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1.	Buckland, Philip I., 1973-, et al. (author) SEAD - The Strategic Environmental Archaeology Database : Progress Report Spring 2014 2014 Reports (other academic/artistic)abstract This report provides an overview of the progress and results of the VR:KFI infrastructure projects 2007-7494 and (825-)2010-5976. It should be considered as a status report in an on-going long-term research infrastructure development project.
2.	Nilsson, R. Henrik, 1976, et al. (author) Mycobiome diversity: high-throughput sequencing and identification of fungi. 2019 In: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109 Research review (peer-reviewed)abstract Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
3.	Sanli, Kemal, et al. (author) Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities 2015 In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 6:1192 Journal article (peer-reviewed)abstract Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.
4.	Kõljalg, Urmas, et al. (author) A price tag on species 2022 In: Research Ideas and Outcomes_RIO. - : Pensoft Publishers. - 2367-7163. ; 8, s. 1-7 Journal article (peer-reviewed)abstract Species have intrinsic value but also partake in a long range of ecosystem services of major economic value to humans. These values have proved hard to quantify precisely, making it all too easy to dismiss them altogether. We outline the concept of the species stock market (SSM), a system to provide a unified basis for valuation of all living species. The SSM amalgamates digitized information from natural history collections, occurrence data, and molecular sequence databases to quantify our knowledge of each species from scientific, societal, and economic points of view. The conceptual trading system will necessarily be very unlike that of the regular stock market, but the looming biodiversity crisis implores us to finally put an open and transparent price tag on symbiosis, deforestation, and pollution
5.	Abarenkov, Kessy, et al. (author) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden) 2016 In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15 Journal article (peer-reviewed)abstract Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
6.	Nilsson, R. Henrik, 1976, et al. (author) Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms 2022 In: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 239-244 Journal article (peer-reviewed)abstract DNA sequencing efforts of environmental and other biological samples disclose unprecedented and largely untapped opportunities for advances in the taxonomy, ecology, and geographical distributions of our living world. To realise this potential, DNA-derived occurrence data (notably sequences with dates and coordinates) – much like traditional specimens and observations – need to be discoverable and interpretable through biodiversity data platforms. The Global Biodiversity Information Facility (GBIF) recently headed a community effort to assemble a set of guidelines for publishing DNA-derived data. These guidelines target the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. They cover a choice of terms using a controlled vocabulary, common pitfalls, and good practices, without going into platform-specific details. Our hope is that they will benefit anyone interested in better exposure of DNA-derived occurrence data through general biodiversity data platforms, including national biodiversity portals. This paper provides a brief rationale and an overview of the guidelines, an up-to-date version of which is maintained at https://doi.org/10.35035/doc-vf1a-nr22. User feedback and interaction are encouraged as new techniques and best practices emerge.
7.	Le Breton, Michael, 1986, et al. (author) Chlorine oxidation of VOCs at a semi-rural site in Beijing: significant chlorine liberation from ClNO2 and subsequent gas- and particle-phase Cl-VOC production 2018 In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 18:17, s. 13013-13030:18, s. 13013-13030 Journal article (peer-reviewed)abstract Nitryl chloride (ClNO2) accumulation at night acts as a significant reservoir for active chlorine and impacts the following day's photochemistry when the chlorine atom is liberated at sunrise. Here, we report simultaneous measurements of N2O5 and a suite of inorganic halogens including ClNO2 and reactions of chloride with volatile organic compounds (Cl-VOCs) in the gas and particle phases utilising the Filter Inlet for Gas and AEROsols time-of-flight chemical ionisation mass spectrometer (FIGAERO-ToF-CIMS) during an intensive measurement campaign 40 km northwest of Beijing in May and June 2016. A maximum mixing ratio of 2900 ppt of ClNO2 was observed with a mean campaign nighttime mixing ratio of 487 ppt, appearing to have an anthropogenic source supported by correlation with SO2, CO and benzene, which often persisted at high levels after sunrise until midday. This was attributed to such high mixing ratios persisting after numerous e-folding times of the photolytic lifetime enabling the chlorine atom production to reach 2.3 x 10(5) molecules cm(-3) from ClNO2 alone, peaking at 09:30 LT and up to 8.4 x 10(5) molecules cm(-3) when including the supporting inorganic halogen measurements. Cl-VOCs were observed in the particle and gas phases for the first time at high time resolution and illustrate how the iodide ToF-CIMS can detect unique markers of chlorine atom chemistry in ambient air from both biogenic and anthropogenic sources. Their presence and abundance can be explained via time series of their measured and steady-state calculated precursors, enabling the assessment of competing OH and chlorine atom oxidation via measurements of products from both of these mechanisms and their relative contribution to secondary organic aerosol (SOA) formation.
8.	Bengtsson-Palme, Johan, 1985, et al. (author) Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data 2013 In: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919 Journal article (peer-reviewed)abstract The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
9.	Posthumanistiska nyckelstexter 2012. - 1 Editorial collection (peer-reviewed)abstract Den här boken introducerar några viktiga författare på samtidsaktuella teoriområden. Donna Haraway, Karen Barad, Rosi Braidotti, Michel Callon, Gilles Deleuze, Félix Guattari, Michel Serres och Annemarie Mol presenteras i boken, som också innehåller översatta texter av dessa namn. Boken ger en bakgrund till och en överblick över ett område i intensiv teoriutveckling. Här presenteras den så kallade materiella, posthumana eller ontologiska vändningen. Här kartläggs grunderna för olika posthumanistiska förhållningssätt till de både mänskliga och icke-mänskliga (djur, miljö, teknik) krafterna i vår värld så som de begreppsliggjorts inom filosofi, feministisk teori, kulturstudier och samhällsvetenskapliga studier av naturvetenskap, medicin och teknik. Genom lästips och en omfattande litteraturlista öppnar boken för fortsatta studier och vidare diskussioner. Avslutningsvis finns också en omfattande ordlista med viktiga nyckelbegrepp som i sig ger en introduktion till ett heterogent forskningsfält. Boken riktar sig till studenter, doktorander och andra nyfikna forskare inom olika tvärvetenskapliga eller disciplinära former av humaniora och samhällsvetenskap.POSTHUMANISTISKA NYCKELTEXTER ger i de inledande kapitlen en överblick och en introduktion till posthumanistiska studier och till materiell-semiotik. Här behandlas tankeströmningar som rör det humanas natur, humanismens etik och humanvetenskapernas framtid. Boken ger en introduktion till det som inom genusvetenskap och tekniksociologi kommit att kallas den ontologiska vändningen mot de materiaaliteter och världsliga relationer som både gör och förgör oss. Här kartläggs grunderna för posthumanistiska förhållningssätt till de både mänskliga och icke-mänskliga (djur, miljö, teknik) dimensionerna av vår värld så som de begreppsliggjorts inom filosofi, feministisk teori, kulturstudier och sociala studier av vetenskap och teknik. POSTHUMANISTISKA NYCKELTEXTER erbjuder introduktioner till viktiga författare och översättningar av nyckeltexter skrivna av Donna Haraway, Karen Barad, Rosi Braidotti, Michel Callon, Gilles Deleuze med Felix Guattari, Michel Serres och Annemarie Mol. Boken innehåller även en omfattande ordlista med viktiga nyckelbegrepp som i sig ger en introduktion till ett mångfaldigt forskningsfält.
