| 1. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Bellm, Eric C., et al.
(author)
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The Zwicky Transient Facility : System Overview, Performance, and First Results
- 2019
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In: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 131:995
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Journal article (peer-reviewed)abstract
- The Zwicky Transient Facility (ZTF) is a new optical time-domain survey that uses the Palomar 48 inch Schmidt telescope. A custom-built wide-field camera provides a 47 deg(2) field of view and 8 s readout time, yielding more than an order of magnitude improvement in survey speed relative to its predecessor survey, the Palomar Transient Factory. We describe the design and implementation of the camera and observing system. The ZTF data system at the Infrared Processing and Analysis Center provides near-real-time reduction to identify moving and varying objects. We outline the analysis pipelines, data products, and associated archive. Finally, we present on-sky performance analysis and first scientific results from commissioning and the early survey. ZTF's public alert stream will serve as a useful precursor for that of the Large Synoptic Survey Telescope.
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| 3. |
- Craddock, Nick, et al.
(author)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Journal article (peer-reviewed)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 4. |
- Farnocchia, Davide, et al.
(author)
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International Asteroid Warning Network Timing Campaign: 2019 XS
- 2022
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In: The Planetary Science Journal. - : Institute of Physics Publishing (IOPP). - 2632-3338. ; 3:7
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Journal article (peer-reviewed)abstract
- As part of the International Asteroid Warning Network's observational exercises, we conducted a campaign to observe near-Earth asteroid 2019 XS around its close approach to Earth on 2021 November 9. The goal of the campaign was to characterize errors in the observation times reported to the Minor Planet Center, which become an increasingly important consideration as astrometric accuracy improves and more fast-moving asteroids are observed. As part of the exercise, a total of 957 astrometric observations of 2019 XS during the encounter were reported and subsequently were analyzed to obtain the corresponding residuals. While the timing errors are typically smaller than 1 s, the reported times appear to be negatively biased, i.e., they are generally earlier than they should be. We also compared the observer-provided position uncertainty with the cross-track residuals, which are independent of timing errors. A large fraction of the estimated uncertainties appear to be optimistic, especially when <0 2. We compiled individual reports for each observer to help identify and remove the root cause of any possible timing error and improve the uncertainty quantification process. We suggest possible sources of timing errors and describe a simple procedure to derive reliable, conservative position uncertainties.
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| 5. |
- Farnocchia, Davide, et al.
(author)
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The Second International Asteroid Warning Network Timing Campaign: 2005 LW3
- 2023
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In: The Planetary Science Journal. - : Institute of Physics (IOP). - 2632-3338. ; 4:11
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Journal article (peer-reviewed)abstract
- The Earth close approach of near-Earth asteroid 2005 LW3 on 2022 November 23 represented a good opportunity for a second observing campaign to test the timing accuracy of astrometric observation. With 82 participating stations, the International Asteroid Warning Network collected 1046 observations of 2005 LW3 around the time of the close approach. Compared to the previous timing campaign targeting 2019 XS, some individual observers were able to significantly improve the accuracy of their reported observation times. In particular, U.S. surveys achieved good timing performance. However, no broad, systematic improvement was achieved compared to the previous campaign, with an overall negative bias persisting among the different observers. The calibration of observing times and the mitigation of timing errors should be important future considerations for observers and orbit computers, respectively.
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| 6. |
- Rhodes, Olin E., et al.
(author)
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Integration of ecosystem science into radioecology : A consensus perspective
- 2020
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 740
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Journal article (peer-reviewed)abstract
- In the Fall of 2016 a workshop was held which brought together over 50 scientists from the ecological and radiological fields to discuss feasibility and challenges of reintegrating ecosystem science into radioecology. There is a growing desire to incorporate attributes of ecosystem science into radiological risk assessment and radioecological research more generally, fueled by recent advances in quantification of emergent ecosystem attributes and the desire to accurately reflect impacts of radiological stressors upon ecosystem function. This paper is a synthesis of the discussions and consensus of the workshop participant's responses to three primary questions, which were: 1) How can ecosystem science support radiological risk assessment? 2) What ecosystem level endpoints potentially could be used for radiological risk assessment? and 3) What inference strategies and associated methods would be most appropriate to assess the effects of radionuclides on ecosystem structure and function? The consensus of the participants was that ecosystem science can and should support radiological risk assessment through the incorporation of quantitative metrics that reflect ecosystem functions which are sensitive to radiological contaminants. The participants also agreed that many such endpoints exit or are thought to exit and while many are used in ecological risk assessment currently, additional data need to be collected that link the causal mechanisms of radiological exposure to these endpoints. Finally, the participants agreed that radiological risk assessments must be designed and informed by rigorous statistical frameworks capable of revealing the causal inference tying radiological exposure to the endpoints selected for measurement.
