| 1. |
- Zamora, Juan Carlos, et al.
(author)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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In: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Journal article (peer-reviewed)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
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| 3. |
- Hurtado, Pilar, et al.
(author)
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Contrasting Environmental Drivers Determine Biodiversity Patterns in Epiphytic Lichen Communities along a European Gradient
- 2020
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In: Microorganisms. - : MDPI. - 2076-2607. ; 8:12
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Journal article (peer-reviewed)abstract
- Assessing the ecological impacts of environmental change on biological communities requires knowledge of the factors driving the spatial patterns of the three diversity facets along extensive environmental gradients. We quantified the taxonomic (TD), functional (FD), and phylogenetic diversity (PD) of lichen epiphytic communities in 23 beech forests along Europe to examine their response to environmental variation (climate, habitat quality, spatial predictors) at a continental geographic scale. We selected six traits related to the climatic conditions in forest ecosystems, the water-use strategy and the nutrient uptake, and we built a phylogenetic tree based on four molecular markers. FD and climate determined TD and PD, with spatial variables also affecting PD. The three diversity facets were primarily shaped by distinct critical predictors, with the temperature diurnal range affecting FD and PD, and precipitation of the wettest month determining TD. Our results emphasize the value of FD for explaining part of TD and PD variation in lichen communities at a broad geographic scale, while highlighting that these diversity facets provide complementary information about the communities' response under changing environmental conditions. Furthermore, traits such as growth form, photobiont type, and reproductive strategy mediated the response of lichen communities to abiotic factors emerging as useful indicators of macroclimatic variations.
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| 4. |
- Jung, Patrick, et al.
(author)
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The underestimated fraction : diversity, challenges and novel insights into unicellular cyanobionts of lichens
- 2024
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In: ISME Communications. - : Oxford University Press. - 2730-6151. ; 4:1
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Research review (peer-reviewed)abstract
- Lichens are remarkable and classic examples of symbiotic organisms that have fascinated scientists for centuries. Yet, it has only been for a couple of decades that significant advances have focused on the diversity of their green algal and/or cyanobacterial photobionts. Cyanolichens, which contain cyanobacteria as their photosynthetic partner, include up to 10% of all known lichens and, as such, studies on their cyanobionts are much rarer compared to their green algal counterparts. For the unicellular cyanobionts, i.e. cyanobacteria that do not form filaments, these studies are even scarcer. Nonetheless, these currently include at least 10 different genera in the cosmopolitan lichen order Lichinales. An international consortium (International Network of CyanoBionts; INCb) will tackle this lack of knowledge. In this article, we discuss the status of current unicellular cyanobiont research, compare the taxonomic resolution of photobionts from cyanolichens with those of green algal lichens (chlorolichens), and give a roadmap of research on how to recondition the underestimated fraction of symbiotic unicellular cyanobacteria in lichens.
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| 5. |
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| 6. |
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| 7. |
- Motiejunaite, Jurga, et al.
(author)
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Lichens, lichenicolous and allied fungi in Asveja Regional Park (Lithuania)
- 2012
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In: Botanica Lithuanica. - 1392-1665. ; 18:2, s. 85-100
-
Journal article (peer-reviewed)abstract
- The paper reports the results of lichenological investigations in Asveja Regional Park (eastern Lithuania). A large part of the study was performed during the joint 18th Symposium of Baltic Mycologists and Lichenologists (BMLS) and Nordic Lichen Society meeting (NLF), September 19–23, 2011. A list of 259 species is presented, 30 of them are new to Lithuania. Arthonia helvola, Bacidina sulphurella, Candelariella lutella, Catillaria croatica, Cladonia conista, Gyalecta derivata, Lecanora quercicola, Leptosphaeria ramalinae, Strigula jamesii, Trichonectria rubefaciens, Verrucaria banatica, V. boblensis, V. christiansenii, V. illinoisensis, V. inornata, V. nigrofusca, V. trabicola, Zwackhiomyces diederichii are recorded for the first time in the Baltic countries. New lichens for Lithuania are: Bacidia incompta, Caloplaca crenulatella, C. pyracea, Catinaria atropurpurea, Lecanora populicola, L. semipallida, Mycobilimbia epixanthoides, Ramalina dilacerata, Verrucaria inaspecta, and new lichenicolous fungi are: Cladosporium licheniphilum, Stigmidium microspilum, Xenonectriella leptalea. Eighteen species included in the Lithuanian Red Data Book were recorded which is the highest number known for any studied area in Lithuania.
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| 8. |
- Thell, Arne, et al.