10.	Wurzbacher, Christian, 1980, et al. (author) Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds. 2017 In: The ISME journal. - : Springer Science and Business Media LLC. - 1751-7370 .- 1751-7362. ; 11:8, s. 1938-1941 Journal article (peer-reviewed)abstract In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.
11.	Tedersoo, Leho, et al. (author) Response to Comment on “Global diversity and geography of soil fungi” 2015 In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 349:6251 Journal article (other academic/artistic)abstract Schadt and Rosling (Technical Comment, 26 June 2015, p. 1438) argue that primer-template mismatches neglected the fungal class Archaeorhizomycetes in a global soil survey. Amplicon-based metabarcoding of nine barcode-primer pair combinations and polymerase chain reaction (PCR)–free shotgun metagenomics revealed that barcode and primer choice and PCR bias drive the diversity and composition of microorganisms in general, but the Archaeorhizomycetes were little affected in the global study. We urge that careful choice of DNA markers and primers is essential for ecological studies using high-throughput sequencing for identification.
12.	Petersson, Jesper, 1974, et al. (author) Off the record: The invisibility work of doctors in a patient-accessible electronic health record information service. 2021 In: Sociology of health & illness. - : Wiley. - 1467-9566 .- 0141-9889. ; 43:5, s. 1270-1285 Journal article (peer-reviewed)abstract In this article, we draw on Michael Lipsky's work on street-level bureaucrats and discretion to analyse a real case setting comprising an interview study of 30 Swedish doctors regarding their experiences of changes in clinical work following patients being given access to medical records information online. We introduce the notion of invisibility work to capture how doctors exercise discretion to preserve the invisibility of their work, in contrast to the well-established notion of invisible work, which denotes work made invisible by parties other than those performing it. We discuss three main forms of invisibility work in relation to records: omitting information, cryptic writing and parallel note writing. We argue that invisibility work is a way for doctors to resolve professional tensions arising from the political decision to provide patients with online access to record information. Although invisibility work is understood by doctors as a solution to government-initiated visibility, we highlight how it can create difficulties for doctors concerning accountability towards patients, peers and authorities.
13.	Unterseher, Martin, et al. (author) Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition 2018 In: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 17:4, s. 489-500 Journal article (peer-reviewed)abstract Multiple biotic and abiotic parameters influence the dynamics of individual fungal species and entire communities. Major drivers for tropical plant endophytes are undoubtedly seasonality, local habitat conditions and biogeography. However, host specialization and tissue preferences also contribute to the structuring of endophytic mycobiomes. To elucidate such specializations and preferences, we sampled two commercially important, unrelated plant species, Amorphophallus albispathus and Camellia sinensis (tea plant) simultaneously at close proximity. The mycobiomes of different tissue types were assessed with high-throughput amplicon sequencing of the internal transcribed spacer DNA region. Both plants hosted different fungal communities and varied in α- and β-diversity, despite their neighboring occurrence. However, the fungal assemblages of Amorphophallus leaflets shared taxa with the mycobiomes of tea leaves, thereby suggesting common driving forces for leaf-inhabiting fungi irrespective of host plant identity. The mycobiome composition and diversity of tea leaves was clearly driven by leaf age. We suggest that the very youngest tea leaves are colonized by stochastic processes, while mycobiomes of old leaves are rather similar as the result of progressive succession. The biodiversity of fungi associated with A. albispathus was characterized by a large number of unclassified OTUs (at genus and species level) and by tissue-specific composition.This study is the first cultivation-independent high-throughput assessment of fungal biodiversity of an Amorphophallus species, and additionally expands the knowledge base on fungi associated with tea plants.
14.	Guo, Y. D., et al. (author) Identification of highly oxygenated organic molecules and their role in aerosol formation in the reaction of limonene with nitrate radical 2022 In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 22:17, s. 11323-11346 Journal article (peer-reviewed)abstract Nighttime NO3-initiated oxidation of biogenic volatile organic compounds (BVOCs) such as monoterpenes is important for the atmospheric formation and growth of secondary organic aerosol (SOA), which has significant impact on climate, air quality, and human health. In such SOA formation and growth, highly oxygenated organic molecules (HOM) may be crucial, but their formation pathways and role in aerosol formation have yet to be clarified. Among monoterpenes, limonene is of particular interest for its high emission globally and high SOA yield. In this work, HOM formation in the reaction of limonene with nitrate radical (NO3) was investigated in the SAPHIR chamber (Simulation of Atmospheric PHotochemistry In a large Reaction chamber). About 280 HOM products were identified, grouped into 19 monomer families, 11 dimer families, and 3 trimer families. Both closed-shell products and open-shell peroxy radicals (RO2 center dot) 2 were observed, and many of them have not been reported previously. Monomers and dimers accounted for 47% and 47% of HOM concentrations, respectively, with trimers making up the remaining 6 %. In the most abundant monomer families, C10H15-17NO6-14, carbonyl products outnumbered hydroxyl products, indicating the importance of RO2 center dot termination by unimolecular dissociation. Both RO2 center dot autoxidation and alkoxy-peroxy pathways were found to be important processes leading to HOM. Time-dependent concentration profiles of monomer products containing nitrogen showed mainly second-generation formation patterns. Dimers were likely formed via the accretion reaction of two monomer RO2 center dot , and HOM-trimers via the accretion reaction between monomer RO2 center dot and dimer RO2 center dot. Trimers are suggested to play an important role in new particle formation (NPF) observed in our experiment. A HOM yield of 1.5%(+1.7%)(-0.7%) was estimated considering only first-generation products. SOA mass growth could be reasonably explained by HOM condensation on particles assuming irreversible uptake of ultra-low volatility organic compounds (ULVOCs), extremely low volatility organic compounds (ELVOCs), and low volatility organic compounds (LVOCs). This work provides evidence for the important role of HOM formed via the limonene +NO3 reaction in NPF and growth of SOA particles.
