Likelihood informed dimension reduction for inverse problems in remote sensing of atmospheric constituent profiles

We use likelihood informed dimension reduction (LIS) (T. Cui et al. 2014) for inverting vertical profile information of atmospheric methane from ground based Fourier transform infrared (FTIR) measurements at Sodankyl\"a, Northern Finland. The measurements belong to the word wide TCCON network for greenhouse gas measurements and, in addition to providing accurate greenhouse gas measurements, they are important for validating satellite observations. LIS allows construction of an efficient Markov chain Monte Carlo sampling algorithm that explores only a reduced dimensional space but still produces a good approximation of the original full dimensional Bayesian posterior distribution. This in effect makes the statistical estimation problem independent of the discretization of the inverse problem. In addition, we compare LIS to a dimension reduction method based on prior covariance matrix truncation used earlier (S. Tukiainen et al. 2016)

On dimension reduction in Gaussian filters

A priori dimension reduction is a widely adopted technique for reducing the computational complexity of stationary inverse problems. In this setting, the solution of an inverse problem is parameterized by a low-dimensional basis that is often obtained from the truncated Karhunen-Loeve expansion of the prior distribution. For high-dimensional inverse problems equipped with smoothing priors, this technique can lead to drastic reductions in parameter dimension and significant computational savings. In this paper, we extend the concept of a priori dimension reduction to non-stationary inverse problems, in which the goal is to sequentially infer the state of a dynamical system. Our approach proceeds in an offline-online fashion. We first identify a low-dimensional subspace in the state space before solving the inverse problem (the offline phase), using either the method of "snapshots" or regularized covariance estimation. Then this subspace is used to reduce the computational complexity of various filtering algorithms - including the Kalman filter, extended Kalman filter, and ensemble Kalman filter - within a novel subspace-constrained Bayesian prediction-and-update procedure (the online phase). We demonstrate the performance of our new dimension reduction approach on various numerical examples. In some test cases, our approach reduces the dimensionality of the original problem by orders of magnitude and yields up to two orders of magnitude in computational savings

Estimation of ECHAM5 climate model closure parameters with adaptive MCMC

Climate models contain closure parameters to which the model climate is sensitive. These parameters appear in physical parameterization schemes where some unresolved variables are expressed by predefined parameters rather than being explicitly modeled. Currently, best expert knowledge is used to define the optimal closure parameter values, based on observations, process studies, large eddy simulations, etc. Here, parameter estimation, based on the adaptive Markov chain Monte Carlo (MCMC) method, is applied for estimation of joint posterior probability density of a small number (<i>n</i>=4) of closure parameters appearing in the ECHAM5 climate model. The parameters considered are related to clouds and precipitation and they are sampled by an adaptive random walk process of the MCMC. The parameter probability densities are estimated simultaneously for all parameters, subject to an objective function. Five alternative formulations of the objective function are tested, all related to the net radiative flux at the top of the atmosphere. Conclusions of the closure parameter estimation tests with a low-resolution ECHAM5 climate model indicate that (i) adaptive MCMC is a viable option for parameter estimation in large-scale computational models, and (ii) choice of the objective function is crucial for the identifiability of the parameter distributions

Parameter variations in prediction skill optimization at ECMWF

Peer reviewe

Population change in breeding boreal waterbirds in a 25-year perspective : What characterises winners and losers?

