bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated Methodology for Determination of Stress Distribution in Human Abdominal Aortic Aneurysm
Authors: Raghavan Madhavan L. , Fillinger Mark F. , Marra Steven P. , Naegelein Bernhard P. , Kennedy Francis E.
Published: August 2005

Knowledge of impending abdominal aortic aneurysm (AAA) rupture can help in surgical planning. Typically, aneurysm diameter is used as the indicator of rupture, but recent studies have hypothesized that pressure-induced biomechanical stress may be a better predictor. Verification of this hypothesis on a large study population with ruptured and unruptured AAA is vital if stress is to be reliably used as a clinical prognosticator for AAA rupture risk. We have developed an automated algorithm to calculate the peak stress in patient-specific AAA models. The algorithm contains a mesh refinement module, finite element analysis module, and a postprocessing visualization module. Several aspects of the methodology used are an improvement over past reported approaches. The entire analysis may be run from a single command and is completed in less than 1h with the peak wall stress recorded for statistical analysis. We have used our algorithm for stress analysis of numerous ruptured and unruptured AAA models and report some of our results here. By current estimates, peak stress in the aortic wall appears to be a better predictor of rupture than AAA diameter. Further use of our algorithm is ongoing on larger study populations to convincingly verify these findings.
That Hemodynamics and Not Material Mismatch is of Primary Concern in Bypass Graft Failure: An Experimental Argument
Authors: O'Brien Thomas , Morris Liam , Walsh Michael , McGloughlin Tim
Published: August 2005

The long term patency of end-to-side peripheral artery bypasses are low due to failure of the graft generally at the distal end of the bypass. Both material mismatch between the graft and the host artery and junction hemodynamics are cited as being major factors in disease formation at the junction. This study uses experimental methods to investigate the major differences in fluid dynamics and wall mechanics at the proximal and distal ends for rigid and compliant bypass grafts. Injection moulding was used to produce idealized transparent and compliant models of the graft/artery junction configuration. An ePTFE graft was then used to stiffen one of the models. These models were then investigated using two-dimensional video extensometry and one-dimensional laser Doppler anemometry to determine the junction deformations and fluid velocity profiles for the rigid and complaint graft anastomotic junctions. Junction strains were evaluated and generally found to be under 5% with a peak stain measured in the stiff graft model junction of 8.3% at 100mmHg applied pressure. Hemodynamic results were found to yield up to 40% difference in fluid velocities for the stiff/compliant comparison but up to 80% for the proximal/distal end comparisons. Similar strain conditions were assumed for the proximal and distal models while significant differences were noted in their associated hemodynamic changes. In contrasting the fluid dynamics and wall mechanics for the proximal and distal anastomoses, it is evident from the results of this study, that junction hemodynamics are the more variable factor.
Finding Life in Old Bones
Authors: Proctor Robert N.
Published: August 2005

The Ape in the Tree
. An Intellectual and Natural History of
Proconsul
.
By Alan Walker and Pat Shipman
. Harvard University Press, Cambridge, MA, 2005. 285 pp. $26.95, £17.95, €24.90. ISBN 0-674-01675-0.

The authors describe the fossils, discoveries, and interpretations of the best-known Miocene ape.
Carbon Flux and Growth in Mature Deciduous Forest Trees Exposed to Elevated CO
2
Authors: Körner Christian , Asshoff Roman , Bignucolo Olivier , Hättenschwiler Stephan , Keel Sonja G. , Peláez-Riedl Susanna , Pepin Steeve , Siegwolf Rolf T. W. , Zotz Gerhard
Published: August 2005

Whether rising atmospheric carbon dioxide (CO
2
) concentrations will cause forests to grow faster and store more carbon is an open question. Using free air CO
2
release in combination with a canopy crane, we found an immediate and sustained enhancement of carbon flux through 35-meter-tall temperate forest trees when exposed to elevated CO
2
. However, there was no overall stimulation in stem growth and leaf litter production after 4 years. Photosynthetic capacity was not reduced, leaf chemistry changes were minor, and tree species differed in their responses. Although growing vigorously, these trees did not accrete more biomass carbon in stems in response to elevated CO
2
, thus challenging projections of growth responses derived from tests with smaller trees.
Nitrogenase Complexes: Multiple Docking Sites for a Nucleotide Switch Protein
Authors: Tezcan F. Akif , Kaiser Jens T. , Mustafi Debarshi , Walton Mika Y. , Howard James B. , Rees Douglas C.
Published: August 2005

Adenosine triphosphate (ATP) hydrolysis in the nitrogenase complex controls the cycle of association and dissociation between the electron donor adenosine triphosphatase (ATPase) (Fe-protein) and its target catalytic protein (MoFe-protein), driving the reduction of dinitrogen into ammonia. Crystal structures in different nucleotide states have been determined that identify conformational changes in the nitrogenase complex during ATP turnover. These structures reveal distinct and mutually exclusive interaction sites on the MoFe-protein surface that are selectively populated, depending on the Fe-protein nucleotide state. A consequence of these different docking geometries is that the distance between redox cofactors, a critical determinant of the intermolecular electron transfer rate, is coupled to the nucleotide state. More generally, stabilization of distinct docking geometries by different nucleotide states, as seen for nitrogenase, could enable nucleotide hydrolysis to drive the relative motion of protein partners in molecular motors and other systems.
Characterization of the Exosporium Basal Layer Protein BxpB of
Bacillus anthracis
Authors: Steichen Christopher T. , Kearney John F. , Turnbough Charles L.
Published: August 2005