15.	Retter, Alice, et al. (author) Exploring the taxonomic composition of two fungal communities on the Swedish west coast through metabarcoding 2019 In: Biodiversity Data Journal. - 1314-2828 .- 1314-2836. ; 7 Journal article (peer-reviewed)abstract Background Fungi are heterotrophic, unicellular or filamentous organisms that exhibit a wide range of different lifestyles as, e.g., symbionts, parasites, and saprotrophs. Mycologists have traditionally considered fungi to be a nearly exclusively terrestrial group of organisms, but it is now known that fungi have a significant presence in aquatic environments as well. We know little about most fungi in limnic and marine systems, including aspects of their taxonomy, ecology, and geographic distribution. The present study seeks to improve our knowledge of fungi in the marine environment. The fungal communities of two coastal marine environments of the Kattegat sea, Sweden, were explored with metabarcoding techniques using the nuclear ribosomal internal transcribed spacer 2 (ITS2) metabarcode. Our data add new information to the current picture of fungal community composition in benthic and coastal habitats in Northern Europe. New information The dataset describes the number of operational taxonomic units (OTUs) and their taxonomic affiliations in two littoral gradients sampled on the Swedish west coast, Gothenburg municipality. Our data include basic diversity indices as well as chemical and edaphic sediment/soil parameters of the sampling sites. From the sites, 3470 and 4315 fungal OTUs, respectively, were recovered. The number of reads were 673,711 and 779,899, respectively, after quality filtering. Within the benthic sites, more than 80% of the sequences could not be classified taxonomically. The phylum composition of the classifiable sequences was dominated in both localities by Dikarya, which made up around 33% of the OTUs. Within Dikarya, Ascomycota was the dominant phylum. Guild assignment failed for more than half of the classifiable OTUs, with undefined saprotrophs being the most common resolved guild. This guild classification was slightly more common in the ocean sediment samples than in the terrestrial ones. Our metadata indicated that ocean sites contain organisms at a lower trophic level and that there are predominantly endophytic, parasitic, and pathogenic fungi in the marine environments. This hints at the presence of interesting and currently poorly understood fungus-driven ecological processes. It is also clear from our results that a very large number of marine fungi are in urgent need of taxonomic study and formal description.
16.	Nilsson, R. Henrik, 1976, et al. (author) The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. 2019 In: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 47:D1 Journal article (peer-reviewed)abstract UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer(ITS) region-and offers all ∼1 000000 public fungal ITS sequences for reference. These are clustered into ∼459000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
17.	Jayasiri, Subashini C., et al. (author) The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts 2015 In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18 Journal article (peer-reviewed)abstract Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
18.	Wang, Y. J., et al. (author) The formation of nitro-aromatic compounds under high NOx and anthropogenic VOC conditions in urban Beijing, China 2019 In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 19:11, s. 7649-7665 Journal article (peer-reviewed)abstract Nitro-aromatic compounds (NACs), as important contributors to the light absorption by brown carbon, have been widely observed in various ambient atmospheres; however, their formation in the urban atmosphere was little studied. In this work, we report an intensive field study of NACs in summer 2016 at an urban Beijing site, characterized by both high-NO(x)and anthropogenic VOC dominated conditions. We investigated the factors that influence NAC formation (e.g., NO2, VOC precursors, RH and photolysis) through quantification of eight NACs, along with major components in fine particulate matter, selected volatile organic compounds, and gases. The average total concentration of the quantified NACs was 6.63 ng m(-3), higher than those reported in other summertime studies (0.14-6.44 ng m(-3)). 4-Nitrophenol (4NP, 32.4 %) and 4-nitrocatechol (4NC, 28.5 %) were the top two most abundant NACs, followed by methyl-nitrocatechol (MNC), methyl-nitrophenol (MNP), and dimethyl-nitrophenol (DMNP). The oxidation of toluene and benzene in the presence of NOx was found to be a more dominant source of NACs than primary biomass burning emissions. The NO2 concentration level was found to be an important factor influencing the secondary formation of NACs. A transition from low- to high-NOx regimes coincided with a shift from organic- to inorganic-dominated oxidation products. The transition thresholds were NO2 similar to 20 ppb for daytime and NO2 similar to 25 ppb for nighttime conditions. Under low-NOx conditions, NACs increased with NO2, while the NO3 concentrations and (NO3-)/NACs ratios were lower, implying organic-dominated products. Under high-NOx conditions, NAC concentrations did not further increase with NO2, while the NO3- concentrations and (NO3-)/NACs ratios showed increasing trends, signaling a shift from organic- to inorganic-dominated products. Nighttime enhancements were observed for 3M4NC and 4M5NC, while daytime enhancements were noted for 4NP, 2M4NP, and DMNP, indicating different formation pathways for these two groups of NACs. Our analysis suggested that the aqueous-phase oxidation was likely the major formation pathway of 4M5NC and 3M5NC, while photo-oxidation of toluene and benzene in the presence of NO2 could be more important for the formation of nitrophenol and its derivatives. Using the (3M4NC+4M5NC) / 4NP ratios as an indicator of the relative contribution of aqueous-phase and gas-phase oxidation pathways to NAC formation, we observed that the relative contribution of aqueous-phase pathways increased at elevated ambient RH and remained constant at RH > 30 %. We also found that the concentrations of VOC precursors (e.g., toluene and benzene) and aerosol surface area acted as important factors in promoting NAC formation, and photolysis as an important loss pathway for nitrophenols.
19.	Cafaro, Philip, et al. (author) Fewer people would help preserve biodiversity: A response to Hughes et al. (2023) 2023 In: Biological Conservation. - 0006-3207. ; 282 Journal article (peer-reviewed)abstract “Smaller human populations are neither a necessary nor sufficient condition for biodiversity conservation,” according to Alice Hughes and colleagues. We agree that reducing human numbers is not sufficient for preserving biodiversity; whether it’s necessary depends on how high we set the bar for successful conservation. If we hope to preserve robust populations of most of the world’s remaining wild species and their habitats, the evidence suggests human populations will have to be considerably reduced.
20.	Zanne, Amy E, et al. (author) Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. 2020 In: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433 Journal article (peer-reviewed)abstract Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
21.	Ritter, Camila, et al. (author) High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia. 2018 In: PeerJ. - : PeerJ. - 2167-8359. ; 6 Journal article (peer-reviewed)abstract Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties.We used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis.Soil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and eukaryotes were more separated among habitat types (terra-firme, várzea, igapó and campina) than between substrates (soil and litter).In spite of the limited sampling (four localities, 39 plots), our results provide a broad-scale view of the physical and chemical correlations of soil and litter biodiversity in a longitudinal transect across the world's largest rainforest. Our methods help to understand links between soil properties, OTU diversity patterns, and community composition and turnover. The lack of strong correlation between OTU diversity in litter and in soil suggests independence of diversity drives of these substrates and highlights the importance of including both measures in biodiversity assessments. Massive sequencing of soil and litter samples holds the potential to complement traditional biological inventories in advancing our understanding of the factors affecting tropical diversity.
22.	Hartmann, Martin, et al. (author) Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests 2012 In: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 6:12, s. 2199-2218 Journal article (peer-reviewed)abstract Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting.
23.	Mohr, Claudia, et al. (author) Molecular identification of organic vapors driving atmospheric nanoparticle growth 2019 In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10 Journal article (peer-reviewed)abstract Particles formed in the atmosphere via nucleation provide about half the number of atmospheric cloud condensation nuclei, but in many locations, this process is limited by the growth of the newly formed particles. That growth is often via condensation of organic vapors. Identification of these vapors and their sources is thus fundamental for simulating changes to aerosol-cloud interactions, which are one of the most uncertain aspects of anthropogenic climate forcing. Here we present direct molecular-level observations of a distribution of organic vapors in a forested environment that can explain simultaneously observed atmospheric nanoparticle growth from 3 to 50nm. Furthermore, the volatility distribution of these vapors is sufficient to explain nanoparticle growth without invoking particle-phase processes. The agreement between observed mass growth, and the growth predicted from the observed mass of condensing vapors in a forested environment thus represents an important step forward in the characterization of atmospheric particle growth.
