| 1. |
- Bécoulet, A., et al.
(författare)
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Science and technology research and development in support to ITER and the Broader Approach at CEA
- 2013
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 53:10
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Tidskriftsartikel (refereegranskat)abstract
- In parallel to the direct contribution to the procurement phase of ITER and Broader Approach, CEA has initiated research & development programmes, accompanied by experiments together with a significant modelling effort, aimed at ensuring robust operation, plasma performance, as well as mitigating the risks of the procurement phase. This overview reports the latest progress in both fusion science and technology including many areas, namely the mitigation of superconducting magnet quenches, disruption-generated runaway electrons, edge-localized modes (ELMs), the development of imaging surveillance, and heating and current drive systems for steady-state operation. The WEST (W Environment for Steady-state Tokamaks) project, turning Tore Supra into an actively cooled W-divertor platform open to the ITER partners and industries, is presented.
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| 2. |
- Crous, P. W., et al.
(författare)
-
Fungal Planet description sheets : 785-867
- 2018
-
Ingår i: Persoonia. - : Naturalis Biodiversity Center. - 0031-5850 .- 1878-9080. ; 41, s. 238-417
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Tidskriftsartikel (refereegranskat)abstract
- Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces angolensis on unknown host plants. Australia, Dothiora cotymbiae on Corymbia citriodora, Neoeucasphaeria eucalypti (incl. Neoeucasphaeria gen. nov.) on Eucalyptus sp., Fumagopsis stellae on Eucalyptus sp., Fusculina eucalyptorum (incl. Fusculinaceae fam. nov.) on Eucalyptus socialis, Harknessia cotymbiicola on Corymbia maculata, Neocelosporium eucalypti (incl. Neocelosporium gen. nov., Neocelosporiaceae fam. nov. and Neocelosporiales ord. nov.) on Eucalyptus cyanophylla, Neophaeomoniella corymbiae on Corymbia citriodora, Neophaeomoniefia eucalyptigena on Eucalyptus pilularis, Pseudoplagiostoma corymbiicola on Corymbia citriodora, Teratosphaeria gracilis on Eucalyptus gracilis, Zasmidium corymbiae on Corymbia citriodora. Brazil, Calonectria hemileiae on pustules of Hemileia vastatrix formed on leaves of Coffea arabica, Calvatia caatinguensis on soil, Cercospora solani-betacei on Solanum betaceum, Clathrus natalensis on soil, Diaporthe poincianellae on Poincianella pyramidalis, Geastrum piquiriunense on soil, Geosmithia carolliae on wing of Carollia perspicillata, Henningsia resupinata on wood, Penicillium guaibinense from soil, Periconia caespitosa from leaf litter, Pseudocercospora styracina on Styrax sp., Simplicillium filiforme as endophyte from Citrullus lanatus, Thozetella pindobacuensis on leaf litter, Xenosonderhenia coussapoae on Coussapoa floccosa. Canary Islands (Spain), Orbilia amarilla on Euphorbia canariensis, Cape Verde Islands, Xylodon jacobaeus on Eucalyptus camaldulensis. Chile, Colletotrichum arboricola on Fuchsia magellanica. Costa Rica, Lasiosphaeria miniovina on tree branch. Ecuador, Ganoderma chocoense on tree trunk. France, Neofitzroyomyces nerii (incl. Neofitzroyomyces gen. nov.) on Nerium oleander. Ghana, Castanediella tereticornis on Eucalyptus tereticornis, Falcocladium africanum on Eucalyptus brassiana, Rachicladosporium corymbiae on Corymbia citriodora. Hungary, Entoloma silvae-frondosae in Carpinus betulus-Pinus sylvestris mixed forest. Iran, Pseudopyricularia persiana on Cyperus sp. Italy, lnocybe roseascens on soil in mixed forest. Laos, Ophiocordyceps houaynhangensis on Coleoptera larva. Malaysia, Monilochaetes melastomae on Melastoma sp. Mexico, Absidia terrestris from soil. Netherlands, Acaulium pannemaniae, Conioscypha boutwelliae, Fusicolla septimanifiniscientiae, Gibellulopsis simonii, Lasionectria hilhorstii, Lectera nordwiniana, Leptodiscella rintelii, Parasarocladium debruynii and Sarocladium dejongiae (incl. Sarocladiaceae fam. nov.) from soil. New Zealand, Gnomoniopsis rosae on Rosa sp. and Neodevriesia metrosideri on Metrosideros sp. Puerto Rico, Neodevriesia coccolobae on Coccoloba uvifera, Neodevriesia tabebuiae and Alfaria tabebuiae on Tabebuia chrysantha. Russia, Amanita paludosa on bogged soil in mixed deciduous forest, Entoloma tiliae in forest of Tilia x europaea, Kwoniella endophytica on Pyrus communis. South Africa, Coniella diospyri on Diospyros mespiliformis, Neomelanconiella combreti (incl. Neomelanconiellaceae fam. nov. and Neomelanconiella gen. nov.) on Combretum sp., Polyphialoseptoria natalensis on unidentified plant host, Pseudorobillarda bolusanthi on Bolusanthus speciosus, Thelonectria pelargonii on Pelargonium sp. Spain, Vermiculariopsiella lauracearum and Anungitopsis lauri on Laurus novocanariensis, Geosmithia xerotolerans from a darkened wall of a house, Pseudopenidiella gallaica on leaf litter. Thailand, Corynespora thailandica on wood, Lareunionomyces loeiensis on leaf litter, Neocochlearomyces chromolaenae (incl. Neocochlearomyces gen. nov.) on Chromolaena odorata, Neomyrmecridium septatum (incl. Neomyrmecridium gen. nov.), Pararamichloridium caricicola on Carex sp., Xenodactylaria thailandica (incl. Xenodactylariaceae fam. nov. and Xenodactylaria gen. nov.), Neomyrmecridium asiaticum and Cymostachys thailandica from unidentified vine. USA, Carolinigaster bonitoi (incl. Carolinigaster gen. nov.) from soil, Penicillium fortuitum from house dust, Phaeotheca shathenatiana (incl. Phaeothecaceae fam. nov.) from twig and cone litter, Pythium wohlseniorum from stream water, Superstratomyces tardicrescens from human eye, Talaromyces iowaense from office air. Vietnam, Fistulinella olivaceoalba on soil. Morphological and culture characteristics along with DNA barcodes are provided.
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| 3. |
- Crous, P. W., et al.
(författare)
-
Fungal Planet description sheets : 951-1041
- 2019
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Ingår i: Persoonia. - : RIJKSHERBARIUM. - 0031-5850 .- 1878-9080. ; 43, s. 223-425
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Tidskriftsartikel (refereegranskat)abstract
- Novel species of fungi described in this study include those from various countries as follows: Antarctica,Apenidiella antarctica from permafrost, Cladosporium fildesense from an unidentified marine sponge. Argentina,Geastrum wrightii on humus in mixed forest. Australia, Golovinomyces glandulariae on Glandularia aristigera,Neoanungitea eucalyptorum on leaves of Eucalyptus grandis, Teratosphaeria corymbiicola on leaves of Corymbiaficifolia, Xylaria eucalypti on leaves of Eucalyptus radiata. Brazil, Bovista psammophila on soil, Fusarium awaxy onrotten stalks of Zea mays, Geastrum lanuginosum on leaf litter covered soil, Hermetothecium mikaniae-micranthae(incl. Hermetothecium gen. nov.) on Mikania micrantha, Penicillium reconvexovelosoi in soil, Stagonosporopsis vannacciifrom pod of Glycine max. British Virgin Isles, Lactifluus guanensis on soil. Canada, Sorocybe oblongisporaon resin of Picea rubens. Chile, Colletotrichum roseum on leaves of Lapageria rosea. China, Setophoma cavernafrom carbonatite in Karst cave. Colombia, Lareunionomyces eucalypticola on leaves of Eucalyptus grandis. CostaRica, Psathyrella pivae on wood. Cyprus, Clavulina iris on calcareous substrate. France, Chromosera ambiguaand Clavulina iris var. occidentalis on soil. French West Indies, Helminthosphaeria hispidissima on dead wood.Guatemala, Talaromyces guatemalensis in soil. Malaysia, Neotracylla pini (incl. Tracyllales ord. nov. and Neotracyllagen. nov.) and Vermiculariopsiella pini on needles of Pinus tecunumanii. New Zealand, Neoconiothyriumviticola on stems of Vitis vinifera, Parafenestella pittospori on Pittosporum tenuifolium, Pilidium novae-zelandiaeon Phoenix sp. Pakistan, Russula quercus-floribundae on forest floor. Portugal, Trichoderma aestuarinum fromsaline water. Russia, Pluteus liliputianus on fallen branch of deciduous tree, Pluteus spurius on decaying deciduous wood or soil. South Africa, Alloconiothyrium encephalarti, Phyllosticta encephalarticola and Neothyrostromaencephalarti (incl. Neothyrostroma gen. nov.) on leaves of Encephalartos sp., Chalara eucalypticola on leaf spots ofEucalyptus grandis x urophylla, Clypeosphaeria oleae on leaves of Olea capensis, Cylindrocladiella postalofficiumon leaf litter of Sideroxylon inerme, Cylindromonium eugeniicola (incl. Cylindromonium gen. nov.) on leaf litter ofEugenia capensis, Cyphellophora goniomatis on leaves of Gonioma kamassi, Nothodactylaria nephrolepidis (incl.Nothodactylaria gen. nov. and Nothodactylariaceae fam. nov.) on leaves of Nephrolepis exaltata, Falcocladiumeucalypti and Gyrothrix eucalypti on leaves of Eucalyptus sp., Gyrothrix oleae on leaves of Olea capensis subsp.macrocarpa, Harzia metro-sideri on leaf litter of Metrosideros sp., Hippopotamyces phragmitis (incl. Hippopotamycesgen. nov.) on leaves of Phragmites australis, Lectera philenopterae on Philenoptera violacea, Leptosilliamayteni on leaves of Maytenus heterophylla, Lithohypha aloicola and Neoplatysporoides aloes on leaves of Aloesp., Millesimomyces rhoicissi (incl. Millesimomyces gen. nov.) on leaves of Rhoicissus digitata, Neodevriesiastrelitziicola on leaf litter of Strelitzia nicolai, Neokirramyces syzygii (incl. Neokirramyces gen. nov.) on leaf spots of Syzygium sp., Nothoramichloridium perseae (incl. Nothoramichloridium gen. nov. and Anungitiomycetaceae fam.nov.) on leaves of Persea americana, Paramycosphaerella watsoniae on leaf spots of Watsonia sp., Penicilliumcuddlyae from dog food, Podocarpomyces knysnanus (incl. Podocarpomyces gen. nov.) on leaves of Podocarpusfalcatus, Pseudocercospora heteropyxidicola on leaf spots of Heteropyxis natalensis, Pseudopenidiella podocarpi,Scolecobasidium podocarpi and Ceramothyrium podocarpicola on leaves of Podocarpus latifolius, Scolecobasidiumblechni on leaves of Blechnum capense, Stomiopeltis syzygii on leaves of Syzygium chordatum, Strelitziomycesknysnanus (incl. Strelitziomyces gen. nov.) on leaves of Strelitzia alba, Talaromyces clemensii from rotting wood ingoldmine, Verrucocladosporium visseri on Carpobrotus edulis. Spain, Boletopsis mediterraneensis on soil, Calycinacortegadensisi on a living twig of Castanea sativa, Emmonsiellopsis tuberculata in fluvial sediments, Mollisia cortegadensison dead attached twig of Quercus robur, Psathyrella ovispora on soil, Pseudobeltrania lauri on leaf litterof Laurus azorica, Terfezia dunensis in soil, Tuber lucentum in soil, Venturia submersa on submerged plant debris.Thailand, Cordyceps jakajanicola on cicada nymph, Cordyceps kuiburiensis on spider, Distoseptispora caricis onleaves of Carex sp., Ophiocordyceps khonkaenensis on cicada nymph. USA, Cytosporella juncicola and Davidiellomycesjuncicola on culms of Juncus effusus, Monochaetia massachusettsianum from air sample, Neohelicomycesmelaleucae and Periconia neobrittanica on leaves of Melaleuca styphelioides x lanceolata, Pseudocamarosporiumeucalypti on leaves of Eucalyptus sp., Pseudogymnoascus lindneri from sediment in a mine, Pseudogymnoascusturneri from sediment in a railroad tunnel, Pulchroboletus sclerotiorum on soil, Zygosporium pseudomasonii onleaf of Serenoa repens. Vietnam, Boletus candidissimus and Veloporphyrellus vulpinus on soil. Morphological andculture characteristics are supported by DNA barcodes.
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| 4. |
- Crous, P. W., et al.
