| 1. |
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- 2019
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Journal article (peer-reviewed)
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| 2. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 3. |
- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 4. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 5. |
- Alexandrov, Ludmil B., et al.
(author)
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Signatures of mutational processes in human cancer
- 2013
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 500:7463, s. 415-421
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Journal article (peer-reviewed)abstract
- All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.
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| 6. |
- Nik-Zainal, Serena, et al.
(author)
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
- 2016
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 534:7605, s. 47-54
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Journal article (peer-reviewed)abstract
- We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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| 7. |
- Nik-Zainal, Serena, et al.
(author)
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Mutational Processes Molding the Genomes of 21 Breast Cancers
- 2012
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In: Cell. - : Elsevier BV. - 1097-4172 .- 0092-8674. ; 149:5, s. 979-993
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Journal article (peer-reviewed)abstract
- All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed "kataegis,'' was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed.
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| 8. |
- Nik-Zainal, Serena, et al.
(author)
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The Life History of 21 Breast Cancers
- 2012
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In: Cell. - : Elsevier BV. - 1097-4172 .- 0092-8674. ; 149:5
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Journal article (peer-reviewed)abstract
- Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We developed algorithms to decipher this narrative and applied them to 21 breast cancers. Mutational processes evolve across a cancer's lifespan, with many emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, and most mutations are found in just a fraction of tumor cells. Every tumor has a dominant subclonal lineage, representing more than 50% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent cell lineages capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.
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| 9. |
- Butler, Andrew, et al.
(author)
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The XXL Survey XVIII. ATCA 2.1 GHz radio source catalogue and source counts for the XXL-South field
- 2018
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 620
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Journal article (peer-reviewed)abstract
- The 2.1 GHz radio source catalogue of the 25 deg(2) ultimate XMM extragalactic survey south (XXL-S) field, observed with the Australia Telescope Compact Array (ATCA), is presented. The final radio mosaic achieved a resolution of similar to 4.8" and a median rms noise of sigma approximate to 41 mu Jy/beam. To date, this is the largest area radio survey to reach this flux density level. A total of 6350 radio components above 5 sigma are included in the component catalogue, 26.4% of which are resolved. Of these components, 111 were merged together to create 48 multiple-component radio sources, resulting in a total of 6287 radio sources in the source catalogue, 25.9% of which were resolved. A survival analysis revealed that the median spectral index of the Sydney University Molonglo Sky Survey (SUMSS) 843 MHz sources in the field is alpha = 0.75, consistent with the values of -0.7 to -0.8 commonly used to characterise radio spectral energy distributions of active galactic nuclei. The 2.1 GHz and 1.4 GHz di ff erential radio source counts are presented and compared to other 1.4 GHz radio surveys. The XXL-S source counts show good agreement with the other surveys.
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| 10. |
- Lindblad-Toh, Kerstin, et al.
(author)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Journal article (peer-reviewed)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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| 11. |
- Moore, Keith J M, et al.
(author)
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Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications
- 2021
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In: Journal of Biomolecular Techniques. - : Association of Biomolecular Resource Facilities. - 1524-0215 .- 1943-4731. ; 32:3, s. 228-275
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Research review (peer-reviewed)abstract
- As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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| 12. |
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| 13. |
- Allen, David B, et al.
(author)
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GH Safety Workshop Position Paper: a critical appraisal of recombinant human growth hormone therapy in children and adults.
- 2016
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In: European Journal of Endocrinology. - 1479-683X. ; 174:2, s. 1-9
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Journal article (peer-reviewed)abstract
- Recombinant human growth hormone (rhGH) has been in use for 30 years, and over that time its safety and efficacy in children and adults has been subject to considerable scrutiny. In 2001, a statement from the GH Research Society (GRS) concluded that 'for approved indications, GH is safe'; however, the statement highlighted a number of areas for on-going surveillance of long-term safety including; cancer risk, impact on glucose homeostasis and use of high dose pharmacological rhGH treatment. Over the intervening years, there have been a number of publications addressing the safety of rhGH with regard to mortality, cancer and cardiovascular risk and the need for longterm surveillance of the increasing number of adults who were treated with rhGH in childhood. Against this backdrop of interest in safety, the European Society of Paediatric Endocrinology (ESPE), the GRS and the Pediatric Endocrine Society (PES) convened a meeting to reappraise the safety of rhGH. The ouput of the meeting is a concise position statement.
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| 14. |
- Andersson, Sarah, et al.
(author)
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Malmbanan Diaries
- 2010
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Reports (other academic/artistic)abstract
- This booklet is a report for a case study visit during four day field trip, a group of nine PhD students and their supervisors – all part of the National Research School for Architecture and Planning in the Urban Landscape, APULA – set out to explore what may be considered the outback of Western Europe’s conurbations, the transnational region of Kiruna -Narvik.Both “remote” and “resourceful”, “threatened” and “thriving” (equally relative notions), this region seemed to offer possibilities to reflect upon many of the current tendencies influencing contemporary planning practice and research.
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| 15. |
- Berglund, Ulla, et al.
(author)
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Landskapsanalys för transportinfrastruktur : en kunskaps- och metodredovisning för utveckling av väg- och järnvägsprojekt i enlighet med den Europeiska Landskapskonventionen
- 2013
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Reports (other academic/artistic)abstract
- Rapporten ”Landskapsanalys för transportinfrastruktur” har tagits fram inom forskningsprojektet ”Bättre landskapsanalys för transportsektorn” (2010-2013) i samverkan mellan SLU och VTI och handlar om hur man kan arbeta med landskapsanalys (LA) i planläggningsprocessen för väg- ochjärnvägsprojekt. Vi kallar den ett kunskapsunderlag, och dess främsta syfte är att förmedla relevantkunskap från forskarsamhället till Trafikverkets landskapsexperter och därmed stödja Trafikverketsmöjligheter att leverera den landskapsanpassade infrastruktur som regeringen kräver.Fokus för arbetet har varit planläggningsfasen, dvs. när man enligt den sammanhållna vägprocessenkommit så långt att vägen/järnvägen ska prövas i en fysisk miljö.
