bluuebunny/crossref_metadata_2025 huggingface dataset:
Pattern of Ca2+ increase determines the type of secretory mechanism activated in dog pancreatic duct epithelial cells
Authors: Jung Seung‐Ryoung , Kim Kyungjin , Hille Bertil , Nguyen Toan D. , Koh Duk‐Su
Published: July 2006

Intracellular calcium concentration ([Ca2+]i) is a key factor controlling secretion from various cell types. We investigated how different patterns of [Ca2+]i signals evoke salt secretion via ion transport mechanisms and mucin secretion via exocytosis in dog pancreatic duct epithelial cells (PDEC). Activation of epithelial P2Y2 receptors by UTP generated two patterns of [Ca2+]i change: 2–10 μm UTP induced [Ca2+]i oscillations, whereas 100 μm UTP induced a sustained [Ca2+]i increase, both in the micromolar range. As monitored by carbon‐fibre amperometry, the sustained [Ca2+]i increase stimulated a larger increase in exocytosis than [Ca2+]i oscillations, despite their similar amplitude. In contrast, patch‐clamp recordings revealed that [Ca2+]i oscillations synchronously activated a K+ current as efficiently as the sustained [Ca2+]i increase. This K+ current was mediated by intermediate‐conductance Ca2+‐activated K+ channels (32 pS at −100 mV) which were sensitive to charybdotoxin and resistant to TEA. Activation of these Ca2+‐dependent K+ channels hyperpolarized the plasma membrane from a resting potential of −40 mV to −90 mV, as monitored in perforated whole‐cell configuration, in turn enhancing Na+‐independent, Cl−‐dependent and DIDS‐sensitive HCO3− secretion, as monitored through changes in intracellular pH. PDEC therefore encode concentrations of purinergic agonists as different patterns of [Ca2+]i changes, which differentially stimulate K+ channels, the Cl−–HCO3− exchanger, and exocytosis. Thus, in addition to amplitude, the temporal pattern of [Ca2+]i increases is an important mechanism for transducing extracellular stimuli into different physiological effects.
Alternative splicing in the C‐terminus of CaV2.2 controls expression and gating of N‐type calcium channels
Authors: Castiglioni Andrew J. , Raingo Jesica , Lipscombe Diane
Published: July 2006

N‐type CaV2.2 calcium channels localize to presynaptic nerve terminals of nociceptors where they control neurotransmitter release. Nociceptive neurons express a unique set of ion channels and receptors important for optimizing their role in transmission of noxious stimuli. Included among these is a structurally and functionally distinct N‐type calcium channel splice isoform, CaV2.2e[37a], expressed in a subset of nociceptors and with limited expression in other parts of the nervous system. CaV2.2[e37a] arises from the mutually exclusive replacement of e37a for e37b in the C‐terminus of CaV2.2 mRNA. N‐type current densities in nociceptors that express a combination of CaV2.2e[37a] and CaV2.2e[37b] mRNAs are significantly larger compared to cells that express only CaV2.2e[37b]. Here we show that e37a supports increased expression of functional N‐type channels and an increase in channel open time as compared to CaV2.2 channels that contain e37b. To understand how e37a affects N‐type currents we compared macroscopic and single‐channel ionic currents as well as gating currents in tsA201 cells expressing CaV2.2e[37a] and CaV2.2e[37b]. When activated, CaV2.2e[37a] channels remain open for longer and are expressed at higher density than CaV2.2e[37b] channels. These unique features of the CaV2.2e[37a] isoform combine to augment substantially the amount of calcium that enters cells in response to action potentials. Our studies of the e37a/e37b splice site reveal a multifunctional domain in the C‐terminus of CaV2.2 that regulates the overall activity of N‐type calcium channels in nociceptors.
The complexity of the mammalian transcriptome
Authors: Gustincich Stefano , Sandelin Albin , Plessy Charles , Katayama Shintaro , Simone Roberto , Lazarevic Dejan , Hayashizaki Yoshihide , Carninci Piero
Published: July 2006

A comprehensive understanding of protein and regulatory networks is strictly dependent on the complete description of the transcriptome of cells. After the determination of the genome sequence of several mammalian species, gene identification is based on in silico predictions followed by evidence of transcription. Conservative estimates suggest that there are about 20 000 protein‐encoding genes in the mammalian genome. In the last few years the combination of full‐length cDNA cloning, cap‐analysis gene expression (CAGE) tag sequencing and tiling arrays experiments have unveiled unexpected additional complexities in the transcriptome. Here we describe the current view of the mammalian transcriptome focusing on transcripts diversity, the growing non‐coding RNA world, the organization of transcriptional units in the genome and promoter structures. In‐depth analysis of the brain transcriptome has been challenging due to the cellular complexity of this organ. Here we present a computational analysis of CAGE data from different regions of the central nervous system, suggesting distinctive mechanisms of brain‐specific transcription.
The Mevalonate Pathway Controls Heart Formation in
Drosophila
by Isoprenylation of Gγ1
Authors: Yi Peng , Han Zhe , Li Xiumin , Olson Eric N.
Published: July 2006

