of domestication in fish is fundamentally important to conservation efforts because of the extensive use of hatcheries to mitigate population declines. Research into the genetic changes associated with the domestication process in many endangered species is impeded by a lack of genomic tools, long generation times, and large space requirements. The study of the genetics of fish domestication could therefore benefit from the introduction of a model system. In this paper, we document behavioral and growth rate differences observed between a domesticated laboratory strain of zebra danio (Danio rerio) and a strain newly introduced into the laboratory from its native habitat in India. Domesticated zebra danio showed a higher degree of surface orientation, a reduced startle response, and higher growth rate compared with wild zebra danio. Wilddomesticated interstrain hybrids were intermediate in phenotype for all traits. When strains were reared together, most interstrain behavioral differences were maintained, indicating a genetic basis underlying the interstrain phenotypic variation. Phenotypic differences observed in this study are consistent with the effects of domestication in other fish species, indicating that the zebra danio can be used as a model system for studying the genetics of the domestication process in fish.
Detecting p53 family proteins in haemocytic leukemia cells ofMytilus edulisfrom Pictou Harbour, Nova Scotia, Canada
Authors: St-Jean S D , Stephens R E , Courtenay S C , Reinisch C L
Published: September 2005

Evaluating patterns of expression of p53-related proteins in cells is a novel approach in defining environmentally linked diseases. We have examined the induction of haemocytic leukemia in Mytilus edulis by municipal and industrial contaminants in Pictou Harbour, Nova Scotia, Canada. We used a murine monoclonal antibody, 1E10, as a diagnostic reagent to detect leukemic cells. We first characterized the reactivity of 1E10 with both normal and leukemic Mytilus haemocytes by confocal microscopy. We then compared p53 gene family expression (p53, p63p73, and p97) in normal versus leukemic haemocytes using a panel of monoclonal and polyclonal antibodies to p53 family proteins. The immunochemical data demonstrate that haemocytic leukemia cells of M. edulis differentially express p63p73 and p97p120 proteins. We subsequently used 1E10 to diagnose haemocytic leukemia in 500 M. edulis previously deployed 6 months earlier in Pictou Harbour. In the field, Mytilus caged near untreated municipal wastewater and bleached kraft pulpmill effluents have a significantly greater chance of developing haemocytic leukemia than do mussels exposed to reference sites.
Genetic influence of parr versus anadromous sires on the life histories of Atlantic salmon (Salmo salar)
Authors: Duston J , Astatkie T , MacIsaac P F
Published: September 2005

The potential for sire size to influence life history patterns from fry to sea age at maturity was established by rearing individually identified half-sibs of a single dam and either small (parr) or large (anadromous) sires in a common tank environment. Male sexual maturity was higher among progeny of small versus large sires at both parr (age 0+, 50% versus 32%, p = 0.065) and grilse stages (age 2+, 23% versus 10%, p = 0.034). In contrast, rates of female grilse (6.8%) and smolt age 1+ (>95%) were independent of sire size. Logistic regression indicated that grilse of small sires had an asymptote body weight (BW) 30% lower than grilse of large sires (1.0 versus 1.4 kg). In comparison, repeated measures analysis of BW, fork length (FL), and condition factor (CF) indicated that growth changes associated with grilsing were independent of sire size and sex. The highest-order interaction for which sire size was significant was day × sire × sex (p < 0.034). Independent of sire size, sexual maturation at both age 0+ and age 2+ was associated with a high CF, whereas smolting at age 1+ was associated with a high BW and FL but low CF.
A risk assessment for Pacific leatherback turtles (Dermochelys coriacea)
Authors: Kaplan I C
Published: September 2005

