bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing prostate, bladder and rectal doses during image guided radiation therapy — need for plan adaptation?
Authors: Varadhan Raj , Hui Susanta K , Way Sarah , Nisi Kurt
Published: August 2009

The primary application of Image‐Guided Radiotherapy (IGRT) in the treatment of localized prostate cancer has been to assist precise dose delivery to the tumor. With the ability to use in‐room Computed Tomography (CT) imaging modalities, the prostate, bladder and rectum can be imaged before each treatment and the actual doses delivered to these organs can be tracked using anatomy of the day. This study evaluates the dosimetric uncertainties caused by interfraction organ variation during IGRT for 10 patients using kilovoltage cone beam CT (kvCBCT) on the Elekta Synergy system and megavoltage CT (MVCT) on the TomoTherapy Hi·Art System. The actual delivered doses to the prostate, bladder and rectum were based on dose recomputation using CT anatomy of the day. The feasibility of dose calculation accuracy in kvCBCT images from the Elekta Synergy system was investigated using the ComTom phantom. Additionally, low contrast resolution, image uniformity, and spatial resolution between the three imaging modalities of kilovoltage CT (kvCT), kvCBCT and MVCT images, were quantitatively evaluated using the Catphan 600 phantom. The Planned Adaptive software was used on the TomoTherapy Hi·Art system to construct a cumulative Dose Volume Histogram (DVH), incorporating anatomical information provided by the daily MVCT scans. The cumulative DVH was examined to identify large deviation (10% or greater) between the planned and delivered mean doses. The study proposes a framework that applies the cumulative DVH to evaluate and adapt plans that are based on actual delivered doses. Due to the large deviation in CT number (›300 HU) between the kvCBCT images and the kvCT, a direct dose recomputation on the kvCBCT images from the Elekta Synergy system was found to be inaccurate. The maximum deviation to the prostate was only 2.7% in our kvCBCT study, when compared to the daily prescribed dose. However, there was a large daily variation in rectum and bladder doses based on the anatomy of the day. The maximum variation in rectum and bladder volumes receiving the percentage of prescribed dose was 12% and 40%, respectively. We have shown that by using Planned Adaptive software on the TomoTherapy Hi·Art system, plans can be adapted based on the image feedback from daily MVCT scans to allow the actual delivered doses to closely track the original planned doses.

PACS number: 87.53.Tf
Time delays and margins in gated radiotherapy
Authors: Smith Wendy L. , Becker Nathan
Published: August 2009

In gated radiotherapy, the accuracy of treatment delivery is determined by the accuracy with which both the imaging and treatment beams are gated. Time delays are of four types: (1) beam on imaging time delay is the time between the target entering the gated region and the first gated image acquisition; (2) beam off imaging time delay is the time between the target exiting a gated region and the last image acquisition; (3) beam on treatment time delay is the time between the target entering the gated region and the treatment beam on; and (4) beam off treatment time delay is the time between the target exiting the gated region and treatment beam off. Asynchronous time delays for the imaging and treatment systems may increase the required internal target volume (ITV) margin. We measured time delay on three fluoroscopy systems, and three linear accelerator treatment beams, varying gating type (amplitude vs. phase), beam energy, dose rate, and period. The average beam on imaging time delays were (amplitude, 1 SD), (phase); while the average beam off imaging time delays were (amplitude) and (phase). The average beam on treatment time delays were (amplitude, 1 SD), (phase); while the average beam off time delays for treatment beams were (amplitude) and (phase). The negative value indicates the images were acquired early, and the positive values show the treatment beam was triggered late. We present a technique for calculating the margin necessary to account for time delays. We found that the difference between these imaging and treatment time delays required a significant increase in the ITV margin in the direction of tumor motion at the gated level.

PACS number: 87.53.Dq
Application of a 3D volumetric display for radiation therapy treatment planning I: quality assurance procedures
Authors: Gong Xing , Kirk Mike , Zusag Tom , Khelashvili Gocha , Chu James , Napoli Josh , Stutsman Sandy
Published: August 2009

To design and implement a set of quality assurance tests for an innovative 3D volumetric display for radiation treatment planning applications. A genuine 3D display (Perspecta Spatial 3D, Actuality‐Systems Inc., Bedford, MA) has been integrated with the Pinnacle TPS (Philips Medical Systems, Madison WI), for treatment planning. The Perspecta 3D display renders a 25 cm diameter volume that is viewable from any side, floating within a translucent dome. In addition to displaying all 3D data exported from Pinnacle, the system provides a 3D mouse to define beam angles and apertures and to measure distance. The focus of this work is the design and implementation of a quality assurance program for 3D displays and specific 3D planning issues as guided by AAPM Task Group Report 53. A series of acceptance and quality assurance tests have been designed to evaluate the accuracy of CT images, contours, beams, and dose distributions as displayed on Perspecta. Three‐dimensional matrices, rulers and phantoms with known spatial dimensions were used to check Perspecta's absolute spatial accuracy. In addition, a system of tests was designed to confirm Perspecta's ability to import and display Pinnacle data consistently. CT scans of phantoms were used to confirm beam field size, divergence, and gantry and couch angular accuracy as displayed on Perspecta. Beam angles were verified through Cartesian coordinate system measurements and by CT scans of phantoms rotated at known angles. Beams designed on Perspecta were exported to Pinnacle and checked for accuracy. Dose at sampled points were checked for consistency with Pinnacle and agreed within 1% or 1 mm. All data exported from Pinnacle to Perspecta was displayed consistently. The 3D spatial display of images, contours, and dose distributions were consistent with Pinnacle display. When measured by the 3D ruler, the distances between any two points calculated using Perspecta agreed with Pinnacle within the measurement error