The early morphogenetic mechanisms involved in heart formation are evolutionarily conserved. A screen for genes that control
Drosophila
heart development revealed a cardiac defect in which pericardial and cardial cells dissociate, which causes loss of cardiac function and embryonic lethality. This phenotype resulted from mutations in the genes encoding HMG-CoA reductase, downstream enzymes in the mevalonate pathway, and G protein Gγ1, which is geranylgeranylated, thus representing an end point of isoprenoid biosynthesis. Our findings reveal a cardial cell–autonomous requirement of Gγ1 geranylgeranylation for heart formation and suggest the involvement of the mevalonate pathway in congenital heart disease.
Climate-Controlled Holocene Occupation in the Sahara: Motor of Africa's Evolution
Authors: Kuper Rudolph , Kröpelin Stefan
Published: July 2006

Radiocarbon data from 150 archaeological excavations in the now hyper-arid Eastern Sahara of Egypt, Sudan, Libya, and Chad reveal close links between climatic variations and prehistoric occupation during the past 12,000 years. Synoptic multiple-indicator views for major time slices demonstrate the transition from initial settlement after the sudden onset of humid conditions at 8500 B.C.E. to the exodus resulting from gradual desiccation since 5300 B.C.E. Southward shifting of the desert margin helped trigger the emergence of pharaonic civilization along the Nile, influenced the spread of pastoralism throughout the continent, and affects sub-Saharan Africa to the present day.
EULAR recommendations for knee and hip osteoarthritis: a critique of the methodology
Authors: Zhang W , Doherty M
Published: July 2006

The quality of the EULAR recommendations for the management of hip and knee osteoarthritis (OA) was evaluated using a validated instrument. The quality and methods were compared with other guidelines and recommendations. EULAR recommendations were found to be among the best for overall quality. They show strengths with respect to scope, rigour of development, and clarity, but weaknesses with respect to stakeholder involvement, applicability, and editorial independence. However, a principal strength is their attempt to fill the gap between guidelines based solely on either research evidence or expert opinion. The methods used to synthesise research evidence (systematic review) and expert opinion (Delphi exercise) are robust. Strength of recommendation, based on combined consideration of research evidence, clinical expertise, and perceived patient preference, is valid and approaches the true essence of “evidence based practice” that considers each of these different forms of evidence.
Physiological left ventricular hypertrophy or hypertrophic cardiomyopathy in an elite adolescent athlete: role of detraining in resolving the clinical dilemma
Authors: Basavarajaiah S , Wilson M , Junagde S , Jackson G , Whyte G , Sharma S
Published: July 2006

The differentiation of physiological left ventricular hypertrophy (LVH) from hypertrophic cardiomyopathy (HCM) can prove challenging for even the most experienced cardiologists. The case is presented of a 17 year old elite swimmer who had electrocardiographic and echocardiographic features that were highly suggestive of HCM. However, indices of diastolic function were normal and cardiopulmonary exercise testing revealed high peak oxygen consumption in keeping with physiological LVH. To resolve the diagnostic dilemma, the patient underwent detraining for eight weeks, after which, there was complete resolution of the changes seen on electrocardiogram and echocardiogram, indicating physiological LVH rather than HCM.
Work design and management in the manufacturing sector: development and validation of the Work Organisation Assessment Questionnaire
Authors: Griffiths A , Cox T , Karanika M , Khan S , Tomás J M
Published: July 2006

Objectives:To examine the factor structure, reliability, and validity of a new context-specific questionnaire for the assessment of work and organisational factors. The Work Organisation Assessment Questionnaire (WOAQ) was developed as part of a risk assessment and risk reduction methodology for hazards inherent in the design and management of work in the manufacturing sector.

Method:Two studies were conducted. Data were collected from 524 white- and blue-collar employees from a range of manufacturing companies. Exploratory factor analysis was carried out on 28 items that described the most commonly reported failures of work design and management in companies in the manufacturing sector. Concurrent validity data were also collected. A reliability study was conducted with a further 156 employees.

Results:Principal component analysis, with varimax rotation, revealed a strong 28-item, five factor structure. The factors were named: quality of relationships with management, reward and recognition, workload, quality of relationships with colleagues, and quality of physical environment. Analyses also revealed a more general summative factor. Results indicated that the questionnaire has good internal consistency and test-retest reliability and validity. Being associated with poor employee health and changes in health related behaviour, the WOAQ factors are possible hazards. It is argued that the strength of those associations offers some estimation of risk. Feedback from the organisations involved indicated that the WOAQ was easy to use and meaningful for them as part of their risk assessment procedures.