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| 16. |
- Berglund, Ulla, et al.
(author)
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Landskapsanalys för transportinfrastruktur : en kunskaps- och metodredovisning för utveckling av väg- och järnvägsprojekt i enlighet med den Europeiska Landskapskonventionen
- 2013
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Reports (other academic/artistic)abstract
- Rapporten ”Landskapsanalys för transportinfrastruktur …” har tagits fram inom forskningsprojektet ”Bättre landskapsanalys för transportsektorn” (2010-2013) i samverkan mellan SLU och VTI och handlar om hur man kan arbeta med landskapsanalys (LA) i planläggningsprocessen för väg- och järnvägsprojekt. Vi kallar den ett kunskapsunderlag, och dess främsta syfte är att förmedla relevant kunskap från forskarsamhället till Trafikverkets landskapsexperter och därmed stödja Trafikverkets möjligheter att leverera den landskapsanpassade infrastruktur som regeringen kräver. Fokus för arbetet har varit planläggningsfasen, dvs. när man enligt den sammanhållna vägprocessen kommit så långt att vägen/järnvägen ska prövas i en fysisk miljö. Den här rapporten tar vid efter det strategiska skede som hanteras i rapporten ”Landskap i långsiktig planering” (Trafikverket 2012). ”Projektet har utförts med utgångspunkt i att LA ska vara en grund på vilken MKBprocessen vilar men också ge viktig bakgrundskunskap för gestaltningsprogrammet (GP). En anledning till projektets tillkomst är de ökade krav på helhetssyn som den Europeiska landskapskonventionen (ECL), som trädde ikraft i Sverige 2011, ställer på projekt som påverkar landskap. Det gäller inte bara landskap som har bedömts som vetenskapligt värdefulla eller har erkänt stora skönhetsvärden, utan också de så kallade vardagslandskap som omger våra städer och samhällen. Det är landskap där många människor bor, arbetar och tillbringar sin fritid och där utbyggnad av transportinfrastruktur får stor påverkan på de värden som är viktiga för brukarna. ELC betonar landskapets betydelse som en del i människors utformande av sin egen identitet såväl som sin gruppidentitet och dessutom allas rätt att vara delaktiga i värderingen av de landskap som berör dem. Europarådet (2008) skriver i sina rekommendationer för implementeringen av ELC att allmänhetens medverkan bör finnas med genom hela planerings- och beslutsprocessen i frågor som rör landskap. För det anför man dels demokratiska skäl, som grundar sig i uppfattningen att alla människor har intressen i landskapet och i den meningen också är sakägare. Dels anförs kunskapsskäl, närmare bestämt att genom allmänhetens medverkan öka medvetenheten om landskapet och dess värden såväl hos allmänheten som hos berörda experter. Arbetet inom projektet har bland annat gått ut på att finna och beskriva metoder som passar att användas i infrastrukturprojekt och som på ett rimligt sätt motsvarar det ELC föreskriver och rekommenderar. Särskilt fokus har satts på frågan om hur den berörda allmänhetens syn på sina landskap ska kunna komplettera och samverka med den expertkunskap som hittills helt dominerat LA inom transportsektorn. Den utgångspunkt som vi valt är den väl beskrivna och prövade metodansatsen ”Landscape Character assessment” (LCA) från Storbritannien, som har ett brett angreppssätt men kan sägas vara mindre välutvecklad när det gäller frågor kring landskapets historia och utveckling. Därför visar vi hur man kan kombinera den med metoden ”Historic Landscape Characterisation” (HLC) och hur man kan arbeta i de båda faserna beskrivnings- respektive bedömningsfas. På svenska benämner vi dessa metoder: landskapskaraktärisering respektive historisk landskapskaraktärisering. Eftersom utvecklingen av allmänhetens medverkan i LA inte är så stark överhuvudtaget har vi också fångat upp och delvis själva utvecklat metoder för dialog med berörda människor, där deras värderingar står i fokus. Det gäller en kartbaserad enkät, kartnålsmetoden, och en variant på gåtursmetoden som vi här kort och gott kallar busstur. Frågan om ljud – inte bara buller – är också ett ämne där LA hittills varit relativt svag. Där har vi bedrivit utvecklingsarbete, som resulterat i en mobilapplikation för karaktärisering av ljudlandskap. I uppdraget för det här projektet har det inte ingått att studera ekologisk landskapsanalys i sig. Däremot har vi redovisat hur vi tänker att den ekologiska analysen, landskapskaraktäriseringen 8 landskapsanalys för transportinfrastruktur och den historiska landskapskaraktäriseringen ska kunna samverka för det eftersträvade helhetsperspektivet. För att nå detta menar vi vidare att metoderna kulturmiljöanalys (DIVE) och strukturanalys också kan ge viktiga bidrag. Vi presenterar kort dessa metoder och deras tänkta roller i LA för väg- och järnvägsprojekt. Landskapskaraktärisering är alltså inte en enhetlig metod utan det vi kallar ansats eller ramverk, som kan anpassas efter projektets art och skala och efter landskapets egenskaper, dess sårbarhet och vilka värden som kan förutses ha betydelse för allmänheten såväl som för vetenskap och andra intressen. I rapporten finns därför information om hur olika specifika metoder kan kombineras och dessutom viss information om hur man kan prioritera i olika fall, vilka underlagsmaterial som kan var lämpliga etc. Kravet på att ge berörd allmänhet såväl som andra sakägare möjlighet att medverka i landskapskaraktäriseringen innebär knappast att specialisterna, landskapsexperterna, får mindre ansvar i processen. Frågan om kommunikation med sakägarna och sammanvägning av olika intressen kräver stor omsorg och skicklighet. I rapporten noterar vi det och ger förslag om hur denna kommunikation ska kunna planeras och utföras på ett effektivt och kvalitativt gott sätt. I många väg- och järnvägsprojekt krävs att en MKB genomförs för att i förväg beskriva vilka konsekevenser för människors hälsa och för miljön som projektet ifråga kan komma att ge upphov till. Vi beskriver i rapporten hur kunskap från den genomförda LA kan användas som underlag för MKB i flera avseenden och vid olika tillfällen i vägplanläggningen. På motsvarande vis vill vi också peka på hur kunskap som tas fram inom LA kan vara till nytta i arbetet med det Gestaltningsprogram (GP) som arbetas fram inom planläggningsprocessen. MKB och GP kan i många fall ses som slutprodukter för en stor del av arbetet med LA. För att LA skall kunna bidra till väg- och järnvägsplanläggning och till MKB och GP behöver krav ställas på dem som har att genomföra LA. Vi har inom ramen för projektet undersökt vad som bör ingå av kvalitets- och kompetenskrav vid upphandling av LA. Detta redovisas i rapporten som ett förslag på vad en upphandling bör innehålla. Avslutningsvis finns i rapporten en översikt och beskrivning i tabellform av exempel på projekt och metoder som vi hänvisat till i texten. Den innehåller uppgifter om sammanhang, genomförande, mm. och länkar eller andra hänvisningar till källor för vidare läsning.
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| 17. |
- Berglund, Ulla, et al.
(author)
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Om landskap och landskapsanalys för väg och järnväg : ett kunskapsunderlag med fokus på begrepp och exempel
- 2011
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Reports (other academic/artistic)abstract
- Landskapets och landskapsanalysens roll i planeringen påverkas av implementeringen av den europeiska landskapskonventionen (ELC) som nyligen inletts i Sverige. Kravet ökar på hantering av landskapsfrågor och på medverkan från allmänheten i till exempel infrastrukturprojekt. Därför behöver olika aktörer få aktuell kunskap om landskap och analys av landskap och så långt möjligt skaffa sig gemensamma referensramar i ämnet. Vägar och järnvägar har en avgörande betydelse för människors möjligheter att uppleva landskap. Samtidigt utgör de ingrepp som kräver kunskap och respekt för de landskap med sina sociala sammanhang som påverkas. Genom ELC har fokus ökat på ”vardagslandskapet”, dvs. de landskap som används och värderas av människor oavsett sådana värden som utomstående experter kan bedöma. Den här rapporten är den första redovisningen i ett forskningsuppdrag från Trafikverket: Bättre landskapsanalys för transportsektorn. Vi kallar den kunskapsunderlag, och den ska vara en källa till bildning och utbildning i frågor som rör landskap och landskapsanalys med fokus på vägoch järnvägsplanering. Arbetet utgår från en bred genomgång av forskning om landskap som fenomen och begrepp, om upplevelse av landskap och om människors möjligheter att påverka landskap och landskapsplanering. Vi har inte begränsat oss till, men särkilt lyft fram sådan kunskap, som har direkt relevans för tranportinfrastruktur och för nordiska förhållanden. Rapporten redogör för ELC: s förhållande till landskapet som sådant och till olika aspekter av landskap. Ett särskilt fokus har lagts på att utreda begreppen landskap och identitet och relatera dem till andra, centrala begrepp som ”plats” och ”karaktär”. Ett avsnitt hanterar allmänhetens medverkan i landskapsanalyser och planering. Vidare diskuteras olika typer av landskapsanalyser och ett antal goda exempel presenteras och gås igenom. Landskapet finns överallt och landskapsbegreppet kan användasi olika skalor, inte bara om stora områden. Det har också relevans likaväl i städer som på landsbygden. Infrastrukturen berör alla slags landskap. Med den här rapporten hoppas vi bidra till ett ökat intresse för landskapet i sin helhet, särskilt hos dem som genom stora projekt sätter avgörande och långvariga avtryck i vår gemensamma livsmiljö
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| 18. |
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| 19. |
- Butler, Andrew, et al.
(author)
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Awareness-raising of landscape in practice. An analysis of Landscape Character Assessments in England
- 2014
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In: Land Use Policy. - : Elsevier BV. - 0264-8377 .- 1873-5754. ; 36, s. 441-449
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Journal article (peer-reviewed)abstract
- Awareness-raising is one of the measures which signatories to the European Landscape Convention are expected to realise, yet it is unclear what awareness-raising entails when related to an ambiguous subject such as landscape. Our study builds a conceptual understanding of awareness-raising of landscape, recognising that it cannot be a purely top-down process but needs to be seen as a "multi-directional transfer of knowledge" or "co-creation of meaning". We have used this conceptual understanding as a lens for analysing practices which in some form help raise awareness of landscape. Document studies of Landscape Character Assessments undertaken in England since 2007 and interviews with key actors involved in Landscape Character Assessments were carried out in order to understand how awareness-raising is addressed. The findings suggest that while often overlooked or recognised as a top down endeavour landscape assessments have potential to develop co-creation of meaning.
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| 20. |
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| 21. |
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| 22. |
- Butler, Andrew
(author)
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Developing theory of public involvement in landscape planning : democratising landscape
- 2014
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Doctoral thesis (other academic/artistic)abstract
- Public involvement has been recognised as a fundamental aspect of landscape planning for over 40 years, and has been more recently legitimised in policy through the European Landscape Convention. However, the practice of public involvement in landscape planning remains questionable. In this thesis I develop the argument that failure in public involvement is founded on a weakness in theoretical understanding within the discipline. Consequently I argue for a strengthening of the theoretical base underpinning public involvement in landscape planning, and seek to contribute to the development of this theory. The research which this thesis builds on examines how public involvement is theorised and practised in landscape planning. The empirical material which supports this analysis has been gathered by examining landscape assessments, which are identified as a key moment in the landscape planning process. I use landscape character assessments, undertaken in England, as a case for analysing how practitioners engage the public and handle their multiple values. In this thesis I expose the dynamics between theory and practice within landscape planning. I argue that an ambiguity in the discipline is created by the presence of plural understandings of landscape. In particular, two contrasting theorisations of landscape drive a gap between the rhetoric of practice, and its conduct. The first theorisation, expressed in the ELC and forming the rhetoric of practice, identifies landscape as a dynamic, holistic entity dependent on perceptions. The second theorisation which is operationalised in the conduct of practice is an objective outsiders’ view, where landscape is understood as a physical surface. I further argue that this confusion relates to a weakness of substantive theory in the landscape planning discipline. Practice builds on procedural theories which have weak substantive grounding, brought about by the discipline being driven and developed by practice, and falling back on an objective outsiders' view of landscape. Such a view of landscape means that landscape planners lack adequate tools for handling the diverse and dynamic values which are experienced in landscape, and therefore have no sound basis for dealing with conflicting values. This thesis contributes to an understanding of the dynamics of landscape planning, and begins to develop a theoretical position, with landscape as a democratic entity as the focus for public involvement. The thesis explores the implications of the theorisation of a democratising landscape for the discipline of landscape planning.
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| 23. |
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| 24. |
- Butler, Andrew
(author)
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Dynamics of integrating landscape values in landscape character assessment: the hidden dominance of the objective outsider
- 2016
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In: Landscape Research. - : Informa UK Limited. - 0142-6397 .- 1469-9710. ; 41, s. 239-252
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Journal article (peer-reviewed)abstract
- While there has been extensive research undertaken on the values which insiders attribute to landscape there is a lack of literature which looks at how planning professionals handle landscape values. In this article, I develop a framework for questioning how landscape values are taken up in landscape planning, with the aim of conceptualising what landscape values mean in practice. This is undertaken through addressing landscape assessment, more specifically analysing how landscape character assessment (LCA) represents a critical point in the framing of landscape values. Through a synthesis of research on landscape values I examine the underlying logic of the LCA documents. I conclude that the values communicated in these assessments tend to be those of ‘objective' outside experts, predominantly based on aesthetics and focusing on the physicality of landscape. This I argue leads to a questioning the legitimacy of the LCA approach.
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| 25. |
- Butler, Andrew, et al.
(author)
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Foraging for identity : the relationships between landscape activities and landscape identity after catastrophic landscape change
- 2019
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In: Landscape research. - : Routledge. - 0142-6397 .- 1469-9710. ; 44:3, s. 303-319
-
Journal article (peer-reviewed)abstract
- In this article, we deal with landscape activities in relation to changing landscape identity after a major wildfire in Sweden in 2014. The aim was to investigate the relationships between 22 landscape activities (before the fire) and 2 components (emotion and cognition) of landscape identity (before and after the fire). A total of 656 respondents living nearby the fire area participated in this study. Before the fire, a positive association was found between the activities of enjoying nature and foraging, and both components of landscape identity. This suggests that the more participants enjoyed nature and picked berries and mushrooms, the stronger their attachment to the landscape (emotion), and the more they remembered and reasoned about the landscape (cognition). Post fire, these relationships were found only between the two components of landscape identity and foraging. This implies a significant role of this type of activity for keeping alive' landscape identity.
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| 26. |
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| 27. |
- Butler, Andrew
(author)
-
Landscape as a developing discourse: contested landscape identities in an area affected by forest fire
- 2016
-
Conference paper (peer-reviewed)abstract
- This paper examines the dynamics involved in legitimising and defining values which ultimately inform the official discourse relating to a landscape. As such it explores which values are legitimized, promoted, subordinated or ignored when a landscape is defined; consequently influencing whose understanding of a landscape is accepted as justified true knowledge and thus informing the aspirations and future direction of that landscape.The empirical basis for this paper is a landscape impacted by the largest forest fire in modern Swedish history and the discourses which develop around this landscape. This paper addresses how local inhabitants, planning authorities and researcher have shaped the understanding and future trajectory of this landscape. The paper finally questions how the developing official discourse relates to the ideal of landscape as promoted through the ELC; a democratic entity.
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| 28. |
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| 29. |
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| 30. |
- Butler, Andrew, et al.
(author)
-
Landscape Character Assessment as an Approach to Understanding Public Interests within the European Landscape Convention
- 2014
-
In: Landscape Research. - : Informa UK Limited. - 0142-6397 .- 1469-9710. ; 39, s. 219-236
-
Journal article (peer-reviewed)abstract
- The European Landscape Convention's (ELC) definition of landscape, "an area, as perceived by people...'', places the public central to any understanding of landscape. This paper argues for 'just' involvement of the public and looks at how the focus of landscape as a perceived entity has been taken up within Landscape Character Assessment (LCA), an approach applied in England and Scotland for implementing the ELC. Based on a conceptual framework grounded in perception as a phenomenological experience of landscape and informed by principles of participation, LCAs from 2007 to 2011 have been assessed as to how public involvement has been considered. The results show that only a quarter of all assessments accessed involved the public, and that among these there is great disparity in the degree to which the public is engaged.
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| 31. |
- Butler, Andrew, et al.
(author)
-
Landscape identity, before and after a forest fire
- 2018
-
In: Landscape research. - : Routledge. - 0142-6397 .- 1469-9710. ; 43:6, s. 878-889
-
Journal article (peer-reviewed)abstract
- Our identity is tied to where we are and how we engage with the landscapes in which we find ourselves. But what happens if the landscape which we use for our everyday life is drastically altered by a catastrophic upheaval, for example, when forest fires ravage the landscape? In this paper, interviews with individuals affected by the largest forest fire in modern Swedish history are used to exemplify our conceptualisation of how landscape identity is impacted by dramatic change. We address the phases of stability, change and progression in relation to the case. Finally, we propose that landscape identity can be utilised as a central concept for engaging with the social aspects of the impact of forest fires.