PACS number: 07.07.Hj, 87.55.Qr, 87.56.Da, 87.55.D‐; Radiation Treatment Planning
Expected clinical impact of the differences between planned and delivered dose distributions in helical tomotherapy for treating head and neck cancer using helical megavoltage CT images
Authors: Mavroidis Panayiotis , Stathakis Sotirios , Gutierrez Alonso , Esquivel Carlos , Shi Chenyu , Papanikolaou Nikos
Published: August 2009

Helical Tomotherapy (HT) has become increasingly popular over the past few years. However, its clinical efficacy and effectiveness continues to be investigated. Pre‐treatment patient repositioning in highly conformal image‐guided radiation therapy modalities is a prerequisite for reducing setup uncertainties. A MVCT image set has to be acquired to account for daily changes in the patient's internal anatomy and setup position. Furthermore, a comparison should be performed to the kVCT study used for dosimetric planning, by a registration process that results in repositioning the patient according to specific transitional and rotational shifts. Different image registration techniques may lead to different repositioning of the patient and, as a result, to varying delivered doses. This study aims to investigate the expected effect of patient setup correction using the Hi·Art TomoTherapy system by employing radiobiological measures such as the biologically effective uniform dose and the complication‐free tumor control probability . In this study, a typical case of lung cancer with metastatic head and neck disease was investigated by developing a Helical Tomotherapy plan. For the TomoTherapy Hi·Art plan, the dedicated tomotherapy treatment planning station was used. Three dose distributions (planned and delivered with and without patient setup correction) were compared based on radiobiological measures by using the index and the concept as the common prescription point of the plans, and plotting the tissue response probabilities against the mean target dose for a range of prescription doses. The applied plan evaluation method shows that, in this cancer case, the planned and delivered dose distributions with and without patient setup correction give a of 81.6%, 80.9% and 72.2%, for a to the planning target volume (PTV) of 78.0Gy, 77.7Gy and 75.4Gy, respectively. The corresponding tumor control probabilities are 86.3%, 85.1% and 75.1%, whereas the total complication probabilities are 4.64%, 4.20% and 2.89%, respectively. HT can encompass the often large PTV required while minimizing the volume of the organs at risk receiving high dose. However, the effectiveness of an HT treatment plan can be considerably deteriorated if an accurate patient setup system is not available. Taking into account the dose‐response relations of the irradiated tumors and normal tissues, a radiobiological treatment plan evaluation can be performed, which may provide a closer association of the delivered treatment with the clinical outcome. In such situations, for effective evaluation and comparison of different treatment plans, traditional dose based evaluation tools can be complemented by the use of diagrams.

PACS number: 87.55.Qr Quality assurance in radiotherapy
The effect of a limited number of projections and reconstruction algorithms on the image quality of megavoltage digital tomosynthesis
Authors: Sarkar Vikren , Shi Chengyu , Rassiah‐Szegedi Prema , Diaz Aidnag , Eng Tony , Papanikolaou Niko
Published: August 2009

In order to investigate the effect of the number of projections on digital tomosynthesis image quality, images were acquired over a 40 degree arc and sampled into sets of 2 to 41 projections used as input to three different reconstruction algorithms: the shift‐and‐add, the Feldkamp‐Davis‐Kress filtered back projection algorithms, and the simultaneous algebraic reconstruction technique. The variation of several image characteristics, such as in‐plane resolution, contrast to noise ratio, artifact spread, volumetric accuracy, and dose, are investigated based on the reconstruction algorithms used and also the number of projections used as source data. The results suggest that only 11 projections are required since the various parameters checked do not improve much past that number. As a reconstruction algorithm, SART did best but took much longer to reconstruct images. Thus, if reconstruction time is a determining factor, filtered back‐projection looks like a better compromise.

PACS number: 87.57.C‐, 87.57.nf, 87.57.Q‐, 87.59.‐e
Evaluation of new data processing algorithms for planar gated ventriculography (MUGA)
Authors: Fair Joanna R. , Heintz Philip H. , Telepak Robert J.
Published: August 2009

Before implementing one of two new LVEF radionuclide gated ventriculogram (MUGA) systems, the results from 312 consecutive parallel patient studies were evaluated. Each gamma‐camera acquisition was simultaneously processed by semi‐automatic Medasys Pinnacle and by fully automatic and semiautomatic Philips nuclear medicine computer systems. The Philips systems yielded LVEF results within percentage points of the Medasys system in fewer than half of the studies. The remaining values were higher or lower than those from the long‐used Medasys system. These differences might have changed cancer patient chemotherapy clinical decisions. As a result, our institution elected not to implement either new system.