(författare)
-
Fungal Planet description sheets: 1182-1283
- 2021
-
Ingår i: Persoonia. - : Naturalis Biodiversity Center. - 0031-5850. ; 46, s. 313-528
-
Tidskriftsartikel (refereegranskat)abstract
- Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indooroopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor (acid) soil, Entoloma pudens on plant debris, amongst grasses. New Zealand, Amorocoelophoma neoregeliae from leaf spots of Neoregelia sp., Aquilomyces metrosideri and Septoriella callistemonis from stem discolouration and leaf spots of Metrosideros sp., Cadophora neoregeliae from leaf spots of Neoregelia sp., Flexuomyces asteliae (incl. Flexuomyces gen. nov.) and Mollisia asteliae from leaf spots of Astelia chathamica, Ophioceras freycinetiae from leaf spots of Freycinetia banksii, Phaeosphaeria caricis-sectae from leaf spots of Carex secta. Norway, Cuphophyllus flavipesoides on soil in semi-natural grassland, Entoloma coracis on soil in calcareous Pinus and Tilia forests, Entoloma cyaneolilacinum on soil semi-natural grasslands, Inocybe norvegica on gravelly soil. Pakistan, Butyriboletus parachinarensis on soil in association with Quercus baloot. Poland, Hyalodendriella bialowiezensis on debris beneath fallen bark of Norway spruce Picea abies. Russia, Bolbitius sibiricus on. moss covered rotting trunk of Populus tremula, Crepidotus wasseri on debris of Populus tremula, Entoloma isborscanum on soil on calcareous grasslands, Entoloma subcoracis on soil in subalpine grasslands, Hydropus lecythiocystis on rotted wood of Betula pendula, Meruliopsis faginea on fallen dead branches of Fagus orientalis, Metschnikowia taurica from fruits of Ziziphus jujube, Suillus praetermissus on soil, Teunia lichenophila as endophyte from Cladonia rangiferina. Slovakia, Hygrocybe fulgens on mowed grassland, Pleuroflammula pannonica from corticated branches of Quercus sp. South Africa, Acrodontium burrowsianum on leaves of unidentified Poaceae, Castanediella senegaliae on dead pods of Senegalia ataxacantha, Cladophialophora behniae on leaves of Behnia sp., Colletotrichum cliviigenum on leaves of Clivia sp., Diatrype dalbergiae on bark of Dalbergia armata, Falcocladium heteropyxidicola on leaves of Heteropyxis canescens, Lapidomyces aloidendricola as epiphyte on brown stem of Aloidendron dichotomum, Lasionectria sansevieriae and Phaeosphaeriopsis sansevieriae on leaves of Sansevieria hyacinthoides, Lylea dalbergiae on Diatrype dalbergiae on bark of Dalbergia armata, Neochaetothyrina syzygii (incl. Neochaetothyrina gen. nov.) on leaves of Syzygium chordatum, Nothophaeomoniella ekebergiae (incl. Nothophaeomoniella gen. nov.) on leaves of Ekebergia pterophylla, Paracymostachys euphorbiae (incl. Paracymostachys gen. nov.) on leaf litter of Euphorbia ingens, Paramycosphaerella pterocarpi on leaves of Pterocarpus angolensis, Paramycosphaerella syzygii on leaf litter of Syzygium chordatum, Parateichospora phoenicicola (incl. Parateichospora gen. nov.) on leaves of Phoenix reclinata, Seiridium syzygii on twigs of Syzygium chordatum, Setophoma syzygii on leaves of Syzygium sp., Starmerella xylocopis from larval feed of an Afrotropical bee Xylocopa caffra, Teratosphaeria combreti on leaf litter of Combretum kraussii, Teratosphaericola leucadendri on leaves of Leucadendron sp., Toxicocladosporium pterocarpi on pods of Pterocarpus angolensis. Spain, Cortinarius bonachei with Quercus ilex in calcareus soils, Cortinarius brunneovolvatus under Quercus ilex subsp. ballota in calcareous soil, Extremopsis radicicola (incl. Extremopsis gen. nov.) from root-associated soil in a wet heathland, Russula quintanensis on acidic soils, Tubaria vulcanica on volcanic lapilii material, Tuber zambonelliae in calcareus soil. Sweden, Elaphomyces borealis on soil under Pinus sylvestris and Betula pubescens. Tanzania, Curvularia tanzanica on inflorescence of Cyperus aromaticus. Thailand, Simplicillium niveum on Ophiocordyceps camponoti-leonardi on underside of unidentified dicotyledonous leaf. USA, Calonectria californiensis on leaves of Umbellularia californica, Exophiala spartinae from surface sterilised roots of Spartina alterniflora, Neophaeococcomyces oklahomaensis from outside wall of alcohol distillery. Vietnam, Fistulinella aurantioflava on soil. Morphological and culture characteristics are supported by DNA barcodes.
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| 5. |
- Crous, P. W., et al.
(författare)
-
Fusarium : more than a node or a foot-shaped basal cell
- 2021
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Ingår i: Studies in mycology. - : CENTRAALBUREAU SCHIMMELCULTURE. - 0166-0616 .- 1872-9797. ; :98
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Tidskriftsartikel (refereegranskat)abstract
- Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
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| 6. |
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| 7. |
- Schoch, CL, et al.
(författare)
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
- 2012
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490. ; 109:16, s. 6241-6246
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Tidskriftsartikel (refereegranskat)abstract
- Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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| 8. |
- Sumaila, U. Rashid, et al.
(författare)
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WTO must ban harmful fisheries subsidies
- 2021
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 374:6567, s. 544-544
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 9. |
- Waszak, S. M., et al.
(författare)
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Germline Elongator mutations in Sonic Hedgehog medulloblastoma
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 580:7803
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Tidskriftsartikel (refereegranskat)abstract
- Cancer genomics has revealed many genes and core molecular processes that contribute to human malignancies, but the genetic and molecular bases of many rare cancers remains unclear. Genetic predisposition accounts for 5 to 10% of cancer diagnoses in children(1,2), and genetic events that cooperate with known somatic driver events are poorly understood. Pathogenic germline variants in established cancer predisposition genes have been recently identified in 5% of patients with the malignant brain tumour medulloblastoma(3). Here, by analysing all protein-coding genes, we identify and replicate rare germline loss-of-function variants across ELP1 in 14% of paediatric patients with the medulloblastoma subgroup Sonic Hedgehog (MBSHH). ELP1 was the most common medulloblastoma predisposition gene and increased the prevalence of genetic predisposition to 40% among paediatric patients with MBSHH. Parent-offspring and pedigree analyses identified two families with a history of paediatric medulloblastoma. ELP1-associated medulloblastomas were restricted to the molecular SHH alpha subtype(4) and characterized by universal biallelic inactivation of ELP1 owing to somatic loss of chromosome arm 9q. Most ELP1-associated medulloblastomas also exhibited somatic alterations in PTCH1, which suggests that germline ELP1 loss-of-function variants predispose individuals to tumour development in combination with constitutive activation of SHH signalling. ELP1 is the largest subunit of the evolutionarily conserved Elongator complex, which catalyses translational elongation through tRNA modifications at the wobble (U-34) position(5,6). Tumours from patients with ELP1-associated MBSHH were characterized by a destabilized Elongator complex, loss of Elongator-dependent tRNA modifications, codon-dependent translational reprogramming, and induction of the unfolded protein response, consistent with loss of protein homeostasis due to Elongator deficiency in model systems(7-9). Thus, genetic predisposition to proteome instability may be a determinant in the pathogenesis of paediatric brain cancers. These results support investigation of the role of protein homeostasis in other cancer types and potential for therapeutic interference.
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| 10. |
- Anney, Richard, et al.
(författare)
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Individual common variants exert weak effects on the risk for autism spectrum disorders.
- 2012
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 21:21, s. 4781-92
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Tidskriftsartikel (refereegranskat)abstract
- While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASD), the contribution of common variation to ASD risk is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating association of individual SNPs, we also sought evidence that common variants, en masse, might affect risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest p-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. By contrast, allele-scores derived from the transmission of common alleles to Stage 1 cases significantly predict case-status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele-score results, it is reasonable to conclude that common variants affect ASD risk but their individual effects are modest.
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| 11. |
- Liebenberg, L., et al.
(författare)
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Tracking science : An alternative for those excluded by citizen science
- 2021
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Ingår i: Citizen Science: Theory and Practice. - : Ubiquity Press. - 2057-4991. ; 6:1, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- In response to recent discussion about terminology, we propose "tracking science" as a term that is more inclusive than citizen science. Our suggestion is set against a post-colonial political background and large-scale migrations, in which "citizen" is becoming an increasingly contentious term. As a diverse group of authors from several continents, our priority is to deliberate a term that is all-inclusive, so that it could be adopted by everyone who participates in science or contributes to scientific knowledge, regardless of socio-cultural background. For example, current citizen science terms used for Indigenous knowledge imply that such practitioners belong to a sub-group that is other, and therefore marginalized. Our definition for "tracking science" does not exclude Indigenous peoples and their knowledge contributions and may provide a space for those who currently participate in citizen science, but want to contribute, explore, and/or operate beyond its confinements. Our suggestion is not that of an immediate or complete replacement of terminology, but that the notion of tracking science can be used to complement the practice and discussion of citizen science where it is contextually appropriate or needed. This may provide a breathing space, not only to explore alternative terms, but also to engage in robust, inclusive discussion on what it means to do science or create scientific knowledge. In our view, tracking science serves as a metaphor that applies broadly to the scientific community-from modern theoretical physics to ancient Indigenous knowledge.
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| 12. |
- Abreu, A., et al.
(författare)
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Priorities for ocean microbiome research
- 2022
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Ingår i: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 7:7, s. 937-947
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Tidskriftsartikel (refereegranskat)abstract
- Studying the ocean microbiome can inform international policies related to ocean governance, tackling climate change, ocean acidification and pollution, and can help promote achievement of multiple Sustainable Development Goals. Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 'life below water'. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals.
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| 13. |
- Eneman, K., et al.
(författare)
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Evaluation of signal enhancement algorithms for hearing instruments
- 2008
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Konferensbidrag (refereegranskat)abstract
- In the frame of the HearCom1 project five promising signal enhancement algorithms are validated for future use in hearing instrument devices. To assess the algorithm performance solely based on simulation experiments, a number of physical evaluation measures have been proposed that incorporate basic aspects of normal and impaired human hearing. Additionally, each of the algorithms has been implemented on a common real-time hardware/software platform, which facilitates a profound subjective validation of the algorithm performance. Recently, a multicenter study has been set up across five different test centers in Belgium, the Netherlands, Germany and Switzerland to perceptually evaluate the selected signal enhancement approaches with normally hearing and hearing impaired listeners.
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| 14. |
- Schoville, Sean D., et al.
(författare)
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A model species for agricultural pest genomics : The genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)
- 2018
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.
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| 15. |
- Manzano-Nunez, Ramiro, et al.
(författare)
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Outcomes and management approaches of resuscitative endovascular balloon occlusion of the aorta based on the income of countries
- 2020
-
Ingår i: World Journal of Emergency Surgery. - : Springer Science and Business Media LLC. - 1749-7922. ; 15:57
-
Tidskriftsartikel (refereegranskat)abstract
- © 2020 The Author(s). Background: Resuscitative endovascular balloon occlusion of the aorta (REBOA) could provide a survival benefit to severely injured patients as it may improve their initial ability to survive the hemorrhagic shock. Although the evidence supporting the use of REBOA is not conclusive, its use has expanded worldwide. We aim to compare the management approaches and clinical outcomes of trauma patients treated with REBOA according to the countries' income based on the World Bank Country and Lending Groups. Methods: We used data from the AORTA (USA) and the ABOTrauma (multinational) registries. Patients were stratified into two groups: (1) high-income countries (HICs) and (2) low-to-middle income countries (LMICs). Propensity score matching extracted 1:1 matched pairs of subjects who were from an LMIC or a HIC based on age, gender, the presence of pupillary response on admission, impeding hypotension (SBP ≤ 80), trauma mechanism, ISS, the necessity of CPR on arrival, the location of REBOA insertion (emergency room or operating room) and the amount of PRBCs transfused in the first 24 h. Logistic regression (LR) was used to examine the association of LMICs and mortality. Results: A total of 817 trauma patients from 14 countries were included. Blind percutaneous approach and surgical cutdown were the preferred means of femoral cannulation in HICs and LIMCs, respectively. Patients from LMICs had a significantly higher occurrence of MODS and respiratory failure. LR showed no differences in mortality for LMICs when compared to HICs; neither in the non-matched cohort (OR = 0.63; 95% CI: 0.36-1.09; p = 0.1) nor in the matched cohort (OR = 1.45; 95% CI: 0.63-3,33; p = 0.3). Conclusion: There is considerable variation in the management practices of REBOA and the outcomes associated with this intervention between HICs and LMICs. Although we found significant differences in multiorgan and respiratory failure rates, there were no differences in the risk-adjusted odds of mortality between the groups analyzed. Trauma surgeons practicing REBOA around the world should joint efforts to standardize the practice of this endovascular technology worldwide.
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| 16. |
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| 17. |
- Berg, Frenk van den, et al.
