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1.
  • Aad, G., et al. (author)
  • 2011
  • swepub:Mat__t (peer-reviewed)
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2.
  • Ademuyiwa, Adesoji O., et al. (author)
  • Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
  • 2016
  • In: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
  • Journal article (peer-reviewed)abstract
    • Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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3.
  • Allan, James, et al. (author)
  • Frontiers, Challenges, and Opportunities for Information Retrieval – Report from SWIRL 2012, The Second Strategic Workshop on Information Retrieval in Lorne
  • 2012
  • In: SIGIR Forum. - : ACM. - 0163-5840. ; 46:1, s. 2-32
  • Journal article (peer-reviewed)abstract
    • During a three-day workshop in February 2012, 45 Information Retrieval researchers met to discuss long-range challenges and opportunities within the field. The result of the workshop is a diverse set of research directions, project ideas, and challenge areas. This report describes the workshop format, provides summaries of broad themes that emerged, includes brief descriptions of all the ideas, and provides detailed discussion of six proposals that were voted "most interesting" by the participants. Key themes include the need to: move beyond ranked lists of documents to support richer dialog and presentation, represent the context of search and searchers, provide richer support for information seeking, enable retrieval of a wide range of structured and unstructured content, and develop new evaluation methodologies.
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4.
  • Ariyawansa, Hiran A., et al. (author)
  • Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
  • 2015
  • In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 75, s. 27-274
  • Journal article (peer-reviewed)abstract
    • This paper is a compilation of notes on 142 fungal taxa, including five new families, 20 new genera, and 100 new species, representing a wide taxonomic and geographic range. The new families, Ascocylindricaceae, Caryosporaceae and Wicklowiaceae (Ascomycota) are introduced based on their distinct lineages and unique morphology. The new Dothideomycete genera Pseudomassariosphaeria (Amniculicolaceae), Heracleicola, Neodidymella and P s e u d o m i c ros p h a e r i o p s i s ( D id y m e l l a c e a e ) , P s e u d o p i t h o m y c e s ( D i d y m o s p h a e r i a c e a e ) , Brunneoclavispora, Neolophiostoma and Sulcosporium (Halotthiaceae), Lophiohelichrysum (Lophiostomataceae), G a l l i i c o l a , Popul o c re s c e n t i a a nd Va g i c o l a (Phaeosphaeriaceae), Ascocylindrica (Ascocylindricaceae), E l o n g a t o p e d i c e l l a t a ( R o u s s o e l l a c e a e ) , Pseudoasteromassaria (Latoruaceae) and Pseudomonodictys (Macrodiplodiopsidaceae) are introduced. The newly described species of Dothideomycetes (Ascomycota) are Pseudomassariosphaeria bromicola (Amniculicolaceae), Flammeascoma lignicola (Anteagloniaceae), Ascocylindrica marina (Ascocylindricaceae) , Lembosia xyliae (Asterinaceae), Diplodia crataegicola and Diplodia galiicola ( B o t r yosphae r i a cea e ) , Caryospor a aquat i c a (Caryosporaceae), Heracleicola premilcurensis and Neodi dymell a thai landi cum (Didymellaceae) , Pseudopithomyces palmicola (Didymosphaeriaceae), Floricola viticola (Floricolaceae), Brunneoclavispora bambusae, Neolophiostoma pigmentatum and Sulcosporium thailandica (Halotthiaceae), Pseudoasteromassaria fagi (Latoruaceae), Keissleriella dactylidicola (Lentitheciaceae), Lophiohelichrysum helichrysi (Lophiostomataceae), Aquasubmersa japonica (Lophiotremataceae) , Pseudomonodictys tectonae (Macrodiplodiopsidaceae), Microthyrium buxicola and Tumidispora shoreae (Microthyriaceae), Alloleptosphaeria clematidis, Allophaeosphaer i a c y t i s i , Allophaeosphae r i a subcylindrospora, Dematiopleospora luzulae, Entodesmium artemisiae, Galiicola pseudophaeosphaeria, Loratospora(Basidiomycota) are introduced together with a new genus Neoantrodiella (Neoantrodiellaceae), here based on both morphology coupled with molecular data. In the class Agaricomycetes, Agaricus pseudolangei, Agaricus haematinus, Agaricus atrodiscus and Agaricus exilissimus (Agaricaceae) , Amanita m e l l e i a l b a , Amanita pseudosychnopyramis and Amanita subparvipantherina (Amanitaceae), Entoloma calabrum, Cora barbulata, Dictyonema gomezianum and Inocybe granulosa (Inocybaceae), Xerocomellus sarnarii (Boletaceae), Cantharellus eucalyptorum, Cantharellus nigrescens, Cantharellus tricolor and Cantharellus variabilicolor (Cantharellaceae), Cortinarius alboamarescens, Cortinarius brunneoalbus, Cortinarius ochroamarus, Cortinarius putorius and Cortinarius seidlii (Cortinariaceae), Hymenochaete micropora and Hymenochaete subporioides (Hymenochaetaceae), Xylodon ramicida (Schizoporaceae), Colospora andalasii (Polyporaceae), Russula guangxiensis and Russula hakkae (Russulaceae), Tremella dirinariae, Tremella graphidis and Tremella pyrenulae (Tremellaceae) are introduced. Four new combinations Neoantrodiella gypsea, Neoantrodiella thujae (Neoantrodiellaceae), Punctulariopsis cremeoalbida, Punctulariopsis efibulata (Punctulariaceae) are also introduced here for the division Basidiomycota. Furthermore Absidia caatinguensis, Absidia koreana and Gongronella koreana (Cunninghamellaceae), Mortierella pisiformis and Mortierella formosana (Mortierellaceae) are newly introduced in the Zygomycota, while Neocallimastix cameroonii and Piromyces irregularis (Neocallimastigaceae) ar e i n t roduced i n the Neocallimastigomycota. Reference specimens or changes in classification and notes are provided for Alternaria ethzedia, Cucurbitaria ephedricola, Austropleospora, Austropleospora archidendri, Byssosphaeria rhodomphala, Lophiostoma caulium, Pseudopithomyces maydicus, Massariosphaeria, Neomassariosphaeria and Pestalotiopsis montellica.
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5.
  • 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.
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6.
  • Walsh, John J., et al. (author)
  • Fungal and bacterial growth following the application of slurry and anaerobic digestate of livestock manure to temperate pasture soils
  • 2012
  • In: Biology and Fertility of Soils. - : Springer Science and Business Media LLC. - 0178-2762 .- 1432-0789. ; 48:8, s. 889-897
  • Journal article (peer-reviewed)abstract
    • How land-application of digestate sourced from anaerobic digestion (AD) of animal waste influences the functioning of a mixed pasture agroecosystem is not well characterised, particularly with regard to the response of the actively growing microbial community. We studied the impact of the liquid AD digestate on the decomposer community in two different soils, seeded with two different common grassland crops; a mixture of either grass or grass/clover in a greenhouse experiment. We studied bacterial (leucine incorporation into bacteria) and fungal (acetate incorporation into ergosterol) growth responses to AD cattle slurry digestate, undigested cattle slurry, mineral fertiliser (NPK and N) added at a rate equivalent to 150 kg N ha(-1), and a no-fertiliser control treatment. Differences in fungal and bacterial growth were evident between the soil and sward types. However, the fertilisers consistently stimulated a higher bacterial growth than the no-fertiliser control, and liquid digestate resulted in a level of bacterial growth higher or equal to that of mineral fertiliser, whilst undigested slurry resulted in lower bacterial growth. These fertiliser effects on bacterial growth mirrored the effects on plant growth. In contrast, the fungal community responded only marginally to fertiliser treatments. We conclude that the application of digestate stimulates the bacterial decomposer community in a similar way to that of mineral fertilisers. Our results suggest that mineral fertiliser can be exchanged for liquid digestate with limited impact on the actively growing soil microbial community that, in turn, regulate important soil processes including nutrient cycling in agricultural soils.
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7.
  • Ahearn, Thomas U., et al. (author)
  • Common variants in breast cancer risk loci predispose to distinct tumor subtypes
  • 2022
  • In: Breast Cancer Research. - : Springer Nature. - 1465-5411 .- 1465-542X. ; 24:1
  • Journal article (peer-reviewed)abstract
    • BackgroundGenome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear.MethodsAmong 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes.ResultsEighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions.ConclusionThis report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
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8.
  • Ando, Shin'ichiro, et al. (author)
  • Colloquium : Multimessenger astronomy with gravitational waves and high-energy neutrinos
  • 2013
  • In: Reviews of Modern Physics. - 0034-6861 .- 1539-0756. ; 85:4, s. 1401-1420
  • Journal article (peer-reviewed)abstract
    • Many of the astrophysical sources and violent phenomena observed in our Universe are potential emitters of gravitational waves and high-energy cosmic radiation, including photons, hadrons, and presumably also neutrinos. Both gravitational waves (GW) and high-energy neutrinos (HEN) are cosmic messengers that may escape much denser media than photons. They travel unaffected over cosmological distances, carrying information from the inner regions of the astrophysical engines from which they are emitted (and from which photons and charged cosmic rays cannot reach us). For the same reasons, such messengers could also reveal new, hidden sources that have not been observed by conventional photon-based astronomy. Coincident observation of GWs and HENs may thus play a critical role in multimessenger astronomy. This is particularly true at the present time owing to the advent of a new generation of dedicated detectors: the neutrino telescopes IceCube at the South Pole and ANTARES in the Mediterranean Sea, as well as the GW interferometers Virgo in Italy and LIGO in the United States. Starting from 2007, several periods of concomitant data taking involving these detectors have been conducted. More joint data sets are expected with the next generation of advanced detectors that are to be operational by 2015, with other detectors, such as KAGRA in Japan, joining in the future. Combining information from these independent detectors can provide original ways of constraining the physical processes driving the sources and also help confirm the astrophysical origin of a GW or HEN signal in case of coincident observation. Given the complexity of the instruments, a successful joint analysis of this combined GW and HEN observational data set will be possible only if the expertise and knowledge of the data is shared between the two communities. This Colloquium aims at providing an overview of both theoretical and experimental state of the art and perspectives for GW and HEN multimessenger astronomy.