PACS: 87.57.U‐ Nuclear medicine imaging
Determination of the photon beam attenuation by the BrainLAB imaging couch: angular and field size dependence
Authors: Njeh Christopher F , Raines Timothy W , Saunders Mark W
Published: August 2009

Highly attenuating radiation treatment couches are no longer useful in the present era of IMRT‐ and IGRT‐utilizing radiotherapy. High tensile strength and low density carbon fiber couch tops present a useful alternative. The objective of this study is to quantify the attenuation of megavoltage photons through BrainLAB imaging couch top and headrest at various angles and field sizes. At normal incidence, the couch attenuated 6 MV photons by 4.9% and 3.4% for and field sizes, respectively. The headrest, alone, attenuated 6 MV photons by 2.5% and 1.6% for the same field sizes. There was no significant attenuation of the 18 MV beam by either the couch or the headrest. We further found attenuation to be gantry angle dependent, with the highest attenuation recorded at 120° – at which angle the couch attenuated the 6 MV photon beam by 10% for the and 8.3% for the field sizes. Similarly, an 18 MV photon beam was attenuated by 3.6% and 3.4% for the and field sizes, respectively. The highest attenuation for the headrest occurred at 110° gantry angle: for the 6 MV photon beam, the headrest attenuation was 6.3% and 5.6% (for the and field sizes, respectively); for the 18 MV, attenuation was 2.3% (for the field size) and 2.1% (for the field size). It would appear, therefore, that BrainLAB imaging couch and headrest in IMRT with posterior beams results in significant decreases in the dose delivered to the target.

PACS number: 87.56.Da
New method for obtaining position and time structure of source in HDR remote afterloading brachytherapy unit utilizing light emission from scintillator
Authors: Kojima Haruna , Hanada Takashi , Katsuta Shoichi , Yorozu Atsunori , Maruyama Koichi
Published: August 2009

When using a HDR remote afterloading brachytherapy unit, results of treatment can be greatly influenced by both source position and treatment time. The purpose of this study is to obtain information on the source of the HDR remote afterloading unit, such as its position and time structure, with the use of a simple system consisting of a plastic scintillator block and a charge‐coupled device (CCD) camera. The CCD camera was used for recording images of scintillation luminescence at a fixed rate of 30 frames per second in real time. The source position and time structure were obtained by analyzing the recorded images. For a preset source‐step‐interval of 5 mm, the measured value of the source position was , with a pixel resolution of 0.07 mm in the recorded images. For a preset transit time of 30 s, the measured value was s, when the time resolution of the CCD camera was 1/30 s. This system enabled us to obtain the source dwell time and movement time. Therefore, parameters such as source position, transit time, dwell time, and movement time at each dwell position can be determined quantitatively using this plastic scintillator‐CCD camera system.

PACS number: 87.53.Jw
Statistical validation of a new helical tomotherapy patient transfer station
Authors: Zhuang Audrey H. , Liu An , Schultheiss Timothy E. , Wong Jeffrey Y.C.
Published: August 2009

The purpose of this work is to evaluate statistically the accuracy of a patient transfer station (PTS), which automatically converts one planning‐station‐generated treatment plan to another one with a different beam model. In our department we have installed two Hi•Art tomotherapy systems (TomoTherapy Inc., Madison, WI), and patients often need to be transferred from one tomotherapy unit to the other. Thirty patients who underwent patient transfer between the two systems were evaluated. For each patient, dose differences between his/her original plan and PTS‐transferred plan were evaluated by comparing doses at 10 randomly selected positions in his/her CT images. The Pearson indexes were calculated to analyze the relationship of the deviations to other parameters, which include absolute dose levels, sites (targets or normal tissues), and the dose accuracy of original plans and that of transferred plans. The dose accuracy of a treatment plan was determined by comparing delivered doses at the center of a solid water phantom to planned doses at the same position. The calculated dose difference between original and transferred plans was, on average, ; the maximum deviation in absolute values was 1.9% in target volumes and 2.5% in normal organs. The errors generated during PTS‐based transferring process were random and did not show correlation with other parameters. The PTS took less than 10 minutes to generate a backup plan, much less than the approximately two hours needed to create a duplicate plan manually. The results show that a PTS‐transferred plan is an acceptable match to the original plan. With a physician's approval, a transferred plan is acceptable for treatment without the necessity of being revalidated in phantom. Thus far, all of our PTS plans have been approved by the treating physician without further optimization.

