A view from above: using Unmanned Aerial Vehicles (UAVs) to enhance ecological understanding of lianas in tropical forest canopies

Lianas play integral roles in structuring community composition, forest regeneration, the maintenance of species diversity and whole-forest level ecosystem processes in tropical forests. With increasing disturbances to forests worldwide, the relative importance of lianas as players in many areas of forest dynamics is expected to increase, with important ramifications for the global carbon cycle. However, our knowledge of lianas is incomplete and biased: (i) towards the Neotropics; and (ii) against the canopy, yet the canopy is where lianas proliferate most. Research in these areas is hampered by the logistical difficulties of studying lianas; the fact that they are time-consuming to survey, and that it is difficult to quantify what is going on in the canopy. This thesis enhances ecological understanding of lianas in tropical forest tree crowns, focusing on the lesser studied Palaeotropics. The development of a novel method to enable faster, cheaper and more canopy-centred assessment of liana than possible with traditional assessment methods is vital for this. A lightweight unmanned aerial vehicle (UAV) was used to assess liana infestation of tropical forest tree canopies in Sabah, Malaysia. By visually interpreting the images, the UAV-derived liana infestation estimates were compared with those derived from traditional ground methods of liana infestation assessment to determine the validity, strengths and weaknesses of using UAVs as a new method for assessing liana infestation of tree canopies. These data were then used to map and monitor liana load in tree crowns: (i) spatially, to elucidate liana-environmental relationships; and (ii) temporally, to monitor the canopy response, including changes in liana infestation, to El Niño drought. UAV-derived estimates of liana infestation correlated strongly with ground-derived data at individual tree and plot level, and across multiple forest types and spatial resolutions. Furthermore, the UAV surveys improved liana infestation assessment for upper canopy layers and were considerably faster and more cost-efficient than ground-based surveys. Liana infestation was significantly spatially aggregated, with tree canopy height and presence of canopy gaps being the most important variables influencing this. Taller trees were less often and less heavily infested by lianas while liana infestation occurred more often and to greater extents in close proximity to canopy gaps. Temporally, tree-level liana infestation and crown area showed significant increases in the aftermath of the 2015/16 El Niño whereas crown greenness and tree leaf cover showed a significant decrease. Furthermore, liana cover was significantly higher for trees that experienced mortality in the aftermath of the El Niño than for those that did not. This thesis presents a novel UAV-based method of capturing data that can be used to assess liana infestation of tropical forest tree crowns at least as accurately as traditional ground data. This novel method promotes reproducibility of results and quality control, and enables additional variables to be derived from the image data. It is more cost-effective, time-efficient and covers larger geographical extents than traditional ground surveys, enabling more comprehensive monitoring of changes in liana infestation over space and time. By utilising the new UAV method, this thesis presents: (i) the largest and most comprehensive continuous assessment of Palaeotropical tree crown liana infestation, and analysis of environmental variables that may influence this, to date; and (ii) the first study assessing short-term temporal change in liana canopy cover and associated alterations in the forest canopy using UAV image data. Examining how and why lianas are distributed in the forest canopy and how this changes through time may help us to determine what variables could determine increases in lianas with environmental change in the future, with important implications for tropical forest carbon storage and sequestration, and provide a step towards more comprehensive testing of ecological theory in tropical forests

A view from above: Unmanned aerial vehicles (UAVs) provide a new tool for assessing liana infestation in tropical forest canopies

1. Tropical forests store and sequester large quantities of carbon, mitigating climate change. Lianas (woody vines) are important tropical forest components, most conspicuous in the canopy. Lianas reduce forest carbon uptake and their recent increase may, therefore, limit forest carbon storage with global consequences for climate change. Liana infestation of tree crowns is traditionally assessed from the ground, which is labour intensive and difficult, particularly for upper canopy layers.2. We used a lightweight unmanned aerial vehicle (UAV) to assess liana infestation of tree canopies from above. It was a commercially available quadcopter UAV with an integrated, standard three‐waveband camera to collect aerial image data for 150 ha of tropical forest canopy. By visually interpreting the images, we assessed the degree of liana infestation for 14.15 ha of forest for which ground‐based estimates were collected simultaneously. We compared the UAV liana infestation estimates with those from the ground to determine the validity, strengths, and weaknesses of using UAVs as a new method for assessing liana infestation of tree canopies.3. Estimates of liana infestation from the UAV correlated strongly with ground‐based surveys at individual tree and plot level, and across multiple forest types and spatial resolutions, improving liana infestation assessment for upper canopy layers. Importantly, UAV‐based surveys, including the image collection, processing, and visual interpretation, were considerably faster and more cost‐efficient than ground‐based surveys. 4. Synthesis and applications. Unmanned aerial vehicle (UAV) image data of tree canopies can be easily captured and used to assess liana infestation at least as accurately as traditional ground data. This novel method promotes reproducibility of results and quality control, and enables additional variables to be derived from the image data. It is more cost‐effective, time‐efficient and covers larger geographical extents than traditional ground surveys, enabling more comprehensive monitoring of changes in liana infestation over space and time. This is important for assessing liana impacts on the global carbon balance, and particularly useful for forest management where knowledge of the location and change in liana infestation can be used for tailored, targeted, and effective management of tropical forests for enhanced carbon sequestration (e.g., REDD+ projects), timber concessions, and forest restoration

