A Latent Variable Approach to Multivariate Quantitative Trait Loci

A novel approach based on latent variable modelling is presented for the analysis of multivariate quantitative and qualitative trait loci. The approach is general in the sense that it enables the joint analysis of many kinds of quantitative and qualitative traits (including count data and censored traits) in a single modelling framework. In the framework, the observations are modelled as functions of latent variables, which are then affected by quantitative trait loci. Separating the analysis in this way means that measurement errors in the phenotypic observations can be included easily in the model, providing robust inferences. The performance of the method is illustrated using two real multivariate datasets, from barley and Scots pine

Multi-frequency VLBA study of the blazar S5 0716+714 during the active state in 2004: I. Inner jet kinematics

We observed the blazar \object{0716+714} with the VLBA during its active state in 2003-2004. In this paper we discuss multi-frequency analysis of the inner jet (first 1 mas) kinematics. The unprecedentedly dense time sampling allows us to trace jet components without misidentification and to calculate the component speeds with good accuracy. In the smooth superluminal jet we were able to identify and track three components over time moving outwards with relatively high apparent superluminal speeds (8.5-19.4 $c$), which contradicts the hypothesis of a stationary oscillating jet in this source. Component ejections occur at a relatively high rate (once in two months), and they are accompanied by mm-continuum outbursts. Superluminal jet components move along wiggling trajectories, which is an indication of actual helical motion. Fast proper motion and rapid decay of the components suggest that this source should be observed with the VLBI at a rate of at least once in one or two months in order to trace superluminal jet components without confusion.Comment: 4 pages, 3 figures, Astronomy & Astrophysics Letter, language corrections adde

The Genome of the "Great Speciator" Provides Insights into Bird Diversification

Among birds, white-eyes (genus Zosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the “great speciator.” The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation

Hardware-efficient compression of neural multi-unit activity

Brain-machine interfaces (BMI) are tools for measuring neural activity in the brain, used to treat numerous conditions. It is essential that the next generation of intracortical BMIs is wireless so as to remove percutaneous connections, i.e. wires, and the associated mechanical and infection risks. This is required for the effective translation of BMIs into clinical applications and is one of the remaining bottlenecks. However, due to cortical tissue thermal dissipation safety limits, the on-implant power consumption must be strictly limited. Therefore, both the neural signal processing and wireless communication power should be minimal, while the implants should provide signals that offer high behavioural decoding performance (BDP). The Multi-Unit Activity (MUA) signal is the most common signal in modern BMIs. However, with an ever-increasing channel count, the raw data bandwidth is becoming prohibitively high due to the associated communication power exceeding the safety limits. Data compression is therefore required. To meet this need, this work developed hardware-efficient static Huffman compression schemes for MUA data. Our final system reduced the bandwidth to 27 bps/channel, compared to the standard MUA rate of 1 kbps/channel. This compression is over an order of magnitude more than has been achieved before, while using only 0.96 uW/channel processing power and 246 logic cells. Our results were verified on 3 datasets and less than 1% loss in BDP was observed. As such, with the use of effective data compression, an order more of MUA channels can be fitted on-implant, enabling the next generation of high-performance wireless intracortical BMIs

Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy

Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated populations originating from the colonization of one single haplotype into an area left available after a glacial retreat. Simulated data were compared with empirical data available from the literature for a species of Pinus that has expanded north after the Last Glacial Maximum. In the evaluation of genetic diversity, homoplasy was found to have little influence on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance estimates (D2sh) were much more affected. The effect of the number of chloroplast microsatellite loci for evaluation of genetic diversity is also discussed

Sex Steroid Hormone Analysis in Human Tear Fluid Using a Liquid Chromatography—Mass Spectrometry Method

The marked sexual dimorphism prevalent in inflammatory/autoimmune diseases is mostly due to sex hormone actions. One common eye disease that disproportionately affects women is dry eye. Thus, our aim was to optimise our highly sensitive liquid chromatography–tandem mass spectrometry method for steroid hormone quantification in tear fluid (TF). We used tears and matched serum samples from 10 heathy individuals. Estrone, estradiol testosterone, progesterone, androstenedione, and dehydroepiandrosterone, were quantified with an HPLC coupled with a Triple Quad 5500 MS. Estrone was measured in 80% of female and 20% of male TF samples (mean ± SD, 68.9 ± 62.2 pmol/L), whereas estradiol was undetectable in tears. Progesterone was identified in half of the female tear samples (2.91 ± 3.47 nmol/L) but in none of the male samples, whereas testosterone was quantifiable only in male tears (0.24 ± 0.1 nmol/L). TF hormone levels were, on average, from 1.4% to 55% of systemic values. Estrone, progesterone, and testosterone levels in tears correlated with the matching serum samples (r = 0.82, 0.79, and 0.85, respectively), but androstenedione and dehydroepiandrosterone showed no correlations. Our LC–MS/MS method could detect five out of the six steroid hormones studied in individual human TF samples and could therefore be used to analyse the role of sex steroids in eye diseases