Leatherback turtles (Dermochelys coriacea) are critically endangered in the eastern and western Pacific Ocean. Here, I estimate the magnitude of two likely causes of their decline: (i) bycatch by longline fishing vessels and (ii) coastal sources of mortality. I calculate point estimates of longline bycatch based on turtle catch rates from the US Hawaii-based fleet and effort data for the international Pacific longline fleet. I estimate the intrinsic growth rate of the population and the magnitude of coastal mortality by fitting a simple logistic model. In the western and central Pacific, coastal sources lead to a 13% annual mortality rate, compared with a point estimate of 12% from longlining. In the eastern Pacific, coastal sources account for a 28% annual mortality rate, compared with a point estimate of only 5% from longlining. A Bayesian risk assessment reveals the importance of reducing coastal sources of mortality, as well as longline bycatch, if the populations are to avoid extinction. International efforts to protect the leatherback should expand beyond focusing solely on longline bycatch and should attempt to reduce coastal harvest of adult females and eggs, as well as reduce bycatch by inshore gears such as gillnets.
Impacts of hydraulic dredging on a macrobenthic community of the Adriatic Sea, Italy
Authors: Morello E B , Froglia C , Atkinson R JA , Moore P G
Published: September 2005

Hydraulic dredging that targets the bivalve Chamelea gallina in the northern and central Adriatic Sea (Italy) has been taking place for over 30 years. Seventy-three commercial dredgers harvest the resource within the sandy coastal area of the Ancona Maritime District (central Adriatic Sea). Despite this chronic disturbance, studies aimed at investigating the impacts of the fishery on the macrobenthic community of the area have never been carried out. To remedy this, sampling was accomplished within an area of the District from which hydraulic dredging was banned, within the framework of a balanced beyond-BACI (before/after, control/impact) experimental design. Data regarding seven groups of species were analysed separately by means of permutational multivariate analysis of variance. No impacts attributable to hydraulic dredging were found upon consideration of the entire sampled macrobenthic community, the Polychaeta, the Crustacea, detritivores, and suspensivores. In contrast, a sustained press impact of fishing was revealed for the Mollusca, and the bivalve Abra alba was found to be particularly susceptible. Abra alba was suggested as a possible impact indicator. A short-lived pulse impact on the predator and scavenger trophic guild was observed and was limited to the 1st sampling day after experimental hydraulic dredging.
Can growth be used as a surrogate measure of walleye (Sander vitreus) abundance change?
Authors: Sass Greg G , Kitchell James F
Published: September 2005

We examined several models to determine the relative contributions of density-dependent and density-independent factors on walleye (Sander vitreus) growth in the ceded territory of Wisconsin from 1990 to 1999. We then used independent data from 2000 to determine how well each model predicted walleye growth and examined several models to determine if growth could be used to predict density. Adult density best predicted the mean size of age-3 males ( [Formula: see text]3m) and age-5 females ( [Formula: see text]5f). Density-independent measures of pH, the morphoedaphic index, maximum depth, and conductance had a positive influence on growth, while adult density negatively affected growth. The solely density-dependent models predicted [Formula: see text]3m and [Formula: see text]5f poorly in 2000. The addition of density-independent factors improved model predictions of [Formula: see text]3m and [Formula: see text]5f. Walleye growth did not predict adult walleye densities. Regional patterns in walleye growth were correlated with surrogate measures of lake productivity and to a lesser extent adult density. Density dependence had a relatively weak affect on growth patterns, suggesting that growth cannot be used as a surrogate method for monitoring abundance change.
Catch-up growth and swimming performance in threespine sticklebacks (Gasterosteus aculeatus): seasonal changes in the cost of compensation
Authors: Álvarez D , Metcalfe N B
Published: September 2005

Compensatory growth is a phase of unusually rapid growth following a period of growth depression. This response allows animals to achieve the same size-for-age as continuously fed contemporaries. We tested the hypothesis that a period of poor growth followed by compensation reduces the swimming abilities of threespine sticklebacks (Gasterosteus aculeatus), even after the period of rapid growth had ceased; we also investigated how the time of year in which the rapid growth occurred affected the possible costs in swimming performance. The threespine sticklebacks showed a compensatory growth response after a period of food shortage, both in winter and in spring. This change in growth trajectory subsequently caused a reduction in ability to withstand high flows, but only when the period of rapid growth occurred just prior to the breeding season. We suggest that threespine sticklebacks may be willing to incur the swimming costs of catch-up growth just prior to the breeding season to maximize their expected reproductive success.
Raman spectroscopic studies on structure I and structure IItrimethylene oxide hydrate
Authors: Subramaniam S , Lance M J , Rawn C J , Chakoumakos B C , Rondinone A J
Published: September 2005

