Abundance distributions for tree species in Great Britain: a two-stage approach to modeling abundance using species distribution modeling and random forest

High-quality abundance data are expensive and time-consuming to collect and often highly limited in availability. Nonetheless, accurate, high-resolution abundance distributions are essential for many ecological applications ranging from species conservation to epidemiology. Producing models that can predict abundance well, with good resolution over large areas, has therefore been an important aim in ecology, but poses considerable challenges. We present a two-stage approach to modeling abundance, combining two established techniques. First, we produce ensemble species distribution models (SDMs) of trees in Great Britain at a fine resolution, using much more common presence–absence data and key environmental variables. We then use random forest regression to predict abundance by linking the results of the SDMs to a much smaller amount of abundance data. We show that this method performs well in predicting the abundance of 20 of 25 tested British tree species, a group that is generally considered challenging for modeling distributions due to the strong influence of human activities. Maps of predicted tree abundance for the whole of Great Britain are provided at 1 km2 resolution. Abundance maps have a far wider variety of applications than presence-only maps, and these maps should allow improvements to aspects of woodland management and conservation including analysis of habitats and ecosystem functioning, epidemiology, and disease management, providing a useful contribution to the protection of British trees. We also provide complete R scripts to facilitate application of the approach to other scenarios

TOI-2257 b: A highly eccentric long-period sub-Neptune transiting a nearby M dwarf

