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Large Regions (large + regions)
Selected AbstractsRejoinder to "Line Transect Sampling in Small and Large Regions"BIOMETRICS, Issue 3 2005G. J. Melville No abstract is available for this article. [source] High density genome-wide DNA profiling reveals a remarkably stable profile in hairy cell leukaemiaBRITISH JOURNAL OF HAEMATOLOGY, Issue 5 2008Francesco Forconi Summary Hairy cell leukaemia (HCL) is a rare B-cell neoplasm for which the molecular mechanisms are largely unknown. High-density genome-wide DNA profiling was performed with Affymetrix 250K arrays to analyse copy number (CN) changes and loss of heterozygosity (LOH) in 16 cases of HCL. Four of 16 cases (25%) demonstrated gross non-recurrent CN deletions. Within the affected regions, we identified genes involved in bone marrow fibrosis (FGF12) and response to treatment (TP53) in individual cases. Large regions (>5 Mb) of LOH without any concomitant DNA CN changes were identified in 5/16 (31%) HCL and were indicative of uniparental disomy UD. The germline origin of UD was demonstrated in one case for which a matched normal sample was available. Overall analysis of LOH showed that identical loci were recurrently targeted in chromosomes 1, 2 and 6. As a whole, however, HCL showed a remarkably stable genome. This finding adds to several other features that are unique to HCL among mature B-cell tumours. [source] Rendering the World Unsafe: ,Vulnerability' as Western DiscourseDISASTERS, Issue 1 2001Gregory Bankoff Disasters seem destined to be major issues of academic enquiry in the new century if for no other reason than that they are inseparably linked to questions of environmental conservation, resource depletion and migration patterns in an increasingly globalised world. Unfortunately, inadequate attention has been directed at considering the historical roots of the discursive framework within which hazard is generally presented, and how that might reflect particular cultural values to do with the way in which certain regions or zones of the world are usually imagined. This paper argues that tropicality, development and vulnerability form part of one and the same essentialising and generalising cultural discourse that denigrates large regions of world as disease-ridden, poverty-stricken and disaster-prone. [source] Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessmentDIVERSITY AND DISTRIBUTIONS, Issue 3 2007Simon Ferrier ABSTRACT Generalized dissimilarity modelling (GDM) is a statistical technique for analysing and predicting spatial patterns of turnover in community composition (beta diversity) across large regions. The approach is an extension of matrix regression, designed specifically to accommodate two types of nonlinearity commonly encountered in large-scaled ecological data sets: (1) the curvilinear relationship between increasing ecological distance, and observed compositional dissimilarity, between sites; and (2) the variation in the rate of compositional turnover at different positions along environmental gradients. GDM can be further adapted to accommodate special types of biological and environmental data including, for example, information on phylogenetic relationships between species and information on barriers to dispersal between geographical locations. The approach can be applied to a wide range of assessment activities including visualization of spatial patterns in community composition, constrained environmental classification, distributional modelling of species or community types, survey gap analysis, conservation assessment, and climate-change impact assessment. [source] A comprehensive framework for global patterns in biodiversityECOLOGY LETTERS, Issue 1 2004Robert E. Ricklefs Abstract The present study proposes to reconcile the different spatial and temporal scales of regional species production and local constraint on species richness. Although interactions between populations rapidly achieve equilibrium and limit membership in ecological communities locally, these interactions occur over heterogeneous environments within large regions, where the populations of species are stably regulated through competition and habitat selection. Consequently, exclusion of species from a region depends on long-term regional-scale environmental change or evolutionary change among interacting populations, bringing species production and extinction onto the same scale and establishing a link between local and regional processes. [source] LAND RICH AND DATA POOR: MODELLING REQUIREMENTS IN AUSTRALIA'S FAR NORTHECONOMIC PAPERS: A JOURNAL OF APPLIED ECONOMICS AND POLICY, Issue 3 2005Natalie Stoeckl Economic models have long been used as a way of organising and presenting information for policy makers interested in large regions,e.g. nations,and recent advances