bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of permafrost degradation on woody vegetation at arctic treeline on the Seward Peninsula, Alaska
Authors: Lloyd Andrea H. , Yoshikawa Kenji , Fastie Christopher L. , Hinzman Larry , Fraver Matthew 
Published: July 2003

AbstractPermafrost degradation leads to substantial changes in soil thermal and hydrologic characteristics. We investigated the effects of changes in active layer thickness and soil drainage on vegetation distribution near the arctic treeline on the Seward Peninsula, Alaska. We measured active layer thickness, soil moisture, density of tall shrub species, cover of low shrub species, and reconstructed white spruce establishment history along transects across the banks of a network of thaw ponds. We found that active layer thickness did not vary along our transects, but soils on thaw pond banks were significantly drier than those on level tundra or in thaw‐pond channels. Thaw‐pond banks were the only sites in which trees successfully established, and shrub communities on thaw‐pond banks were taller and more dominated by tall shrub species like willow and shrub birch. The data suggest that the establishment of tree and tall shrub species at the arctic treeline can be limited by the availability of well‐drained microsites, and the response of these species to regional climatic changes will be constrained by the availability of such microsites and thus contingent upon further degradation of the permafrost. Copyright © 2003 John Wiley & Sons, Ltd.
A model for regional‐scale estimation of temporal and spatial variability of active layer thickness and mean annual ground temperatures
Authors: Sazonova T. S. , Romanovsky V. E. 
Published: July 2003

AbstractHigh‐latitude ecosystems where the mean annual ground surface temperature is around or below 0°C are highly sensitive to global warming. This is largely because these regions contain vast areas of permafrost, which begins to thaw when the mean annual temperature rises above freezing. The Geophysical Institute Permafrost Lab has developed a new interactive geographical information systems (GIS) model to estimate the long‐term response of permafrost to changes in climate. An analytical approach is used for calculating both active layer thickness (ALT) and mean annual ground temperatures (MAGTs). When applied to long‐term (decadal or longer time scale) averages, this approach shows an accuracy of ±0.2–0.4°C for MAGTs and ±0.1–0.3 m for ALT calculations. The relative errors do not exceed 32% for ALT calculations, but typically they are between 10 and 25%. A spatial statistical analysis of the data from 32 sites in Siberia indicated a confidence level of 75% to have a deviation between measured and calculated MAGTs of 0.2–0.4°C. A detailed analysis has been performed for two regional transects in Alaska and eastern Siberia that has validated the use of the model. The results obtained from this analysis show that a more economical (in terms of computational time) analytical approach could be successfully used instead of a full‐scale numerical model in the regional and global scale analysis of permafrost spatial and temporal dynamics. This project has been a successful contribution to the Arctic Climate Impact Assessment project. Copyright © 2003 John Wiley & Sons, Ltd.
Shrinking thermokarst ponds and groundwater dynamics in discontinuous permafrost near council, Alaska
Authors: Yoshikawa Kenji , Hinzman Larry D. 
Published: July 2003

AbstractThe purpose of this study was to characterize the geomorphological processes controlling the dynamics of ponds and to identify and characterize groundwater infiltration and surface water dynamics for a tundra terrain located in discontinuous permafrost near Council, Alaska. Thermokarst processes and permafrost degradation were studied, focusing upon the interaction between surface and groundwater systems via an open talik. Synthetic aperture radar (SAR) data were used for classification of terrain units and surface water properties, while historical aerial photographs and satellite images (IKONOS) were used for assessment of pond shrinking and recent thermokarst progression. Geophysical surveys (ground penetrating radar and DC resistivity) were conducted to detect permafrost thickness and talik formations. Temperature boreholes and hydrological observation wells were monitored throughout the year and provided ground truth for validation of remotely‐sensed data and geophysical surveys. Field and laboratory analyses enabled quantitative determination of subsurface hydrologic and thermal properties. We found many areas where alluvium deposits and ice‐wedge polygonal terrain had developed thermokarst features within the last 20 years. Thermokarst ponds located over ice‐wedge terrain have decreased in surface area since at least the early 20th Century. Small thermokarst features initially developed into tundra ponds perched over permafrost in response to some local disturbance to the surface. These thermokarst ponds grew larger and initiated large taliks that completely penetrated the permafrost. These taliks allowed internal drainage throughout the year causing the ponds to shrink under recent climatic conditions. Shrinking pond surface areas may become a common feature in the discontinuous permafrost regions as a consequence of warming climate and thawing permafrost. Copyright © 2003 John Wiley & Sons, Ltd.
Vegetation‐soil‐thaw‐depth relationships along a low‐arctic bioclimate gradient, Alaska: synthesis of information from the ATLAS studies
Authors: Walker D. A. , Jia G. J. , Epstein H. E. , Raynolds M. K. , Chapin III F. S. , Copass C. , Hinzman L. D. , Knudson J. A. , Maier H. A. , Michaelson G. J. , Nelson F. , Ping C. L. , Romanovsky V. E. , Shiklomanov N. 
Published: July 2003

