GTM through time

The standard GTM (generative topographic mapping) algorithm assumes that the data on which it is trained consists of independent, identically distributed (iid) vectors. For time series, however, the iid assumption is a poor approximation. In this paper we show how the GTM algorithm can be extended to model time series by incorporating it as the emission density in a hidden Markov model. Since GTM has discrete hidden states we are able to find a tractable EM algorithm, based on the forward-backward algorithm, to train the model. We illustrate the performance of GTM through time using flight recorder data from a helicopter

A geometrically motivated coordinate system for exploring spacetime dynamics in numerical-relativity simulations using a quasi-Kinnersley tetrad

We investigate the suitability and properties of a quasi-Kinnersley tetrad and a geometrically motivated coordinate system as tools for quantifying both strong-field and wave-zone effects in numerical relativity (NR) simulations. We fix the radial and latitudinal coordinate degrees of freedom of the metric, using the Coulomb potential associated with the quasi-Kinnersley transverse frame. These coordinates are invariants of the spacetime and can be used to unambiguously fix the outstanding spin-boost freedom associated with the quasi-Kinnersley frame (resulting in a preferred quasi-Kinnersley tetrad (QKT)). In the limit of small perturbations about a Kerr spacetime, these coordinates and QKT reduce to Boyer-Lindquist coordinates and the Kinnersley tetrad, irrespective of the simulation gauge choice. We explore the properties of this construction both analytically and numerically, and we gain insights regarding the propagation of radiation described by a super-Poynting vector. We also quantify in detail the peeling properties of the chosen tetrad and gauge. We argue that these choices are particularly well suited for a rapidly converging wave-extraction algorithm as the extraction location approaches infinity, and we explore numerically the extent to which this property remains applicable on the interior of a computational domain. Using a number of additional tests, we verify that the prescription behaves as required in the appropriate limits regardless of simulation gauge. We explore the behavior of the geometrically motivated coordinate system in dynamical binary-black-hole NR mergers, and find them useful for visualizing features in NR simulations such as the spurious "junk" radiation. Finally, we carefully scrutinize the head-on collision of two black holes and, for example, the way in which the extracted waveform changes as it moves through the computational domain.Comment: 30 pages, 17 figures, 2 table

Selective deforestation and exposure of African wildlife to bat-borne viruses

Proposed mechanisms of zoonotic virus spillover often posit that wildlife transmission and amplification precede human outbreaks. Between 2006 and 2012, the palm Raphia farinifera, a rich source of dietary minerals for wildlife, was nearly extirpated from Budongo Forest, Uganda. Since then, chimpanzees, black-and-white colobus, and red duiker were observed feeding on bat guano, a behavior not previously observed. Here we show that guano consumption may be a response to dietary mineral scarcity and may expose wildlife to bat-borne viruses. Videos from 2017–2019 recorded 839 instances of guano consumption by the aforementioned species. Nutritional analysis of the guano revealed high concentrations of sodium, potassium, magnesium and phosphorus. Metagenomic analyses of the guano identified 27 eukaryotic viruses, including a novel betacoronavirus. Our findings illustrate how “upstream” drivers such as socioeconomics and resource extraction can initiate elaborate chains of causation, ultimately increasing virus spillover risk

Selective deforestation and exposure of African wildlife to bat-borne viruses

Proposed mechanisms of zoonotic virus spillover often posit that wildlife transmission and amplification precede human outbreaks. Between 2006 and 2012, the palm Raphia farinifera, a rich source of dietary minerals for wildlife, was nearly extirpated from Budongo Forest, Uganda. Since then, chimpanzees, black-and-white colobus, and red duiker were observed feeding on bat guano, a behavior not previously observed. Here we show that guano consumption may be a response to dietary mineral scarcity and may expose wildlife to bat-borne viruses. Videos from 2017–2019 recorded 839 instances of guano consumption by the aforementioned species. Nutritional analysis of the guano revealed high concentrations of sodium, potassium, magnesium and phosphorus. Metagenomic analyses of the guano identified 27 eukaryotic viruses, including a novel betacoronavirus. Our findings illustrate how “upstream” drivers such as socioeconomics and resource extraction can initiate elaborate chains of causation, ultimately increasing virus spillover risk.Peer reviewe

The Ariel payload electrical and electronic architecture: a summary of the current design and implementation status

Ariel is the M4 mission of the ESA’s Cosmic Vision Program 2015-2025, whose aim is to characterize by lowresolution transit spectroscopy the atmospheres of over one thousand warm and hot exoplanets orbiting nearby stars. It has been selected by ESA in March 2018 and adopted in November 2020 to be flown, then, in 2029. It is the first survey mission dedicated to measuring the chemical composition and thermal structures of the atmospheres of hundreds of transiting exoplanets, in order to enable planetary science far beyond the boundaries of the Solar System. The Payload (P/L) is based on a cold section (PLM – Payload Module) working at cryogenic temperatures and a warm section, located within the Spacecraft (S/C) Service Vehicle Module (SVM) and hosting five warm units operated at ambient temperature (253-313 K). The P/L and its electrical, electronic and data handling architecture has been designed and optimized to perform transit spectroscopy from space during primary and secondary planetary eclipses in order to achieve a large set of unbiased observations to shed light and fully understand the nature of exoplanets atmospheres, retrieving information about planets interior and determining the key factors affecting the formation and evolution of planetary systems

Particulate matter exposure during pregnancy is associated with birth weight, but not gestational age, 1962-1992: a cohort study

<p>Abstract</p> <p>Background</p> <p>Exposure to air pollutants is suggested to adversely affect fetal growth, but the evidence remains inconsistent in relation to specific outcomes and exposure windows.</p> <p>Methods</p> <p>Using birth records from the two major maternity hospitals in Newcastle upon Tyne in northern England between 1961 and 1992, we constructed a database of all births to mothers resident within the city. Weekly black smoke exposure levels from routine data recorded at 20 air pollution monitoring stations were obtained and individual exposures were estimated via a two-stage modeling strategy, incorporating temporally and spatially varying covariates. Regression analyses, including 88,679 births, assessed potential associations between exposure to black smoke and birth weight, gestational age and birth weight standardized for gestational age and sex.</p> <p>Results</p> <p>Significant associations were seen between black smoke and both standardized and unstandardized birth weight, but not for gestational age when adjusted for potential confounders. Not all associations were linear. For an increase in whole pregnancy black smoke exposure, from the 1^st(7.4 μg/m³) to the 25^th(17.2 μg/m³), 50^th(33.8 μg/m³), 75^th(108.3 μg/m³), and 90^th(180.8 μg/m³) percentiles, the adjusted estimated decreases in birth weight were 33 g (SE 1.05), 62 g (1.63), 98 g (2.26) and 109 g (2.44) respectively. A significant interaction was observed between socio-economic deprivation and black smoke on both standardized and unstandardized birth weight with increasing effects of black smoke in reducing birth weight seen with increasing socio-economic disadvantage.</p> <p>Conclusions</p> <p>The findings of this study progress the hypothesis that the association between black smoke and birth weight may be mediated through intrauterine growth restriction. The associations between black smoke and birth weight were of the same order of magnitude as those reported for passive smoking. These findings add to the growing evidence of the harmful effects of air pollution on birth outcomes.</p

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder