Workflow for the generation of expert-derived training and validation data: a view to global scale habitat mapping

Our ability to completely and repeatedly map natural environments at a global scale have increased significantly over the past decade. These advances are from delivery of a range of on-line global satellite image archives and global-scale processing capabilities, along with improved spatial and temporal resolution satellite imagery. The ability to accurately train and validate these global scale-mapping programs from what we will call “reference data sets” is challenging due to a lack of coordinated financial and personnel resourcing, and standardized methods to collate reference datasets at global spatial extents. Here, we present an expert-driven approach for generating training and validation data on a global scale, with the view to mapping the world’s coral reefs. Global reefs were first stratified into approximate biogeographic regions, then per region reference data sets were compiled that include existing point data or maps at various levels of accuracy. These reference data sets were compiled from new field surveys, literature review of published surveys, and from individually sourced contributions from the coral reef monitoring and management agencies. Reference data were overlaid on high spatial resolution satellite image mosaics (3.7 m × 3.7 m pixels; Planet Dove) for each region. Additionally, thirty to forty satellite image tiles; 20 km × 20 km) were selected for which reference data and/or expert knowledge was available and which covered a representative range of habitats. The satellite image tiles were segmented into interpretable groups of pixels which were manually labeled with a mapping category via expert interpretation. The labeled segments were used to generate points to train the mapping models, and to validate or assess accuracy. The workflow for desktop reference data creation that we present expands and up-scales traditional approaches of expert-driven interpretation for both manual habitat mapping and map training/validation. We apply the reference data creation methods in the context of global coral reef mapping, though our approach is broadly applicable to any environment. Transparent processes for training and validation are critical for usability as big data provide more opportunities for managers and scientists to use global mapping products for science and conservation of vulnerable and rapidly changing ecosystems

Dynamic Imprints of Colliding-wind Dust Formation from WR 140

Carbon-rich Wolf-Rayet (WR) binaries are a prominent source of carbonaceous dust that contribute to the dust budget of galaxies. The “textbook” example of an episodic dust-producing WR binary, WR 140 (HD 193793), provides us with an ideal laboratory for investigating the dust physics and kinematics in an extreme environment. This study is among the first to utilize two separate JWST observations, from Cycle 1 ERS (2022 July) and Cycle 2 (2023 September), to measure WR 140’s dust kinematics and confirm its morphology. To measure the proper motions and projected velocities of the dust shells, we performed a novel point-spread function (PSF) subtraction to reduce the effects of the bright diffraction spikes and carefully aligned the Cycle 2 to the Cycle 1 images. At 7.7 μm, through the bright feature common to 16 dust shells (C1), we find an average dust shell proper motion of 390 ± 29 mas yr−1, which equates to a projected velocity of 2714 ± 188 km s−1 at a distance of 1.64 kpc. Our measured speeds are constant across all visible shells and consistent with previously reported dust expansion velocities. Our observations not only prove that these dusty shells are astrophysical (i.e., not associated with any PSF artifact) and originate from WR 140, but also confirm the “clumpy” morphology of the dust shells, in which identifiable substructures within certain shells persist for at least 14 months from one cycle to the next. These results support the hypothesis that clumping in the wind collision region is required for dust production in WR binaries

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

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

New global area estimates for coral reefs from high-resolution mapping

Summary: Coral reefs underpin the environmental, social, and economic fabrics of much of the world's tropical coast. Yet, the fine-scale distribution and composition of coral reefs have never been reported consistently across the planet. Here, we present new area estimates enabled by global geomorphic zone and benthic substrate maps at 5 m pixel resolution. We revise global coral reef estimates to 348,361 km2 of shallow coral reefs and 80,213 km2 (46,237–106,319 km2, 95% confidence interval) of coral habitat. The mapping used more than 1.5 million training samples supported by 480+ data contributions to deploy a coral reef classification of over 100 trillion pixels from the Sentinel-2 satellites and the Planet Dove CubeSat constellation. The publicly available maps are accessible via the Allen Coral Atlas and Google Earth Engine and are already being used by thousands of people to improve the conservation, management, and research of coral reef ecosystems. Science for society: Coral reefs possess a quarter of all marine life and contribute to the well-being and livelihoods of a billion people worldwide. Maps of ecosystems underpin many science and conservation activities, but until recently, there were no consistent high-resolution maps of the world’s coral reefs. In this paper, we describe new global coral reef maps from the Allen Coral Atlas, detailing the underlying methodology and our new understanding of the global distribution of coral reefs. The transparent and repeatable nature of our mapping framework allows the maps to be updated based on user feedback, and the ease of access has led to downstream applications such as coral bleaching monitoring and usage in scientific, management, and conservation activities. Hundreds of thousands of people have already accessed the maps, and they are already being used directly around the world for marine spatial planning, marine protected areas, environmental accounting and assessments, restoration, and education

