905 resultados para Challenge posed by omics data to compositional analysis-paucity of independent samples (n)


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The number of remote sensing platforms and sensors rises almost every year, yet much work on the interpretation of land cover is still carried out using either single images or images from the same source taken at different dates. Two questions could be asked of this proliferation of images: can the information contained in different scenes be used to improve the classification accuracy and, what is the best way to combine the different imagery? Two of these multiple image sources are MODIS on the Terra platform and ETM+ on board Landsat7, which are suitably complementary. Daily MODIS images with 36 spectral bands in 250-1000 m spatial resolution and seven spectral bands of ETM+ with 30m and 16 days spatial and temporal resolution respectively are available. In the UK, cloud cover may mean that only a few ETM+ scenes may be available for any particular year and these may not be at the time of year of most interest. The MODIS data may provide information on land cover over the growing season, such as harvest dates, that is not present in the ETM+ data. Therefore, the primary objective of this work is to develop a methodology for the integration of medium spatial resolution Landsat ETM+ image, with multi-temporal, multi-spectral, low-resolution MODIS \Terra images, with the aim of improving the classification of agricultural land. Additionally other data may also be incorporated such as field boundaries from existing maps. When classifying agricultural land cover of the type seen in the UK, where crops are largely sown in homogenous fields with clear and often mapped boundaries, the classification is greatly improved using the mapped polygons and utilising the classification of the polygon as a whole as an apriori probability in classifying each individual pixel using a Bayesian approach. When dealing with multiple images from different platforms and dates it is highly unlikely that the pixels will be exactly co-registered and these pixels will contain a mixture of different real world land covers. Similarly the different atmospheric conditions prevailing during the different days will mean that the same emission from the ground will give rise to different sensor reception. Therefore, a method is presented with a model of the instantaneous field of view and atmospheric effects to enable different remote sensed data sources to be integrated.

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The authors would like to thank the College of Life Sciences of Aberdeen University and Marine Scotland Science which funded CP's PhD project. Skate tagging experiments were undertaken as part of Scottish Government project SP004. We thank Ian Burrett for help in catching the fish and the other fishermen and anglers who returned tags. We thank José Manuel Gonzalez-Irusta for extracting and making available the environmental layers used as environmental covariates in the environmental suitability modelling procedure. We also thank Jason Matthiopoulos for insightful suggestions on habitat utilization metrics as well as Stephen C.F. Palmer, and three anonymous reviewers for useful suggestions to improve the clarity and quality of the manuscript.

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Tässä työssä perehdytään soodakattiloiden vesikiertomallin rakentamiseen. Työn päätavoitteena on kehittää simulointimallia varten taulukkolaskentapohja, jonka avulla soodakattilan lämpövuotietoja on yksinkertaista ja nopeaa käsitellä ja siirtää Apros 6 -simulointiohjelmaan. Lisäksi tarkoituksena on pyrkiä automatisoimaan työvaiheet mahdollisimman pitkälle, jolloin vesikiertolaskennan tekeminen yksinkertaistuisi, yhtenäistyisi ja tarkentuisi. Tämä on mahdollista Excel- makrojen ja Apros 6:n uusien toimintojen avulla. Apros 6:ssa on nyt mahdollista hyödyntää SCL- komentotiedostoja, joiden avulla sujuva tiedonsiirto Aproksen ja Excelin välillä vodaan toteuttaa. Vesikiertolaskentaan käytettävän datan käsittely on aikaisemmin ollut työlästä ja sen tarkkuus on pitkälti riippunut mallintajasta. Tässä diplomityössä päästään hyödyntämään uusimpia ja realistisempia soodakattiloiden CFD- malleja, joiden avulla pystytään luomaan aikaisempaa tarkemmat lämpövuojakaumat soodakattilan lämpöpinnoille. Tämä muutos parantaa vesikiertolaskennan tarkkuutta. Työn kokeellisessa osassa uutta Excel laskentatyökalua ja uusia lämpövuoarvoja testataan käytännössä. Eräs vanha Apros- vesikiertomalli päivitetään uusilla lämpövuoarvoilla ja sen rakenteeseen tehdään muutoksia tarkkuuden parantamiseksi. Uuden mallin toimivuutta testataan myös 115 %:n kapasiteetilla ja tutkitaan kuinka kyseinen vesikiertopiiri reagoi suurempaan lämpötehoon. Näitä kolmea eri tilannetta vertaillaan toisiinsa ja tarkastellaan eroavaisuuksia niiden vesi-höyrypiireissä.