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| 7. |
- Striano, Brendan M, et al.
(author)
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Displaced Supracondylar Humerus Fractures in Toddlers
- 2020
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In: Orthopedics. - : SLACK, Inc.. - 1938-2367 .- 0147-7447. ; 43:5, s. 421-424
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Journal article (peer-reviewed)abstract
- Gartland type III fracture is the most troublesome type of supracondylar humerus fracture. These injuries most often occur in school age children, but they are seen in pediatric patients of all ages. The goal of this study was to analyze toddlers with Gartland type III fractures to identify clinically significant differences compared with older children. A retrospective cohort study was conducted with 94 toddlers (<3 years) and 378 older children (3 to 12 years). Factors including demographics, mechanism of injury, additional injuries, location of trauma, pin configuration, postoperative complications, follow-up time, and compliance with the treatment plan were collected and compared. The study included 94 toddlers (59% girls, 2.11±0.64 years) and 378 older children (48% girls, 6.32±1.89 years), chosen at random, who were treated between 2000 and 2015. Among toddlers, fractures were more likely to occur at home (P<.001) and to be the result of suspected nonaccidental trauma (P<.001). Older children had more additional injuries (P<.001), but were no more likely to have an open fracture (P=.59) or a flexion-type fracture (P=.42). Older children were more likely to undergo open reduction (P=.03), whereas toddlers were more likely to be treated with a medial pin (P<.001). Toddlers experienced more cubitus varus (P<.001) and loss of reduction (P=.02). No difference was found in length of follow-up (P=.83) or compliance with the treatment plan (P=.11). This study provides novel insights into clinical differences between toddlers and older children with Gartland type III fractures. Knowledge of these differences can facilitate the delivery of targeted, age-specific care for patients with type III supracondylar humerus fractures. [Orthopedics. 2020;43(5);e421-e424.].
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| 8. |
- Swartling, Fredrik Johansson, et al.
(author)
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Pleiotropic role for MYCN in medulloblastoma
- 2010
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In: Genes & Development. - : Cold Spring Harbor Laboratory. - 0890-9369 .- 1549-5477. ; 24:10, s. 1059-1072
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Journal article (peer-reviewed)abstract
- Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Sonic Hedgehog (SHH) signaling drives a minority of MB, correlating with desmoplastic pathology and favorable outcome. The majority, however, arises independently of SHH and displays classic or large cell anaplastic (LCA) pathology and poor prognosis. To identify common signaling abnormalities, we profiled mRNA, demonstrating misexpression of MYCN in the majority of human MB and negligible expression in normal cerebella. We clarified a role in pathogenesis by targeting MYCN (and luciferase) to cerebella of transgenic mice. MYCN-driven MB showed either classic or LCA pathologies, with Shh signaling activated in approximately 5% of tumors, demonstrating that MYCN can drive MB independently of Shh. MB arose at high penetrance, consistent with a role for MYCN in initiation. Tumor burden correlated with bioluminescence, with rare metastatic spread to the leptomeninges, suggesting roles for MYCN in both progression and metastasis. Transient pharmacological down-regulation of MYCN led to both clearance and senescence of tumor cells, and improved survival. Targeted expression of MYCN thus contributes to initiation, progression, and maintenance of MB, suggesting a central role for MYCN in pathogenesis.
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| 9. |
- Vogt, Marissa F., et al.
