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- In ’t Veld, Sjors G.J.G., et al.
(författare)
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Detection and localization of early- and late-stage cancers using platelet RNA
- 2022
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Ingår i: Cancer Cell. - : Elsevier. - 1535-6108 .- 1878-3686. ; 40:9, s. 999-1009.e6
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Tidskriftsartikel (refereegranskat)abstract
- Cancer patients benefit from early tumor detection since treatment outcomes are more favorable for less advanced cancers. Platelets are involved in cancer progression and are considered a promising biosource for cancer detection, as they alter their RNA content upon local and systemic cues. We show that tumor-educated platelet (TEP) RNA-based blood tests enable the detection of 18 cancer types. With 99% specificity in asymptomatic controls, thromboSeq correctly detected the presence of cancer in two-thirds of 1,096 blood samples from stage I–IV cancer patients and in half of 352 stage I–III tumors. Symptomatic controls, including inflammatory and cardiovascular diseases, and benign tumors had increased false-positive test results with an average specificity of 78%. Moreover, thromboSeq determined the tumor site of origin in five different tumor types correctly in over 80% of the cancer patients. These results highlight the potential properties of TEP-derived RNA panels to supplement current approaches for blood-based cancer screening.
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- Richards, Stephen, et al.
(författare)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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- Hartley, Philippa, et al.
(författare)
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SKA Science Data Challenge 2: analysis and results
- 2023
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Ingår i: Monthly Notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 523:2, s. 1967-1993
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Tidskriftsartikel (refereegranskat)abstract
- The Square Kilometre Array Observatory (SKAO) will explore the radio sky to new depths in order to conduct transformational science. SKAO data products made available to astronomers will be correspondingly large and complex, requiring the application of advanced analysis techniques to extract key science findings. To this end, SKAO is conducting a series of Science Data Challenges, each designed to familiarize the scientific community with SKAO data and to drive the development of new analysis techniques. We present the results from Science Data Challenge 2 (SDC2), which invited participants to find and characterize 233 245 neutral hydrogen (H i) sources in a simulated data product representing a 2000 h SKA-Mid spectral line observation from redshifts 0.25-0.5. Through the generous support of eight international supercomputing facilities, participants were able to undertake the Challenge using dedicated computational resources. Alongside the main challenge, 'reproducibility awards' were made in recognition of those pipelines which demonstrated Open Science best practice. The Challenge saw over 100 participants develop a range of new and existing techniques, with results that highlight the strengths of multidisciplinary and collaborative effort. The winning strategy - which combined predictions from two independent machine learning techniques to yield a 20 per cent improvement in overall performance - underscores one of the main Challenge outcomes: that of method complementarity. It is likely that the combination of methods in a so-called ensemble approach will be key to exploiting very large astronomical data sets.
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- Lopez-Garcia, SC, et al.
(författare)
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Treatment and long-term outcome in primary distal renal tubular acidosis
- 2019
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Ingår i: Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. - : Oxford University Press (OUP). - 1460-2385. ; 34:6, s. 981-991
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Tidskriftsartikel (refereegranskat)
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- Wagenveld, Jonah D., et al.
(författare)
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The MeerKAT Absorption Line Survey: Homogeneous continuum catalogues towards a measurement of the cosmic radio dipole
- 2023
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 673
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Tidskriftsartikel (refereegranskat)abstract
- The number counts of homogeneous samples of radio sources are a tried and true method of probing the large-scale structure of the Universe, as most radio sources outside the Galactic plane are at cosmological distances. As such, they are expected to trace the cosmic radio dipole, an anisotropy analogous to the dipole seen in the cosmic microwave background (CMB). Results have shown that although the cosmic radio dipole matches the direction of the CMB dipole, it has a significantly larger amplitude. This unexplained result challenges our assumption of the Universe being isotropic, which can have large repercussions for the current cosmological paradigm. Though significant measurements have been made, sensitivity to the radio dipole is generally hampered by systematic effects that can cause large biases in the measurement. Here we assess these systematics with data from the MeerKAT Absorption Line Survey (MALS), a blind search for absorption lines with pointings centred on bright radio sources. With the sensitivity and field of view of MeerKAT, thousands of sources are observed in each pointing, allowing for the possibility of measuring the cosmic radio dipole given enough pointings. We present the analysis of ten MALS pointings, focusing on systematic effects that could lead to an inhomogeneous catalogue. We describe the calibration and creation of full band continuum images and catalogues, producing a combined catalogue containing 16 307 sources and covering 37.5 square degrees of sky down to a sensitivity of 10 μJy beam-1. We measure the completeness, purity, and flux recovery statistics for these catalogues using simulated data. We investigate different source populations in the catalogues by looking at flux densities and spectral indices and how they might influence source counts. Using the noise characteristics of the pointings, we find global measures that can be used to correct for the incompleteness of the catalogue, producing corrected number counts down to 100-200 μJy. We show that we can homogenise the catalogues and properly account for systematic effects. We determine that we can measure the dipole to 3significance with 100 MALS pointings.
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- Carlsson, Per, et al.
(författare)
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Better Grid Integration of Distributed Generation Using Supply - Demand Matching
- 2005
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Konferensbidrag (populärvet., debatt m.m.)abstract
- In the future electricity grids it is expected that the share of Distributed Generation and intermittent generators will rise. Because of that the conventional top-down-approach of grid control is no longer sufficient and the need arises to find new mechanisms for balancing supply and demand of electricity.Using new developments in ICT technology ECN and EnerSearch have developed an alternative concept of balancing supply and demand of electricity, supply-demand matching. This facilitates the introduction of a large amount of small scale distributed generation (including RES) within the lower levels of the power grid.We show several scenarios that may benefit from supply-demand matching. One scenario investigates the impact of distributed supply - demand matching (SDM) in a residential area. In the scenario a cluster of 40 houses, all connected to the same low-voltage distribution grid cell (LV-cell), is simulated. The LV-cell is externally connected to a medium voltage network. Through this connection power can be obtained from and delivered to other parts of the network. The influence of the SDM has been evaluated in terms of the possibilities to improve the overall match of local demand and supply (i.e. improvement of the local match), and decrease the dependency upon externally supplied power. The added value of SDM has been evaluated in terms of financial value of the locally generated power, and in terms of compliance to user preferences.Another scenario investigates the case of a program responsible partner having intermittent production such as a wind turbine. Due to uncertainty in the power forecast financial risk is at stake when trading the power. We add different suppliers and consumers to the portfolio, who have elasticity in their load patterns, such as a CHP-installation controlling the building temperature of a cooling device controlling a cold store. We use this elasticity as a local reserve capacity to be controlled by the program responsible partner in order to overcome the uncertainty of its intermittent production.At the conference we will present the simulation results for these scenarios within the above sketched distributed power market. The case studies will show the benefits for cost effective operation of distributed energy resources (DER); reduction of power flow through substations, thus avoiding distribution and transmission cost; controlling unbalance in intermittent renewables generation such as PV or wind. To validate the results of the simulations an experiment is being prepared.
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