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A microbiopsy system for fast excision and transfer of biological specimens from donor to high-pressure freezer was developed. With a modified, commercially available, Promag 1.2 biopsy gun, tissue samples can be excised with a size small enough (0.6 mm x 1.2 mm x 0.3 mm) to be easily transferred into a newly designed specimen platelet. A self-made transfer unit allows fast transfer of the specimen from the needle into the specimen platelet. The platelet is then fixed in a commercially available specimen holder of a high-pressure freezing machine (EM PACT, Leica Microsystems, Vienna, Austria) and frozen therein. The time required by a well-instructed (but not experienced) person to execute all steps is in the range of half a minute. This period is considered short enough to maintain the excised tissue pieces close to their native state. We show that a range of animal tissues (liver, brain, kidney and muscle) are well preserved. To prove the quality of freezing achieved with the system, we show vitrified ivy leaves high-pressure frozen in the new specimen platelet.

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Soil aggregation is an index of soil structure measured by mean weight diameter (MWD) or scaling factors often interpreted as fragmentation fractal dimensions (D-f). However, the MWD provides a biased estimate of soil aggregation due to spurious correlations among aggregate-size fractions and scale-dependency. The scale-invariant D-f is based on weak assumptions to allow particle counts and sensitive to the selection of the fractal domain, and may frequently exceed a value of 3, implying that D-f is a biased estimate of aggregation. Aggregation indices based on mass may be computed without bias using compositional analysis techniques. Our objective was to elaborate compositional indices of soil aggregation and to compare them to MWD and D-f using a published dataset describing the effect of 7 cropping systems on aggregation. Six aggregate-size fractions were arranged into a sequence of D-1 balances of building blocks that portray the process of soil aggregation. Isometric log-ratios (ilrs) are scale-invariant and orthogonal log contrasts or balances that possess the Euclidean geometry necessary to compute a distance between any two aggregation states, known as the Aitchison distance (A(x,y)). Close correlations (r>0.98) were observed between MWD, D-f, and the ilr when contrasting large and small aggregate sizes. Several unbiased embedded ilrs can characterize the heterogeneous nature of soil aggregates and be related to soil properties or functions. Soil bulk density and penetrater resistance were closely related to A(x,y) with reference to bare fallow. The A(x,y) is easy to implement as unbiased index of soil aggregation using standard sieving methods and may allow comparisons between studies. (C) 2012 Elsevier B.V. All rights reserved.

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Data in germplasm collections contain a mixture of data types; binary, multistate and quantitative. Given the multivariate nature of these data, the pattern analysis methods of classification and ordination have been identified as suitable techniques for statistically evaluating the available diversity. The proximity (or resemblance) measure, which is in part the basis of the complementary nature of classification and ordination techniques, is often specific to particular data types. The use of a combined resemblance matrix has an advantage over data type specific proximity measures. This measure accommodates the different data types without manipulating them to be of a specific type. Descriptors are partitioned into their data types and an appropriate proximity measure is used on each. The separate proximity matrices, after range standardisation, are added as a weighted average and the combined resemblance matrix is then used for classification and ordination. Germplasm evaluation data for 831 accessions of groundnut (Arachis hypogaea L.) from the Australian Tropical Field Crops Genetic Resource Centre, Biloela, Queensland were examined. Data for four binary, five ordered multistate and seven quantitative descriptors have been documented. The interpretative value of different weightings - equal and unequal weighting of data types to obtain a combined resemblance matrix - was investigated by using principal co-ordinate analysis (ordination) and hierarchical cluster analysis. Equal weighting of data types was found to be more valuable for these data as the results provided a greater insight into the patterns of variability available in the Australian groundnut germplasm collection. The complementary nature of pattern analysis techniques enables plant breeders to identify relevant accessions in relation to the descriptors which distinguish amongst them. This additional information may provide plant breeders with a more defined entry point into the germplasm collection for identifying sources of variability for their plant improvement program, thus improving the utilisation of germplasm resources.