Fifteen essential science advances needed for effective restoration of the world's forest landscapes

There has never been a more pressing and opportune time for science and practice to collaborate towards restoration of the world's forests. Multiple uncertainties remain for achieving successful, long-term forest landscape restoration (FLR). In this article, we use expert knowledge and literature review to identify knowledge gaps that need closing to advance restoration practice, as an introduction to a landmark theme issue on FLR and the UN Decade on Ecosystem Restoration. Aligned with an Adaptive Management Cycle for FLR, we identify 15 essential science advances required to facilitate FLR success for nature and people. They highlight that the greatest science challenges lie in the conceptualization, planning and assessment stages of restoration, which require an evidence base for why, where and how to restore, at realistic scales. FLR and underlying sciences are complex, requiring spatially explicit approaches across disciplines and sectors, considering multiple objectives, drivers and trade-offs critical for decision-making and financing. The developing tropics are a priority region, where scientists must work with stakeholders across the Adaptive Management Cycle. Clearly communicated scientific evidence for action at the outset of restoration planning will enable donors, decision makers and implementers to develop informed objectives, realistic targets and processes for accountability. This article paves the way for 19 further articles in this theme issue, with author contributions from across the world. This introduction article is part of the theme issue ‘Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration’

Landscape‐scale drivers of liana load across a Southeast Asian forest canopy differ to the Neotropics

1. Lianas (woody vines) are a key component of tropical forests, known to reduce forest carbon storage and sequestration and to be increasing in abundance. Analysing how and why lianas are distributed in forest canopies at landscape scales will help us determine the mechanisms driving changes in lianas over time. This will improve our understanding of liana ecology and projections of tropical forest carbon storage now and into the future. Despite competing hypotheses on the mechanisms driving spatial patterning of lianas, few studies have integrated multiple tree-level biotic and abiotic factors in an analytical framework. None have done so in the Palaeotropics, which are biogeographically and evolutionarily distinct from the Neotropics, where most research on lianas has been conducted.2. We used an unoccupied aerial system (UAS; drone) to assess liana load in 50- ha of Palaeotropical forest canopy in Southeast Asia. We obtained data on hypothesised drivers of liana spatial distribution in the forest canopy, including disturbance, tree characteristics, soil chemistry and topography, from the UAS, from airborne LiDAR and from ground surveys. We integrated these in a comprehensive analytical framework to extract variables at an individual-tree level and evaluated the relative strengths of the hypothesised drivers and their ability to predict liana distributions through boosted regression tree (BRT) modelling.3. Tree height and distance to canopy gaps were the two most important predictors of liana load, with relative contribution values in BRT models of 34.60%–45.39% and 7.93%–10.19%, respectively. Our results suggest that taller trees were less often and less heavily infested by lianas than shorter trees, opposite to Neotropical findings. Lianas also occurred more often, and to a greater extent, in tree crowns close to canopy gaps and to neighbouring trees with lianas in their crown.4. Synthesis. Despite their known importance and prevalence in tropical forests, lianas are not well understood, particularly in the Palaeotropics. Examining 2428 trees across 50-ha of Palaeotropical forest canopy in Southeast Asia, we find support for the hypothesis that canopy gaps promote liana infestation. However, we also found that liana presence and load declined with tree height, which is opposite to well-established Neotropical findings. This suggests a fundamental difference between Neotropical and Southeast Asian forests. Considering that most liana literature has focused on the Neotropics, this highlights the need for additional studies in other biogeographic regions to clarify potential differences and enable us to better understand liana impacts on tropical forest ecology, carbon storage and sequestration

From Big Society to Shared Society? Geographies of social cohesion and encounter in the UK’s National Citizen Service

This article explores and expands debates on the geographies of social cohesion and encounter, specifically in relation to young people and informal citizenship training. Three questions drive our agenda in this paper. First, how do certain youth spaces get enrolled into wider political discourses, functioning as geographical expressions of government visions to create a political legacy? Second, how are these spaces engineered and operate on-the-ground? Finally, how do young people understand their experiences of such spaces? To address these questions, we use the example of ‘National Citizen Service’ – a youth programme operating in England and Northern Ireland – to raise critical questions about the wider politics of spaces of informal education and attempts by the state to ‘make’ citizens and future neighbours. The article examines the rationale for this growing scheme, targeted at 15–17 year olds and designed to foster a ‘more cohesive, responsible and engaged society’. Drawing on original fieldwork with key architects, stakeholders and young people, we analyse the narratives that underlie NCS and its expansion – specifically around social cohesion and citizenship education. We explore the idea of ‘social mix’ as one of NCS’ guiding principles and its place as part of state narratives about the ‘Big Society’ and ‘Shared Society’

Identification of the top TESS objects of interest for atmospheric characterization of transiting exoplanets with JWST