(författare)
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Results of the European collaborative project "Product Uniformity Control" to improve the inline sensing of mechanical properties and microstructure of automotive steels
- 2018
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Ingår i: e-Journal of Nondestructive Testing (eJNDT). - 1435-4934. ; 23:8
-
Tidskriftsartikel (refereegranskat)abstract
- A European consortium consisting of four major steel manufacturers and ten academic technology institutes has conducted a research and development project, called “Product Uniformity Control“ (PUC) in the period 2013 to 2017. This project aimed to develop and improve non-destructive (inline) measurement techniques to characterise the (uniformity of the) microstructure of steel strip products. In this project, a multitude of strip steel samples from various stages of production have been collected from the four participating steel manufacturers. The samples have been characterised in various ways, namely on their (1) non-destructive measurement parameters using different techniques suited for inline evaluation, (2) fundamental ultrasonic and electromagnetic properties (wave speed, ultrasonic attenuation, magnetisation loops, coercive field), (3) tensile properties (stress-strain curves) and (4) microstructure (by optical micrographs and EBSD images). The correlations between these different characterisations will be addressed. Besides the experimental characterisation, a strong accent has been on modelling activities: during the project, fundamental models have been developed to describe, starting from 2D and 3D microstructures, the ultrasonic and magnetic properties, which are next used as input to sensor models that predict the output of the inline measurement systems. This contribution presents the recent results of experimental work, which underlines the importance of associated modelling studies for the interpretation of the measurement data for the benefit of inline characterisation of the mechanical properties complementary to traditional destructive tensile testing.
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| 18. |
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| 19. |
- Huttner, A., et al.
(författare)
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A dose-dependent plasma signature of the safety and immunogenicity of the rVSV-Ebola vaccine in Europe and Africa
- 2017
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Ingår i: Science Translational Medicine. - : American Association for the Advancement of Science (AAAS). - 1946-6234 .- 1946-6242. ; 9:385
-
Tidskriftsartikel (refereegranskat)abstract
- The 2014-2015 Ebola epidemic affected several African countries, claiming more than 11,000 lives and leaving thousands with ongoing sequelae. Safe and effective vaccines could prevent or limit future outbreaks. The recombinant vesicular stomatitis virus-vectored Zaire Ebola (rVSV-ZEBOV) vaccine has shown marked immunogenicity and efficacy in humans but is reactogenic at higher doses. To understand its effects, we examined plasma samples from 115 healthy volunteers from Geneva who received low-dose (LD) or high-dose (HD) vaccine or placebo. Fifteen plasma chemokines/cytokines were assessed at baseline and on days 1, 2 to 3, and 7 after injection. Significant increases in monocyte-mediated MCP-1/CCL2, MIP-1 beta/CCL4, IL-6, TNF-alpha, IL-1Ra, and IL-10 occurred on day 1. A signature explaining 68% of cytokine/chemokine vaccine-response variabilitywas identified. Its score was higher in HD versus LD vaccinees and was associated positively with vaccine viremia and negatively with cytopenia. It was higher in vaccinees with injection-site pain, fever, myalgia, chills, and headache; higher scores reflected increasing severity. In contrast, HD vaccinees who subsequently developed arthritis had lower day 1 scores than other HD vaccinees. Vaccine dose did not influence the signature despite its influence on specific outcomes. The Geneva-derived signature associated strongly (rho = 0.97) with that of a cohort of 75 vaccinees from a parallel trial in Lambarene, Gabon. Its score in Geneva HD vaccinees with subsequent arthritis was significantly lower than that in Lambarene HD vaccinees, none of whom experienced arthritis. This signature, which reveals monocytes' critical role in rVSV-ZEBOV immunogenicity and safety across doses and continents, should prove useful in assessments of other vaccines.
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| 20. |
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| 21. |
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| 22. |
- Van Den Berg, F. D., et al.
(författare)
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Product uniformity control - A research collaboration of european steel industries to non-destructive evaluation of microstructure and mechanical properties
- 2018
-
Ingår i: Stud. Appl. Electromagn. Mech.. - : IOS Press. - 9781614998358 ; 43, s. 120-129
-
Konferensbidrag (refereegranskat)abstract
- In steel manufacturing, the conventional method to determine the mechanical properties and microstructure is by offline, destructive (lab-)characterisation of sample material that is typically taken from the head or the tail of the coil. Since coils can be up to 7 km long, the samples are not always representative for the main coil body. Also, the time delay (typically a few days) between the actual production and the availability of the characterisation results implies that these results cannot be exploited for real-time adaptation of the process settings. Information about the microstructure and material properties can also be obtained from electromagnetic (EM) and ultrasonic (US) parameters, which can be measured in real-time, non-destructively, and over the full length of the steel strip product. With the aim to improve the consistency in product quality by use of inline EM and US measurements, a European project called "Product Uniformity Control" (PUC) has been set up as a broad collaboration between 4 major European Steel Manufacturers and 10 Universities / Research institutes. Using both numerical simulations and experimental characterisations, we study the inline measured EM and US parameters in regard of the microstructural and mechanical properties. In this way, we aim to establish an improved understanding of their mutual relationships, and to apply this knowledge in existing and new nondestructive evaluation techniques. In this paper, the concerted approach of modelling and experimental validation will be addressed, and results of this work will be shown in combination with inline measured data.
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| 23. |
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| 24. |
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| 25. |
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| 26. |
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| 27. |
- Berg, Frenk van den, et al.
(författare)
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How the EU project “Online Microstructure Analytics” advances inline sensing of microstructure during steel manufacturing
- 2023
-
Ingår i: Research and Review Journal of Nondestructive Testing (ReJNDT). - Lisabon : NDT.net GmbH & Co. KG. - 2941-4989. ; 1:1
-
Tidskriftsartikel (refereegranskat)abstract
- Weight savings in mobility and transport are mandatory in order to reduce CO2 emissions and energy consumption. The steel industry offers weight saving solutions by a growing portfolio of Advanced High Strength Steel (AHSS) products. AHSS owe their strength to their largely refined and complex microstructures, containing multiple metallurgical phases. Optimal control of the thermo-mechanical processing of AHSS requires inline sensors for real-time monitoring of evolution and consistency of microstructure and material properties.
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| 28. |
- Bernabé, S., et al.
(författare)
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Highly integrated VCSEL-based 10Gb/s miniature optical sub-assembly
- 2005
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Ingår i: Proceedings - Electronic Components and Technology Conference. - Lake Buena Vista, FL : IEEE. ; , s. 1333-1338
-
Konferensbidrag (refereegranskat)abstract
- In order to fit with the present and future needs of the Datacom transceiver market, newly designed high rate transmitter optical subassemblies (TOSAs) have to be compact, low cost and compatible with mass production. We propose here an innovative design strategy that reaches all these targets by integrating a 10Gbps 850nmVCSEL laser diode and its laser driver with other functionalities (e.g. power monitoring and thermal monitoring) in a small form factor package. Taking advantages of the optical properties of the VCSEL and using flip-chip techniques, the transmitter exhibits excellent hyperfrequency performances and compatibility with mass production due to the use of collective manufacturing technologies and passive optical alignment. This versatile approach is also applicable to high rate receivers, parallel optics emitters, and singlemode low cost transmitter integrating long wavelength VCSELs.