Bacillus anthracis
spores, the cause of anthrax, are enclosed by a prominent loose-fitting structure called the exosporium. The exosporium is composed of a basal layer and an external hair-like nap. The filaments of the hair-like nap are apparently formed by a single collagen-like glycoprotein called BclA, whereas several different proteins form or are tightly associated with the basal layer. In this study, we used immunogold electron microscopy to demonstrate that BxpB (also called ExsF) is a component of the exosporium basal layer. Binding to the basal layer by an anti-BxpB monoclonal antibody was greatly increased by the loss of BclA. We found that BxpB and BclA are part of a stable complex that appears to include the putative basal layer protein ExsY and possibly other proteins. Previous results suggested that BxpB was glycosylated; however, our results indicate that it is not a glycoprotein. We showed that
ΔbxpB
spores, which lack BxpB, contain an exosporium devoid of hair-like nap even though the
ΔbxpB
strain produces normal levels of BclA. These results indicated that BxpB is required for the attachment of BclA to the exosporium. Finally, we found that the efficiency of production of
ΔbxpB
spores and their resistance properties were similar to those of wild-type spores. However,
ΔbxpB
spores germinate faster than wild-type spores, indicating that BxpB suppresses germination. This effect did not appear to be related to the absence from
ΔbxpB
spores of a hair-like nap or of enzymes that degrade germinants.
A Novel β-Peptidyl Aminopeptidase (BapA) from Strain 3-2W4 Cleaves Peptide Bonds of Synthetic β-Tri- and β-Dipeptides
Authors: Geueke Birgit , Namoto Kenji , Seebach Dieter , Kohler Hans-Peter E.
Published: August 2005

A novel bacterial strain that was capable of growing on the β-tripeptide H-βhVal-βhAla-βhLeu-OH as the sole carbon and nitrogen source was isolated from an enrichment culture. On the basis of physiological characterization, partial 16S rRNA sequencing, and fatty acid analysis, strain 3-2W4 was identified as a member of the familySphingomonadaceae. Growth on the β-tripeptide and the β-dipeptide H-βhAla-βhLeu-OH was observed, and emerging metabolites were characterized. Small amounts of a persisting metabolite, the N-acetylated β-dipeptide, were identified in both media. According to dissolved organic carbon measurements, 74 to 80% of the available carbon was dissimilated. The β-peptide-degrading enzyme was purified from the crude cell extract of cells from strain 3-2W4 grown on complex medium. The enzyme was composed of two subunits, and the N-terminal sequences of both were determined. With this information, it was possible to identify the complete nucleotide sequence and to deduce the primary structure of the genebapA. The gene encoded a β-peptidyl aminopeptidase (BapA) of 402 amino acids that was synthesized as preprotein with a signal sequence of 29 amino acids. The enzyme was cleaved into two subunits (residues 30 to 278 and 279 to 402). It belonged to the N-terminal nucleophile (Ntn) hydrolase superfamily.
Identification of Residues Responsible for the Defective Virulence Gene Regulator Mga Produced by a Natural Mutant ofStreptococcus pyogenes
Authors: Vahling Cheryl M. , McIver Kevin S.
Published: August 2005

Mga is a transcriptional regulator in the pathogenStreptococcus pyogenesthat positively activates several important virulence genes involved in colonization and immune evasion in the human host. A naturally occurring mutant of Mga that is defective in its ability to activate transcription has been identified in the serotype M50 strain B514-Sm. Sequence alignment of the defective M50 Mga with the fully functional Mga from serotypes M4 and M49 revealed only three amino acid changes that might result in a defective protein. Electrophoretic mobility shift assays using purified M50 and M4 maltose binding protein-Mga found that both exhibited DNA-binding activity towards regulated promoters. Thus, the significance of each residue for the functionality of M50 Mga was explored through introduction of “gain-of-function” mutations based on M4 Mga. Transcriptional studies of the mutant alleles under both constitutive (PrpsL) and autoactivated (Pmga4) promoters illustrated that an arginine-to-methionine change at position 461 of M50 Mga protein fully restored activation of downstream genes. Western blot analyses of steady-state Mga levels suggest that the M461 residue may play a role in overall conformation and protein stability of Mga. However, despite the conservation of the M461 protein among all other Mga proteins, it does not appear to be necessary for activity in a divergent M6 Mga. These studies highlight the potential differences that exist between divergent Mga proteins in this important human pathogen.
Regulation of the
Bacillus subtilis ytmI
Operon, Involved in Sulfur Metabolism
Authors: Burguière Pierre , Fert Juliette , Guillouard Isabelle , Auger Sandrine , Danchin Antoine , Martin-Verstraete Isabelle
Published: August 2005

