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Inferring redshift and galaxy properties via a multi-task neural net with probabilistic outputs : an application to simulated MOONS spectra
Get PDFFunding: F.B acknowledges support from the INAF ‘Fundamental Astrophysics‘ programs 2022 & 2023. E.D.T. was supported by the European Research Council (ERC) under grant agreement no. 10104075. A.M., F.M., F.B. and G.C. acknowledge support from grant PRIN-MUR 2020ACSP5K_002 financed by European Union – Next Generation EU. VW and NFB acknowledge Science and Technologies Facilities Council (STFC) grants ST/V000861/1 and ST/Y00275X/1.The era of large-scale astronomical surveys demands innovative approaches for rapid and accurate analysis of extensive spectral data, and a promising direction in which to address this challenge is offered by machine learning. Here, we introduce a new pipeline, M-TOPnet (Multi-Task network Outputting Probabilities), which employs a convolutional neural network with residual learning to simultaneously derive redshift and other key physical properties of galaxies from their spectra. Our tool efficiently encodes spectral information into a latent space, employing distinct downstream branches for each physical quantity, thereby benefiting from multi-task learning. Notably, our method handles the redshift output as a probability distribution, allowing for a more refined and robust estimation of this critical parameter. We demonstrate preliminary results using simulated data from the MOONS instrument, which will soon be operating at the ESO/VLT. We highlight the effectiveness of our tool in accurately predicting the redshift, stellar mass, and star formation rate of galaxies at z ≳ 1 − 3, even for faint sources (mH ∼ 24) for which traditional methods often struggle. Through analysis of the output probability distributions, we demonstrate that our pipeline enables robust quality screening of the results, achieving accuracy rates of up to 99% in redshift determination (defined as predictions within |Δz|< 0.01 relative to the true redshift) with 8 h exposure spectra, while automatically identifying potentially problematic cases. Our pipeline thus emerges as a powerful solution for the upcoming challenges in observational astronomy, combining precision, interpretability, and efficiency, all aspects that are crucial for analysing the massive datasets expected from next-generation instruments.Peer reviewe
Range-wide salamander densities reveal a key component of terrestrial vertebrate biomass in eastern North American forests
Get PDFCharacterizing the population density of species is a central interest in ecology. Eastern North America is the global hotspot for biodiversity of plethodontid salamanders, an inconspicuous component of terrestrial vertebrate communities, and among the most widespread is the eastern red-backed salamander, Plethodon cinereus. Previous work suggests population densities are high with significant geographic variation, but comparisons among locations are challenged by lack of standardization of methods and failure to accommodate imperfect detection. We present results from a large-scale research network that accounts for detection uncertainty using systematic survey protocols and robust statistical models. We analysed mark-recapture data from 18 study areas across much of the species range. Estimated salamander densities ranged from 1950 to 34 300 salamanders ha-1, with a median of 9965 salamanders ha-1. We compared these results to previous estimates for P. cinereus and other abundant terrestrial vertebrates. We demonstrate that overall the biomass of P. cinereus, a secondary consumer, is of similar or greater magnitude to widespread primary consumers such as white-tailed deer (Odocoileus virginianus) and Peromyscus mice, and two to three orders of magnitude greater than common secondary consumer species. Our results add empirical evidence that P. cinereus, and amphibians in general, are an outsized component of terrestrial vertebrate communities in temperate ecosystems.Peer reviewe
Bonobo gestures, meanings, and context
Get PDFFunding: The author is currently funded by the European Union’s 8th Framework Programme, Horizon 2020, under grant agreement no 802719.Although you might not know what a “gesture” is (yet), most people reading this book probably have some experience with gestures. Waving, bowing, clapping, nodding, pantomiming, and pointing, are just some of the many gestures that you may have encountered. As humans, we use many conventionalized gestures that we learn throughout our lives and regularly produce gestures alongside language (Goldin-Meadow 2005). One way of examining the evolution of human gesture, and potentially human language, is to study gestural communication in other species. Researchers in great ape gestural communication tend to define a gesture as an intentional, mechanically ineffective movement of the limbs, head, or body that is used to communicate (Townsend et al. 2016). All great apes use gestures to communicate (Call and Tomasello 2007), and there is growing evidence of gestural communication across the primate taxa (Macaca mulatta, M. nemestrina, M. arctoides, Maestripieri 2005; Macaca radiata, Gupta and Sinha 2016; Macaca Sylvanus, Hesler and Fischer 2007; Papio anubis, Bourjade et al. 2014)
Poloidal field line resonances driven by a fast wave
Get PDFThis research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project #483 (The Identification and Classification of 3D Alfvén Resonances). The authors are grateful to ISSI for funding the Team and hosting its meetings. ANW was partially funded by the Science and Technology Facilities Council (STFC) Grant (ST/N000609/1). KT was supported by NASA 80NSSC19K0259. JKS was funded by STFC Grant ST/W00089X/1. AWD is funded by NSFC (RFIS-III Grant 42350710200). TKY acknowledges support from STFC UKRI Grant ST/W00089X/1 and NERC UKRI Grant NE/V000748/1. LO and IRM were supported by funding from the Canadian Space Agency. IRM was also funded by a Discovery Grant from the Canadian NSERC.We present numerical simulations of the excitation of resonant poloidal Alfvén waves. The resulting Alfvén waves could be loosely described as “high‐m” (m is the azimuthal wave number) in as much as the azimuthal scale of the wave is much less than the scale in the direction normal to L‐shells. Such waves are generally excited by wave‐particle interactions. In this article we show how resonant poloidal Alfvén waves can be excited by a fast mode (of large azimuthal scale) in a cold plasma. The key property that enables this is a three‐dimensional equilibrium, which facilitates the process of phasemixing in the azimuthal direction. We show that the classification of resonant Alfvén waves as high‐m and low‐m has limited applicability in 3D inhomogeneous media and suggest an alternative classification be based on the excitation mechanism.Peer reviewe
Warming nondormant tree roots advances aboveground spring phenology in temperate trees
Get PDFFunding: This study was funded by the Deutsche Forschungsgemeinschaft (DFG MA 8130/1-1, KR 3309/9-1).• Climate warming advances the onset of tree growth in spring, but above- and belowground phenology are not always synchronized. These differences in growth responses may result from differences in root and bud dormancy dynamics, but root dormancy is largely unexplored. • We measured dormancy in roots and leaf buds of Fagus sylvatica and Populus nigra by quantifying the warming sum required to initiate above- and belowground growth in October, January and February. We furthermore carried out seven experiments, manipulating only the soil and not air temperature before or during tree leaf-out to evaluate the potential of warmer roots to influence budburst timing using seedlings and adult trees of F. sylvatica and seedlings of Betula pendula. • Root dormancy was virtually absent in comparison with the much deeper winter bud dormancy. Roots were able to start growing immediately as soils were warmed during the winter. Interestingly, higher soil temperature advanced budburst across all experiments, with soil temperature possibly accounting for c. 44% of the effect of air temperature in advancing aboveground spring phenology per growing degree hour. • Therefore, differences in root and bud dormancy dynamics, together with their interaction, likely explain the nonsynchronized above- and belowground plant growth responses to climate warming.Peer reviewe
Design, recruitment and baseline characteristics of the LENS trial
Get PDFFunding: LENS was primarily funded by the National Institute for Health and Care Research (NIHR), Health Technology Assessment Programme (14/49/84). The Nuffield Department of Population Health (NDPH), University of Oxford, covered the costs of storing, packaging and preparation for mailing of study treatment. LENS is coordinated by the Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), NDPH, University of Oxford; CTSU receives funding from the UK Medical Research Council (MRC), the British Heart Foundation and Health Data Research (HDR) UK. During the conduct of the trial, David Preiss was also supported by a University of Oxford BHF Centre of Research Excellence Senior Transition Fellowship (RE/13/1/30181), MRC (MC_UU_12026) and HDR UK (OXFD1 & HDRUK2023.0025).Background Findings from cardiovascular outcome trials suggest that treatment with fenofibrate may reduce the progression of diabetic retinopathy. However, no dedicated large-scale randomised trials have yet investigated this hypothesis. Methods LENS is a streamlined randomised double-masked placebo-controlled trial, based in Scotland, assessing whether treatment with fenofibrate (145 mg tablet daily or, in the context of impaired renal function, on alternate days) in people with early retinopathy reduces progression to referable diabetic retinopathy (defined in NHS Scotland's Diabetic Eye Screening grading scheme as referable background or proliferative retinopathy, or referable maculopathy in either eye) or treatment with retinal laser, intravitreal injections or vitrectomy. Adults with diabetes mellitus and non-referable retinopathy (mild background retinopathy in both eyes or observable background retinopathy in one/both eyes at the most recent NHS retinal screening assessment; or observable maculopathy in one/both eyes in the previous 3 years) were eligible. Potential participants were identified from routinely collected healthcare data and followed up using regular contact from the research team and linkage to national electronic morbidity, mortality, biochemistry and retinal screening records. Study treatment was mailed to participants. Results Between 18 September 2018 and 27 July 2021, 1151 participants were randomised. Their mean age was 61 (SD 12) years, 312 (27%) were female and 305 (26%) had type 1 diabetes. 