Conclusions:The studies reported here describe a model of the hazards to employee health and health related behaviour inherent in the design and management of work in the manufacturing sector. It offers an instrument for their assessment. The scales derived which form the WOAQ were shown to be reliable, valid, and meaningful to the user population.
Protein transport in the plant secretory pathwayThis review is one of a selection of papers published in the Special Issue on Plant Cell Biology.
Authors: Hanton Sally L. , Brandizzi Federica
Published: July 2006

The study of the plant secretory pathway is a relatively new field, developing rapidly over the last 30 years. Many exciting discoveries have already been made in this area, but as old questions are answered new ones become apparent. Our understanding of the functions and mechanisms of the plant secretory pathway is constantly expanding, in part because of the development of new technologies, mainly in bioimaging. The increasing accessibility of these new tools in combination with more established methods provides an ideal way to increase knowledge of the secretory pathway in plants. In this review we discuss recent developments in understanding protein transport between organelles in the plant secretory pathway.
Changing spaces: the Arabidopsis mucilage secretory cells as a novel system to dissect cell wall production in differentiating cellsThis review is one of a selection of papers published in the Special Issue on Plant Cell Biology.
Authors: Western Tamara L.
Published: July 2006

As the outer boundary of plant cells, the cell wall is integral to all aspects of plant growth, development, and interactions with the environment. Dicot primary cell walls are composed of a network of cellulose, hemicellulose and proteins embedded in a matrix of acidic pectins. Pectins are synthesized in the Golgi apparatus by the sequential addition of nucleotide sugars by glycosyltransferases, following which they are secreted to the apoplast. During their differentiation, the mucilage secretory cells (MSCs) of the Arabidopsis seed coat undergo sequential biosynthesis and secretion of a primarily pectinaceous mucilage followed by secondary cell wall production. Several genes affecting MSC differentiation have been identified with roles ranging from the production of nucleotide sugar substrates for pectin synthesis to putative cell wall modification enzymes to transcription factors required to control MSC differentiation. These preliminary studies of the MSCs demonstrate that they will play a valuable role in gene discovery related to cell wall production and modification. Furthermore, they have the potential to become an important system in which to study the interaction and regulation of pectin biosynthetic factors in differentiating cells. These results will contribute to answering the important question of how cell wall production and modification occur throughout a growing plant living in a complex environment.
Plastid protein delivery: coping with diversityThis review is one of a selection of papers published in the Special Issue on Plant Cell Biology.
Authors: Ko Kenton , Chan Kelvin , Karakasis Katherine , Pedram Babak
Published: July 2006

Plastids play a central role in a variety of biosynthetic activities such as photosynthesis, amino acid synthesis, and oil production. Many of these activities depend on the compartment’s ability to adapt appropriately to the ever-changing environment of a plant cell. The pressure to adapt can arise from both internal and external sources. The complex nature of these adaptation activities is likely to be mirrored in the diversity of proteins being transported in a given situation. This diversity can be manifested at all molecular levels of the proteins, from different transit signal-bearing preproteins to different structural versions of the same preprotein. Unanticipated changes can also arise spontaneously upon exposing the population of translocating proteins to environmental stress, for example heat or cold. It is therefore important for plastids to maintain a responsive and efficient protein transport process to accommodate all situations, immediately or for the longer-term. By drawing on existing evidence, this review explores specific structural features or schemes for adapting the plastid protein delivery process and speculates on other adaptation possibilities for future consideration.
When microspores decide to become embryos — cellular and molecular changesThis review is one of a selection of papers published in the Special Issue on Plant Cell Biology.
Authors: Pauls K. Peter , Chan John , Woronuk Grant , Schulze Derek , Brazolot Janice
Published: July 2006

Cultured microspores can be induced to develop into fully functional haploid embryos instead of mature pollen. The ability of these cells to change their development in response to environmental stimuli is an exceptional example of totipotency in plants. Discovering the triggers of embryo development in microspore cultures could lead to a greater understanding of the early stages of embryogenesis in plants and might be used to increase the range of crop plants to which microspore culture can be applied for the production of double haploid homozygous lines. The information might also help to define the general characteristics of pluripotent cells in any organism. In this review, the changes that occur in cellular organization and gene expression in early-stage microspore cultures of several species are discussed. Responding cells in these cultures enlarge, their nuclei are repositioned to their cell centres, and their cytoplasms become filled with fragmented vacuoles. We used flow cytometry to track cellular changes in canola ( Brassica napus L.) microspore cultures as well as microarray analyses and real-time PCR to compare gene expression in embryogenic and nonembryogenic cells. A model for embryogenic cell activation in plants that involves alkalinization, Ca2+ signaling, and changes in GTPase activity that lead to significant changes in gene expression is discussed.
Morphological and systematic reinterpretation of two enigmatic edrioasteroids (Echinodermata) from Canada
Authors: Sumrall Colin D , Gahn Forest J
Published: July 2006

Reinterpretation of two enigmatic Canadian edrioasteroids, Thresherodiscus ramosus Foerste, 1914 from the Upper Ordovician Verulam Formation of Ontario and Lispidecodus plinthotus Kesling, 1967 from the Lower Mississippian Banff Formation of Alberta, shows that previous accounts of these taxa were largely erroneous. Unlike other isorophid edrioasteroids, Thresherodiscus has branching ambulacra, an unusual hydro-gonopore, differentiated interambulacral plates bearing respiratory structures, and ambulacra that extend onto the peripheral rim. Except for the turreted thecal shape, Lispidecodus is a rather typical discocystinid edrioasteroid. Phylogenetic analysis weakly supports the placement of Thresherodiscus within Agelacrinitidae and strongly places Lispidecodus within Discocystinae.
A record of post-glacial moraine deposition and tephra stratigraphy from Otokomi Lake, Rose Basin, Glacier National Park, Montana
Authors: MacLeod David Matthew , Osborn Gerald , Spooner Ian
Published: July 2006