The YtlI regulator of
Bacillus subtilis
activates the transcription of the
ytmI
operon encoding an
l
-cystine ABC transporter, a riboflavin kinase, and proteins of unknown function. The expression of the
ytlI
gene and the
ytmI
operon was high with methionine and reduced with sulfate. Using deletions and site-directed mutagenesis, a
cis
-acting DNA sequence important for YtlI-dependent regulation was identified upstream from the −35 box of
ytmI
. Gel mobility shift assays confirmed that YtlI specifically interacted with this sequence. The replacement of the sulfur-regulated
ytlI
promoter by the
xylA
promoter led to constitutive expression of a
ytmI
′
-lacZ
fusion in a
ytlI
mutant, suggesting that the repression of
ytmI
expression by sulfate was mainly at the level of YtlI synthesis. We further showed that the YrzC regulator negatively controlled
ytlI
expression while this repressor also acted on
ytmI
expression via YtlI. The cascade of regulation observed in
B. subtilis
is conserved in
Listeria
spp. Both a YtlI-like regulator and a
ytmI
-type operon are present in
Listeria
spp. Indeed, the Lmo2352 protein from
Listeria monocytogenes
was able to replace YtlI for the activation of
ytmI
expression and a lmo2352′
-lacZ
fusion was repressed in the presence of sulfate via YrzC in
B. subtilis
. A common motif, AT(A/T)ATTCCTAT, was found in the promoter region of the
ytlI
and lmo2352 genes. Deletion of part of this motif or the introduction of point mutations in this sequence confirmed its involvement in
ytlI
regulation.
ExploringLactobacillus plantarumGenome Diversity by Using Microarrays
Authors: Molenaar Douwe , Bringel Françoise , Schuren Frank H. , de Vos Willem M. , Siezen Roland J. , Kleerebezem Michiel
Published: August 2005

Lactobacillus plantarumis a versatile and flexible species that is encountered in a variety of niches and can utilize a broad range of fermentable carbon sources. To assess if this versatility is linked to a variable gene pool, microarrays containing a subset of small genomic fragments ofL. plantarumstrain WCFS1 were used to perform stringent genotyping of 20 strains ofL. plantarumfrom various sources. The gene categories with the most genes conserved in all strains were those involved in biosynthesis or degradation of structural compounds like proteins, lipids, and DNA. Conversely, genes involved in sugar transport and catabolism were highly variable between strains. Moreover, besides the obvious regions of variance, like prophages, other regions varied between the strains, including regions encoding plantaricin biosynthesis, nonribosomal peptide biosynthesis, and exopolysaccharide biosynthesis. In many cases, these variable regions colocalized with regions of unusual base composition. Two large regions of flexibility were identified between 2.70 and 2.85 and 3.10 and 3.29 Mb of the WCFS1 chromosome, the latter being close to the origin of replication. The majority of genes encoded in these variable regions are involved in sugar metabolism. This functional overrepresentation and the unusual base composition of these regions led to the hypothesis that they represented lifestyle adaptation regions inL. plantarum. The present study consolidates this hypothesis by showing that there is a high degree of gene content variation amongL. plantarumstrains in genes located in these regions of the WCFS1 genome. Interestingly, based on our genotyping dataL. plantarumstrains clustered into two clearly distinguishable groups, which coincided with an earlier proposed subdivision of this species based on conventional methods.
Effects of Nitrogen and Carbon Sources on Transcription of Soluble Methyltransferases in
Methanosarcina mazei
Strain Gö1
Authors: Veit Katharina , Ehlers Claudia , Schmitz Ruth A.
Published: August 2005

The methanogenic archaeon
Methanosarcina mazei
strain Gö1 uses versatile carbon sources and is able to fix molecular nitrogen with methanol as carbon and energy sources. Here, we demonstrate that when growing on trimethylamine (TMA), nitrogen fixation does not occur, indicating that ammonium released during TMA degradation is sufficient to serve as a nitrogen source and represses
nif
gene induction. We further report on the transcriptional regulation of soluble methyltransferases, which catalyze the initial step of methylamine consumption by methanogenesis, in response to different carbon and nitrogen sources. Unexpectedly, we obtained conclusive evidence that transcription of the

mtmB
2
C
2

operon, encoding a monomethylamine (MMA) methyltransferase and its corresponding corrinoid protein, is highly increased under nitrogen limitation when methanol serves as a carbon source. In contrast, transcription of the homologous

mtmB
1
C
1

operon is not affected by the nitrogen source but appears to be increased when TMA is the sole carbon and energy source. In general, transcription of operons encoding dimethylamine (DMA) and TMA methyltransferases and methylcobalamine:coenzyme M methyltransferases is not regulated in response to the nitrogen source. However, in all cases transcription of one of the homologous operons or genes is increased by TMA or its degradation products DMA and MMA.
The N-Terminal Domain of Enterococcal Surface Protein, Esp, Is Sufficient for Esp-Mediated Biofilm Enhancement inEnterococcus faecalis
Authors: Tendolkar Preeti M. , Baghdayan Arto S. , Shankar Nathan
Published: August 2005