24.	Andersson, Erik, et al. (author) Ambio fit for the 2020s 2022 In: Ambio. - : Springer Nature. - 0044-7447 .- 1654-7209. ; 51:5, s. 1091-1093 Journal article (peer-reviewed)
25.	Falk Erhag, Hanna, et al. (author) A Multidisciplinary Approach to Capability in Age and Ageing 2022 Book (other academic/artistic)abstract This open access book provides insight on how to interpret capability in ageing – one’s individual ability to perform actions in order to reach goals one has reason to value – from a multidisciplinary approach. With for the first time in history there being more people in the world aged 60 years and over than there are children below the age of 5, the book describes this demographic trends as well as the large global challenges and important societal implications this will have such as a worldwide increase in the number of persons affected with dementia, and in the ratio of retired persons to those still in the labor market. Through contributions from many different research areas, it discussed how capability depends on interactions between the individual (e.g. health, genetics, personality, intellectual capacity), environment (e.g. family, friends, home, work place), and society (e.g. political decisions, ageism, historical period). The final chapter by the editors summarizes the differences and similarities in these contributions. As such this book provides an interesting read for students, teachers and researchers at different levels and from different fields interested in capability and multidisciplinary research.
26.	Farewell, Anne, 1961 (author) Rising to the Top: Promoting Deeper Learning in the Laboratory 2018 In: National Center for Case Study Teaching in Science. Book chapter (peer-reviewed)abstract Inquiry-based labs differ from cookbook labs in that inquiry-based labs contain an element of experimentation. A cookbook lab can be performed by a student without understanding any of the theory connected with the exercise whereas inquiry-based labs require a degree of conceptual knowledge for a student to perform the lab. Inquiry-based labs also strengthen and deepen students understanding of topics discussed in lectures or reading assignments. There are many variations and degrees of inquiry in these labs ranging from a lab that is entirely designed by the students to those that include small questions requiring that the students predict the outcomes of a lab or fill in missing information (guided inquiry). A simple specific example of a cookbook lab would be instructing students to measure volume changes between ice and liquid water. The students would be given step by step instructions to follow and would not need to apply any conceptual knowledge. An inquiry based lab on the same topic would allow the students to design their own experiment to discover how the volume of liquid water differs from that of ice. One goal of this activity is to introduce inquiry-based lab design. Beyond lab design, lab supervision is crucial to encouraging students to use their conceptual knowledge when doing a practical lab. Lab assistants or teachers who are involved in the lab can use student questions to encourage deeper understanding. This case study includes a role-play exercise for this skill. This case study has been designed to be used in science education courses for both graduate student laboratory assistants and lecturers or professors in natural sciences at the university or college level. It includes discussion and role-play of a hypothetical laboratory. No specific knowledge of biology or chemistry is needed beyond high school level to complete this task, though knowledge of the existence of microorganisms (yeast) and proteins is assumed. In addition, this activity is suitable for participants with little or no pedagogics training.
27.	Gallego-Urrea, Julian A., 1977, et al. (author) Analysis of behavior and toxicity to Pseudokirchneriella subcapitata of Titanium Dioxide nanoparticles 2009 In: 4th International Conference on the Environmental Effects of Nanoparticles and Nanomaterials. Vienna, Austria, September 2009. Conference paper (other academic/artistic)
28.	Dodig Crnkovic, Gordana, 1955 (author) Natural Computational Architectures for Cognitive Info-Communication 2021 Journal article (other academic/artistic)abstract Recent comprehensive overview of 40 years of research in cognitive architectures, (Kotseruba and Tsotsos 2020), evaluates modelling of the core cognitive abilities in humans, but only marginally addresses biologically plausible approaches based on natural computation. This mini review presents a set of perspectives and approaches which have shaped the development of biologically inspired computational models in the recent past that can lead to the development of biologically more realistic cognitive architectures. For describing continuum of natural cognitive architectures, from basal cellular to human-level cognition, we use evolutionary info-computational framework, where natural/ physical/ morphological computation leads to evolution of increasingly complex cognitive systems. Forty years ago, when the first cognitive architectures have been proposed, understanding of cognition, embodiment and evolution was different. So was the state of the art of information physics, bioinformatics, information chemistry, computational neuroscience, complexity theory, selforganization, theory of evolution, information and computation. Novel developments support a constructive interdisciplinary framework for cognitive architectures in the context of computing nature, where interactions between constituents at different levels of organization lead to complexification of agency and increased cognitive capacities. We identify several important research questions for further investigation that can increase understanding of cognition in nature and inspire new developments of cognitive technologies. Recently, basal cell cognition attracted a lot of interest for its possible applications in medicine, new computing technologies, as well as micro- and nanorobotics. Bio-cognition of cells connected into tissues/organs, and organisms with the group (social) levels of information processing provides insights into cognition mechanisms that can support the development of new AI platforms and cognitive robotics.
29.	Amundin, Mats, et al. (author) A proposal to use distributional models to analyse dolphin vocalisation 2017 In: Proceedings of the 1st International Workshop on Vocal Interactivity in-and-between Humans, Animals and Robots, VIHAR 2017. - 9782956202905 ; , s. 31-32 Conference paper (peer-reviewed)abstract This paper gives a brief introduction to the starting points of an experimental project to study dolphin communicative behaviour using distributional semantics, with methods implemented for the large scale study of human language.
30.	Wu, R. R., et al. (author) Molecular composition and volatility of multi-generation products formed from isoprene oxidation by nitrate radical 2021 In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 21:13, s. 10799-10824 Journal article (peer-reviewed)abstract Isoprene oxidation by nitrate radical (NO3) is a potentially important source of secondary organic aerosol (SOA). It is suggested that the second or later-generation products are the more substantial contributors to SOA. However, there are few studies investigating the multi-generation chemistry of isoprene-NO3 reaction, and information about the volatility of different isoprene nitrates, which is essential to evaluate their potential to form SOA and determine their atmospheric fate, is rare. In this work, we studied the reaction between isoprene and NO3 in the SAPHIR chamber (Julich) under near-atmospheric conditions. Various oxidation products were measured by a high-resolution time-offlight chemical ionization mass spectrometer using Br as the reagent ion. Most of the products detected are organic nitrates, and they are grouped into monomers (C-4 and C-5 products) and dimers (C-10 products) with 1-3 nitrate groups according to their chemical composition. Most of the observed products match expected termination products observed in previous studies, but some compounds such as monomers and dimers with three nitrogen atoms were rarely reported in the literature as gas-phase products from isoprene oxidation by NO3. Possible formation mechanisms for these compounds are proposed. The multi-generation chemistry of isoprene and NO3 is characterized by taking advantage of the time behavior of different products. In addition, the vapor pressures of diverse isoprene nitrates are calculated by different parametrization methods. An estimation of the vapor pressure is also derived from their condensation behavior. According to our results, isoprene monomers belong to intermediate-volatility or semi-volatile organic compounds and thus have little effect on SOA formation. In contrast, the dimers are expected to have low or extremely low volatility, indicating that they are potentially substantial contributors to SOA. However, the monomers constitute 80% of the total explained signals on average, while the dimers contribute less than 2 %, suggesting that the contribution of isoprene NO3 oxidation to SOA by condensation should be low under atmospheric conditions. We expect a SOA mass yield of about 5% from the wall-loss- and dilution-corrected mass concentrations, assuming that all of the isoprene dimers in the low- or extremely low-volatility organic compound (LVOC or ELVOC) range will condense completely.