in information technology make the goal of developing models for decision makers in other locales a realistic one. The research on which this paper focuses was part of large project investigating the feasibility and desirability of developing a multi-disciplinary computer model of the Australian Savannas. In the large project, researchers were broken in to three teams: those considering the biophysical, demographic, and economic aspects of the modelling problem. This paper presents findings from part of the economic component of the investigation: that which sought information from key local ,stakeholders' about the type of information that would be useful to them. Responses indicate that many of Australia's existing economic models are capable of providing the ,right' type of information; but at too coarse a geographic scale for those in remote regions. Evidently, there is a need for developing other models. [source] Quantitative tools for perfecting species listsENVIRONMETRICS, Issue 2 2002Michael W. Palmer Abstract A substantial body of literature has accumulated on the topic of the estimation of species richness by extrapolation. However, most of these methods rely on an objective sampling of nature. This condition is difficult to meet and seldom achieved for large regions. Furthermore, scientists conducting biological surveys often already have preliminary but subjectively gathered species lists, and would like to assess the completeness of such lists, and/or to find a way to perfect them. We propose several strategies for utilizing external data (such as might be obtained using GIS) to aid in the completion of species lists. These include: (i) using existing species lists to develop predictive models; (ii) using the uniqueness of the environment as a guide to find underrepresented species; (iii) using spectral heterogeneity to locate environmentally heterogeneous regions; (iv) combining surveys with statistical model-building in an iterative manner. We demonstrate the potential of these approaches using simulation and case studies from Oklahoma. Copyright © 2002 John Wiley & Sons, Ltd. [source] The common fragile site FRA16D and its associated gene WWOX are highly conserved in the mouse at Fra8E1GENES, CHROMOSOMES AND CANCER, Issue 2 2002Kurt A. Krummel Recently, several common fragile sites (CFSs) have been cloned and characterized, including the two most frequently observed in the human population, FRA3B and FRA16D. In addition to their high frequency of breakage, FRA3B and FRA16D colocalize with genes crossing large regions of breakage. At FRA3B, the fragile histidine triad (FHIT) gene spans more than 1 Mb, and at FRA16D, the WWOX gene spans more than 750 kb. It has also been shown that in Mus musculus, a CFS Fra14A2 and the mouse Fhit gene are conserved in the orthologous region of the genome. In this study, we positioned the ortholog to WWOX (Wox1) at chromosome band 8E1 in the mouse genome. To determine whether, like Fra14A2 and Fhit, Fra8E1 and Wox1 colocalized in the mouse, we prepared bacterial and yeast artificial chromosome probes, and we hybridized them to aphidicolin-treated mouse metaphase chromosomes. Our data demonstrate that Wox1 colocalizes with Fra8E1. Furthermore, the sequence from this region, including introns, is highly conserved over at least a 100-kb region. This evolutionary conservation suggests that the two most active CFSs share many features, and that CFSs and their associated genes may be necessary for cell survival. © 2002 Wiley-Liss, Inc. [source] The greening and browning of Alaska based on 1982,2003 satellite dataGLOBAL ECOLOGY, Issue 4 2008David Verbyla Abstract Aim To examine the trends of 1982,2003 satellite-derived normalized difference vegetation index (NDVI) values at several spatial scales within tundra and boreal forest areas of Alaska. Location Arctic and subarctic Alaska. Methods Annual maximum NDVI data from the twice monthly Global Inventory Modelling and Mapping Studies (GIMMS) NDVI 1982,2003 data set with 64-km2 pixels were extracted from a spatial hierarchy including three large regions: ecoregion polygons within regions, ecozone polygons within boreal ecoregions and 100-km climate station buffers. The 1982,2003 trends of mean annual maximum NDVI values within each area, and within individual pixels, were computed using simple linear regression. The relationship between NDVI and temperature and precipitation was investigated within climate station buffers. Results, At the largest spatial scale of polar, boreal and maritime regions, the strongest trend was a negative trend in NDVI within the boreal region. At a finer scale of ecoregion polygons, there was a strong positive NDVI trend in cold arctic tundra areas, and a strong negative trend in interior boreal forest areas. Within boreal ecozone polygons, the weakest negative