| 1. |
- 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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| 2. |
- 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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| 3. |
- 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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| 4. |
- Michalowski, M. J., et al.
(författare)
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The second-closest gamma-ray burst: Sub-luminous GRB 111005A with no supernova in a super-solar metallicity environment
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 616
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Tidskriftsartikel (refereegranskat)abstract
- We report the detection of the radio afterglow of a long gamma-ray burst (GRB) 111005A at 5-345 GHz, including very long baseline interferometry observations with a positional error of 0.2 mas. The afterglow position is coincident with the disc of a galaxy ESO 58049 at z = 0.01326 (∼1″ from its centre), which makes GRB 111005A the second-closest GRB known to date, after GRB 980425. The radio afterglow of GRB 111005A was an order of magnitude less luminous than those of local low-luminosity GRBs, and obviously less luminous than those of cosmological GRBs. The radio flux was approximately constant and then experienced an unusually rapid decay a month after the GRB explosion. Similarly to only two other GRBs, we did not find the associated supernovae (SNe), despite deep near- and mid-infrared observations 1-9 days after the GRB explosion, reaching ∼20 times fainter than other SNe associated with GRBs. Moreover, we measured a twice-solar metallicity for the GRB location. The low y-ray and radio luminosities, rapid decay, lack of a SN, and super-solar metallicity suggest that GRB 111005A represents a rare class of GRB that is different from typical core-collapse events. We modelled the spectral energy distribution of the GRB 111005A host finding that it is a moderately star-forming dwarf galaxy, similar to the host of GRB 980425. The existence of two local GRBs in such galaxies is still consistent with the hypothesis that the GRB rate is proportional to the cosmic star formation rate (SFR) density, but suggests that the GRB rate is biased towards low SFRs. Using the far-infrared detection of ESO 580-49, we conclude that the hosts of both GRBs 111005A and 980425 exhibit lower dust content than what would be expected from their stellar masses and optical colors.
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| 5. |
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| 6. |
- Mulay, A. L., et al.
(författare)
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Borderline personality disorder diagnosis in a new key
- 2019
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Ingår i: Borderline Personality Disorder and Emotion Dysregulation. - : Springer Science and Business Media LLC. - 2051-6673. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Conceptualizations of personality disorders (PD) are increasingly moving towards dimensional approaches. The definition and assessment of borderline personality disorder (BPD) in regard to changes in nosology are of great importance to theory and practice as well as consumers. We studied empirical connections between the traditional DSM-5 diagnostic criteria for BPD and Criteria A and B of the Alternative Model for Personality Disorders (AMPD). Method Raters of varied professional backgrounds possessing substantial knowledge of PDs (N = 20) characterized BPD criteria with the four domains of the Level of Personality Functioning Scale (LPFS) and 25 pathological personality trait facets. Mean AMPD values of each BPD criterion were used to support a nosological cross-walk of the individual BPD criteria and study various combinations of BPD criteria in their AMPD translation. The grand mean AMPD profile generated from the experts was compared to published BPD prototypes that used AMPD trait ratings and the DSM-5-III hybrid categorical-dimensional algorithm for BPD. Divergent comparisons with DSM-5-III algorithms for other PDs and other published PD prototypes were also examined. Results Inter-rater reliability analyses showed generally robust agreement. The AMPD profile for BPD criteria rated by individual BPD criteria was not isomorphic with whole-person ratings of BPD, although they were highly correlated. Various AMPD profiles for BPD were generated from theoretically relevant but differing configurations of BPD criteria. These AMPD profiles were highly correlated and showed meaningful divergence from non-BPD DSM-5-III algorithms and other PD prototypes. Conclusions Results show that traditional DSM BPD diagnosis reflects a common core of PD severity, largely composed of LPFS and the pathological traits of anxiousness, depressively, emotional lability, and impulsivity. Results confirm the traditional DSM criterion-based BPD diagnosis can be reliably cross-walked with the full AMPD scheme, and both approaches share substantial construct overlap. This relative equivalence suggests the vast clinical and research literatures associated with BPD may be brought forward with DSM-5-III diagnosis of BPD.
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| 7. |
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| 8. |
- 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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