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| 29. |
- Breton, Gwenna, et al.
(författare)
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Lactase Persistence Alleles Reveal Partial East African Ancestry of Southern African Khoe Pastoralists
- 2014
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 24:8, s. 852-858
-
Tidskriftsartikel (refereegranskat)abstract
- The ability to digest milk into adulthood, lactase persistence (LP), as well as specific genetic variants associated with LP, is heterogeneously distributed in global populations [1-4]. These variants were most likely targets of selection when some populations converted from hunter-gatherer to pastoralist or farming lifestyles [5-7]. Specific LP polymorphisms are associated with particular geographic regions and populations [1-4, 8-10]; however, they have not been extensively studied in southern Africa. We investigate the LP-regulatory region in 267 individuals from 13 southern African populations (including descendants of hunter-gatherers, pastoralists, and agropastoralists), providing the first comprehensive study of the LP-regulatory region in a large group of southern Africans. The "East African" LP single-nucleotide polymorphism (SNP) (14010G>C) was found at high frequency (>20%) in a strict pastoralist Khoe population, the Nama of Namibia, suggesting a connection to East Africa, whereas the "European" LP SNP (13910C>T) was found in populations of mixed ancestry. Using genome-wide data from various African populations, we identify admixture (13%) in the Nama, from an Afro-Asiatic group dating to >1,300 years ago, with the remaining fraction of their genomes being from San hunter-gatherers. We also find evidence of selection around the LCT gene among Khoe-speaking groups, and the substantial frequency of the 14010C variant among the Nama is best explained by adaptation to digesting milk. These genome-local and genome-wide results support a model in which an East African group brought pastoralist practices to southern Africa and admixed with local hunter-gatherers to form the ancestors of Khoe people.
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| 30. |
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| 31. |
- Cantwell, C. D., et al.
(författare)
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Nektar plus plus : An open-source spectral/hp element framework
- 2015
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Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655. ; 192, s. 205-219
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Tidskriftsartikel (refereegranskat)abstract
- Nektar++ is an open-source software framework designed to support the development of high-performance scalable solvers for partial differential equations using the spectral/hp element method. High-order methods are gaining prominence in several engineering and biomedical applications due to their improved accuracy over low-order techniques at reduced computational cost for a given number of degrees of freedom. However, their proliferation is often limited by their complexity, which makes these methods challenging to implement and use. Nektar++ is an initiative to overcome this limitation by encapsulating the mathematical complexities of the underlying method within an efficient C++ framework, making the techniques more accessible to the broader scientific and industrial communities. The software supports a variety of discretisation techniques and implementation strategies, supporting methods research as well as application-focused computation, and the multi-layered structure of the framework allows the user to embrace as much or as little of the complexity as they need. The libraries capture the mathematical constructs of spectral/hp element methods, while the associated collection of pre-written PDE solvers provides out-of-the-box application-level functionality and a template for users who wish to develop solutions for addressing questions in their own scientific domains. Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland No. of lines in distributed program, including test data, etc.: 1052456 No. of bytes in distributed program, including test data, etc.: 42851367 External routines: Boost, PFTW, MPI, BLAS, LAPACK and METIS (www.cs.umn.edu) Nature of problem: The Nektar++ framework is designed to enable the discretisation and solution of time-independent or time-dependent partial differential equations. Running time: The tests provided take a few minutes to run. Runtime in general depends on mesh size and total integration time.
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| 32. |
- Doherty, Tanya, et al.
(författare)
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Early cessation of breastfeeding amongst women in South Africa : an area needing urgent attention to improve child health
- 2012
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Ingår i: BMC Pediatrics. - : Springer Science and Business Media LLC. - 1471-2431. ; 12, s. 105-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Breastfeeding is a critical component of interventions to reduce child mortality. Exclusive breastfeeding practice is extremely low in South Africa and there has been no improvement in this over the past ten years largely due to fears of HIV transmission. Early cessation of breastfeeding has been found to have negative effects on child morbidity and survival in several studies in Africa. This paper reports on determinants of early breastfeeding cessation among women in South Africa.Methods: This is a sub group analysis of a community-based cluster-randomized trial (PROMISE EBF) promoting exclusive breastfeeding in three South African sites (Paarl in the Western Cape Province, and Umlazi and Rietvlei in KwaZulu-Natal) between 2006 and 2008 (ClinicalTrials.gov no: NCT00397150). Infant feeding recall of 22 food and fluid items was collected at 3, 6, 12 and 24 weeks postpartum. Women's experiences of breast health problems were also collected at the same time points. 999 women who ever breastfed were included in the analysis. Univariable and multivariable logistic regression analysis adjusting for site, arm and cluster, was performed to determine predictors of stopping breastfeeding by 12 weeks postpartum.Results: By 12 weeks postpartum, 20% of HIV-negative women and 40% of HIV-positive women had stopped all breastfeeding. About a third of women introduced other fluids, most commonly formula milk, within the first 3 days after birth. Antenatal intention not to breastfeed and being undecided about how to feed were most strongly associated with stopping breastfeeding by 12 weeks (Adjusted odds ratio, AOR 5.6, 95% CI 3.4 - 9.5 and AOR 4.1, 95% CI 1.6 - 10.8, respectively). Also important was self-reported breast health problems associated with a 3-fold risk of stopping breastfeeding (AOR 3.1, 95% CI 1.7 - 5.7) and the mother having her own income doubled the risk of stopping breastfeeding (AOR 1.9, 95% CI 1.3 - 2.8).Conclusion: Early cessation of breastfeeding is common amongst both HIV-negative and positive women in South Africa. There is an urgent need to improve antenatal breastfeeding counselling taking into account the challenges faced by working women as well as early postnatal lactation support to prevent breast health problems.
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| 33. |
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| 34. |
- Doherty, Tanya, et al.
