Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects

BackgroundThe patterns of mutation vary both within and across genomes. It has been shown for a few mammals that mutation rates vary within the genome, while for unknown reasons, the sensu stricto yeasts have uniform rates instead. The generality of these observations has been unknown. Here we examine silent site substitutions in a more expansive set (20 mammals, 27 fungi, 4 insects) to determine why some genomes demonstrate this mosaic distribution and why others are uniform.ResultsWe applied several intragene and intergene correlation tests to measure regional substitution patterns. Assuming that silent sites are a reasonable approximation to neutrally mutating sequence, our results show that all multicellular eukaryotes exhibit mutational heterogeneity. In striking contrast, all fungi are mutationally uniform - with the exception of three Candida species: C. albicans, C. dubliniensis, and C. tropicalis. We speculate that aspects of replication timing may be responsible for distinguishing these species. Our analysis also reveals classes of genes whose silent sites behave anomalously with respect to the mutational background in many species, indicating prevalent selective pressures. Genes associated with nucleotide binding or gene regulation have consistently low silent substitution rates in every mammalian species, as well as multiple fungi. On the other hand, receptor genes repeatedly exhibit high silent substitution rates, suggesting they have been influenced by diversifying selection.ConclusionOur findings provide a framework for understanding the regional mutational properties of eukaryotes, revealing a sharp difference between fungi and multicellular species. They also elucidate common selective pressures acting on eukaryotic silent sites, with frequent evidence for both purifying and diversifying selection

Finsler geometry on higher order tensor fields and applications to high angular resolution diffusion imaging.

We study 3D-multidirectional images, using Finsler geometry. The application considered here is in medical image analysis, specifically in High Angular Resolution Diffusion Imaging (HARDI) (Tuch et al. in Magn. Reson. Med. 48(6):1358–1372, 2004) of the brain. The goal is to reveal the architecture of the neural fibers in brain white matter. To the variety of existing techniques, we wish to add novel approaches that exploit differential geometry and tensor calculus. In Diffusion Tensor Imaging (DTI), the diffusion of water is modeled by a symmetric positive definite second order tensor, leading naturally to a Riemannian geometric framework. A limitation is that it is based on the assumption that there exists a single dominant direction of fibers restricting the thermal motion of water molecules. Using HARDI data and higher order tensor models, we can extract multiple relevant directions, and Finsler geometry provides the natural geometric generalization appropriate for multi-fiber analysis. In this paper we provide an exact criterion to determine whether a spherical function satisfies the strong convexity criterion essential for a Finsler norm. We also show a novel fiber tracking method in Finsler setting. Our model incorporates a scale parameter, which can be beneficial in view of the noisy nature of the data. We demonstrate our methods on analytic as well as simulated and real HARDI data

Cognitive Assessment Tools Recommended in Geriatric Oncology Guidelines: A Rapid Review.

Cognitive assessment is a cornerstone of geriatric care. Cognitive impairment has the potential to significantly impact multiple phases of a person's cancer care experience. Accurately identifying this vulnerability is a challenge for many cancer care clinicians, thus the use of validated cognitive assessment tools are recommended. As international cancer guidelines for older adults recommend Geriatric Assessment (GA) which includes an evaluation of cognition, clinicians need to be familiar with the overall interpretation of the commonly used cognitive assessment tools. This rapid review investigated the cognitive assessment tools that were most frequently recommended by Geriatric Oncology guidelines: Blessed Orientation-Memory-Concentration test (BOMC), Clock Drawing Test (CDT), Mini-Cog, Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MoCA), and Short Portable Mental Status Questionnaire (SPMSQ). A detailed appraisal of the strengths and limitations of each tool was conducted, with a focus on practical aspects of implementing cognitive assessment tools into real-world clinical settings. Finally, recommendations on choosing an assessment tool and the additional considerations beyond screening are discussed

Self-supervised generative adverrsarial network for depth estimation in laparoscopic images

