| 41. |
- Jamin, Soazik P., et al.
(författare)
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Combined RNA/tissue profiling identifies novel Cancer/testis genes
- 2021
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Ingår i: Molecular Oncology. - : John Wiley & Sons. - 1574-7891 .- 1878-0261. ; 15:11, s. 3003-3023
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Tidskriftsartikel (refereegranskat)abstract
- Cancer/Testis (CT) genes are induced in germ cells, repressed in somatic cells, and derepressed in somatic tumors, where these genes can contribute to cancer progression. CT gene identification requires data obtained using standardized protocols and technologies. This is a challenge because data for germ cells, gonads, normal somatic tissues, and a wide range of cancer samples stem from multiple sources and were generated over substantial periods of time. We carried out a GeneChip-based RNA profiling analysis using our own data for testis and enriched germ cells, data for somatic cancers from the Expression Project for Oncology, and data for normal somatic tissues from the Gene Omnibus Repository. We identified 478 candidate loci that include known CT genes, numerous genes associated with oncogenic processes, and novel candidates that are not referenced in the Cancer/Testis Database (). We complemented RNA expression data at the protein level for SPESP1, GALNTL5, PDCL2, and C11orf42 using cancer tissue microarrays covering malignant tumors of breast, uterus, thyroid, and kidney, as well as published RNA profiling and immunohistochemical data provided by the Human Protein Atlas (). We report that combined RNA/tissue profiling identifies novel CT genes that may be of clinical interest as therapeutical targets or biomarkers. Our findings also highlight the challenges of detecting truly germ cell-specific mRNAs and the proteins they encode in highly heterogenous testicular, somatic, and tumor tissues.
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| 42. |
- Jiguet, Frederic, et al.
(författare)
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Desert crossing strategies of migrant songbirds vary between and within species
- 2019
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Each year, billions of songbirds cross large ecological barriers during their migration. Understanding how they perform this incredible task is crucial to predict how global change may threaten the safety of such journeys. Earlier studies based on radar suggested that most songbirds cross deserts in intermittent flights at high altitude, stopping in the desert during the day, while recent tracking with light loggers suggested diurnal prolongation of nocturnal flights and common non-stop flights for some species. We analyzed light intensity and temperature data obtained from geolocation loggers deployed on 130 individuals of ten migratory songbird species, and show that a large variety of strategies for crossing deserts exists between, but also sometimes within species. Diurnal stopover in the desert is a common strategy in autumn, while most species prolonged some nocturnal flights into the day. Nonstop flights over the desert occurred more frequently in spring than in autumn, and more frequently in foliage gleaners. Temperature recordings suggest that songbirds crossed deserts with flight bouts performed at various altitudes according to species and season, along a gradient ranging from low above ground in autumn to probably >2000 m above ground level, and possibly at higher altitude in spring. High-altitude flights are therefore not the general rule for crossing deserts in migrant songbirds. We conclude that a diversity of migration strategies exists for desert crossing among songbirds, with variations between but also within species.
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| 43. |
- Kockert, Hansjochen, et al.
(författare)
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UV-induced dissociation of CH2BrI probed by intense femtosecond XUV pulses
- 2022
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Ingår i: JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 55:1
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Tidskriftsartikel (refereegranskat)abstract
- The ultraviolet (UV)-induced dissociation and photofragmentation of gas-phase CH2BrI molecules induced by intense femtosecond extreme ultraviolet (XUV) pulses at three different photon energies are studied by multi-mass ion imaging. Using a UV-pump-XUV-probe scheme, charge transfer between highly charged iodine ions and neutral CH2Br radicals produced by C-I bond cleavage is investigated. In earlier charge-transfer studies, the center of mass of the molecules was located along the axis of the bond cleaved by the pump pulse. In the present case of CH2BrI, this is not the case, thus inducing a rotation of the fragment. We discuss the influence of the rotation on the charge transfer process using a classical over-the-barrier model. Our modeling suggests that, despite the fact that the dissociation is slower due to the rotational excitation, the critical interatomic distance for charge transfer is reached faster. Furthermore, we suggest that charge transfer during molecular fragmentation may be modulated in a complex way.
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| 44. |
- Kolman, Krzysztof, 1986, et al.