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9.
  • Aston, Eoghan A., et al. (author)
  • Scale-dependent spatial patterns in benthic communities around a tropical island seascape
  • 2019
  • In: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 42:3, s. 578-590
  • Journal article (peer-reviewed)abstract
    • Understanding and predicting patterns of spatial organization across ecological communities is central to the field of landscape ecology, and a similar line of inquiry has begun to evolve sub-tidally among seascape ecologists. Much of our current understanding of the processes driving marine community patterns, particularly in the tropics, has come from small-scale, spatially-discrete data that are often not representative of the broader seascape. Here we expand the spatial extent of seascape ecology studies and combine spatially-expansive in situ digital imagery, oceanographic measurements, spatial statistics, and predictive modeling to test whether predictable patterns emerge between coral reef benthic competitors across scales in response to intra-island gradients in physical drivers. We do this around the entire circumference of a remote, uninhabited island in the central Pacific (Jarvis Island) that lacks the confounding effects of direct human impacts. We show, for the first time, that competing benthic groups demonstrate predictable scaling patterns of organization, with positive autocorrelation in the cover of each group at scales < similar to 1 km. Moreover, we show how gradients in subsurface temperature and surface wave power drive spatially-abrupt transition points in group dominance, explaining 48-84% of the overall variation in benthic cover around the island. Along the western coast, we documented ten times more sub-surface cooling-hours than any other part of the coastline, with events typically resulting in a drop of 1-4 degrees C over a period of < 5 h. These high frequency temperature fluctuations are indicative of upwelling induced by internal waves and here result in localized nitrogen enrichment (NO2 + NO3) that promotes hard coral dominance around 44% of the island's perimeter. Our findings show that, in the absence of confounding direct human impacts, the spatial organization of coral reef benthic competitors are predictable and somewhat bounded across the seascape by concurrent gradients in physical drivers.
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10.
  • Baret, Bruny, et al. (author)
  • Multimessenger science reach and analysis method for common sources of gravitational waves and high-energy neutrinos
  • 2012
  • In: Physical Review D. - 1550-7998 .- 1550-2368. ; 85:10, s. 103004-
  • Journal article (peer-reviewed)abstract
    • We present the baseline multimessenger analysis method for the joint observations of gravitational waves (GW) and high-energy neutrinos (HEN), together with a detailed analysis of the expected science reach of the joint search. The analysis method combines data from GW and HEN detectors, and uses the blue-luminosity-weighted distribution of galaxies. We derive expected GW + HEN source rate upper limits for a wide range of source parameters covering several emission models. Using published sensitivities of externally triggered searches, we derive joint upper limit estimates both for the ongoing analysis with the initial LIGO-Virgo GW detectors with the partial IceCube detector (22 strings) HEN detector and for projected results to advanced LIGO-Virgo detectors with the completed IceCube (86 strings). We discuss the constraints these upper limits impose on some existing GW + HEN emission models.
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11.
  • Brem, Jürgen, et al. (author)
  • Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors
  • 2022
  • In: Nature Chemistry. - : Springer Nature. - 1755-4330 .- 1755-4349. ; 14:1, s. 15-24
  • Journal article (peer-reviewed)abstract
    • Carbapenems are vital antibiotics, but their efficacy is increasingly compromised by metallo-β-lactamases (MBLs). Here we report the discovery and optimization of potent broad-spectrum MBL inhibitors. A high-throughput screen for NDM-1 inhibitors identified indole-2-carboxylates (InCs) as potential β-lactamase stable β-lactam mimics. Subsequent structure-activity relationship studies revealed InCs as a new class of potent MBL inhibitor, active against all MBL classes of major clinical relevance. Crystallographic studies revealed a binding mode of the InCs to MBLs that, in some regards, mimics that predicted for intact carbapenems, including with respect to maintenance of the Zn(II)-bound hydroxyl, and in other regards mimics binding observed in MBL-carbapenem product complexes. InCs restore carbapenem activity against multiple drug-resistant Gram-negative bacteria and have a low frequency of resistance. InCs also have a good in vivo safety profile, and when combined with meropenem show a strong in vivo efficacy in peritonitis and thigh mouse infection models.
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12.
  • Calabon, Mark Seasat, et al. (author)
  • Phylogenetic assessment and taxonomic revision of Halobyssothecium and Lentithecium (Lentitheciaceae, Pleosporales)
  • 2021
  • In: Mycological progress. - : Springer Nature. - 1617-416X .- 1861-8952. ; 20:5, s. 701-720
  • Journal article (peer-reviewed)abstract
    • Our studies on lignicolous aquatic fungi in Thailand, Sweden, and the UK resulted in the collection of three new Halobyssothecium species (H. bambusicola, H. phragmitis, H. versicolor) assigned to Lentitheciaceae (Pleosporales, Dothideomycetes). Multi-loci phylogenetic analyses of the combined large subunit, small subunit, internal transcribed spacers of ribosomal DNA, and the translation elongation factor 1-alpha sequence data enabled a revision of the taxa assigned to Lentithecium and the transfer of L. cangshanense, L. carbonneanum, L. kunmingense, L. unicellulare, and L. voraginesporum to Halobyssothecium. Collection of an asexual morph of L. lineare and phylogenetic analysis confirmed its taxonomic placement in Keissleriella. Detailed descriptions and illustrations of H. bambusicola, H. phragmitis, and H. versicolor are provided.
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13.
  • Callaghan, Terry V., et al. (author)
  • Ecosystem change and stability over multiple decades in the Swedish subarctic : complex processes and multiple drivers
  • 2013
  • In: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 368:1624
  • Journal article (peer-reviewed)abstract
    • The subarctic environment of northernmost Sweden has changed over the past century, particularly elements of climate and cryosphere. This paper presents a unique geo-referenced record of environmental and ecosystem observations from the area since 1913. Abiotic changes have been substantial. Vegetation changes include not only increases in growth and range extension but also counterintuitive decreases, and stability: all three possible responses. Changes in species composition within the major plant communities have ranged between almost no changes to almost a 50 per cent increase in the number of species. Changes in plant species abundance also vary with particularly large increases in trees and shrubs (up to 600%). There has been an increase in abundance of aspen and large changes in other plant communities responding to wetland area increases resulting from permafrost thaw. Populations of herbivores have responded to varying management practices and climate regimes, particularly changing snow conditions. While it is difficult to generalize and scale-up the site-specific changes in ecosystems, this very site-specificity, combined with projections of change, is of immediate relevance to local stakeholders who need to adapt to new opportunities and to respond to challenges. Furthermore, the relatively small area and its unique datasets are a microcosm of the complexity of Arctic landscapes in transition that remains to be documented.
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14.
  • Christiansen, Sara Nysom, et al. (author)
  • Patient-reported outcomes in axial spondyloarthritis and psoriatic arthritis patients treated with secukinumab for 24 months in daily clinical practice
  • 2024
  • In: Seminars in Arthritis and Rheumatism. - 0049-0172 .- 1532-866X. ; 65
  • Journal article (peer-reviewed)abstract
    • Objectives: In patients with axial spondyloarthritis (axSpA) or psoriatic arthritis (PsA) initiating secukinumab, we aimed to assess and compare the proportion of patients achieving 6-, 12- and 24-month patient-reported outcomes (PRO) remission and the 24-month retention rates. Patients and methods: Patients with axSpA or PsA from 16 European registries, who initiated secukinumab in routine care were included. PRO remission rates were defined as pain, fatigue, Patient Global Assessment (PGA) ≤2 (Numeric Rating Scale (NRS) 0–10) and Health Assessment Questionnaire (HAQ) ≤0.5, for both axSpA and PsA, and were calculated as crude values and adjusted for drug adherence (LUNDEX). Comparisons of axSpA and PsA remission rates were performed using logistic regression analyses (unadjusted and adjusted for multiple confounders). Kaplan-Meier plots with log-rank test and Cox regression analyses were conducted to assess and compare secukinumab retention rates. Results: We included 3087 axSpA and 3246 PsA patients initiating secukinumab. Crude pain, fatigue, PGA and HAQ remission rates were higher in axSpA than in PsA patients, whereas LUNDEX-adjusted remission rates were similar. No differences were found between the patient groups after adjustment for confounders. The 24-month retention rates were similar in axSpA vs. PsA in fully adjusted analyses (HR [95 %CI] = 0.92 [0.84–1.02]). Conclusion: In this large European real-world study of axSpA and PsA patients treated with secukinumab, we demonstrate for the first time a comparable effectiveness in PRO remission and treatment retention rates between these two conditions when adjusted for confounders.
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15.
  • Edwards, Gareth, et al. (author)
  • Editorial: What makes a good article for leadership? Thoughts and views from our associate editors, part 1
  • 2024
  • In: Leadership. - 1742-7150. ; 20:1, s. 3-8
  • Journal article (other academic/artistic)abstract
    • This issue of Leadership marks our first full year as Co-Editors-in-Chief. As we highlighted in our introductory editorial (Edwards and Schedlitzki, 2023) we see our role as striving to develop the community of the journal in its endeavour to be a key, critical and contemporary voice for leadership studies. To continue this journey, and to help contributors frame and develop their work for submission to the journal, we have invited some of our Associate Editors to share their thoughts on the following questions:1. What do you look for in a strong article, suitable for submission to Leadership?2. What do you see as a critical contribution to leadership studies?3. Can you highlight and/or explore some past articles published in Leadership that exemplify your views?In this editorial we will hear from three of our associate editors - Brigid Carroll, Magnus Larsson and Owain Smolović Jones. As you will see below, they push us towards key thinking around criticality as an edge, encouragement to engage with the complexity of leadership as a phenomenon and promoting ideas around critical companionship. We hope that you enjoy the read!
