| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 3. |
- Khatri, C, et al.
(författare)
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Outcomes after perioperative SARS-CoV-2 infection in patients with proximal femoral fractures: an international cohort study
- 2021
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Ingår i: BMJ open. - : BMJ. - 2044-6055. ; 11:11, s. e050830-
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Tidskriftsartikel (refereegranskat)abstract
- Studies have demonstrated high rates of mortality in people with proximal femoral fracture and SARS-CoV-2, but there is limited published data on the factors that influence mortality for clinicians to make informed treatment decisions. This study aims to report the 30-day mortality associated with perioperative infection of patients undergoing surgery for proximal femoral fractures and to examine the factors that influence mortality in a multivariate analysis.SettingProspective, international, multicentre, observational cohort study.ParticipantsPatients undergoing any operation for a proximal femoral fracture from 1 February to 30 April 2020 and with perioperative SARS-CoV-2 infection (either 7 days prior or 30-day postoperative).Primary outcome30-day mortality. Multivariate modelling was performed to identify factors associated with 30-day mortality.ResultsThis study reports included 1063 patients from 174 hospitals in 19 countries. Overall 30-day mortality was 29.4% (313/1063). In an adjusted model, 30-day mortality was associated with male gender (OR 2.29, 95% CI 1.68 to 3.13, p<0.001), age >80 years (OR 1.60, 95% CI 1.1 to 2.31, p=0.013), preoperative diagnosis of dementia (OR 1.57, 95% CI 1.15 to 2.16, p=0.005), kidney disease (OR 1.73, 95% CI 1.18 to 2.55, p=0.005) and congestive heart failure (OR 1.62, 95% CI 1.06 to 2.48, p=0.025). Mortality at 30 days was lower in patients with a preoperative diagnosis of SARS-CoV-2 (OR 0.6, 95% CI 0.6 (0.42 to 0.85), p=0.004). There was no difference in mortality in patients with an increase to delay in surgery (p=0.220) or type of anaesthetic given (p=0.787).ConclusionsPatients undergoing surgery for a proximal femoral fracture with a perioperative infection of SARS-CoV-2 have a high rate of mortality. This study would support the need for providing these patients with individualised medical and anaesthetic care, including medical optimisation before theatre. Careful preoperative counselling is needed for those with a proximal femoral fracture and SARS-CoV-2, especially those in the highest risk groups.Trial registration numberNCT04323644
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| 4. |
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| 5. |
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| 6. |
- Abe, K., et al.
(författare)
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J-PARC Neutrino Beamline Upgrade Technical Design Report
- 2019
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Rapport (refereegranskat)abstract
- In this document, technical details of the upgrade plan of the J-PARC neutrino beamline for the extension of the T2K experiment are described. T2K has proposed to accumulate data corresponding to 2×1022 protons-on-target in the next decade, aiming at an initial observation of CP violation with 3σ or higher significance in the case of maximal CP violation. Methods to increase the neutrino beam intensity, which are necessary to achieve the proposed data increase, are described.
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| 7. |
- Abe, K., et al.
(författare)
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Neutron tagging following atmospheric neutrino events in a water Cherenkov detector
- 2022
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Ingår i: Journal of Instrumentation. - : Institute of Physics (IOP). - 1748-0221. ; 17:10
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Tidskriftsartikel (refereegranskat)abstract
- We present the development of neutron-tagging techniques in Super-Kamiokande IV using a neural network analysis. The detection efficiency of neutron capture on hydrogen is estimated to be 26%, with a mis-tag rate of 0.016 per neutrino event. The uncertainty of the tagging efficiency is estimated to be 9.0%. Measurement of the tagging efficiency with data from an Americium-Beryllium calibration agrees with this value within 10%. The tagging procedure was performed on 3,244.4 days of SK-IV atmospheric neutrino data, identifying 18,091 neutrons in 26,473 neutrino events. The fitted neutron capture lifetime was measured as 218 +/- 9 mu s.
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| 8. |
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| 9. |
- Thoma, B, et al.