Enterococci have emerged as one of the leading causes of nosocomial bloodstream, surgical site, and urinary tract infections. More recently, enterococci have been associated with biofilms, which are bacterial communities attached to a surface and encased in an extracellular polymeric matrix. The enterococcal cell surface-associated protein, Esp, enhances biofilm formation byEnterococcus faecalisin a glucose-dependent manner. Mature Esp consists of a nonrepeat N-terminal domain and a central region made up of two types of tandem repeats followed by a C-terminal membrane-spanning and anchor domain. This study was undertaken to localize the specific domain(s) of Esp that plays a role in Esp-mediated biofilm enhancement. To achieve this objective, we constructed in-frame deletion mutants expressing truncated forms of Esp in an isogenic background. By comparing strains expressing the mutant forms of Esp to those expressing wild-type Esp, we found that the strain expressing Esp lacking the N-terminal domain formed biofilms that were quantitatively less in biovolume than the strain expressing wild-type Esp. Furthermore, anE. faecalisstrain expressing only the N-terminal domain of Esp fused to a heterologous protein anchor formed biofilms that were quantitatively similar to those formed by a strain expressing full-length Esp. This suggested that the minimal region contributing to Esp-mediated biofilm enhancement inE. faecaliswas confined to the nonrepeat N-terminal domain. Expression of full-lengthE. faecalisEsp in heterologous host systems ofesp-deficientLactococcus lactisandEnterococcus faeciumdid not enhance biofilm formation as was observed forE. faecalis. These results suggest that Esp may require interaction with an additionalE. faecalis-specific factor(s) to result in biofilm enhancement.
Xanthomonas campestris
pv. campestris Possesses a Single Gluconeogenic Pathway That Is Required for Virulence
Authors: Tang Dong-Jie , He Yong-Qiang , Feng Jia-Xun , He Bao-Ren , Jiang Bo-Le , Lu Guang-Tao , Chen Baoshan , Tang Ji-Liang
Published: August 2005

Disruption of
ppsA
, a key gene in gluconeogenesis, of
Xanthomonas campestris
pv. campestris resulted in the failure of the pathogen to grow in medium with pyruvate or C
4
-dicarboxylates as the sole carbon source and a significant reduction in virulence, indicating that
X. campestris
pv. campestris possesses only the malic enzyme-PpsA route in gluconeogenesis, which is required for virulence.
Acquisition of Insertion Sequences and the GBSi1 Intron by
Streptococcus agalactiae
Isolates Correlates with the Evolution of the Species
Authors: Héry-Arnaud Geneviève , Bruant Guillaume , Lanotte Philippe , Brun Stella , Rosenau Agnès , van der Mee-Marquet Nathalie , Quentin Roland , Mereghetti Laurent
Published: August 2005

The prevalence of insertion sequences IS
1548
, IS
861
, IS
1381
, and ISSa4 and of the group II intron GBSi1 within
Streptococcus agalactiae
human isolates strongly correlates with the genetic lineages obtained by multilocus sequence typing. Our results yielded an evolutionary scheme for the acquisition of these genetic elements linked to the ecosystems from which the isolates were obtained.
A randomised controlled intervention study on prevention of work related skin problems among gut cleaners in swine slaughterhouses
Authors: Flyvholm M-A , Mygind K , Sell L , Jensen A , Jepsen K F
Published: August 2005

Aims:To evaluate the effect of an intervention to reduce work related skin problems in gut cleaning departments in Danish swine slaughterhouses. The intervention consisted of an evidence based prevention programme and a documented method for implementation.

Methods:Randomised controlled intervention study with a one year follow up. The intervention included educational activities and evidence based recommendations. The effect of the intervention was evaluated by telephone interviews using a standardised questionnaire based on the Nordic Occupational Skin Questionnaire (NOSQ-2002) with modified and additional questions on exposure, preventive measures, information, and discussions on prevention of skin problems, etc.

Results:A total of 644 (87.5%) responded at the baseline interview and 622 (71.6%) at the one year follow up interview. A total of 495 participated in both interviews (67.3%). In the intervention departments the frequency of eczema on hands or forearms within the past three months at follow up was reduced significantly from 56.2% at baseline to 41.0% at follow up, while a slight non-significant increase was observed in the comparison departments (from 45.9% to 50.2%). The intervention activities resulted in more frequent use of protective gloves in general and the use of cotton gloves worn underneath rubber and plastic gloves. At follow up three times as many in the intervention departments used the recommended high fat skin care products introduced as part of the intervention activities. At follow up, discussion of skin problems was increased in the intervention group while no changes were observed in the comparison group.

Conclusions:A significant 27% relative reduction of occupational eczema in a high risk group was feasible through implementation of an evidence based prevention programme.
Respiratory disease and cardiovascular morbidity
Authors: Koskela R-S , Mutanen P , Sorsa J-A , Klockars M
Published: August 2005

Background:Work related dust exposure is a risk factor for acute and chronic respiratory irritation and inflammation. Exposure to dust and cigarette smoke predisposes to exogenous viral and bacterial infections of the respiratory tract. Respiratory infection can also act as a risk factor in the development of atherosclerotic and coronary artery disease.

Aims:To investigate the association of dust exposure and respiratory diseases with ischaemic heart disease (IHD) and other cardiovascular diseases (CVDs).

Methods:The study comprised 6022 dust exposed (granite, foundry, cotton mill, iron foundry, metal product, and electrical) workers hired in 1940–76 and followed until the end of 1992. National mortality and morbidity registers and questionnaires were used. The statistical methods were person-year analysis and Cox regression.

Results:Co-morbidity from cardiovascular and respiratory diseases ranged from 17% to 35%. In at least 60% of the co-morbidity cases a respiratory disease preceded a cardiovascular disease. Chronic bronchitis, pneumonia, and upper respiratory track infections predicted IHD in granite workers (rate ratio (RR) = 1.9; 95% CI 1.38 to 2.72), foundry workers (2.1; 1.48 to 2.93), and iron foundry workers (1.7; 1.16 to 2.35). Dust exposure was not a significant predictor of IHD or other CVD in any group. Dust exposure was related to respiratory morbidity. Thus, some respiratory diseases appeared to act as intermediate variables in the association of dust exposure with IHD.