trends were from areas with a maritime climate or colder mountainous ecozones, while the strongest negative trends were from warmer basin ecozones. The trends from climate station buffers were similar to ecoregion trends, with no significant trends from Bering tundra buffers, significant increasing trends among arctic tundra buffers and significant decreasing trends among interior boreal forest buffers. The interannual variability of NDVI among the arctic tundra buffers was related to the previous summer warmth index. The spatial pattern of increasing tundra NDVI at the pixel level was related to the west-to-east spatial pattern in changing climate across arctic Alaska. There was no significant relationship between interannual NDVI and precipitation or temperature among the boreal forest buffers. The decreasing NDVI trend in interior boreal forests may be due to several factors including increased insect/disease infestations, reduced photosynthesis and a change in root/leaf carbon allocation in response to warmer and drier growing season climate. Main conclusions There was a contrast in trends of 1982,2003 annual maximum NDVI, with cold arctic tundra significantly increasing in NDVI and relatively warm and dry interior boreal forest areas consistently decreasing in NDVI. The annual maximum NDVI from arctic tundra areas was strongly related to a summer warmth index, while there were no significant relationships in boreal areas between annual maximum NDVI and precipitation or temperature. Annual maximum NDVI was not related to spring NDVI in either arctic tundra or boreal buffers. [source] High-resolution mapping of the 8p23.1 beta-defensin cluster reveals strictly concordant copy number variation of all genes,HUMAN MUTATION, Issue 10 2008Marco Groth Abstract One unexpected feature of the human genome is the high structural variability across individuals. Frequently, large regions of the genome show structural polymorphisms and many vary in their abundance. However, accurate methods for the characterization and typing of such copy number variations (CNV) are needed. The defensin cluster at the human region 8p23.1 is one of the best studied CNV regions due to its potential clinical relevance for innate immunity, inflammation, and cancer. The region can be divided into two subclusters, which harbor predominantly either alpha- or beta-defensin genes. Previous studies assessing individual copy numbers gave different results regarding whether the complete beta-defensin cluster varies or only particular genes therein. We applied multiplex ligation-dependent probe amplification (MLPA) to measure defensin locus copy numbers in 42 samples. The data show strict copy number concordance of all 10 loci typed within the beta-defensin cluster in each individual, while seven loci within the alpha-defensin cluster are consistently found as single copies per chromosome. The exception is DEFA3, which is located within the alpha-defensin cluster and was found to also differ in copy number interindividually. Absolute copy numbers ranged from two to nine for the beta-defensin cluster and zero to four for DEFA3. The CNV-typed individuals, including HapMap samples, are publicly available and may serve as a universal reference for absolute copy number determination. On this basis, MLPA represents a reliable technique for medium- to high-throughput typing of 8p23.1 defensin CNV in association studies for diverse clinical phenotypes. Hum Mutat 0,1,8, 2008. © 2008 Wiley-Liss, Inc. [source] Spatial variability of snowmelt timing from AMSR-E and SSM/I passive microwave sensors, Pelly River, Yukon Territory, CanadaHYDROLOGICAL PROCESSES, Issue 12 2007Joan M. Ramage Abstract Spring snow melt run-off in high latitude and snow-dominated drainage basins is generally the most significant annual hydrological event. Melt timing, duration, and flow magnitude are highly variable and influence regional climate, geomorphology, and hydrology. Arctic and sub-arctic regions have sparse long-term ground observations and these snow-dominated hydrologic regimes are sensitive to the rapidly warming climate trends that characterize much of the northern latitudes. Passive microwave brightness temperatures are sensitive to changes in the liquid water content of the snow pack and make it possible to detect incipient melt, diurnal melt-refreeze cycles, and the approximate end of snow cover on the ground over large regions. Special Sensor Microwave Imager (SSM/I) and Advanced Microwave Scanning Radiometer for EOS (AMSR-E) passive microwave brightness temperatures (Tb) and diurnal amplitude variations (DAV) are used to investigate the spatial variability of snowmelt onset timing (in two stages, ,DAV onset' and ,melt onset') and duration for a complex sub-arctic landscape during 2005. The satellites are sensitive to small percentages of