(författare)
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An international, interprofessional investigation of the self-reported podcast listening habits of emergency clinicians: A METRIQ Study
- 2020
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Ingår i: CJEM. - : Springer Science and Business Media LLC. - 1481-8043 .- 1481-8035. ; 22:1, s. 112-117
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Tidskriftsartikel (refereegranskat)abstract
- ObjectivesPodcasts are increasingly being used for medical education. A deeper understanding of usage patterns would inform both producers and researchers of medical podcasts. We aimed to determine how and why podcasts are used by emergency medicine and critical care clinicians.MethodsAn international interprofessional sample (medical students, residents, physicians, nurses, physician assistants, and paramedics) was recruited through direct contact and a multimodal social media (Twitter and Facebook) campaign. Each participant completed a survey outlining how and why they utilize medical podcasts. Recruitment materials included an infographic and study website.Results390 participants from 33 countries and 4 professions (medicine, nursing, paramedicine, physician assistant) completed the survey. Participants most frequently listened to medical podcasts to review new literature (75.8%), learn core material (75.1%), and refresh memory (71.8%). The majority (62.6%) were aware of the ability to listen at increased speeds, but most (76.9%) listened at 1.0 x (normal) speed. All but 25 (6.4%) participants concurrently performed other tasks while listening. Driving (72.3%), exercising (39.7%), and completing chores (39.2%) were the most common. A minority of participants used active learning techniques such as pausing, rewinding, and replaying segments of the podcast. Very few listened to podcasts multiple times.ConclusionsAn international cohort of emergency clinicians use medical podcasts predominantly for learning. Their listening habits (rarely employing active learning strategies and frequently performing concurrent tasks) may not support this goal. Further exploration of the impact of these activities on learning from podcasts is warranted.
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| 10. |
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| 11. |
- Willeit, P., et al.
(författare)
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Carotid Intima-Media Thickness Progression as Surrogate Marker for Cardiovascular Risk: Meta-Analysis of 119 Clinical Trials Involving 100 667 Patients
- 2020
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Ingår i: Circulation. - 1524-4539. ; 142:7, s. 621-642
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: To quantify the association between effects of interventions on carotid intima-media thickness (cIMT) progression and their effects on cardiovascular disease (CVD) risk. METHODS: We systematically collated data from randomized, controlled trials. cIMT was assessed as the mean value at the common-carotid-artery; if unavailable, the maximum value at the common-carotid-artery or other cIMT measures were used. The primary outcome was a combined CVD end point defined as myocardial infarction, stroke, revascularization procedures, or fatal CVD. We estimated intervention effects on cIMT progression and incident CVD for each trial, before relating the 2 using a Bayesian meta-regression approach. RESULTS: We analyzed data of 119 randomized, controlled trials involving 100 667 patients (mean age 62 years, 42% female). Over an average follow-up of 3.7 years, 12 038 patients developed the combined CVD end point. Across all interventions, each 10 μm/y reduction of cIMT progression resulted in a relative risk for CVD of 0.91 (95% Credible Interval, 0.87-0.94), with an additional relative risk for CVD of 0.92 (0.87-0.97) being achieved independent of cIMT progression. Taken together, we estimated that interventions reducing cIMT progression by 10, 20, 30, or 40 μm/y would yield relative risks of 0.84 (0.75-0.93), 0.76 (0.67-0.85), 0.69 (0.59-0.79), or 0.63 (0.52-0.74), respectively. Results were similar when grouping trials by type of intervention, time of conduct, time to ultrasound follow-up, availability of individual-participant data, primary versus secondary prevention trials, type of cIMT measurement, and proportion of female patients. CONCLUSIONS: The extent of intervention effects on cIMT progression predicted the degree of CVD risk reduction. This provides a missing link supporting the usefulness of cIMT progression as a surrogate marker for CVD risk in clinical trials.
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| 12. |
- Barlow, Natasha L. M., et al.
(författare)
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Lack of evidence for a substantial sea-level fluctuation within the Last Interglacial
- 2018
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Ingår i: Nature Geoscience. - : Springer Science and Business Media LLC. - 1752-0894 .- 1752-0908. ; 11:9, s. 627-634
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Forskningsöversikt (refereegranskat)abstract
- During the Last Interglacial, global mean sea level reached approximately 6 to 9 m above the present level. This period of high sea level may have been punctuated by a fall of more than 4 m, but a cause for such a widespread sea-level fall has been elusive. Reconstructions of global mean sea level account for solid Earth processes and so the rapid growth and decay of ice sheets is the most obvious explanation for the sea-level fluctuation. Here, we synthesize published geomorphological and stratigraphic indicators from the Last Interglacial, and find no evidence for ice-sheet regrowth within the warm interglacial climate. We also identify uncertainties in the interpretation of local relative sea-level data that underpin the reconstructions of global mean sea level. Given this uncertainty, and taking into account our inability to identify any plausible processes that would cause global sea level to fall by 4 m during warm climate conditions, we question the occurrence of a rapid sea-level fluctuation within the Last Interglacial. We therefore recommend caution in interpreting the high rates of global mean sea-level rise in excess of 3 to 7 m per 1,000 years that have been proposed for the period following the Last Interglacial sea-level lowstand.
