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- Abarenkov, Kessy, et al.
(författare)
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The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
- 2024
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Ingår i: Nucleic Acids Research. - 0305-1048 .- 1362-4962. ; 52:D1, s. D791-D797
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Tidskriftsartikel (refereegranskat)abstract
- UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into similar to 2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms. Graphical Abstract
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- Abarenkov, Kessy, et al.
(författare)
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The curse of the uncultured fungus
- 2022
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Ingår i: MycoKeys. - 1314-4057 .- 1314-4049. ; 86, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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| 4. |
- Abarenkov, Kessy, et al.
(författare)
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The curse of the uncultured fungus
- 2022
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :86, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget lowresolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length that represent truly unidentifiable fungal taxa - and what proportion of them that would have deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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- Ahlberg, Erik, et al.
(författare)
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"Vi klimatforskare stödjer Greta och skolungdomarna"
- 2019
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Ingår i: Dagens nyheter (DN debatt). - 1101-2447.
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- DN DEBATT 15/3. Sedan industrialiseringens början har vi använt omkring fyra femtedelar av den mängd fossilt kol som får förbrännas för att vi ska klara Parisavtalet. Vi har bara en femtedel kvar och det är bråttom att kraftigt reducera utsläppen. Det har Greta Thunberg och de strejkande ungdomarna förstått. Därför stödjer vi deras krav, skriver 270 klimatforskare.
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- Badinlou, Farzaneh, et al.
(författare)
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Trajectories of mental health outcomes following COVID-19 infection: a prospective longitudinal study
- 2024
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Ingår i: BMC PUBLIC HEALTH. - : BioMed Central Ltd. - 1471-2458. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe COVID-19 pandemic has triggered a global mental health crisis. Yet, we know little about the lasting effects of COVID-19 infection on mental health. This prospective longitudinal study aimed to investigate the trajectories of mental health changes in individuals infected with COVID-19 and to identify potential predictors that may influence these changes.MethodsA web-survey that targeted individuals that had been infected with COVID-19 was used at three time-points: T0 (baseline), T1 (six months), and T2 (twelve months). The survey included demographics, questions related to COVID-19 status, previous psychiatric diagnosis, post-COVID impairments, fatigue, and standardized measures of depression, anxiety, insomnia. Linear mixed models were used to examine changes in depression, anxiety, and insomnia over time and identify factors that impacted trajectories of mental health outcomes.ResultsA total of 236 individuals completed assessments and was included in the longitudinal sample. The participants' age ranged between 19 and 81 years old (M = 48.71, SD = 10.74). The results revealed notable changes in mental health outcomes over time. The trajectory of depression showed significant improvement over time while the trends in anxiety and insomnia did not exhibit significant changes over time. Younger participants and individuals who experienced severe COVID-19 infection in the acute phase were identified as high-risk groups with worst mental ill-health. The main predictors of the changes in the mental health outcomes were fatigue and post-COVID impairments.ConclusionsThe findings of our study suggest that mental health outcomes following COVID-19 infection exhibit a dynamic pattern over time. The study provides valuable insights into the mental health trajectory following COVID-19 infection, emphasizing the need for ongoing assessment, support, and interventions tailored to the evolving mental health needs of this population.
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| 9. |
- Blom, Tobias, et al.
(författare)
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An In-Situ Prepared Nano-Manipulator Tip for Electrical Characterization of Free Standing Graphene Like Sheets Inside a Focused Ion Beam/Scanning Electron Microscope
- 2011
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Ingår i: Journal of Nanoelectronics and Optoelectronics. - : American Scientific. - 1555-130X .- 1555-1318. ; 6:2, s. 162-168
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Tidskriftsartikel (refereegranskat)abstract
- Although contacting and moving atoms has been demonstrated using probe techniques, for many nano-objects, a fast and reproducible nano-probe technique is needed to acquire a large number of electrical measurements on nano-objects that are often similar but not the identical. Nano-manipulators have become a common tool in many scanning electron microscopes (SEM) and focussed ion beam devices (FIB). They can be rapidly and reproducibly moved from one nano-object to another. In this work we present a procedure to obtain reproducible electrical measurements of nano- to micron-sized objects by using a sharp, tungsten tip with well defined surface properties. The tip is a part of a manipulator and is sharpened in-situ by using the gallium ion beam inside a focused ion beam/scanning electron microscope (FIB/SEM). The contact resistance between a Au surface and the tip is 70 kΩ before the sharpening procedure and 10 Ω after sharpening. The leakage current of the total set-up of 10pA makes it possible to measure currents through a variety of nano-objects. This measurement technique is applied to measure the resistance of as grown, water treated and two HCl treated carbon nanosheets (CNS). These CNS vary in size and morphology. Using this nano-contacting set-up, we could obtain measurements of more than 400 different CNS. The obtained histograms allow us to observe a clear decrease of the resistance between original and 3 hour acid treated CNSs. We observe that longer periods of exposure of the CNS to the HCl do not further modify the resistance.
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