liquid water, and therefore represent ,incipient melt', a condition somewhat earlier than a traditional definition of a melting snowpack. Incipient melt dates and duration are compared to topography, land cover, and hydrology to investigate the strength and significance of melt timing in heterogeneous landscapes in the Pelly River, a major tributary to the Yukon River. Microwave-derived melt onset in this region in 2005 occurred from late February to late April. Upland areas melt 1,2 weeks later than lowland areas and have shorter transition periods. Melt timing and duration appear to be influenced by pixel elevation, aspect, and uniformity as well as other factors such as weather and snow mass distribution. The end of the transition season is uniform across sensors and across the basin in spite of a wide variety of pixel characteristics. Copyright © 2007 John Wiley & Sons, Ltd. [source] Identification of 2 putative critical segments of 17q gain in neuroblastoma through integrative genomicsINTERNATIONAL JOURNAL OF CANCER, Issue 5 2008Jo Vandesompele Abstract Partial gain of chromosome arm 17q is the most frequent genetic change in neuroblastoma (NB) and constitutes the strongest independent genetic factor for adverse prognosis. It is assumed that 1 or more genes on 17q contribute to NB pathogenesis by a gene dosage effect. In the present study, we applied chromosome 17 tiling path BAC arrays on a panel of 69 primary tumors and 28 NB cell lines in order to reduce the current smallest region of gain and facilitate identification of candidate dosage sensitive genes. In all tumors and cell lines with 17q gain, large distal segments were consistently present in extra copies and no interstitial gains were observed. In addition to these large regions of distal gain with breakpoints proximal to coordinate 44.3 Mb (17q21.32), smaller regions of gain (distal to coordinate 60 Mb at 17q24.1) were found superimposed on the larger region in a minority of cases. Positional gene enrichment analysis for 17q genes overexpressed in NB showed that dosage sensitive NB oncogenes are most likely located in the gained region immediately distal to the most distal breakpoint of the 2 breakpoint regions. Interestingly, comparison of gene expression profiles between primary tumors and normal fetal adrenal neuroblasts revealed 2 gene clusters on chromosome 17q that are overexpressed in NB, i.e. a region on 17q21.32 immediately distal to the most distal breakpoint (in cases with single regions of gain) and 17q24.1, a region coinciding with breakpoints leading to superimposed gain. © 2007 Wiley-Liss, Inc. [source] Human papillomavirus type distribution in invasive cervical cancer and high-grade cervical lesions: A meta-analysis updateINTERNATIONAL JOURNAL OF CANCER, Issue 3 2007Jennifer S. Smith Abstract Data on human papillomavirus (HPV) type distribution in invasive and pre-invasive cervical cancer is essential to predict the future impact of HPV16/18 vaccines and HPV-based screening tests. A meta-analyses of HPV type distribution in invasive cervical cancer (ICC) and high-grade squamous intraepithelial lesions (HSIL) identified a total of 14,595 and 7,094 cases, respectively. In ICC, HPV16 was the most common, and HPV18 the second most common, type in all continents. Combined HPV16/18 prevalence among ICC cases was slightly higher in Europe, North America and Australia (74,77%) than in Africa, Asia and South/Central America (65,70%). The next most common HPV types were the same in each continent, namely HPV31, 33, 35, 45, 52 and 58, although their relative importance differed somewhat by region. HPV18 was significantly more prevalent in adeno/adenosquamous carcinoma than in squamous cell carcinoma, with the reverse being true for HPV16, 31, 33, 52 and 58. Among HSIL cases, HPV16/18 prevalence was 52%. However, HPV 16, 18 and 45 were significantly under-represented, and other high-risk HPV types significantly over-represented in HSIL compared to ICC, suggesting differences in type-specific risks for progression. Data on HPV-typed ICC and HSIL cases were particularly scarce from large regions of Africa and Central Asia. © 2007 Wiley-Liss, Inc. [source] A novel dual-mode predictive control strategy for constrained Wiener systemsINTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL, Issue 9 2010Hai-Tao Zhang Abstract In process industry, there exist many Wiener systems with input magnitude constraints for which, however, most of the existing control algorithms cannot guarantee to have sufficiently large regions of asymptotic stability. In this paper, the subspace method is applied to separate the nonlinear and linear blocks in a constrained multi-input/multi-output (MIMO) Wiener system and a novel dual-mode nonlinear model predictive control algorithm is developed to maximize the region of the asymptotic