31.	Okenwa-Emegwa, Leah, 1973-, et al. (author) Lessons Learned from Teaching Nursing Students about Equality, Equity, Human Rights, and Forced Migration through Roleplay in an Inclusive Classroom 2020 In: Sustainability. - Basel : MDPI. - 2071-1050. ; 12:17 Journal article (peer-reviewed)abstract Inclusive education, sustainable development, and core nursing values all share common goals of promoting diversity, equity, social justice, and inclusion. However, prevailing norms of exclusion may shape health systems and healthcare workers’ attitudes and threaten inclusive patient care. Ongoing global conflicts and violence resulting in growing patient diversity in terms of ethnicity and migration status have led to questions regarding healthcare systems’ preparedness for inclusive nursing. Diversity-rich classrooms and collaborative learning methods, like role play, are inclusive strategies that may be useful in nursing education. The purpose of this paper is to present lessons learned from incorporating role play about forced migration in inclusive nursing classrooms. Various diversity-rich nursing student groups participated in a two-hour role play on forced migration facilitated by youth volunteers from the Swedish Red Cross Society between 2017 and 2019. This study is based on the amplified analysis of qualitative data materials, in the form of notes and summarized feedbacks, obtained from evaluating the role play as a teaching-learning activity. Three themes were identified, specifically, knowledge exchange, existential reflections, and empathy evoked. Findings suggest that working collaboratively in an inclusive environment may improve nursing students’ understanding of the vulnerabilities created by forced migration and to be better prepared for promoting social justice for this group in health care settings.
32.	Tedersoo, Leho, et al. (author) Novel soil-inhabiting clades fill gaps in the fungal tree of life 2017 In: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5 Journal article (peer-reviewed)abstract Background - Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. Results - We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. Conclusions - This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
33.	Sigvald, Roland, et al. (author) Molecular identification of bloodmeals and species composition in Culicoides biting midges 2013 In: Medical and Veterinary Entomology. - : Wiley. - 0269-283X .- 1365-2915. ; 27, s. 104-112 Journal article (peer-reviewed)abstract Investigations of host preferences in haematophagous insects, including Culicoides biting midges (Diptera: Ceratopogonidae), are critical in order to assess transmission routes of vector-borne diseases. In this study, we collected and morphologically identified 164 blood-engorged Culicoides females caught in both light traps and permanent 12-m high suction traps during 20082010 in Sweden. Molecular analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene in the biting midges was performed to verify species classification, discern phylogenetic relationships and uncover possible cryptic species. Bloodmeal analysis using universal vertebrate cytochrome b primers revealed a clear distinction in host selection between mammalophilic and ornithophilic Culicoides species. Host sequences found matches in horse (n = 59), sheep (n = 39), cattle (n = 26), Eurasian elk (n = 1) and 10 different bird species (n = 18). We identified 15 Culicoides species previously recorded in Scandinavia and four additional species haplotypes that were distinctly different from the described species. All ornithophilic individuals (n = 23) were caught exclusively in the suction traps, as were, interestingly, almost all mammalophilic species (n = 41), indicating that many biting midge species may be able to cover long distances after completing a bloodmeal. These results add new information on the composition of Culicoides species and their host preferences and their potential long-distance dispersal while blood-engorged.
34.	Elliott, David R., et al. (author) Bacterial and Fungal Communities in a Degraded Ombrotrophic Peatland Undergoing Natural and Managed Re-Vegetation 2015 In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5 Journal article (peer-reviewed)abstract The UK hosts 15–19% of global upland ombrotrophic (rain fed) peatlands that are estimated to store 3.2 billion tonnes of carbon and represent a critical upland habitat with regard to biodiversity and ecosystem services provision. Net production is dependent on an imbalance between growth of peat-forming Sphagnum mosses and microbial decomposition by microorganisms that are limited by cold, acidic, and anaerobic conditions. In the Southern Pennines, land-use change, drainage, and over 200 years of anthropogenic N and heavy metal deposition have contributed to severe peatland degradation manifested as a loss of vegetation leaving bare peat susceptible to erosion and deep gullying. A restoration programme designed to regain peat hydrology, stability and functionality has involved re-vegetation through nurse grass, dwarf shrub and Sphagnum re-introduction. Our aim was to characterise bacterial and fungal communities, via high-throughput rRNA gene sequencing, in the surface acrotelm/mesotelm of degraded bare peat, long-term stable vegetated peat, and natural and managed restorations. Compared to long-term vegetated areas the bare peat microbiome had significantly higher levels of oligotrophic marker phyla (Acidobacteria, Verrucomicrobia, TM6) and lower Bacteroidetes and Actinobacteria, together with much higher ligninolytic Basidiomycota. Fewer distinct microbial sequences and significantly fewer cultivable microbes were detected in bare peat compared to other areas. Microbial community structure was linked to restoration activity and correlated with soil edaphic variables (e.g. moisture and heavy metals). Although rapid community changes were evident following restoration activity, restored bare peat did not approach a similar microbial community structure to non-eroded areas even after 25 years, which may be related to the stabilisation of historic deposited heavy metals pollution in long-term stable areas. These primary findings are discussed in relation to bare peat oligotrophy, re-vegetation recalcitrance, rhizosphere-microbe-soil interactions, C, N and P cycling, trajectory of restoration, and ecosystem service implications for peatland restoration.
35.	Contemporary Natural Philosophy and Philosophies - Part 1 2019 Editorial collection (peer-reviewed)abstract The book is open acces and can be downloaded from: https://www.mdpi.com/books/pdfview/book/1331
36.	Mamontov, Eugen, 1955, et al. (author) Mathematical models and numerical simulation results for oncogeny: Specific problems and different tools for various user communities 2008 In: Abstracts Booklet. CancerSim2008 — Euroconference on Modelling and Simulation of Cancer Growth and Therapy, 19-21 May, Turin, Italy; N. Bellomo and G. Forni (Chairmen) http://www.cancersim2008.org. Conference paper (peer-reviewed)
37.	Némethy, Sándor, 1955, et al. (author) Collection, cultivation and processing of medical plants, herbs and spices in the Balaton Ecomuseum – herbal medicine as intangible cultural heritage 2020 In: Ecocycles. - : Ecocycles. - 2416-2140. ; 6:1, s. 52-87 Journal article (peer-reviewed)abstract The Balaton Ecomuseum, which is being continuously developed since 2017, will have a holistic approach, where the objectives of the ecomuseum embrace the whole cultural landscape of Lake Balaton as one unit with several thematic routes in one system and shall not be restricted to one particular subject area or a part of local heritage. One of these thematic routes is the recently developingHerbs and Spices Network, led by Zánka Herb Valley Visitor and Training Centre based on the collection, cultivation and processing of medicinal plants, herbs and spices. The place of herbs and spices in the diet needs to be considered in reviewing health benefits, including definitions of the food category and the way in which benefits might be viewed, and therefore researched.Here we describe the already established system of the Zánka Herb Valley Visitor and Training Centre, the potential of the Balaton Region in the development of herbal medicine illustrated by the scientific presentation of the 30 most collected herbs in the region and examples of other herbal centres, which are intended to become a part of the network. Herbalmedicine, as an important part of the intangible cultural heritage, with hundreds of years old recipes for herbal concoctionshas been known since ancient times before science related to modern medicine developed and continues to be used for generationsuntil now. Furthermore, the medical effects of many agricultural crops should be better understood, such as the grapevine, which is being investigated for its medical compounds or the medicinal properties of other fruits and vegetables not sufficiently known to the general public. In this study we present a new system of the culture and interactive education of the collection, cultivation and use of medicinal plants, herbs and spices applying a learning by doing approach and a network embracing the whole area of the Balaton Ecomuseum.
38.	Hallquist, Mattias, 1969, et al. (author) Photochemical smog in China: scientific challenges and implications for air-quality policies 2016 In: National Science Review. - : Oxford University Press (OUP). - 2095-5138 .- 2053-714X. ; 3:4, s. 401-403 Journal article (peer-reviewed)abstract In large areas of China severe air pollution events pose a significant threat to human health, ecosystems and climate. Current reduction of primary emissions will also affect secondary pollutants such as ozone (O3) and particulate matter (PM), but the magnitude of the effects is uncertain. Major scientific challenges are related to the formation of O3 and secondary particulate matter including Secondary Organic Aerosols (SOA). Large uncertainties also remain regarding the interactions of soot, SOA and O3 under the influence of different SO2, NOX and VOC concentrations. To improve the understanding of these secondary atmospheric interactions in China, scientific areas of central importance for photochemically induced air pollutants have been identified. In addition to the scientific challenges, results from research need to be synthesized across several disciplines and communicated to stakeholders affected by air pollution and to policy makers responsible for developing abatement strategies. Development of these science-policy interactions can benefit from experience gained under the UN ECE Convention on Long Range Transboundary Air Pollution (LRTAP)
39.	Li, J. J., et al. (author) Characterization of Aerosol Aging Potentials at Suburban Sites in Northern and Southern China Utilizing a Potential Aerosol Mass (Go:PAM) Reactor and an Aerosol Mass Spectrometer 2019 In: Journal of Geophysical Research-Atmospheres. - : American Geophysical Union (AGU). - 2169-897X .- 2169-8996. ; 124:10, s. 5629-5649 Journal article (peer-reviewed)abstract Aerosol mass spectrometry was used to characterize submicron aerosols before and after aging in a Gothenburg Potential Aerosol Mass (Go:PAM) reactor at two suburban sites in China, one in northern China at Changping (CP), Beijing, and a second in southern China at Hong Kong (HK). Organic aerosol (OA) dominated in the ambient nonrefractory particulate matter <1m (NR-PM1) for both CP (42-71%) and HK (43-61%), with a large contribution from secondary OA factors that were semivolatile oxygenated (SVOOA) and low-volatility oxygenated (LVOOA). Under constant OH exposure, OA enhancement (78-98%) dominated the NR-PM1 mass increment at both sites, while nitrate was enhanced the most among the inorganic species (7-9%). Overall, the CP site exhibited higher OA oxidation potential and more enhancement of SVOOA than LVOOA (7.5 vs. 2.7g/m(3)), but the reverse was observed in HK (0.8 vs. 2.6g/m(3)). In CP, more enhancement of the less oxygenated SVOOA suggests that aerosol aging was more sensitive to the abundant locally emitted primary OA and volatile organic compound precursors. On the contrary, the more formation of the highly oxidized LVOOA in HK indicates that aerosol aging mainly escalated the degree of oxygenation of OA as ambient aerosol was already quite aged and there was a lack of volatile organic compound precursors. The comparative measurements using the same oxidation system reveal distinct key factors and mechanisms that influence secondary aerosol formation in two suburban locations in China, providing scientific insights to assist formulation of location-specific mitigation measures of secondary pollution. Plain Language Summary Atmospheric submicron particles have significant impacts on the climate and human health. A large part of these particles are formed secondarily through successive aging of primary emissions. To study such aging processes, we used a reactor that can provide highly oxidizing conditions to simulate the oxidation of ambient aerosols at accelerated rates. An online mass spectrometer was connected after the reactor to measure changes in aerosol mass concentration and chemical composition between the ambient samples and the oxidized ones. We presented the first comparative measurements of the aging potentials of ambient aerosols in two suburban sites in northern and southern China (Changping District in Beijing, and Hong Kong). Results showed that generally aerosols at the Changping site had higher aging potentials after passing through the oxidation reactor, probably due to more local emissions of precursors, while air masses in Hong Kong were already in a higher oxidation state with lower aging potentials, mainly because of strong impacts from long-range transported pollution sources. Distinct aerosol aging pathways related to different ambient precursors were observed at the two sites. Understanding of the different characteristics of aerosol aging processes can lead to advances in air quality modeling and pollution management.
40.	Salvador, Christian Mark, 1989, et al. (author) Ambient nitro-aromatic compounds - biomass burning versus secondary formation in rural China 2021 In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 21:3, s. 1389-1406 Journal article (peer-reviewed)abstract Nitro-aromatic compounds (NACs) were measured hourly at a rural site in China during wintertime to monitor the changes due to local and regional impacts of biomass burning (BB). Concurrent and continuous measurements of the concentrations of 16 NACs in the gas and particle phases were performed with a time-of-flight chemical ionization mass spectrometer (CIMS) equipped with a Filter Inlet for Gases and AEROsols (FIGAERO) unit using iodide as the reagent ion. NACs accounted for <2 % of the mass concentration of organic matter (OM) and total particulate matter (PM), but the total particle mass concentrations of these compounds can reach as high as 1000 ng m(-3) (299 ng m(-3) avg), suggesting that they may contribute significantly to the radiative forcing effects of atmospheric particles. Levels of gas-phase NACs were highest during the daytime (15:00-16:00 local time, LT), with a smaller night-time peak around 20:00LT. Box-model simulations showed that this occurred because the rate of NAC production from gas-phase sources exceeded the rate of loss, which occurred mainly via the OH reaction and to a lesser degree via photolysis. Data gathered during extended periods with high contributions from primary BB sources (resulting in 40 %-60 % increases in NAC concentrations) were used to characterize individual NACs with respect to gas-particle partitioning and the contributions of regional secondary processes (i.e. photochemical smog). On days without extensive BB, secondary formation was the dominant source of NACs, and NAC levels correlated strongly with the ambient ozone concentration. Analyses of individual NACs in the regionally aged plumes sampled on these days allowed precursors such as phenol and catechol to be linked to their NAC derivatives (i.e. nitrophenol and nitrocatechol). Correlation analysis using the high time resolution data and box-model simulation results constrained the relationships between these compounds and demonstrated the contribution of secondary formation processes. Furthermore, 13 of 16 NACS were classified according to primary or secondary formation process. Primary emission was the dominant source (accounting for 60 %-70 % of the measured concentrations) of 5 of the 16 studied NACs, but secondary formation was also a significant source. Photochemical smog thus has important effects on brown carbon levels even during wintertime periods dominated by primary air pollution in rural China.
