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

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

Urbanisation lowers great tit Parus major breeding success at multiple spatial scales

While numerous studies have reported negative effects of urbanisation on birds, few have examined the role of urban scale in influencing breeding success. Furthermore, many studies have relied on qualitative rather than quantitative assessments of urbanisation. This study sought to address these issues by testing the effects of urbanisation, measured at two spatial scales, on the breeding success of great tits Parus major. A nested study design, incorporating over 400 nestboxes, was used in study sites across northern Belgium with a priori quantified degrees of urbanisation at both local and regional scales. All measured breeding parameters were found to vary at one or both spatial scales of urbanisation; in more urbanised areas great tits displayed advanced laying dates but lower breeding success compared to rural areas, with smaller clutch sizes, lower nestling masses and fewer fledglings per egg. Importantly, urbanisation effects were not limited to big cities as birds breeding in gardens or parks in small towns also had comparatively low success. We found that both regional- and local-scale urbanisation had consistent significant effects on laying date, clutch size and nestling mass, while the number of fledglings per egg was negatively influenced by local-scale urbanisation only. Results of this study therefore highlight the importance of utilising multiple spatial scales in analysing urbanisation effects, as well as the potential negative impact of local urbanisation on breeding success. This calls for further investigation into mechanisms driving urbanisation effects and how these may vary at different scales