stability. Simulation results are presented to demonstrate the virtues of this new control algorithm. The limitation is the requirement that the state and input matrices of the Wiener system's linear block should be accurately identified. Copyright © 2009 John Wiley & Sons, Ltd. [source] Spatial arrangement and macrodomain organization of bacterial chromosomesMOLECULAR MICROBIOLOGY, Issue 1 2005Frédéric Boccard Summary Recent developments in fluorescence microscopy have shown that bacterial chromosomes have a defined spatial arrangement that preserves the linear order of genes on the genetic map. These approaches also revealed that large portions of the chromosome in Escherichia coli or Bacillus subtilis are concentrated in the same cellular space, suggesting an organization as large regions defined as macrodomains. In E. coli, two macrodomains of 1 Mb containing the replication origin (Ori) and the replication terminus (Ter) have been shown to relocalize at specific steps of the cell cycle. A genetic analysis of the collision probability between distant DNA sites in E. coli has confirmed the presence of macrodomains by revealing the existence of large regions that do not collide with each other. Two macrodomains defined by the genetic approach coincide with the Ori and Ter macrodomains, and two new macrodomains flanking the Ter macrodomain have been identified. Altogether, these results indicate that the E. coli chromosome has a ring organization with four structured and two less-structured regions. Implications for chromosome dynamics during the cell cycle and future prospects for the characterization and understanding of macrodomain organization are discussed. [source] Evaluation of the anti-vascular effects of combretastatin in rodent tumours by dynamic contrast enhanced MRINMR IN BIOMEDICINE, Issue 2 2002Ross J. Maxwell The anti-vascular effects of the tubulin binding agent, disodium combretastatin A-4 3- O -phosphate (CA-4-P), have been investigated in the rat P22 carcinosarcoma by measurements of radiolabelled iodoantipyrine uptake and dynamic contrast-enhanced MRI. The iodoantipyrine estimates of absolute tumour blood flow showed a reduction from 0.35 to 0.04,ml g,1 min,1 6,h after 10,mg kg,1 CA-4-P and to <0.01,ml g,1 min,1 after 100,mg kg,1. Tumour blood flow recovered to control values 24,h after 10,mg kg,1 CA-4-P, but there was no recovery by 24,h after the higher dose. Dynamic contrast-enhanced MR images were obtained at 4.7 T, following injection of 0.1,mmol kg,1 Gd-DTPA and analysed assuming a model arterial input function. A parameter, Ktrans, which is related to blood flow rate and permeability of the tumour vasculature to Gd-DTPA, was calculated from the uptake data. Ktrans showed a reduction from 0.34 to 0.11 min,1 6,h after 10,mg kg,1 CA-4-P and to 0.07 min,1 after 100,mg kg,1. Although the magnitude of changes in Ktrans was smaller than that in tumour blood flow, the time course and dose-dependency patterns were very similar. The apparent extravascular extracellular volume fraction, ,e, showed a four-fold reduction 6,h after 100,mg kg,1 CA-4-P, possibly associated with vascular shutdown within large regions of the tumour. These results suggest that Ktrans values for Gd-DTPA uptake into tumours could be a useful non-invasive indicator of blood flow changes induced by anti-vascular agents such as combretastatin. Copyright © 2002 John Wiley & Sons, Ltd. [source] Genotyping single nucleotide polymorphisms using intact polymerase chain reaction products by electrospray quadrupole mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 18 2001James J. Walters Both single nucleotide polymorphisms (SNPs) and mutations are commonly observed in the gene encoding the tumor suppressor protein, p53. SNPs occur at specific locations within genes whereas mutations may be distributed across large regions of genes. When determining nucleotide differences, mass spectrometry is the only method other than Sanger sequencing which offers direct structural information. Electrospray ionization (ESI) quadrupole mass spectrometry (MS) analysis of intact polymerase chain reaction (PCR) products was performed following a simple purification and on-line heating to limit ion adduction. The PCR products were amplified directly from genomic DNA rather than plasmids, as in our previous work. Two known polymorphisms of the p53 gene were genotyped. A cytosine (C) or guanine (G) transversion, designated C,,,G (G,,,C on the opposite strand), were each detected by a 40.0,Da change upon ESI quadrupole MS analysis. Using known PCR products as standards, the genotypes determined for 10 human samples corresponded with restriction fragment length polymorphism (RFLP) analysis. Cytosine/thymine (T) transitions, designated C,,,T (G,,,A on the opposite strand), were also genotyped by ESI-MS. This SNP is