Conclusion:Dust exposure had only a small direct effect on IHD and other CVD. IHD morbidity was associated with preceding respiratory morbidity. A chronic infectious respiratory tract disease appeared to play an independent role in the development of IHD.
Asthma, chronic bronchitis, and exposure to irritant agents in occupational domestic cleaning: a nested case-control study
Authors: Medina-Ramón M , Zock J P , Kogevinas M , Sunyer J , Torralba Y , Borrell A , Burgos F , Antó J M
Published: August 2005

Background:Women employed in domestic cleaning are at increased risk for symptoms of obstructive lung disease, but the agents responsible are unknown.

Aims:To investigate common tasks and products in occupational domestic cleaning in relation to respiratory morbidity.

Methods:Case-control study in domestic cleaning women nested within a large population based survey of women aged 30–65 years; 160 domestic cleaning women with asthma symptoms, chronic bronchitis symptoms, or both and 386 without a history of respiratory symptoms were identified. Detailed exposures were evaluated for 40 cases who reported still having symptoms at the recruitment interview, and 155 controls who reported not having symptoms. All tasks performed and products used when cleaning houses were determined in a face-to-face interview. Lung function, methacholine challenge, and serum IgE testing were performed. Personal exposure measurements of airborne chlorine and ammonia were performed in a subsample. Associations between asthma, chronic bronchitis, and cleaning exposures were evaluated using multiple logistic regression analysis.

Results:Airborne chlorine (median level 0–0.4 ppm) and ammonia (0.6–6.4 ppm) were detectable during occupational domestic cleaning activities. Cases used bleach more frequently than controls; adjusted odds ratio (OR) for intermediate exposure was 3.3 (95% CI 0.9 to 11) and for high exposure 4.9 (1.5 to 15). Other independent associations included accidental inhalation of vapours and gases from cleaning agents and washing dishes. These associations were more pronounced for cases with asthma symptoms than for those with symptoms of chronic bronchitis, but were not related to sensitisation to common allergens.

Conclusions:Asthma symptoms in domestic cleaning women are associated with exposure to bleach and possibly other irritant agents. The public health impact of the use of irritant cleaning products could be widespread since the use of these products is common both in the workplace and at home.
Accuracy of a semiquantitative method for Dermal Exposure Assessment (DREAM)
Authors: van Wendel de Joode B , Vermeulen R , van Hemmen J J , Fransman W , Kromhout H
Published: August 2005

Background:The authors recently developed a Dermal Exposure Assessment Method (DREAM), an observational semiquantitative method to assess dermal exposures by systematically evaluating exposure determinants using pre-assigned default values.

Aim:To explore the accuracy of the DREAM method by comparing its estimates with quantitative dermal exposure measurements in several occupational settings.

Methods:Occupational hygienists observed workers performing a certain task, whose exposure to chemical agents on skin or clothing was measured quantitatively simultaneously, and filled in the DREAM questionnaire. DREAM estimates were compared with measurement data by estimating Spearman correlation coefficients for each task and for individual observations. In addition, mixed linear regression models were used to study the effect of DREAM estimates on the variability in measured exposures between tasks, between workers, and from day to day.

Results:For skin exposures, spearman correlation coefficients for individual observations ranged from 0.19 to 0.82. DREAM estimates for exposure levels on hands and forearms showed a fixed effect between and within surveys, explaining mainly between-task variance. In general, exposure levels on clothing layer were only predicted in a meaningful way bydetailedDREAM estimates, which comprised detailed information on the concentration of the agent in the formulation to which exposure occurred.

Conclusions:The authors expect that the DREAM method can be successfully applied for semiquantitative dermal exposure assessment in epidemiological and occupational hygiene surveys of groups of workers with considerable contrast in dermal exposure levels (variability between groups >1.0). For surveys with less contrasting exposure levels, quantitative dermal exposure measurements are preferable.
Precision riparian buffers for the control of nonpoint source pollutant loading into surface water: A review
Authors: Polyakov Viktor , Fares Ali , Ryder Micah H
Published: August 2005

Numerous studies have shown the effectiveness of riparian buffers in reducing sediment, pathogen, and nutrient loads into surface and groundwater in agricultural catchments. Reported retention rates of sediment, N, and P were as high as 97%, 85%, and 84%, respectively. Often, however, riparian buffers fail to perform their protective functions due to low adaptability of their designs to local settings. This is caused by our inadequate understanding of the conditions under which riparian buffers perform the best at field scale. Therefore, a precision oriented approach based on thorough analysis of spatially variable characteristics of landscape has to be undertaken in riparian buffer construction. Such an approach has a potential to improve the protective qualities and the economic viability of the riparian buffers. This paper gives an overview of the current level of research on riparian buffers and discusses the importance of spatial variability of local conditions on their performance. It presents the approaches for precision buffer design and its practical implementation and highlights the directions for future development of precision conservation. Key words: riparian buffer, vegetative filter, water quality, precision conservation.
Global correlation of the radiolarian faunal change across the TriassicJurassic boundary
Authors: Carter Elizabeth S , Hori Rie S
Published: August 2005