(author)
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New or interesting lichens and lichenicolous fungi from the Vadstena area, Östergötland, Sweden
- 2014
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In: Graphis Scripta. - 0901-7593. ; 26:1-2, s. 15-33
-
Journal article (peer-reviewed)abstract
- Results from the excursion of the 20th biennial symposium in Vadstena 11–15 August 2013 are presented. Eight localities in and around Vadstena were visited. Forty-three species are reported as new to the province Östergötland [Ostrogothia], three of which are new to the Nordic countries: Lecanora compallens, Polycoccum kerneri and Tremella caloplacae, five are new to Sweden: Cornutispora ciliata, Pyrenula chlorospila, Thelidium cf. rimulosum, Verrucaria ochrostoma and V. polystictoides, and the following are new to Östergötland: Bagliettoa baldensis, B. calciseda, Briancoppinsia cytospora, Calogaya arnoldii ssp. obliterata, Clypeococcum hypocenomycis, Cornutispora lichenicola, Endococcus exerrans, Fuscidea arboricola, Illosporium carneum, Lepraria elobata, L. jackii, L. vouauxii, Leptochidium albociliatum, Lichenoconium lecanorae, Lichenochora weillii, Marchandiobasidium aurantiacum, Micarea byssacea, Monodictys anaptychiae, M. epilepraria, Parmelia serrana, Phaeosporobolus alpinus, Placopyrenium canellum, Porpidia soredizodes, Pyrenidium actinellum, Rinodina turfacea, Stereocaulon rivulorum, Syzygospora physciacearum, Thelenella muscorum, Tremella phaeophysciae, T. ramalinae, Trichonectria rubefaciens, Verrucaria dolosa, V. inaspecta, V. infumata and V. memnonia.
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| 9. |
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| 10. |
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| 11. |
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| 12. |
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| 13. |
- Ariyawansa, Hiran A., et al.
(author)
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Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
- 2015
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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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| 14. |
- Armstrong, Ellie E., et al.
(author)
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Draft Genome Sequence and Annotation of the Lichen-Forming Fungus Arthonia radiata
- 2018
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In: Microbiology Resource Announcements. - : AMER SOC MICROBIOLOGY. - 2576-098X. ; 6:14
-
Journal article (peer-reviewed)abstract
- We report here the draft de novo genome assembly, transcriptome assembly, and annotation of the lichen-forming fungus Arthonia radiata (Pers.) Ach., the type species for Arthoniomycetes, a class of lichen-forming, lichenicolous, and saprobic Ascomycota. The genome was assembled using overlapping paired-end and mate pair libraries and sequenced on an Illumina HiSeq 2500 instrument.
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| 15. |
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| 16. |
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| 17. |
- Arup, Ulf, et al.
(author)
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Lavar Lichenes
- 2015
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In: Rödlistade arter i Sverige 2015. - 9789187853104 ; , s. 72-79
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Book chapter (other academic/artistic)
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| 18. |
- Arup, Ulf, et al.
(author)
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Om att kurera svampar.
- 2007
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In: Puggehatten. - 1100-7109. ; 2007:1, s. 6-8
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Journal article (peer-reviewed)
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| 19. |
- Arup, Ulf, et al.
(author)
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Professor Ingvar Kärnfelt - a birthday tribute
- 2009
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In: The Lichenologist. - Cambridge : Cambridge University Press. - 0024-2829 .- 1096-1135. ; 41:5, s. 453-456
-
Journal article (other academic/artistic)abstract
- On 19 July 2009 Ingvar Kärnefelt celebrated his 65th birthday. This could have meant that we, his former students, would be celebrating him in his retirement from his position as head of the Biological Museums at Lund University. We are grateful that this is not the case, as Ingvar will carry on, probably for at least one or two more years. Instead, we celebrate Ingvar because he is the main reason for all of us having studied lichenology in Lund. This special issue of The Lichenologist is dedicated to him as a birthday tribute in honour of his long and fruitful lichenological career. The main authors of all the papers in this issue are former students of Ingvar. For several of us he has not only acted as supervisor but later also as the director of the Botanical Museum where we meet him in our daily work.
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| 20. |
- Arup, Ulf, et al.
(author)
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Rödlista över lavar Lichenes
- 2020
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In: Rödlistade arter i Sverige 2020. - 9789187853548 - 9789187853555 ; , s. 89-96
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Book chapter (other academic/artistic)
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| 21. |
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| 22. |
- Arup, Ulf, et al.