N.S., R.W. and B.-O.D. acknowledge support from the Swiss National Science Foundation (PP00P2-163967 and PP00P2-190080). M.N.G. acknowledges support from MIT's Kavli Institute as a Juan Carlos Torres Fellow and from the European Space Agency (ESA) as an ESA Research Fellow. A.A.B., B.S.S.and I.A.S. acknowledge the support of the Ministry of Science and Higher Education of the Russian Federation under the grant 075-15-2020-780 (N13.1902.21.0039). L.D. is an F.R.S.-FNRS Postdoctoral Researcher. B.V.R. thanks the Heising-Simons Foundation for support. This publication benefits from the support of the French Community of Belgium in the context of the FRIA Doctoral Grant awarded to M.T. and E.J. acknowledges DGAPA for his postdoctoral fellowship. Y.G.M.C. acknowledges support from UNAM-DGAPA PAPIIT BG-101321. D.D. acknowledges support from the TESS Guest Investigator Program grant 80NSSC19K1727 and NASA Exoplanet Research Program grant 18-2XRP18_2-0136. We acknowledge support from the Centre for Space and Habitability (CSH) of the University of Bern. Part of this work received support from the National Centre for Competence in Research PlanetS, supported by the Swiss National Science Foundation (SNSF). Funding for the TESS mission is provided by NASA's Science Mission Directorate. We acknowledge the use of public TESS data from pipelines at the TESS Science Office and at the TESS Science Processing Operations Center. This research has made use of the Exoplanet Follow-up Observation Program website, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program. Resources supporting this work were provided by the NASA High-End Computing (HEC) Program through the NASA Advanced Supercomputing (NAS) Division at Ames Research Center for the production of the SPOC data products. This paper includes data collected by the TESS mission that are publicly available from the Mikulski Archive for Space Telescopes (MAST). This work is based upon observations carried out at the Observatorio Astronomico Nacional on the Sierra de San Pedro Martir (OAN-SPM), Baja California, Mexico. We warmly thank the entire technical staff of the Observatorio Astronomico Nacional at San Pedro Martir in Mexico for their unfailing support to SAINT-EX operations, namely: E. Cadena, T. Calvario, E. Colorado, F. Diaz, A. Franco, B. Garcia, C. Guerrero, G. Guisa, F. Guillen, A. Landa, L. Figueroa, B. Hernandez, J. Herrera, E. Lopez, E. Lugo, B. Martinez, G. Melgoza, F. Montalvo, J.M. Nunez, J.L. Ochoa, I. Plauchu, F. Quiroz, H. Riesgo, H. Serrano, T. Verdugo, I. Zavala. The research leading to these results has received funding from the European Research Council (ERC) under the FP/2007-2013 ERC grant agreement nffi 336480, and under the European Union's Horizon 2020 research and innovation programme (grants agreements nffi 679030 and 803193/BEBOP); from an Actions de Recherche Concertee (ARC) grant, financed by the Wallonia-Brussels Federation, from the Balzan Prize Foundation, from the BEL-SPO/BRAIN2.0 research program (PORTAL project), from the Science and Technology Facilities Council (STFC; grant nffi ST/S00193X/1), and from F.R.S-FNRS (Research Project ID T010920F). This work was also partially supported by a grant from the Simons Foundation (PI: Queloz, grant number 327127), as well as by the MERAC foundation (PI: Triaud). PI: Gillon is F.R.S.-FNRS Senior Research Associate. TRAPPIST is funded by the Belgian Fund for Scientific Research (Fond National de la Recherche Scientifique, FNRS) under the grant PDR T.0120.21, with the participation of the Swiss National Science Fundation (SNF). M.G. and E.J. are F.R.S.-FNRS Senior Research Associate. This work makes use of observations from the LCOGT network. Part of the LCOGT telescope time was granted by NOIRLab through the Mid-Scale Innovations Program (MSIP). M.S.I.P. is funded by NSF. Some of the observations in the paper made use of the High-Resolution Imaging instrument(s) `Alopeke (and/or Zorro). `Alopeke (and/or Zorro) was funded by the NASA Exoplanet Exploration Program and built at the NASA Ames Research Center by Steve B. Howell, Nic Scott, Elliott P. Horch, and Emmett Quigley. Data were reduced using a software pipeline originally written by Elliott Horch and Mark Everett. `Alopeke (and/or Zorro) was mounted on the Gemini North (and/or South) telescope of the international Gemini Observatory, a program of NSF's OIR Lab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation, on behalf of the Gemini partnership: the National Science Foundation (United States), National Research Council (Canada), Agencia Nacional de Investigacion y Desarrollo (Chile), Ministerio de Ciencia, Tecnologia e Innovacion (Argentina), Ministerio da Ciencia, Tecnologia, Inovacoes e Comunicacoes (Brazil), and Korea Astronomy and Space Science Institute (Republic of Korea). This research has made use of the NASA Exoplanet Archive, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program. This research made use of exoplanet (Foreman-Mackey et al. 2021a,b) and its dependencies (Agol et al. 2020; Kumar et al. 2019; Astropy Collaboration 2013, 2018; Kipping 2013; Luger et al. 2019; Salvatier et al. 2016; Theano Development Team 2016). Additional use of software packages AstroImageJ (Collins et al. 2017) and TAPIR (Jensen 2013).Context. Thanks to the relative ease of finding and characterizing small planets around M-dwarf stars, these objects have become cornerstones in the field of exoplanet studies. The current paucity of planets in long-period orbits around M dwarfs makes such objects particularly compelling as they provide clues about the formation and evolution of these systems. Aims. In this study we present the discovery of TOI-2257 b (TIC 198485881), a long-period (35 d) sub-Neptune orbiting an M3 star at 57.8 pc. Its transit depth is about 0.4%, large enough to be detected with medium-size, ground-based telescopes. The long transit duration suggests the planet is in a highly eccentric orbit (e similar to 0.5), which would make it the most eccentric planet known to be transiting an M-dwarf star. Methods. We combined TESS and ground-based data obtained with the 1.0-meter SAINT-EX, 0.60-meter TRAPPIST-North, and 1.2-meter FLWO telescopes to find a planetary size of 2.2 R-circle plus and an orbital period of 35.19 days. In addition, we make use of archival data, high-resolution imaging, and vetting packages to support our planetary interpretation. Results. With its long period and high eccentricity, TOI-2257 b falls into a novel slice of parameter space. Despite the planet's low equilibrium temperature (similar to 256 K), its host star's small size (R-* = 0.311 +/- 0.015) and relative infrared brightness (K-mag = 10.7) make it a suitable candidate for atmospheric exploration via transmission spectroscopy.Swiss National Science Foundation (SNSF)European Commission PP00P2-163967 PP00P2-190080MIT's Kavli InstituteEuropean Space Agency European CommissionMinistry of Science and Higher Education of the Russian Federation 075-15-2020-780 (N13.1902.21.0039)Heising-Simons FoundationFrench Community of BelgiumDGAPAPrograma de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT) Universidad Nacional Autonoma de Mexico BG-101321TESS Guest Investigator Program 80NSSC19K1727NASA Exoplanet Research Program 18-2XRP18_2-0136Centre for Space and Habitability (CSH) of the University of BernSwiss National Science Foundation (SNSF)European Research Council (ERC) 336480Actions de Recherche Concertee (ARC) grant - Wallonia-Brussels FederationUK Research & Innovation (UKRI)Science & Technology Facilities Council (STFC)Science and Technology Development Fund (STDF) ST/S00193X/1Fonds de la Recherche Scientifique - FNRS T010920FSimons Foundation 327127MERAC foundationFonds de la Recherche Scientifique - FNRS PDR T.0120.21Swiss National Science Foundation (SNSF)National Science Foundation (NSF)NASA Exoplanet Exploration Program NASA's Science Mission DirectorateEuropean Research Council (ERC) 679030 803193/BEBOPBalzan Prize Foundation BEL-SPO/BRAIN2.0 research program (PORTAL project

Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease

Genetic determinants of cognition are poorly characterized, and their relationship to genes that confer risk for neurodevelopmental disease is unclear. Here we performed a systems-level analysis of genome-wide gene expression data to infer gene-regulatory networks conserved across species and brain regions. Two of these networks, M1 and M3, showed replicable enrichment for common genetic variants underlying healthy human cognitive abilities, including memory. Using exome sequence data from 6,871 trios, we found that M3 genes were also enriched for mutations ascertained from patients with neurodevelopmental disease generally, and intellectual disability and epileptic encephalopathy in particular. M3 consists of 150 genes whose expression is tightly developmentally regulated, but which are collectively poorly annotated for known functional pathways. These results illustrate how systems-level analyses can reveal previously unappreciated relationships between neurodevelopmental disease–associated genes in the developed human brain, and provide empirical support for a convergent gene-regulatory network influencing cognition and neurodevelopmental disease

Calcium control of triphasic hippocampal STDP

Bush D, Jin Y. Calcium control of triphasic hippocampal STDP. Journal of Computational Neuroscience. 2012;33(3):495-514.Synaptic plasticity is believed to represent the neural correlate of mammalian learning and memory function. It has been demonstrated that changes in synaptic conductance can be induced by approximately synchronous pairings of pre- and post- synaptic action potentials delivered at low frequencies. It has also been established that NMDAr-dependent calcium influx into dendritic spines represents a critical signal for plasticity induction, and can account for this spike-timing dependent plasticity (STDP) as well as experimental data obtained using other stimulation protocols. However, subsequent empirical studies have delineated a more complex relationship between spike-timing, firing rate, stimulus duration and post-synaptic bursting in dictating changes in the conductance of hippocampal excitatory synapses. Here, we present a detailed biophysical model of single dendritic spines on a CA1 pyramidal neuron, describe the NMDAr-dependent calcium influx generated by different stimulation protocols, and construct a parsimonious model of calcium driven kinase and phosphatase dynamics that dictate the probability of stochastic transitions between binary synaptic weight states in a Markov model. We subsequently demonstrate that this approach can account for a range of empirical observations regarding the dynamics of synaptic plasticity induced by different stimulation protocols, under regimes of pharmacological blockade and metaplasticity. Finally, we highlight the strengths and weaknesses of this parsimonious, unified computational synaptic plasticity model, discuss differences between the properties of cortical and hippocampal plasticity highlighted by the experimental literature, and the manner in which further empirical and theoretical research might elucidate the cellular basis of mammalian learning and memory function

TOI-2257 b : a highly eccentric long-period sub-Neptune transiting a nearby M dwarf

Context. Thanks to the relative ease of finding and characterizing small planets around M-dwarf stars, these objects have become cornerstones in the field of exoplanet studies. The current paucity of planets in long-period orbits around M dwarfs makes such objects particularly compelling as they provide clues about the formation and evolution of these systems. Aims. In this study we present the discovery of TOI-2257 b (TIC 198485881), a long-period (35 d) sub-Neptune orbiting an M3 star at 57.8 pc. Its transit depth is about 0.4%, large enough to be detected with medium-size, ground-based telescopes. The long transit duration suggests the planet is in a highly eccentric orbit (e ~ 0.5), which would make it the most eccentric planet known to be transiting an M-dwarf star. Methods. We combined TESS and ground-based data obtained with the 1.0-meter SAINT-EX, 0.60-meter TRAPPIST-North, and 1.2-meter FLWO telescopes to find a planetary size of 2.2 R⊕ and an orbital period of 35.19 days. In addition, we make use of archival data, high-resolution imaging, and vetting packages to support our planetary interpretation. Results. With its long period and high eccentricity, TOI-2257 b falls into a novel slice of parameter space. Despite the planet’s low equilibrium temperature (~256 K), its host star’s small size (R* = 0.311 ± 0.015) and relative infrared brightness (Kmag = 10.7) make it a suitable candidate for atmospheric exploration via transmission spectroscopy