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| 32. |
- Butler, Andrew
(author)
-
Landscape's physiognomic structure: conceptual development and practical applications
- 2018
-
In: Landscape Research. - : Informa UK Limited. - 0142-6397 .- 1469-9710. ; 43, s. 410-427
-
Journal article (peer-reviewed)abstract
- The past decade has seen an increased interest in approaches for the identification and assessment of landscapes, which has been, in part, a response to the European Landscape Convention (ELC). In this article, we review landscape physiognomy, an important component of the Polish approach to the assessment and identification of its landscape. We address the relevance of physiognomy both in relation to the ELC and to the landscape character assessments approach, and then explore the theoretical basis of landscape physiognomic structure. We also expand the existing classification of landscape interiors; this is followed by combining three approaches: (1) physical geography in the field of comprehensive classification of natural landscapes; (2) landscape ecology studies on the spatial structure of land cover patches against the landscape matrix' and (3) the theory of landscape interiors. Presented ideas create the outline of the concept of landscape's physiognomic structure.
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| 33. |
- Butler, Anne M., et al.
(author)
-
Novel Loci Associated With PR Interval in a Genome-Wide Association Study of 10 African American Cohorts
- 2012
-
In: Circulation: Cardiovascular Genetics. - 1942-325X. ; 5:6, s. 639-646
-
Journal article (peer-reviewed)abstract
- Background-The PR interval, as measured by the resting, standard 12-lead ECG, reflects the duration of atrial/atrioventricular nodal depolarization. Substantial evidence exists for a genetic contribution to PR, including genome-wide association studies that have identified common genetic variants at 9 loci influencing PR in populations of European and Asian descent. However, few studies have examined loci associated with PR in African Americans. Methods and Results-We present results from the largest genome-wide association study to date of PR in 13 415 adults of African descent from 10 cohorts. We tested for association between PR (ms) and approximate to 2.8 million genotyped and imputed single-nucleotide polymorphisms. Imputation was performed using HapMap 2 YRI and CEU panels. Study-specific results, adjusted for global ancestry and clinical correlates of PR, were meta-analyzed using the inverse variance method. Variation in genome-wide test statistic distributions was noted within studies (lambda range: 0.9-1.1), although not after genomic control correction was applied to the overall meta-analysis (lambda: 1.008). In addition to generalizing previously reported associations with MEIS1, SCN5A, ARHGAP24, CAV1, and TBX5 to African American populations at the genome-wide significance level (P<5.0x10(-8)), we also identified a novel locus: ITGA9, located in a region previously implicated in SCN5A expression. The 3p21 region harboring SCN5A also contained 2 additional independent secondary signals influencing PR (P<5.0x10-8). Conclusions-This study demonstrates the ability to map novel loci in African Americans as well as the generalizability of loci associated with PR across populations of African, European, and Asian descent. (Circ Cardiovasc Genet. 2012;5:639-646.)
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| 34. |
- Butler, Andrew, et al.
(author)
-
“There will be mushrooms again” – Foraging, landscape and forest fire
- 2021
-
In: Journal of Outdoor Recreation. - : Elsevier. - 2213-0780 .- 2213-0799. ; 33
-
Journal article (peer-reviewed)abstract
- In this paper, we address the relevance of recreational foraging, picking berries and mushrooms, for developing connection to nature and what happens when that practice is interrupted by drastic landscape change. We use the site of the largest forest fire in modern Swedish history as a case to examining the relevance of foraging. In previous studies, positive associations have been observed between the activity of picking berries and mushrooms with landscape-identity prior to forest fires. The results suggest that the more participants enjoyed foraging, the stronger their attachment to the landscape as well as memories and reasoning about the landscape. These relationships remainedafter the area has been drastically altered by fire, implying a significant role of foraging for keeping “alive” the positive feelings and memories of the forest landscape. Through questionnaires and semistructured interviews, we examine why individuals forage, what foraging meant for them before the event and how they relate to the landscape and foraging after the fire. Our findings suggest that these connections are built on an interplay between place, practice and intimate knowledge. We conclude that foraging play an essential role in defining and developing connections to landscape which can act as the basis for stewardship of the landscape. Management implications: • In order to facilitate reconnection to the landscape after a forest fire there is a need to understand how individuals and communities related to the landscape before the fire. • Foraging will always be reliant on issues of access, and specific management regimes. • Cultural values and small-scale activities play an essential role in defining and developing connections to landscape. Connections which can ultimately inform a sense of responsibility and stewardship. • Activities such as foraging are reliant on more than just the affordance provided by the physical and visual character of a landscape.
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| 35. |
- Calderon, Camilo, et al.
(author)
-
Navigating swift and slow planning: planners' balancing act in the design of participatory processes
- 2024
-
In: European Planning Studies. - : Informa UK Limited. - 0965-4313 .- 1469-5944. ; 32, s. 390-409
-
Journal article (peer-reviewed)abstract
- Pressing sustainability challenges and increased influence of neoliberal ideas in planning have resulted in strong demands to 'speed up', and increase efficiency in, planning processes. Meanwhile, the reported risks that such emphasis on speed have for participatory decision-making and continuous calls for increased deliberation in planning, following the ideas of communicative planning theory, suggest that planning processes ought to 'slow down'. These dual pressures for swift and slow planning have been discussed within Nordic planning studies as an 'either-or' tension by which decision-making processes are either swift yet exclusive and technical-based and/or market-driven or participatory and deliberative but time-consuming. This paper provides insights into how deliberative planners navigate the double pressure for swift and slow planning in the design of participatory planning processes. It is based on a case study in Uppsala, Sweden where demands for swift decision-making and for participation following deliberative ideals were noticeable. The case study shows planners striving in different ways to balance the contradicting demands for swift and slow planning through their process design choices. These findings provide inspiration to reimagine the deliberative turn in planning as a 'balancing act' between equally important demands for participation and deliberation, and for faster and more efficient planning.
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| 36. |
- Calderon, Camilo, et al.
(author)
-
Towards the development of landscape democracy: a theoretical contribution
- 2016
-
Conference paper (peer-reviewed)abstract
- Participatory approaches have gained recognition through the European Landscape Convention (Council of Europe 2000), yet still remain questionable within landscape planning. Practitioners struggle to operationalise landscape as dynamic, holistic and democratic as defined in the ELC. This is due to: 1) weakness of substantive theory in landscape planning, with practice engaging with an impoverished understanding of landscape; and 2) a focus on normative ideals of how participation ought to be as opposed to the realpolitik of these practices. As such, practitioners fail to handle the diverse, dynamic values experienced in landscape, and the conflicts and power relations of participatory processes. By forwarding an understanding of the dynamics of landscape planning, and the differences, conflicts and power relations that are present in participatory processes, the paper develops a theorisation of landscape as a democratic entity.