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16.
  • Freitag, Daniel F., et al. (author)
  • Cardiometabolic effects of genetic upregulation of the interleukin 1 receptor antagonist: a Mendelian randomisation analysis
  • 2015
  • In: The Lancet Diabetes & Endocrinology. - 2213-8595. ; 3:4, s. 243-253
  • Journal article (peer-reviewed)abstract
    • Background To investigate potential cardiovascular and other effects of long-term pharmacological interleukin 1 (IL-1) inhibition, we studied genetic variants that produce inhibition of IL-1, a master regulator of inflammation. Methods We created a genetic score combining the effects of alleles of two common variants (rs6743376 and rs1542176) that are located upstream of IL1RN, the gene encoding the IL-1 receptor antagonist (IL-1Ra; an endogenous inhibitor of both IL-1 alpha and IL-1 beta); both alleles increase soluble IL-1Ra protein concentration. We compared effects on inflammation biomarkers of this genetic score with those of anakinra, the recombinant form of IL-1Ra, which has previously been studied in randomised trials of rheumatoid arthritis and other inflammatory disorders. In primary analyses, we investigated the score in relation to rheumatoid arthritis and four cardiometabolic diseases (type 2 diabetes, coronary heart disease, ischaemic stroke, and abdominal aortic aneurysm; 453 411 total participants). In exploratory analyses, we studied the relation of the score to many disease traits and to 24 other disorders of proposed relevance to IL-1 signalling (746 171 total participants). Findings For each IL1RN minor allele inherited, serum concentrations of IL-1Ra increased by 0.22 SD (95% CI 0.18-0.25; 12.5%; p=9.3 x 10(-33)), concentrations of interleukin 6 decreased by 0.02 SD (-0.04 to -0.01; -1,7%; p=3.5 x 10(-3)), and concentrations of C-reactive protein decreased by 0.03 SD (-0.04 to -0.02; -3.4%; p=7.7 x 10(-14)). We noted the effects of the genetic score on these inflammation biomarkers to be directionally concordant with those of anakinra. The allele count of the genetic score had roughly log-linear, dose-dependent associations with both IL-1Ra concentration and risk of coronary heart disease. For people who carried four IL-1Ra-raising alleles, the odds ratio for coronary heart disease was 1.15 (1.08-1.22; p=1.8 x 10(-6)) compared with people who carried no IL-1Ra-raising alleles; the per-allele odds ratio for coronary heart disease was 1.03 (1.02-1.04; p=3.9 x 10(-10)). Perallele odds ratios were 0.97 (0.95-0.99; p=9.9 x 10(-4)) for rheumatoid arthritis, 0.99 (0.97-1.01; p=0.47) for type 2 diabetes, 1.00 (0.98-1.02; p=0.92) for ischaemic stroke, and 1.08 (1.04-1.12; p=1.8 x 10(-5)) for abdominal aortic aneurysm. In exploratory analyses, we observed per-allele increases in concentrations of proatherogenic lipids, including LDL-cholesterol, but no clear evidence of association for blood pressure, glycaemic traits, or any of the 24 other disorders studied. Modelling suggested that the observed increase in LDL-cholesterol could account for about a third of the association observed between the genetic score and increased coronary risk. Interpretation Human genetic data suggest that long-term dual IL-1 alpha/beta inhibition could increase cardiovascular risk and, conversely, reduce the risk of development of rheumatoid arthritis. The cardiovascular risk might, in part, be mediated through an increase in proatherogenic lipid concentrations. Copyright (C) The Interleukin 1 Genetics Consortium. Open Access article distributed under the terms of CC-BY-NC-ND.
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17.
  • Garcia-Martin, E. Elena, et al. (author)
  • Sources, Composition, and Export of Particulate Organic Matter Across British Estuaries
  • 2023
  • In: Journal of Geophysical Research - Biogeosciences. - : American Geophysical Union (AGU). - 2169-8953 .- 2169-8961. ; 128:4
  • Journal article (peer-reviewed)abstract
    • Estuaries receive and process a large amount of particulate organic carbon (POC) prior to its export into coastal waters. Studying the origin of this POC is key to understanding the fate of POC and the role of estuaries in the global carbon cycle. Here, we evaluated the concentrations of POC, as well as particulate organic nitrogen (PON), and used stable carbon and nitrogen isotopes to assess their sources across 13 contrasting British estuaries during five different sampling campaigns over 1 year. We found a high variability in POC and PON concentrations across the salinity gradient, reflecting inputs, and losses of organic material within the estuaries. Catchment land cover appeared to influence the contribution of POC to the total organic carbon flux from the estuary to coastal waters, with POC contributions >36% in estuaries draining catchments with a high percentage of urban/suburban land, and <11% in estuaries draining catchments with a high peatland cover. There was no seasonal pattern in the isotopic composition of POC and PON, suggesting similar sources for each estuary over time. Carbon isotopic ratios were depleted (-26.7 +/- 0.42 parts per thousand, average +/- sd) at the lowest salinity waters, indicating mainly terrigenous POC (TPOC). Applying a two-source mixing model, we observed high variability in the contribution of TPOC at the highest salinity waters between estuaries, with a median value of 57%. Our results indicate a large transport of terrigenous organic carbon into coastal waters, where it may be buried, remineralized, or transported offshore. Plain Language Summary Estuaries transport and process a large amount terrigenous particulate organic matter (i.e., carbon and nitrogen) prior to its export to coastal waters. In order to understand the fate of organic carbon and the role of estuaries in the global carbon cycle it is essential to improve our knowledge on its composition, origin, and amount of carbon transported. We quantified the elemental concentrations and stable isotopes composition of carbon and nitrogen to quantify the amount of terrigenous particulate organic matter transported by 13 British estuaries, which drain catchments of diverse land cover under different hydrological conditions. We found a great variability in particulate organic carbon (POC) and particulate organic nitrogen concentrations across the salinity gradient, implying inputs, and losses of material within the estuaries. Each estuary had similar sources of particulate material throughout the year. In most of the estuaries, the POC had a terrigenous origin at the lowest salinity waters. The terrigenous organic carbon contribution decreased toward coastal waters with an average contribution of 57% at the highest salinity waters, indicating a large transport of terrigenous organic carbon into coastal waters.
  •  
18.
  • Hassett, Brandon, et al. (author)
  • Global diversity and geography of planktonic marine fungi
  • 2020
  • In: Botanica Marina. - : Walter de Gruyter GmbH. - 0006-8055 .- 1437-4323. ; 63:2, s. 121-139
  • Journal article (peer-reviewed)abstract
    • Growing interest in understanding the relevance of marine fungi to food webs, biogeochemical cycling, and biological patterns necessitates establishing a context for interpreting future findings. To help establish this context, we summarize the diversity of cultured and observed marine planktonic fungi from across the world. While exploring this diversity, we discovered that only half of the known marine fungal species have a publicly available DNA locus, which we hypothesize will likely hinder accurate high-throughput sequencing classification in the future, as it does currently. Still, we reprocessed >600 high-throughput datasets and analyzed 4.9×109 sequences (4.8×109 shotgun metagenomic reads and 1.0×108 amplicon sequences) and found that every fungal phylum is represented in the global marine planktonic mycobiome; however, this mycobiome is generally predominated by three phyla: the Ascomycota, Basidiomycota, and Chytridiomycota. We hypothesize that these three clades are the most abundant due to a combination of evolutionary histories, as well as physical processes that aid in their dispersal. We found that environments with atypical salinity regimes (>5 standard deviations from the global mean: Red Sea, Baltic Sea, sea ice) hosted higher proportions of the Chytridiomycota, relative to open oceans that are dominated by Dikarya. The Baltic Sea and Mediterranean Sea had the highest fungal richness of all areas explored. An analysis of similarity identified significant differences between oceanographic regions. There were no latitudinal gradients of marine fungal richness and diversity observed. As more high-throughput sequencing data become available, expanding the collection of reference loci and genomes will be essential to understanding the ecology of marine fungi.
  •  
19.
  • Heap, Graham A., et al. (author)
  • HLA-DQA1-HLA-DRB1 variants confer susceptibility to pancreatitis induced by thiopurine immunosuppressants
  • 2014
  • In: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 46:10, s. 1131-1134
  • Journal article (peer-reviewed)abstract
    • Pancreatitis occurs in approximately 4% of patients treated with the thiopurines azathioprine or mercaptopurine. Its development is unpredictable and almost always leads to drug withdrawal. We identified patients with inflammatory bowel disease (IBD) who had developed pancreatitis within 3 months of starting these drugs from 168 sites around the world. After detailed case adjudication, we performed a genome-wide association study on 172 cases and 2,035 controls with IBD. We identified strong evidence of association within the class II HLA region, with the most significant association identified at rs2647087 (odds ratio 2.59, 95% confidence interval 2.07-3.26, P = 2 x 10(-16)). We replicated these findings in an independent set of 78 cases and 472 controls with IBD matched for drug exposure. Fine mapping of the H LA region identified association with the HLA-DQA1*02:01-HLA-DRB1*07:01 haplotype. Patients heterozygous at rs2647087 have a 9% risk of developing pancreatitis after administration of a thiopurine, whereas homozygotes have a 17% risk.
  •  
20.