96% had bilateral mild background retinopathy and 10% had observable maculopathy. Conclusions LENS will provide a robust evaluation of the efficacy of treating people at risk of progression of diabetic retinopathy with fenofibrate. Results are anticipated in mid-2024.Peer reviewe
scikit-eo : a Python package for remote sensing data analysis
Get PDFIn recent years, a growing body of space-borne and drone imagery has become available with increasing spatial and temporal resolutions. This remotely sensed data has enabled researchers to address and tackle a broader range of challenges effectively by using novel tools and data. However, analysts spend an important amount of time finding the adequate libraries to read and process remotely sensed data. With an increasing amount of open access data, there is a growing need to account for effective open source tools to read, process and execute analysis that contributes to underpin patterns, changes and trends that are critical for environmental studies. Applications that integrate spatial-temporal data are used to study a variety of complex environmental processes, such as monitoring and assessment of land cover changes (Chaves et al., 2020), crop classifications (Pott et al., 2021), deforestation (Tarazona et al., 2018), impact on urbanization level (Trinder & Liu, 2020) and climate change impacts (Yang et al., 2013). Other complex environmental processes that are monitored by integrating spatial-temporal data are assessments of glacier retreat (Hugonnet et al., 2018), related hydrological change (Huss & Hock, 2018), biodiversity conservation (Cavender-Bares et al., 2022) and disaster management (Kucharczyk & Hugenholtz, 2021). To bridge the gaps in remotely sensed data processing tools, we here introduce scikit-eo, a brand-new Python package for satellite remote sensing analysis. Unlike other tools, it is a centralized, scalable, and open-source toolkit due to its flexibility in being adapted into large dataset processing pipelines. It provides central access to the most commonly used Python functions in remote sensing analysis for environmental studies, including machine learning methods. scikit-eo stands out with its ability to be used in various settings, from a lecturer room to a crucial part of any Python environment in a research project. The majority of the tools included in scikit-eo are derived from peer-reviewed scientific publications, ensuring their reliability and accuracy. By integrating this diverse set of tools, scikit-eo allows to focus on analyzing the results of data rather than being bogged down by complex lines of code. With its centralized structure, integrated use cases, and example data, scikit-eo empowers to optimize resources and dedicate more attention to the meaningful interpretation of findings in a more efficient way.Peer reviewe
Quantifying the importance of an L4 or L5 magnetograph for modelling the global solar magnetic field
No full textCurrently, space weather observations and predictions are primarily made using observations from the L1 Lagrange point (on the Sun-Earth line). A mission to place a satellite at the L5 viewpoint (60° behind Earth) has been proposed to enhance our space weather predictive capabilities. This thesis explores the potential impact of an additional magnetograph at L5, as well as at the L4 viewpoint (60° in front of the Earth). We first conduct a study utilising a spherical harmonic magnetic flux transport (MFT) and potential field source surface (PFSS) combined model to simulate the Sun’s global magnetic field. We also perform a study employing an MFT and 3D magnetofrictional combined model. In both studies, the first simulation run is called a “Reference Sun” simulation, which assumes a full 360° longitude view of the Sun to produce synthetic bipole data. This simulation, along with every simulation in this thesis, is conducted over 4 solar cycles.
In the first study, we conduct 12 “limited data” simulations, where we vary the limited field of view (FOV; L1, L1+L5 or L1+L4+L5), the inclusion of rotational updates (RUs) and the initial polar field strength (B0). For the most accurate scenario, with the addition of an L4 or L5 magnetograph, we find accuracy increases of 38–40% for different flux quantities, 5–9% for the Br polarities, 23–37% for the Br error, 4–13% for the Br correlation, 24–28% for the heliospheric current sheet (HCS) location and 2–3% for the connectivity of the photospheric field.