The sedimentary record of Otokomi Lake, Glacier National Park, Montana, was studied to determine the age of an adjacent Crowfoot moraine. The presence of Mt. St. Helens Jy ash near the bottom of the longest percussion core limits drainage basin deglaciation to before 11 400 14C years before present (BP), although 14 100 BP is the estimated basal age of the core. Correlative shifts in loss on ignition, coarse (>1 mm) grain size, magnetic susceptibility, and X-ray gray-scale data at a depth of 185 cm are interpreted to be related to a sedimentary change in Otokomi Lake brought about by the deposition of the adjacent Crowfoot moraine. The estimated age of the moraine is 10 590 BP, which is within the Younger Dryas interval. This information supports the hypothesis that Crowfoot moraines represent a regional western North American response to Younger Dryas cooling.
Protecting marine biodiversity: a comparison of individual habitat quotas and marine protected areas
Authors: Holland Daniel S , Schnier Kurt E
Published: July 2006

Fisheries managers in the United States are required to identify and mitigate the adverse impacts of fishing activity on essential fish habitat (EFH). There are additional concerns that the viability of sessile noncommercial species, animals that are habitat dependent and (or) are themselves constituents of fishery habitat, may be threatened by fishing activities. We propose a system of individual habitat quotas (IHQ) to achieve habitat conservation and species protection cost effectively. Individual quotas of habitat impact units would be distributed to fishers with an aggregate quota set to maintain a target habitat "stock". Using a dynamic, spatially explicit fishery simulation model, we explore the efficiency and effectiveness of an IHQ policy versus marine protected areas (MPAs) for conserving habitat-dependent, sessile species of unknown spatial distributions. Our findings indicate that an IHQ policy with a conservatively established habitat target is better suited to the protection of sessile nontarget species than a rotating or fixed MPA policy.
Recovery from acidification in Nova Scotia: temporal trends and critical loads for 20 headwater lakes
Authors: Whitfield C J , Aherne J , Watmough S A , Dillon P J , Clair T A
Published: July 2006

The chemical response of 20 headwater lakes in Nova Scotia to reduced acid deposition was investigated using trend analysis, and the need for further reductions was assessed using two steady-state, critical load models. Significant decreases were observed in the concentration of nonmarine sulphate (SO42) and hydrogen (H+) at four wet deposition monitoring stations across Atlantic Canada since 1984. Dominant trends in surface water were decreasing SO42concentrations, with little improvement in alkalinity and H+. Based on the Steady State Water Chemistry (SSWC) and First-order Acidity Balance (FAB) models, and using a critical chemical limit for acid-neutralizing capacity of 20 µmolc·L1, critical load is exceeded at 9 and 13 of the 20 study lakes, respectively. Application of the SSWC model suggests that sulphur (S) deposition must be reduced by 37.3 mmolc·m2·year1from 1997 levels to prevent critical load exceedance at 95% of the study lakes. Using the FAB model, the minimum reductions in nitrogen and S deposition necessary to protect 95% of the study lakes are 32.7 and 42.1 mmolc·m2·year1, respectively. Additional reductions beyond those proposed for 2030 are required to minimize critical load exceedance and promote recovery in alkalinity and pH of surface waters at the study catchments.
Depth-specific patterns in benthicplanktonic food web relationships in Lake Superior
Authors: Sierszen Michael E , Peterson Gregory S , Scharold Jill V
Published: July 2006

In an investigation of the spatial characteristics of Laurentian Great Lakes food webs, we examined the trophic relationship between benthic amphipods (Diporeia) and plankton in Lake Superior. We analyzed the carbon and nitrogen stable isotope ratios of Diporeia and plankton at stations in water column depths of 4300 m. Neither δ15N nor δ13C of plankton from the upper 50 m of the water column varied significantly with station depth. Diporeia isotope ratios exhibited depth-specific patterns reflecting changes in food sources and food web relationships with plankton. Diporeia was 13C enriched at station depths of <40 m, reflecting increased dietary importance of benthic algae. There was a systematic increase in Diporeia δ15N with depth, which appeared to result from a combination of dietary shifts in the nearshore and decompositional changes in Diporeia's principal food, sedimented plankton, in deep habitats. Diporeia δ13C and δ15N together described changes in food web isotope baseline with depth. They also discriminated three depth strata representing photic, mid-depth, and profundal zones. These findings have implications for our understanding of Great Lakes food webs and analyses of trophic position within them, the ecology of zoobenthos and plankton communities, and sampling designs for large lakes.
Improving the precision of design-based scallop drag surveys using adaptive allocation methods
Authors: Smith Stephen J , Lundy Mark J
Published: July 2006