Dynamic Imprints of Colliding-wind Dust Formation from WR 140

This article was originally published in The Astrophysical Journal Letters. The version of record is available at: https://doi.org/10.3847/2041-8213/ad9aa9. © 2025. The Author(s). Published by the American Astronomical Society. Original content from this work may be used under the terms of the Creative Commons Attribution 4.0 licence (https://creativecommons.org/licenses/by/4.0/). Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI.Carbon-rich Wolf–Rayet (WR) binaries are a prominent source of carbonaceous dust that contribute to the dust budget of galaxies. The "textbook" example of an episodic dust-producing WR binary, WR 140 (HD 193793), provides us with an ideal laboratory for investigating the dust physics and kinematics in an extreme environment. This study is among the first to utilize two separate JWST observations, from Cycle 1 ERS (2022 July) and Cycle 2 (2023 September), to measure WR 140's dust kinematics and confirm its morphology. To measure the proper motions and projected velocities of the dust shells, we performed a novel point-spread function (PSF) subtraction to reduce the effects of the bright diffraction spikes and carefully aligned the Cycle 2 to the Cycle 1 images. At 7.7 μm, through the bright feature common to 16 dust shells (C1), we find an average dust shell proper motion of 390 ± 29 mas yr−1, which equates to a projected velocity of 2714 ± 188 km s−1 at a distance of 1.64 kpc. Our measured speeds are constant across all visible shells and consistent with previously reported dust expansion velocities. Our observations not only prove that these dusty shells are astrophysical (i.e., not associated with any PSF artifact) and originate from WR 140, but also confirm the "clumpy" morphology of the dust shells, in which identifiable substructures within certain shells persist for at least 14 months from one cycle to the next. These results support the hypothesis that clumping in the wind collision region is required for dust production in WR binaries.The work of E.P.L. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the U.S. National Science Foundation. J.L.H. acknowledges support from the National Science Foundation under award AST-1816944. T.O. acknowledges support by the Japan Society for the Promotion of Science (JSPS) KAKENHI grant No. JP24K07087. N.D.R. is grateful for support from the Cottrell Scholar Award #CS-CSA-2023-143 sponsored by the Research Corporation for Science Advancement. J.S.-B. acknowledges the support received from the UNAM PAPIIT project IA 105023. C.M.P.R. acknowledges support from NASA Chandra Theory grant TM3-24001X. This material is based upon work supported by NASA under award number 80GSFC24M0006 and based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract number NAS 5-03127 for JWST. These observations are associated with programs #3823 and #1349. Support for program #3823 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127. We thank the anonymous reviewer for insightful feedback that improved the quality of this manuscript. We thank Christopher Packham and Mason Leist for their valuable discussions about the MIRI PSF subtraction