Dense depth estimation and 3D reconstruction of a surgical scene are crucial steps in computer assisted surgery. Recent work has shown that depth estimation from a stereo image pair could be solved with convolutional neural networks. However, most recent depth estimation models were trained on datasets with per-pixel ground truth. Such data is especially rare for laparoscopic imaging, making it hard to apply supervised depth estimation to real surgical applications. To overcome this limitation, we propose SADepth, a new self-supervised depth estimation method based on Generative Adversarial Networks. It consists of an encoder-decoder generator and a discriminator to incorporate geometry constraints during training. Multi-scale outputs from the generator help to solve the local minima caused by the photometric reprojection loss, while the adversarial learning improves the framework generation quality. Extensive experiments on two public datasets show that SADepth outperforms recent state-of-the-art unsupervised methods by a large margin, and reduces the gap between supervised and unsupervised depth estimation in laparoscopic images

Spatio-temporal variability and principal components of the particle number size distribution in an urban atmosphere

A correct description of fine (diameter <1 μm) and ultrafine (<0.1 μm) aerosol particles in urban areas is of interest for particle exposure assessment but also basic atmospheric research. We examined the spatio-temporal variability of atmospheric aerosol particles (size range 3–800 nm) using concurrent number size distribution measurements at a maximum of eight observation sites in and around Leipzig, a city in Central Europe. Two main experiments were conducted with different time span and number of observation sites (2 years at 3 sites; 1 month at 8 sites). A general observation was that the particle number size distribution varied in time and space in a complex fashion as a result of interaction between local and far-range sources, and the meteorological conditions. To identify statistically independent factors in the urban aerosol, different runs of principal component (PC) analysis were conducted encompassing aerosol, gas phase, and meteorological parameters from the multiple sites. Several of the resulting PCs, outstanding with respect to their temporal persistence and spatial coverage, could be associated with aerosol particle modes: a first accumulation mode ("droplet mode", 300–800 nm), considered to be the result of liquid phase processes and far-range transport; a second accumulation mode (centered around diameters 90–250 nm), considered to result from primary emissions as well as aging through condensation and coagulation; an Aitken mode (30–200 nm) linked to urban traffic emissions in addition to an urban and a rural Aitken mode; a nucleation mode (5–20 nm) linked to urban traffic emissions; nucleation modes (3–20 nm) linked to photochemically induced particle formation; an aged nucleation mode (10–50 nm). Additional PCs represented only local sources at a single site, or infrequent phenomena. In summary, the analysis of size distributions of high time and size resolution yielded a surprising wealth of statistical aerosol components occurring in the urban atmosphere over one single city. A paradigm on the behaviour of sub-μm urban aerosol particles is proposed, with recommendations how to efficiently monitor individual sub-fractions across an entire city

Mobility particle size spectrometers: Calibration procedures and measurement uncertainties

Mobility particle size spectrometers (MPSS) belong to the essential instruments in aerosol science that determine the particle number size distribution (PNSD) in the submicrometer size range. Following calibration procedures and target uncertainties against standards and reference instruments are suggested for a complete MPSS quality assurance program: (a) calibration of the CPC counting efficiency curve (within 5% for the plateau counting efficiency; within 1 nm for the 50% detection efficiency diameter), (b) sizing calibration of the MPSS, using a certified polystyrene latex (PSL) particle size standard at 203 nm (within 3%), (c) intercomparison of the PNSD of the MPSS (within 10% and 20% of the dN/dlogDP concentration for the particle size range 20–200 and 200–800 nm, respectively), and (d) intercomparison of the integral PNC of the MPSS (within 10%). Furthermore, following measurement uncertainties have been investigated: (a) PSL particle size standards in the range from 100 to 500 nm match within 1% after sizing calibration at 203 nm. (b) Bipolar diffusion chargers based on the radioactive nuclides Kr85, Am241, and Ni63 and a new ionizer based on corona discharge follow the recommended bipolar charge distribution, while soft X-ray-based charges may alter faster than expected. (c) The use of a positive high voltage supply show a 10% better performance than a negative one. (d) The intercomparison of the integral PNC of an MPSS against the total number concentration is still within the target uncertainty at an ambient pressure of approximately 500 hPa

Mobility particle size spectrometers: Calibration procedures and measurement uncertainties