(author)
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Öländsk tegellav Psora vallesiaca på Öland och Gotland 2007
- 2008
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Reports (other academic/artistic)abstract
- SAMMANFATTNINGÖländsk tegellavPsora vallesiaca är rödlistad som akut hotad (CR). Arten var fram till2005 känd från en lokal på Öland, där den blev funnen 1970. Under 2004–2006 hittadesfyra nya lokaler på Gotland under samma period togs ett åtgärdsprogram fram för attsäkerställa artens fortlevnad i landet. I åtgärdsprogrammet föreslogs en inventering påÖland och Gotland för att försöka finna nya lokaler i landet och för att få ett bättre greppom ekologi, status och utbredning. I denna rapport redovisas resultaten av dennainventering, som utfördes 2007.Inga nya lokaler hittades på Öland och chansen att finna nya lokaler där får nu anses somsmå. På Gotland hittades fem nya lokaler, varav några med flera dellokaler. Totalt är nu tioaktuella lokaler kända i landet. På Gotland har arten noterats på sammanlagt 34 block elleravsatser och täcker nästan 900 cm2. Lokalerna är spridda på ön, i norr och öster samt längsti söder. Tre av lokalerna ligger i ett naturreservat och de andra är utan formellt skydd.Det är nu, genom de nya fynden, möjligt att beskriva artens ekologi mer i detalj. Denuppträder oftast på väl vittrade kalkstensblock, men även på avsatser. Laven skyr dock denhårda revkalkstenen som bygger upp de flesta raukar, klintar och hällmarker. Man finnerarten huvudsakligen på sidan av blocken och avsatserna, bara mer sällan på ovansidan.Lokalerna bör vara ljusa, helt öppna till halvöppna med gles buskvegetation eller spriddaträd. Under dessa förhållanden är arten oftast fertil och mår väl. Under skuggigareförhållanden mår arten sämre och är ofta steril. Ungefär samma förhållanden gäller desssläkting falsk guldskivlavPsora testacea, som dock påträffas på något hårdare, elleråtminstone inte så vittrad kalksten, men inte heller den växer på revkalksten. Bara på enlokal uppträder arterna tillsammans och intrycket är därför att om den ena arten finns på enlokal är sannolikheten inte så stor att den andra finns.Under inventeringen besöktes de allra flesta områden på Gotland som har gynnsammaförhållanden för öländsk tegellav. Dessa områden är inte speciellt många då kalkstenen påde flesta ställen är för hård och inte tillräckligt vittrad. Mörkertalet för arten bör därför,enligt vår bedömning inte vara så stort. Trots det kan det finnas oupptäckta lokaler ellerdelpopulationer.Flertalet av de aktuella lokalerna hålls mer eller mindre öppna genom bete. Igenväxning ärsåledes inte något större problem idag, men är något man på sikt måsta bevaka. En avlokalerna bör dock röjas omgående. Stenbrottsverksamhet skulle också kunna utgöra etthot mot någon av lokalerna.Uppföljningen av åtgärdsprogrammet bör nu koncentrera sig på att se till att de tio kändalokalerna har så gynnsamma förutsättningar som möjligt för öländsk tegellav. Vissövervakning bör ske, dels på de lokaler där skötselåtgärder görs, dels på några av derikligaste lokalerna.
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| 23. |
- Axelsson, Sara, 1975-
(author)
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Resin acids in commercial products and the work environment of Swedish wood pellets production : Analytical methodology, occurrence and exposure
- 2012
-
Doctoral thesis (other academic/artistic)abstract
- The aims of the work this thesis is based upon were to develop convenient analytical procedures for determining resin acids in biological and environmental matrices, and apply them to enhance understanding of the occurrence, exposure to and uptake by exposed individuals of resin acids. Particular focus has been on the workplace environment of the Swedish wood pellets industry. Sample extraction procedures and high-performance liquid chromatography/electrospray ionisation-mass spectrometry (HPLC/ESI-MS) methodologies were developed for measuring resin acids in dust, skin and urine samples. Chromatographic separation of abietic (AA) and pimaric acid was achieved by using a polar-embedded C12 stationary phase. The HPLC/ESI-MS method avoids undesirable oxidation of AA, which was found to occur during the derivatisation step in the standard MDHS 83/2 gas chromatography/flame ionisation detection (GC/FID) methodology, leading to false observations of both AA and the oxidation product 7-oxodehydroabietic acid (7-OXO). Personal exposures to resin acids in the Swedish wood pellet production industry were found to be lower, on average, than the British Occupational Exposure Limit for rosin (50 µg/m3). The oxidised resin acid 7-OXO, was detected in both dust and skin samples indicating the presence of allergenic resin acids. A correlation between air and post-shift urinary concentrations of dehydroabietic acid (DHAA), and a trend towards an increase in urinary 7-OXO during work shifts, were also observed. Whether the increase in 7-OXO was due to direct uptake or metabolism of other resin acids cannot be concluded from the results. An efficient HPLC/UV methodology with diode-array detection was developed for screening commercial products for rosin that could be used in laboratories lacking mass spectrometers. Very high concentrations of free resin acids were detected in depilatory wax strips using the method.
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| 24. |
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| 25. |
- Dalmo, Johanna, et al.
(author)
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Evaluation of retinol binding protein 4 and carbamoylated haemoglobin as potential renal toxicity biomarkers in adult mice treated with Lu-177-octreotate
- 2014
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In: EJNMMI Research. - : Springer Science and Business Media LLC. - 2191-219X. ; 4:59
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Journal article (peer-reviewed)abstract
- Background: The kidneys are regarded as one of the main dose-limiting organs in the treatment of neuroendocrine tumours with Lu-177-[DOTA(0), Tyr(3)]-octreotate (Lu-177-octreotate), despite the successful use of kidney uptake blocking agents such as lysine and arginine. To avoid renal toxicity but still give each patient as high amount of Lu-177-octreotate as possible, there is a need for methods/biomarkers that indicate renal injury in an early stage of the treatment. The aim of this study was to investigate the potential of using urinary retinol binding protein 4 (RBP4) and carbamoylated haemoglobin (Hb) in blood as biomarkers of nephrotoxic effects on adult mice after Lu-177-octreotate treatment. Methods: Adult BALB/c nude mice were injected with 60 MBq or 120 MBq of Lu-177-octreotate or with saline (control). Urine was collected before injection and concentrations of urinary RBP4 and creatinine were determined 14 to 90 days after injection Blood samples were collected after 90 days, and carbamoylated N-terminal valine in Hb, formed from urea, was measured as valine hydantoin (VH) after detachment from Hb. Results: The RBP4 values increased with administered activity and time. For the 60 and 120 MBq groups, statistically significantly higher RBP4 levels (p <0.05) were found at day 60 and 90 compared to baseline, also at day 30 for 120 MBq group. For VH, the mean values were similar for the 60 MBq and control groups, while a small increase was observed for the 120 MBq group; but there were no statistically significant differences between any of the groups (p >0.05). No morphological changes in the kidney tissue were found. Conclusions: Urinary RBP4 is a promising new biomarker for radiation-induced renal toxicity. For the conditions used in this experiment, carbamoylated Hb (from urea) measured as VH may not be a sufficiently sensitive biomarker to be used for renal toxicity.