PACS number: 87.55.km, 87.55.D‐
Nitrate uptake by plant rootsThis paper is one of a selection published in a Special Issue comprising papers presented at the 50th Annual Meeting of the Canadian Society of Plant Physiologists (CSPP) held at the University of Ottawa, Ontario, in June 2008.
Authors: Glass Anthony D.M.
Published: August 2009

Nitrate is a major source of N for plant growth, particularly under aerobic agricultural conditions. This nutrient is absorbed from soil solution by both high-affinity and low-affinity transport systems that were first defined physiologically and subsequently by molecular genetic means. This minireview presents an abbreviated history of developments in plant inorganic ion uptake, the physiology of nitrate uptake, and recent developments in the molecular genetic characterization of nitrate transport systems.
Site- and species-specific patterns of metal bioavailability in edible plantsThis paper is one of a selection published in a Special Issue comprising papers presented at the 50th Annual Meeting of the Canadian Society of Plant Physiologists (CSPP) held at the University of Ottawa, Ontario, in June 2008.
Authors: Murray Hollydawn , Thompson Karen , Macfie Sheila M.
Published: August 2009

Differences in metal uptake between plant species and soil types were compared to assess the safe use of mildly contaminated soils for the growth of edible food crops. Accumulation of metals in five plant species grown in each of three field soils and a commercial soil were evaluated in a controlled environment. Metal bioavailability varied more with plant species than with type of soil. Among a number of physical and chemical soil properties that were measured, high metal content and low percent organic matter were the best predictors of increased metal bioavailability. Contamination levels of metals measured in soil and vegetable samples were used to calculate bioconcentration factors and hazard quotients. The results indicated significant differences between plant species. The species accumulating the most metal was carrot, and the most mobile element was cadmium. Some hazard quotients exceeded the threshold value of 1, even in soils considered uncontaminated by current guidelines. Overall, these results reinforce the need to include soil characteristics when setting threshold guidelines for metal content of agricultural soils and indicate the need for species-specific planting guidelines.
Geologist-controlled trends versus computer-controlled trends: introducing a high-resolution approach to subsurface structural mapping using well-log data, trend surface analysis, and geospatial analysisA companion paper to Mei, S. 2009. New insights on faults in the Peace River Arch region, northwest Alberta, based on existing well-log data and refined trend surface analysis. Canadian Journal of Earth Sciences, 46(1): 41–65.
Authors: Mei Shilong
Published: August 2009

This paper introduces a refined trend surface analysis (TSA) for detecting faults with small, metre-scale offsets (5–20 m). Conventional TSA uses a global polynomial method to model the trend; the power of the polynomial (e.g., first, second, or third order) is the only parameter for input. The refined approach is different in that it uses local-fit techniques to generate the trend. The refined approach provides greater flexibility for inputting geological knowledge in the trend surface modelling process. This results in a trend surface with the maximum amount of unwanted information, which is removed from the residual surface after removal of the trend from the data, leaving features of interest optimally highlighted in the residuals. Such a trend is referred to as a geologist-controlled trend to differentiate it from the trend surface modelled by conventional TSA, which is primarily a computer-controlled global polynomial surface. The refined approach goes one step beyond conventional TSA by incorporating advanced geostatistics for modelling the trend, interpolating the resultant residuals, and then extracting formation-top offset patterns from the residual surface using spatial analysis. Modelling the geologist-controlled trend in the refined approach results in higher resolution in detecting formation-top offsets and higher accuracy in digitizing fault locations, compared with various techniques that have been traditionally used in subsurface structure mapping of the West Canada Sedimentary Basin (WCSB) (e.g., structural and isopach contour mapping, cross-section construction, and seismic and aeromagnetic data interpretation). The refined approach is demonstrated using the Basal Fish Scale Zone in the Peace River Arch region as an example.
Stratigraphy of the Fort Selkirk Volcanogenic Complex in central Yukon and its paleoclimatic significance: Ar/Ar and paleomagnetic data
Authors: Nelson Faye E. , Barendregt René W. , Villeneuve Mike
Published: August 2009

Brunhes, Matuyama, Kaena, and Mammoth age basaltic lava flows (Tertiary–Quaternary Selkirk Volcanics) were sampled in west-central Yukon. The mean characteristic remanent magnetization (ChRM) direction of the flows sampled in this and previous studies has a declination of 348.7° and an inclination of 70.8° (n = 42, k = 99.6, α95 = 2.2°) (all on lower hemisphere). The time range represented in this study (ca. 3.25 to ca. 0.004 Ma) is great enough to have confidently averaged secular variation. Sediment associated with the basalt has a mean declination of 7.6° and inclination of 78.8° (n = 5, k = 5.6, α95 = 35.7°). A new 40Ar–39Ar date on the reversely magnetized basal basalts at Ne Ch’e Ddhäwa places the eruption in the Mammoth subchron of the Gauss Normal Chron. The newly dated basal basalt at Ne Ch’e Ddhäwa precedes the initial continental glaciation in Yukon and is older than the Fort Selkirk vent (Lower Mushroom), which was previously thought to be the oldest eruption at Fort Selkirk Volcanic Complex (FSVC). This basal flow at Mushroom is dated at 1.82 ± 0.03 Ma and the uppermost flow is reproducibly dated at 1.36 ± 0.04 Ma. Till on the flanks of a subglacial volcanic mound called Ne Ch’e Ddhäwa (informal) is older than previously thought; its reverse magnetization indicates an Early Pleistocene age rather than the Reid glaciation, which falls during the Brunhes Normal Chron. The paleomagnetism of Tertiary–Quaternary Selkirk Volcanics outcrops outside the FSVC was studied for the first time. The ChRM direction of basalt at the northern edge of the northern Cordillera volcanic province agrees with FSVC directions, suggesting that this flow reflects the same period of volcanism. This suggests that an Eocene K–Ar date, previously thought to be unreliable, may well be correct.
Paleomagnetism and U–Pb geochronology of the Lac de Gras diabase dyke swarm, Slave Province, Canada: implications for relative drift of Slave and Superior provinces in the PaleoproterozoicGeological Survey of Canada Contribution 20080350.
Authors: Buchan Kenneth L. , LeCheminant Anthony N. , van Breemen Otto
Published: August 2009

