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| 2. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 3. |
- Epp, Alexandra, et al.
(författare)
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Sialylation of IgG antibodies inhibits IgG-mediated allergic reactions
- 2018
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Ingår i: Journal of Allergy and Clinical Immunology. - : Elsevier BV. - 1097-6825 .- 0091-6749. ; 141:1, s. 8-402
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Tidskriftsartikel (refereegranskat)abstract
- In presence of high allergen dosis besides IgE also IgG antibodies can induce allergic reactions, whose severity is dependent on the induced type of IgG Fc glycosylation, what should be considered for new AIT protocols containing new adjuvants.
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| 4. |
- George, Julie, et al.
(författare)
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Comprehensive genomic profiles of small cell lung cancer
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 524:7563, s. 47-U73
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Tidskriftsartikel (refereegranskat)abstract
- We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Dex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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| 5. |
- Griessl, René, et al.
(författare)
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A Scalable, Heterogeneous Hardware Platform for Accelerated AIoT based on Microservers
- 2023
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Ingår i: Shaping the Future of IoT with Edge Intelligence How Edge Computing Enables the Next Generation of IoT Applications. - 9788770040273 ; , s. 179-196
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Performance and energy efficiency are key aspects of next-generation AIoT hardware. This chapter presents a scalable, heterogeneous hardware platform for accelerated AIoT based on microserver technology. It integrates several accelerator platforms based on technologies like CPUs, embedded GPUs, FPGAs, or specialized ASICs, supporting the full range of the cloud−edgeIoT continuum. The modular microserver approach enables the integrationof different, heterogeneous accelerators into one platform. Benchmarking the various accelerators takes performance, energy efficiency, and accuracy into account. The results provide a solid overview of available accelerator solutions and guide hardware selection for AIoT applications from the far edge to the cloud.
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| 6. |
- Griessl, R., et al.
(författare)
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Evaluation of heterogeneous AIoT Accelerators within VEDLIoT
- 2023
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Ingår i: Proceedings -Design, Automation and Test in Europe, DATE. - 1530-1591. ; 2023-April
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Konferensbidrag (refereegranskat)abstract
- Within VEDLIoT, a project targeting the development of energy-efficient Deep Learning for distributed AIoT applications, several accelerator platforms based on technologies like CPUs, embedded GPUs, FPGAs, or specialized ASICs are evaluated. The VEDLIoT approach is based on modular and scalable cognitive IoT hardware platforms. Modular microserver technology enables the integration of different, heterogeneous accelerators into one platform. Benchmarking of the different accelerators takes into account performance, energy efficiency and accuracy. The results in this paper provide a solid overview regarding available accelerator solutions and provide guidance for hardware selection for AIoT applications from far edge to cloud. VEDLIoT is an H2020 EU project which started in November 2020. It is currently in an intermediate stage. The focus is on the considerations of the performance and energy efficiency of hardware accelerators. Apart from the hardware and accelerator focus presented in this paper, the project also covers toolchain, security and safety aspects. The resulting technology is tested on a wide range of AIoT applications.
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| 7. |
- Bergström, Per, 1980, et al.
(författare)
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Testing the potential for improving quality of sediments impacted by mussel farms using bioturbating polychaete worms
- 2017
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Ingår i: Aquaculture Research. - : Hindawi Limited. - 1365-2109 .- 1355-557X. ; 48:1, s. 161-176
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Tidskriftsartikel (refereegranskat)abstract
- Biodeposits from farmed mussels severely influence the biogeochemistry of sediments by increasing the levels of organic matter (OM). Mitigation of such negative impacts is important for the development of sustainable aquaculture operations. As a step towards developing methods for remediation of coastal sediments affected by mussel farming, the effects of the polychaete, Hediste diversicolor was evaluated experimentally. In a series of field- and laboratory experiments we tested hypotheses about the effects of polychaetes on sediment oxygen consumption, nutrient fluxes and sulphide pools under different polychaete densities and sedimentation regimes. The experimental results support the idea that polychaetes can mitigate negative effects on the benthic environment beneath mussel farms. H.diversicolor oxidized the sediment and generally enhanced the oxygen consumption, and thus the decomposition of OM. The accumulation of pore water sulphides were reduced and fluxes of nutrients across the sediment-water interface increased. Additional calculations suggest that the effects of polychaetes were mainly indirect and driven by increased microbial activity due to the borrowing activity of the polychaetes. Trends of increasing decomposition with increasing polychaete density suggest that the decomposition could be further enhanced by higher densities. Overall, we concluded that H.diversicolor is a potentially strong candidate for remediation of mussel farm sediments. The results show that sediments inhabited by H.diversicolor have high assimilative capacity of OM and oxygen conditions are significantly improved following the addition of polychaetes at naturally occurring densities. However, technological developments are needed in order to allow the approach to be used in practice.
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| 8. |
- Petersen, Jens Kjerulf, et al.
(författare)
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Reference conditions and EQOs for aquatic vegetation and macrozoobenthos.
- 2005
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Ingår i: Final report from The project RETRO - ”Reference conditions and typologies for aquatic vegetation and macrozoobenthos in the Skagerrak and Kattegat” - is an 2002-4 RTD-project funded by Nordic Council of Ministers involving partners from Denmark, Norway and Sweden..
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 9. |
- Wright, SC, et al.
(författare)
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A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 667-
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Tidskriftsartikel (refereegranskat)abstract
- Class F receptors are considered valuable therapeutic targets due to their role in human disease, but structural changes accompanying receptor activation remain unexplored. Employing population and cancer genomics data, structural analyses, molecular dynamics simulations, resonance energy transfer-based approaches and mutagenesis, we identify a conserved basic amino acid in TM6 in Class F receptors that acts as a molecular switch to mediate receptor activation. Across all tested Class F receptors (FZD4,5,6,7, SMO), mutation of the molecular switch confers an increased potency of agonists by stabilizing an active conformation as assessed by engineered mini G proteins as conformational sensors. Disruption of the switch abrogates the functional interaction between FZDs and the phosphoprotein Dishevelled, supporting conformational selection as a prerequisite for functional selectivity. Our studies reveal the molecular basis of a common activation mechanism conserved in all Class F receptors, which facilitates assay development and future discovery of Class F receptor-targeting drugs.
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| 10. |
- Zhang, J., et al.
(författare)
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Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Through advanced mechanistic modeling and the generation of large high-quality datasets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show that mechanistic and machine learning models can be combined to enable accurate genotype-to-phenotype predictions. We use a genome-scale model to pinpoint engineering targets, efficient library construction of metabolic pathway designs, and high-throughput biosensor-enabled screening for training diverse machine learning algorithms. From a single data-generation cycle, this enables successful forward engineering of complex aromatic amino acid metabolism in yeast, with the best machine learning-guided design recommendations improving tryptophan titer and productivity by up to 74 and 43%, respectively, compared to the best designs used for algorithm training. Thus, this study highlights the power of combining mechanistic and machine learning models to effectively direct metabolic engineering efforts.
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