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| 26. |
- Dillman, Karen L., et al.
(author)
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New records, range extensions and nomenclatural innovations for lichens and lichenicolous fungi from Alaska, USA
- 2012
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In: Herzogia. - : Herzogia. - 0018-0971. ; 25:2, s. 177-210
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Journal article (peer-reviewed)abstract
- New records, range extensions and nomenclatural innovations for lichens and lichenicolous fungi from Alaska, U.S.A. - Herzogia 25: 177-210. Surveys of lichens and lichenicolous fungi have been taking place in the U.S. state of Alaska for more than 160 years, but until now assessing the full extent of their diversity has been hampered by the lack of a comprehensive and synonymized baseline inventory. In this paper we will begin to redress this by resolving outstanding nomenclatural issues and providing voucher data for a forthcoming catalog of Alaskan lichens, specifically: 1) synonymization,and/or resolution of status of species previously reported from Alaska, with emphasis on Alaskan types; 2) species new to the Alaska lichen biota; and 3) biogeographically significant new records from within Alaska. We report 91 species new to the flora of Alaska, including 65 lichens, three saprophytic calicioid fungi and 23 lichenicolous fungi. Of these, we report thirteen species, Biatora sphaeroidiza, Biatorella conspurcans, Chaenothecopsis arthoniae, Collemopsidium foveolatum, Dactylospora frigida, Halospora discrepans, Lecanora bryopsora, Opegrapha geographicola, Peltigera lyngei, Petractis clausa, Protoblastenia cyclospora, Thelocarpon impressellum and Usnea cylindrica as new to North America. In addition, Arthonia pruinata and Flavocetraria minuscula are new to Canada and Adelococcus alpestris new to the United States. We further place the following five names into synonymy: Lecania disceptans (Nyl.) Lynge [= Halecania alpivaga (Th.Fr.) M.Mayrhofer], Lecidea pallidella Nyl. [= Lecania subfuscula (Nyl.) S.Ekman], Lempholemma triptodes (Nyl.) Zahlbr. Leciophysma finmarkicum Th.Fr.), Polyblastia obtenta (Nyl.) Lynge [= Sporodictyon terrestre (Th.Fr.) S.Savic & Tibell], and Verrucaria pernigrata Nyl. [= Protothelenella sphinctrinoides (Nyl.) H.Mayrhofer & Poelt]. We propose restoring the long overlooked taxon Polyblastia exalbida (Nyl.) Zahlbr., currently known only from Alaska, to the North American lichen checklist. Finally, we propose the new combination Puttea caesia (Fr.) M.Svensson & T.Sprib. to replace Lecidea symmictella Nyl., which becomes a synonym.
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| 27. |
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| 28. |
- Främling, Kary, 1965-, et al.
(author)
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Comparison of Contextual Importance and Utility with LIME and Shapley Values
- 2021
-
In: Explainable and Transparent AI and Multi-Agent Systems. - Cham : Springer. - 9783030820169 - 9783030820176 ; , s. 39-54
-
Conference paper (peer-reviewed)abstract
- Different explainable AI (XAI) methods are based on different notions of ‘ground truth’. In order to trust explanations of AI systems, the ground truth has to provide fidelity towards the actual behaviour of the AI system. An explanation that has poor fidelity towards the AI system’s actual behaviour can not be trusted no matter how convincing the explanations appear to be for the users. The Contextual Importance and Utility (CIU) method differs from currently popular outcome explanation methods such as Local Interpretable Model-agnostic Explanations (LIME) and Shapley values in several ways. Notably, CIU does not build any intermediate interpretable model like LIME, and it does not make any assumption regarding linearity or additivity of the feature importance. CIU also introduces the value utility notion and a definition of feature importance that is different from LIME and Shapley values. We argue that LIME and Shapley values actually estimate ‘influence’ (rather than ‘importance’), which combines importance and utility. The paper compares the three methods in terms of validity of their ground truth assumption and fidelity towards the underlying model through a series of benchmark tasks. The results confirm that LIME results tend not to be coherent nor stable. CIU and Shapley values give rather similar results when limiting explanations to ‘influence’. However, by separating ‘importance’ and ‘utility’ elements, CIU can provide more expressive and flexible explanations than LIME and Shapley values.
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| 29. |
- Hagström, Mikael, et al.
(author)
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Exkursionsrapport till Närke våren 2017
- 2017
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In: Lavbulletinen. - 1651-6435. ; 2017, s. 75-79
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Journal article (pop. science, debate, etc.)abstract
- SLF’s vårexkursion gick till trakterna av Kumla och Örebro med Mikael Hagström som arrangör. En god skara människor hade slutit upp och trotsade de initialt urusla vädret, men som tur var bättrade det sig. Med på exkursionen var Martin Westberg, Samantha Fernandez Brime, Ulf Arup, Emil Persson, Sten Svantesson, Stefan Ekman, Linnea Eide-Ekman, Måns Svensson, Lovisa Fogelberg, Ola Hammarström, Jesper Wadstein, Björn Owe-Larsson, Toni Berglund, Anders Carlberg och Per Larsson.