Precise comparison of the change in radiolarian faunas 3.5 m above a UPb zircon dated 199.6 ± 0.3 Ma tuff and approximately coincident with a negative δ13C anomaly in the Queen Charlotte Islands, B.C. (Canada) with Inuyama (Japan) sequences indicates that major global changes occurred across the TriassicJurassic (TJ) boundary. Nearly 20 genera and over 130 Rhaetian species disappeared at the end of the Triassic. The index genera Betraccium and Risella disappear and the final appearance of Globolaxtorum tozeri, Livarella valida, and Pseudohagiastrum giganteum sp. nov. are also diagnostic for the end of the Triassic. The low-diversity Hettangian survival fauna immediately above the boundary is composed mainly of small, primitive spumellarians with spongy or irregularly latticed meshwork and rod-like spines, and new genera Charlottea, Udalia, and Parahsuum s.l. first appear in the lowest Hettangian in both localities. Irrespective of different sedimentation rates and sedimentary environments, such as shelf to upper slope (Queen Charlotte Islands) and deep sea below carbonate compensation depth (CCD; Inuyama), radiolarians show a similar turnover pattern at the TJ boundary.
Predation on winter flounder (Pseudopleuronectes americanus) eggs by the sand shrimp (Crangon septemspinosa)
Authors: Taylor David L , Danila Donald J
Published: August 2005

This study estimated rates of sand shrimp (Crangon septemspinosa) predation on winter flounder (Pseudopleuronectes americanus) eggs and examined the effect of temperature on density-dependent mortality of early-stage flounder. In laboratory experiments, shrimp feeding rates on flounder eggs were positively correlated with temperature and shrimp size. Immunological assays of shrimp stomach contents indicated that 7.2% of shrimp collected from the Niantic River (Connecticut) had flounder eggs in their stomachs. Incidence of egg predation was highest in February (20%) and decreased continuously into early April (1.2%). In a deterministic model simulating predator-induced mortality of flounder eggs during a spawning season, shrimp consumed 0.4%49.7% of the total flounder spawn. Variations in shrimp population abundance and size structure accounted for the greatest variability in egg mortality. Water temperature during the spawning season presumably alters the population dynamics of early-stage flounder. In a long-term survey, the number of yolk-sac flounder larvae in warm years (≥4.3 °C) was depressed at high egg densities, indicating strong compensatory processes that increased egg mortality and limited the abundance of larvae. Failure of flounder to produce strong year-classes of larvae during warm years, possibly resulting from altered trophic dynamics, may explain the inability of stocks to recover from previous overexploitation.
A continuum of life history tactics in a brown trout (Salmo trutta) population
Authors: Cucherousset Julien , Ombredane Dominique , Charles Katia , Marchand Frédéric , Baglinière Jean-Luc
Published: August 2005

Life history tactics of the brown trout (Salmo trutta) population of the Oir River (Normandy, France) were studied using passive integrated transponder (PIT) tagging data of five consecutive cohorts (5900 individuals) monitored between 1995 and 2002. Results demonstrate that (i) life history traits vary among cohorts, chiefly caused by environmental variability, (ii) juvenile growth, particularly second-year growth, plays an important role in the determination of the growing environment and trout exhibit variable migratory behaviour (from remaining in the natal brook to migrating in the sea) related to their juvenile growth rate, and (iii) the description of life history tactics (including juvenile growth, fine-scale migratory behaviour, and reproduction) can be clarified. Tactics are expressed along a continuum in time (age to reproduce) and space (distance of migration). Flexible life history tactics varying with juvenile growth is consistent with previous studies, but the use of empiric data on growth and migration from PIT tagging allows refining the description of life history tactics, taking into account their continuous distribution in time and space.
A bioeconomic analysis of management strategies for rebuilding and maintenance of the NSS rock lobster (Jasus edwardsii) stock in southern New Zealand
Authors: Holland Daniel S , Bentley Nokome , Lallemand Philippe
Published: August 2005

We evaluated alternative management strategies for the Otago and Southland rock lobster (Jasus edwardsii) fisheries in New Zealand. We compare a number of decision-rule-based management strategies and assess amalgamation of the two separate quota management areas that currently comprise the fishery. The analysis combines a spatial sex- and length-structured simulation model of the fishery with an economic module that converts catches and effort into revenues and costs. We compare performance of alternative management strategies using a variety of biological and economic performance indicators relevant to a range of management objectives identified by stakeholders. The results demonstrate the importance of modelling economic performance, since the relative performance of different management strategies differ when considering catch versus net revenues. The analysis also reveals important distributional issues, since some strategies that increase the overall value of the fishery create both winners and losers.
Ecotypic differentiation of native rainbow trout (Oncorhynchus mykiss) populations from British Columbia
Authors: Keeley E R , Parkinson E A , Taylor E B
Published: August 2005

We sampled 34 native rainbow trout (Oncorhynchus mykiss) populations over a wide geographic area of British Columbia to determine whether variation in morphology is related to differences in habitat or fish community characteristics experienced by a population. After correcting for differences in body size, the most dramatic differences occurred in external characteristics between stream- and lake-dwelling populations. Rainbow trout from streams had more robust bodies with larger caudal peduncles and heads and longer paired fins than rainbow trout from lakes. Unlike other lake populations, piscivorous rainbow trout populations had relatively large heads and mouths that were more similar in size to those of stream-dwelling populations. We found fewer differences in the size of internal organs across ecotypes, producing little predictive ability of these characteristics to differentiate populations of rainbow trout. We also sampled 27 additional rainbow trout populations with unknown fish communities to determine how well large-scale patterns predict morphological differentiation over a smaller spatial scale. Of the five ecotypes that we detected at a smaller scale, the largest differences again occurred between stream and lake populations. Our data suggest that external morphological variation among populations of rainbow trout covaries with ecological conditions at a variety of spatial scales, particularly between lakes and rivers.
Estimation of change in lifetime egg production from length frequency data
Authors: O'Farrell Michael R , Botsford Louis W
Published: August 2005