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| 13. |
- Bentley, Michael J., et al.
(författare)
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A community-based geological reconstruction of Antarctic Ice Sheet deglaciation since the Last Glacial Maximum
- 2014
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 100, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- A robust understanding of Antarctic Ice Sheet deglacial history since the Last Glacial Maximum is important in order to constrain ice sheet and glacial-isostatic adjustment models, and to explore the forcing mechanisms responsible for ice sheet retreat. Such understanding can be derived from a broad range of geological and glaciological datasets and recent decades have seen an upsurge in such data gathering around the continent and Sub-Antarctic islands. Here, we report a new synthesis of those datasets, based on an accompanying series of reviews of the geological data, organised by sector. We present a series of timeslice maps for 20 ka, 15 ka, 10 ka and 5 ka, including grounding line position and ice sheet thickness changes, along with a clear assessment of levels of confidence. The reconstruction shows that the Antarctic Ice sheet did not everywhere reach the continental shelf edge at its maximum, that initial retreat was asynchronous, and that the spatial pattern of deglaciation was highly variable, particularly on the inner shelf. The deglacial reconstruction is consistent with a moderate overall excess ice volume and with a relatively small Antarctic contribution to meltwater pulse la. We discuss key areas of uncertainty both around the continent and by time interval, and we highlight potential priorities for future work. The synthesis is intended to be a resource for the modelling and glacial geological community.
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| 14. |
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| 16. |
- Moore, S. A., et al.
(författare)
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Wristband Accelerometers to motiVate arm Exercise after Stroke (WAVES) : Study protocol for a pilot randomized controlled trial
- 2016
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Ingår i: Trials. - : BioMed Central. - 1745-6215. ; 17:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Loss of upper limb function affects up to 85 % of acute stroke patients. Recovery of upper limb function requires regular intensive practise of specific upper limb tasks. To enhance intensity of practice interventions are being developed to encourage patients to undertake self-directed exercise practice. Most interventions do not translate well into everyday activities and stroke patients continue to find it difficult remembering integration of upper limb movements into daily activities. A wrist-worn device has been developed that monitors and provides 'live' upper limb activity feedback to remind patients to use their stroke arm in daily activities (The CueS wristband). The aim of this trial is to assess the feasibility of a multi-centre, observer blind, pilot randomised controlled trial of the CueS wristband in clinical stroke services. Methods/design: This pilot randomised controlled feasibility trial aims to recruit 60 participants over 15 months from North East England. Participants will be within 3 months of stroke which has caused new reduced upper limb function and will still be receiving therapy. Each participant will be randomised to an intervention or control group. Intervention participants will wear a CueS wristband (between 8 am and 8 pm) providing "live" feedback towards pre-set movement goals through a simple visual display and vibration prompts whilst undertaking a 4-week upper limb therapy programme (reviewed twice weekly by an occupational/physiotherapist). Control participants will also complete the 4-week upper limb therapy programme but will wear a 'sham' CueS wristband that monitors upper limb activity but provides no feedback. Outcomes will determine study feasibility in terms of recruitment, retention, adverse events, adherence and collection of descriptive clinical and accelerometer motor performance data at baseline, 4 weeks and 8 weeks. Discussion: The WAVES study will address an important gap in the evidence base by reporting the feasibility of undertaking an evaluation of emerging and affordable technology to encourage impaired upper limb activity after stroke. The study will establish whether the study protocol can be supported by clinical stroke services, thereby informing the design of a future multi-centre randomised controlled trial of clinical and cost-effectiveness.
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| 17. |
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| 18. |
- Clason, Caroline C., et al.
(författare)
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Controls on the early Holocene collapse of the Bothnian Sea Ice Stream
- 2016
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Ingår i: Journal of Geophysical Research - Earth Surface. - 2169-9003 .- 2169-9011. ; 121:12, s. 2494-2513
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Tidskriftsartikel (refereegranskat)abstract
- New high-resolution multibeam data in the Gulf of Bothnia reveal for the first time the subglacial environment of a Bothnian Sea Ice Stream. The geomorphological record suggests that increased meltwater production may have been important in driving rapid retreat of Bothnian Sea Ice during deglaciation. Here we apply a well-established, one-dimensional flow line model to simulate ice flow through the Gulf of Bothnia and investigate controls on retreat of the ice stream during the post-Younger Dryas deglaciation of the Fennoscandian Ice Sheet. The relative influence of atmospheric and marine forcings are investigated, with the modeled ice stream exhibiting much greater sensitivity to surface melting, implemented through surface mass balance and hydrofracture-induced calving, than to submarine melting or relative sea level change. Such sensitivity is supported by the presence of extensive meltwater features in the geomorphological record. The modeled ice stream does not demonstrate significant sensitivity to changes in prescribed ice stream width or overall bed slope, but local variations in basal topography and ice stream width result in nonlinear retreat of the grounding line, notably demonstrating points of short-lived retreat slowdown on reverse bed slopes. Retreat of the ice stream was most likely governed by increased ice surface meltwater production, with the modeled retreat rate less sensitive to marine forcings despite the marine setting.