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| 30. |
- Hammarström, Ola, et al.
(author)
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SLFs exkursion till västra Jämtland 6-9 augusti 2020
- 2021
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In: Lavbulletinen. - : Svensk Lichenologisk Förening. - 1651-6435. ; :1, s. 30-40
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Journal article (pop. science, debate, etc.)abstract
- SLF återvänder gång på gång till Jämtland av förklarliga skäl. I början av augusti samlades ett gäng på 25 laventusiaster i västra Jämtland för några dagars lavjakt i de fina miljöerna kring Kallsjön.
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| 31. |
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| 32. |
- Hurtado, P., et al.
(author)
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Disentangling functional trait variation and covariation in epiphytic lichens along a continent-wide latitudinal gradient
- 2020
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In: Proceedings of the Royal Society of London. Biological Sciences. - : ROYAL SOC. - 0962-8452 .- 1471-2954. ; 287:1922
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Journal article (peer-reviewed)abstract
- Characterizing functional trait variation and covariation, and its drivers, is critical to understand the response of species to changing environmental conditions. Evolutionary and environmental factors determine how traits vary among and within species at multiple scales. However, disentangling their relative contribution is challenging and a comprehensive trait-environment framework addressing such questions is missing in lichens. We investigated the variation in nine traits related to photosynthetic performance, water use and nutrient acquisition applying phylogenetic comparative analyses in lichen epiphytic communities on beech across Europe. These poikilohydric organisms offer a valuable model owing to their inherent limitations to buffer contrasting environmental conditions. Photobiont type and growth form captured differences in certain physiological traits whose variation was largely determined by evolutionary processes (i.e. phylogenetic history), although the intraspecific component was non-negligible. Seasonal temperature fluctuations also had an impact on trait variation, while nitrogen content depended on photobiont type rather than nitrogen deposition. The inconsistency of trait covariation among and within species prevented establishing major resource use strategies in lichens. However, we did identify a general pattern related to the water-use strategy. Thus, to robustly unveil lichen responses under different climatic scenarios, it is necessary to incorporate both among and within-species trait variation and covariation.
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| 33. |
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| 34. |
- Jonsson, Lina, 1982, et al.
(author)
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Examining neurodevelopmental problems in 15q11.2 (BP1-BP2) copy number variation carriers at ages 9/12 and 18 in a Swedish twin sample
- 2023
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In: Molecular Genetics & Genomic Medicine. - 2324-9269. ; 11:8
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Journal article (peer-reviewed)abstract
- BackgroundSeveral copy number variations (CNVs) are associated with increased risk for neurodevelopmental and psychiatric disorders. The CNV 15q11.2 (BP1-BP2) deletion has been associated with learning difficulties, attention deficit hyperactivity disorder (ADHD), epilepsy, and brain morphology; however, many carriers present mild or no symptoms. Carrying the reciprocal duplication does not seem to confer risk for these disorders or traits. Our aim was to examine the impact of carrying either 15q11.2 deletion and reciprocal duplication on neurodevelopmental problems in a population-based sample of children. MethodsTwins with genotype and phenotype information in the Child and Adolescent Twin Study in Sweden (CATSS) were included (N = 12,040). We included measures of neurodevelopmental problems (NDPs), including learning problems, from the questionnaire Autism-Tics, ADHD, and other Comorbidities inventory (A-TAC) at age 9/12, ADHD and autism spectrum disorder (ASD) questionnaires at age 18, as well as information about lifetime psychiatric diagnoses and epileptic seizures. We tested the association between these phenotypic measurements and carrying the 15q11.2 deletion, the reciprocal duplication, and other CNVs with previously reported strong associations with neurodevelopmental and psychiatric disorders (i.e., psychiatric CNVs). ResultsWe identified 57 carriers of the 15q11.2 deletion, 75 carriers of the reciprocal duplication, and 67 carriers of other psychiatric CNVs. We did not find an increased risk for NDPs or psychiatric diagnoses in the 15q11.2 deletion carriers. For 15q11.2 duplication carriers, we found an increased risk for math learning problems and fewer self-reported ADHD symptoms at age 18 but not for other NDPs. In line with previous studies, we found an increased risk of NDPs and other evaluated phenotypes in carriers of psychiatric CNVs. ConclusionsOur results support previous findings that carrying 15q11.2 deletion does not have a large effect on NDPs in children.
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| 35. |
- Joosse, Sofie, et al.
(author)
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Critical, Engaged and Change-oriented Scholarship in Environmental Communication. Six Methodological Dilemmas to Think with
- 2020
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In: Environmental Communication. - : Informa UK Limited. - 1752-4032 .- 1752-4040. ; 14, s. 758-771
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Journal article (peer-reviewed)abstract
- While calls for critical, engaged and change-oriented scholarship in environmental communication (EC) abound, few articles discuss what this may practically entail. With this article, we aim to contribute to a discussion in EC about the methodological implications of such scholarship. Based on our combined experience in EC research and drawing from a variety of academic fields, we describe six methodological dilemmas that we encounter in our research practice and that we believe are inherent to such scholarship. These dilemmas are (1) grasping communication; (2) representing others; (3) involving people in research; (4) co-producing knowledge; (5) engaging critically; and (6) relating to conflict. This article does not offer solutions to these complex dilemmas. Rather, our dilemma descriptions are meant to help researchers think through methodological issues in critical, engaged and change-oriented EC research. The article also helps to translate the dilemmas to the reality of research projects through a set of questions, aimed to support a sensitivity to, and understanding of, the dilemmas in context.