  • Hodson, Elise, et al. (author)
  • Evaluating Social Impact of Smart City Technologies and Services: Methods, Challenges, Future Directions
  • 2023
  • In: MULTIMODAL TECHNOLOGIES AND INTERACTION. - : MDPI. - 2414-4088. ; 7:3
  • Journal article (peer-reviewed)abstract
    • This study examines motivations, definitions, methods and challenges of evaluating the social impacts of smart city technologies and services. It outlines concepts of social impact assessment and discusses how social impact has been included in smart city evaluation frameworks. Thematic analysis is used to investigate how social impact is addressed in eight smart city projects that prioritise human-centred design across a variety of contexts and development phases, from design research and prototyping to completed and speculative projects. These projects are notable for their emphasis on human, organisational and natural stakeholders; inclusion, participation and empowerment; new methods of citizen engagement; and relationships between sustainability and social impact. At the same time, there are gaps in the evaluation of social impact in both the smart city indexes and the eight projects. Based on our analysis, we contend that more coherent, consistent and analytical approaches are needed to build narratives of change and to comprehend impacts before, during and after smart city projects. We propose criteria for social impact evaluation in smart cities and identify new directions for research. This is of interest for smart city developers, researchers, funders and policymakers establishing protocols and frameworks for evaluation, particularly as smart city concepts and complex technologies evolve in the context of equitable and sustainable development.
  •  
21.
  • Izquierdo, Milagros, 1963-, et al. (author)
  • Groups of automorphisms of Riemann surfaces and maps of genus p + 1 where p is prime
  • 2020
  • In: Annales Academiæ Scientiarum Fennicæ Mathematica. - Helsinki, Finland : Academia Scientiarum Fennica. - 1239-629X .- 1798-2383. ; 46:2, s. 839-867
  • Journal article (peer-reviewed)abstract
    • We classify compact Riemann surfaces of genus g, where g−1 is a prime p, whichhave a group of automorphisms of order ρ(g−1) for some integer ρ ≥ 1, and determine isogeny decompositions of the corresponding Jacobian varieties. This extends results of Belolipetzky and the second author for ρ > 6, and of the first and third authors for ρ = 3,4,5 and 6. As a corollary we classify the orientably regular hypermaps (including maps) of genus p +1, together with the non-orientable regular hypermaps of characteristic − p, with automorphism group of order divisible by the prime p; this extends results of Conder, Širáň and Tucker for maps.
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22.
  • Izquierdo, Milagros, 1963-, et al. (author)
  • Groups of Automorphisms of Riemann Surfaces and Maps of Genus p+1 Where p is Prime
  • 2021
  • In: Annales Fennici Mathematici. - : The Finnish Mathematical Society. - 2737-0690 .- 2737-114X. ; 46:2, s. 839-867
  • Journal article (peer-reviewed)abstract
    • We classify compact Riemann surfaces of genus g, where g−1 is a prime p, which have a group of automorphisms of order ρ(g−1)for some integer ρ≥1, and determine isogeny decompositions of the corresponding Jacobian varieties. This extends results of Belolipetzky and the second author for ρ>6, and of the first and third authors for ρ= 3, 4, 5 and 6. As a corollary we classify the orientably regular hypermaps (including maps) of genus p+1, together with the non-orientable regular hypermaps of characteristic −p, with automorphism group of order divisible by the prime p; this extends results of Conder, Širáň and Tucker for maps.
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23.
  • Jayasiri, Subashini C., et al. (author)
  • The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
  • 2015
  • In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18
  • Journal article (peer-reviewed)abstract
    • Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
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24.
  • Jones, Gareth, et al. (author)
  • Phylogeny of new marine Dothideomycetes and Sordariomycetes from mangroves and deep-sea sediments
  • 2020
  • In: Botanica Marina. - : Walter de Gruyter GmbH. - 0006-8055 .- 1437-4323. ; 63:2, s. 155-181
  • Journal article (peer-reviewed)abstract
    • This paper documents six new saprobic marine fungi and one new genus based on morphology and multi-gene phylogenies. Three Dothideomycetes, and members of the Pleosporales, are introduced: Pseudo-massariosphaeria triseptata sp. nov. was recognized as a mangrove species in Amniculicolaceae, and Salsuginea phoenicis sp. nov. was discovered as a second member of Salsugineaceae. A new genus Raghukumaria with Raghukumaria keshaphalae sp. nov., recovered from mangroves, is phylogenetically sister to Halomassarina and nests in the Trematosphaeriaceae. Three new species are referred to the Sordariomycetes: Coniochaeta marina (Coniochaetales, Coniochaetaceae) on driftwood; Fusicolla bharatavarshae (Hypocreales, Nectriaceae) is introduced with asexual and sexual morphs, on decayed mangrove wood of Avicennia marina; and Fusarium sedimenticola (Hypocreales, Nectriaceae) is new to the Fusarium solani species complex (FSSC) from deep-sea sediment.
  •  
25.
  • Kapoor, Pooja Middha, et al. (author)
  • Combined associations of a polygenic risk score and classical risk factors with breast cancer risk
  • 2021
  • In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 113:3, s. 329-337
  • Journal article (peer-reviewed)abstract
    • We evaluated the joint associations between a new 313-variant PRS (PRS313) and questionnaire-based breast cancer risk factors for women of European ancestry, using 72 284 cases and 80 354 controls from the Breast Cancer Association Consortium. Interactions were evaluated using standard logistic regression and a newly developed case-only method for breast cancer risk overall and by estrogen receptor status. After accounting for multiple testing, we did not find evidence that per-standard deviation PRS313 odds ratio differed across strata defined by individual risk factors. Goodness-of-fit tests did not reject the assumption of a multiplicative model between PRS313 and each risk factor. Variation in projected absolute lifetime risk of breast cancer associated with classical risk factors was greater for women with higher genetic risk (PRS313 and family history) and, on average, 17.5% higher in the highest vs lowest deciles of genetic risk. These findings have implications for risk prevention for women at increased risk of breast cancer. 
  •  
26.
  • Kierkegaard, Amelie, et al. (author)
  • A mass balance of tri-hexabrominated diphenyl ethers in lactating cows.
  • 2009
  • In: Environmental Science and Technology. - : American Chemical Society. - 0013-936X .- 1520-5851. ; 43:7, s. 2602-2607
  • Journal article (peer-reviewed)abstract
    • Beef and dairy products can be important vectors of human exposure to polybrominated diphenylethers (BDEs), and hence an understanding of BDE transfer from feed to cows' milk and tissue is important for BDE exposure assessment The fate of tri- to hexaBDEs in lactating cows exposed to a naturally contaminated diet was studied by analyzing feed, feces, and milk samples from a mass balance study. Tissue distribution was studied in one cowslaughtered afterthe experiment The carryover rates from feed to milk ranged from 0.15 to 0.35 for the major congeners. Lower values were observed for several of the tetrabrominated congeners, and this was attributed to metabolism. The dietary absorption efficiency decreased with increasing octanol-water partition coefficient of the BDE congener. The absorption behavior was consistent with a model based on chemical lipophilicity, but agreed less well with a model based on effective molecular diameter, and it violated Lipinski's "rule of 5". The lipid normalized concentrations were similar in all tissues analyzed including liver and milk, suggesting that tissue distribution is governed by partitioning into lipids. Overall, the behavior of the tri- to hexaBDEs was consistent with that observed for other classes of halogenated aromatic contaminants such as PCBs and PCDD/Fs, but it differed markedly from the behavior of the hepta- decaBDEs.
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27.
  •  
28.
  • Kropp, Heather, et al. (author)
  • Shallow soils are warmer under trees and tall shrubs across Arctic and Boreal ecosystems
  • 2021
  • In: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 16:1
  • Journal article (peer-reviewed)abstract
    • Soils are warming as air temperatures rise across the Arctic and Boreal region concurrent with the expansion of tall-statured shrubs and trees in the tundra. Changes in vegetation structure and function are expected to alter soil thermal regimes, thereby modifying climate feedbacks related to permafrost thaw and carbon cycling. However, current understanding of vegetation impacts on soil temperature is limited to local or regional scales and lacks the generality necessary to predict soil warming and permafrost stability on a pan-Arctic scale. Here we synthesize shallow soil and air temperature observations with broad spatial and temporal coverage collected across 106 sites representing nine different vegetation types in the permafrost region. We showed ecosystems with tall-statured shrubs and trees (>40 cm) have warmer shallow soils than those with short-statured tundra vegetation when normalized to a constant air temperature. In tree and tall shrub vegetation types, cooler temperatures in the warm season do not lead to cooler mean annual soil temperature indicating that ground thermal regimes in the cold-season rather than the warm-season are most critical for predicting soil warming in ecosystems underlain by permafrost. Our results suggest that the expansion of tall shrubs and trees into tundra regions can amplify shallow soil warming, and could increase the potential for increased seasonal thaw depth and increase soil carbon cycling rates and lead to increased carbon dioxide loss and further permafrost thaw.
  •  
29.
  • Loranty, Michael M., et al. (author)
  • Reviews and syntheses : Changing ecosystem influences on soil thermal regimes in northern high-latitude permafrost regions
  • 2018
  • In: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 15:17, s. 5287-5313
  • Research review (peer-reviewed)abstract
    • Soils in Arctic and boreal ecosystems store twice as much carbon as the atmosphere, a portion of which may be released as high-latitude soils warm. Some of the uncertainty in the timing and magnitude of the permafrost-climate feedback stems from complex interactions between ecosystem properties and soil thermal dynamics. Terrestrial ecosystems fundamentally regulate the response of permafrost to climate change by influencing surface energy partitioning and the thermal properties of soil itself. Here we review how Arctic and boreal ecosystem processes influence thermal dynamics in permafrost soil and how these linkages may evolve in response to climate change. While many of the ecosystem characteristics and processes affecting soil thermal dynamics have been examined individually (e.g., vegetation, soil moisture, and soil structure), interactions among these processes are less understood. Changes in ecosystem type and vegetation characteristics will alter spatial patterns of interactions between climate and permafrost. In addition to shrub expansion, other vegetation responses to changes in climate and rapidly changing disturbance regimes will affect ecosystem surface energy partitioning in ways that are important for permafrost. Lastly, changes in vegetation and ecosystem distribution will lead to regional and global biophysical and biogeochemical climate feedbacks that may compound or offset local impacts on permafrost soils. Consequently, accurate prediction of the permafrost carbon climate feedback will require detailed understanding of changes in terrestrial ecosystem distribution and function, which depend on the net effects of multiple feedback processes operating across scales in space and time.