Raman spectra were collected from structure I (sI) and structure II (sII) trimethylene oxide (TMO) hydrates at various temperatures and used to assign the vibrational modes, investigate the ordering of TMO molecules inside the cage structure, and to determine possible interactions between the guest and the host lattice. Only Raman spectra from sI hydrate could be analyzed since the low concentration of TMO prevented sII peaks from being resolved. Comparison of the Raman spectra of liquid, solid, and enclathrated TMO (sI) showed Raman shifts to higher wave numbers for the enclathrated TMO; mainly among the ring modes. The ring and (or) skeletal modes around 930 cm1 and the asymmetric CH2 stretching mode around 2970 cm1, showed shifts greater than 10 cm1. These observed changes are interpreted on the basis of the "loose-cage  tight-cage" model, which interprets the shift as arising from strain induced by the hydrate cage on the guest TMO molecules in the 62 cages. In addition, variable temperature Raman studies, in the temperatures ranging from 103 to 203 K, showed no evidence of ordering and (or) reorientation of host molecules. PACS No.: 78.30.-j
Sensitivity studies and first validation of stratospheric ozone profile retrievals from Odin/OSIRIS observations of limb-scattered solar radiation
Authors: Savigny C von , McDade I C , Griffioen E , Haley C S , Sioris C E , Llewellyn E J
Published: September 2005

An error analysis and first validation results are presented for a method of retrieving stratospheric ozone density profiles from spectra of limb-scattered solar radiation, as measured with the OSIRIS instrument on the Odin satellite. The sensitivity study includes geophysical parameters such as ground albedo, stratospheric aerosols, cloud cover, and conditions in the background atmosphere, as well as instrumental parameters such as instrument noise, polarization sensitivity of the spectrograph, and levels of internal and external straylight. The dominating sources of error within the 1540 km altitude range are found to be stratospheric aerosols, ground albedo, and clouds, with each individual error being generally well below 5%. The total error in this altitude range is estimated to be on the order of 10% for an individual retrieved profile. A comparison of colocated measurements from OSIRIS and the POAM III occultation instrument during August of 2001 at northern-hemisphere mid-latitudes shows agreement to within about 5% between 15 and 35 km. The ozone densities from OSIRIS are found to be systematically lower than those from POAM III.PACS Nos.: 42.68.Ca, 82.33.Tb
A home-built lock-in amplifier for laser frequency stabilization
Authors: Sowka K , Weel M , Cauchi S , Cockins L , Kumarakrishnan A
Published: September 2005

We describe an inexpensive lock-in amplifier that can be built using discrete off-the-shelf RF components and home-built analog circuits. This lock-in has been used in a feedback loop to lock the frequency of a laser to an atomic transition. The frequency stability was tested by trapping rubidium atoms. The feedback loop involves obtaining a modulated saturated absorption signal from a vapor cell using an acousto-optic modulator to modulate the laser frequency. The absorption signal is sent to the lock-in to generate an error signal, proportional to the first derivative of the absorption, which is fed back to the laser to complete the feedback loop. We also demonstrate a simplified optical setup for viewing the saturated absorption spectrum. In this case, the signal consists of narrow saturated absorption spectra riding on top of a Doppler-broadened pedestal. We show that it is possible to greatly reduce the effect of this background and lock the laser to the atomic resonance by modifying the home-built lock-in to generate an error signal proportional to the third derivative of the absorption. The results of this work can be adapted for advanced undergraduate laboratory work.PACS Nos.: 01.50Pa, 07.50.e, 42.62Fi, 42.60Fc
Remediation of flare pit soils using supercritical fluid extraction
Authors: Nagpal V , Guigard S E
Published: September 2005