The percentage of unfished lifetime egg production (LEP) has been used to represent persistence in precautionary fisheries management, but estimation of this reference point requires substantial data and it is sensitive to errors in natural mortality rate. We present an estimation method that quantifies the change in LEP by a fishery when only length frequency samples, one early in the fishery and one recent, are available for assessment. Using simulated length frequency data with known parameter values, estimates of LEP had undetectable bias when challenged with random sampling variability and sample sizes as low as 100. Simulation of artificial data with (i) growth parameters that differed from the estimation model, (ii) transient size structures, and (iii) recruitment variability led to predictably biased estimates. In a direct comparison with the spawning potential ratio reference point, fractional LEP was much less sensitive to errors in natural mortality rate. Application of this method to length frequency data for blue rockfish (Sebastes mystinus) for years between 1980 and 2003 suggests that during this interval, LEP has been reduced to levels of concern.
Food partitioning within the species-rich benthic fish community of Lake Malawi, East Africa
Authors: Duponchelle F , Ribbink A J , Msukwa A , Mafuka J , Mandere D , Bootsma H
Published: August 2005

Temporal diet patterns were studied for nine species of haplochromine cichlids in Lake Malawi, East Africa, using a combination of stable isotope and stomach content analyses. The results illustrate the complementarity of the two approaches in elucidating dietary differences. Evidence was found that benthic algal production contributed to the energy requirements of offshore fishes that occupy depths between 10 and 30 m. The importance of the lake fly Chaoborus edulis as a food source for demersal fishes was confirmed, supporting the recent hypothesis that deep demersal fish production is principally sustained through the pelagic food chain rather than from benthic detrital sources. Isotopic differences were observed among species with apparently similar diets, feeding behavior, and depth preferences, suggesting that important resource partitioning exists among Lake Malawi benthic haplochromine cichlids.
Effects of tree size and position on pipe model ratios in Scots pine
Authors: Berninger Frank , Coll Lluis , Vanninen Petteri , Mäkelä Annikki , Palmroth Sari , Nikinmaa Eero
Published: August 2005

We investigate how the foliage mass to wood area ratios depend on tree and stand characteristics of previously collected data from Scots pine (Pinus sylvestris L.). Our analysis allowed a separation of the relationship between stem and branch cross-sectional areas and the relationship between the branch cross-sectional area and foliage mass. We studied how these relationships varied within and between stands. The lowest site fertility class had a higher foliage mass to stem area ratio than better sites. The relative height of a tree in the stand (Φ) was the major factor that determined the variation in the relationship between the branch cross-sectional area and the stem cross-sectional area. Models based on absolute height or tree diameter were usually weaker. Models based on Φ were simpler, since no other variables were able to explain between-stand variation in the presence of Φ. We were able to predict changes in the branchiness of the tree but not in the foliage mass supported per unit of branch area.
Landscape-level interactions of prefire vegetation, burn severity, and postfire vegetation over a 16-year period in interior Alaska
Authors: Epting Justin , Verbyla David
Published: August 2005

Landsat imagery was used to study the relationship between a remotely sensed burn severity index and prefire vegetation and the postfire vegetation response related to burn severity within a 1986 burn in interior Alaska. Vegetation was classified prior to the fire and 16 years after the fire, and a chronosequence of remotely sensed vegetation index values was analyzed as a surrogate of vegetation recovery. Remotely sensed burn severity varied by vegetation class, with needle-leaf forest classes experiencing higher burn severity than broadleaf forest or broadleaf shrubland classes. Burn severity varied by cover within needle-leaf classes. Elevation also had an influence on burn severity, presumably as a result of there being less fuel above the treeline. Several large broadleaf areas at the fire perimeter appeared to act as fire breaks. A remotely sensed vegetation index peaked 814 years after the fire, and increase in the vegetation index was highest within the highest burn severity class. Self-replacement appeared to be the dominant successional pathway, with prefire needle-leaf forest classes mostly succeeding to needle-leaf woodland and with prefire broadleaf forest mostly succeeding to broadleaf shrubland. Because the remotely sensed indices were based on reflected solar radiation, they are likely indicative of surface properties, such as canopy destruction and surface charring, rather than subsurface properties, such as postfire depth of organic soil.
Genotype × shade effects for western hemlock
Authors: Johnson G R , Cartwright C
Published: August 2005

Western hemlock (Tsuga heterophylla (Raf.) Sarg.) families were grown under different levels of shade for 2 or 3 years at two nursery sites to determine whether families performed differently relative to one another in the different shade environments. Differences were found both for levels of shade and families, but no family × shade interaction was found. Results suggest that families selected in full-sun environments (clearcuts or farm fields) may be well suited for use in silvicultural systems where seedlings are planted in understory conditions.
A comparison of alternative methods for estimating the self-thinning boundary line
Authors: Zhang Lianjun , Bi Huiquan , Gove Jeffrey H , Heath Linda S
Published: August 2005

