| 1. |
- Mendoza, Patricia, et al.
(författare)
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DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as an Alk target in the Drosophila visceral mesoderm
- 2021
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Ingår i: Development. - : The Company of Biologists. - 0950-1991 .- 1477-9129. ; 148:23
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Tidskriftsartikel (refereegranskat)abstract
- Development of the Drosophila visceral muscle depends on Anaplastic Lymphoma Kinase (Alk) receptor tyrosine kinase (RTK) signaling, which specifies founder cells (FCs) in the circular visceral mesoderm (VM). Although Alk activation by its ligand Jelly Belly (Jeb) is well characterized, few target molecules have been identified. Here, we used targeted DamID (TaDa) to identify Alk targets in embryos overexpressing Jeb versus embryos with abrogated Alk activity, revealing differentially expressed genes, including the Snail/Scratch family transcription factor Kahuli (Kah). We confirmed Kah mRNA and protein expression in the VM, and identified midgut constriction defects in Kah mutants similar to those of pointed (pnt). ChIP and RNA-Seq data analysis defined a Kah target-binding site similar to that of Snail, and identified a set of common target genes putatively regulated by Kah and Pnt during midgut constriction. Taken together, we report a rich dataset of Alk-responsive loci in the embryonic VM and functionally characterize the role of Kah in the regulation of embryonic midgut morphogenesis.
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| 2. |
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| 3. |
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| 4. |
- Adman, Per, et al.
(författare)
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171 forskare: ”Vi vuxna bör också klimatprotestera”
- 2019
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Ingår i: Dagens nyheter (DN debatt). - Stockholm. - 1101-2447.
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- DN DEBATT 26/9. Vuxna bör följa uppmaningen från ungdomarna i Fridays for future-rörelsen och protestera eftersom det politiska ledarskapet är otillräckligt. Omfattande och långvariga påtryckningar från hela samhället behövs för att få de politiskt ansvariga att utöva det ledarskap som klimatkrisen kräver, skriver 171 forskare i samhällsvetenskap och humaniora.
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| 5. |
- Andersson, Alma, et al.
(författare)
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Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases. While transcriptomics have enhanced our understanding for cancer, spatial transcriptomics enable the characterisation of cellular interactions. Here, the authors integrate single cell data with spatial information for HER2 + tumours and develop tools for the prediction of interactions between tumour-infiltrating cells.
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| 6. |
- Andersson, Alma, et al.
(författare)
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Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships
- 2020
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra-and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. We integrate and spatially map tumor-associated types from single cell data to find: segregated epithelial cells, interactions between B and T-cells and myeloid cells, co-localization of macrophage and T-cell subsets. A model is constructed to infer presence of tertiary lymphoid structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define novel interactions between tumor-infiltrating cells in breast cancer and provide tools generalizing across tissues and diseases.
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| 7. |
- Andersson, Linnéa, et al.
(författare)
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Evaluating pore space in macroporous ceramics with water-based porosimetry
- 2013
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Ingår i: Journal of The American Ceramic Society. - : Wiley. - 0002-7820 .- 1551-2916. ; 96:6, s. 1916-1922
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Tidskriftsartikel (refereegranskat)abstract
- We show that water-based porosimetry (WBP), a facile, simple, and nondestructive porosimetry technique, accurately evaluates both the pore size distribution and throat size distribution of sacrificially templated macroporous alumina. The pore size distribution and throat size distribution derived from the WBP evaluation in uptake (imbibition) and release (drainage) mode, respectively, were corroborated by mercury porosimetry and X-ray micro-computed tomography (μ-CT). In contrast with mercury porosimetry, the WBP also provided information on the presence of “dead-end pores” in the macroporous alumina.
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| 8. |
- Andersson, Richard, et al.
(författare)
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One algorithm to rule them all? : An evaluation and discussion of ten eye movement event-detection algorithms
- 2017
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Ingår i: Behavior Research Methods. - : Springer Science and Business Media LLC. - 1554-3528. ; 49:2, s. 616-637
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Tidskriftsartikel (refereegranskat)abstract
- Almost all eye-movement researchers use algorithms to parse raw data and detect distinct types of eye movement events, such as fixations, saccades, and pursuit, and then base their results on these. Surprisingly, these algorithms are rarely evaluated. We evaluated the classifications of ten eye-movement event detection algorithms, on data from an SMI HiSpeed 1250 system, and compared them to manual ratings of two human experts. The evaluation focused on fixations, saccades, and post-saccadic oscillations. The evaluation used both event duration parameters, and sample-by-sample comparisons to rank the algorithms. The resulting event durations varied substantially as a function of what algorithm was used. This evaluation differed from previous evaluations by considering a relatively large set of algorithms, multiple events, and data from both static and dynamic stimuli. The main conclusion is that current detectors of only fixations and saccades work reasonably well for static stimuli, but barely better than chance for dynamic stimuli. Differing results across evaluation methods make it difficult to select one winner for fixation detection. For saccade detection, however, the algorithm by Larsson, Nyström and Stridh (IEEE Transaction on Biomedical Engineering, 60(9):2484–2493,2013) outperforms all algorithms in data from both static and dynamic stimuli. The data also show how improperly selected algorithms applied to dynamic data misestimate fixation and saccade properties.
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| 10. |
- Axelsson, Magnus, et al.
(författare)
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Measuring energy dependent polarization in soft γ-rays using Compton scattering in PoGOLite
- 2007
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Ingår i: Astroparticle Physics. - : Elsevier BV. - 0927-6505. ; 28:3, s. 327-337
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Tidskriftsartikel (refereegranskat)abstract
- Linear polarization in X- and γ-rays is an important diagnostic of many astrophysical sources, foremost giving information about their geometry, magnetic fields, and radiation mechanisms. However, very few X-ray polarization measurements have been made, and then only mono-energetic detections, whilst several objects are assumed to have energy dependent polarization signatures. In this paper, we investigate whether detection of energy dependent polarization from cosmic sources is possible using the Compton technique, in particular with the proposed PoGOLite balloon-experiment, in the 25–100 keV range. We use Geant4 simulations of a PoGOLite model and input photon spectra based on Cygnus X-1 and accreting magnetic pulsars (100 mCrab). Effective observing times of 6 and 35 h were simulated, corresponding to a standard and a long duration flight, respectively. Both smooth and sharp energy variations of the polarization are investigated and compared to constant polarization signals using chi-square statistics. We can reject constant polarization, with energy, for the Cygnus X-1 spectrum (in the hard state), if the reflected component is assumed to be completely polarized, whereas the distinction cannot be made for weaker polarization. For the accreting pulsar, constant polarization can be rejected in the case of polarization in a narrow energy band with at least 50% polarization, and similarly for a negative step distribution from 30% to 0% polarization.
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