(author)
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Electron densities in the ionosphere of Mars : A comparison of MARSIS and radio occultation measurements
- 2016
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In: Journal of Geophysical Research - Space Physics. - 2169-9380 .- 2169-9402. ; 121:10, s. 10241-10257
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Journal article (peer-reviewed)abstract
- Radio occultation electron densities measurements from the Mariner 9 and Viking spacecraft, which orbited Mars in the 1970s, have recently become available in a digital format. These data are highly complementary to the radio occultation electron density profiles from Mars Global Surveyor, which were restricted in solar zenith angle and altitude. Wehave compiled data from the Mariner 9, Viking, and Mars Global Surveyor radio occultation experiments for comparison to electron density measurements made by Mars AdvancedRadar for SubsurfaceandIonosphere Sounding (MARSIS), the topside radar sounder on Mars Express, and MARSIS-based empirical density models. Wefind that the electron densities measured by radio occultation are in generally good agreement with the MARSIS data and model, especially near the altitude of the peak electron density but that the MARSIS data and model display a larger plasma scale height than the radio occultation profiles at altitudes between the peak density and 200 km. Consequently, the MARSIS-measured and model electron densities are consistently larger than radio occultation densities at altitudes similar to 200-300 km. Finally, we have analyzed transitions in the topside ionosphere, at the boundary between the photochemically controlled and transport-controlled regions, and identified the average transition altitude, or altitude at which a change in scale height occurs. The average transition altitude is similar to 200 km in the Mariner 9 and Viking radio occultation profiles and in profiles of the median MARSIS radar sounding electron densities.
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| 10. |
- Žliobaitė, Indrė, et al.
(author)
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The NOW Database of Fossil Mammals
- 2023
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In: Evolution of Cenozoic Land Mammal Faunas and Ecosystems: 25 years of the NOW database of fossil mammals. - : Springer. ; , s. 33-42
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Book chapter (peer-reviewed)abstract
- NOW (New and Old Worlds) is a global database of fossil mammal occurrences, currently containing around 68,000 locality-species entries. The database spans the last 66 million years, with its primary focus on the last 23 million years. Whereas the database contains records from all continents, the main focus and coverage of the database historically has been on Eurasia. The database includes primarily, but not exclusively, terrestrial mammals. It covers a large part of the currently known mammalian fossil record, focusing on classical and actively researched fossil localities. The database is managed in collaboration with an international advisory board of experts. Rather than a static archive, it emphasizes the continuous integration of new knowledge of the community, data curation, and consistency of scientific interpretations. The database records species occurrences at localities worldwide, as well as ecological characteristics of fossil species, geological contexts of localities and more. The NOW database is primarily used for two purposes: (1) queries about occurrences of particular taxa, their characteristics and properties of localities in the spirit of an encyclopedia; and (2) large scale research and quantitative analyses of evolutionary processes, patterns, reconstructing past environments, as well as interpreting evolutionary contexts. The data are fully open, no logging in or community membership is necessary for using the data for any purpose.
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| 11. |
- Flynn, Alison B., et al.
(author)
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Future Directions for Systems Thinking in Chemistry Education : Putting the Pieces Together
- 2019
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In: Journal of Chemical Education. - : AMER CHEMICAL SOC. - 0021-9584 .- 1938-1328. ; 96:12, s. 3000-3005
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Journal article (peer-reviewed)abstract
- The International Union of Pure & Applied Chemistry (IUPAC) launched a global project in 2017 to infuse systems thinking into chemistry education, motivated in part by the desire to help equip chemists and citizens to better address the complex, global challenges our society currently faces. One important early outcome of the IUPAC Systems Thinking in Chemistry Education (STICE) project is this special issue of the Journal of Chemical Education, which provides a key reference point for the rapidly emerging literature on the incorporation of systems thinking into chemistry education, including its application to green and sustainable chemistry. The STICE project outcomes to date include reviewing systems thinking approaches in other STEM fields, articulating a framework for STICE, identifying aspects of learning theories relevant to learning systems thinking skills in chemistry, using systems thinking approaches to integrate green and sustainability chemistry concepts into university-level chemistry classrooms, and identifying considerations for assessing systems thinking in chemistry education. The authors of this article, who, with others, have provided leadership to the STICE project, conclude this Journal's special issue by briefly reviewing progress to date and identifying three main areas of future work for the application of systems thinking in chemistry education: (1) developing systems thinking resources for chemistry educators and students, (2) identifying chemistry education research needed to investigate and improve systems thinking approaches, and (3) investigating opportunities to apply chemistry-related systems thinking approaches in broader educational contexts. Our intention is to recommend potential opportunities, stimulate conversations, and motivate actions required to successfully equip learners with systems thinking skills in chemistry, such that these learners, citizens of our countries and our planet, are better positioned to interpret and address complex global challenges.