AbstractDifferences in the summer insulative value of the zonal vegetation mat affect the depth of thaw along the Arctic bioclimate gradient. Toward the south, taller, denser plant canopies and thicker organic horizons counter the effects of warmer temperatures, so that there is little correspondence between active layer depths and summer air temperature. We examined the interactions between summer warmth, vegetation (biomass, Leaf Area Index, Normalized Difference Vegetation Index), soil (texture and pH), and thaw depths at 17 sites in three bioclimate subzones of the Arctic Slope and Seward Peninsula, Alaska. Total plant biomass in subzones C, D, and E averaged 421 g m−2, 503 g m−2, and 1178 g m−2 respectively. Soil organic horizons averaged 4 cm in subzone C, 8 cm in subzone D, and 14 cm in subzone E. The average late‐August thaw depths in subzones C, D, and E were 44 cm, 55 cm, and 47 cm respectively. Non‐acidic soils in equivalent climates generally have shorter‐stature sedge‐dominated canopies and many frost boils, and consequently have thicker active layers than acidic soils. The trends reported here are useful for palaeo‐ecological reconstructions and predictions of future ecosystem changes in the Low Arctic. Climate change will not lead to uniform thickening of the active layer, and could lead to shallower active layers in some presently dry areas due to paludification. Copyright © 2003 John Wiley & Sons, Ltd.
On the analysis of viral load endpoints in HIV vaccine trials
Authors: Hudgens Michael G. , Hoering Antje , Self Steven G. 
Published: July 2003

AbstractFirst generation HIV vaccines are not likely to provide complete protection from HIV‐1 infection. Therefore, it is important to assess a vaccine's effect on disease progression and infectiousness of infected vaccinees in an efficacy trial; however, direct assessment of such vaccine effects is not feasible within current trial designs. Viral load in HIV‐infected individuals correlates with infectiousness and disease progression in a natural history setting, and thus is a reasonable candidate for a surrogate outcome in vaccine efficacy trials. We consider comparisons of viral load of infected vaccinees to that of infected trial participants in the control group. Dramatic differences in viral loads between these groups would suggest a vaccine effect on disease progression. However, modest differences, even if statistically significant, could be consistent with an imperfect vaccine effect on susceptibility to infection and not an effect on disease progression, that is, a selection effect of the vaccine. Thus, the usual statistical tests for no difference between groups do not test the biologically and clinically relevant hypothesis. We propose a model for the possible selective effects of a vaccine and develop several test statistics for assessing a direct effect of the vaccine on viral load given this selection model. Finite sample properties of these tests are evaluated using computer simulations. Copyright © 2003 John Wiley & Sons, Ltd.
Multivariate meta‐analysis
Authors: Nam In‐Sun , Mengersen Kerrie , Garthwaite Paul 
Published: July 2003

