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- Bratulic, Sinisa, 1981, et al.
(författare)
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The Translational Status of Cancer Liquid Biopsies
- 2021
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Ingår i: Regenerative Engineering and Translational Medicine. - : Springer Science and Business Media LLC. - 2364-4133 .- 2364-4141. ; 7:3, s. 312-352
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Tidskriftsartikel (refereegranskat)abstract
- Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research. Lay Summary: Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
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| 2. |
- Bossini, D., et al.
(författare)
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Ultrafast Amplification and Nonlinear Magnetoelastic Coupling of Coherent Magnon Modes in an Antiferromagnet
- 2021
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 127:7
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the role of domain walls in the ultrafast magnon dynamics of an antiferromagnetic NiO single crystal in a pump-probe experiment with variable pump photon energy. Analyzing the amplitude of the energy-dependent photoinduced ultrafast spin dynamics, we detect a yet unreported coupling between the material's characteristic terahertz- and gigahertz-magnon modes. We explain this unexpected coupling between two orthogonal eigenstates of the corresponding Hamiltonian by modeling the magnetoelastic interaction between spins in different domains. We find that such interaction, in the nonlinear regime, couples the two different magnon modes via the domain walls and it can be optically exploited via the exciton-magnon resonance.
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| 4. |
- Zamani, Neda, et al.
(författare)
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Unsupervised genome-wide recognition of local relationship patterns
- 2013
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 14, s. 347-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUNDPhenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion.RESULTSWe developed Saguaro, a combination of a Hidden Markov Model (HMM) and a Self Organising Map (SOM), to characterise local phylogenetic relationships among aligned sequences using cacti, matrices of pair-wise distance measures. While the HMM determines the genomic boundaries from aligned sequences, the SOM hypothesises new cacti in an unsupervised and iterative fashion based on the regions that were modelled least well by existing cacti. After testing the software on simulated data, we demonstrate the utility of Saguaro by testing two different data sets: (i) 181 Dengue virus strains, and (ii) 5 primate genomes. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to incomplete lineage sorting in the second dataset. Intriguingly for the primate data, Saguaro also classified an additional ~3% of the genome as most incompatible with the expected species phylogeny. A substantial fraction of these regions was found to overlap genes associated with both the innate and adaptive immune systems.CONCLUSIONSSaguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses. We have successfully demonstrated Saguaro's utility with two contrasting data sets, one containing many members with short sequences (Dengue viral strains: n = 181, genome size = 10,700 nt), and the other with few members but complex genomes (related primate species: n = 5, genome size = 3 Gb), suggesting that the software is applicable to a wide variety of experimental populations. Saguaro is written in C++, runs on the Linux operating system, and can be downloaded from http://saguarogw.sourceforge.net/.
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| 5. |
- Rosvall, Per-Åke, et al.
(författare)
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Yrkesämnena och skolans demokratiuppdrag
- 2020
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- Yrkesämnena och yrkesläraren befinner sig i skärningspunkten mellan utbildning och yrkesliv. Inom yrkesprogram finns en stark tradition av att innehållet är tydligt kopplat till arbetsplatspraktiker och undervisningen sker genom specifika moment och arbetsuppgifter. Som en följd av detta har demokrati- och medborgarfostran ofta hamnat i skymundan, trots att det står i läroplanen att förberedelse för demokratiskt deltagande ska genomsyra all undervisning. Därför behöver yrkesprogrammen förstärkas på områden där eleverna ges redskap att påverka och utöva inflytande. I den här boken synliggörs hur undervisning i yrkesämnen är och kan vara en väsentlig del av skolans demokratiska uppdrag. Författarna fördjupar resonemang om läroplaner och undervisningspraktik i förhållande till medborgarfrågor relaterade till klass, kön och etnicitet. Utifrån verkliga exempel diskuteras bland annat vilka kunskaper yrkesämnesundervisningen ger i att problematisera rådande förhållanden på arbetsplatsen och det vidare yrkeslivet. Vilka möjligheter ges för elever att delta i samtal om hur arbetet ska organiseras och vad som skapar yrkets förutsättningar, till exempel i arbetslag, i fackförbund och inom politiken? Yrkesämnena och skolans demokratiuppdrag bygger på resultat från forskningsprojektet Kritiskt tänkande i yrkesämnesundervisning? Medborgarskapande i yrkesprogrammens styrdokument och klassrumspraktik. Bokens författare Per-Åke Rosvall och Maria Rönnlund är docenter i pedagogiskt arbete, Kristina Ledman är lektor i pedagogik vid Umeå universitet och Mattias Nylund är docent i pedagogik vid Göteborgs universitet.
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