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As the gap between processor and memory continues to grow Memory performance becomes a key performance bottleneck for many applications. Compilers therefore increasingly seek to modify an application’s data layout to improve cache locality and cache reuse. Whole program Structure Layout [WPSL] transformations can significantly increase the spatial locality of data and reduce the runtime of programs that use link-based data structures, by increasing the cache line utilization. However, in production compilers WPSL transformations do not realize the entire performance potential possible due to a number of factors. Structure layout decisions made on the basis of whole program aggregated affinity/hotness of structure fields, can be sub optimal for local code regions. WPSL is also restricted in applicability in production compilers for type unsafe languages like C/C++ due to the extensive legality checks and field sensitive pointer analysis required over the entire application. In order to overcome the issues associated with WPSL, we propose Region Based Structure Layout (RBSL) optimization framework, using selective data copying. We describe our RBSL framework, implemented in the production compiler for C/C++ on HP-UX IA-64. We show that acting in complement to the existing and mature WPSL transformation framework in our compiler, RBSL improves application performance in pointer intensive SPEC benchmarks ranging from 3% to 28% over WPSL

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Rapid adaptation and tolerance is a phenomenon experienced by a variety of organisms typically because of new and harsh environments. Mimulus guttatus, a plant commonly seen on the west coast of the United States, is a prime example as it has rapidly evolved to soil contamination by copper due to mining in California in the last 150 years. There have been two hypotheses posed by researchers as to the genetic basis of how organisms have evolved so quickly which I set out to study: 1) There is a low frequency of tolerant genotypes in the ancestral population otherwise known as standing variation or 2) new mutations occurred once exposed to a new environment. In the past, researchers found it difficult to distinguish between the two because they lacked the technology we have today for DNA analysis. I used four different populations of M. guttatus from varying locations in order to address which hypothesis was valid. I conducted both survival assays of these populations and DNA analysis of known tolerant and non-tolerant lines using a copper oxidase gene. I found that there was at least some degree of tolerance in all populations in the survival assays, supporting the hypothesis of standing variation. I also found patterns within DNA analysis suggesting the copper oxidase gene would be useful for further study to verify the standing variation hypothesis. The results from this experiment helps in understanding rapid evolution not just in the context of soil contamination by metals but also ties back to why an alarming number of species are not able to adapt to our constantly changing world.

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Over recent years, the focus in road safety has shifted towards a greater understanding of road crash serious injuries in addition to fatalities. Police reported crash data are often the primary source of crash information; however, the definition of serious injury within these data is not consistent across jurisdictions and may not be accurately operationalised. This study examined the linkage of police-reported road crash data with hospital data to explore the potential for linked data to enhance the quantification of serious injury. Data from the Queensland Road Crash Database (QRCD), the Queensland Hospital Admitted Patients Data Collection (QHAPDC), Emergency Department Information System (EDIS), and the Queensland Injury Surveillance Unit (QISU) for the year 2009 were linked. Nine different estimates of serious road crash injury were produced. Results showed that there was a large amount of variation in the estimates of the number and profile of serious road crash injuries depending on the definition or measure used. The results also showed that as the definition of serious injury becomes more precise the vulnerable road users become more prominent. These results have major implications in terms of how serious injuries are identified for reporting purposes. Depending on the definitions used, the calculation of cost and understanding of the impact of serious injuries would vary greatly. This study has shown how data linkage can be used to investigate issues of data quality. It has also demonstrated the potential improvements to the understanding of the road safety problem, particularly serious injury, by conducting data linkage.

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Inter-simple sequence repeat (ISSR) analysis was used to assess genetic diversity among 10 pairs of male and female Laminaria gametophytes. A total of 58 amplification loci was obtained from 10 selected ISSR primers, of which 34 revealed polymorphism among the gametophytes. Genetic distances were calculated with the Dice coefficient ranging from 0.006 to 0.223. A dendrogram based on the unweighted pair-group method arithmetic (UPGMA) average showed that most male and female gametophytes of the same species were clustered together and that 10 pairs of gametophytes were divided into four groups. This was generally consistent with the taxonomic categories. The main group consisted of six pairs of gametophytes, which were selected from Laminaria japonica Aresch. by intensive inbreeding through artificial hybridization. One specific marker was cloned, but was not converted successfully into a sequence characterized amplified region (SCAR) marker. Our results demonstrate the feasibility of applying ISSR markers to evaluate Laminaria germplasm diversities.