Supercritical fluid extraction (SFE) is a promising remediation technology for contaminated soils. This work investigates the use of SFE to remove petroleum hydrocarbons (PHCs) from flare pit soils. Extractions were performed on two flare pit soils at pressures ranging from 11.0 to 24.1 MPa and at temperatures ranging from 40 to 80 °C in an attempt to identify the best extraction conditions and to understand the effects of pressure, temperature, supercritical fluid flow rate, soil type, and extraction time on the extraction efficiency. For the conditions studied, the efficiency of the SFE process appeared to be solvent-density dependent. Conditions of 24.1 MPa and 40 °C (highest supercritical fluid density) yielded the highest extraction efficiency for both soils (89% for the sand and 80% for the loam). An increase in temperature at a fixed pressure led to a decrease in the extraction efficiency while an increase in pressure at a fixed temperature led to an increase in the extraction efficiency. The treated soils appeared to be drier, grainy, and lighter coloured than the soil prior to extraction.Key words: supercritical fluid extraction (SFE), supercritical carbon dioxide, flare pit soils, contaminated soil, soil remediation, biorecalcitrant petroleum hydrocarbons.
Nitrifier population dynamics in a bench-scale conventional activated sludge reactor following an induced perturbation
Authors: Simm R A , Ramey W D , Mavinic D S
Published: September 2005

An instantaneous increase in reactor free ammonia concentration resulted in a gradual decrease in nitrite oxidizer activity that was coincidental with an increase in the nitrous oxide emissions from the reactor. Microbial community analysis using RNA slot blotting techniques indicated that Nitrospira, and not Nitrobacter, populations appeared to be most affected by this induced perturbation. It is hypothesized that competition for nitrite and possibly oxygen between ammonia oxidizers and Nitrospira, and not free ammonia stress, was the true cause of impaired nitrite oxidizer activity. Key words: ammonia inhibition, fatty acid methyl esters, free ammonia, molecular methods, nitrification, nitrite, Nitrobacter, Nitrospira, nitrous oxide, RNA slot blotting, wastewater treatment.
Runoff and phosphorus export patterns in large forested watersheds on the western Canadian Boreal Plain before and for 4 years after wildfire
Authors: Burke J M , Prepas E E , Pinder S
Published: September 2005

We examined water and phosphorus export patterns in four large (130 to 247 km2) Boreal Plain watersheds (two burned and two reference) before and for 4 years after wildfire and the influence of precipitation intensity and timing on these patterns. Time series analysis of the one burned and one reference watershed monitored before and after fire demonstrated that relative to changes in the reference watershed over the same time period, runoff and dissolved and particulate phosphorus exports were higher in the burned watershed during the four post-fire years than before the fire (P = 0.001). Comparison of post-fire means in all four watersheds monitored for the post-fire years demonstrated that mean water and particulate phosphorus exports were 1.6 (P = 0.01) and 3.7 (P = 0.03) times higher in burned than reference watersheds, respectively. A similar pattern existed for dissolved phosphorus exports, but differences were not significant (P = 0.13). Thus, the pre- vs. post-fire comparison was consistent with, and more powerful than, the post-fire treatment vs. reference comparison. As of year 4 post-fire, burned watersheds continued to export more water and particulate phosphorus per unit area than reference watersheds, particularly during peak flow periods. Key words: watershed disturbance, boreal forest, stream, water quality, fire, phosphorus, runoff.
Measurement of growth rate of ammonia oxidizing bacteria in partially submerged rotating biological contactor by fluorescent in situ hybridization (FISH)
Authors: Jang Am , Okabe Satoshi , Watanabe Yoshimasa , Kim In S , Bishop Paul L
Published: September 2005

Optimization of the nitrification processes in biofilms is important for effective nitrogen removal because nitrification in an aerobic biofilm is considered to be a less than reliable process. Thus, one of the main factors to improve biological nitrogen removal processes is a better understanding of the microbiology and population dynamics of ammonia oxidizing bacteria (AOB) in wastewater treatment biofilms. Although the AOB in wastewater treatment have been qualitatively and quantitatively studied, information on their actual populations and activities is still limited. Therefore, the areal cell density of AOB in domestic wastewater biofilms on a partially submerged rotating biological contactor (RBC) was determined by fluorescent in situ hybridization (FISH) with a set of 16S rRNA-targeted oligonucleotide probes. The growth kinetics of the in situ AOB was also studied. Although low numbers of AOB were found at the deeper layers where oxygen was depleted, they were primarily detected in the upper and middle layers of the biofilm. The maximum specific growth rate (µb,max) and half saturation constant (Ks) of AOB in the biofilm were 0.32 d–1 and 1.7 mM/L of NH4+, respectively. Key words: ammonia oxidizing bacteria (AOB), fluorescent in situ hybridization (FISH), growth rate, rotating biological contactor (RBC).
Lateral stress changes and shaft friction for model displacement piles in sand
Authors: Lehane Barry M , White David J
Published: September 2005