AbstractMeta‐analysis is now a standard statistical tool for assessing the overall strength and interesting features of a relationship, on the basis of multiple independent studies. There is, however, recent acknowledgement of the fact that in many applications responses are rarely uniquely determined. Hence there has been some change of focus from a single response to the analysis of multiple outcomes. In this paper we propose and evaluate three Bayesian multivariate meta‐analysis models: two multivariate analogues of the traditional univariate random effects models which make different assumptions about the relationships between studies and estimates, and a multivariate random effects model which is a Bayesian adaptation of the mixed model approach. Our preferred method is then illustrated through an analysis of a new data set on parental smoking and two health outcomes (asthma and lower respiratory disease) in children. Copyright © 2003 John Wiley & Sons, Ltd.
Novel designs for multi‐arm clinical trials with survival outcomes with an application in ovarian cancer
Authors: Royston Patrick , Parmar Mahesh K. B. , Qian Wendi 
Published: July 2003

AbstractWith the increasing pace of drug development, it is not unusual for several promising treatment regimens to be ready simultaneously for testing in a randomized phase III setting. Various limiting factors, including the time needed to transfer research results to clinical practice and a narrow ‘window of opportunity’, may make it unfeasible to perform trials to test such regimens sequentially against a control treatment in a traditional two‐arm parallel group design. We present an approach to trial design based on eliminating inferior contenders at an early stage, allowing through to a second stage only treatments that show a predefined degree of advantage against a control treatment. The first stage of testing utilizes a marker known to be a valid intermediate outcome measure or surrogate for the definitive outcome. The experimental arms are compared pairwise with control according to this intermediate outcome measure. Arms that survive the comparison enter a second stage of patient accrual culminating in comparisons against control on the outcome measure of primary interest. We show how the design may be realized in practice by considering hypothetically distinct trials at stages 1 and 2, each with their own operating characteristics. The overall operating characteristics are computed from the stage 1 and 2 size and power and the correlation between the treatment effects on the intermediate and primary outcome measures according to a bivariate Normal approximation. The correlation is estimated by bootstrapping individual patient data from previous trials. We illustrate the general approach in a design of a real trial of four new chemotherapy regimens for advanced ovarian cancer. The intermediate outcome measure is progression‐free survival. An international randomized controlled trial using the new design is already under way. Copyright © 2003 John Wiley & Sons, Ltd.
Estimating the distribution of lag in the effect of short‐term exposures and interventions: adaptation of a non‐parametric regression spline model
Authors: Rachet B. , Abrahamowicz M. , Sasco A. J. , Siemiatycki J. 
Published: July 2003

AbstractInformation on the distribution of lag duration between exposure or intervention and the subsequent changes in risk can help in assessing the impact of exposure, predicting cost‐effectiveness of intervention, and understanding the underlying biological mechanisms. Previous approaches focused more on optimizing the strength of the exposure–disease association than on directly estimating lag duration. We propose an alternative approach applicable to the analysis of the lagged effects of binary exposure variables. The density function of the distribution of lags is estimated based on flexible modelling of changes in hazard ratio of exposed versus unexposed subjects. The methodology is evaluated in a simulation study and is applied to the Framingham data to investigate the lagged effect of smoking cessation on coronary heart disease risk. Copyright © 2003 John Wiley & Sons, Ltd.
Titrating and evaluating multi‐drug regimens within subjects
Authors: Shih Margaret , Gennings Chris , Chinchilli Vernon M. , Carter Walter H. 
Published: July 2003

AbstractThe dosing of combination therapies is commonly undertaken empirically by practising physicians, and a coherent algorithm to approach the problem of combination dosing is currently lacking. Current methods of evaluating multiple drug combinations in clinical trials fail to provide information regarding the location of more effective doses when the combination is not found to differ from the standard, even though the absence of a difference does not necessarily mean the new combination is ineffective. Moreover, in studies where the new combination is found more effective, often a large proportion of the study participants obtain no benefit from the trial. Even with early stopping rules, the time these subjects spend on inferior treatments can have lasting detrimental effects, leading to problems with patient enrolment and adherence to study protocol. This paper describes an evolutionary operation (EVOP) direct‐search procedure to titrate combination doses within individual patients. The Nelder–Mead simplex direct‐search algorithm is used to titrate combinations of drugs within individual subjects. Desirability functions are utilized to define the main response of interest and additional responses or constraints. Statistical methodology for determining whether the titrated treatment combination has resulted in an improvement in subject response and for evaluating for therapeutic synergism is developed. Inferences can then be made about the efficacy of the combination or about the individual drugs that comprise the combination. The advantages of this approach include affording every patient the potential to benefit from the combination under study and permitting the consideration of multiple endpoints simultaneously. Copyright © 2003 John Wiley & Sons, Ltd.
Predictive accuracy and explained variation
Authors: Schemper Michael 
Published: July 2003