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| 36. |
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| 37. |
- Kosuthova, Alica, et al.
(author)
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A revision of the Rostania occultata (Collemataceae) complex in Fennoscandia
- 2022
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In: The Lichenologist. - : Cambridge University Press. - 0024-2829 .- 1096-1135. ; 54:1, s. 13-24
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Journal article (peer-reviewed)abstract
- The Rostania occultata species complex ('Collema occultatum s. lat.') is revised in Fennoscandia and found to consist of four species, all epiphytes on deciduous trees: Rostania effusa A. Kosuth., M. Westb. & Wedin sp. nov., R. occultata (Bagl.) Otalora et al., R. pallida A. Kosuth., M. Westb. & Wedin sp. nov. and R. populina (Th. Fr.) A. Kosuth., M. Westb. & Wedin comb. nov. Rostania effusa and R. pallida are newly described from humid habitats in old-growth boreal coniferous forests, usually with a mixture of deciduous trees, and from similar areas in the subalpine birch-dominated forests of Fennoscandia. Rostania effusa is characterized by apothecia with red-brown apothecium discs and an excipulum thallinum with a simple pseudocortex and cubic to oblong, muriform spores. Rostania pallida has apothecia with whitish to pale yellowish discs and an excipulum thallinum with a distinct cellular pseudocortex, and ellipsoid, muriform mature spores that are often constricted at the centre. A lectotype is designated for Collema quadratum J. Lahm ex Korb. The new combination Rostania populina is introduced for the species recognized until now as the variety Rostania occultata var. populina (Th. Fr.) Perlmutter & Rivas Plata. A key to the six species in Rostania s. str. is included.
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| 38. |
- Kosuthova, Alica, et al.
(author)
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A revision of the Rostania occultata (Collemataceae) complex in Fennoscandia
- 2022
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In: The Lichenologist. - : Cambridge University Press (CUP). - 0024-2829 .- 1096-1135. ; 54:1, s. 13-24
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Journal article (peer-reviewed)abstract
- The Rostania occultata species complex (‘Collema occultatum s. lat.’) is revised in Fennoscandia and found to consist of four species, all epiphytes on deciduous trees: Rostania effusa A. Košuth., M. Westb. & Wedin sp. nov., R. occultata (Bagl.) Otálora et al., R. pallida A. Košuth., M. Westb. & Wedin sp. nov. and R. populina (Th. Fr.) A. Košuth., M. Westb. & Wedin comb. nov. Rostania effusa and R. pallida are newly described from humid habitats in old-growth boreal coniferous forests, usually with a mixture of deciduous trees, and from similar areas in the subalpine birch-dominated forests of Fennoscandia. Rostania effusa is characterized by apothecia with red-brown apothecium discs and an excipulum thallinum with a simple pseudocortex and cubic to oblong, muriform spores. Rostania pallida has apothecia with whitish to pale yellowish discs and an excipulum thallinum with a distinct cellular pseudocortex, and ellipsoid, muriform mature spores that are often constricted at the centre. A lectotype is designated for Collema quadratum J. Lahm ex Körb. The new combination Rostania populina is introduced for the species recognized until now as the variety Rostania occultata var. populina (Th. Fr.) Perlmutter & Rivas Plata. A key to the six species in Rostania s. str. is included.
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| 39. |
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| 40. |
- Kosuthova, Alica, 1978-, et al.
(author)
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Rostania revised : testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes )
- 2019
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :47, s. 17-33
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Journal article (peer-reviewed)abstract
- Here, we test the current generic delimitation of Rostania (Collemataceae, Peltigerales, Ascomycota) utilizing molecular phylogeny and morphological investigations. Using DNA sequence data from the mitochondrial SSU rDNA and two nuclear protein-coding genes (MCM7 and β-tubulin) and utilizing parsimony, maximum likelihood and Bayesian phylogenetic methods, Rostania is shown to be non-monophyletic in the current sense. A new generic delimitation of Rostania is thus proposed, in which the genus is monophyletic, and three species (Rostania coccophylla, R. paramensis, R. quadrifida) are excluded and transferred to other genera. Rostania occultata is further non-monophyletic, and a more detailed investigation of species delimitations in Rostania s. str. is needed. The new combinations Leptogium paramense and Scytinium quadrifidum are proposed.
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| 41. |
- Košuthová, Alica, 1978-, et al.
