Bayesian quantification for coherent anti-Stokes Raman scattering spectroscopy

We propose a Bayesian statistical model for analyzing coherent anti-Stokes Raman scattering (CARS) spectra. Our quantitative analysis includes statistical estimation of constituent line-shape parameters, underlying Raman signal, error-corrected CARS spectrum, and the measured CARS spectrum. As such, this work enables extensive uncertainty quantification in the context of CARS spectroscopy. Furthermore, we present an unsupervised method for improving spectral resolution of Raman-like spectra requiring little to no \textit{a priori} information. Finally, the recently-proposed wavelet prism method for correcting the experimental artefacts in CARS is enhanced by using interpolation techniques for wavelets. The method is validated using CARS spectra of adenosine mono-, di-, and triphosphate in water, as well as, equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose

Introduction to Dynamic Linear Models for Time Series Analysis

Dynamic linear models (DLM) offer a very generic framework to analyse time series data. Many classical time series models can be formulated as DLMs, including ARMA models and standard multiple linear regression models. The models can be seen as general regression models where the coefficients can vary in time. In addition, they allow for a state space representation and a formulation as hierarchical statistical models, which in turn is the key for efficient estimation by Kalman formulas and by Markov chain Monte Carlo (MCMC) methods. A dynamic linear model can handle non-stationary processes, missing values and non-uniform sampling as well as observations with varying accuracies. This chapter gives an introduction to DLM and shows how to build various useful models for analysing trends and other sources of variability in geodetic time series.Comment: A chapter submitted to a book with a proposed title: Geodetic Time Series Analysis and Applications, editors. J.-P. Montillet and M. Bo

Spatial and temporal variation in community composition of herbivorous insects on Neoboutonia macrocalyx in a primary tropical rain forest

Spatial and temporal variation of tropical insect communities has rarely been studied, although such variation influences estimates of global species richness. Therefore, we compared spatial and temporal variation of herbivorous insect communities on Neoboutonia macrocalyx trees among seven sites over 1 y in a primary tropical rain forest in Kibale National Park, Uganda. The distance between the study sites varied from 4.8 to 31.2 km and altitudinal differences ranged from 20 to 242 m. Permutational multivariate analysis of variance (PERMANOVA) revealed significant spatial changes in community composition of the herbivorous insects and study sites differed also in insect abundance (6.9-26.2 individuals m−2 of leaf area). This is likely to be caused by differences in vegetation, altitude and microclimate among the study sites. The similarity of insect species composition was negatively correlated with geographic and altitudinal distances among sites and positively correlated with the similarity of tree community composition. Species richness varied significantly between sampling dates, ranging from 33 to 41 species. Also community compositions changed between sampling dates, which likely follows from marked seasonal changes in climate and the phenology of other host plants used by the generalist insect species also living on Neoboutonia macrocalyx. In general our study supports the idea of high variability of herbivorous insect communities in primary rain forests even at a small spatial scale. This should be considered when estimations of insect biodiversity are mad

A minor role of asparaginase in predisposing to cerebral venous thromboses in adult acute lymphoblastic leukemia patients

Cerebral venous thrombosis (CVT) covers up to a third of all venous thromboses (VTs) detected in patients with acute lymphoblastic leukemia (ALL). It usually hampers patients' lives and may also endanger efficient leukemia treatment. Although many factors have been suggested to account for an elevated risk of VTs in patients with ALL, there still is a lack of studies focusing on CVTs and especially in the setting of adult ALL patients. We studied in our retrospective population-based cohort the occurrence, characteristics, as well as risk factors for VTs in 186 consecutively diagnosed Finnish adult ALL patients treated with a national pediatric-inspired treatment protocol ALL2000. In the risk factor analyses for VTs we found a distinction of the characteristics of the patients acquiring CVT from those with other kinds of VTs or without thrombosis. In contrast to previous studies we were also able to compare the effects of asparaginase in relation to CVT occurrence. Notably, more than half of the CVTs were diagnosed prior the administration of asparaginase which accentuates the role of other risk factors on the pathophysiology of CVT compared to truncal or central venous line (CVL) VTs in adult ALL patients

European Red List of Habitats Part 1. Marine habitats

The European Red List of Habitats provides an overview of the risk of collapse (degree of endangerment) of marine, terrestrial and freshwater habitats in the European Union (EU28) and adjacent regions (EU28+), based on a consistent set of categories and criteria, and detailed data and expert knowledge from involved countries1. A total of 257 benthic marine habitat types were assessed. In total, 19% (EU28) and 18% (EU28+) of the evaluated habitats were assessed as threatened in categories Critically Endangered, Endangered and Vulnerable. An additional 12% were Near Threatened in the EU28 and 11% in the EU28+. These figures are approximately doubled if Data Deficient habitats are excluded. The percentage of threatened habitat types differs across the regional seas. The highest proportion of threatened habitats in the EU28 was found in the Mediterranean Sea (32%), followed by the North-East Atlantic (23%), the Black Sea (13%) and then the Baltic Sea (8%). There was a similar pattern in the EU28+. The most frequently cited pressures and threats were similar across the four regional seas: pollution (eutrophication), biological resource use other than agriculture or forestry (mainly fishing but also aquaculture), natural system modifications (e.g. dredging and sea defence works), urbanisation and climate change. Even for habitats where the assessment outcome was Data Deficient, the Red List assessment process has resulted in the compilation of a substantial body of useful information to support the conservation of marine habitats

A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers

L.) is an economically important crop, exhibiting unique features such as outstanding resistance to biotic and abiotic stresses and high nutrient use efficiency. This species presents a challenge to geneticists and breeders due to its large genome containing a high proportion of repetitive sequences, self incompatibility, severe inbreeding depression and tissue culture recalcitrance. The genomic resources currently available for rye are underdeveloped in comparison with other crops of similar economic importance. The aim of this study was to create a highly saturated, multilocus linkage map of rye via consensus mapping, based on Diversity Arrays Technology (DArT) markers.Recombinant inbred lines (RILs) from 5 populations (564 in total) were genotyped using DArT markers and subjected to linkage analysis using Join Map 4.0 and Multipoint Consensus 2.2 software. A consensus map was constructed using a total of 9703 segregating markers. The average chromosome map length ranged from 199.9 cM (2R) to 251.4 cM (4R) and the average map density was 1.1 cM. The integrated map comprised 4048 loci with the number of markers per chromosome ranging from 454 for 7R to 805 for 4R. In comparison with previously published studies on rye, this represents an eight-fold increase in the number of loci placed on a consensus map and a more than two-fold increase in the number of genetically mapped DArT markers.Through the careful choice of marker type, mapping populations and the use of software packages implementing powerful algorithms for map order optimization, we produced a valuable resource for rye and triticale genomics and breeding, which provides an excellent starting point for more in-depth studies on rye genome organization