The paper describes a series of tests performed in a drum centrifuge on instrumented model displacement piles in normally consolidated sand. These tests examined the influence of the pile installation method, the stress level, and the pile aspect ratio on the increase in lateral effective stress on the pile shaft during static load testing to failure. A parallel series of constant normal load and constant normal stiffness (CNS) laboratory interface shear experiments was performed to assist interpretation of the centrifuge tests. It is shown that although the cycling associated with pile installation results in a progressive reduction in the stationary horizontal effective stress acting on a pile shaft and densification of the sand in a shear band close to the pile shaft, this sand dilates strongly during subsequent shearing to failure in a static load test. The dilation (the amount of which depends on the cyclic history) is constrained by the surrounding soil and therefore leads to large increases in lateral effective stresses and hence to large increases in mobilized shaft friction. The increase in lateral stress is shown to be related to the radial stiffness of the soil mass constraining dilation of the shear band and to be consistent with measurements made in appropriate CNS interface shear tests. The paper's findings assist in the extrapolation of model-scale pile test results to full-scale conditions.Key words: sand, displacement pile, centrifuge tests, shaft friction.
Infiltration into an embankment reinforced by nonwoven geotextiles
Authors: Iryo T , Rowe R K
Published: September 2005

The hydraulic behaviour of permeable geosynthetics within unsaturated embankments subjected to infiltration is examined using the finite element method. The van Genuchten  Mualem model is employed to evaluate unsaturated hydraulic characteristics for both the soil and nonwoven geotextile. Using pore-water pressures obtained from the finite element analysis, stability analyses are conducted for the embankments, and the contribution of the nonwoven geo textile to stability is evaluated with reference to the observed performance of instrumented embankments. A numerical study is also conducted to examine the effect of geotextile configuration on the performance of reinforced embankments subject to infiltration. This study shows that nonwoven geotextiles may retard water flow in situations where the pore pressure is negative, whereas they act as a drainage material in situations where pore pressures are positive. It is also shown that the contribution of the nonwoven geotextile to the stability of the embankment as a drainage material is much less substantial than its role as a reinforcing material.Key words: nonwoven geotextile, drainage, unsaturated, embankment, stability.
Modelling species fate and porous media effects for landfill leachate flow
Authors: Cooke A J , Rowe R K , Rittmann B E
Published: September 2005

A numerical, multiple-species, reactive transport model, coupled to models of kinetic biodegradation, precipitation, and particle attachment and detachment for predicting landfill leachate-induced clogging in porous media for one-dimensional flow systems, is described. The finite-element method is used for transport modelling, with reactions incorporated into point-source or sink terms. The species modelled include three volatile fatty acids, active and inert suspended biomass, dissolved calcium, and inorganic particles. The clog matter consists of active biofilm, inert biofilm, and inorganic solids. A biofilm model is used to simulate the growth and decay of active biomass and removal of substrate. Precipitate accumulation and calcium removal are simulated by a model of calcium carbonate precipitation. Interphase movement between clog matter and fluid includes the processes of attachment and detachment. A geometric representation of the porous media allows porosity and specific surface to be estimated from the thickness of the accumulated clog matter. The porosity of the media can thus change spatially and temporally. The behaviour of the model is demonstrated with a hypothetical example.Key words: clogging, landfills, leachate collection systems, modelling, biofilms, mineral precipitation.
Development and verification of a numerical model for the analysis of geosynthetic-reinforced soil segmental walls under working stress conditions
Authors: Hatami Kianoosh , Bathurst Richard J
Published: September 2005