(författare)
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Severe events in the first 6 months of life in a cohort of HIV-unexposed infants from South Africa : effects of low birthweight and breastfeeding status
- 2014
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Ingår i: Tropical medicine & international health. - : Wiley. - 1360-2276 .- 1365-3156. ; 19:10, s. 1162-1169
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE:To report on risk factors for severe events (hospitalisation or infant death) within the first half of infancy amongst HIV-unexposed infants in South Africa.METHODS:South African data from the multisite community-based cluster-randomised trial PROMISE EBF promoting exclusive breastfeeding in three sub-Saharan countries from 2006 to 2008 were used. The South African sites were Paarl in the Western Cape Province, and Umlazi and Rietvlei in KwaZulu-Natal. This analysis included 964 HIV-negative mother-infant pairs. Data on severe events and infant feeding practices were collected at 3, 6, 12 and 24 weeks post-partum. We used a stratified extended Cox model to examine the association between the time to the severe event and covariates including birthweight, with breastfeeding status as a time-dependent covariate.RESULTS:Seventy infants (7%) experienced a severe event. The median age at first hospitalisation was 8 weeks, and the two main reasons for hospitalisation were cough and difficult breathing followed by diarrhoea. Stopping breastfeeding before 6 months (HR 2.4; 95% CI 1.2-5.1) and low birthweight (HR 2.4; 95% CI 1.3-4.3) were found to increase the risk of a severe event, whilst maternal completion of high school education was protective (HR 0.3; 95% CI 0.1-0.7).CONCLUSIONS:A strengthened primary healthcare system incorporating promotion of breastfeeding and appropriate caring practices for low birthweight infants (such as kangaroo mother care) are critical. Given the leading reasons for hospitalisation, early administration of oral rehydration therapy and treatment of suspected pneumonia are key interventions needed to prevent hospitalisation in young infants.
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| 35. |
- Lombard, Vincent, et al.
(författare)
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A hierarchical classification of polysaccharide lyases for glycogenomics
- 2010
-
Ingår i: Biochemical Journal. - 0264-6021 .- 1470-8728. ; 432, s. 437-444
-
Tidskriftsartikel (refereegranskat)abstract
- Carbohydrate-active enzymes face huge substrate diversity in a highly selective manner using only a limited number of available folds. They are therefore subjected to multiple divergent and convergent evolutionary events. This and their frequent modularity render their functional annotation in genomes difficult in a number of cases. In the present paper, a classification of polysaccharide lyases (the enzymes that cleave polysaccharides using an elimination instead of a hydrolytic mechanism) is shown thoroughly for the first time. Based on the analysis of a large panel of experimentally characterized polysaccharide lyases, we examined the correlation of various enzyme properties with the three levels of the classification: fold, family and subfamily. The resulting hierarchical classification, which should help annotate relevant genes in genomic efforts, is available and constantly updated at the Carbohydrate-Active Enzymes Database (http://www.cazy.org).
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| 36. |
- Pierella Karlusich, Juan José, et al.
(författare)
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Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods
- 2021
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
-
Tidskriftsartikel (refereegranskat)abstract
- Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2-2000m). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2m) to mesoplankton (180-2000 mu m) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 mu m). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 mu m) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow. Nitrogen fixation by diazotrophs is critical for marine primary production. Using Tara Oceans datasets, this study combines a quantitative image analysis pipeline with metagenomic mining to provide an improved global overview of diazotroph abundance, diversity and distribution.
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| 37. |
- Schlebusch, Carina, 1977-, et al.
(författare)
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Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens
- 2020
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 37:10, s. 2944-2954
-
Tidskriftsartikel (refereegranskat)abstract
- The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.
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| 38. |
- Schlebusch, Carina M., et al.
(författare)
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MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa
- 2013
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 13, s. 56-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The current San and Khoe populations are remnant groups of a much larger and widely dispersed population of hunter-gatherers and pastoralists, who had exclusive occupation of southern Africa before the influx of Bantu-speakers from 2 ka (ka = kilo annum [thousand years] old/ago) and sea-borne immigrants within the last 350 years. Here we use mitochondrial DNA (mtDNA) to examine the population structure of various San and Khoe groups, including seven different Khoe-San groups (Ju/'hoansi, !Xun, /Gui+//Gana, Khwe, not equal Khomani, Nama and Karretjie People), three different Coloured groups and seven other comparative groups. MtDNA hyper variable segments I and II (HVS I and HVS II) together with selected mtDNA coding region SNPs were used to assign 538 individuals to 18 haplogroups encompassing 245 unique haplotypes. Data were further analyzed to assess haplogroup histories and the genetic affinities of the various San, Khoe and Coloured populations. Where possible, we tentatively contextualize the genetic trends through time against key trends known from the archaeological record. Results: The most striking observation from this study was the high frequencies of the oldest mtDNA haplogroups (L0d and L0k) that can be traced back in time to similar to 100 ka, found at high frequencies in Khoe-San and sampled Coloured groups. Furthermore, the L0d/k sub-haplogroups were differentially distributed in the different Khoe-San and Coloured groups and had different signals of expansion, which suggested different associated demographic histories. When populations were compared to each other, San groups from the northern parts of southern Africa (Ju speaking: !Xun, Ju/'hoansi and Khoe-speaking: /Gui+//Gana) grouped together and southern groups (historically Tuu speaking: not equal Khomani and Karretjie People and some Coloured groups) grouped together. The Khoe group (Nama) clustered with the southern Khoe-San and Coloured groups. The Khwe mtDNA profile was very different from other Khoe-San groups with high proportions of Bantu-speaking admixture but also unique distributions of other mtDNA lineages. Conclusions: On the whole, the research reported here presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the Khoe-San and Coloured populations of southern Africa.
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| 39. |
- Schlebusch, Carina M., et al.
(författare)
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The disappearing San of southeastern Africa and their genetic affinities
- 2016
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Ingår i: Human Genetics. - : Springer Science and Business Media LLC. - 0340-6717 .- 1432-1203. ; 135:12, s. 1365-1373
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Tidskriftsartikel (refereegranskat)abstract
- Southern Africa was likely exclusively inhabited by San hunter-gatherers before similar to 2000 years ago. Around that time, East African groups assimilated with local San groups and gave rise to the Khoekhoe herders. Subsequently, Bantu-speaking farmers, arriving from the north (similar to 1800 years ago), assimilated and displaced San and Khoekhoe groups, a process that intensified with the arrival of European colonists similar to 350 years ago. In contrast to the western parts of southern Africa, where several Khoe-San groups still live today, the eastern parts are largely populated by Bantu speakers and individuals of non-African descent. Only a few scattered groups with oral traditions of Khoe-San ancestry remain. Advances in genetic research open up new ways to understand the population history of southeastern Africa. We investigate the genomic variation of the remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using similar to 2.2 million genetic markers, combined with comparative published data sets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the parallel to Xegwi San) and Bantu speakers. Specifically, we found that the Lake Chrissie San are closely related to the current southern San groups (i.e., the Karretjie people). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. This study illustrates how genetic tools can be used to assess hypotheses about the ancestry of people who seemingly lost their historic roots, only recalling a vague oral tradition of their origin.