Clinical validation of automated and rapid mariPOC SARS-CoV-2 antigen test

Publisher Copyright: © 2021, The Author(s).COVID-19 diagnostics was quickly ramped up worldwide early 2020 based on the detection of viral RNA. However, based on the scientific knowledge for pre-existing coronaviruses, it was expected that the SARS-CoV-2 RNA will be detected from symptomatic and at significant rates also from asymptomatic individuals due to persistence of non-infectious RNA. To increase the efficacy of diagnostics, surveillance, screening and pandemic control, rapid methods, such as antigen tests, are needed for decentralized testing and to assess infectiousness. A novel automated mariPOC SARS-CoV-2 test was developed for the detection of conserved structural viral nucleocapsid proteins. The test utilizes sophisticated optical laser technology for two-photon excitation and individual detection of immunoassay solid-phase particles. We validated the new method against qRT-PCR. Sensitivity of the test was 100.0% (13/13) directly from nasopharyngeal swab specimens and 84.4% (38/45) from swab specimens in undefined transport mediums. Specificity of the test was 100.0% (201/201). The test's limit of detection was 2.7 TCID50/test. It showed no cross-reactions. Our study shows that the new test can detect infectious individuals already in 20 min with clinical sensitivity close to qRT-PCR. The mariPOC is a versatile platform for syndromic testing and for high capacity infection control screening of infectious individuals.Peer reviewe

Difficulties in administration of oral medication formulations to pet cats: an e-survey of cat owners

The purpose here was to determine the problems cat owners encounter in medicating their cats with orally administered drugs at home. The study was carried out as an open e-questionnaire survey addressed to cat owners in which the authors focused on the oral administration route. A total of 46 completed questionnaires were included in the survey. In the study, 46 cats received 67 orally administered drugs. Approximately half of the drugs were registered for use in cats by the European Medicines Agency (54 per cent), and there were also off-label drugs registered for human (36 per cent) and canine medication (7.4 per cent) and an ex tempore drug (3.0 per cent). The owners were unable to give the doses as prescribed for their cats for one-fourth of the medications (16/67). Drugs that were registered for feline medication were significantly more palatable than drugs registered for other species (odds ratio (OR) 4.9), and liquid formulations were significantly more palatable than solid formulations (OR 4.8). However, most of the owners (22/38) preferred a solid dosage form, while few (4/38) chose a liquid formulation. The results indicate that there is still a need for more palatable and easily administered oral drugs for cats.Peer reviewe

COVID-19 cases in spectators returning to Finland from UEFA Euro 2020 matches in Saint Petersburg

UEFA Euro 2020 tournament was scheduled to take place in 2020, but due to the coronavirus disease 2019 (COVID-19) pandemic was rescheduled to start on 11 June 2021. Approximately 4500 Finnish spectators participated, travelling between Finland and Russia during the period of 16 to 30 June to attend matches played on 16 and 21 June. A total of 419 persons returning from Russia or with a connection to Russia were detected positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Of the 321 sequenced samples 303 turned out to be of the Delta variant. None of these cases was hospitalised. In the following weeks findings of the Delta variant increased rapidly. Thus, EURO 2020 travel-related imported cases likely facilitated this rapid surge of Delta variant, but this impact would likely have been seen with the typical increase in the number of travellers entering Finland later in the summer.Peer reviewe

Studying genetics of adaptive variation in model organisms: flowering time variation in Arabidopsis lyrata

Arabidopsis thaliana has emerged as a model organism for plant developmental genetics, but it is also now being widely used for population genetic studies. Outcrossing relatives of A. thaliana are likely to provide suitable additional or alternative species for studies of evolutionary and population genetics. We have examined patterns of adaptive flowering time variation in the outcrossing, perennial A. lyrata. In addition, we examine the distribution of variation at marker genes in populations form North America and Europe. The probability of flowering in this species differs between southern and northern populations. Northern populations are much less likely to flower in short than in long days. A significant daylength by region interaction shows that the northern and southern populations respond differently to the daylength. The timing of flowering also differs between populations, and is made shorter by long days, and in some populations, by vernalization. North American and European populations show consistent genetic differentiation over microsatellite and isozyme loci and alcohol dehydrogenase sequences. Thus, the patterns of variation are quite different from those in A. thaliana, where flowering time differences show little relationship to latitude of origin and the genealogical trees of accessions vary depending on the genomic region studied. The genetic architecture of adaptation can be compared in these species with different life historie