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30.
  • Michelsen, Brigitte, et al. (author)
  • Real-World Six- and Twelve-Month Drug Retention, Remission, and Response Rates of Secukinumab in 2,017 Patients With Psoriatic Arthritis in Thirteen European Countries
  • 2022
  • In: Arthritis Care and Research. - : Wiley. - 2151-464X .- 2151-4658. ; 74:7, s. 1205-1218
  • Journal article (peer-reviewed)abstract
    • Objective: There is a lack of real-life studies on interleukin-17 (IL-17) inhibition in psoriatic arthritis (PsA). We assessed real-life 6- and 12-month effectiveness (i.e., retention, remission, low disease activity [LDA], and response rates) of the IL-17 inhibitor secukinumab in PsA patients overall and across 1) number of prior biologic/targeted synthetic disease-modifying antirheumatic drugs (b/tsDMARDs), 2) years since diagnosis, and 3) European registries. Methods: Thirteen quality registries in rheumatology participating in the European Spondyloarthritis Research Collaboration Network provided longitudinal, observational data collected as part of routine care for secondary use. Data were pooled and analyzed with Kaplan-Meier plots, log rank tests, Cox regression, and multiple linear and logistic regression analyses. Results: A total of 2,017 PsA patients started treatment with secukinumab between 2015 and 2018. Overall secukinumab retention rates were 86% and 76% after 6 and 12 months, respectively. Crude (LUNDEX adjusted) 6-month remission/LDA (LDA including remission) rates for the 28-joint Disease Activity Index for Psoriatic Arthritis, the Disease Activity Score in 28 joints using the C-reactive protein level, and the Simplified Disease Activity Index (SDAI) were 13%/46% (11%/39%), 36%/55% (30%/46%), and 13%/56% (11%/47%), and 12-month rates were 11%/46% (7%/31%), 39%/56% (26%/38%), and 16%/62% (10%/41%), respectively. Clinical Disease Activity Index remission/LDA rates were similar to the SDAI rates. Six-month American College of Rheumatology 20%/50%/70% improvement criteria responses were 34%/19%/11% (29%/16%/9%); 12-month rates were 37%/21%/11% (24%/14%/7%). Secukinumab effectiveness was significantly better for b/tsDMARD-naive patients, similar across time since diagnosis (<2/2–4/>4 years), and varied significantly across the European registries. Conclusion: In this large real-world study on secukinumab treatment in PsA, 6- and 12-month effectiveness was comparable to that in previous observational studies of tumor necrosis factor inhibitors. Retention, remission, LDA, and response rates were significantly better for b/tsDMARD-naive patients, were independent of time since diagnosis, and varied significantly across the European countries.
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31.
  • Middha, Pooja K., et al. (author)
  • A genome-wide gene-environment interaction study of breast cancer risk for women of European ancestry
  • 2023
  • In: Breast Cancer Research. - : BioMed Central (BMC). - 1465-5411 .- 1465-542X. ; 25:1
  • Journal article (peer-reviewed)abstract
    • Background Genome-wide studies of gene-environment interactions (GxE) may identify variants associated with disease risk in conjunction with lifestyle/environmental exposures. We conducted a genome-wide GxE analysis of similar to 7.6 million common variants and seven lifestyle/environmental risk factors for breast cancer risk overall and for estrogen receptor positive (ER +) breast cancer. Methods Analyses were conducted using 72,285 breast cancer cases and 80,354 controls of European ancestry from the Breast Cancer Association Consortium. Gene-environment interactions were evaluated using standard unconditional logistic regression models and likelihood ratio tests for breast cancer risk overall and for ER + breast cancer. Bayesian False Discovery Probability was employed to assess the noteworthiness of each SNP-risk factor pairs. Results Assuming a 1 x 10(-5) prior probability of a true association for each SNP-risk factor pairs and a Bayesian False Discovery Probability < 15%, we identified two independent SNP-risk factor pairs: rs80018847(9p13)-LINGO2 and adult height in association with overall breast cancer risk (ORint = 0.94, 95% CI 0.92-0.96), and rs4770552(13q12)-SPATA13 and age at menarche for ER + breast cancer risk (ORint = 0.91, 95% CI 0.88-0.94). Conclusions Overall, the contribution of GxE interactions to the heritability of breast cancer is very small. At the population level, multiplicative GxE interactions do not make an important contribution to risk prediction in breast cancer.
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32.
  • Mueller, Stefanie H., et al. (author)
  • Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
  • 2023
  • In: Genome Medicine. - : BioMed Central (BMC). - 1756-994X. ; 15
  • Journal article (peer-reviewed)abstract
    • Background: Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.Methods: We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.Results: In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 x 10(-6)) and AC058822.1 (P = 1.47 x 10(-4)), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C.Conclusions: Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 x 10(-5)), demonstrating the importance of diversifying study cohorts.
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33.
  • Ornbjerg, Lykke Midtboll, et al. (author)
  • One-Third of European Patients With Axial Spondyloarthritis Reach Pain Remission With Routine Care Tumor Necrosis Factor Inhibitor Treatment
  • 2023
  • In: JOURNAL OF RHEUMATOLOGY. - : The Journal of Rheumatology. - 0315-162X .- 1499-2752. ; 50:8, s. 1009-1019
  • Journal article (peer-reviewed)abstract
    • Objective. To investigate the distribution of patient-reported outcomes (PROs) in patients with axial spondyloarthritis (axSpA) initiating a tumor necrosis factor inhibitor ( TNFi), to assess the proportion reaching PRO "remission" across registries and treatment series, and to compare patients registered to fulfill the modified New York (mNY) criteria for ankylosing spondylitis (AS) vs patients with nonradiographic axSpA (nr-axSpA). Methods. Fifteen European registries contributed PRO scores for pain, fatigue, patient global assessment (PtGA), Bath Ankylosing Spondylitis (AS) Disease Activity Index (BASDAI), Bath AS Functional Index (BASFI), and Health Assessment Questionnaire (HAQ) from 19,498 patients with axSpA. Changes in PROs and PRO remission rates (definitions: <= 20 mm for pain, fatigue, PtGA, BASDAI, and BASFI; <= 0.5 for HAQ) were calculated at 6, 12, and 24 months of treatment. Results. Heterogeneity in baseline characteristics and outcomes between registries were observed. In pooled data, 6 months after the start of a first TNFi, pain score was reduced by approximately 60% (median at baseline/6/12/24 months: 65/25/20/20 mm) in patients on treatment. Similar patterns were observed for fatigue (68/32/30/25 mm), PtGA (66/29/21/20 mm), BASDAI (58/26/21/19 mm), BASFI (46/20/16/16 mm), and HAQ (0.8/0.4/0.2/0.2). Patients with AS (n = 3281) had a slightly better response than patients with nr-axSpA (n = 993). The Lund Efficacy Index (LUNDEX)-adjusted remission rates at 6 months for pain/fatigue/PtGA/BASDAI/BASFI/HAQ were 39%/30%/38%/34%/35%/48% for the AS cohort and 30%/21%/26%/24%/33%/47% for the nr-axSpA cohort. Better PRO responses were seen with a first TNFi compared to a second and third TNFi. Conclusion. Patients with axSpA starting a TNFi achieved high PRO remission rates, most pronounced in those fulfilling the mNY criteria and for the first TNFi.
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34.
  • Pang, Ka-Lai, et al. (author)
  • Recent progress in marine mycological research in different countries, and prospects for future developments worldwide
  • 2023
  • In: Botanica Marina. - : Walter de Gruyter. - 0006-8055 .- 1437-4323. ; 66:4, s. 239-269
  • Journal article (peer-reviewed)abstract
    • Early research on marine fungi was mostly descriptive, with an emphasis on their diversity and taxonomy, especially of those collected at rocky shores on seaweeds and driftwood. Subsequently, further substrata (e.g. salt marsh grasses, marine animals, seagrasses, sea foam, seawater, sediment) and habitats (coral reefs, deep-sea, hydrothermal vents, mangroves, sandy beaches, salt marshes) were explored for marine fungi. In parallel, research areas have broadened from micro-morphology to ultrastructure, ecophysiology, molecular phylogenetics, biogeography, biodeterioration, biodegradation, bioprospecting, genomics, proteomics, transcriptomics and metabolomics. Although marine fungi only constitute a small fraction of the global mycota, new species of marine fungi continue to be described from new hosts/substrata of unexplored locations/habitats, and novel bioactive metabolites have been discovered in the last two decades, warranting a greater collaborative research effort. Marine fungi of Africa, the Americas and Australasia are under-explored, while marine Chytridiomycota and allied taxa, fungi associated with marine animals, the functional roles of fungi in the sea, and the impacts of climate change on marine fungi are some of the topics needing more attention. In this article, currently active marine mycologists from different countries have written on the history and current state of marine fungal research in individual countries highlighting their strength in the subject, and this represents a first step towards a collaborative inter- and transdisciplinary research strategy.
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35.