Understanding drivers of variation and trends in biodiversity change is a general scientific challenge, but also crucial for conservation and management. Previous research shows that patterns of increase and decrease are not always consistent at different spatial scales, calling for approaches combining the latter. We here explore the idea that functional traits of species may help explaining divergent population trends. Complementing a previous community level study, we here analyse data about breeding waterbirds on 58 wetlands in boreal Fennoscandia, covering gradients in latitude as well as trophic status. We used linear mixed models to address how change in local abundance over 25 years in 25 waterbird species are associated with life history traits, diet, distribution, breeding phenology, and habitat affinity. Mean abundance increased in 10 species from 1990/1991 to 2016, whereas it decreased in 15 species. Local population increases were associated with species that are early breeders and have small clutches, an affinity for luxurious wetlands, an herbivorous diet, and a wide breeding range rather than a southern distribution. Local decreases, by contrast, were associated with species having large clutches and invertivorous diet, as well as being late breeders and less confined to luxurious wetlands. The three species occurring on the highest number of wetlands all decreased in mean abundance. The fact that early breeders have done better than late fits well with previous research about adaptability to climate change, that is, response to earlier springs. We found only limited support for the idea that life history traits are good predictors of wetland level population change. Instead, diet turned out to be a strong candidate for an important driver of population change, as supported by a general decrease of invertivores and a concomitant increase of large herbivores. In a wider perspective, future research needs to address whether population growth of large-bodied aquatic herbivores affects abundance of co-occurring invertivorous species, and if so, if this is due to habitat alteration, or to interference or exploitative competition.Peer reviewe

MicroRNA profiling in ischemic injury of the gracilis muscle in rats

<p>Abstract</p> <p>Background</p> <p>To profile the expression of microRNAs (miRNAs) and their potential target genes in the gracilis muscles following ischemic injury in rats by monitoring miRNA and mRNA expression on a genome-wide basis.</p> <p>Methods</p> <p>Following 4 h of ischemia and subsequent reperfusion for 4 h of the gracilis muscles, the specimens were analyzed with an Agilent rat miRNA array to detect the expressed miRNAs in the experimental muscles compared to those from the sham-operated controls. Their expressions were subsequently quantified by real-time reverse transcription polymerase chain reaction (real-time RT-PCR) to determine their expression pattern after different durations of ischemia and reperfusion. In addition, the expression of the mRNA in the muscle specimens after 4 h of ischemia and reperfusion for 1, 3, 7, and 14 d were detected with the Agilent Whole Rat Genome 4 × 44 k oligo microarray. A combined approach using a computational prediction algorithm that included miRanda, PicTar, TargetScanS, MirTarget2, RNAhybrid, and the whole genome microarray experiment was performed by monitoring the mRNA:miRNA association to identify potential target genes.</p> <p>Results</p> <p>Three miRNAs (miR-21, miR-200c, and miR-205) of 350 tested rat miRNAs were found to have an increased expression in the miRNA array. Real-time RT-PCR demonstrated that, with 2-fold increase after 4 h of ischemia, a maximum 24-fold increase at 7 d, and a 7.5-fold increase at 14 d after reperfusion, only the miR-21, but not the miR-200c or miR-205 was upregulated throughout the experimental time. In monitoring the target genes of miR-21 in the expression array at 1, 3, 7, 14 d after reperfusion, with persistent expression throughout the experiment, we detected the same 4 persistently downregulated target genes (<it>Nqo1</it>, <it>Pdpn</it>, <it>CXCL3</it>, and <it>Rad23b</it>) with the prediction algorithms miRanda and RNAhybrid, but no target gene was revealed with PicTar, TargetScanS, and MirTarget2.</p> <p>Conclusions</p> <p>This study revealed 3 upregulated miRNAs in the gracilis muscle following ischemic injury and identified 4 potential target genes of miR-21 by examining miRNAs and mRNAs expression patterns in a time-course fashion using a combined approach with prediction algorithms and a whole genome expression array experiment.</p

Interaction of climate change with effects of conspecific and heterospecific density on reproduction

We studied the relationship between temperature and the coexistence of great titParus majorand blue titCyanistes caeruleus, breeding in 75 study plots across Europe and North Africa. We expected an advance in laying date and a reduction in clutch size during warmer springs as a general response to climate warming and a delay in laying date and a reduction in clutch size during warmer winters due to density-dependent effects. As expected, as spring temperature increases laying date advances and as winter temperature increases clutch size is reduced in both species. Density of great tit affected the relationship between winter temperature and laying date in great and blue tit. Specifically, as density of great tit increased and temperature in winter increased both species started to reproduce later. Density of blue tit affected the relationship between spring temperature and blue and great tit laying date. Thus, both species start to reproduce earlier with increasing spring temperature as density of blue tit increases, which was not an expected outcome, since we expected that increasing spring temperature should advance laying date, while increasing density should delay it cancelling each other out. Climate warming and its interaction with density affects clutch size of great tits but not of blue tits. As predicted, great tit clutch size is reduced more with density of blue tits as temperature in winter increases. The relationship between spring temperature and density on clutch size of great tits depends on whether the increase is in density of great tit or blue tit. Therefore, an increase in temperature negatively affected the coexistence of blue and great tits differently in both species. Thus, blue tit clutch size was unaffected by the interaction effect of density with temperature, while great tit clutch size was affected in multiple ways by these interactions terms.Peer reviewe