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| 37. |
- Carleo, Ilaria, et al.
(author)
-
The Multiplanet System TOI-421*
- 2020
-
In: Astronomical Journal. - : American Astronomical Society. - 1538-3881 .- 0004-6256. ; 160:3
-
Journal article (peer-reviewed)abstract
- We report the discovery of a warm Neptune and a hot sub-Neptune transiting TOI-421 (BD-14 1137, TIC 94986319), a bright (V = 9.9) G9 dwarf star in a visual binary system observed by the Transiting Exoplanet Survey Satellite (TESS) space mission in Sectors 5 and 6. We performed ground-based follow-up observations-comprised of Las Cumbres Observatory Global Telescope transit photometry, NIRC2 adaptive optics imaging, and FIbre-fed Echelle Spectrograph, CORALIE, High Accuracy Radial velocity Planet Searcher, High Resolution echelle Spectrometer, and Planet Finder Spectrograph high-precision Doppler measurements-and confirmed the planetary nature of the 16 day transiting candidate announced by the TESS team. We discovered an additional radial velocity signal with a period of five days induced by the presence of a second planet in the system, which we also found to transit its host star. We found that the inner mini-Neptune, TOI-421 b, has an orbital period of P-b = 5.19672 +/- 0.00049 days, a mass of M-b = 7.17 +/- 0.66 M-circle plus, and a radius of R-b = R-circle plus, whereas the outer warm Neptune, TOI-421 c, has a period of P-c = 16.06819 +/- 0.00035 days, a mass of M-c = 16.42(-1.04)(+1.06)M(circle plus), a radius of R-c = 5.09(-0.15)(+0.16)R(circle plus), and a density of rho(c) = 0.685(-0.072)(+0.080) cm(-3). With its characteristics, the outer planet (rho(c) = 0.685(-0.0072)(+0.080) cm(-3)) is placed in the intriguing class of the super-puffy mini-Neptunes. TOI-421 b and TOI-421 c are found to be well-suited for atmospheric characterization. Our atmospheric simulations predict significant Ly alpha transit absorption, due to strong hydrogen escape in both planets, as well as the presence of detectable CH4 in the atmosphere of TOI-421 c if equilibrium chemistry is assumed.
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| 38. |
- Fenstermacher, M.E., et al.
(author)
-
DIII-D research advancing the physics basis for optimizing the tokamak approach to fusion energy
- 2022
-
In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:4
-
Journal article (peer-reviewed)abstract
- DIII-D physics research addresses critical challenges for the operation of ITER and the next generation of fusion energy devices. This is done through a focus on innovations to provide solutions for high performance long pulse operation, coupled with fundamental plasma physics understanding and model validation, to drive scenario development by integrating high performance core and boundary plasmas. Substantial increases in off-axis current drive efficiency from an innovative top launch system for EC power, and in pressure broadening for Alfven eigenmode control from a co-/counter-I p steerable off-axis neutral beam, all improve the prospects for optimization of future long pulse/steady state high performance tokamak operation. Fundamental studies into the modes that drive the evolution of the pedestal pressure profile and electron vs ion heat flux validate predictive models of pedestal recovery after ELMs. Understanding the physics mechanisms of ELM control and density pumpout by 3D magnetic perturbation fields leads to confident predictions for ITER and future devices. Validated modeling of high-Z shattered pellet injection for disruption mitigation, runaway electron dissipation, and techniques for disruption prediction and avoidance including machine learning, give confidence in handling disruptivity for future devices. For the non-nuclear phase of ITER, two actuators are identified to lower the L-H threshold power in hydrogen plasmas. With this physics understanding and suite of capabilities, a high poloidal beta optimized-core scenario with an internal transport barrier that projects nearly to Q = 10 in ITER at ∼8 MA was coupled to a detached divertor, and a near super H-mode optimized-pedestal scenario with co-I p beam injection was coupled to a radiative divertor. The hybrid core scenario was achieved directly, without the need for anomalous current diffusion, using off-axis current drive actuators. Also, a controller to assess proximity to stability limits and regulate β N in the ITER baseline scenario, based on plasma response to probing 3D fields, was demonstrated. Finally, innovative tokamak operation using a negative triangularity shape showed many attractive features for future pilot plant operation.
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| 39. |
- Green, Jonathan M. H., et al.
(author)
-
Research priorities for managing the impacts and dependencies of business upon food, energy, water and the environment
- 2017
-
In: Sustainability Science. - : Springer Science and Business Media LLC. - 1862-4065 .- 1862-4057. ; 12:2, s. 319-331
-
Journal article (peer-reviewed)abstract
- Delivering access to sufficient food, energy and water resources to ensure human wellbeing is a major concern for governments worldwide. However, it is crucial to account for the 'nexus' of interactions between these natural resources and the consequent implications for human wellbeing. The private sector has a critical role in driving positive change towards more sustainable nexus management and could reap considerable benefits from collaboration with researchers to devise solutions to some of the foremost sustainability challenges of today. Yet opportunities are missed because the private sector is rarely involved in the formulation of deliverable research priorities. We convened senior research scientists and influential business leaders to collaboratively identify the top forty questions that, if answered, would best help companies understand and manage their food-energy-water-environment nexus dependencies and impacts. Codification of the top order nexus themes highlighted research priorities around development of pragmatic yet credible tools that allow businesses to incorporate nexus interactions into their decision-making; demonstration of the business case for more sustainable nexus management; identification of the most effective levers for behaviour change; and understanding incentives or circumstances that allow individuals and businesses to take a leadership stance. Greater investment in the complex but productive relations between the private sector and research community will create deeper and more meaningful collaboration and cooperation.
