| 1. |
- Yarza, P., et al.
(författare)
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Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names
- 2013
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 36:1, s. 69-73
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Tidskriftsartikel (refereegranskat)abstract
- High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 “orphan” species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these “orphan” species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.
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| 2. |
- Murray, Alison E., et al.
(författare)
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Roadmap for naming uncultivated Archaea and Bacteria
- 2020
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Ingår i: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 5:8, s. 987-994
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Tidskriftsartikel (refereegranskat)abstract
- The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.
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| 3. |
- Chambers, Josephine M., et al.
(författare)
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Co-productive agility and four collaborative pathways to sustainability transformations
- 2022
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Ingår i: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 72
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Tidskriftsartikel (refereegranskat)abstract
- Co-production, the collaborative weaving of research and practice by diverse societal actors, is argued to play an important role in sustainability transformations. Yet, there is still poor understanding of how to navigate the tensions that emerge in these processes. Through analyzing 32 initiatives worldwide that co-produced knowledge and action to foster sustainable social-ecological relations, we conceptualize 'co-productive agility' as an emergent feature vital for turning tensions into transformations. Co-productive agility refers to the willingness and ability of diverse actors to iteratively engage in reflexive dialogues to grow shared ideas and actions that would not have been possible from the outset. It relies on embedding knowledge production within processes of change to constantly recognize, reposition, and navigate tensions and opportunities. Co-productive agility opens up multiple pathways to transformation through: (1) elevating marginalized agendas in ways that maintain their integrity and broaden struggles for justice; (2) questioning dominant agendas by engaging with power in ways that challenge assumptions, (3) navigating conflicting agendas to actively transform interlinked paradigms, practices, and structures; (4) exploring diverse agendas to foster learning and mutual respect for a plurality of perspectives. We explore six process considerations that vary by these four pathways and provide a framework to enable agility in sustainability transformations. We argue that research and practice spend too much time closing down debate over different agendas for change - thereby avoiding, suppressing, or polarizing tensions, and call for more efforts to facilitate better interactions among different agendas.
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| 4. |
- Chambers, Josephine M., et al.
(författare)
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Six modes of co-production for sustainability
- 2021
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Ingår i: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 4, s. 983-996
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Tidskriftsartikel (refereegranskat)abstract
- Co-production includes diverse aims, terminologies and practices. This study explores such diversity by mapping differences in how 32 initiatives from 6 continents co-produce diverse outcomes for the sustainable development of ecosystems at local to global scales. The promise of co-production to address complex sustainability challenges is compelling. Yet, co-production, the collaborative weaving of research and practice, encompasses diverse aims, terminologies and practices, with poor clarity over their implications. To explore this diversity, we systematically mapped differences in how 32 initiatives from 6 continents co-produce diverse outcomes for the sustainable development of ecosystems at local to global scales. We found variation in their purpose for utilizing co-production, understanding of power, approach to politics and pathways to impact. A cluster analysis identified six modes of co-production: (1) researching solutions; (2) empowering voices; (3) brokering power; (4) reframing power; (5) navigating differences and (6) reframing agency. No mode is ideal; each holds unique potential to achieve particular outcomes, but also poses unique challenges and risks. Our analysis provides a heuristic tool for researchers and societal actors to critically explore this diversity and effectively navigate trade-offs when co-producing sustainability.
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| 5. |
- Klenk, T., et al.
(författare)
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Taking women on boards : a comparative analysis of public policies in higher education
- 2022
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Ingår i: Policy Reviews in Higher Education. - : Informa UK Limited. - 2332-2969 .- 2332-2950. ; 6:2, s. 128-152
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Tidskriftsartikel (refereegranskat)abstract
- There is growing interest in the underlying mechanisms affecting female leaders in Higher Education (HE). This article compares four countries–Germany, Norway, Poland and Sweden to identify key structural conditions (enablers and barriers) for female representation in academia by studying the regulative framework of government policy. Two research questions are guiding the analysis: first, what (if any) policy instruments are chosen to increase the number of female leaders in HE? Second, to what extent does this choice of instruments mirror either sectorial logic (HE) or national policy styles? The empirical results of the article show that while processes of policy diffusion are observable at the sectoral level, gender equality policies and instrument choice differ considerably in the four countries under consideration. The article thus concludes that national policy styles need to be understood as enabling and disabling policy factors for gender equality in HE shaping the process of translating diffused models decisively.
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| 6. |
- Kurz, MW, et al.
(författare)
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FMR1 alleles in Parkinson's disease: relation to cognitive decline and hallucinations, a longitudinal study
- 2007
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Ingår i: Journal of geriatric psychiatry and neurology. - : SAGE Publications. - 0891-9887 .- 1552-5708. ; 20:2, s. 89-92
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Tidskriftsartikel (refereegranskat)abstract
- Carriers of expanded alleles of the fragile X mental retardation ( FMR1) gene may display parkinsonism, cognitive decline, and behavioral changes. The authors screened 2 male groups of patients affected with Parkinson's disease (PD) (n = 137). One group (n = 56) was followed longitudinally for up to 12 years. Length of CGG repeats in PD patients was compared with healthy controls (n = 310). In addition, the association of the number of CGG repeats with cognitive decline or hallucinations was studied in the longitudinally followed PD group. The authors found no repeats in the premutation range (55-200 CGG repeats) and no significant difference in the proportion of intermediate-size (41-54 CGG repeats) carriers between the PD and the control groups. Using linear regression, the number of CGG repeats was not related to motor or cognitive progression. However, the marked cognitive decline in 2 patients carrying intermediate-size alleles points to a possible association. More studies with larger PD samples are warranted. ( J Geriatr Psychiatry Neurol 2007;20:89-92)
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| 7. |
- Kyrpides, Nikos C, et al.
(författare)
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Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.
- 2014
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1545-7885. ; 12:8
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Tidskriftsartikel (refereegranskat)abstract
- Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
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| 8. |
- Naghavi, N., et al.
(författare)
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Buffer layers and transparent conducting oxides for chalcopyrite Cu(In,Ga)(S,Se)(2) based thin film photovoltaics : Present status and current developments
- 2010
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Ingår i: Progress in Photovoltaics. - : Wiley. - 1062-7995 .- 1099-159X. ; 18:6, s. 411-433
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Tidskriftsartikel (refereegranskat)abstract
- The aim of the present contribution is to give a review on the recent work concerning Cd-free buffer and window layers in chalcopyrite solar cells using various deposition techniques as well as on their adaptation to chalcopyrite-type absorbers such as Cu(In,Ga)Se-2, CuInS2, or Cu(In,Ga)(S,Se)(2). The corresponding solar-cell performances, the expected technological problems, and current attempts for their commercialization will be discussed. The most important deposition techniques developed in this paper are chemical bath deposition, atomic layer deposition, ILGAR deposition, evaporation, and spray deposition. These deposition methods were employed essentially for buffers based on the following three materials: In2S3, ZnS, Zn1-xMgxO.
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