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- Hartley, Philippa, et al.
(author)
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SKA Science Data Challenge 2: analysis and results
- 2023
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In: Monthly Notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 523:2, s. 1967-1993
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Journal article (peer-reviewed)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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| 5. |
- In ’t Veld, Sjors G.J.G., et al.
(author)
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Detection and localization of early- and late-stage cancers using platelet RNA
- 2022
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In: Cancer Cell. - : Elsevier. - 1535-6108 .- 1878-3686. ; 40:9, s. 999-1009.e6
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Journal article (peer-reviewed)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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| 7. |
- Michalowski, M. J., et al.
(author)
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Massive stars formed in atomic hydrogen reservoirs : H i observations of gamma-ray burst host galaxies
- 2015
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 582
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Journal article (peer-reviewed)abstract
- Long gamma-ray bursts (GRBs), among the most energetic events in the Universe, are explosions of massive and short-lived stars, so they pinpoint locations of recent star formation. However, several GRB host galaxies have recently been found to be deficient in molecular gas (H-2), believed to be the fuel of star formation. Moreover, optical spectroscopy of GRB afterglows implies that the molecular phase constitutes only a small fraction of the gas along the GRB line of sight. Here we report the first ever 21 cm line observations of GRB host galaxies, using the Australia Telescope Compact Array, implying high levels of atomic hydrogen (HI), which suggests that the connection between atomic gas and star formation is stronger than previously thought. In this case, it is possible that star formation is directly fuelled by atomic gas (or that the HI- to- H-2 conversion is very efficient, which rapidly exhaust molecular gas), as has been theoretically shown to be possible. This can happen in low-metallicity gas near the onset of star formation because cooling of gas (necessary for star formation) is faster than the HI- to- H-2 conversion. Indeed, large atomic gas reservoirs, together with low molecular gas masses, stellar, and dust masses are consistent with GRB hosts being preferentially galaxies which have very recently started a star formation episode after accreting metal-poor gas from the intergalactic medium. This provides a natural route for forming GRBs in low-metallicity environments. The gas inflow scenario is also consistent with the existence of the companion HI object with no optical counterpart similar to 19 kpc from the GRB 060505 host, and with the fact that the HI centroids of the GRB 980425 and 060505 hosts do not coincide with optical centres of these galaxies, but are located close to the GRB positions.
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| 8. |
- Richards, Stephen, et al.
(author)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Journal article (peer-reviewed)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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| 9. |
- Michalowski, Michal J., et al.
(author)
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Molecular gas masses of gamma-ray burst host galaxies
- 2018
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 617
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Journal article (peer-reviewed)abstract
- Context. Long gamma-ray bursts (GRBs) can potentially be used as a tool to study star formation and recent gas accretion onto galaxies. However, the information about gas properties of GRB hosts is scarce. In particular, very few carbon monoxide (CO) line detections of individual GRB hosts have been reported. It has also been suggested that GRB hosts have lower molecular gas masses than expected from their star formation rates (SFRs). Aims. The objectives of this paper are to analyse molecular gas properties of the first substantial sample of GRB hosts and test whether they are deficient in molecular gas. Methods. We obtained CO(2-1) observations of seven GRB hosts with the APEX and IRAM 30 m telescopes. We analysed these data together with all other hosts with previous CO observations. From these observations we calculated the molecular gas masses of these galaxies and compared them with the expected values based on their SFRs and metallicities. Reults. We obtained detections for 3 GRB hosts (980425, 080207, and 111005A) and upper limits for the remaining 4 (031203, 060505, 060814, and 100316D). In our entire sample of 12 CO-observed GRB hosts, 3 are clearly deficient in molecular gas, even taking into account their metallicity (980425, 060814, and 080517). Four others are close to the best-fit line for other star-forming galaxies on the SFR-M-H2 plot (051022, 060505, 080207, and 100316D). One host is clearly molecule rich (111005A). Finally, the data for 4 GRB hosts are not deep enough to judge whether they are molecule deficient (000418, 030329, 031203, and 090423). The median value of the molecular gas depletion time, M-H2/SFR, of GRB hosts is similar to 0.3 dex below that of other star-forming galaxies, but this result has low statistical significance. A Kolmogorov-Smirnov test performed on M-H2/SFR shows an only similar to 2 sigma difference between GRB hosts and other galaxies. This difference can partly be explained by metallicity effects, since the significance decreases to similar to 1 sigma for M-H2/SFR versus metallicity. Conclusions. We found that any molecular gas deficiency of GRB hosts has low statistical significance and that it can be attributed to their lower metallicities; and thus the sample of GRB hosts has molecular properties that are consistent with those of other galaxies, and they can be treated as representative star-forming galaxies. However, the molecular gas deficiency can be strong for GRB hosts if they exhibit higher excitations and/or a lower CO-to-H-2 conversion factor than we assume, which would lead to lower molecular gas masses than we derive. Given the concentration of atomic gas recently found close to GRB and supernova sites, indicating recent gas inflow, our results about the weak molecular deficiency imply that such an inflow does not enhance the SFRs significantly, or that atomic gas converts efficiently into the molecular phase, which fuels star formation. Only if the analysis of a larger GRB host sample reveals molecular deficiency (especially close to the GRB position) would this support the hypothesis of star formation that is directly fuelled by atomic gas.