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| 12. |
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| 13. |
- Liew, Jean W, et al.
(author)
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A scoping review of how early-stage knee osteoarthritis has been defined
- 2023
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In: Osteoarthritis and Cartilage. - 1063-4584. ; 31:9, s. 1234-1241
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Research review (peer-reviewed)abstract
- BACKGROUND: Early-stage knee osteoarthritis (KOA) classification criteria will enable consistent identification and trial recruitment of individuals with knee osteoarthritis (OA) at an earlier stage of the disease when interventions may be more effective. Toward this goal, we identified how early-stage KOA has been defined in the literature.METHODS: We performed a scoping literature review in PubMed, EMBASE, Cochrane, and Web of Science, including human studies where early-stage KOA was included as a study population or outcome. Extracted data included demographics, symptoms/history, examination, laboratory, imaging, performance-based measures, gross inspection/histopathologic domains, and the components of composite early-stage KOA definitions.RESULTS: Of 6142 articles identified, 211 were included in data synthesis. An early-stage KOA definition was used for study inclusion in 194 studies, to define study outcomes in 11 studies, and in the context of new criteria development or validation in six studies. The element most often used to define early-stage KOA was Kellgren-Lawrence (KL) grade (151 studies, 72%), followed by symptoms (118 studies, 56%), and demographic characteristics (73 studies, 35%); 14 studies (6%) used previously developed early-stage KOA composite criteria. Among studies defining early-stage KOA radiographically, 52 studies defined early-stage KOA by KL grade alone; of these 52, 44 (85%) studies included individuals with KL grade 2 or higher in their definitions.CONCLUSION: Early-stage KOA is variably defined in the published literature. Most studies included KL grades of 2 or higher within their definitions, which reflects established or later-stage OA. These findings underscore the need to develop and validate classification criteria for early-stage KOA.
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| 14. |
- Mitra, Aditee, et al.
(author)
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Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition : Incorporation of Diverse Mixotrophic Strategies
- 2016
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In: Protist. - : Elsevier BV. - 1434-4610 .- 1618-0941. ; 167:2, s. 106-120
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Journal article (peer-reviewed)abstract
- Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic "phytoplankton" and phagotrophic "microzooplankton". However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding, we propose a new functional grouping of planktonic protists in an ecophysiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking phagotrophic capacity, (iii) constitutive mixotrophs (CMs) as phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accordingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their frameworks. (C) 2016 The Authors. Published by Elsevier GmbH.
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| 15. |
- Mullan, Rebecca J, et al.
(author)
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Systematic reviewers commonly contact study authors but do so with limited rigor.
- 2009
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In: Journal of Clinical Epidemiology. - : Elsevier BV. - 0895-4356 .- 1878-5921. ; 62:2, s. 138-142
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Journal article (peer-reviewed)abstract
- OBJECTIVES: Author contact can enhance the quality of systematic reviews. We conducted a systematic review of the practice of author contact in recently published systematic reviews to characterize its prevalence, quality, and results. STUDY DESIGN AND SETTING: Eligible studies were systematic reviews of efficacy published in 2005-2006 in the 25 journals with the highest impact factor publishing systematic reviews in clinical medicine and the Cochrane Library, identified by searching MEDLINE, EMBASE, and the Cochrane Library. Two researchers determined whether and why reviewers contacted authors. To assess the accuracy of the abstracted data, we surveyed reviewers by e-mail. RESULTS: Forty-six (50%) of the 93 eligible systematic reviews published in top journals and 46 (85%) of the 54 eligible Cochrane reviews reported contacting authors of eligible studies. Requests were made most commonly for missing information: 40 (76%) clinical medicine reviews and 45 (98%) Cochrane reviews. One hundred and nine of 147 (74%) reviewers responded to the survey, and reported a higher rate of author contact than apparent from the published record. CONCLUSION: Although common, author contact is not a universal feature of systematic reviews published in top journals and the Cochrane Library. The conduct and reporting of author contact purpose, procedures, and results require improvement.
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| 16. |
- Rich, Rebecca L., et al.
(author)
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A global benchmark study using affinity-based biosensors
- 2009
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In: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 386:2, s. 194-216
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Journal article (peer-reviewed)abstract
- To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.
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