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| 40. |
- Sundin, Anders, 1954-, et al.
(författare)
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ENETS Consensus Guidelines for the Standards of Care in Neuroendocrine Tumors : Radiological, Nuclear Medicine & Hybrid Imaging.
- 2017
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Ingår i: Neuroendocrinology. - : S. Karger AG. - 0028-3835 .- 1423-0194. ; 105:3, s. 212-244
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Tidskriftsartikel (refereegranskat)abstract
- Contrast-enhanced computed tomography (CT) of the neckthorax-abdomen and pelvis, including 3-phase examination of the liver, constitutes the basic imaging for primary neuroendocrine tumor (NET) diagnosis, staging, surveillance, and therapy monitoring. CT characterization of lymph nodes is difficult because of inadequate size criteria (short axis diameter), and bone metastases are often missed. Contrast-enhanced magnetic resonance imaging (MRI) including diffusion-weighted imaging is preferred for the examination of the liver, pancreas, brain and bone. MRI may miss small lung metastases. MRI is less well suited than CT for the examination of extended body areas because of the longer examination procedure. Ultrasonography (US) frequently provides the initial diagnosis of liver metastases and contrast-enhanced US is excellent to characterize liver lesions that remain equivocal on CT/MRI. US is the method of choice to guide the biopsy needle for the histopathological NET diagnosis. US cannot visualize thoracic NET lesions for which CTguided biopsy therefore is used. Endocopic US is the most sensitive method to diagnose pancreatic NETs, and additionally allows for biopsy. Intraoperative US facilitates lesion detection in the pancreas and liver. Somatostatin receptor imaging should be a part of the tumor staging, preoperative imaging and restaging, for which 68 Ga-DOTA-somatostatin analog PET/CT is recommended, which is vastly superior to somatostatin receptor scintigraphy, and facilitates the diagnosis of most types of NET lesions, for example lymph node metastases, bone metastases, liver metastases, peritoneal lesions, and primary small intestinal NETs. (18)FDG-PET/CT is better suited for G3 and high G2 NETs, which generally have higher glucose metabolism and less somatostatin receptor expression than low-grade NETs, and additionally provides prognostic information.
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| 41. |
- Weickert, Martin O., et al.
(författare)
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Changes in Weight Associated With Telotristat Ethyl in the Treatment of Carcinoid Syndrome
- 2018
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Ingår i: Clinical Therapeutics. - : ELSEVIER. - 0149-2918 .- 1879-114X. ; 40:6, s. 952-962
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: In the placebo-controlled Phase III TELE-STAR (Telotristat Etiprate for Somatostatin Analogue Not Adequately Controlled Carcinoid Syndrome) trial, the oral tryptophan hydroxylase inhibitor telotristat ethyl significantly reduced bowel movement (BM) frequency during a 12-week, double-blind treatment period in 135 patients with metastatic neuroendocrine tumors with carcinoid syndrome and >= 4 BMs per day. Patients (mean [SD] age, 63.5 [8.9] years; mean [SD] body mass index, 24.9 [4.9] kg/m(2)) received placebo, telotristat ethyl 250 mg, or telotristat ethyl 500 mg 3 times per day (TID) in addition to somatostatin analogue therapy. Weight loss is associated with uncontrolled carcinoid syndrome and may be associated with reduced survival.Methods: Assessment of the occurrence of weight change >= 3% at week 12 was prespecified in the statistical analysis plan.Findings: In 120 patients with weight data available, weight gain >= 3% was observed in 2 of 39 patients (5.1%) taking placebo [1.1), 7 of 41 (17.1%) taking telotristat ethyl 250 mg TID, and 13 of 40 (32.5%) taking telotristat ethyl 500 mg TID (P = 0.0017) at week 12. Weight loss >= 3% was observed in 5 of 39 patients (12.8%) taking placebo TID, 4 of 41 (9.8%) taking telotristat ethyl 250 mg TID, and 6 of 40 (15.0%) taking telotristat ethyl 500 mg TID (P = 0.77). Biochemical and metabolic parameters of serum albumin and cholesterol significantly increased (P = 0.02 and P = 0.001, respectively) in patients gaining weight and decreased in patients who lost weight, suggesting an improvement in overall nutritional status.
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| 42. |
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| 43. |
- Yao, James C., et al.
(författare)
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Everolimus for advanced pancreatic neuroendocrine tumors
- 2011
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Ingår i: New England Journal of Medicine. - 0028-4793 .- 1533-4406. ; 364:6, s. 514-523
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Everolimus, an oral inhibitor of mammalian target of rapamycin (mTOR), has shown antitumor activity in patients with advanced pancreatic neuroendocrine tumors, in two phase 2 studies. We evaluated the agent in a prospective, randomized, phase 3 study. METHODS: We randomly assigned 410 patients who had advanced, low-grade or intermediate-grade pancreatic neuroendocrine tumors with radiologic progression within the previous 12 months to receive everolimus, at a dose of 10 mg once daily (207 patients), or placebo (203 patients), both in conjunction with best supportive care. The primary end point was progression-free survival in an intention-to-treat analysis. In the case of patients in whom radiologic progression occurred during the study, the treatment assignments could be revealed, and patients who had been randomly assigned to placebo were offered open-label everolimus. RESULTS: The median progression-free survival was 11.0 months with everolimus as compared with 4.6 months with placebo (hazard ratio for disease progression or death from any cause with everolimus, 0.35; 95% confidence interval [CI], 0.27 to 0.45; P<0.001), representing a 65% reduction in the estimated risk of progression or death. Estimates of the proportion of patients who were alive and progression-free at 18 months were 34% (95% CI, 26 to 43) with everolimus as compared with 9% (95% CI, 4 to 16) with placebo. Drug-related adverse events were mostly grade 1 or 2 and included stomatitis (in 64% of patients in the everolimus group vs. 17% in the placebo group), rash (49% vs. 10%), diarrhea (34% vs. 10%), fatigue (31% vs. 14%), and infections (23% vs. 6%), which were primarily upper respiratory. Grade 3 or 4 events that were more frequent with everolimus than with placebo included anemia (6% vs. 0%) and hyperglycemia (5% vs. 2%). The median exposure to everolimus was longer than exposure to placebo by a factor of 2.3 (38 weeks vs. 16 weeks). CONCLUSIONS: Everolimus, as compared with placebo, significantly prolonged progression-free survival among patients with progressive advanced pancreatic neuroendocrine tumors and was associated with a low rate of severe adverse events. (Funded by Novartis Oncology; RADIANT-3 ClinicalTrials.gov number, NCT00510068.).
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