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| 40. |
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| 41. |
- Iglesias, Maria Jesus, et al.
(author)
-
Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism
- 2023
-
In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
-
Journal article (peer-reviewed)abstract
- Venous thromboembolism (VTE) is a common, multi-causal disease with potentially serious short- and long-term complications. In clinical practice, there is a need for improved plasma biomarker-based tools for VTE diagnosis and risk prediction. Here we show, using proteomics profiling to screen plasma from patients with suspected acute VTE, and several case-control studies for VTE, how Complement Factor H Related 5 protein (CFHR5), a regulator of the alternative pathway of complement activation, is a VTE-associated plasma biomarker. In plasma, higher CFHR5 levels are associated with increased thrombin generation potential and recombinant CFHR5 enhanced platelet activation in vitro. GWAS analysis of ~52,000 participants identifies six loci associated with CFHR5 plasma levels, but Mendelian randomization do not demonstrate causality between CFHR5 and VTE. Our results indicate an important role for the regulation of the alternative pathway of complement activation in VTE and that CFHR5 represents a potential diagnostic and/or risk predictive plasma biomarker.
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| 42. |
- Ihantola, Petri, et al.
(author)
-
Educational Data Mining and Learning Analytics in Programming : Literature Review and Case Studies
- 2016
-
In: Proceedings of the 2015 ITiCSE on Working Group Reports. - New York, NY, USA : ACM Digital Library. - 9781450341462 ; , s. 41-63
-
Conference paper (peer-reviewed)abstract
- Educational data mining and learning analytics promise better understanding of student behavior and knowledge, as well as new information on the tacit factors that contribute to student actions. This knowledge can be used to inform decisions related to course and tool design and pedagogy, and to further engage students and guide those at risk of failure. This working group report provides an overview of the body of knowledge regarding the use of educational data mining and learning analytics focused on the teaching and learning of programming. In a literature survey on mining students' programming processes for 2005-2015, we observe a significant increase in work related to the field. However, the majority of the studies focus on simplistic metric analysis and are conducted within a single institution and a single course. This indicates the existence of further avenues of research and a critical need for validation and replication to better understand the various contributing factors and the reasons why certain results occur. We introduce a novel taxonomy to analyse replicating studies and discuss the importance of replicating and reproducing previous work. We describe what is the state of the art in collecting and sharing programming data. To better understand the challenges involved in replicating or reproducing existing studies, we report our experiences from three case studies using programming data. Finally, we present a discussion of future directions for the education and research community.
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| 43. |
- Ji, Xuemei, et al.
(author)
-
Identification of susceptibility pathways for the role of chromosome 15q25.1 in modifying lung cancer risk
- 2018
-
In: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 9, s. 1-15
-
Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) identified the chromosome 15q25.1 locus as a leading susceptibility region for lung cancer. However, the pathogenic pathways, through which susceptibility SNPs within chromosome 15q25.1 affects lung cancer risk, have not been explored. We analyzed three cohorts with GWAS data consisting 42,901 individuals and lung expression quantitative trait loci (eQTL) data on 409 individuals to identify and validate the underlying pathways and to investigate the combined effect of genes from the identified susceptibility pathways. The KEGG neuroactive ligand receptor interaction pathway, two Reactome pathways, and 22 Gene Ontology terms were identified and replicated to be significantly associated with lung cancer risk, with P values less than 0.05 and FDR less than 0.1. Functional annotation of eQTL analysis results showed that the neuroactive ligand receptor interaction pathway and gated channel activity were involved in lung cancer risk. These pathways provide important insights for the etiology of lung cancer.
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| 44. |
- Ji, Xuemei, et al.
(author)
-
Protein-altering germline mutations implicate novel genes related to lung cancer development
- 2020
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
-
Journal article (peer-reviewed)abstract
- Few germline mutations are known to affect lung cancer risk. We performed analyses of rare variants from 39,146 individuals of European ancestry and investigated gene expression levels in 7,773 samples. We find a large-effect association with an ATM L2307F (rs56009889) mutation in adenocarcinoma for discovery (adjusted Odds Ratio=8.82, P=1.18x10(-15)) and replication (adjusted OR=2.93, P=2.22x10(-3)) that is more pronounced in females (adjusted OR=6.81 and 3.19 and for discovery and replication). We observe an excess loss of heterozygosity in lung tumors among ATM L2307F allele carriers. L2307F is more frequent (4%) among Ashkenazi Jewish populations. We also observe an association in discovery (adjusted OR=2.61, P=7.98x10(-22)) and replication datasets (adjusted OR=1.55, P=0.06) with a loss-of-function mutation, Q4X (rs150665432) of an uncharacterized gene, KIAA0930. Our findings implicate germline genetic variants in ATM with lung cancer susceptibility and suggest KIAA0930 as a novel candidate gene for lung cancer risk. In lung cancer, relatively few germline mutations are known to impact risk. Here the authors looked at rare variants in 39,146 individuals and find novel germline mutations associated with risk, as well as implicating ATM and a new candidate gene for lung cancer risk.
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| 45. |
- Knez, Igor, et al.
(author)
-
Before and after a natural disaster : disruption in emotion component of place-identity and wellbeing
- 2018
-
In: Journal of Environmental Psychology. - : Academic Press. - 0272-4944 .- 1522-9610. ; 55, s. 11-17
-
Journal article (peer-reviewed)abstract
- The aim was to investigate relationships between emotion and cognition components of place-identity and wellbeing, before and after a natural disaster. A total of 656 respondents, living near the area of the largest forest and landscape fire in modern times in Sweden, participated in this study. Before the disaster, a positive association was found between place-identity and wellbeing, indicating that the stronger emotions participants evolved to the place, as well as remembered more and thought about the place, the stronger wellbeing they experienced at the site. After the disaster, the strength of this relationship decreased more than twice, accounted for by the weakening of the emotion-wellbeing link. Accordingly, participants almost lost their emotional bond to the area but maintained their memories and thoughts about the site intact and, by that, their positive wellbeing associations with the location. This indicates tentatively the phenomenon of post-traumatic growth, type of resilience involving operations of cognitive appraisal. © 2017 Elsevier Ltd
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| 46. |
- Knez, Igor, 1959-, et al.