Lac de Gras diabase dykes trend north to NNE across the central Slave Province of the Canadian Shield. U–Pb baddeleyite ages of 2023 ± 2 and 2027 ± 4 Ma are interpreted as dyke emplacement ages. These ages are similar to that of the Booth River igneous complex, exposed along the margins of Kilohigok Basin near the northern end of the dyke swarm. Ten paleomagnetic sites (from four to six dykes) yield a mean paleopole at 11.8°N, 92.1°W (dm = 8.4°, dp = 6.0°). A positive baked contact test where a Lac de Gras dyke crosscuts a NE-trending Malley dyke demonstrates that this pole is primary. It represents the first key Paleoproterozoic pole from the Slave Province and, hence, the first Paleoproterozoic Slave pole suitable for reconstructing paleocontinents. Although a direct comparison is not available with precisely dated paleopoles of identical age from other Archean cratons, a comparison is made with a sequence of precisely dated poles from Superior Province dyke swarms, including those 40–50 million years older and 25 million years younger. It yields two options depending on the relative magnetic polarity assumed for data from the two cratons. The two cratons were either at similar latitudes, but not in their present relative orientations, when the swarms were emplaced, or separated in latitude by ∼40°–60°. In either case, they may have drifted separately or formed part of a single (super)continent that subsequently broke up with the two cratons drifting separately to attain their present configuration. Additional key paleopoles are required to distinguish between these interpretations.
Impacts of supplementation: genetic diversity in supplemented and unsupplemented populations of summer chum salmon (Oncorhynchus keta) in Puget Sound (Washington, USA)
Authors: Small Maureen P. , Currens Ken , Johnson Thom H. , Frye Alice E. , Von Bargen Jennifer F.
Published: August 2009

In supplementation programs, hatcheries employ wild-origin fish as brood stock and their offspring are allowed into wild spawning areas. Resource managers use supplementation to support imperiled salmonid populations, seeking to increase census size and possibly effective population size (Ne), while minimizing risks of genetic diversity loss and domestication from hatchery intervention. Here we document impacts of 5–10 years of supplementation on threatened summer-run chum salmon ( Oncorhynchus keta ) in Hood Canal (HC) and Strait of Juan de Fuca (SJF) in Washington State and compare them genetically with unsupplemented summer- and fall-run chum salmon from HC and South Puget Sound. Microsatellite allele frequencies identified four run-timing and geographic groups. HC and SJF summer chum salmon genetic relationships followed a metapopulation pattern of isolation by distance, similar to patterns prior to supplementation, suggesting that supplementation minimally impacted population structure. In most supplemented subpopulations, we detected no effects on diversity and Ne, but high variance in individual pairwise relatedness values indicated over-representation of family groups. In two subpopulations, hatchery impacts (decreased diversity and lower Ne) were confounded with extreme bottlenecks. Rebounds in census sizes in all subpopulations suggest that general survivorship has improved and that possible hatchery effects on genetic diversity will be overcome.
The Lake Huron pelagic fish community: persistent spatial pattern along biomass and species composition gradients
Authors: Warner David M. , Schaeffer Jeffrey S. , O’Brien Timothy P.
Published: August 2009

Spatial patterns in the biomass of pelagic fish in Lake Huron have persisted over 10 years even though biomass decreased 86% and the fish community shifted from dominance by non-native species (rainbow smelt, Osmerus mordax ) to dominance by native species (bloater, Coregonus hoyi ). Based on multivariate analyses of acoustic biomass data and abiotic variables from the years 1997, 2004, 2005, and 2007, the strength of relationships between abiotic variables (primarily bottom depth) and fish community composition gradients decreased with fish biomass, suggesting that at high biomass, the influence of the measured abiotic variables is minimal. We observed consistently higher biomass in the North Channel and Georgian Bay than in the Main Basin, and as a result, we conclude that these smaller basins are likely important contributors to lakewide fish biomass, production, and dynamics. These results suggest that at current biomass levels, efforts to understand ecology, population dynamics, and lakewide abundance need to incorporate the effects of depth and geographic variation on fish distributions and ecology.
Population effects and changes in life history traits in relation to phase transitions induced by long-term fishery harvesting: European hake (Merluccius merluccius) off the Balearic Islands
Authors: Hidalgo Manuel , Massutí Enric , Guijarro Beatriz , Moranta Joan , Ciannelli Lorenzo , Lloret Josep , Oliver Pere , Stenseth Nils Christian
Published: August 2009