The paper describes a numerical model that was developed to simulate the response of three instrumented, full-scale, geosynthetic-reinforced soil walls under working stress conditions. The walls were constructed with a fascia column of solid modular concrete units and clean, uniform sand backfill on a rigid foundation. The soil reinforcement comprised different arrangements of a weak biaxial polypropylene geogrid reinforcement material. The properties of backfill material, the method of construction, the wall geometry, and the boundary conditions were otherwise nominally the same for each structure. The performance of the test walls up to the end of construction was simulated with the finite-difference-based Fast Lagrangian Analysis of Continua (FLAC) program. The paper describes FLAC program implementation, material properties, constitutive models for component materials, and predicted results for the model walls. The results predicted with the use of nonlinear elastic-plastic models for the backfill soil and reinforcement layers are shown to be in good agreement with measured toe boundary forces, vertical foundation pressures, facing displacements, connection loads, and reinforcement strains. Numerical results using a linear elastic-plastic model for the soil also gave good agreement with measured wall displacements and boundary toe forces but gave a poorer prediction of the distribution of strain in the reinforcement layers.Key words: numerical modelling, retaining walls, reinforced soil, geosynthetics, FLAC.
Unusual drawdown curves for a pumping test in an unconfined aquifer at Lachenaie, Quebec: field data and numerical modeling
Authors: Chapuis Robert P , Chenaf Djaouida , Acevedo Nelson , Marcotte Denis , Chouteau Michel
Published: September 2005

An unconfined aquifer was instrumented with monitoring wells over a surface area of about 100 m × 100 m. The aquifer is a sand deposit overlying a thick nonfissured layer of Champlain Sea clay. The paper presents the results of a pumping test at a constant flow rate. None of the curves of drawdown versus time presented the S shape of current theories; however, all drawdowns indicated that the aquifer was homogeneous. The values for the specific yield were too low and varied with distance and time instead of being constant. The theories for steady and unsteady states provided different values for the saturated hydraulic conductivity. To understand the field behavior that differs from theoretical predictions, the pumping test conditions were modeled numerically using a finite element method. The transmissivity was derived from the Dupuit equation, and different curves for capillary retention and unsaturated permeability were examined. The numerical drawdowns agree with the experimental drawdowns. Several numerical models were investigated. All of them solved the inverse problem correctly for steady-state conditions and fairly well for transient conditions with highly nonlinear characteristic functions. The best solution to the transient problem was obtained using trial and error, by considering how the drawdown curves might be modified due to anisotropy and stratification. According to these field tests and the numerical analysis, the S shape is not the rule, and a different shape can be perfectly normal due to the complexity of unsaturated flow.Key words: pumping, unconfined aquifer, permeability, drawdown, numerical modeling.
Time domain reflectometry for water content and density of soils: study of soil-dependent calibration constants
Authors: Drnevich V P , Ashmawy A K , Yu X , Sallam A M
Published: September 2005

The paper studies the soil-dependent calibration constants used for determining water content and density of soil using time domain reflectometry (TDR), specifically, to establish the typical soil calibration values and study the extent of the uncertainty in calibration factors on measurement accuracy. The TDR method described here makes use of a calibration equation normalized by soil dry density, which involves two soil-dependent constants, a and b. Both a and b have physical significance, with the value of a related to the apparent dielectric constant of the dry density – normalized dry soil solids and the value of b related to the apparent dielectric constant of the pore fluid. From theoretical predictions, typical values of a are around 1.0, and typical values of b are around 9. Practically, the constants a and b are obtained through calibration tests performed in conjunction with standard compaction tests. Experimental study shows that calibration constants fall within the ranges from theoretical predictions. Tests on five soil mixtures provided average values of a = 0.945 and b = 8.76, while 11 clean sands resulted in average values of a = 1.0 and b = 8.5. The study also shows that there are no significant effects of compaction energy on the measured values of a and b. Sensitivity analyses indicate that variations in a and b both cause variations in TDR-determined water content and density, but the variations are typically within acceptable limits for engineering application purpose. Results from TDR tests on simulated field experiments are consistent with the sensitivity analyses.Key words: time domain reflectometry, TDR, calibration constants, water content, dry density, sensitivity.
Change in leachate chemistry and porosity as leachate permeates through tire shreds and gravel
Authors: McIsaac Reagan , Rowe R Kerry
Published: September 2005

