Seasonal cycle and source analyses of aerosol optical properties in a semi-urban environment at Puijo station in Eastern Finland

We introduce a four-year (in 2006–2010) continuous data set of aerosol optical properties at Puijo in Kuopio, Finland. We study the annual and diurnal variation of the aerosol scattering and absorption coefficients, hemispheric backscattering fraction, scattering Ångström exponent, and single scattering albedo, whose median values over this period were 7.2 Mm<sup>−1</sup> (at 550 nm), 1.0 Mm<sup>−1</sup> (at 637 nm), 0.15, 1.93 (between 450 and 550 nm), and 0.85, respectively. The scattering coefficient peaked in the spring and autumn, being 2–4 times those in the summer and winter. An exception was the summer of 2010, when the scattering coefficient was elevated to ~300 Mm<sup>−1</sup> by plumes from forest fires in Russia. The absorption coefficient peaked in the winter when soot-containing particles derived from biomass burning were present. The higher relative absorption coefficients resulted in lower single scattering albedo in winter. The optical properties varied also with wind direction and time of the day, indicating the effect of the local pollutant sources and the age of the particles. Peak values in the single scattering albedo were observed when the wind blew from a paper mill and from the sector without local pollutant sources. These observations were linked, respectively, to the sulphate-rich aerosol from the paper mill and the oxygenated organics in the aged aerosol, which both are known to increase the scattering characteristics of aerosols. Decreases in the single scattering albedo in the morning and afternoon, distinct in the summertime, were linked to the increased traffic density at these hours. The scattering and absorption coefficients of residential and long-range transported aerosol (two separate cloud events) were found to be decreased by clouds. The effect was stronger for the scattering than absorption, indicating preferential activation of the more hygroscopic aerosol with higher scattering characteristics

Genes in the postgenomic era

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype

Solar Intensity X-Ray and Particle Spectrometer SIXS : Instrument Design and First Results

The Solar Intensity X-ray and particle Spectrometer (SIXS) on the BepiColombo Mercury Planetary Orbiter ("Bepi") measures the direct solar X-rays, energetic protons, and electrons that bombard, and interact with, the Hermean surface. The interactions result in X-ray fluorescence and scattering, and particle induced X-ray emission (PIXE), i.e. "glow" of the surface in X-rays. Simultaneous monitoring of the incident and emitted radiation enables derivation of the abundances of some chemical elements and scattering properties of the outermost surface layer of the planet, and it may reveal other sources of X-ray emission, due to, for example, weak aurora-like phenomena in Mercury's exosphere. Mapping of the Hermean X-ray emission is the main task of the MIXS instrument onboard BepiColombo. SIXS data will also be used for investigations of the solar X-ray corona and solar energetic particles (SEP), both in the cruise phase and the passes of the Earth, Venus and Mercury before the arrival at Mercury's orbit, and the final science phase at Mercury's orbit. These observations provide the first-ever opportunity for in-situ measurements of the propagation of SEPs, their interactions with the interplanetary magnetic field, and space weather phenomena in multiple locations throughout the inner solar system far away from the Earth, and more extensively at Mercury's orbit. In this paper we describe the scientific objectives, design and calibrations, operational principles, and scientific performance of the final SIXS instrument launched to the mission to planet Mercury onboard BepiColombo. We also provide the first analysis results of science observations with SIXS, that were made during the Near-Earth Commissioning Phase and early cruise phase operations in 2018-19, including the background X-ray sky observations and "first light" observations of the Sun with the SIXS X-ray detection system (SIXS-X), and in-situ energetic electron and proton observations with the SIXS Particle detection system (SIXS-P).Peer reviewe

Genome-wide fine-scale recombination rate variation in Drosophila melanogaster

Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem, in particular because of the high background recombination rate. In this paper, a new computational method is developed to address this challenge. Through an extensive simulation study, it is demonstrated that the method allows more accurate inference, and exhibits greater robustness to the effects of natural selection and noise, compared to a well-used previous method developed for studying fine-scale recombination rate variation in the human genome. As an application, a genome-wide analysis of genetic variation data is performed for two Drosophila melanogaster populations, one from North America (Raleigh, USA) and the other from Africa (Gikongoro, Rwanda). It is shown that fine-scale recombination rate variation is widespread throughout the D. melanogaster genome, across all chromosomes and in both populations. At the fine-scale, a conservative, systematic search for evidence of recombination hotspots suggests the existence of a handful of putative hotspots each with at least a tenfold increase in intensity over the background rate. A wavelet analysis is carried out to compare the estimated recombination maps in the two populations and to quantify the extent to which recombination rates are conserved. In general, similarity is observed at very broad scales, but substantial differences are seen at fine scales. The average recombination rate of the X chromosome appears to be higher than that of the autosomes in both populations, and this pattern is much more pronounced in the African population than the North American population. The correlation between various genomic features—including recombination rates, diversity, divergence, GC content, gene content, and sequence quality—is examined using the wavelet analysis, and it is shown that the most notable difference between D. melanogaster and humans is in the correlation between recombination and diversity