Funding: Funding for the TESS mission is provided by NASA's Science Mission Directorate. 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). MSIP is funded by NSF. This paper is based on observations made with the MuSCAT3 instrument, developed by the Astrobiology Center and under financial support by JSPS KAKENHI (grant No. JP18H05439) and JST PRESTO (grant No. JPMJPR1775), at Faulkes Telescope North on Maui, HI, operated by the Las Cumbres Observatory. This paper makes use of data from the MEarth Project, which is a collaboration between Harvard University and the Smithsonian Astrophysical Observatory. The MEarth Project acknowledges funding from the David and Lucile Packard Fellowship for Science and Engineering, the National Science Foundation under grant Nos. AST-0807690, AST-1109468, AST-1616624 and AST-1004488 (Alan T. Waterman Award), the National Aeronautics and Space Administration under grant No. 80NSSC18K0476 issued through the XRP Program, and the John Templeton Foundation. C.M. would like to gratefully acknowledge the entire Dragonfly Telephoto Array team, and Bob Abraham in particular, for allowing their telescope bright time to be put to use observing exoplanets. B.J.H. acknowledges support from the Future Investigators in NASA Earth and Space Science and Technology (FINESST) program (grant No. 80NSSC20K1551) and support by NASA under grant No. 80GSFC21M0002. K.A.C. and C.N.W. acknowledge support from the TESS mission via subaward s3449 from MIT. D.R.C. and C.A.C. acknowledge support from NASA through the XRP grant No. 18-2XRP18_2-0007. C.A.C. acknowledges that this research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004). S.Z. and A.B. acknowledge support from the Israel Ministry of Science and Technology (grant No. 3-18143). The research leading to these results has received funding from the ARC grant for Concerted Research Actions, financed by the Wallonia-Brussels Federation. TRAPPIST is funded by the Belgian Fund for Scientific Research (Fond National de la Recherche Scientifique, FNRS) under the grant No. PDR T.0120.21. The postdoctoral fellowship of K.B. is funded by F.R.S.-FNRS grant No. T.0109.20 and by the Francqui Foundation. H.P.O.'s contribution has been carried out within the framework of the NCCR PlanetS supported by the Swiss National Science Foundation under grant Nos. 51NF40_182901 and 51NF40_205606. F.J.P. acknowledges financial support from the grant No. CEX2021-001131-S funded by MCIN/AEI/ 10.13039/501100011033. A.J. acknowledges support from ANID—Millennium Science Initiative—ICN12_009 and from FONDECYT project 1210718. Z.L.D. acknowledges the MIT Presidential Fellowship and that this material is based upon work supported by the National Science Foundation Graduate Research Fellowship under grant No. 1745302. P.R. acknowledges support from the National Science Foundation grant No. 1952545. This work is partly supported by JSPS KAKENHI grant Nos. JP17H04574, JP18H05439, JP21K20376; JST CREST grant No. JPMJCR1761; and Astrobiology Center SATELLITE Research project AB022006. This publication benefits from the support of the French Community of Belgium in the context of the FRIA Doctoral Grant awarded to M.T. D.D. acknowledges support from TESS Guest Investigator Program grant Nos. 80NSSC22K1353, 80NSSC22K0185, and 80NSSC23K0769. A.B. acknowledges the support of M.V. Lomonosov Moscow State University Program of Development. T.D. was supported in part by the McDonnell Center for the Space Sciences. V.K. acknowledges support from the youth scientific laboratory project, topic FEUZ-2020-0038.JWST has ushered in an era of unprecedented ability to characterize exoplanetary atmospheres. While there are over 5000 confirmed planets, more than 4000 Transiting Exoplanet Survey Satellite (TESS) planet candidates are still unconfirmed and many of the best planets for atmospheric characterization may remain to be identified. We present a sample of TESS planets and planet candidates that we identify as “best-in-class” for transmission and emission spectroscopy with JWST. These targets are sorted into bins across equilibrium temperature Teq and planetary radius Rp and are ranked by a transmission and an emission spectroscopy metric (TSM and ESM, respectively) within each bin. We perform cuts for expected signal size and stellar brightness to remove suboptimal targets for JWST. Of the 194 targets in the resulting sample, 103 are unconfirmed TESS planet candidates, also known as TESS Objects of Interest (TOIs). We perform vetting and statistical validation analyses on these 103 targets to determine which are likely planets and which are likely false positives, incorporating ground-based follow-up from the TESS Follow-up Observation Program to aid the vetting and validation process. We statistically validate 18 TOIs, marginally validate 31 TOIs to varying levels of confidence, deem 29 TOIs likely false positives, and leave the dispositions for four TOIs as inconclusive. Twenty-one of the 103 TOIs were confirmed independently over the course of our analysis. We intend for this work to serve as a community resource and motivate formal confirmation and mass measurements of each validated planet. We encourage more detailed analysis of individual targets by the community.Peer reviewe

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

OBJECTIVE: Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired β-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology. RESEARCH DESIGN AND METHODS: We have conducted a meta-analysis of genome-wide association tests of ∼2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates. RESULTS: Nine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 × 10(-4)), improved β-cell function (P = 1.1 × 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets. CONCLUSIONS: We have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis