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1.	Clark, Andrew G., et al. (author) Evolution of genes and genomes on the Drosophila phylogeny 2007 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218 Journal article (peer-reviewed)abstract Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
2.	Craddock, Nick, et al. (author) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls 2010 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720 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.
3.	Richards, Stephen, et al. (author) Genome Sequence of the Pea Aphid Acyrthosiphon pisum 2010 In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313- Journal article (peer-reviewed)abstract Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
4.	Bellm, Eric C., et al. (author) The Zwicky Transient Facility : System Overview, Performance, and First Results 2019 In: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 131:995 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.
5.	Bianco, Federica B., et al. (author) Optimization of the Observing Cadence for the Rubin Observatory Legacy Survey of Space and Time : A Pioneering Process of Community-focused Experimental Design 2022 In: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 258:1 Journal article (peer-reviewed)abstract Vera C. Rubin Observatory is a ground-based astronomical facility under construction, a joint project of the National Science Foundation and the U.S. Department of Energy, designed to conduct a multipurpose 10 yr optical survey of the Southern Hemisphere sky: the Legacy Survey of Space and Time. Significant flexibility in survey strategy remains within the constraints imposed by the core science goals of probing dark energy and dark matter, cataloging the solar system, exploring the transient optical sky, and mapping the Milky Way. The survey's massive data throughput will be transformational for many other astrophysics domains and Rubin's data access policy sets the stage for a huge community of potential users. To ensure that the survey science potential is maximized while serving as broad a community as possible, Rubin Observatory has involved the scientific community at large in the process of setting and refining the details of the observing strategy. The motivation, history, and decision-making process of this strategy optimization are detailed in this paper, giving context to the science-driven proposals and recommendations for the survey strategy included in this Focus Issue.
6.	Elsik, Christine G., et al. (author) The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution 2009 In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528 Journal article (peer-reviewed)abstract To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
7.	Estrada, Karol, et al. (author) Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. 2012 In: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 44:5, s. 491-501 Journal article (peer-reviewed)abstract Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We identified 56 loci (32 new) associated with BMD at genome-wide significance (P < 5 × 10(-8)). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways. However, we also discovered loci that were localized to genes not known to have a role in bone biology. Fourteen BMD-associated loci were also associated with fracture risk (P < 5 × 10(-4), Bonferroni corrected), of which six reached P < 5 × 10(-8), including at 18p11.21 (FAM210A), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility.
8.	Fedorets, Grigori, et al. (author) Discovering Earth’s transient moons with the Large Synoptic Survey Telescope 2020 In: Icarus. - : Elsevier. - 0019-1035 .- 1090-2643. ; 338 Journal article (peer-reviewed)abstract Earth's temporarily-captured orbiters (TCOs) are a sub-population of near-Earth objects (NEOs). TCOs can provide constraints for NEO population models in the 1–10-metre-diameter range, and they are outstanding targets for in situ exploration of asteroids due to a low requirement on Δv. So far there has only been a single serendipitous discovery of a TCO. Here we assess in detail the possibility of their discovery with the upcoming Large Synoptic Survey Telescope (LSST), previously identified as the primary facility for such discoveries. We simulated observations of TCOs by combining a synthetic TCO population with an LSST survey simulation. We then assessed the detection rates, detection linking and orbit computation, and sources for confusion. Typical velocities of detectable TCOs will range from 1∘/day to 50∘/day, and typical apparent V magnitudes from 21 to 23. Potentially-hazardous asteroids have observational characteristics similar to TCOs, but the two populations can be distinguished based on their orbits with LSST data alone. We predict that a TCO can be discovered once every year with the baseline moving-object processing system (MOPS). The rate can be increased to one TCO discovery every two months if tools complementary to the baseline MOPS are developed for the specific purpose of discovering these objects.