The fundamental validity of the self-thinning "law" has been debated over the last three decades. A long-standing concern centers on how to objectively select data points for fitting the self-thinning line and the most appropriate regression method for estimating the two coefficients. Using data from an even-aged Pinus strobus L. stand as an example, we show that quantile regression (QR), deterministic frontier function (DFF), and stochastic frontier function (SFF) methods have the potential to produce an upper limiting boundary line above all plots for the maximum sizedensity relationship, without subjectively selecting a subset of data points based on predefined criteria. On the other hand, ordinary least squares (OLS), corrected ordinary least squares (COLS), and reduced major axis (RMA) methods are sensitive to the data selected for model fitting and may produce self-thinning lines with inappropriate slopes. However, statistical inference is very difficult with the DFF and QR methods. Although SFF produces a self-thinning line lower than the upper limiting boundary line because of the nature of the method, it can easily produce the statistics for inference on the model coefficients, given that there are no significant departures from underlying distributional assumptions.
Growth response of spruce infected by Inonotus tomentosus in Alaska and interactions with spruce beetle
Authors: Lewis Kathy J , Thompson R Douglas , Trummer Lori
Published: August 2005

Thirty-eight trees from Alaska's Kenai Peninsula and 39 from the interior near Fairbanks (Delta Junction) were sampled by detailed stem dissections to determine the impact of tomentosus root disease [Inonotus tomentosus (Fr.: Fr.) S. Teng] on growth and decay volume in spruce, with and without the influence of past spruce beetle activity in stands. Disease severity was assessed by the number of primary roots (out of four) infected and by the average proportion of root cross-section area colonized by stain and (or) decay. Butt rot volumes were positively related to disease severity at both locations, but only the Delta Junction trees showed a significant negative relationship between relative volume increment and disease severity. Substantial mortality of spruce, caused by the spruce beetle (Dendroctonus rufipennis (Kirby)), has occurred on the Kenai Peninsula since the late 1970s. Mortality of overstory spruce trees released surviving trees from competition, causing compensatory growth in healthy to moderately infected trees, which masked the effect of the root disease. We found that the magnitude of growth release was negatively related to disease severity and that the mean proportion of root cross-section with decay or stain was a better estimator of disease impact on tree growth.
ATOMICALLY FLAT III-ANTIMONIDE EPILAYERS GROWN USING LIQUID PHASE EPITAXY
Authors: KUMAR ANIKA , SRIDARAN SUJATHA , DUTTA P. S.
Published: August 2005

A novel process has been developed which allows the growth of device grade ultra-smooth epitaxial layers of antimonide based III-V compounds with a controlled thickness using Liquid Phase Epitaxy (LPE). GaSb epilayers (with thickness in the range of 20-50 m) on GaSb single crystalline substrates have been grown with a root mean square surface roughness of less than 1 nm over an area of 5 §←5 m .
MBE-Grown AlGaN/GaN HEMTs on SiC
Authors: RAJAN SIDDHARTH , CHAKRABORTY ARPAN , MISHRA UMESH K. , POBLENZ CHRISTIANE , WALTEREIT PATRICK , SPECK JAMES S.
Published: August 2005

We report on the development of AlGaN/GaN high-electron mobility transistors (HEMTs) grown on SiC using plasma-assisted molecular beam epitaxy (MBE). In this work, we show that performance comparable to state-of-the-art AlGaN/GaN HEMTs can be achieved using MBE-grown material. Buffer leakage was an important limiting factor for these devices. The use of either carbon-doped buffers, or low Al/N ratio in the nucleation layer growth were effective in reducing buffer leakage. Studies varying the thickness and concentration of the carbon doping were carried out to determine the effect of different carbon doping profiles on the insulating and dispersive properties of buffers, On devices without field plates, at 4 GHz an output power density of 12 W/mm was obtained with a power-added efficiency (PAE) of 46 % and gain of 14 dB. 15.6 W/mm with PAE of 56 % was obtained from these devices after field-plating. Two-tone linearity measurements of these devices were also carried out. At a C/I 3 level of 30 dBc, the devices measured had an output power of 1.9 W/mm with a PAE of 53 %. The effect of the Al/N ratio in the AlN nucleation layer on buffer leakage was studied. N -rich conditions yielded highly insulating GaN buffers without carbon doping. At 4 GHz, devices without field plates delivered 4.8 W/mm with a PAE of 62 %. At a higher drain bias (50 V), 8.1 W/mm with a PAE of 38 % was achieved.
HIGH LINEARITY GaN HEMT POWER AMPLIFIER WITH PRE-LINEARIZATION GATE DIODE
Authors: XIE SHOUXUAN , PAIDI VAMSI , HEIKMAN STEN , SHEN LIKUN , CHINI ALESSANDRO , MISHRA UMESH K. , RODWELL MARK J. W. , LONG STEPHEN I.
Published: August 2005

A high linearity MMIC RF power amplifier is reported in the AlGaN/GaN HEMT technology. In order to obtain high linearity, a pre-linearization gate diode is added at the input to compensate for the nonlinear input capacitance C gs of the GaN HEMT device. Another single-ended Class B power amplifier without the gate diode is also designed for comparison. The circuit with the pre-linearization gate diode demonstrates at least 4dB improvement on 3rd order intermodulation distortion (IMD3) performance over the one without the diode over the useful power range in two-tone measurement.