RNA-sequencing has revolutionized biomedical research and, in particular, our ability to study gene alternative splicing. The problem has important implications for human health, as alternative splicing may be involved in malfunctions at the cellular level and multiple diseases. However, the high-dimensional nature of the data and the existence of experimental biases pose serious data analysis challenges. We find that the standard data summaries used to study alternative splicing are severely limited, as they ignore a substantial amount of valuable information. Current data analysis methods are based on such summaries and are hence sub-optimal. Further, they have limited flexibility in accounting for technical biases. We propose novel data summaries and a Bayesian modeling framework that overcome these limitations and determine biases in a non-parametric, highly flexible manner. These summaries adapt naturally to the rapid improvements in sequencing technology. We provide efficient point estimates and uncertainty assessments. The approach allows to study alternative splicing patterns for individual samples and can also be the basis for downstream analyses. We found a several fold improvement in estimation mean square error compared popular approaches in simulations, and substantially higher consistency between replicates in experimental data. Our findings indicate the need for adjusting the routine summarization and analysis of alternative splicing RNA-seq studies. We provide a software implementation in the R package *

Abstract. Measuring vertical profiles of the particle light-absorption coefficient by using absorption photometers may face the challenge of fast changes in relative humidity (RH). These absorption photometers determine the particle light-absorption coefficient due to a change in light attenuation through a particle-loaded filter. The filter material, however, takes up or releases water with changing relative humidity (RH in %), thus influencing the light attenuation. A sophisticated set of laboratory experiments was therefore conducted to investigate the effect of fast RH changes (dRH ∕ dt) on the particle light-absorption coefficient (σabs in Mm−1) derived with two absorption photometers. The RH dependence was examined based on different filter types and filter loadings with respect to loading material and areal loading density. The Single Channel Tricolor Absorption Photometer (STAP) relies on quartz-fiber filter, and the microAeth® MA200 is based on a polytetrafluoroethylene (PTFE) filter band. Furthermore, three cases were investigated: clean filters, filters loaded with black carbon (BC), and filters loaded with ammonium sulfate. The filter areal loading densities (ρ*) ranged from 3.1 to 99.6 mg m−2 in the case of the STAP and ammonium sulfate and 1.2 to 37.6 mg m−2 in the case the MA200. Investigating BC-loaded cases, ρBC* was in the range of 2.9 to 43.0 and 1.1 to 16.3 mg m−2 for the STAP and MA200, respectively. Both instruments revealed opposing responses to relative humidity changes (ΔRH) with different magnitudes. The STAP shows a linear dependence on relative humidity changes. The MA200 is characterized by a distinct exponential recovery after its filter was exposed to relative humidity changes. At a wavelength of 624 nm and for the default 60 s running average output, the STAP reveals an absolute change in σabs per absolute change of RH (Δσabs∕ΔRH) of 0.14 Mm−1 %−1 in the clean case, 0.29 Mm−1 %−1 in the case of BC-loaded filters, and 0.21 Mm−1 %−1 in the case filters loaded with ammonium sulfate. The 60 s running average of the particle light-absorption coefficient at 625 nm measured with the MA200 revealed a response of around −0.4 Mm−1 %−1 for all three cases. Whereas the response of the STAP varies over the different loading materials, in contrast, the MA200 was quite stable. The response was, for the STAP, in the range of 0.17 to 0.24 Mm−1 %−1 and, in the case of ammonium sulfate loading and in the BC-loaded case, 0.17 to 0.62 Mm−1 %−1. In the ammonium sulfate case, the minimum response shown by the MA200 was −0.42 with a maximum of −0.36 Mm−1 %−1 and a minimum of −0.42 and maximum −0.37 Mm−1 %−1 in the case of BC. A linear correction function for the STAP was developed here. It is provided by correlating 1 Hz resolved recalculated particle light-absorption coefficients and RH change rates. The linear response is estimated at 10.08 Mm−1 s−1 %−1. A correction approach for the MA200 is also provided; however, the behavior of the MA200 is more complex. Further research and multi-instrument measurements have to be conducted to fully understand the underlying processes, since the correction approach resulted in different correction parameters across various experiments. However, the exponential recovery after the filter of the MA200 experienced a RH change could be reproduced. However, the given correction approach has to be estimated with other RH sensors as well, since each sensor has a different response time. And, for the given correction approaches, the uncertainties could not be estimated, which was mainly due to the response time of the RH sensor. Therefore, we do not recommend using the given approaches. But they point in the right direction, and despite the imperfections, they are useful for at least estimating the measurement uncertainties due to relative humidity changes. Due to our findings, we recommend using an aerosol dryer upstream of absorption photometers to reduce the RH effect significantly. Furthermore, when absorption photometers are used in vertical measurements, the ascending or descending speed through layers of large relative humidity gradients has to be low to minimize the observed RH effect. But this is simply not possible in some scenarios, especially in unmixed layers or clouds. Additionally, recording the RH of the sample stream allows correcting for the bias during post-processing of the data. This data correction leads to reasonable results, according to the given example in this study.

No abstract

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

We propose regression models for curve-valued responses in two or more dimensions, where only the image but not the parametrization of the curves is of interest. Examples of such data are handwritten letters, movement paths or outlines of objects. In the square-root-velocity framework, a parametrization invariant distance for curves is obtained as the quotient space metric with respect to the action of re-parametrization, which is by isometries. With this special case in mind, we discuss the generalization of 'linear' regression to quotient metric spaces more generally, before illustrating the usefulness of our approach for curves modulo re-parametrization. We address the issue of sparsely or irregularly sampled curves by using splines for modeling smooth conditional mean curves. We test this model in simulations and apply it to human hippocampal outlines, obtained from Magnetic Resonance Imaging scans. Here we model how the shape of the irregularly sampled hippocampus is related to age, Alzheimer's disease and sex.