Herophilus and Erasistratus on the hēgemonikon

This is the author accepted manuscript. The final version is available from Cambridge University Press via the DOI in this record.In Alexandria at some point in the early third century bc, Herophilus of Chalcedon identified the nerves as a distinct system within the body, traced their origins to the brain, and recognised their role in transmitting sensation and voluntary motion. His discovery was based on dissection and vivisection, not only of animals, but also of human beings. Herophilus’ younger contemporary Erasistratus also integrated these findings into his rather bolder physiology. The implications of this discovery were of course wide-ranging. From a modern perspective, it is now widely celebrated as having established, for the first time on something like a scientific basis, that the brain has more or less the functions that we now ascribe to it. Likewise, in antiquity, Galen relied heavily on Herophilus’ discovery in his proof that the rational soul is located in the brain. As we shall see, it also had an impact on Stoic psychology. What exactly Herophilus and Erasistratus saw as its implications, however, is a different question, and the difficulties in answering it are considerable given the state of the evidence

Creating and curating an archive: Bury St Edmunds and its Anglo-Saxon past

This contribution explores the mechanisms by which the Benedictine foundation of Bury St Edmunds sought to legitimise and preserve their spurious pre-Conquest privileges and holdings throughout the Middle Ages. The archive is extraordinary in terms of the large number of surviving registers and cartularies which contain copies of Anglo-Saxon charters, many of which are wholly or partly in Old English. The essay charts the changing use to which these ancient documents were put in response to threats to the foundation's continued enjoyment of its liberties. The focus throughout the essay is to demonstrate how pragmatic considerations at every stage affects the development of the archive and the ways in which these linguistically challenging texts were presented, re-presented, and represented during the Abbey’s history

Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease

BACKGROUND: Patients with atherosclerotic vascular disease remain at high risk for cardiovascular events despite effective statin-based treatment of low-density lipoprotein (LDL) cholesterol levels. The inhibition of cholesteryl ester transfer protein (CETP) by anacetrapib reduces LDL cholesterol levels and increases high-density lipoprotein (HDL) cholesterol levels. However, trials of other CETP inhibitors have shown neutral or adverse effects on cardiovascular outcomes. METHODS: We conducted a randomized, double-blind, placebo-controlled trial involving 30,449 adults with atherosclerotic vascular disease who were receiving intensive atorvastatin therapy and who had a mean LDL cholesterol level of 61 mg per deciliter (1.58 mmol per liter), a mean non-HDL cholesterol level of 92 mg per deciliter (2.38 mmol per liter), and a mean HDL cholesterol level of 40 mg per deciliter (1.03 mmol per liter). The patients were assigned to receive either 100 mg of anacetrapib once daily (15,225 patients) or matching placebo (15,224 patients). The primary outcome was the first major coronary event, a composite of coronary death, myocardial infarction, or coronary revascularization. RESULTS: During the median follow-up period of 4.1 years, the primary outcome occurred in significantly fewer patients in the anacetrapib group than in the placebo group (1640 of 15,225 patients [10.8%] vs. 1803 of 15,224 patients [11.8%]; rate ratio, 0.91; 95% confidence interval, 0.85 to 0.97; P=0.004). The relative difference in risk was similar across multiple prespecified subgroups. At the trial midpoint, the mean level of HDL cholesterol was higher by 43 mg per deciliter (1.12 mmol per liter) in the anacetrapib group than in the placebo group (a relative difference of 104%), and the mean level of non-HDL cholesterol was lower by 17 mg per deciliter (0.44 mmol per liter), a relative difference of -18%. There were no significant between-group differences in the risk of death, cancer, or other serious adverse events. CONCLUSIONS: Among patients with atherosclerotic vascular disease who were receiving intensive statin therapy, the use of anacetrapib resulted in a lower incidence of major coronary events than the use of placebo. (Funded by Merck and others; Current Controlled Trials number, ISRCTN48678192 ; ClinicalTrials.gov number, NCT01252953 ; and EudraCT number, 2010-023467-18 .)