Periodic scientific surveys of commercially exploited fish and invertebrate species are a major source of monitoring data for tracking population trends and evaluating fisheries management plans. The precision of the estimates is important for assessing their quality, as well as being used directly in population models and decision rules. For design-based surveys, precision is partly a function of the survey design and can be improved for the commonly used stratified random design through the judicious definition of strata boundaries and sample-to-strata allocation schemes. In this study, we used adaptive allocation schemes to improve the precision of sea scallop (Placopecten magellanicus) surveys in 1999 and 2004 over the standard stratified random design. The adaptive surveys for both years were more efficient (smaller variance of the mean) than the standard stratified random surveys that had been used. Greater gains in efficiency were obtained for the 2004 survey in which scallops were more abundant (stratified mean of 227 scallops per tow) than in 1999 (stratified mean of 73 scallops per tow). The 2004 survey also benefitted from having tows allocated proportionally to stratum size at the first phase of sampling. Adaptive allocation methods appear to work best for small area surveys with one or few target species.
Survival of Arctic cod larvae (Boreogadus saida) in relation to sea ice and temperature in the Northeast Water Polynya (Greenland Sea)
Authors: Fortier Louis , Sirois Pascal , Michaud Josée , Barber David
Published: July 2006

We tested the hypothesis that the survival of Arctic cod larvae (Boreogadus saida) is limited at sea ice cover >50% and sea surface temperature (SST) <0 °C. In 1993 in the Northeast Water Polynya, a spring cohort (14 May  15 June) was hatched under heavy ice cover (58%91%) and cold SST (1.7 to 1.0 °C) and a summer cohort (21 June  21 July) under low ice cover (4%31%) and above-zero SST (1.5 to 3.9 °C). Consistent with the hypothesis, the spring cohort had almost completely vanished by age 10 days (first feeding stage), while the summer cohort survived well and dominated the population by the end of our sampling in early August. By then, the few surviving spring larvae were on average 5.7 mm longer than summer larvae (18.6 vs. 12.9 mm). A retrospective analysis of ice cover in the polynya (1979 to 2003) indicated that first-feeding larvae of the spring cohort encountered good survival conditions (sea ice <50% and SST >0 °C) in only 12% of the years compared with 80% for the summer cohort. The survival advantage provided by a larger size at the onset of Arctic winter could explain the evolutionary persistence of a spring cohort despite the low probability of initial survival.
A 500-year context for the recent surge in sockeye salmon (Oncorhynchus nerka) abundance in the Alagnak River, Alaska
Authors: Schindler Daniel E , Leavitt Peter R , Johnson Susan P , Brock Curtis S
Published: July 2006

Returns of sockeye salmon (Oncorhynchus nerka) to the Alagnak River in Bristol Bay, Alaska, during the last 3 years were unprecedented in the last five decades. Enumerated run sizes averaged about 1 million fish from 1955 to 2002 but surged unexpectedly to average 5.4 million fish in 20032005. These huge returns currently pose a challenge to management of Bristol Bay sockeye for several reasons, including that it is unclear whether the recent surge in abundance is a new phenomenon or if it has arisen as part of interdecadal population variability. To answer this question we used changes in lake sedimentary δ15N coupled with an isotope-mixing model to estimate historical abundances of sockeye salmon populations in this ecosystem. Our analyses show that periods of high salmon abundance have occurred every ~100 years during the last five centuries, interspersed by prolonged periods of substantially lower abundance. We suggest that the recent high returns are an expression of the long-term variability that is characteristic of this stock and will be a relatively transient phenomenon.
When do marine reserves increase fishery yield?
Authors: Hart Deborah R
Published: July 2006

An age-structured model is developed for analyzing the effects of marine reserves and other long-term closures on fishery yield, assuming larvae are well-mixed and that exchange of adults between the open and closed areas is negligible. A number of analytic results are derived, including a formula for the gradient of yield with respect to fishing mortality and closure fraction. Increasing the closure fraction at equilibrium spawning stock biomass (SSB), B, will increase yield if and only if s′(B) > 1/b0(0), where s′(B) is the slope of the stockrecruitment curve at B and b0(0) is SSB per recruit at zero fishing mortality. Conditions for the level of closure required to prevent stock collapse are also derived. Applications of the theory to canary rockfish (Sebastes pinniger) and Georges Bank sea scallop (Placopecten magellanicus) illustrate that long-term closures increase yield only at low SSB associated with fishing mortalities greater than FMSY and with low closure fractions. The theory presented here gives simple analytic and graphical techniques for predicting the effects of long-term closures on yield and stock persistence.
Fleet dynamics and fishermen behavior: lessons for fisheries managers
Authors: Branch Trevor A , Hilborn Ray , Haynie Alan C , Fay Gavin , Flynn Lucy , Griffiths Jennifer , Marshall Kristin N , Randall Jeffrey K , Scheuerell Jennifer M , Ward Eric J , Young Mark
Published: July 2006