AbstractMeasures of the predictive accuracy of regression models quantify the extent to which covariates determine an individual outcome. Explained variation measures the relative gains in predictive accuracy when prediction based on covariates replaces unconditional prediction. A unified concept of predictive accuracy and explained variation based on the absolute prediction error is presented for models with continuous, binary, polytomous and survival outcomes. The measures are given both in a model‐based formulation and in a formulation directly contrasting observed and expected outcomes. Various aspects of application are demonstrated by examples from three forms of regression models. It is emphasized that the likely degree of absolute or relative predictive accuracy often is low even if there are highly significant and relatively strong covariates. Copyright © 2003 John Wiley & Sons, Ltd.
Over‐expression of wild‐type and mutant HFE in a human melanocytic cell line reveals an intracellular bridge between MHC class I pathway and transferrin iron uptake
Authors: Fergelot Patricia , Orhant Magali , Thénié Agnès , Loyer Pascal , Ropert‐Bouchet Martine , Lohyer Stéphanie , Le Gall Jean‐Yves , Mosser Jean 
Published: July 2003

AbstractHereditary hemochromatosis (HH) is a frequent recessive disorder of iron metabolism characterised by systemic iron overload. In Northern Europe, more than 90% of HH patients are homozygous for a mis‐sense mutation (C282Y) in the HFE1 gene product. The HFE protein is the heavy chain of a MHC class I‐related molecule and associates with β2 microglobulin and the transferrin receptor. Its precise roles in iron metabolism and in the pathophysiology of HH are still unclear. In order to identify the cellular processing of HFE, an important step towards the understanding of the function of the protein, we stably over‐expressed the wild type and mutated forms fused to the Green Fluorescent Protein in a melanocytic MHC class I expressing cell line, the Mel Juso cell line. In wild type and mutant clones, the fusion proteins were not detected at the cell surface but only in the cytoplasm. Their sub‐cellular localisation was determined by co‐labelling of cells with organite‐specific antibodies and confocal microscopy. HFE‐GFP followed initially HLA class I intracellular processing but co‐localised with transferrin in early endosomes without recycling at the cell surface. The C282Y‐GFP fusion protein followed a different folding pathway to exit endoplasmic reticulum. Over‐expression of the wild‐type protein lead to a decrease in diferric transferrin uptake. Our model will be of use in the elucidation of the functional interaction between intracellular HFE and iron transporters transferrin/transferrin receptor complexes and Slc11A2 (also named N‐Ramp2 or DMT1) in different endosomal compartments.
The Different Characteristics of Dupuytren’s Disease Fibroblasts Derived from Either Nodule or Cord: Expression of α-Smooth Muscle Actin and the Response to Stimulation by TGF-β1
Authors: BISSON M. A. , MCGROUTHER D. A. , MUDERA V. , GROBBELAAR A. O. 
Published: July 2003