discriminated by a 15.0,Da change on one strand (C,,,T) and a 16.0,Da change on the other (G,,,A). Appropriate sample preparation and instrumental configuration (including heated sample inlet syringe and MS source), to limit adducts, are both vital for successful ESI quadrupole MS analysis of intact PCR products. Copyright © 2001 John Wiley & Sons, Ltd. [source] Impact study of the 2003 North Atlantic THORPEX Regional CampaignTHE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 615 2006Nadia Fourrié Abstract An experiment took place during autumn 2003 with the aim of testing the feasibility of an operational targeting of observations over the North Atlantic Ocean in the context of the international programme THORPEX. The purpose of this paper is to evaluate the impact of these additional observations in the French operational model ARPEGE during the last three weeks of the campaign. Results are shown for large regions over and around the North Atlantic Ocean and for specific verification areas. Over Europe, the addition of observations is slightly beneficial for the forecast, mostly in the low troposphere over wide areas and above 100 hPa. However, the impact of extra data is more significant but also more mixed for the dedicated verification areas: they are case, forecast-range and level dependent. In addition, the information content is studied with the Degrees of Freedom for Signal (DFS) for the evaluation of the observation impact on the analysis of one case of December 2003. Firstly, the variations of the DFS have been illustrated in a simplified data assimilation system. It has been found for that case that satellite data have the most important global contribution to the overall analysis, especially the humidity sensitive infrared radiances. For the conventional data, the wind measurements of the aircraft and from the geostationary satellites are the most informative. For the targeted area, the data from aircraft and the dropsondes have the largest DFS. It has been noted that the DFS of the dropsondes located in the sensitivity maximum is larger than the other one even if there is no link between the DFS and the forecast. However, the impact of the dropsondes grows with respect to the forecast range and leads to an improvement of the forecast for this case. Copyright © 2006 Royal Meteorological Society [source] Hydrological seasonal forecast over France: feasibility and prospectsATMOSPHERIC SCIENCE LETTERS, Issue 2 2010J.-P. Céron Abstract This article presents a first evaluation of a hydrological forecasting suite at seasonal time scales over France. The hydrometeorological model SAFRAN-ISBA-MODCOU is forced by seasonal forecasts from the DEMETER project for the March,April,May period. Despite a simple downscaling method, the atmospheric forcings are reasonably well represented at the finest scale. The computed soil moisture shows some predictability with large regions of correlation above 0.3. Probabilistic scores for soil moisture and river flows for four different catchments are higher than that for atmospheric variables. These results suggest to go further for building an operational hydrological seasonal forecast system. Copyright © 2010 Royal Meteorological Society [source] MRSA in Austria,an overviewCLINICAL MICROBIOLOGY AND INFECTION, Issue 3 2008K. Krziwanek Abstract The aim of this study was to provide an overview of predominant and sporadic methicillin-resistant Staphylococcus aureus (MRSA) strains in large regions of Austria, and to compare the results with those from other European countries. In total, 1439 MRSA isolates, collected routinely between January 1996 and June 2006 from five Austrian federal provinces, were investigated. The isolates were confirmed as MRSA using mecA/femA multiplex PCR assays. Genes encoding Panton-Valentine leukocidin (PVL), which are characteristic of community-acquired MRSA, were also detected by PCR. Subtyping was performed using SmaI macrorestriction digestion of genomic DNA, followed by pulsed-field gel electrophoresis (PFGE) and cluster analysis. Isolates that could not be assigned to clusters were further analysed by spa typing and/or multilocus sequence typing. The predominant clones detected in Austria were ST228 (southern German epidemic clone), ST5 (Rhine-Hessen MRSA), the ST8 Austrian clone and CC8/ST8. Whereas the frequencies of lineages corresponding to ST247, ST45 and ST22 remained comparably low, an increase in the frequency of lineages corresponding to ST5 and to ST228 was recorded. Overall, 20 different MRSA types and 321 subtypes were recognised according to PFGE analysis. The prevalence of different strains varied considerably in the different Austrian regions. When compared to other European countries, the situation in Austria was most similar to that found in Germany. [source] | |||||||||||||||||||||||||