We review fleet dynamics and fishermen behavior from an economic and sociological basis in developing fisheries, in mature fisheries near full exploitation, and in senescent fisheries that are overexploited and overcapitalized. In all cases, fishing fleets behave rationally within the imposed regulatory structures. Successful, generalist fishermen who take risks often pioneer developing fisheries. At this stage, regulations and subsidies tend to encourage excessive entry and investments, creating the potential for serial depletion. In mature fisheries, regulations often restrict season length, vessel and gear types, fishing areas, and fleet size, causing or exacerbating the race for fish and excessive investment, and are typically unsuccessful except when combined with dedicated access privileges (e.g., territorial rights, individual quotas). In senescent fisheries, vessel buyback programs must account for the fishing power of individuals and their vessels. Subsidies should be avoided as they prolong the transition towards alternative employment. Fisheries managers need to create individual incentives that align fleet dynamics and fishermen behavior with the intended societal goals. These incentives can be created both through management systems like dedicated access privileges and through market forces.
Propagation of laser beams formed by unstable resonators with different magnifications
Authors: Saghafi S , Withford M J , Piper J A
Published: July 2006

Laser beams generated from high-magnification on-axis unstable resonators using hard-edged axial scraper mirrors and output couplers consisting of axial spot reflectors typically have an annular distribution in the near field (i.e., a flat-top profile with a hole in the middle for an axially coupled beam). We employ a new model, based on the flattened Gaussian beam (FGB) concept, to describe the propagation of such annular near-field beams. The superposition of two FGBs, whose flatness and steepness of edges are controlled by defined parameters (i.e., the beam width and the order), is used to analyze the output beam intensity profile along the propagation axis. We apply this model to characterize the output beams of copper vapour lasers employing unstable resonators of different magnifications (M = 80, 200, and 400). We show that once the model is fitted to the beam intensity profile at any two positions along the axis of propagation, it can be used to predict the beam shape at any position.PACS Nos.: 42.55.–f, 42.55.Lt, 42.60.–v
Hydrogenic system confined to a two-dimensional circular disc
Authors: Patil S H , Varshni Y P
Published: July 2006

Some general properties of a hydrogenic system confined to a circular disc are analyzed. Based on these, simple and accurate expressions are developed for the energies, critical radii, and some other properties, for all the states and all radii of confinement. Model wave functions are considered for some states, which give accurate values for the energies and other properties, and provide an insight into their physical structure. PACS Nos.: 3.65.Ge, 73.21.La, 78.67.Hc
Two electrons in a simple harmonic potential
Authors: Patil S H , Varshni Y P
Published: July 2006

Some structural properties of energy eigenfunctions of two electrons in a simple harmonic potential are analyzed. Simple expressions are obtained for the energy spectrum based on a model potential, and on a model wave function. These expressions give accurate values for the energy eigenvalues and provide a physical insight into their structure.PACS Nos.: 3.65.Ge, 73.21.La, 78.67.Hc
Can the effect of sand fabric on plastic hardening be determined using a self-bored pressuremeter?
Authors: Shuttle D A
Published: July 2006

At working levels of strain, prior to peak strength, soil fabric has a large effect on the mobilized stress–strain response. Fabric is also known to affect the number of cycles to liquefaction in loose sands. Better quality analyses require that the effect of fabric on plastic hardening be included in any parameter selection, but measurement of this fabric effect is difficult. Fabric is sensitive to soil disturbance and hence is most appropriately measured in situ, but the effect of density and fabric may have similar effects on in situ tests, which complicates the determination of each of these independent state variables. This paper investigates whether the pressuremeter, an in situ test whose loading may be idealized as simple cylindrical cavity expansion, is able to differentiate between the effects of density and fabric. A realistic critical state constitutive soil model, NorSand, is used for the investigation in detailed finite element simulations of pressuremeter tests. Resolution of the competing effects of the state parameter ψ and fabric is challenging and cannot be achieved from pressuremeter data alone.Key words: fabric, pressuremeter, sand, state, numerical modelling, critical state.
Pressure-controlled cavity expansion in clay
Authors: Au Alfred SK , Yeung Albert T , Soga Kenichi
Published: July 2006

Experimental studies and numerical simulation of experiments were conducted on pressure-controlled cavity expansion in clay. The modified Cam-clay model was used to describe the clay behaviour. The experimental data are in good agreement with the simulation results, indicating that the adopted numerical simulation procedure is a plausible and reliable technique to study the fundamental behaviour of pressure-controlled cavity expansion. A new parameter, cavity aspect ratio (CAR), was defined to better describe the cavity shape. Different phenomena during the cavity expansion process are thus studied numerically, and the results are presented in this paper.Key words: pressure-controlled cavity expansion, numerical simulation, laboratory investigation, modified Cam-clay model, cavity aspect ratio (CAR), ABAQUS.
Effects of sample disturbance and consolidation procedures on measured shear strength of soft marine Norwegian clays
Authors: Lunne Tom , Berre Toralv , Andersen Knut H , Strandvik Stein , Sjursen Morten
Published: July 2006