Mechanisms behind the onset and progression of Dupuytren’s disease are poorly understood. Both myofibroblasts and transforming growth factor beta 1 (TGF-β1) have been implicated. We studied fibroblast cultures derived from nodules or cords of Dupuytren’s contracture tissue to determine the proportion of myofibroblasts present in comparison with flexor retinaculum fibroblast cultures. We identified myofibroblasts by immunohistochemical staining for α-SMA. We then investigated the effects of TGF-β1 stimulation on these fibroblasts. Basal myofibroblast/fibroblast proportions were 9.7% in nodule cell cultures, 2.7% in cord cell cultures and only 1.3% in flexor retinaculum cell cultures. Nodule and cord myofibroblast proportions increased to 25.4% and 24.2%, respectively, in response to TGF-β1 treatment. Flexor retinaculum cell cultures showed no response to TGF-β1 stimulation. Fibroblasts cultured from specific regions of Dupuytren’s tissue retain myofibroblast features in culture. TGF-β1 stimulation causes an increased myofibroblast phenotype to similar levels in both nodule and cord, suggesting that previously quiescent cord fibroblasts can be reactivated to become myofibroblasts by TGF-β1. This could be an underlying reason for high recurrence rates seen after surgery or progression following injury.
A comparison of direct macrofaunal mortality using three types of clam dredges
Authors: Gaspar M.B , Leitão F , Santos M.N , Chícharo L , Dias M.D , Chícharo A , Monteiro C.C 
Published: July 2003

Abstract
The white clam Spisula solida is harvested along the entire coast of Portugal using mechanical dredges. In this study, the total direct mortality of the macrobenthic community caused by three types of clam dredges (north dredge—ND, traditional dredge—TD, and the metallic grid dredge—GD) used in the S. solida fishery was determined and compared. The relationship between mortality and catching efficiency for each type of dredge was also assessed. Our results showed significant differences for total direct mortality between the ND and both the GD and TD dredges. This difference was largely attributed to the mortality of animals that died in the dredge track as a direct result of the physical damage inflicted by the dredge passing. It was also found that the damage to uncaught individuals is directly related to gear efficiency. The lower catching efficiency of the ND (64%) led to a higher proportion of damaged individuals being left in the dredge path, when compared with the more efficient GD (98%) and TD (90%) dredges. Short and long-term implications of the impact of dredging on the composition of benthic communities are discussed. From fisheries management and ecological points of view, there are obvious advantages to introduce into the bivalve dredge fisheries more efficient and selective dredges in order to reduce the number of damaged individuals and by-catch, and consequently decreasing the impact on the macrobenthic communities.
Winter and spring changes in condition factor and energy reserves of wild cod compared with changes observed during food-deprivation in the laboratory
Authors: Dutil Jean-Denis , Lambert Yvan , Chabot Denis 
Published: July 2003

Abstract
Atlantic cod were food-deprived for a period of 84 days at three temperatures (2, 6, 10°C), and changes in the liver, gonads and somatic weights, and muscle and liver water contents were monitored and compared with changes observed in wild cod over winter in the northern Gulf of St. Lawrence. Total lack of food during the period January–April would have caused condition to decline to a level at which very high mortality takes place. Actual changes in condition in wild cod were less than predicted from the laboratory experiments except during the period April–May at the onset of spawning. Thus, wild cod were able to meet part of the metabolic costs during winter through occasional feeding, as confirmed by stomach content data. We conclude that previous estimates of natural mortality associated with poor condition in spring were not biased by the selective mortality of poor-condition fish in winter.
Using AMOEBAs to display multispecies, multifleet fisheries advice
Authors: Collie Jeremy S. , Gislason Henrik , Vinther Morten 
Published: July 2003

Abstract
In multispecies fish communities, predation levels change dynamically in response to changes in the abundance of predator and prey species, as influenced by the fisheries that exploit them. In addition to community-level metrics, it remains necessary to track the abundance of each species relative to its biological reference point. In situations with many interacting species, exploited by multiple fishing fleets, it can be complicated to illustrate how the effort of each fleet will affect the abundance of each species. We have adapted the AMOEBA approach to graph the reference levels of multiple interacting species exploited by multiple fleets. This method is illustrated with 10 species and eight fishing fleets in the North Sea. We fit a relatively simple response-surface model to the predictions of a fully age-structured multispecies model. The response-surface model links the AMOEBA for fishing effort to separate AMOEBAs for spawning stock biomass, fishing mortality, and yield. Ordination is used to give the shape of the AMOEBAs functional meaning by relating fish species to the fleets that catch them. The aim is to present the results of dynamic multispecies models in a format that can be readily understood by decision makers. Interactive versions of the AMOEBAs can be used to identify desirable combinations of effort levels and to test the compatibility of the set of single-species biological reference points.