(author)
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Species delimitation in the cyanolichen genus Rostania
- 2020
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In: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 115
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Journal article (peer-reviewed)abstract
- BackgroundIn this study, we investigate species limits in the cyanobacterial lichen genus Rostania (Collemataceae, Peltigerales, Lecanoromycetes). Four molecular markers (mtSSU rDNA, β-tubulin, MCM7, RPB2) were sequenced and analysed with two coalescent-based species delimitation methods: the Generalized Mixed Yule Coalescent model (GMYC) and a Bayesian species delimitation method (BPP) using a multispecies coalescence model (MSC), the latter with or without an a priori defined guide tree.ResultsSpecies delimitation analyses indicate the presence of eight strongly supported candidate species. Conclusive correlation between morphological/ecological characters and genetic delimitation could be found for six of these. Of the two additional candidate species, one is represented by a single sterile specimen and the other currently lacks morphological or ecological supporting evidence.ConclusionsWe conclude that Rostania includes a minimum of six species: R. ceranisca, R. multipunctata, R. occultata 1, R. occultata 2, R. occultata 3, and R. occultata 4,5,6. Three distinct Nostoc morphotypes occur in Rostania, and there is substantial correlation between these morphotypes and Rostania thallus morphology.
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| 42. |
- Kärnefelt, Ingvar, et al.
(author)
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Candelaria fruticans found in Southern Africa
- 2001
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In: Mycotaxon. - 0093-4666. ; 80:1, s. 465-467
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Journal article (peer-reviewed)abstract
- The distribution and habitat ecology of Candelaria fruticans Poelt & Oberw. is discussed and a distribution map is provided, The distribution pattern is shared by a few species occurring on both sides of the Atlantic Ocean in mainly the subtropical and tropical zones.
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| 43. |
- Leavitt, Steven D., et al.
(author)
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Multiple, Distinct Intercontinental Lineages but Isolation of Australian Populations in a Cosmopolitan Lichen-Forming Fungal Taxon, Psora decipiens (Psoraceae, Ascomycota)
- 2018
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In: Frontiers in Microbiology. - : FRONTIERS MEDIA SA. - 1664-302X. ; 9
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Journal article (peer-reviewed)abstract
- Multiple drivers shape the spatial distribution of species, including dispersal capacity, niche incumbency, climate variability, orographic barriers, and plate tectonics. However, biogeographic patterns of fungi commonly do not fit conventional expectations based on studies of animals and plants. Fungi, in general, are known to occur across exceedingly broad, intercontinental distributions, including some important components of biological soil crust communities (BSCs). However, molecular data often reveal unexpected biogeographic patterns in lichenized fungal species that are assumed to have cosmopolitan distributions. The lichen-forming fungal species Psora decipiens is found on all continents, except Antarctica and occurs in BSCs across diverse habitats, ranging from hot, arid deserts to alpine habitats. In order to better understand factors that shape population structure in cosmopolitan lichen-forming fungal species, we investigated biogeographic patterns in the cosmopolitan taxon P. decipiens, along with the closely related taxa P. crenata and P. saviczii. We generated a multi-locus sequence dataset based on a worldwide sampling of these taxa in order to reconstruct evolutionary relationships and explore phylogeographic patterns. Both P. crenata and P. decipiens were not recovered as monophyletic; and P. saviczii specimens were recovered as a monophyletic clade closely related to a number of lineages comprised of specimens representing P. decipiens. Striking phylogeographic patterns were observed for P. crenata, with populations from distinct geographic regions belonging to well-separated, monophyletic lineages. South African populations of P. crenata were further divided into well-supported sub-clades. While well-supported phylogenetic substructure was also observed for the nominal taxon P. decipiens, nearly all lineages were comprised of specimens collected from intercontinental populations. However, all Australian specimens representing P. decipiens were recovered within a single well-supported monophyletic clade consisting solely of Australian samples. Our study supports up to 10 candidate species-level lineages in P. decipiens, based on genealogical concordance and coalescent-based species delimitation analyses. Our results support the general pattern of the biogeographic isolation of lichen-forming fungal populations in Australia, even in cases where closely related congeners have documented intercontinental distributions. Our study has important implications for understanding factors influencing diversification and distributions of lichens associated with BSC.
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| 44. |
- Lidell, Martin, 1970, et al.
(author)
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The Adipocyte-Expressed Forkhead Transcription Factor Foxc2 Regulates Metabolism Through Altered Mitochondrial Function
- 2011
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In: Diabetes. - 0012-1797. ; 60:2, s. 427-435
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Journal article (peer-reviewed)abstract
- OBJECTIVE: Previous findings demonstrate that enhanced expression of the forkhead transcription factor Foxc2 in adipose tissue leads to a lean and insulin-sensitive phenotype. These findings prompted us to further investigate the role of Foxc2 in the regulation of genes of fundamental importance for metabolism and mitochondrial function. RESEARCH DESIGN AND METHODS: The effects of Foxc2 on expression of genes involved in mitochondriogenesis and mitochondrial function were assessed by quantitative real-time PCR. The potential of a direct transcriptional regulation of regulated genes was tested in promoter assays, and mitochondrial morphology was investigated by electron microscopy. Mitochondrial function was tested by measuring oxygen consumption and extracellular acidification rates as well as palmitate oxidation. RESULTS: Enhanced expression of FOXC2 in adipocytes or in cells with no endogenous Foxc2 expression induces mitochondriogenesis and an elongated mitochondrial morphology. Together with increased aerobic metabolic capacity, increased palmitate oxidation, and upregulation of genes encoding respiratory complexes and of brown fat-related genes, Foxc2 also specifically induces mitochondrial fusion genes in adipocytes. Among tested forkhead genes, Foxc2 is unique in its ability to trans-activate the nuclear-encoded mitochondrial transcription factor A (mtTFA/Tfam) gene--a master regulator of mitochondrial biogenesis. In human adipose tissue the expression levels of mtTFA/Tfam and of fusion genes also correlate with that of Foxc2. CONCLUSIONS: We previously showed that a high-calorie diet and insulin induce Foxc2 in adipocytes; the current findings identify a previously unknown role for Foxc2 as an important metabo-regulator of mitochondrial morphology and metabolism.