Mobility particle size spectrometers (MPSS) belong to the essential instruments in aerosol science that determine the particle number size distribution (PNSD) in the submicrometer size range. Following calibration procedures and target uncertainties against standards and reference instruments are suggested for a complete MPSS quality assurance program: (a) calibration of the CPC counting efficiency curve (within 5% for the plateau counting efficiency; within 1 nm for the 50% detection efficiency diameter), (b) sizing calibration of the MPSS, using a certified polystyrene latex (PSL) particle size standard at 203 nm (within 3%), (c) intercomparison of the PNSD of the MPSS (within 10% and 20% of the dN/dlogDP concentration for the particle size range 20–200 and 200–800 nm, respectively), and (d) intercomparison of the integral PNC of the MPSS (within 10%). Furthermore, following measurement uncertainties have been investigated: (a) PSL particle size standards in the range from 100 to 500 nm match within 1% after sizing calibration at 203 nm. (b) Bipolar diffusion chargers based on the radioactive nuclides Kr85, Am241, and Ni63 and a new ionizer based on corona discharge follow the recommended bipolar charge distribution, while soft X-ray-based charges may alter faster than expected. (c) The use of a positive high voltage supply show a 10% better performance than a negative one. (d) The intercomparison of the integral PNC of an MPSS against the total number concentration is still within the target uncertainty at an ambient pressure of approximately 500 hPa. Copyright © 2018 Published with license by American Association for Aerosol Research

An episode of extremely high PM concentrations over Central Europe caused by dust emitted over the southern Ukraine

International audienceOn 24 March 2007, the atmosphere over Central Europe was affected by an episode of exceptionally high mass concentrations of aerosol particles, most likely caused by a dust storm in the Southern Ukraine on the preceding day. At ground-based measurement stations in Slovakia, the Czech Republic, Poland and Germany PM10 mass concentrations rose to values between 200 and 1400 ?g m?3. An evaluation of PM10 measurements from 360 monitoring stations showed that the dust cloud advanced along a narrow corridor at speeds of up to 70 km h?1. According to lidar observations over Leipzig, Germany, the high aerosol concentrations were confined to a homogeneous boundary layer of 1800 m height. The wavelength dependence of light extinction using both lidar and sun photometer measurements suggested the dominance of coarse particles during the main event. At a wavelength of 532 nm, relatively high volume extinction coefficients (300?400 Mm?1) and a particle optical depth of 0.65 was observed. In-situ measurements with an aerodynamic particle sizer at Melpitz, Germany, confirmed the presence of a coarse particle mode with a mode diameter >2 ?m, whose maximum concentration coincided with that of PM10. A chemical particle analysis confirmed the dominance of non-volatile and insoluble matter in the coarse mode as well as high enrichments of Ti and Fe, which are characteristic of soil dust. A combination of back trajectory calculations and satellite images allowed to identify the dust source with confidence: On 23 March 2007, large amounts of dust were emitted from dried-out farmlands in the southern Ukraine, facilitated by wind gusts up to 100 km h?1. The unusual vertical stability and confined height of this dust layer as well as the rapid transport under dry conditions led to the conservation of high aerosol mass concentrations along the transect and thus to the extraordinary high aerosol concentrations over Central Europe. Our observations demonstrate the capacity of a combined apparatus of in situ and remote sensing measurements to characterise such a dust with a variety of aerosol parameters. As a conclusion, the description of dust emission, transport and transformation processes needs to be improved, especially when facing the possible effects of further anthropogenic desertification and climate change

Atmospheric aerosols at the Pierre Auger Observatory and environmental implications

The Pierre Auger Observatory detects the highest energy cosmic rays. Calorimetric measurements of extensive air showers induced by cosmic rays are performed with a fluorescence detector. Thus, one of the main challenges is the atmospheric monitoring, especially for aerosols in suspension in the atmosphere. Several methods are described which have been developed to measure the aerosol optical depth profile and aerosol phase function, using lasers and other light sources as recorded by the fluorescence detector. The origin of atmospheric aerosols traveling through the Auger site is also presented, highlighting the effect of surrounding areas to atmospheric properties. In the aim to extend the Pierre Auger Observatory to an atmospheric research platform, a discussion about a collaborative project is presented.Comment: Regular Article, 16 pages, 12 figure