After many decades of research, the issue of sample disturbance is still important as regards to determining reliable and representative soil parameters for foundation design in soft clays. Parallel laboratory tests have been carried out on high-quality block samples and ordinary piston tube samples from 12 deposits of soft Norwegian marine clays. Undrained triaxial and direct simple shear (DSS) tests on samples reconsolidated to the in situ effective stresses show that sample disturbance has a significant effect on the measured stress–strain–strength behaviour: the more disturbed the sample, the lower the shear stress at small strains and the higher the shear stress at large strains. Breakdown of the clay structure, including cementation bonds, is the assumed cause of lower shear resistance at small strains, whereas at large strains the shear resistance is governed mainly by the water content, which for soft clay samples, reconsolidated to the in situ effective stresses, will be lower, and the strength thereby higher, the more disturbed the sample. The work described herein also includes the effects of the consolidation procedure; in addition to the reconsolidation technique, both stress history and normalized soil engineering properties (SHANSEP) and delayed consolidation tests have been carried out.Key words: soft clays, sample disturbance, consolidation procedures, stress–strain–strength behaviour, stress–strain–time behaviour.
Analyzing the effects of stand thinning on microclimates with semiparametric smoothing splines
Authors: Guan Biing T , Weng Shih-Hao , Kuo Shing-Rong , Chang Tsung-Yi , Hsu Hsin-Wu , Shen Chieh-Wen
Published: July 2006

Monitoring the effects of stand thinning on microclimates is an integral part of any thinning experiment. It is through its modifications of microclimates that thinning alters important ecological processes. An efficient analysis of microclimate-monitoring data should address both the effects of thinning regimes on, and the temporal response trends of, microclimates. Probably because of the difficulties in modeling temporal trends parametrically, an examination of the existing literature on thinning showed that only a few studies have attempted to address the second aspect. We propose the use of semiparametric smoothing splines to analyze monitoring data from thinning experiments. First, the concept of a smoothing spline is briefly described. We then provide an example in which semiparametric mixed-effects smoothing-spline models were used to analyze microclimate-monitoring data from a thinning experiment. The proposed approach not only successfully detected the effects of thinning, but also revealed interesting temporal trends. For each of the microclimatic variables, we also compared the performance of the fitted semiparametric model with that of a parametric model. In general, the semiparametric model performed better than its parametric counterpart. We also addresse some concerns in using the proposed approach.
Spatial analysis enhances modelling of a wide variety of traits in forest genetic trials
Authors: Dutkowski Gregory W , Costa e Silva João , Gilmour Arthur R , Wellendorf Hubert , Aguiar Alexandre
Published: July 2006

Spatial analysis of progeny trial data improved predicted genetic responses by more than 10% for around 20 of the 216 variables tested, although, in general, the gains were more modest. The spatial method partitions the residual variance into an independent component and a two-dimensional spatially autocorrelated component and is fitted using REML. The largest improvements in likelihood were for height. Traits that exhibit little spatial structure (stem counts, form, and branching) did not respond as often. The spatial component represented up to 50% of the total residual variance, usually subsuming design-based blocking effects. The autocorrelation tended to be high for growth, indicating a smooth environmental surface, it tended to be small for measures of health, indicating patchiness, and otherwise the autocorrelation was intermediate. Negative autocorrelations, indicating competition, were present in only 10% of diameter measurements for the largest diameter square planted trials, and between nearest trees with rectangular planting at smaller diameters. Bimodal likelihood surfaces indicate that competition may be present, but not dominant, in other cases. Modelling of extraneous effects yielded extra genetic gain only in a few trials with severely asymmetric autocorrelations. Block analysis of resolvable incomplete-block or row–column designs was better than randomized complete-block analysis, but spatial analysis was even better.
Stand-level prediction of balsam fir mortality in relation to spruce budworm defoliation
Authors: Pothier David , Mailly Daniel
Published: July 2006

Stand production and sustained yield calculations are largely affected by tree mortality, which can be caused by many factors such as competition, insect damage, or climatic events. In the eastern Canadian boreal forest, spruce budworm (Choristoneura fumiferana (Clem.)) defoliation can produce varying levels of mortality in balsam fir (Abies balsamea (L.) Mill.) stands. This mortality was estimated for the entire range of balsam fir in Quebec, Canada, using historical records of insect defoliation and permanent sample plot (PSP) inventories for the 19702003 period, which includes the last insect outbreak. A two-step approach was used to model balsam fir mortality at the stand level. The first step predicts the probability that all balsam fir trees within a PSP will survive during a given time interval. The second step quantifies the amount of mortality for PSP observation periods during which mortality actually occurred. The whole model shows that spruce budworm defoliation may account for between 6% and 100% of the merchantable volume lost due to mortality, depending on outbreak severity. A model evaluation made with an independent data set indicates that the model is unbiased, although the prediction error is relatively large at the stand level but decreases with increasing prediction horizon.
Ectomycorrhizal fungal communities of nursery-inoculated seedlings outplanted on clear-cut sites in northern Alberta
Authors: Gagné André , Jany Jean-Luc , Bousquet Jean , Khasa Damase P
Published: July 2006