Shifting Attention From Theory to Practice in Philosophy of Biology

Traditional approaches in philosophy of biology focus attention on biological concepts, explanations, and theories, on evidential support and inter-theoretical relations. Newer approaches shift attention from concepts to conceptual practices, from theories to practices of theorizing, and from theoretical reduction to reductive retooling. In this article, I describe the shift from theory-focused to practice-centered philosophy of science and explain how it is leading philosophers to abandon fundamentalist assumptions associated with traditional approaches in philosophy of science and to embrace scientific pluralism. This article comes in three parts, each illustrating the shift from theory-focused to practice-centered epistemology. The first illustration shows how shifting philosophical attention to conceptual practice reveals how molecular biologists succeed in identifying coherent causal strands within systems of bewildering complexity. The second illustration suggests that analyzing how a multiplicity of alternative models function in practice provides an illuminating approach for understanding the nature of theoretical knowledge in evolutionary biology. The third illustration demonstrates how framing reductionism in terms of the reductive retooling of practice offers an informative perspective for understanding why putting DNA at the center of biological research has been incredibly productive throughout much of biology. Each illustration begins by describing how traditional theory-focused philosophical approaches are laden with fundamentalist assumptions and then proceeds to show that shifting attention to practice undermines these assumptions and motivates a philosophy of scientific pluralism

Solar Intensity X-Ray and Particle Spectrometer SIXS: Instrument Design and First Results

The Solar Intensity X-ray and particle Spectrometer (SIXS) on the BepiColombo Mercury Planetary Orbiter ("Bepi") measures the direct solar X-rays, energetic protons, and electrons that bombard, and interact with, the Hermean surface. The interactions result in X-ray fluorescence and scattering, and particle induced X-ray emission (PIXE), i.e. "glow" of the surface in X-rays. Simultaneous monitoring of the incident and emitted radiation enables derivation of the abundances of some chemical elements and scattering properties of the outermost surface layer of the planet, and it may reveal other sources of X-ray emission, due to, for example, weak aurora-like phenomena in Mercury's exosphere. Mapping of the Hermean X-ray emission is the main task of the MIXS instrument onboard BepiColombo. SIXS data will also be used for investigations of the solar X-ray corona and solar energetic particles (SEP), both in the cruise phase and the passes of the Earth, Venus and Mercury before the arrival at Mercury's orbit, and the final science phase at Mercury's orbit. These observations provide the first-ever opportunity for in-situ measurements of the propagation of SEPs, their interactions with the interplanetary magnetic field, and space weather phenomena in multiple locations throughout the inner solar system far away from the Earth, and more extensively at Mercury's orbit. In this paper we describe the scientific objectives, design and calibrations, operational principles, and scientific performance of the final SIXS instrument launched to the mission to planet Mercury onboard BepiColombo. We also provide the first analysis results of science observations with SIXS, that were made during the Near-Earth Commissioning Phase and early cruise phase operations in 2018-19, including the background X-ray sky observations and "first light" observations of the Sun with the SIXS X-ray detection system (SIXS-X), and in-situ energetic electron and proton observations with the SIXS Particle detection system (SIXS-P)

Configurational asymmetry in vernier offset detection

Two psychophysical experiments were conducted at the horizontal and vertical orientations respectively, demonstrating substantial main effect of configuration, but no effect of offset direction on vernier acuity. In Experiment 1, a pair of horizontal bars were arranged side by side with a large gap between them. The observers were, on average, significantly better at discriminating a vertical offset if the right-hand bar was below the left-hand bar than vice versa, regardless of which bar they experienced as displaced and which as constant. A similar asymmetry was evident in Experiment 2 where observers judged horizontal offset for a pair of vertically oriented bars, where one was placed above the other. In this case average performance was better if the upper bar was on the right of the lower bar rather than on its left. There were large individual variations in the asymmetrical trend, but the effect could not be explained by subjective response bias. Furthermore, vernier acuity improved significantly and the asymmetry decreased more or less as a function of training. The average asymmetrical trend was consistent across training days and across two orientations, which indicates that the processing of line vernier stimuli is possibly configuration-specific in the cardinal orientation

Human V6: functional characterisation and localisation.

Human visual area V6, in the parieto-occipital sulcus, is thought to have an important role in the extraction of optic flow for the monitoring and guidance of self-motion (egomotion) because it responds differentially to egomotion-compatible optic flow when compared to: (a) coherent but egomotion-incompatible flow (Cardin & Smith, 2010), and (b) incoherent motion (Pitzalis et al., 2010). It is not clear, however, whether V6 responds more strongly to egomotion-incompatible global motion than to incoherent motion. This is relevant not only for determining the functional properties of V6, but also in order to choose optimal stimuli for localising V6 accurately with fMRI. Localisation with retinotopic mapping is difficult and there is a need for a simple, reliable method. We conducted an event-related 3T fMRI experiment in which participants viewed a display of dots which either: a) followed a time-varying optic flow trajectory in a single, egomotion-compatible (EC) display; b) formed an egomotion-incompatible (EI) 3 × 3 array of optic flow patches; or c) moved randomly (RM). Results from V6 show an ordering of response magnitudes: EC > EI > RM. Neighbouring areas V3A and V7 responded more strongly to EC than to RM, but about equally to EC and EI. Our results suggest that although V6 may have a general role in the extraction of global motion, in clear contrast to neighbouring motion areas it is especially concerned with encoding EC stimuli. They suggest two strategies for localising V6: (1) contrasting EC and EI; or (2) contrasting EC and RM, which is more sensitive but carries a risk of including voxels from neighbouring regions that also show a EC > RM preference