Dynamic Imprints of Colliding-wind Dust Formation from WR 140

Carbon-rich Wolf–Rayet (WR) binaries are a prominent source of carbonaceous dust that contribute to the dust budget of galaxies. The "textbook" example of an episodic dust-producing WR binary, WR 140 (HD 193793), provides us with an ideal laboratory for investigating the dust physics and kinematics in an extreme environment. This study is among the first to utilize two separate JWST observations, from Cycle 1 ERS (2022 July) and Cycle 2 (2023 September), to measure WR 140's dust kinematics and confirm its morphology. To measure the proper motions and projected velocities of the dust shells, we performed a novel point-spread function (PSF) subtraction to reduce the effects of the bright diffraction spikes and carefully aligned the Cycle 2 to the Cycle 1 images. At 7.7 μm, through the bright feature common to 16 dust shells (C1), we find an average dust shell proper motion of 390 ± 29 mas yr⁻¹, which equates to a projected velocity of 2714 ± 188 km s⁻¹ at a distance of 1.64 kpc. Our measured speeds are constant across all visible shells and consistent with previously reported dust expansion velocities. Our observations not only prove that these dusty shells are astrophysical (i.e., not associated with any PSF artifact) and originate from WR 140, but also confirm the "clumpy" morphology of the dust shells, in which identifiable substructures within certain shells persist for at least 14 months from one cycle to the next. These results support the hypothesis that clumping in the wind collision region is required for dust production in WR binaries.The work of E.P.L. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the U.S. National Science Foundation. J.L.H. acknowledges support from the National Science Foundation under award AST-1816944. T.O. acknowledges support by the Japan Society for the Promotion of Science (JSPS) KAKENHI grant No. JP24K07087. N.D.R. is grateful for support from the Cottrell Scholar Award #CS-CSA-2023-143 sponsored by the Research Corporation for Science Advancement. J.S.-B. acknowledges the support received from the UNAM PAPIIT project IA 105023. C.M.P.R. acknowledges support from NASA Chandra Theory grant TM3-24001X. This material is based upon work supported by NASA under award number 80GSFC24M0006 and based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract number NAS 5-03127 for JWST. These observations are associated with programs #3823 and #1349. Support for program #3823 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127. We thank the anonymous reviewer for insightful feedback that improved the quality of this manuscript. We thank Christopher Packham and Mason Leist for their valuable discussions about the MIRI PSF subtraction.https://iopscience.iop.org/article/10.3847/2041-8213/ad9aa

Large-scale and long-term wildlife research and monitoring using camera traps: a continental synthesis

Camera traps are widely used in wildlife research and monitoring, so it is imperative to understand their strengths, limitations, and potential for increasing impact. We investigated a decade of use of wildlife cameras (2012–2022) with a case study on Australian terrestrial vertebrates using a multifaceted approach. We (i) synthesised information from a literature review; (ii) conducted an online questionnaire of 132 professionals; (iii) hosted an in-person workshop of 28 leading experts representing academia, non-governmental organisations (NGOs), and government; and (iv) mapped camera trap usage based on all sources. We predicted that the last decade would have shown: (i) exponentially increasing sampling effort, a continuation of camera usage trends up to 2012; (ii) analytics to have shifted from naive presence/absence and capture rates towards hierarchical modelling that accounts for imperfect detection, thereby improving the quality of outputs and inferences on occupancy, abundance, and density; and (iii) broader research scales in terms of multi-species, multi-site and multi-year studies. However, the results showed that the sampling effort has reached a plateau, with publication rates increasing only modestly. Users reported reaching a saturation point in terms of images that could be processed by humans and time for complex analyses and academic writing. There were strong taxonomic and geographic biases towards medium–large mammals (>500 g) in forests along Australia's southeastern coastlines, reflecting proximity to major cities. Regarding analytical choices, bias-prone indices still accounted for ~50% of outputs and this was consistent across user groups. Multi-species, multi-site and multiple-year studies were rare, largely driven by hesitancy around collaboration and data sharing. There is no widely used repository for wildlife camera images and the Atlas of Living Australia (ALA) is the dominant repository for sharing tabular occurrence records. However, the ALA is presence-only and thus is unsuitable for creating detection histories with absences, inhibiting hierarchical modelling. Workshop discussions identified a pressing need for collaboration to enhance the efficiency, quality and scale of research and management outcomes, leading to the proposal of a Wildlife Observatory of Australia (WildObs). To encourage data standards and sharing, WildObs should (i) promote a metadata collection app; (ii) create a tagged image repository to facilitate artificial intelligence/machine learning (AI/ML) computer vision research in this space; (iii) address the image identification bottleneck via the use of AI/ML-powered image-processing platforms; (iv) create data commons for detection histories that are suitable for hierarchical modelling; and (v) provide capacity building and tools for hierarchical modelling. Our review highlights that while Australia's investments in monitoring biodiversity with cameras position it to be a global leader in this context, realising that potential requires a paradigm shift towards best practices for collecting, curating, sharing and analysing ‘Big Data’. Our findings and framework have broad applicability outside Australia to enhance camera usage to meet conservation and management objectives ranging from local to global scales. This review articulates a country/continental observatory approach that is also suitable for international collaborative wildlife research networks

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 b-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 3 10-4), improved b-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