The second study conducts three limited data simulations using bipole data from L1, L1+L5, and L1+L4+L5 FOVs, including RUs and reducing B0 to ensure correct polar field oscillations. In addition to the quantities investigated in the first study, we can examine the non-potential and free magnetic energy, the electric current and the global non-potential magnetic field with this simulating method. Including L5 data with L1, we find accuracy increases of 32–38% for globally integrated quantities, 15–25% for the 3D magnetic field, 10–36% for the 2D spatial distributions of non-potential quantities and 26% for the HCS. Similarly, including L4 with L1+L5 improves the accuracy by 11–37% for globally integrated quantities, 9–17% for the magnetic field, 16– 39% for the 2D non-potential quantities and 13% for the HCS. These potential improvements in modelling accuracy indicate more reliable space weather predictions and the importance for future space programs to incorporate L5 and L4 observations."This research was supported by the UK’s Science and Technology Facilities Council (STFC) Doctoral Training Partnership Grant ST/S505717/1."--Fundin
Evaluating Diuretics in Normal Care (EVIDENCE) : protocol of a cluster randomised controlled equivalence trial of prescribing policy to compare the effectiveness of thiazide-type diuretics in hypertension
Get PDFIntroduction Healthcare systems must use treatments that are effective and safe. Regulators licensed many currently used older medications before introducing the stringent evidential requirements imposed on modern treatments. Also, there has been little encouragement to carry out within-class, head-to-head comparisons of licensed medicines. For commonly prescribed drugs, even small differences in effectiveness or safety could have significant public health implications. However, conventional clinical trials that randomise individual subjects are costly and unwieldy. Such trials are also often criticised as having low external validity. We describe an approach to rapidly generate externally valid evidence of comparative safety and effectiveness using the example of two widely used diuretics for the management of hypertension. Methods and analysis The EVIDENCE (Evaluating Diuretics in Normal Care) study has a prospective, cluster-randomised, open-label, blinded end-point design. By randomising prescribing policy in primary care practices, the study compares the safety and effectiveness of commonly used diuretics in treating hypertension. Participating practices are randomised 1:1 to a policy of prescribing either indapamide or bendroflumethiazide when clinically indicated. Suitable patients who are not already taking the policy diuretic are switched accordingly. All patients taking the study medications are written to explaining the rationale for changing the prescribing policy and notifying them they can opt-out of any switch. The prescribing policies’ effectiveness and safety will be compared using rates of major adverse cardiovascular events (hospitalisation with myocardial infarction, heart failure or stroke or cardiovascular death), routinely collected in national healthcare administrative datasets. The study will seek to recruit 250 practices to provide a study population of approximately 50,000 individuals with a mean follow-up time of two years. A primary intention-to-treat time-to-event analysis will be used to estimate the relative effect of the two policies.Peer reviewe
Quantitative proteomics identifies plasma protein alterations that associate with metabolic and thrombotic profile changes after bariatric surgery
Get PDFFunding: This work was supported by the School of Medicine, University of St Andrews. H.A. is supported by a Tenovus Scotland-funded PhD studentship (ref: T19-05).Objective Roux-en-Y gastric bypass (RYGB) surgery has been shown to lead to favourable health outcomes in obese patients. However, the molecular changes that occur and how they relate to clinical measures are poorly understood. Here we characterise the proteomic alterations that occur in plasma of RYGB patients before and 9 months after surgery using quantitative proteomics. Methods Plasma proteomics was performed by sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) to identify and quantify differentially abundant proteins. Relationships between significantly altered proteins and clinical markers were examined. A gene set enrichment analysis was also conducted to identify altered pathways. Results From the proteomic analysis, 27 proteins increased, and 43 proteins decreased in abundance 9 months after surgery, providing insights into the physiological changes that accompany weight loss. Proteins including sex hormone binding globulin (SHBG), inter-alpha-trypsin inhibitor heavy chain 3 (ITIH3), and apolipoprotein D (APOD), which increased in abundance post-surgery, highlight improvements in lipid regulation, insulin sensitivity, and inflammation. Proteins involved in coagulation, including α2-macroglobulin, kallikrein-B1, prothrombin, factor (FX, FXI, and FXII), exhibited reduced levels, aligning with a decreased in thrombotic potential. Conclusions These findings provide a mechanistic understanding of how bariatric surgery leads to systemic changes in metabolic and haemostatic pathways, thus favourably modulating the risk of developing cardiovascular disease.Peer reviewe
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