(author)
-
I can still see, hear and smell the fire : Cognitive, emotional and personal consequences of a natural disaster, and the impact of evacuation
- 2021
-
In: Journal of Environmental Psychology. - : Elsevier. - 0272-4944 .- 1522-9610. ; 74
-
Journal article (peer-reviewed)abstract
- We investigated the effects of evacuation experience on autobiographical memory, sensory-perceptual re-experiencing, emotions, and personal consequentiality of a natural disaster one year after. A total of 601 individuals participated, living nearby the area of the largest fire in modern times in Sweden. It was shown that evacuated (first-hand experience) compared to not-evacuated (second-hand experience) participants thought and talked more about the fire. Evacuated residents also mentally traveled back and re-lived the disaster more; as well as saw the fire, heard its sound, smelled it more, and felt more anxious, enraged, and emotionally strong. Moreover, evacuated compared to not-evacuated participants estimated that their life and view of the world had changed due to the natural disaster. All this suggests that the psychology of dramatically charged events, such as natural disasters, differs notably between individuals “being there” and those “hearing the news”, indicating a factual flashbulb memory as a result of the first-hand experience.
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| 47. |
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| 48. |
- Li, Yafang, et al.
(author)
-
Genetic interaction analysis among oncogenesis-related genes revealed novel genes and networks in lung cancer development
- 2019
-
In: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 10:19, s. 1760-1774
-
Journal article (peer-reviewed)abstract
- The development of cancer is driven by the accumulation of many oncogenesis-related genetic alterations and tumorigenesis is triggered by complex networks of involved genes rather than independent actions. To explore the epistasis existing among oncogenesis-related genes in lung cancer development, we conducted pairwise genetic interaction analyses among 35,031 SNPs from 2027 oncogenesis-related genes. The genotypes from three independent genome-wide association studies including a total of 24,037 lung cancer patients and 20,401 healthy controls with Caucasian ancestry were analyzed in the study. Using a two-stage study design including discovery and replication studies, and stringent Bonferroni correction for multiple statistical analysis, we identified significant genetic interactions between SNPs in RGL1:RAD51B (OR=0.44, p value=3.27x10-11 in overall lung cancer and OR=0.41, p value=9.71x10-11 in non-small cell lung cancer), SYNE1:RNF43 (OR=0.73, p value=1.01x10-12 in adenocarcinoma) and FHIT:TSPAN8 (OR=1.82, p value=7.62x10-11 in squamous cell carcinoma) in our analysis. None of these genes have been identified from previous main effect association studies in lung cancer. Further eQTL gene expression analysis in lung tissues provided information supporting the functional role of the identified epistasis in lung tumorigenesis. Gene set enrichment analysis revealed potential pathways and gene networks underlying molecular mechanisms in overall lung cancer as well as histology subtypes development. Our results provide evidence that genetic interactions between oncogenesis-related genes play an important role in lung tumorigenesis and epistasis analysis, combined with functional annotation, provides a valuable tool for uncovering functional novel susceptibility genes that contribute to lung cancer development by interacting with other modifier genes.
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| 49. |
- Li, Yafang, et al.
(author)
-
Genome-wide interaction study of smoking behavior and non-small cell lung cancer risk in Caucasian population
- 2018
-
In: Carcinogenesis. - : Oxford University Press (OUP). - 0143-3334 .- 1460-2180. ; 39:3, s. 336-346
-
Journal article (peer-reviewed)abstract
- Non-small cell lung cancer is the most common type of lung cancer. Both environmental and genetic risk factors contribute to lung carcinogenesis. We conducted a genome-wide interaction analysis between single nucleotide polymorphisms (SNPs) and smoking status (never- versus ever-smokers) in a European-descent population. We adopted a two-step analysis strategy in the discovery stage: we first conducted a case-only interaction analysis to assess the relationship between SNPs and smoking behavior using 13 336 non-small cell lung cancer cases. Candidate SNPs with P-value <0.001 were further analyzed using a standard case-control interaction analysis including 13 970 controls. The significant SNPs with P-value <3.5 × 10-5 (correcting for multiple tests) from the case-control analysis in the discovery stage were further validated using an independent replication dataset comprising 5377 controls and 3054 non-small cell lung cancer cases. We further stratified the analysis by histological subtypes. Two novel SNPs, rs6441286 and rs17723637, were identified for overall lung cancer risk. The interaction odds ratio and meta-analysis P-value for these two SNPs were 1.24 with 6.96 × 10-7 and 1.37 with 3.49 × 10-7, respectively. In addition, interaction of smoking with rs4751674 was identified in squamous cell lung carcinoma with an odds ratio of 0.58 and P-value of 8.12 × 10-7. This study is by far the largest genome-wide SNP-smoking interaction analysis reported for lung cancer. The three identified novel SNPs provide potential candidate biomarkers for lung cancer risk screening and intervention. The results from our study reinforce that gene-smoking interactions play important roles in the etiology of lung cancer and account for part of the missing heritability of this disease.
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| 50. |
- Lundberg, Jon O., et al.
(author)
-
Nitrate and nitrite in biology, nutrition and therapeutics
- 2009
-
In: Nature Chemical Biology. - : Springer Science and Business Media LLC. - 1552-4450 .- 1552-4469. ; 5:12, s. 865-869
-
Journal article (peer-reviewed)abstract
- Inorganic nitrate and nitrite from endogenous or dietary sources are metabolized in vivo to nitric oxide (NO) and other bioactive nitrogen oxides. The nitrate-nitrite-NO pathway is emerging as an important mediator of blood flow regulation, cell signaling, energetics and tissue responses to hypoxia. The latest advances in our understanding of the biochemistry, physiology and therapeutics of nitrate, nitrite and NO were discussed during a recent 2-day meeting at the Nobel Forum, Karolinska Institutet in Stockholm.
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