Seedlings from three conifer species (Pinus contorta Doug. ex Loud. var. latifolia Englem., Picea glauca (Moench) Voss, and Picea mariana (Mill.) BSP) were planted on two clear-cut sites in Alberta, Canada, after inoculation in the nursery with strains of six different ectomycorrhizal species (Hebeloma longicaudum, Laccaria bicolor,Paxillus involutus,Pisolithus tinctorius,Rhizopogon vinicolor, and Suillus tomentosus). Five and 6 years after planting, morphological characterization and molecular typing techniques (internal transcribed spacer  restriction fragment length polymorphism (ITS-RFLP) and simple sequence repeat (SSR) markers) were used to identify the ectomycorrhizal fungal communities and to assess the occurrence of the inoculated ectomycorrhizal fungi on host roots. Ectomy corrhi zae recovered from the roots of the planted trees on each of the two sites showed little diversity, with a total of 16 and 19 ITS-RFLP patterns corresponding to 11 and 13 ectomycorrhizal taxa, respectively. The most abundant ectomycorrhizal fungi found on colonized roots were ascomycetes and the widespread basidiomycete Amphinema byssoides. Amongst the six introduced fungal strains, only L. bicolor UAMH 8232 was detected on one site after 5 and 6 years, as determined using six SSR markers. Although not detected after 5 years, some of the introduced strains might have had a positive effect on the early growth of the trees before their replacement by competing species, because significant differences in plot volume index were detected between inoculation and control treatments.
Evaluation of the economic impacts of length and diameter measurement error on mechanical harvesters and processors operating in pine stands
Authors: Marshall Hamish D , Murphy Glen E , Boston Kevin
Published: July 2006

Value recovery studies from around the world have shown that on average mechanical log-making systems lose 18% of the potential value compared to 11% for motor manual systems. One of the potential reasons for their poor value recovery performance is the level of accuracy of their stem diameter and length measurements. Numerous studies have looked at the level of error in both the diameter and length measurements made by mechanical harvesters and processors; however, few have looked at the economic impacts of these errors. The paper investigates the economic impacts in terms of value loss of six different harvesting operations in three different pine species. The accuracy and precision of the measurements recorded in this study were similar to those of other studies from around the world. A simulation model was developed to estimate the value loss caused by these errors. The results of the simulation model showed that the operations were losing between 3% and 23% of the potential value because of measurement errors. Further analysis showed that the industry should concentrate on increasing the precision of the length and diameter measurements to optimize gains from reducing the measurement error rates.
Classification and regression tree based survival analysis in oak-dominated forests of Missouri's Ozark highlands
Authors: Fan Zhaofei , Kabrick John M , Shifley Stephen R
Published: July 2006

Tree survival or mortality is a stochastic process and highly variable over time and space. Many factors contribute to this process, including tree age, tree size, competition, drought, insects, and diseases. Traditional parametric approaches to modeling tree survival or mortality are often unable to capture this variation, especially in natural, mixed-species forests. We analyzed tree survival in Missouri Ozark oak forests using a combination of classification and regression tree (CART) and survival analysis of more than 35 000 trees with DBH >11 cm measured four times between 1992 and 2002. We employed a log-rank test with CART to classify trees into seven disjoint survival groups and used a nonparametric KaplanMeier (product limit) method to estimate tree survival rate and construct confidence intervals for each survival group. We found that tree species, crown class, DBH, and basal area of larger trees were the variables most closely associated with differences in tree survival rates. In these mature oak forests, mortality for the red oak species group was three to six times greater than for the white oak, hickory, or shortleaf pine species group. The results provide practical information to guide development of silvicultural prescriptions to reduce losses to mortality.
Postfire dynamics of black spruce coarse woody debris in northern boreal forest of Quebec
Authors: Boulanger Yan , Sirois Luc
Published: July 2006

In this study, postfire coarse woody debris (CWD) dynamics in northern Quebec, Canada, were assessed using a 29-year chronosequence. Postfire woody-debris storage, decomposition rates, and variation of nitrogen and carbon contents of black spruce CWD (Picea mariana (Mill.) BSP) are estimated. The decomposition rate for postfire snags is exceptionally slow (k = 0.00), while the decomposition rate for logs (k = 0.019–0.021) is within previously recorded values for the boreal forest. The low decomposition rate for snags could be related to low moisture content associated with the position of debris and fast bark shedding. Given the low CWD decomposition rates and CWD storage (21.3–66.8 m3·ha–1), carbon losses from postfire CWD are relatively low, varying between 35.5 and 128.8 kg·ha–1·year–1 at the study sites. The nitrogen content in CWD drops quickly between living trees and snags and increases slightly with time since fire in logs. Nitrogen content is not related to wood density or to moisture content of deadwood. Rapid loss of nitrogen is associated with fast decomposition of subcortical tissues, leaching, and insect comminution. The increase in nitrogen content at the oldest site could result from asymbiotic nitrogen fixation, although a longer time span in the chronosequence would probably have revealed a greater nitrogen gain in increasingly decayed CWD.