In 1980 and 1995, the European hake ( Merluccius merluccius ) population off the Balearic Islands (northwestern Mediterranean) underwent changes at both the individual level and the population level. There was a sharp decrease in abundance that coincided with a change in the seasonal catch-per-unit-effort pattern in 1980. A new population scenario emerged after 1980 characterized by an increase in the intrinsic growth rate and a decrease in carrying capacity; however, catchability remained the same. An age-structure truncation could have caused these changes, making the population more dependent on year-to-year recruitment. A change in size structure also occurred in 1995, which was evidenced by a sudden decrease in the mean length-at-age (L) and abundance of recruits and a change in the density-dependent effect on recruits. As the Mediterranean trawl fishery mainly harvests recruits and juveniles and fishery harvesting induces adaptive changes in life history traits, the sharp decrease in L of recruits could be explained as a growth reduction due to the selective pressure to stay under mesh size for longer and thus maximize survival until reproduction. These individual and population transitions explain the changes in the response to the environmental forcing observed in the European hake off the Balearic Islands.
Estimating exploitation rates of migrating yellowtail flounder (Limanda ferruginea) using multistate mark–recapture methods incorporating tag loss and variable reporting rates
Authors: Cowen Laura , Walsh Stephen John , Schwarz Carl James , Cadigan Noel , Morgan Joanne
Published: August 2009

Multistate mark–recapture models can be used to model migration through stratification of the study area into states (location). However, the incorporation of both tag loss and reporting rates is new to the multistate paradigm. We develop a migration model for fish that incorporates tag loss and reporting rates but has as its primary purpose the modelling of exploitation and natural mortality rates. This model is applied to a 2000–2004 yellowtail flounder ( Limanda ferruginea ) tagging study on the Grand Bank of Newfoundland, Canada. We found that exploitation rates varied over both location and years, ranging from 0.000 to 0.047. Migration into the centre of the Grand Bank (state 2) was three times higher than migration out. The estimate of the instantaneous annual natural mortality rate was 0.256, which is equivalent to an annual survival rate of 0.880. We describe how these mortality estimates will be quite valuable in specifying an assessment model for this stock.
Drawing the lines: resolving fishery management units with simple fisheries data
Authors: Cope Jason M. , Punt André E.
Published: August 2009

The task of assessing marine resources should begin with defining management units. Often this step is overlooked or defined at temporal scales irrelevant to management needs. Additionally, traditional methods to define stock structure can be data intensive and (or) cost prohibitive and thus not available for emerging or data-limited fisheries. We present an approach that uses commonly available fisheries data (catch and effort) to delineate management units for dynamically independent populations. Spatially explicit standardized indices of abundance are grouped using a two-step partitioning cluster analysis that includes abundance index uncertainty. This “management unit estimator” is tested via simulation and found generally to recover the true number of management units across data of different temporal length, sample size, and quality. Management units are then determined for four species with varying ecologies, fishery histories, and data issues that exemplify the challenges of applying this method to messy data sets. Defining management units via relative abundance incorporates changes in population connectivity in relation to current removals and environmental conditions and creates consistency of index use within assessments. The two-step clustering approach is simple and widely applicable to situations wherein the clustering metric contains uncertainty.
Geographic, anthropogenic, and habitat influences on Great Lakes coastal wetland fish assemblages
Authors: Trebitz Anett S. , Brazner John C. , Danz Nicholas P. , Pearson Mark S. , Peterson Gregory S. , Tanner Danny K. , Taylor Debra L. , West Corlis W. , Hollenhorst Thomas P.
Published: August 2009

We analyzed data from coastal wetlands across the Laurentian Great Lakes to identify fish assemblage patterns and relationships to habitat, watershed condition, and regional setting. Nonmetric multidimensional scaling (NMDS) ordination of electrofishing catch-per-effort data revealed an overriding geographic and anthropogenic stressor gradient that appeared to structure fish composition via impacts on water clarity and vegetation structure. Wetlands in Lakes Erie and Michigan with agricultural watersheds, turbid water, little submerged vegetation, and a preponderance of generalist, tolerant fishes occupied one end of this gradient, while wetlands in Lake Superior with largely natural watersheds, clear water, abundant submerged vegetation, and diverse fishes occupied the other. Fish composition was also related to wetland morphology, hydrology, exposure, and substrate, but this was only evident within low-disturbance wetlands. Anthropogenic stress appears to homogenize fish composition among wetlands and mask other fish–habitat associations. Because land use is strongly spatially patterned across the Great Lakes and aquatic vegetation is a key habitat element that responds to both biogeography and disturbance, it is difficult to disentangle natural from anthropogenic drivers of coastal wetland fish composition.
Is ambient chitobiase activity a monitoring tool for impacts on secondary production in lotic systems?
Authors: Conley Justin M. , Schorr Mark S. , Hanson Mark L. , Symes Steven J. , Richards Sean M.
Published: August 2009