  • Rowney, Francis M, et al. (author)
  • Environmental DNA reveals links between abundance and composition of airborne grass pollen and respiratory health
  • 2021
  • In: Current Biology. - : Elsevier BV. - 1879-0445 .- 0960-9822. ; 31:9, s. 4-2003
  • Journal article (peer-reviewed)abstract
    • Grass (Poaceae) pollen is the most important outdoor aeroallergen,1 exacerbating a range of respiratory conditions, including allergic asthma and rhinitis ("hay fever").2-5 Understanding the relationships between respiratory diseases and airborne grass pollen with a view to improving forecasting has broad public health and socioeconomic relevance. It is estimated that there are over 400 million people with allergic rhinitis6 and over 300 million with asthma, globally,7 often comorbidly.8 In the UK, allergic asthma has an annual cost of around US$ 2.8 billion (2017).9 The relative contributions of the >11,000 (worldwide) grass species (C. Osborne et al., 2011, Botany Conference, abstract) to respiratory health have been unresolved,10 as grass pollen cannot be readily discriminated using standard microscopy.11 Instead, here we used novel environmental DNA (eDNA) sampling and qPCR12-15 to measure the relative abundances of airborne pollen from common grass species during two grass pollen seasons (2016 and 2017) across the UK. We quantitatively demonstrate discrete spatiotemporal patterns in airborne grass pollen assemblages. Using a series of generalized additive models (GAMs), we explore the relationship between the incidences of airborne pollen and severe asthma exacerbations (sub-weekly) and prescribing rates of drugs for respiratory allergies (monthly). Our results indicate that a subset of grass species may have disproportionate influence on these population-scale respiratory health responses during peak grass pollen concentrations. The work demonstrates the need for sensitive and detailed biomonitoring of harmful aeroallergens in order to investigate and mitigate their impacts on human health.
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36.
  • Rydell, Jens, et al. (author)
  • Testing the performances of automated identification of bat echolocation calls : A request for prudence
  • 2017
  • In: Ecological Indicators. - : Elsevier BV. - 1470-160X. ; 78, s. 416-420
  • Journal article (peer-reviewed)abstract
    • Echolocating bats are surveyed and studied acoustically with bat detectors routinely and worldwide, yet identification of species from calls often remains ambiguous or impossible due to intraspecific call variation and/or interspecific overlap in call design. To overcome such difficulties and to reduce workload, automated classifiers of echolocation calls have become popular, but their performance has not been tested sufficiently in the field. We examined the absolute performance of two commercially available programs (SonoChiro and Kaleidoscope) and one freeware package (BatClassify). We recorded noise from rain and calls of seven common bat species with Pettersson real-time full spectrum detectors in Sweden. The programs could always (100%) distinguish rain from bat calls, usually (68–100%) identify bats to group (Nyctalus/Vespertilio/Eptesicus, Pipistrellus, Myotis, Plecotus, Barbastella) and usually (83–99%) recognize typical calls of some species whose echolocation pulses are structurally distinct (Pipistrellus pygmaeus, Barbastella barbastellus). Species with less characteristic echolocation calls were not identified reliably, including Vespertilio murinus (16–26%), Myotis spp. (4–93%) and Plecotus auritus (0–89%). All programs showed major although different shortcomings and the often poor performance raising serious concerns about the use of automated classifiers for identification to species level in research and surveys. We highlight the importance of validating output from automated classifiers, and restricting their use to specific situations where identification can be made with high confidence. For comparison we also present the result of a manual identification test on a random subset of the files used to test the programs. It showed a higher classification success but performances were still low for more problematic taxa.
  •  
37.
  • Sanchez, Xavier, 1971-, et al. (author)
  • Identification of Parameters That Predict Sport Climbing Performance
  • 2019
  • In: Frontiers in Psychology. - Lausanne : Frontiers Media S.A.. - 1664-1078. ; 10
  • Journal article (peer-reviewed)abstract
    • In recent years, extreme sport-related pursuits including climbing have emerged not only as recreational activities but as competitive sports. Today, sport climbing is a rapidly developing, competitive sport included in the 2020 Olympic Games official program. Given recent developments, the understanding of which factors may influence actual climbing performance becomes critical. The present study aimed at identifying key performance parameters as perceived by experts in predicting actual lead sport climbing performance. Ten male (Mage = 28, SD = 6.6 years) expert climbers (7a+ to 8b on-sight French Rating Scale of Difficulty), who were also registered as climbing coaches, participated in semi-structured interviews. Participants’ responses were subjected to inductive-deductive content analysis. Several performance parameters were identified: passing cruxes, strength and conditioning aspects, interaction with the environment, possessing a good climbing movement repertoire, risk management, route management, mental balance, peer communication, and route preview. Route previewing emerged as critical when it comes to preparing and planning ascents, both cognitively and physically. That is, when optimizing decision making in relation to progressing on the route (ascent strategy forecasting) and when enhancing strategic management in relation to the effort exerted on the route (ascent effort forecasting). Participants described how such planning for the ascent allows them to: select an accurate and comprehensive movement repertoire relative to the specific demands of the route and reject ineffective movements; optimize effective movements; and link different movements upward. As the sport of climbing continues to develop, our findings provide a basis for further research that shall examine further how, each of these performance parameters identified, can most effectively be enhanced and optimized to influence performance positively. In addition, the present study provides a comprehensive view of parameters to consider when planning, designing and delivering holistic and coherent training programs aimed at enhancing climbing performance. © 2019 Sanchez, Torregrossa, Woodman, Jones and Llewellyn.
  •  
38.
  • Satizabal, Claudia L., et al. (author)
  • Genetic architecture of subcortical brain structures in 38,851 individuals
  • 2019
  • In: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:11, s. 1624-
  • Journal article (peer-reviewed)abstract
    • Subcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen and thalamus, using genome-wide association analyses in almost 40,000 individuals from CHARGE, ENIGMA and UK Biobank. We show that variability in subcortical volumes is heritable, and identify 48 significantly associated loci (40 novel at the time of analysis). Annotation of these loci by utilizing gene expression, methylation and neuropathological data identified 199 genes putatively implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, inflammation/infection and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease.
  •  
39.
  • Senanayake, Indunil C., et al. (author)
  • Fungal diversity notes 1611–1716: taxonomic and phylogenetic contributions on fungal genera and species emphasis in south China
  • 2023
  • In: Fungal Diversity. - 1560-2745 .- 1878-9129. ; 122, s. 161-403
  • Journal article (peer-reviewed)abstract
    • This article is the 15th contribution in the Fungal Diversity Notes series, wherein 115 taxa from three phyla, nine classes, 28 orders, 48 families, and 64 genera are treated. Fungal taxa described and illustrated in the present study include a new family, five new genera, 61 new species, five new combinations, one synonym, one new variety and 31 records on new hosts or new geographical distributions. Ageratinicolaceae fam. nov. is introduced and accommodated in Pleosporales. The new genera introduced in this study are Ageratinicola, Kevinia, Pseudomultiseptospora (Parabambusicolaceae), Marasmiellomycena, and Vizzinia (Porotheleaceae). Newly described species are Abrothallus altoandinus, Ageratinicola kunmingensis, Allocryptovalsa aceris, Allophoma yuccae, Apiospora cannae, A. elliptica, A. pallidesporae, Boeremia wisteriae, Calycina papaeana, Clypeococcum lichenostigmoides, Coniochaeta riskali-shoyakubovii, Cryphonectria kunmingensis, Diaporthe angustiapiculata, D. campylandrae, D. longipapillata, Diatrypella guangdongense, Dothiorella franceschinii, Endocalyx phoenicis, Epicoccum terminosporum, Fulvifomes karaiensis, F. pannaensis, Ganoderma ghatensis, Hysterobrevium baoshanense, Inocybe avellaneorosea, I. lucida, Jahnula oblonga, Kevinia lignicola, Kirschsteiniothelia guangdongensis, Laboulbenia caprina, L. clavulata, L. cobiae, L. cosmodisci, L. nilotica, L. omalii, L. robusta, L. similis, L. stigmatophora, Laccaria rubriporus, Lasiodiplodia morindae, Lyophyllum agnijum, Marasmiellomycena pseudoomphaliiformis, Melomastia beihaiensis, Nemania guangdongensis, Nigrograna thailandica, Nigrospora ficuum, Oxydothis chinensis, O. yunnanensis, Petriella thailandica, Phaeoacremonium chinensis, Phialocephala chinensis, Phytophthora debattistii, Polyplosphaeria nigrospora, Pronectria loweniae, Seriascoma acutispora, Setoseptoria bambusae, Stictis anomianthi, Tarzetta tibetensis, Tarzetta urceolata, Tetraploa obpyriformis, Trichoglossum beninense, and Tricoderma pyrrosiae. We provide an emendation for Urnula ailaoshanensis Agaricus duplocingulatoides var. brevisporus introduced as a new variety based on morphology and phylogeny.
  •  
40.
  • Shu, Xiang, et al. (author)
  • Associations of obesity and circulating insulin and glucose with breast cancer risk : a Mendelian randomization analysis
  • 2019
  • In: International Journal of Epidemiology. - : OXFORD UNIV PRESS. - 0300-5771 .- 1464-3685. ; 48:3, s. 795-806
  • Journal article (peer-reviewed)abstract
    • Background: In addition to the established association between general obesity and breast cancer risk, central obesity and circulating fasting insulin and glucose have been linked to the development of this common malignancy. Findings from previous studies, however, have been inconsistent, and the nature of the associations is unclear. Methods: We conducted Mendelian randomization analyses to evaluate the association of breast cancer risk, using genetic instruments, with fasting insulin, fasting glucose, 2-h glucose, body mass index (BMI) and BMI-adjusted waist-hip-ratio (WHRadj BMI). We first confirmed the association of these instruments with type 2 diabetes risk in a large diabetes genome-wide association study consortium. We then investigated their associations with breast cancer risk using individual-level data obtained from 98 842 cases and 83 464 controls of European descent in the Breast Cancer Association Consortium. Results: All sets of instruments were associated with risk of type 2 diabetes. Associations with breast cancer risk were found for genetically predicted fasting insulin [odds ratio (OR) = 1.71 per standard deviation (SD) increase, 95% confidence interval (CI) = 1.26-2.31, p = 5.09 x 10(-4)], 2-h glucose (OR = 1.80 per SD increase, 95% CI = 1.3 0-2.49, p = 4.02 x 10(-4)), BMI (OR = 0.70 per 5-unit increase, 95% CI = 0.65-0.76, p = 5.05 x 10(-19)) and WHRadj BMI (OR = 0.85, 95% CI = 0.79-0.91, p = 9.22 x 10(-6)). Stratified analyses showed that genetically predicted fasting insulin was more closely related to risk of estrogen-receptor [ER]-positive cancer, whereas the associations with instruments of 2h glucose, BMI and WHRadj BMI were consistent regardless of age, menopausal status, estrogen receptor status and family history of breast cancer. Conclusions: We confirmed the previously reported inverse association of genetically predicted BMI with breast cancer risk, and showed a positive association of genetically predicted fasting insulin and 2-h glucose and an inverse association of WHRadj BMI with breast cancer risk. Our study suggests that genetically determined obesity and glucose/insulin-related traits have an important role in the aetiology of breast cancer.