Rubber tire shreds are an attractive potential alternative to conventional gravel in the drainage layer of leachate collection systems at the base of landfills, yet the clogging and thus the long-term performance of tire shreds in this application is not known. This paper presents the results of an experimental investigation into the clogging potential of rubber tire shreds used as part of a leachate collection system at the base of a landfill when permeated with leachate. Experimental columns filled with two different rubber tire shreds and a conventional gravel drainage material were used to study the spatial and temporal variation of leachate characteristics and porosity changes within the drainage materials. It is shown that there are significant differences in the pore structures of the drainage materials and that these differences affect clog development and the length of time it takes for the hydraulic conductivity to drop below a threshold of 105 m/s. The gravel is found to have a service life at least three times greater than that of an equivalent thickness of compressed (at 150 kPa) tire shred.Key words: tire shreds, landfill, clogging, hydraulic conductivity, porosity, leachate collection.
Predicted genetic gains and testing efficiency from two loblolly pine clonal trials
Authors: Isik Fikret , Goldfarb Barry , LeBude Anthony , Li Bailian , McKeand Steve
Published: September 2005

Clonal field trials were established at two sites using rooted cuttings from 450 clones of eight full-sib families of loblolly pine (Pinus taeda L.). Height, survival, fusiform rust infection (caused by Cronartium quercuum (Berk) Miyabe ex Shirai f.sp. fusiforme), bole straightness, and diameter were measured after four growing seasons. There were significant differences among full-sib families and among clones within families for all traits studied. Moderately high within-family repeatabilities of clone means (0.50 to 0.75) for growth traits and a very high within-family repeatability of clone means (0.94) for fusiform rust infection were estimated. When the best eight clones were selected regardless of family structure, the volume yield was 52% greater than that of the unimproved seedlings at two sites. Selection of the best two clones from each of four families produced only slightly lower estimated genetic gains than the above scenario. The probability of fusiform rust infection ranged from 0.08 to 0.93 among clones at the South Carolina site. Predicted genetic gain for rust resistance was relatively insensitive to selection intensity, as there were numerous clones with high apparent resistance. The number of ramets per clone necessary to reliably characterize performance on one site was estimated to be between four and six. These results contribute to estimates of the gains available from clonal forestry and will help guide clonal testing and selection programs. Implementation of clonal forestry and cost issues are discussed.
Ecosystem and understory water and energy exchange for a mature, naturally regenerated pine flatwoods forest in north Florida
Authors: Powell Thomas L , Starr Gregory , Clark Kenneth L , Martin Timothy A , Gholz Henry L
Published: September 2005

Eddy covariance was used to measure energy fluxes from July 2000 – June 2002 above the tree canopy and above the understory in a mature, naturally regenerated slash pine (Pinus elliottii Engelm. var. elliottii) – longleaf pine (Pinus palustris Mill.) flatwoods forest. Understory latent energy (λE) and sensible heat (H) fluxes accounted for 45% and 55% of whole-ecosystem fluxes, respectively, with strong seasonal variation in the proportion of λE attributable to the understory. The partitioning of net radiation (Rnet) to λE and H also changed seasonally, with half-hourly mean ecosystem H in the winter peaking at 175 W·m–2, almost twice as large as λE. In contrast, half-hourly ecosystem λE and H remained almost equal throughout the day in July and August, with mean midday peaks of approximately 200 W·m–2. Maximum hourly evapotranspiration (ET) in the months of July and August was 0.32 and 0.29 mm·h–1 for 2000 and 2001, respectively. For a variety of environmental conditions, mean daily ET was approximately 2.7 mm in the summer and 1.3 mm in the winter. Annual ET for the first year was 832 mm, or 87% of annual precipitation (956 mm). Although leaf area index was higher in the second year, annual ET was only 676 mm, which is considerably lower than that of the previous year, but it still accounted for approximately the same proportion (84%) of the much lower annual precipitation (811 mm). Canopy conductance declined as soils dried, changing patterns of partitioning of Rnet to λE.