41.	Unraveling the logics of landscape 2014 Editorial collection (other academic/artistic)abstract Despite conceptual oscillations through times, the concept of landscape remains highly subjective, whereupon unraveling its 'logics' opens up to a plurality of interpretations. Accordingly, by focusing on the interconnections present in the non-haphazard production of landscape, this publication elaborates on how the rural landscape is valued, monitored, changed, harbored, used and misused, be it through actions, representations or metaphors. This book covers a broad range of topics, with contributions from scholars from more than 30 countries.
42.	Sonesten, Lars (author) Miljöövervakningen av Sveriges sjöar och vattendrag : Representativiteten av den kontrollerande miljöövervakningen 2013 Reports (other academic/artistic)abstract Samtliga ytvattenkategorier inom ett vattendistrikt ska omfattas av övervakningsprogram inklusive övervakningsnät för kontrollerande övervakning som upprättas enligt kap. 7 VFF. En översyn av hur representativt Sveriges kontrollerade övervakningsnät är har tidigare inte kunnat utföras på grund av omfattande kvalitetsbrister i länsstyrelserna och vattenmyndigheternas datasystem VISS (VattenInformationsSystem Sverige). Kvaliteten på informationen i VISS har under senare år genomgått en omfattande kvalitetssäkring, vilket har gett förutsättningarna för att nu kunna genomföra den sammanställning och översyn över den svenska miljöövervakningen av sjöar och vattendrag. Denna översyn har varit starkt önskad under flera år, då det finns ett stort behov av att se över och analysera hur ett representativt samordnat kontrollerande övervakningsprogram skulle kunna se ut. Översynen sker mot bakgrund av den samlade vatten övervakning som bedrivs i Sverige, bland annat för att optimera befintlig övervakning och att kunna förstärka den där brister har identifierats. Arbetet är också viktigt för att säkerställa att kommande rapporteringar såväl internationellt som nationellt blir så bra som möjligt.Uppdraget för projektet Representativ kontrollerande miljöövervakning (RepKöp) syftar till att ta fram ett förslag på hur ett representativt kontrollerande övervakningsprogram med avseende på (vattentyper), kvalitetsfaktorer och statusklasser bör se ut på nationell och distriktsnivå i Sverige. Förslaget tas fram mot bakgrund av den samlade vattenövervakningen som bedrivs i Sverige idag och mot bakgrund av vad behövs för att uppfylla vattendirektivets krav på kontrollerande övervakning av vattenförekomster.Resultaten från översynen är tänkta att dels fungera som underlag för att underlätta Havs och vattenmyndighetens och Vattenmyndigheternas arbete inför rapporteringen 2012, men framför allt ska projektet ge underlag för att ta fram optimerade övervakningsprogram för sjöar och vattendrag till en långsiktig plan med en första anhalt 2016. För att RepKÖP ska få praktisk betydelse i övervakningsSverige skall projektet resultera i ett underlag för framtida revision av befintliga övervakningsprogram för respektive distrikt.Arbetet inom RepKöp är uppdelat i flera delar, vilka tillsammans ska fungera som vägledning till:• Vattenförvaltningens arbete med kontrollerande övervakning• Upplägg av nationell och regional miljöövervakningMålgruppen för arbetet är i första hand:• Vattenmyndigheter• Länsstyrelserna• Naturvårdsverket• Havs och vattenmyndigheten• Datavärdar och utförare av miljöövervakningFöreliggande rapport är en sammanställning och analys av miljöövervakningen av svenska sjöar och vattendrag så som de beskrevs i VISS vid datauttaget för sjöar i oktober 2011 och vattendrag i maj 2012. Sammanställningen av informationen från VISS har initierat en hel del korrigeringar i systemet, men tyvärr har det inte av praktiska skäl varit möjligt att ta hänsyn till dessa i arbetet. Man skall vara medveten om att VISS är en levande databas som ständigt uppdateras och korrigeras, vilket gör att endast en ”ögonblicksbild” kan analyseras. Detta gör att när analysen är färdig har verkligheten med stor sannolikhet redan till viss del hunnit förändrats.
43.	Tedersoo, Leho, et al. (author) Standardizing metadata and taxonomic identification in metabarcoding studies 2015 In: GigaScience. - : Oxford University Press (OUP). - 2047-217X .- 2047-217X. ; 4 Journal article (peer-reviewed)abstract High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.
44.	Le Breton, Michael, 1986, et al. (author) Online gas- and particle-phase measurements of organosulfates, organosulfonates and nitrooxy organosulfates in Beijing utilizing a FIGAERO ToF-CIMS 2018 In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 18:14, s. 10355-10371 Journal article (peer-reviewed)abstract A time-of-flight chemical ionization mass spectrometer (CIMS) utilizing the Filter Inlet for Gas and Aerosol (FIGAERO) was deployed at a regional site 40 km north-west of Beijing and successfully identified and measured 17 sulfur-containing organics (SCOs are organo/nitrooxy organosulfates and sulfonates) with biogenic and anthropogenic precursors. The SCOs were quantified using laboratory-synthesized standards of lactic acid sulfate and nitrophenol organosulfate (NP OS). The variation in field observations was confirmed by comparison to offline measurement techniques (orbitrap and high-performance liquid chromatography, HPLC) using daily averages. The mean total (of the 17 identified by CIMS) SCO particle mass concentration was 210 +/- 110 ng m(-3) and had a maximum of 540 ng m(-3), although it contributed to only 2 +/- 1% of the organic aerosol (OA). The CIMS identified a persistent gas-phase presence of SCOs in the ambient air, which was further supported by separate vapour-pressure measurements of NP OS by a Knudsen Effusion Mass Spectrometer (KEMS). An increase in relative humidity (RH) promoted partitioning of SCO to the particle phase, whereas higher temperatures favoured higher gas-phase concentrations. Biogenic emissions contributed to only 19% of total SCOs measured in this study. Here, C10H16NSO7, a monoterpene-derived SCO, represented the highest fraction (10 %) followed by an isoprene-derived SCO. The anthropogenic SCOs with polycyclic aromatic hydrocarbon (PAH) and aromatic precursors dominated the SCO mass loading (51 %) with C11H11SO7, derived from methyl naphthalene oxidation, contributing to 40 ng m(-3) and 0.3% of the OA mass. Anthropogenic-related SCOs correlated well with benzene, although their abundance depended highly on the photochemical age of the air mass, tracked using the ratio between pinonic acid and its oxidation product, acting as a qualitative photochemical clock. In addition to typical anthropogenic and biogenic precursors the biomass-burning precursor nitrophenol (NP) provided a significant level of NP OS. It must be noted that the contribution analysis here is only representative of the detected SCOs. There are likely to be many more SCOs present which the CIMS has not identified. Gas- and particle-phase measurements of glycolic acid suggest that partitioning towards the particle phase promotes glycolic acid sulfate production, contrary to the current formation mechanism suggested in the literature. Furthermore, the HSO4 center dot H2SO4- cluster measured by the CIMS was utilized as a qualitative marker for acidity and indicates that the production of total SCOs is efficient in highly acidic aerosols with high SO42- and organic content. This dependency becomes more complex when observing individual SCOs due to variability of specific VOC precursors.