  •  
41.
  • Sim, Thomas G., et al. (author)
  • Regional variability in peatland burning at mid-to high-latitudes during the Holocene
  • 2023
  • In: Quaternary Science Reviews. - : Elsevier. - 0277-3791 .- 1873-457X. ; 305
  • Journal article (peer-reviewed)abstract
    • Northern peatlands store globally-important amounts of carbon in the form of partly decomposed plant detritus. Drying associated with climate and land-use change may lead to increased fire frequency and severity in peatlands and the rapid loss of carbon to the atmosphere. However, our understanding of the patterns and drivers of peatland burning on an appropriate decadal to millennial timescale relies heavily on individual site-based reconstructions. For the first time, we synthesise peatland macrocharcoal re-cords from across North America, Europe, and Patagonia to reveal regional variation in peatland burning during the Holocene. We used an existing database of proximal sedimentary charcoal to represent regional burning trends in the wider landscape for each region. Long-term trends in peatland burning appear to be largely climate driven, with human activities likely having an increasing influence in the late Holocene. Warmer conditions during the Holocene Thermal Maximum (similar to 9e6 cal. ka BP) were associated with greater peatland burning in North America's Atlantic coast, southern Scandinavia and the Baltics, and Patagonia. Since the Little Ice Age, peatland burning has declined across North America and in some areas of Europe. This decline is mirrored by a decrease in wider landscape burning in some, but not all sub-regions, linked to fire-suppression policies, and landscape fragmentation caused by agricultural expansion. Peatlands demonstrate lower susceptibility to burning than the wider landscape in several instances, probably because of autogenic processes that maintain high levels of near-surface wetness even during drought. Nonetheless, widespread drying and degradation of peatlands, particularly in Europe, has likely increased their vulnerability to burning in recent centuries. Consequently, peatland restoration efforts are important to mitigate the risk of peatland fire under a changing climate. Finally, we make recommendations for future research to improve our understanding of the controls on peatland fires.(c) 2023 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
  •  
42.
  • Strittmatter, Nicole, et al. (author)
  • Holistic Characterization of a Salmonella Typhimurium Infection Model Using Integrated Molecular Imaging
  • 2021
  • In: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 32:12, s. 2791-2802
  • Journal article (peer-reviewed)abstract
    • A more complete and holistic view on host-microbe interactions is needed to understand the physiological and cellular barriers that affect the efficacy of drug treatments and allow the discovery and development of new therapeutics. Here, we developed a multimodal imaging approach combining histopathology with mass spectrometry imaging (MSI) and same section imaging mass cytometry (IMC) to study the effects of Salmonella Typhimurium infection in the liver of a mouse model using the S. Typhimurium strains SL3261 and SL1344. This approach enables correlation of tissue morphology and specific cell phenotypes with molecular images of tissue metabolism. IMC revealed a marked increase in immune cell markers and localization in immune aggregates in infected tissues. A correlative computational method (network analysis) was deployed to find metabolic features associated with infection and revealed metabolic clusters of acetyl carnitines, as well as phosphatidylcholine and phosphatidylethanolamine plasmalogen species, which could be associated with pro-inflammatory immune cell types. By developing an IMC marker for the detection of Salmonella LPS, we were further able to identify and characterize those cell types which contained S. Typhimurium.
  •  
43.
  • Suominen, Hanna, et al. (author)
  • Overview of the ShARe/CLEF eHealth Evaluation Lab 2013
  • 2013
  • In: Information Access Evaluation. Multilinguality, Multimodality, and Visualization. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783642408014 - 9783642408021 ; , s. 212-231
  • Conference paper (peer-reviewed)abstract
    • Discharge summaries and other free-text reports in healthcare transfer information between working shifts and geographic locations. Patients are likely to have difficulties in understanding their content, because of their medical jargon, non-standard abbreviations, and ward-specific idioms. This paper reports on an evaluation lab with an aim to support the continuum of care by developing methods and resources that make clinical reports in English easier to understand for patients, and which helps them in finding information related to their condition. This ShARe/CLEFeHealth2013 lab offered student mentoring and shared tasks: identification and normalisation of disorders (1a and 1b) and normalisation of abbreviations and acronyms (2) in clinical reports with respect to terminology standards in healthcare as well as information retrieval (3) to address questions patients may have when reading clinical reports. The focus on patients’ information needs as opposed to the specialised information needs of physicians and other healthcare workers was the main feature of the lab distinguishing it from previous shared tasks. De-identified clinical reports for the three tasks were from US intensive care and originated from the MIMIC II database. Other text documents for Task 3 were from the Internet and originated from the Khresmoi project. Task 1 annotations originated from the ShARe annotations. For Tasks 2 and 3, new annotations, queries, and relevance assessments were created. 64, 56, and 55 people registered their interest in Tasks 1, 2, and 3, respectively. 34 unique teams (3 members per team on average) participated with 22, 17, 5, and 9 teams in Tasks 1a, 1b, 2 and 3, respectively. The teams were from Australia, China, France, India, Ireland, Republic of Korea, Spain, UK, and USA. Some teams developed and used additional annotations, but this strategy contributed to the system performance only in Task 2. The best systems had the F1 score of 0.75 in Task 1a; Accuracies of 0.59 and 0.72 in Tasks 1b and 2; and Precision at 10 of 0.52 in Task 3. The results demonstrate the substantial community interest and capabilities of these systems in making clinical reports easier to understand for patients. The organisers have made data and tools available for future research and development.
  •  
44.
  • Tibell, Sanja, et al. (author)
  • A conspectus of the filamentous marine fungi of Sweden
  • 2020
  • In: Botanica Marina. - : Walter de Gruyter GmbH. - 0006-8055 .- 1437-4323. ; 63:2, s. 141-153
  • Journal article (peer-reviewed)abstract
    • Marine filamentous fungi have been little studied in Sweden, which is remarkable given the depth and width of mycological studies in the country since the time of Elias Fries. Seventy-four marine fungi are listed for Sweden based on historical records and recent collections, of which 16 are new records for the country. New records for the country are based on morphological identification of species mainly from marine wood, and most of them from the Swedish West Coast. In some instances, the identifications have been made by comparisons of sequences obtained from cultures with reference sequences in GenBank. Corollospora angusta, Corollospora filiformis, and Corollospora pulchella, previously known from tropical/subtropical areas, are recorded for the first time for Sweden. The arctic Havispora longyearbyensis was also found. Kalmusia longispora and Neocamarosporium calvescens were reported for the first time from marine habitats.
  •  
45.
  • Tibell, Sanja, et al. (author)
  • Marine fungi of the Baltic Sea
  • 2020
  • In: Mycology. - : Informa UK Limited. - 2150-1203 .- 2150-1211. ; 11:3, s. 195-213
  • Journal article (peer-reviewed)abstract
    • Vast parts of the Baltic Sea have been mycologically neglected and are still awaiting exploration. Here we summarise earlier records of marine fungi from the Baltic, supplementing them with discoveries from fieldwork in Sweden in 2019. Although marine fungal diversity is clearly attenuated in the brackish water of the Baltic Sea, a substantial number has still been discovered. Here we list 77 species from the Baltic Sea, whereas after a critical assessment a further 18 species have been excluded as records of marine fungi. The species have mainly been identified by their morphological features, supplemented by DNA-based diagnostics. Most of the species have their main distributions in temperate areas of the Atlantic Ocean. Some of the Baltic species discovered here represent far disjunctions to tropical waters while only a very few are until now only recorded for the Baltic Sea. In this paper two species belong in Basidiomycota, while the most ascomyceteous speciose classes are Sordariomycetes (with 42 species) and Dothideomycetes (24). Halosphaeriaceae is the most speciose family in marine habitats, as also in the Baltic Sea, represented here by 29 species. Three species are new to Europe, and in addition 13 to the Baltic Sea and 13 to Sweden.
  •  
46.
  • Voigt, Christian C., et al. (author)
  • The Impact of Light Pollution on Bats Varies According to Foraging Guild and Habitat Context
  • 2021
  • In: BioScience. - : Oxford University Press (OUP). - 0006-3568 .- 1525-3244. ; 71:10, s. 1103-1109
  • Research review (peer-reviewed)abstract
    • We Review How Different Bat Guilds Respond To Artificial Light At Night (Alan) And Assess How The Impacts Can Vary According To Ecological Context. All Studied European Species Respond Negatively To Alan Close To Roosts And Drinking Sites, And The Impacts Occur Across A Wide Range Of Light Colors And Intensities. Most Bat Species Are Sensitive To Alan When Commuting And Foraging. Although Narrow-Space-Foraging Bat Species Consistently Avoid Alan When Foraging, Open And Edge-Space-Foraging Species May Exploit Insects Lured By Alan. Therefore, Alan Acts As An Environmental Filter On Bat Assemblages. Considering The Detrimental Effect Of Alan On Insects, We Conclude That Alan Probably Has Negative Impacts On All Bat Species, Even On Those Foraging At Streetlights. The Sprawl Of Alan May Be A Key Factor Driving The Decline Of Bat Diversity Globally, And The Current Trajectory Of Increasing Alan Is Therefore Of Considerable Concern For Bat Conservation.
  •  
47.