Chitobiase is one of two enzymes responsible for cleaving the chitin polymers that form arthropod exoskeletons and has been found to be predictive of secondary production for marine and freshwater zooplankton. Since chitobiase is released into water during molting by aquatic arthropods, it is possible that ambient chitobiase activity may be a useful proxy of secondary production in aquatic systems. In the present study, surface water samples from the upper Tennessee River basin, USA, were collected and analyzed for chitobiase to determine how enzyme levels vary with season, water depth, and proximity to sewage treatment outfalls. Additionally, chitobiase activity was correlated with three pharmaceutical compounds to assess if changes in chitobiase activity were associated with contaminants derived from sewage treatment plants. Chitobiase activity was significantly (p < 0.05) elevated in the fall relative to other seasons. Further, chitobiase activity displayed significant positive correlation (p < 0.05) between surface and subsurface samples and was negatively correlated (p < 0.05) with pharmaceutical concentrations in summer samples. These results indicate the potential for chitobiase as an assessment tool in estimating secondary production and as an ecotoxicological indictor.
Monitoring and potential control of sea lice using an LED-based light trap
Authors: Novales Flamarique Iñigo , Gulbransen Christina , Galbraith Moira , Stucchi Dario
Published: August 2009

Sea lice are ectoparasitic copepods that threaten salmon farming aquaculture and the viability of wild salmon populations. To control infestations on farmed salmon, several chemotherapeutants have been developed, but these are invasive (often causing fish stress and loss in production), costly, may induce parasite resistance over time, and their impact on the environment is a major social concern. Here, we show that a light-emitting diode (LED)-based light trap can be used to monitor sea lice presence on fish and in the water. The performance of the light trap was tested in experimental tanks and in the ocean. Plankton net tows were also performed to compare catches with those from light traps. The light trap caught ~70% of salmon lice larval stages loaded onto a tank and ~24% of the adults. It also acted as a delousing agent by removing ~8% of adult salmon lice infective on Chinook salmon ( Oncorhynchus tshawytscha ) smolts in tank experiments. In the ocean, the light trap caught 21 sea lice (10 Lepeophtheirus salmonis and 11 Caligus clemensi ), comprising free-swimming and attached stages, while plankton net tows failed to capture any. We conclude that light traps constitute an effective, noninvasive, environmentally friendly method to monitor sea lice.
Pavement subsurface drainage: importance of appropriate subbase materials
Authors: Lebeau Marc , Konrad Jean-Marie
Published: August 2009

Past and current research has clearly established the detrimental effects of inadequate subsurface drainage within a road environment. In response, pavement engineers have developed a number of theoretical models to establish the lateral drainage requirements of pavements. The intention of the present paper is to extend current drainage design by accounting for the presence of a pervious subbase layer. A parametric study of an extended form of the time to drain problem was performed while focusing on the effect of subbase material characteristics under saturated and unsaturated conditions. The numerical results established that the addition of a suitable subbase material can shift drainage time from days to minutes by combining the effects of gravity, seepage distance, and discharge area to enhance vertical water movement. Although increasing saturated hydraulic conductivity of the subbase material was generally shown to favour vertical drainage, it also created a capillary barrier effect that hindered downward flow. The results of this analysis emphasize the importance and relevance of subbase material selection for improving the drainage quality of dense-graded base materials, which display excellent bearing capacity and remain stable under repeated loading.
Use of large-diameter, cast–in situ concrete pipe piles for embankment over soft clay
Authors: Liu Han-Long , Chu Jian , Deng An
Published: August 2009

A new method of using large-diameter, cast–in situ concrete pipe (PCC) piles for embankments over soft clay is introduced in this paper. This PCC pile method offers a relatively quick and cost-effective way for soil improvement as compared with other existing soil improvement methods. The principles and construction techniques involved in this method are described. Full-scale model tests were conducted to evaluate the quality and performance of piles and the responses of the surrounding soils. Methods that can be used to check the quality of the pipe piles are elaborated. A case study that illustrates the application of this method in a piled embankment over soft clay is presented.
10 m standpipe tests on oil sands tailings: long-term experimental results and prediction
Authors: Jeeravipoolvarn S. , Scott J. D. , Chalaturnyk R. J.
Published: August 2009

Three large 10 m high standpipe tests were set up at the University of Alberta in 1982 to simulate large-scale compression behavior of oil sands tailings in a controlled environment. The objectives of the tests were to study material behavior and to provide consolidation performance for theoretical verification. Three tailings materials (fine tailings and two mixes of fine tailings and sand) were used. Test results showed that the fine tailings, standpipe 1, strained more than 30% over a 25 year monitoring period by self-weight with very little to no effective stress developing, while the mix of fine tailings and sand, standpipe 3, compressed with a significant effective stress development. The tailings in standpipe 1 can be regarded as a class of material where a reduction in volume is not governed by a unique relationship between effective stress and void ratio, whereas the tailings in standpipe 3 can be categorized as slurry with conventional behavior. To investigate the capability of the finite strain consolidation theory on these tailings, a numerical model with appropriate material constitutive relationships was developed and used to make predictions. Numerical results, compared with the performance of the standpipe tests, indicated that the theory overestimated the compression behavior of the standpipe 1 material, but it could predict the standpipe 3 consolidation behavior.
Case studies on bermed excavation in Taipei silty soil
Authors: Liao H. J. , Lin C. C.
Published: August 2009