9.	Forouzanfar, Mohammad H, et al. (author) Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks in 188 countries, 1990-2013 : a systematic analysis for the Global Burden of Disease Study 2013. 2015 In: The Lancet. - 0140-6736 .- 1474-547X. ; 386:10010, s. 2287-2323 Journal article (peer-reviewed)abstract BACKGROUND: The Global Burden of Disease, Injuries, and Risk Factor study 2013 (GBD 2013) is the first of a series of annual updates of the GBD. Risk factor quantification, particularly of modifiable risk factors, can help to identify emerging threats to population health and opportunities for prevention. The GBD 2013 provides a timely opportunity to update the comparative risk assessment with new data for exposure, relative risks, and evidence on the appropriate counterfactual risk distribution.METHODS: Attributable deaths, years of life lost, years lived with disability, and disability-adjusted life-years (DALYs) have been estimated for 79 risks or clusters of risks using the GBD 2010 methods. Risk-outcome pairs meeting explicit evidence criteria were assessed for 188 countries for the period 1990-2013 by age and sex using three inputs: risk exposure, relative risks, and the theoretical minimum risk exposure level (TMREL). Risks are organised into a hierarchy with blocks of behavioural, environmental and occupational, and metabolic risks at the first level of the hierarchy. The next level in the hierarchy includes nine clusters of related risks and two individual risks, with more detail provided at levels 3 and 4 of the hierarchy. Compared with GBD 2010, six new risk factors have been added: handwashing practices, occupational exposure to trichloroethylene, childhood wasting, childhood stunting, unsafe sex, and low glomerular filtration rate. For most risks, data for exposure were synthesised with a Bayesian meta-regression method, DisMod-MR 2.0, or spatial-temporal Gaussian process regression. Relative risks were based on meta-regressions of published cohort and intervention studies. Attributable burden for clusters of risks and all risks combined took into account evidence on the mediation of some risks such as high body-mass index (BMI) through other risks such as high systolic blood pressure and high cholesterol.FINDINGS: All risks combined account for 57·2% (95% uncertainty interval [UI] 55·8-58·5) of deaths and 41·6% (40·1-43·0) of DALYs. Risks quantified account for 87·9% (86·5-89·3) of cardiovascular disease DALYs, ranging to a low of 0% for neonatal disorders and neglected tropical diseases and malaria. In terms of global DALYs in 2013, six risks or clusters of risks each caused more than 5% of DALYs: dietary risks accounting for 11·3 million deaths and 241·4 million DALYs, high systolic blood pressure for 10·4 million deaths and 208·1 million DALYs, child and maternal malnutrition for 1·7 million deaths and 176·9 million DALYs, tobacco smoke for 6·1 million deaths and 143·5 million DALYs, air pollution for 5·5 million deaths and 141·5 million DALYs, and high BMI for 4·4 million deaths and 134·0 million DALYs. Risk factor patterns vary across regions and countries and with time. In sub-Saharan Africa, the leading risk factors are child and maternal malnutrition, unsafe sex, and unsafe water, sanitation, and handwashing. In women, in nearly all countries in the Americas, north Africa, and the Middle East, and in many other high-income countries, high BMI is the leading risk factor, with high systolic blood pressure as the leading risk in most of Central and Eastern Europe and south and east Asia. For men, high systolic blood pressure or tobacco use are the leading risks in nearly all high-income countries, in north Africa and the Middle East, Europe, and Asia. For men and women, unsafe sex is the leading risk in a corridor from Kenya to South Africa.INTERPRETATION: Behavioural, environmental and occupational, and metabolic risks can explain half of global mortality and more than one-third of global DALYs providing many opportunities for prevention. Of the larger risks, the attributable burden of high BMI has increased in the past 23 years. In view of the prominence of behavioural risk factors, behavioural and social science research on interventions for these risks should be strengthened. Many prevention and primary care policy options are available now to act on key risks.FUNDING: Bill & Melinda Gates Foundation.
10.	Fresard, Laure, et al. (author) Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts 2019 In: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919 Journal article (peer-reviewed)abstract It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
11.	Hall, Lynne, et al. (author) Map reading with an empathic robot tutor 2016 In: ACMIEEE International Conference on Human-Robot Interaction. - Piscataway, NJ : IEEE. - 2167-2121. - 9781467383707 Conference paper (peer-reviewed)
12.	Heinze, Karolin, et al. (author) Validated biomarker assays confirm ARID1A loss is confounded with MMR deficiency, CD8 TIL infiltration, and provides no independent prognostic value in endometriosis-associated ovarian carcinomas. 2021 In: The Journal of pathology. - : Wiley. - 1096-9896 .- 0022-3417. ; 256:4, s. 388-401 Journal article (peer-reviewed)abstract ARID1A (BAF250a) is a component of the SWI/SNF chromatin modifying complex, plays an important tumour suppressor role, and is considered prognostic in several malignancies. However, in ovarian carcinomas there are contradictory reports on its relationship to outcome, immune response, and correlation with clinicopathological features. We assembled a series of 1,623 endometriosis-associated ovarian carcinomas, including 1,078 endometrioid (ENOC) and 545 clear cell (CCOC) ovarian carcinomas through combining resources of the Ovarian Tumor Tissue Analysis (OTTA) Consortium, the Canadian Ovarian Unified Experimental Resource (COEUR), local, and collaborative networks. Validated immunohistochemical surrogate assays for ARID1A mutations were applied to all samples. We investigated associations between ARID1A loss/mutation, clinical features, outcome, CD8+ tumour-infiltrating lymphocytes (CD8+ TIL), and DNA mismatch repair deficiency (MMRd). ARID1A loss was observed in 42% of CCOC and 25% of ENOC. We found no associations between ARID1A loss and outcomes, stage, age, or CD8+ TIL status in CCOC. Similarly, we found no association with outcome or stage in endometrioid cases. In ENOC, ARID1A loss was more prevalent in younger patients (p=0.012), and associated with MMRd (p<0.001), and presence of CD8+ TIL (p=0.008). Consistent with MMRd being causative of ARID1A mutations, in a subset of ENOC we also observed an association between ARID1A loss-of-function mutation as a result of small indels (p=0.035, versus single nucleotide variants). In ENOC, the association between ARID1A loss, CD8+ TIL, and age, appears confounded by MMRd status. Although this observation does not explicitly rule out a role for ARID1A influence on CD8+ TIL infiltration in ENOC, given current knowledge regarding MMRd, it seems more likely that effects are dominated by the hypermutation phenotype. This large dataset with consistently applied biomarker assessment now provides a benchmark for the prevalence of ARID1A loss-of-function mutations in endometriosis-associated ovarian cancers and brings clarity to the prognostic significance. This article is protected by copyright. All rights reserved.
13.	Jedicke, Robert, et al. (author) Earth's Minimoons: Opportunities for Science and Technology 2018 In: Frontiers in Astronomy and Space Sciences. - : Frontiers Media S.A.. - 2296-987X. ; 5 Research review (peer-reviewed)abstract Twelve years ago the Catalina Sky Survey discovered Earth's first known natural geocentric object other than the Moon, a few-meter diameter asteroid designated 2006 RH120. Despite significant improvements in ground-based telescope and detector technology in the past decade the asteroid surveys have not discovered another temporarily-captured orbiter (TCO; colloquially known as minimoons) but the all-sky fireball system operated in the Czech Republic as part of the European Fireball Network detected a bright natural meteor that was almost certainly in a geocentric orbit before it struck Earth's atmosphere. Within a few years the Large Synoptic Survey Telescope (LSST) will either begin to regularly detect TCOs or force a re-analysis of the creation and dynamical evolution of small asteroids in the inner solar system. The first studies of the provenance, properties, and dynamics of Earth's minimoons suggested that there should be a steady state population with about one 1- to 2-m diameter captured objects at any time, with the number of captured meteoroids increasing exponentially for smaller sizes. That model was then improved and extended to include the population of temporarily-captured flybys (TCFs), objects that fail to make an entire revolution around Earth while energetically bound to the Earth-Moon system. Several different techniques for discovering TCOs have been considered but their small diameters, proximity, and rapid motion make them challenging targets for existing ground-based optical, meteor, and radar surveys. However, the LSST's tremendous light gathering power and short exposure times could allow it to detect and discover many minimoons. We expect that if the TCO population is confirmed, and new objects are frequently discovered, they can provide new opportunities for (1) studying the dynamics of the Earth-Moon system, (2) testing models of the production and dynamical evolution of small asteroids from the asteroid belt, (3) rapid and frequent low delta-v missions to multiple minimoons, and (4) evaluating in-situ resource utilization techniques on asteroidal material. Here we review the past decade of minimoon studies in preparation for capitalizing on the scientific and commercial opportunities of TCOs in the first decade of LSST operations.
14.	Jones, Steven, et al. (author) Antonyms in English : Construals Constructions and Canonicity 2012 Book (other academic/artistic)
15.	Jones, Steven, et al. (author) Googling for opposites: a phraseological approach to assessing antonym canonicity 2005 Conference paper (peer-reviewed)
16.	Jones, Steven, et al. (author) Googling for opposites: a web-based study of antonym canonicity 2007 In: Corpora. - 1755-1676. ; 2:2, s. 129-154 Journal article (peer-reviewed)abstract This paper seeks to explain why some semantically-opposed word pairs are more likely to be seen as canonical antonyms (for example, cold/hot) than others (icy/scorching, cold/fiery, freezing/hot, etc.). Specifically, it builds on research which has demonstrated that, in discourse, antonyms are inclined to favour certain frames, such as ‘X and Y alike’, ‘from X to Y’ and ‘either X or Y’ (Justeson and Katz, 1991; etc.), and to serve a limited range of discourse functions (Jones, 2002). Our premise is that the more canonical an antonym pair is, the greater the fidelity with which it will occupy such frames. Since an extremely large corpus is needed to identify meaningful patterns of co-occurrence, we turn to Internet data for this research. As well as enabling the notion of antonym canonicity to be revisited from a more empirical perspective, this approach also allows us to evaluate the appropriateness (and assess the risks) of using the World Wide Web as a corpus for studies into certain types of low-frequency textual phenomena.