  • Wanasinghe, Dhanushka N., et al. (author)
  • Fungal diversity notes 709–839 : taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae
  • 2018
  • In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 89:1, s. 1-236
  • Journal article (peer-reviewed)abstract
    • This paper is the seventh in the Fungal Diversity Notes series, where 131 taxa accommodated in 28 families are mainly described from Rosa (Rosaceae) and a few other hosts. Novel fungal taxa are described in the present study, including 17 new genera, 93 new species, four combinations, a sexual record for a species and new host records for 16 species. Bhatiellae, Cycasicola, Dactylidina, Embarria, Hawksworthiana, Italica, Melanocucurbitaria, Melanodiplodia, Monoseptella, Uzbekistanica, Neoconiothyrium, Neopaucispora, Pararoussoella, Paraxylaria, Marjia, Sporormurispora and Xenomassariosphaeria are introduced as new ascomycete genera. We also introduce the new species Absidia jindoensis, Alternaria doliconidium, A. hampshirensis, Angustimassarina rosarum, Astragalicola vasilyevae, Backusella locustae, Bartalinia rosicola, Bhatiellae rosae, Broomella rosae, Castanediella camelliae, Coelodictyosporium rosarum, Comoclathris rosae, C. rosarum, Comoclathris rosigena, Coniochaeta baysunika, C. rosae, Cycasicola goaensis, Dactylidina shoemakeri, Dematiopleospora donetzica, D. rosicola, D. salsolae, Diaporthe rosae, D. rosicola, Endoconidioma rosae-hissaricae, Epicoccum rosae, Hawksworthiana clematidicola, H. lonicerae, Italica achilleae, Keissleriella phragmiticola, K. rosacearum, K. rosae, K. rosarum, Lophiostoma rosae, Marjia tianschanica, M. uzbekistanica, Melanocucurbitaria uzbekistanica, Melanodiplodia tianschanica, Monoseptella rosae, Mucor fluvius, Muriformistrickeria rosae, Murilentithecium rosae, Neoascochyta rosicola, Neoconiothyrium rosae, Neopaucispora rosaecae, Neosetophoma rosarum, N. rosae, N. rosigena, Neostagonospora artemisiae, Ophiobolus artemisiicola, Paraconiothyrium rosae, Paraphaeosphaeria rosae, P. rosicola, Pararoussoella rosarum, Parathyridaria rosae, Paraxylaria rosacearum, Penicillium acidum, P. aquaticum, Phragmocamarosporium rosae, Pleospora rosae, P. rosae-caninae, Poaceicola agrostina, P. arundinicola, P. rosae, Populocrescentia ammophilae, P. rosae, Pseudocamarosporium pteleae, P. ulmi-minoris, Pseudocercospora rosae, Pseudopithomyces rosae, Pseudostrickeria rosae, Sclerostagonospora lathyri, S. rosae, S. rosicola, Seimatosporium rosigenum, S. rosicola, Seiridium rosarum, Setoseptoria arundelensis, S. englandensis, S. lulworthcovensis, Sigarispora agrostidis, S. caryophyllacearum, S. junci, S. medicaginicola, S. rosicola, S. scrophulariae, S. thymi, Sporormurispora atraphaxidis, S. pruni, Suttonomyces rosae, Umbelopsis sinsidoensis, Uzbekistanica rosae-hissaricae, U. yakutkhanika, Wojnowicia rosicola, Xenomassariosphaeria rosae. New host records are provided for Amandinea punctata, Angustimassarina quercicola, Diaporthe rhusicola, D. eres, D. foeniculina, D. rudis, Diplodia seriata, Dothiorella iberica, Lasiodiplodia theobromae, Lecidella elaeochroma, Muriformistrickeria rubi, Neofusicoccum australe, Paraphaeosphaeria michotii, Pleurophoma pleurospora, Sigarispora caulium and Teichospora rubriostiolata. The new combinations are Dactylidina dactylidis (=Allophaeosphaeria dactylidis), Embarria clematidis (=Allophaeosphaeria clematidis), Hawksworthiana alliariae (=Dematiopleospora alliariae) and Italica luzulae (=Dematiopleospora luzulae).This study also provides some insights into the diversity of fungi on Rosa species and especially those on Rosa spines that resulted in the characterisation of eight new genera, 45 new species, and nine new host records. We also collected taxa from Rosa stems and there was 31% (20/65) overlap with taxa found on stems with that on spines.Because of the limited and non-targeted sampling for comparison with collections from spines and stems of the same host and location, it is not possible to say that the fungi on spines of Rosa differ from those on stems. The study however, does illustrate how spines are interesting substrates with high fungal biodiversity. This may be because of their hard structure resulting in slow decay and hence are suitable substrates leading to fungal colonisation. All data presented herein are based on morphological examination of specimens, coupled with phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.
  •  
48.
  • 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.
  •  
49.
  • Worrillow, Lisa, et al. (author)
  • Polymorphic MLH1 and risk of cancer after methylating chemotherapy for Hodgkin lymphoma
  • 2008
  • In: Journal of Medical Genetics. - : BMJ. - 0022-2593 .- 1468-6244. ; 45:3, s. 142-146
  • Journal article (peer-reviewed)abstract
    • Background and objective: Methylating agents are effective chemotherapy agents for Hodgkin lymphoma, but are associated with the development of second primary cancers. Cytotoxicity of methylating agents is mediated primarily by the DNA mismatch repair (MMR) system. Loss of MLH1, a major component of DNA MMR, results in tolerance to the cytotoxic effects of methylating agents and persistence of mutagenised cells at high risk of malignant transformation. We hypothesised that a common substitution in the basal promoter of MLH1 (position-93, rs1800734) modifies the risk of cancer after methylating chemotherapy. Methods: 133 patients who developed cancer following chemotherapy and/or radiotherapy (n = 133), 420 patients diagnosed with de novo myeloid leukaemia, 242 patients diagnosed with primary Hodgkin lymphoma, and 1177 healthy controls were genotyped for the MLH1 -93 polymorphism by allelic discrimination polymerase chain reaction (PCR) and restriction fragment length polymorphism assay. Odds ratios and 95% confidence intervals for cancer risk by MLH1 -93 polymorphism status, and stratified by previous exposure to methylating chemotherapy, were calculated using unconditional logistic regression. Results: Carrier frequency of the MLH1 -93 variant was higher in patients who developed therapy related acute myeloid leukaemia (t-AML) (75.0%, n = 12) or breast cancer (53.3%. n = 15) after methylating chemotherapy for Hodgkin lymphoma compared to patients without previous methylating exposure (t-AML, 30.4%, n = 69; breast cancer patients, 27.2%, n = 22). The MLH1 -93 variant allele was also over-represented in t-AML cases when compared to de novo AML cases (36.9%, n = 420) and healthy controls (36.3%, n = 952), and was associated with a significantly increased risk of developing t-AML (odds ratio 5.31, 95% confidence interval 1.40 to 20.15), but only in patients previously treated with a methylating agent. Conclusions: These data support the hypothesis that the common polymorphism at position - 93 in the core promoter of MLH1 defines a risk allele for the development of cancer after methylating chemotherapy for Hodgkin lymphoma. However, replication of this finding in larger studies is suggested.
  •  
50.
  • Ørnbjerg, Lykke M., et al. (author)
  • Patient-Reported Outcomes (PROs) and PRO Remission Rates in 12,262 Biologic-Naïve Patients With Psoriatic Arthritis Treated With Tumor Necrosis Factor Inhibitors in Routine Care
  • 2024
  • In: Journal of Rheumatology. - 0315-162X. ; 51:4, s. 378-389
  • Journal article (peer-reviewed)abstract
    • Objective. To evaluate patient-reported outcomes (PROs) after initiation of tumor necrosis factor inhibitor (TNFi) treatment in European real-world patients with psoriatic arthritis (PsA). Further, to investigate PRO remission rates across treatment courses, registries, disease duration, sex, and age at disease onset. Methods. Visual analog scale or numerical rating scale scores for pain, fatigue, patient global assessment (PtGA), and the Health Assessment Questionnaire–Disability Index (HAQ-DI) from 12,262 patients with PsA initiating a TNFi in 13 registries were pooled. PRO remission rates (pain ≤ 1, fatigue ≤ 2, PtGA ≤ 2, and HAQ-DI ≤ 0.5) were calculated for patients still on the treatment. Results. For the first TNFi, median pain score was reduced by approximately 50%, from 6 to 3, 3, and 2; as were fatigue scores, from 6 to 4, 4, and 3; PtGA scores, from 6 to 3, 3, and 2; and HAQ-DI scores, from 0.9 to 0.5, 0.5, and 0.4 at baseline, 6, 12, and 24 months, respectively. Six-month Lund Efficacy Index (LUNDEX)–adjusted remission rates for pain, fatigue, PtGA, and HAQ-DI scores were 24%, 31%, 36%, and 43% (first TNFi); 14%, 19%, 23%, and 29% (second TNFi); and 9%, 14%, 17%, and 20% (third TNFi), respectively. For biologic-naïve patients with disease duration < 5 years, 6-month LUNDEX-adjusted remission rates for pain, fatigue, PtGA, and HAQ-DI scores were 22%, 28%, 33%, and 42%, respectively. Corresponding rates for patients with disease duration > 10 years were 27%, 32%, 41%, and 43%, respectively. Remission rates were 33%, 40%, 45%, and 56% for men and 17%, 23%, 24%, and 32% for women, respectively. For patients aged < 45 years at diagnosis, 6-month LUNDEX-adjusted remission rate for pain was 29% vs 18% for patients ≥ 45 years. Conclusion. In 12,262 biologic-naïve patients with PsA, 6 months of treatment with a TNFi reduced pain by approximately 50%. Marked differences in PRO remission rates across treatment courses, registries, disease duration, sex, and age at onset of disease were observed, emphasizing the potential influence of factors other than disease activity on PROs.
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