Effects of interspecific coexistence on laying date and clutch size in two closely related species of hole-nesting birds

Coexistence between great tits Parus major and blue tits Cyanistes caeruleus, but also other hole‐nesting taxa, constitutes a classic example of species co‐occurrence resulting in potential interference and exploitation competition for food and for breeding and roosting sites. However, the spatial and temporal variations in coexistence and its consequences for competition remain poorly understood. We used an extensive database on reproduction in nest boxes by great and blue tits based on 87 study plots across Europe and Northern Africa during 1957–2012 for a total of 19,075 great tit and 16,729 blue tit clutches to assess correlative evidence for a relationship between laying date and clutch size, respectively, and density consistent with effects of intraspecific and interspecific competition.In an initial set of analyses, we statistically controlled for a suite of site‐specific variables. We found evidence for an effect of intraspecific competition on blue tit laying date (later laying at higher density) and clutch size (smaller clutch size at higher density), but no evidence of significant effects of intraspecific competition in great tits, nor effects of interspecific competition for either species.To further control for site‐specific variation caused by a range of potentially confounding variables, we compared means and variances in laying date and clutch size of great and blue tits among three categories of difference in density between the two species. We exploited the fact that means and variances are generally positively correlated. If interspecific competition occurs, we predicted a reduction in mean and an increase in variance in clutch size in great tit and blue tit when density of heterospecifics is higher than the density of conspecifics, and for intraspecific competition, this reduction would occur when density of conspecifics is higher than the density of heterospecifics. Such comparisons of temporal patterns of means and variances revealed evidence, for both species, consistent with intraspecific competition and to a smaller extent with interspecific competition.These findings suggest that competition associated with reproductive behaviour between blue and great tits is widespread, but also varies across large spatial and temporal scales.</div

Interspecific variation in the relationship between clutch size, laying date and intensity of urbanization in four species of hole-nesting birds

The increase in size of human populations in urban and agricultural areas has resulted in considerable habitat conversion globally. Such anthropogenic areas have specific environmental characteristics, which influence the physiology, life history, and population dynamics of plants and animals. For example, the date of bud burst is advanced in urban compared to nearby natural areas. In some birds, breeding success is determined by synchrony between timing of breeding and peak food abundance. Pertinently, caterpillars are an important food source for the nestlings of many bird species, and their abundance is influenced by environmental factors such as temperature and date of bud burst. Higher temperatures and advanced date of bud burst in urban areas could advance peak caterpillar abundance and thus affect breeding phenology of birds. In order to test whether laying date advance and clutch sizes decrease with the intensity of urbanization, we analyzed the timing of breeding and clutch size in relation to intensity of urbanization as a measure of human impact in 199 nest box plots across Europe, North Africa, and the Middle East (i.e., the Western Palearctic) for four species of hole-nesters: blue tits (Cyanistes caeruleus), great tits (Parus major), collared flycatchers (Ficedula albicollis), and pied flycatchers (Ficedula hypoleuca). Meanwhile, we estimated the intensity of urbanization as the density of buildings surrounding study plots measured on orthophotographs. For the four study species, the intensity of urbanization was not correlated with laying date. Clutch size in blue and great tits does not seem affected by the intensity of urbanization, while in collared and pied flycatchers it decreased with increasing intensity of urbanization. This is the first large-scale study showing a species-specific major correlation between intensity of urbanization and the ecology of breeding. The underlying mechanisms for the relationships between life history and urbanization remain to be determined. We propose that effects of food abundance or quality, temperature, noise, pollution, or disturbance by humans may on their own or in combination affect laying date and/or clutch size