17.	Jones, Steven, et al. (author) Using web data to investigate antonym canonicity 2007 Conference paper (peer-reviewed)
18.	Klionsky, Daniel J., et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy 2012 In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544 Research review (peer-reviewed)abstract In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
19.	Lindblad-Toh, Kerstin, et al. (author) Genome sequence, comparative analysis and haplotype structure of the domestic dog. 2005 In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19 Journal article (peer-reviewed)abstract Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
20.	Lochner, Michelle, et al. (author) The Impact of Observing Strategy on Cosmological Constraints with LSST 2022 In: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 259:2 Journal article (peer-reviewed)abstract The generation-defining Vera C. Rubin Observatory will make state-of-the-art measurements of both the static and transient universe through its Legacy Survey for Space and Time (LSST). With such capabilities, it is immensely challenging to optimize the LSST observing strategy across the survey's wide range of science drivers. Many aspects of the LSST observing strategy relevant to the LSST Dark Energy Science Collaboration, such as survey footprint definition, single-visit exposure time, and the cadence of repeat visits in different filters, are yet to be finalized. Here, we present metrics used to assess the impact of observing strategy on the cosmological probes considered most sensitive to survey design; these are large-scale structure, weak lensing, type Ia supernovae, kilonovae, and strong lens systems (as well as photometric redshifts, which enable many of these probes). We evaluate these metrics for over 100 different simulated potential survey designs. Our results show that multiple observing strategy decisions can profoundly impact cosmological constraints with LSST; these include adjusting the survey footprint, ensuring repeat nightly visits are taken in different filters, and enforcing regular cadence. We provide public code for our metrics, which makes them readily available for evaluating further modifications to the survey design. We conclude with a set of recommendations and highlight observing strategy factors that require further research.
21.	Murphy, M. Lynne, et al. (author) Discourse functions of antonymy: a cross-linguistic investigation of Swedish and English 2009 In: Journal of Pragmatics. - : Elsevier BV. - 0378-2166 .- 1879-1387. ; 41:11, s. 2159-2184 Journal article (peer-reviewed)abstract Jones (2002) identified several discourse functions of antonymy, each of which is loosely associated with a number of contrastive constructions in written English. Subsequent work (Jones, 2006; Jones and Murphy, 2005; Murphy and Jones, 2008) demonstrated that these functions are found in other modalities/registers of English, albeit with some differences in distribution. This article takes a first step in exploring discourse functions of antonymy in a language other than English. Because binary contrast has the potential to interact in different ways with the values and thought patterns of different cultures, we hypothesized that other languages differ from English in the ways in which antonyms are used in discourse. In this study of antonyms in Swedish, translational near-equivalents of pairs used by Jones were searched in the Swedish Parole corpus, and more than 4300 instances of co-occurring antonyms were found and analyzed in their sentential contexts. While the same range of antonym discourse functions is found in English and Swedish, the proportions of those functions differ significantly between the two languages. This paper both describes their functions (and the form of the functions) in Swedish and reflects on the similarities and differences with English.We ascribe some of the differences to the idiomaticity of certain componential expressions and discuss the possibility that certain cultural values affect some categories.
22.	Naghavi, Mohsen, et al. (author) Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013 2015 In: The Lancet. - 1474-547X .- 0140-6736. ; 385:9963, s. 117-171 Journal article (peer-reviewed)abstract Background Up-to-date evidence on levels and trends for age-sex-specifi c all-cause and cause-specifi c mortality is essential for the formation of global, regional, and national health policies. In the Global Burden of Disease Study 2013 (GBD 2013) we estimated yearly deaths for 188 countries between 1990, and 2013. We used the results to assess whether there is epidemiological convergence across countries. Methods We estimated age-sex-specifi c all-cause mortality using the GBD 2010 methods with some refinements to improve accuracy applied to an updated database of vital registration, survey, and census data. We generally estimated cause of death as in the GBD 2010. Key improvements included the addition of more recent vital registration data for 72 countries, an updated verbal autopsy literature review, two new and detailed data systems for China, and more detail for Mexico, UK, Turkey, and Russia. We improved statistical models for garbage code redistribution. We used six different modelling strategies across the 240 causes; cause of death ensemble modelling (CODEm) was the dominant strategy for causes with sufficient information. Trends for Alzheimer's disease and other dementias were informed by meta-regression of prevalence studies. For pathogen-specifi c causes of diarrhoea and lower respiratory infections we used a counterfactual approach. We computed two measures of convergence (inequality) across countries: the average relative difference across all pairs of countries (Gini coefficient) and the average absolute difference across countries. To summarise broad findings, we used multiple decrement life-tables to decompose probabilities of death from birth to exact age 15 years, from exact age 15 years to exact age 50 years, and from exact age 50 years to exact age 75 years, and life expectancy at birth into major causes. For all quantities reported, we computed 95% uncertainty intervals (UIs). We constrained cause-specific fractions within each age-sex-country-year group to sum to all-cause mortality based on draws from the uncertainty distributions. Findings Global life expectancy for both sexes increased from 65.3 years (UI 65.0-65.6) in 1990, to 71.5 years (UI 71.0-71.9) in 2013, while the number of deaths increased from 47.5 million (UI 46.8-48.2) to 54.9 million (UI 53.6-56.3) over the same interval. Global progress masked variation by age and sex: for children, average absolute diff erences between countries decreased but relative diff erences increased. For women aged 25-39 years and older than 75 years and for men aged 20-49 years and 65 years and older, both absolute and relative diff erences increased. Decomposition of global and regional life expectancy showed the prominent role of reductions in age-standardised death rates for cardiovascular diseases and cancers in high-income regions, and reductions in child deaths from diarrhoea, lower respiratory infections, and neonatal causes in low-income regions. HIV/AIDS reduced life expectancy in southern sub-Saharan Africa. For most communicable causes of death both numbers of deaths and age-standardised death rates fell whereas for most non-communicable causes, demographic shifts have increased numbers of deaths but decreased age-standardised death rates. Global deaths from injury increased by 10.7%, from 4.3 million deaths in 1990 to 4.8 million in 2013; but age-standardised rates declined over the same period by 21%. For some causes of more than 100 000 deaths per year in 2013, age-standardised death rates increased between 1990 and 2013, including HIV/AIDS, pancreatic cancer, atrial fibrillation and flutter, drug use disorders, diabetes, chronic kidney disease, and sickle-cell anaemias. Diarrhoeal diseases, lower respiratory infections, neonatal causes, and malaria are still in the top five causes of death in children younger than 5 years. The most important pathogens are rotavirus for diarrhoea and pneumococcus for lower respiratory infections. Country-specific probabilities of death over three phases of life were substantially varied between and within regions. Interpretation For most countries, the general pattern of reductions in age-sex specifi c mortality has been associated with a progressive shift towards a larger share of the remaining deaths caused by non-communicable disease and injuries. Assessing epidemiological convergence across countries depends on whether an absolute or relative measure of inequality is used. Nevertheless, age-standardised death rates for seven substantial causes are increasing, suggesting the potential for reversals in some countries. Important gaps exist in the empirical data for cause of death estimates for some countries; for example, no national data for India are available for the past decade.
23.	Neubeck, Lis, et al. (author) The Core Curriculum for Cardiovascular Nurses and Allied Professionals 2023 In: European Journal of Cardiovascular Nursing. - : OXFORD UNIV PRESS. - 1474-5151 .- 1873-1953. ; 22:7, s. e62-e113 Journal article (peer-reviewed)abstract This 2023 update of the Core Curriculum in Cardiovascular Nursing (2015) embraces the formation of the Association of Cardiovascular Nursing and Allied Professionals and reflects the diverse professional backgrounds of our members, including nurses, allied health professionals, and healthcare scientists (in this document referred to collectively as Nurses and Allied Professionals).
24.	Obaid, Mohammad, 1982, et al. (author) Endowing a Robotic Tutor with Empathic Qualities: Design and Pilot Evaluation 2018 In: International Journal of Humanoid Robotics. - 0219-8436 .- 1793-6942. ; 15:6 Journal article (peer-reviewed)abstract As increasingly more research efforts are geared towards creating robots that can teach and interact with children in educational contexts, it has been speculated that endowing robots with artificial empathy may facilitate learning. In this paper, we provide a background to the concept of empathy, and how it factors into learning. We then present our approach to equipping a robotic tutor with several empathic qualities, describing the technical architecture and its components, a map-reading learning scenario developed for an interactive multitouch table, as well as the pedagogical and empathic strategies devised for the robot. We also describe the results of a pilot study comparing the robotic tutor with these empathic qualities against a version of the tutor without them. The pilot study was performed with 26 school children aged 10-11 at their school. Results revealed that children in the test condition indeed rated the robot as more empathic than children in the control condition. Moreover, we explored several related measures, such as relational status and learning effect, yet no other significant differences were found. We further discuss these results and provide insights into future directions.
25.	Richards, Stephen, et al. (author) The genome of the model beetle and pest Tribolium castaneum. 2008 In: Nature. - 1476-4687. ; 452:7190, s. 949-55 Journal article (peer-reviewed)abstract Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
26.	Sayers, Dave, et al. (author) The Dawn of the Human-Machine Era : A forecast of new and emerging language technologies 2021 Reports (other academic/artistic)abstract New language technologies are coming, thanks to the huge and competing private investment fuelling rapid progress; we can either understand and foresee their effects, or be taken by surprise and spend our time trying to catch up. This report scketches out some transformative new technologies that are likely to fundamentally change our use of language. Some of these may feel unrealistically futuristic or far-fetched, but a central purpose of this report - and the wider LITHME network - is to illustrate that these are mostly just the logical development and maturation of technologies currently in prototype. But will everyone benefit from all these shiny new gadgets? Throughout this report we emphasise a range of groups who will be disadvantaged and issues of inequality. Important issues of security and privacy will accompany new language technologies. A further caution is to re-emphasise the current limitations of AI. Looking ahead, we see many intriguing opportunities and new capabilities, but a range of other uncertainties and inequalities. New devices will enable new ways to talk, to translate, to remember, and to learn. But advances in technology will reproduce existing inequalities among those who cannot afford these devices, among the world’s smaller languages, and especially for sign language. Debates over privacy and security will flare and crackle with every new immersive gadget. We will move together into this curious new world with a mix of excitement and apprehension - reacting, debating, sharing and disagreeing as we always do. Plug in, as the human-machine era dawns.
27.	Schwamb, Megan E., et al. (author) A Software Roadmap for Solar System Science with the Large Synoptic Survey Telescope 2019 In: Research Notes of the AAS. - : Institute of Physics (IOP). - 2515-5172. ; 3:3 Journal article (peer-reviewed)abstract The 8.4 m Large Synoptic Survey Telescope (LSST) will provide an unprecedented view of the Solar System (Ivezić et al. 2008; LSST Science Collaboration et al. 2009). LSST will detect millions of asteroids and tens of thousands of distant Solar System bodies, within approximately 16 and 24.5 mag (in r-band). Over a ten year period, most of these minor planets will receive hundreds of observations divided between 6 filters (ugrizy). What specifically LSST project will deliver for Solar System detections will soon be updated in the LSST Data Products Definition Document (DPDD; Jurić et al. 2013). A preliminary version of the new LSST Solar System data products schema is available at http://ls.st/ssd and http://ls.st/oug.The LSST Solar System Science Collaboration (SSSC; http://www.lsstsssc.org) produced a science roadmap (Schwamb et al. 2018) which outlines the collaboration's highest ranked research priorities utilizing LSST. To achieve these science goals, the SSSC has identified crucial software products and tools that will be required but will not be provided by the LSST project. These will have to be developed by the SSSC and the broader planetary community. To spur this effort, we present below this list of LSST community software development tasks.
28.	Schwamb, Megan E., et al. (author) Tuning the Legacy Survey of Space and Time (LSST) Observing Strategy for Solar System Science 2023 In: Astrophysical Journal Supplement Series. - : Iop Publishing Ltd. - 0067-0049 .- 1538-4365. ; 266:2 Journal article (peer-reviewed)abstract The Vera C. Rubin Observatory is expected to start the Legacy Survey of Space and Time (LSST) in early to mid-2025. This multiband wide-field synoptic survey will transform our view of the solar system, with the discovery and monitoring of over five million small bodies. The final survey strategy chosen for LSST has direct implications on the discoverability and characterization of solar system minor planets and passing interstellar objects. Creating an inventory of the solar system is one of the four main LSST science drivers. The LSST observing cadence is a complex optimization problem that must balance the priorities and needs of all the key LSST science areas. To design the best LSST survey strategy, a series of operation simulations using the Rubin Observatory scheduler have been generated to explore the various options for tuning observing parameters and prioritizations. We explore the impact of the various simulated LSST observing strategies on studying the solar system's small body reservoirs. We examine what are the best observing scenarios and review what are the important considerations for maximizing LSST solar system science. In general, most of the LSST cadence simulations produce +/- 5% or less variations in our chosen key metrics, but a subset of the simulations significantly hinder science returns with much larger losses in the discovery and light-curve metrics.
29.	Trabert, Britton, et al. (author) The Risk of Ovarian Cancer Increases with an Increase in the Lifetime Number of Ovulatory Cycles : An Analysis from the Ovarian Cancer Cohort Consortium (OC3) 2020 In: Cancer Research. - : AMER ASSOC CANCER RESEARCH. - 0008-5472 .- 1538-7445. ; 80:5, s. 1210-1218 Journal article (peer-reviewed)abstract Repeated exposure to the acute proinflammatory environment that follows ovulation at the ovarian surface and distal fallopian tube over a woman's reproductive years may increase ovarian cancer risk. To address this, analyses included individual-level data from 558,709 naturally menopausal women across 20 prospective cohorts, among whom 3,246 developed invasive epithelial ovarian cancer (2,045 serous, 319 endometrioid, 184 mucinous, 121 clear cell, 577 other/unknown). Cox models were used to estimate multivariable-adjusted HRs between lifetime ovulatory cycles (LOC) and its components and ovarian cancer risk overall and by histotype. Women in the 90th percentile of LOC (>514 cycles) were almost twice as likely to be diagnosed with ovarian cancer than women in the 10th percentile (<294) [HR (95% confidence interval): 1.92 (1.60-2.30)]. Risk increased 14% per 5-year increase in LOC (60 cycles) [(1.10-1.17)]; this association remained after adjustment for LOC components: number of pregnancies and oral contraceptive use [1.08 (1.04-1.12)]. The association varied by histotype, with increased risk of serous [1.13 (1.09-1.17)], endometrioid [1.20 (1.10-1.32)], and clear cell [1.37 (1.18-1.58)], but not mucinous [0.99 (0.88-1.10), P-heterogeneity = 0.01] tumors. Heterogeneity across histotypes was reduced [P-heterogeneity = 0.15] with adjustment for LOC components [1.08 serous, 1.11 endometrioid, 1.26 clear cell, 0.94 mucinous]. Although the 10-year absolute risk of ovarian cancer is small, it roughly doubles as the number of LOC rises from approximately 300 to 500. The consistency and linearity of effects strongly support the hypothesis that each ovulation leads to small increases in the risk of most ovarian cancers, a risk that cumulates through life, suggesting this as an important area for identifying intervention strategies.
30.	Visvanathan, Kala, et al. (author) Circulating vitamin D and breast cancer risk : an international pooling project of 17 cohorts 2023 In: European Journal of Epidemiology. - : Springer Science+Business Media B.V.. - 0393-2990 .- 1573-7284. ; 38, s. 11-29 Journal article (peer-reviewed)abstract Laboratory and animal research support a protective role for vitamin D in breast carcinogenesis, but epidemiologic studies have been inconclusive. To examine comprehensively the relationship of circulating 25-hydroxyvitamin D [25(OH)D] to subsequent breast cancer incidence, we harmonized and pooled participant-level data from 10 U.S. and 7 European prospective cohorts. Included were 10,484 invasive breast cancer cases and 12,953 matched controls. Median age (interdecile range) was 57 (42–68) years at blood collection and 63 (49–75) years at breast cancer diagnosis. Prediagnostic circulating 25(OH)D was either newly measured using a widely accepted immunoassay and laboratory or, if previously measured by the cohort, calibrated to this assay to permit using a common metric. Study-specific relative risks (RRs) for season-standardized 25(OH)D concentrations were estimated by conditional logistic regression and combined by random-effects models. Circulating 25(OH)D increased from a median of 22.6 nmol/L in consortium-wide decile 1 to 93.2 nmol/L in decile 10. Breast cancer risk in each decile was not statistically significantly different from risk in decile 5 in models adjusted for breast cancer risk factors, and no trend was apparent (P-trend = 0.64). Compared to women with sufficient 25(OH)D based on Institute of Medicine guidelines (50– < 62.5 nmol/L), RRs were not statistically significantly different at either low concentrations (< 20 nmol/L, 3% of controls) or high concentrations (100– < 125 nmol/L, 3% of controls; ≥ 125 nmol/L, 0.7% of controls). RR per 25 nmol/L increase in 25(OH)D was 0.99 [95% confidence intervaI (CI) 0.95–1.03]. Associations remained null across subgroups, including those defined by body mass index, physical activity, latitude, and season of blood collection. Although none of the associations by tumor characteristics reached statistical significance, suggestive inverse associations were seen for distant and triple negative tumors. Circulating 25(OH)D, comparably measured in 17 international cohorts and season-standardized, was not related to subsequent incidence of invasive breast cancer over a broad range in vitamin D status.
31.	Wang, Xiaoliang, et al. (author) Genome-wide interaction analysis of menopausal hormone therapy use and breast cancer risk among 62,370 women 2022 In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 12:1 Journal article (peer-reviewed)abstract Use of menopausal hormone therapy (MHT) is associated with increased risk for breast cancer. However, the relevant mechanisms and its interaction with genetic variants are not fully understood. We conducted a genome-wide interaction analysis between MHT use and genetic variants for breast cancer risk in 27,585 cases and 34,785 controls from 26 observational studies. All women were post-menopausal and of European ancestry. Multivariable logistic regression models were used to test for multiplicative interactions between genetic variants and current MHT use. We considered interaction p-values < 5 x 10(-8) as genome-wide significant, and p-values < 1 x 10(-5) as suggestive. Linkage disequilibrium (LD)-based clumping was performed to identify independent candidate variants. None of the 9.7 million genetic variants tested for interactions with MHT use reached genome-wide significance. Only 213 variants, representing 18 independent loci, had p-values < 1 x 10(5). The strongest evidence was found for rs4674019 (p-value = 2.27 x 10(-7)), which showed genome-wide significant interaction (p-value = 3.8 x 10(-8)) with current MHT use when analysis was restricted to population-based studies only. Limiting the analyses to combined estrogen-progesterone MHT use only or to estrogen receptor (ER) positive cases did not identify any genome-wide significant evidence of interactions. In this large genome-wide SNP-MHT interaction study of breast cancer, we found no strong support for common genetic variants modifying the effect of MHT on breast cancer risk. These results suggest that common genetic variation has limited impact on the observed MHT-breast cancer risk association.
32.	Wentzensen, Nicolas A., et al. (author) Ovarian cancer risk factors by histologic subtypes : evidence for etiologic heterogeneity 2015 In: Cancer Research. - 0008-5472 .- 1538-7445. ; 75 Journal article (other academic/artistic)
33.	Wentzensen, Nicolas, et al. (author) Ovarian Cancer Risk Factors by Histologic Subtype : An Analysis From the Ovarian Cancer Cohort Consortium 2016 In: Journal of Clinical Oncology. - : AMER SOC CLINICAL ONCOLOGY. - 0732-183X .- 1527-7755. ; 34:24, s. 2888-2898 Journal article (peer-reviewed)abstract Purpose: An understanding of the etiologic heterogeneity of ovarian cancer is important for improving prevention, early detection, and therapeutic approaches. We evaluated 14 hormonal, reproductive, and lifestyle factors by histologic subtype in the Ovarian Cancer Cohort Consortium (OC3).Patients and Methods: Among 1.3 million women from 21 studies, 5,584 invasive epithelial ovarian cancers were identified (3,378 serous, 606 endometrioid, 331 mucinous, 269 clear cell, 1,000 other). By using competing-risks Cox proportional hazards regression stratified by study and birth year and adjusted for age, parity, and oral contraceptive use, we assessed associations for all invasive cancers by histology. Heterogeneity was evaluated by likelihood ratio test.Results: Most risk factors exhibited significant heterogeneity by histology. Higher parity was most strongly associated with endometrioid (relative risk [RR] per birth, 0.78; 95% CI, 0.74 to 0.83) and clear cell (RR, 0.68; 95% CI, 0.61 to 0.76) carcinomas (P value for heterogeneity [P-het] < .001). Similarly, age at menopause, endometriosis, and tubal ligation were only associated with endometrioid and clear cell tumors (P-het ≤ .01). Family history of breast cancer (P-het = .008) had modest heterogeneity. Smoking was associated with an increased risk of mucinous (RR per 20 pack-years, 1.26; 95% CI, 1.08 to 1.46) but a decreased risk of clear cell (RR, 0.72; 95% CI, 0.55 to 0.94) tumors (P-het = .004). Unsupervised clustering by risk factors separated endometrioid, clear cell, and low-grade serous carcinomas from high-grade serous and mucinous carcinomas.Conclusion: The heterogeneous associations of risk factors with ovarian cancer subtypes emphasize the importance of conducting etiologic studies by ovarian cancer subtypes. Most established risk factors were more strongly associated with nonserous carcinomas, which demonstrate challenges for risk prediction of serous cancers, the most fatal subtype.
34.	Werren, John H, et al. (author) Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. 2010 In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 327:5963, s. 343-8 Journal article (peer-reviewed)abstract We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.

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