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| 19. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 20. |
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| 23. |
- Hurlen, L., et al.
(författare)
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The plant panel : Feasibility study of an interactive large screen concept for process monitoring and operation
- 2015
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Ingår i: 9th International Topical Meeting on Nuclear Plant Instrumentation, Control, and Human-Machine Interface Technologies, NPIC and HMIT 2015. - : American Nuclear Society. - 9781510808096 ; , s. 2587-2596
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Konferensbidrag (refereegranskat)abstract
- Control room modernization projects worldwide are currently replacing or supplementing traditional wall-sized "boards" with computerized solutions. These solutions typically consist of multiple small screens that the operators need to navigate and arrange. Shared overview displays have been introduced to compensate for some of their perceived shortcomings, such as increased workload and a loss of process overview. This paper presents a study that investigates the feasibility of taking this approach a step further. Could we utilize modern screen technology to improve operator performance by introducing what we have called a "Plant Panel": a single, all-purpose, wall-sized, interactive display that shows the whole nuclear process in a coherent manner, blending detailed component and system information with useful plant overview information? To address this question we developed a prototype of the Plant Panel limited to the reactor-side of a Boiling Water Reactor and tested it with a number of potential users. This prototype is a 1.5 × 4 meter paper mock-up of the Plant Panel with an overlay of digitally projected interface elements. This study indicates that the Plant Panel concept may have several strengths compared to current computerized control room designs. The results of the feasibility tests show that features of the design related to supporting collaboration and process overview seem particularly promising. The main feasibility concern was related to how users could potentially lose their overview when positioned too close to the display. We recommend that further work should address this issue particularly, as well as exploring the areas for improvements that users identified.
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| 24. |
- Jacquet, Jennifer, et al.
(författare)
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Support US OCTOPUS Act to keep octopuses wild.
- 2024
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Ingår i: Science (New York, N.Y.). - 1095-9203. ; 385:6710, s. 721-722
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Tidskriftsartikel (refereegranskat)abstract
- Commercial octopus farming is incapable of meeting welfare requirements, unsustainable, and unnecessary for sustenance. Although no commercial octopus farms currently exist, a Spanish seafood company plans to build one in the Canary Islands for Octopus vulgaris. In March, the US state of Washington banned octopus farming. Similar legislation has been introduced in California and Hawai‘i . Now, the federal government is proposing action. The US Congress should pass the OCTOPUS Act, a federal law that would prohibit commercial octopus aquaculture in the United States and the import of commercially farmed octopus or octopus products.
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| 25. |
- Mead, AJ, et al.
(författare)
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Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation
- 2017
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Ingår i: The Journal of experimental medicine. - : Rockefeller University Press. - 1540-9538 .- 0022-1007. ; 214:7, s. 2005-2021
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Tidskriftsartikel (refereegranskat)abstract
- Although previous studies suggested that the expression of FMS-like tyrosine kinase 3 (Flt3) initiates downstream of mouse hematopoietic stem cells (HSCs), FLT3 internal tandem duplications (FLT3 ITDs) have recently been suggested to intrinsically suppress HSCs. Herein, single-cell interrogation found Flt3 mRNA expression to be absent in the large majority of phenotypic HSCs, with a strong negative correlation between Flt3 and HSC-associated gene expression. Flt3-ITD knock-in mice showed reduced numbers of phenotypic HSCs, with an even more severe loss of long-term repopulating HSCs, likely reflecting the presence of non-HSCs within the phenotypic HSC compartment. Competitive transplantation experiments established that Flt3-ITD compromises HSCs through an extrinsically mediated mechanism of disrupting HSC-supporting bone marrow stromal cells, with reduced numbers of endothelial and mesenchymal stromal cells showing increased inflammation-associated gene expression. Tumor necrosis factor (TNF), a cell-extrinsic potent negative regulator of HSCs, was overexpressed in bone marrow niche cells from FLT3-ITD mice, and anti-TNF treatment partially rescued the HSC phenotype. These findings, which establish that Flt3-ITD–driven myeloproliferation results in cell-extrinsic suppression of the normal HSC reservoir, are of relevance for several aspects of acute myeloid leukemia biology.
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