Bermed excavation (deep excavation supported by an excavation wall and a berm) can be an economical method for basement construction in urban areas if ground movement around the excavation is not the primary concern and the excavation site is large and (or) irregular in shape. This paper reviews three bermed excavation projects carried out in the Taipei Basin. One project was successful, one was successful after near failure, and one was a failure. Ironically, extensive ground improvement work had been done for the near-failure and failure cases; but no ground improvement was done for the successful case. It is of interest to find the similarities and differences among these bermed excavation projects. The causes of instability that result in unsuccessful bermed excavation projects and the applications of limit equilibrium analysis to the stability of bermed excavation are also discussed here. These three cases show that the existence of grout columns does not help to effectively increase the stability of the berm if the original safety factor against sliding of a berm slope is less than 1.0 and the improvement ratio of grout columns is low (say <20%).
Artificial neural network (ANN) models for determining hydraulic conductivity of compacted fine-grained soils
Authors: Erzin Yusuf , Gumaste S. D. , Gupta A. K. , Singh D. N.
Published: August 2009

This study deals with development of artificial neural networks (ANNs) and multiple regression analysis (MRA) models for determining hydraulic conductivity of fine-grained soils. To achieve this, conventional falling-head tests, oedometer falling-head tests, and centrifuge tests were conducted on silty sand and marine clays compacted at different dry densities and moisture contents. Further, results obtained from ANN and MRA models were compared vis-à-vis experimental results. The performance indices such as the coefficient of determination, root mean square error, mean absolute error, and variance were used to assess the performance of these models. The ANN models exhibit higher prediction performance than the MRA models based on their performance indices. It has been demonstrated that the ANN models developed in the study can be employed for determining hydraulic conductivity of compacted fine-grained soils quite efficiently.
Permeability tensor and representative elementary volume of saturated cracked soil
Authors: Li J. H. , Zhang L. M. , Wang Y. , Fredlund D. G.
Published: August 2009

Cracks are prevalent in near-ground-surface soils and provide preferential pathways for fluid flow. Cracks increase water infiltration or contaminant solute transport into soils. This paper studies the development of a permeability tensor and a representative elementary volume (REV) for saturated cracked soils. First, a method of generating random crack networks based on the statistical parameters of the crack geometry is presented. Then, the permeability tensor and REV for a crack network are studied by modeling water flow through the generated random crack networks. Finally, the permeability tensor for a cracked soil is obtained by combining the crack network and the soil matrix, and the properties of the permeability tensor and the REV for the cracked soils are investigated. Results show that the permeability tensor can be used to represent the permeability anisotropy of a cracked soil. An REV can be readily established when the crack network is relatively dense. An REV can be defined and the contribution of the crack network to permeability is small when a crack network exists in homogeneous sands. An REV is harder to establish and the hydraulic conductivity is dominated by the random crack network when a sparse crack network exists in clays.
Quasi-classical trajectory calculation of the Ba + HBr chemical reaction
Authors: Xia Wen Wen , Lu Ning , Zhong Haiyang , Yao Li
Published: August 2009

The results of the reaction between Ba atom and HBr are studied by using the quasi-classical trajectory (QCT) calculation on extended London–Eyring–Polanyi–Sato (LEPS) potential-energy surface (PES). The vibrational distribution, reaction cross section, and rotational alignment of the product BaBr have been calculated. The calculations predict that the reaction cross section decreases, while the translation energy and rotational energy increase with the increasing of collision energy. It has been found that low collision energy favors the abstraction reaction, whereas high collision energy leads to an insertion reaction. The calculated results agree with the experimental data and some relative theoretical results as well.
Commercial ZrO2 as a new, efficient, and reusable catalyst for the one-step synthesis of quinolines in solvent-free conditions
Authors: Hosseini-Sarvari Mona
Published: August 2009

Commercially available zirconia (ZrO2) is reported as an extremely efficient catalyst for the synthesis of quinolines. A one-step reaction of 2-aminoarylketones and a carbonyl compound (Friedlander reaction) took place under solvent-free conditions to afford the corresponding quinolines in good-to-high yields in the presence of ZrO2. Furthermore, the catalyst is reused several times without any significant loss of its catalytic activity.
Studies on chemo- and diastereo-selectivity of the Diels–Alder reactions of sulfinyltoluquinones with cyclopentadiene
Authors: de Sousa Andrea L. F. , Filho José E. P. Cardoso , Wladislaw Blanka , Marzorati Liliana , Di Vitta Claudio
Published: August 2009

Sulfinyltoluquinones (2a–2c) were submitted to thermal or catalyzed [4+2] cycloaddition reactions with cyclopentadiene. For p-tolylsulfinyltoluquinones (2b) and (2c), almost complete C2–C3-chemo- and unlike-diastereoselectivity was achieved by catalysis with ZnBr2, yielding adducts 6. Under thermal conditions, Diels–Alder reaction took place at the C5–C6 double bonds of quinones 2a–2c, generating mixtures of diastereoisomeric like- and unlike-adducts 4.