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| 10. |
- Mulay, A. L., et al.
(author)
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Borderline personality disorder diagnosis in a new key
- 2019
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In: Borderline Personality Disorder and Emotion Dysregulation. - : Springer Science and Business Media LLC. - 2051-6673. ; 6:1
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Journal article (peer-reviewed)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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| 11. |
- Carlsson, Per, et al.
(author)
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Better Grid Integration of Distributed Generation Using Supply - Demand Matching
- 2005
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Conference paper (pop. science, debate, etc.)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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| 12. |
- Michalowski, M. J., et al.
(author)
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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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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 616
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Journal article (peer-reviewed)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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| 14. |
- Albusoda, A., et al.
(author)
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A fresh look at IBS-opportunities for systems medicine approaches
- 2017
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In: Neurogastroenterology and Motility. - : Wiley. - 1350-1925. ; 29:3
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Journal article (peer-reviewed)abstract
- NeuroGUT is a EU-funded initial training network (ITN) of 14 research projects in neurogastroenterology that have employed an equal number of early-stage researchers. Neurogut trainees haveamong other activitiesattended an international conference on irritable bowel syndrome (IBS) in Bologna in 2016 and were asked to critically review and evaluate the current knowledge on IBS for their respective research activities, and to state what they were missing. Most appreciated were the topics brain imaging of gut activity, the role of the gut microbiota, the pharmacology of gut functions, the IBS-IBD interrelation, the new Rome IV criteria, the role of gas, and the placebo response in functional disorders. Missed were more detailed coverage of high-resolution manometry, functional brain imaging, advanced systems medicine approaches and bioinformatics technology, better sub-classification of IBS patients, and the development of disease biomarkers, extended at the molecular (genetic/epigenetic, proteonomic) level. They summarize that despite excellent specialized research, there is a gap open that should be filled with systems medicine. For this, it would be necessary that medical research learns even more from the data sciences and other basic disciplines, for example, information technology and system biology, and also welcomes a change in paradigm that enhances open sharing of data, information, and resources.
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| 15. |
- Tauber, Marie, et al.
(author)
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Landscape of mast cell populations across organs in mice and humans
- 2023
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In: Journal of Experimental Medicine. - : ROCKEFELLER UNIV PRESS. - 0022-1007 .- 1540-9538. ; 220:10
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Journal article (peer-reviewed)abstract
- Mast cells (MCs) are tissue-resident immune cells that exhibit homeostatic and neuron-associated functions. Here, we combined whole-tissue imaging and single-cell RNA sequencing datasets to generate a pan-organ analysis of MCs in mice and humans at steady state. In mice, we identify two mutually exclusive MC populations, MrgprB2(+) connective tissue-type MCs and MrgprB2(neg) mucosal-type MCs, with specific transcriptomic core signatures. While MrgprB2(+) MCs develop in utero independently of the bone marrow, MrgprB2(neg) MCs develop after birth and are renewed by bone marrow progenitors. In humans, we unbiasedly identify seven MC subsets (MC1-7) distributed across 12 organs with different transcriptomic core signatures. MC1 are preferentially enriched in the bladder, MC2 in the lungs, and MC4, MC6, and MC7 in the skin. Conversely, MC3 and MC5 are shared by most organs but not skin. This comprehensive analysis offers valuable insights into the natural diversity of MC subtypes in both mice and humans. Combining whole-tissue imaging and single-cell RNA sequencing datasets, Tauber et al. present a pan-organ analysis of mast cells in mice and humans at steady state, revealing an unexpected heterogeneity of mast cell populations across tissues and species.
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| 16. |
- Wagenveld, Jonah D., et al.
(author)
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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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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 673
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Journal article (peer-reviewed)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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