45.	Barthel, Stephan, 1968-, et al. (author) Biocultural Refugia : Combating the Erosion of Diversity in Landscapes of Food Production 2013 In: Ecology and Society. - 1708-3087. ; 18:4, s. UNSP 71- Journal article (peer-reviewed)abstract There is urgent need to both reduce the rate of biodiversity loss caused by industrialized agriculture and feed morepeople. The aim of this paper is to highlight the role of places that harbor traditional ecological knowledge, artifacts, and methodswhen preserving biodiversity and ecosystem services in landscapes of food production. We use three examples in Europe ofbiocultural refugia, defined as the physical places that not only shelter farm biodiversity, but also carry knowledge and experiencesabout practical management of how to produce food while stewarding biodiversity and ecosystem services. Memory carriersinclude genotypes, landscape features, oral, and artistic traditions and self-organized systems of rules, and as such reflect adiverse portfolio of practices on how to deal with unpredictable change. We find that the rich biodiversity of many regionallydistinct cultural landscapes has been maintained through different smallholder practices developed in relation to localenvironmental fluctuations and carried within biocultural refugia for as long as millennia. Places that transmit traditionalecological knowledge and practices hold important lessons for policy makers since they may provide genetic and culturalreservoirs — refugia — for the wide array of species that have co-evolved with humans in Europe for more than 6000 thousandyrs. Biodiversity restoration projects in domesticated landscapes can employ the biophysical elements and cultural practicesembedded in biocultural refugia to create locally adapted small-scale mosaics of habitats that allow species to flourish and adaptto change. We conclude that such insights must be included in discussions of land-sparing vs. land-sharing when producingmore food while combating loss of biodiversity. We found the latter strategy rational in domesticated landscapes with a longhistory of agriculture
46.	Kylin, Henrik, et al. (author) Evaluating threats to an endangered species by proxy : air pollution as threat to the blue swallow (Hirundo atrocaerulea) in South Africa 2011 In: Environmental Science and Pollution Research. - : Springer. - 0944-1344 .- 1614-7499. ; 18:2, s. 282-290 Journal article (peer-reviewed)abstract Background, aim, and scope: The blue swallow (Hirundo atrocaerulea) is one of the most threatened bird species in southern Africa. Among terrestrial birds, its plumage is known to be the most water repellent, an adaptation to foraging on the wing in dense fog. Despite this uniqueadaptation, the nesting success of the blue swallow at the Blue Swallow Natural Heritage Site (BSNHS) is lower during years with high incidence of fog. As the phenomenon is not observed at other nesting sites, we hypothesized that this is due to changes in the air chemistry at the BSNHS. In the immediate proximity of the BSNHS, plantations of exotic trees (e.g., pines and eucalypts), rich in volatile organic compounds (VOCs), are dominant features. In addition, air pollution from the Johannesburg area is transported with the surface winds and mix withVOCs released from exotic trees. Together with the high humidity and high elevation, these conditions may result in the formation of sulphonates. Sulphonates are strong detergents, and the presence of these in the fog could lead to decreased water repellence of the plumage. This study was performed in order to determine the occurrence and distribution of sulphonates in the BSNHS and to compare these with sulphonates formed in other locations in South Africa. Because the blue swallow is endangered, pine needles were used as proxy to detect formation of sulphonates.Methods: We sampled pine needles with different exposure to air pollutants, in climates with different humidity, and at different elevation and analyzed these for sulphonates using mass spectrometry.Results: Pine needles from high elevations and the BSNHS, with high humidity, and exposure to air pollution contained significantly higher concentrations of sulphonates than pine needles from low elevations or from high elevations with a dryer climate or a different combination of air pollutants.Conclusions: These findings lead to two conclusions. First, the occurrence and distribution of sulphonates may be explained by chemical reactions between sulphur dioxide and organic compounds in the humid air induced by ultraviolet radiation. Second, elevated concentrations of sulphonates in the fog could affect the water repellence of the blue swallow plumage, possibly decreasing their capacity to forage in the fog. We cannot prove conclusively that this is the reason why the number of blue swallows atthe BSNHS has decreased dramatically, but for endangered species, we may have to rely on proxies to draw conclusions about outside threats. All such information should be valuable in devising protection plans for species under threat.Recommendations and perspectives: The use of proxies to elucidate threats to endangered species should be evaluated in a broad scale. The mist-belt habitat in general is threatened by many human activities. These findings indicate that air pollution and the proximity of volatile organic compound (VOC) sources close to mist-belt habitat refuges may be an unrecognised conservation threat to the animals inhabiting them.
47.	Vitalis Pemunta, Ngambouk, 1973, et al. (author) Modern State Law: Regulating Tradition or Protecting the Environment in the Mankon Kingdom of Northwest Cameroon? 2019 In: Endemic Species. Eusebio Cano Carmona (red.). - London, United Kingdom : Intechopen. - 9781839623547 Book chapter (peer-reviewed)abstract Most African countries including Cameroon find themselves in a situation of legal pluralism and at crossroads with implications for the sustainable management of natural resources. Traditional institutions and knowledge systems have been hailed as invaluable mechanisms for the conservation of flora and fauna. This chapter examines the conflict between traditional institutions and State law in the hierarchically stratified Mankon Kingdom of the Grassfield region of Northwest Cameroon where the latter prohibits the harvesting of culturally valuable plant and animal species for myriad ritual ceremonies and for therapeutic purposes. It demonstrates that the lack of cultural sensitivity can be antithetical to conservation initiatives. In other words, there is the need to align current legislative regulations for the management of natural species with the traditional use of territory, gender roles as well as to raise the cultural and educational level of the population through sensitization on the need to conserve the natural environment on which their culture depends for its survival.
48.	Garmash, O., et al. (author) Multi-generation OH oxidation as a source for highly oxygenated organic molecules from aromatics 2020 In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 20:1, s. 515-537 Journal article (peer-reviewed)abstract Recent studies have recognised highly oxygenated organic molecules (HOMs) in the atmosphere as
49.	Schoch, Conrad L., et al. (author) Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi 2014 In: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21 Journal article (peer-reviewed)abstract DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
50.	Keune, Hans, et al. (author) Defining Nature 2022 In: Visseren-Hamakers, I., & Kok, M. (Eds.). (2022). Transforming Biodiversity Governance. Cambridge: Cambridge University Press.Transforming biodiversity governance. - Cambridge : Cambridge University Press. - 9781108856348 ; , s. 25-42 Book chapter (peer-reviewed)

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