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| 45. |
- Malmström, Martin, et al.
(author)
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Skrivkris, skolkris och samhällskris
- 2021
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In: Skolans kriser : Historiska perspektiv på utbildningsformer och skoldebatter - Historiska perspektiv på utbildningsformer och skoldebatter. - Lund : Nordic Academic Press. - 9789188909787 ; , s. 203-231
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Book chapter (other academic/artistic)
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| 46. |
- Martin, E M, et al.
(author)
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Molecular and neuroanatomical characterization of single neurons in the mouse medullary gigantocellular reticular nucleus.
- 2011
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In: The Journal of comparative neurology. - : Wiley. - 1096-9861 .- 0021-9967. ; 519:13, s. 2574-93
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Journal article (peer-reviewed)abstract
- Medullary gigantocellular reticular nucleus (mGi) neurons have been ascribed a variety of behaviors, many of which may fall under the concepts of either arousal or motivation. Despite this, many details of the connectivity of mGi neurons, particularly in reference to those neurons with ascending axons, remain unknown. To provide a neuroanatomical and molecular characterization of these cells, with reference to arousal and level-setting systems, large medullary reticular neurons were characterized with retrograde dye techniques and with real-time reverse transcriptase PCR (RT-PCR) analyses of single-neuron mRNA expression in the mouse. We have shown that receptors consistent with participation in generalized arousal are expressed by single mGi neurons and that receptors from different families of arousal-related neurotransmitters are rarely coexpressed. Through retrograde labeling, we have shown that neurons with ascending axons and neurons with descending axons tend to form like-with-like clusters, a finding that is consistent across age and gender. In comparing the two groups of retrogradely labeled neurons in neonatal animals, those neurons with axons that ascend to the midbrain show markers for GABAergic or coincident GABAergic and glutamatergic function; in contrast, approximately 60% of the neurons with axons that descend to the spinal cord are glutamatergic. We discuss the mGi's relationship to the voluntary and emotional motor systems and speculate that neurons in the mGi may represent a mammalian analogue to Mauthner cells, with a separation of function for neurons with ascending and descending axons.
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| 47. |
- Millanes, Ana M., et al.
(author)
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Crittendenia gen. nov., a new lichenicolous lineage in the Agaricostilbomycetes (Pucciniomycotina), and a review of the biology, phylogeny and classification of lichenicolous heterobasidiomycetes
- 2021
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In: The Lichenologist. - : Cambridge University Press. - 0024-2829 .- 1096-1135. ; 53:1, s. 103-116
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Research review (peer-reviewed)abstract
- The lichenicolous 'heterobasidiomycetes' belong in the Tremellomycetes (Agaricomycotina) and in the Pucciniomycotina. In this paper, we provide an introduction and review of these lichenicolous taxa, focusing on recent studies and novelties of their classification, phylogeny and evolution. Lichen-inhabiting fungi in the Pucciniomycotina are represented by only a small number of species included in the genera Chionosphaera, Cyphobasidium and Lichenozyma. The phylogenetic position of the lichenicolous representatives of Chionosphaera has, however, never been investigated by molecular methods. Phylogenetic analyses using the nuclear SSU, ITS, and LSU ribosomal DNA markers reveal that the lichenicolous members of Chionosphaera form a monophyletic group in the Pucciniomycotina, distinct from Chionosphaera and outside the Chionosphaeraceae. The new genus Crittendenia is described to accommodate these lichen-inhabiting species. Crittendenia is characterized by minute synnemata-like basidiomata, the presence of clamp connections and aseptate tubular basidia from which 4-7 spores discharge passively, often in groups. Crittendenia, Cyphobasidium and Lichenozyma are the only lichenicolous lineages known so far in the Pucciniomycotina, whereas Chionosphaera does not include any lichenicolous taxa.
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| 48. |
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| 49. |
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| 50. |
- Millanes, Ana M., et al.
(author)
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Three new species in the Biatoropsis usnearum complex
- 2016
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In: Herzogia. - : Herzogia. - 0018-0971. ; 29:2, s. 337-354
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Journal article (peer-reviewed)abstract
- Three new species of Biatoropsis are formally described based on our previous molecular studies, and on additional molecular, morphological, and ecological data. Biatoropsis protousneae sp. nov. is confined to Protousnea dusenii. Biatoropsis minuta sp. nov. is characterized by the small and brown to black basidiomatal galls, and by growing on Usnea barbata and U. lapponica. Biatoropsis hafellneri sp. nov. is distinguished by 2-celled basidia with cells that elongate laterally at maturity, and by growing on species of the Usnea fragilescens aggregate. A fourth Biatoropsis species is left unnamed, and two other lineages are not described, all waiting for the study of additional material.
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