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Background: There is insufficient evidence for the efficacy of comprehensive multiple risk factor interventions by pharmacists in the primary prevention of cardiovascular disease (CVD). Given the proven benefits of pharmacist interventions for individual risk factors, it is essential that evidence for a comprehensive approach to care be generated so that pharmacists remain key members of the health care team for individuals at risk of initial onset of CVD. Objective: To establish the feasibility of an intervention delivered by community pharmacists to reduce the risk of primary onset of CVD.
Methods: A single-cohort intervention study was undertaken in 2008-2009. Twelve community pharmacists from 10 pharmacies who were trained to provide lifestyle and medicine management support to reduce CVD risk recruited 70 at-risk participants aged 50-74 years who were free from diabetes or CVD. Participants received a baseline assessment to establish CVD risk and health behaviors. An assessment report provided to patients and pharmacists was used to collaboratively establish treatment goals and, over 5 sessions, implement treatment strategies. Follow-up assessment at 6 months measured changes in baseline parameters. The primary outcome was the average change to overall 5-year risk of CVD onset.
Results:
Sixty-seven participants were included in the analysis. The mean participant age was 60 years and 73% were female. We observed a 25% (95% CI 17 to 33) proportional risk reduction in overall CVD risk. Significant reductions also occurred in mean blood pressure (-11/-5 mm Hg) and waist circumference (-1.3 cm), with trends toward improvement for most other observed risk factors.
Conclusions: Findings support previous evidence of positive cardiovascular health outcomes following pharmacist intervention in other patient groups; we recommend generating randomized controlled trial evidence for a primary prevention population.

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Cytomegalovirus (CMV) infection is associated with significant morbidity and mortality in transplant recipients. Resistance against ganciclovir is increasingly observed. According to current guidelines, direct drug resistance testing is not always performed due to high costs and work effort, even when resistance is suspected.

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In the present study, proxy data concerning changes in atmospheric CO2 and climatic conditions from the Late Eocene to the Early Miocene were acquired by applying palaeobotanical methods. Fossil floras from 10 well-documented locations in Saxony, Germany, were investigated with respect to (1) stomatal density/index of fossil leaves from three different taxa (Eotrigonobalanus furcinervis, Laurophyllum pseudoprinceps and Laurophyllum acutimontanum), (2) the coexistence approach (CA) based on nearest living relatives (NLR) and (3) leaf margin analysis (LMA). Whereas the results of approach (1) indicate changes in atmospheric CO2 concentration, approaches (2) and (3) provide climate data. The results of the analysis of stomatal parameters indicate that the atmospheric CO2 concentration was higher during the Late Eocene than during the Early Oligocene and increased towards the Late Oligocene. A lower atmospheric pCO2 level after the Late Eocene is also suggested by an increase in marine palaeoproductivity at this time. From the Late Oligocene onwards, no changes in atmospheric CO2 concentration can be detected with the present data. For the considered sites, the results of the coexistence approach and of the leaf margin analysis document a significant cooling event from the Late Eocene to the Early Oligocene. The pCO2 decrease from the Late Eocene to the Early Oligocene indicated by the stomatal data raised in this study was thus coupled to a temperature decrease which is reflected by the present datasets. From the Early Oligocene onwards, however, no further fundamental climate change can be inferred for the considered locations. The pCO2 increase from the Early Oligocene to the Late Oligocene, which is indicated by the present data, is thus not accompanied by a climate change at the considered sites. A warming event during the Late Oligocene is, however, recorded by marine climate archives. According to the present data, no change in pCO2 occurred during the cooling event at the Oligocene/Miocene boundary, which is also indicated by marine data. The quality and validity of stomatal parameters as sensors for atmospheric CO2 concentration are discussed.