(författare)
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pH-Controlled assembly of polyelectrolyte layers on silica nanoparticles in concentrated suspension
- 2022
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Ingår i: Journal of Colloid and Interface Science. - : Elsevier BV. - 1095-7103 .- 0021-9797. ; 615, s. 265-272
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Tidskriftsartikel (refereegranskat)abstract
- Hypothesis: Preparation of suspensions of nanoparticles (>1 wt%) coated with a polyelectrolyte multilayers is a challenging task because of the risk of flocculation when a polyelectrolyte is added to a suspension of oppositely charged nanoparticles. This situation can be avoided if the charge density of the polymers and particles is controlled during mixing so as to separate mixing and adsorption events. Experiments: The cationic polyethylenimine (PEI) and the anionic carboxymethylcellulose (CMC) were used as weak polyelectrolytes. Polyelectrolyte multilayers build-up was conducted by reducing the charge of one of the components during the addition of the next component. Charge density was controlled by tuning pH. Analysis of the suspension of coated nanoparticles was done by means of dynamic light scattering, electrophoresis and small angle x-ray scattering measurements, while quartz crystal microbalance was used to study the build-up process on flat silica surfaces. Findings: Charge density, controlled through pH, can be used as a tool to avoid flocculation during layer-by-layer deposition of polyelectrolytes on 20 nm silica particles at high concentration (∼40 wt%). When added to silica at pH 3, PEI did not induce flocculation. Adsorption was triggered by raising the pH to 11, pH at which CMC could be added. The pH was then lowered to 3. The process was repeated, and up to five polyelectrolyte layers were deposited on concentrated silica nanoparticles while inducing minimal aggregation.
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| 45. |
- Konold, Patrick E., et al.
(författare)
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Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs
- 2024
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Ingår i: NATURE METHODS. - : NATURE PORTFOLIO. - 1548-7091 .- 1548-7105.
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Tidskriftsartikel (refereegranskat)abstract
- Detecting microsecond structural perturbations in biomolecules has wide relevance in biology, chemistry and medicine. Here we show how MHz repetition rates at X-ray free-electron lasers can be used to produce microsecond time-series of protein scattering with exceptionally low noise levels of 0.001%. We demonstrate the approach by examining J alpha helix unfolding of a light-oxygen-voltage photosensory domain. This time-resolved acquisition strategy is easy to implement and widely applicable for direct observation of structural dynamics of many biochemical processes. The MHz repetition rates available at second-generation X-ray free-electron lasers enable the collection of microsecond time-resolved X-ray scattering data with exceptionally low noise, providing insights into protein structural dynamics.
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| 46. |
- Kraus, Stefan, et al.
(författare)
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Planet Formation Imager (PFI) : Science vision and key requirements
- 2016
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Ingår i: Optical and Infrared Interferometry and Imaging V. - : SPIE. - 9781510601932 ; 9907
-
Konferensbidrag (refereegranskat)abstract
- The Planet Formation Imager (PFI) project aims to provide a strong scientific vision for ground-based optical astronomy beyond the upcoming generation of Extremely Large Telescopes. We make the case that a breakthrough in angular resolution imaging capabilities is required in order to unravel the processes involved in planet formation. PFI will be optimised to provide a complete census of the protoplanet population at all stellocentric radii and over the age range from 0.1 to ∼100 Myr. Within this age period, planetary systems undergo dramatic changes and the final architecture of planetary systems is determined. Our goal is to study the planetary birth on the natural spatial scale where the material is assembled, which is the "Hill Sphere" of the forming planet, and to characterise the protoplanetary cores by measuring their masses and physical properties. Our science working group has investigated the observational characteristics of these young protoplanets as well as the migration mechanisms that might alter the system architecture. We simulated the imprints that the planets leave in the disk and study how PFI could revolutionise areas ranging from exoplanet to extragalactic science. In this contribution we outline the key science drivers of PFI and discuss the requirements that will guide the technology choices, the site selection, and potential science/technology tradeoffs.
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| 47. |
- Lehikoinen, Aleksi, et al.
(författare)
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Wintering bird communities are tracking climate change faster than breeding communities
- 2021
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Ingår i: Journal of Animal Ecology. - : Wiley. - 0021-8790 .- 1365-2656. ; 90:5, s. 1085-1095
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Tidskriftsartikel (refereegranskat)abstract
- Global climate change is driving species' distributions towards the poles and mountain tops during both non-breeding and breeding seasons, leading to changes in the composition of natural communities. However, the degree of season differences in climate-driven community shifts has not been thoroughly investigated at large spatial scales. We compared the rates of change in the community composition during both winter (non-breeding season) and summer (breeding) and their relation to temperature changes. Based on continental-scale data from Europe and North America, we examined changes in bird community composition using the community temperature index (CTI) approach and compared the changes with observed regional temperature changes during 1980–2016. CTI increased faster in winter than in summer. This seasonal discrepancy is probably because individuals are less site-faithful in winter, and can more readily shift their wintering sites in response to weather in comparison to the breeding season. Regional long-term changes in community composition were positively associated with regional temperature changes during both seasons, but the pattern was only significant during summer due to high annual variability in winter communities. Annual changes in community composition were positively associated with the annual temperature changes during both seasons. Our results were broadly consistent across continents, suggesting some climate-driven restructuring in both European and North American avian communities. Because community composition has changed much faster during the winter than during the breeding season, it is important to increase our knowledge about climate-driven impacts during the less-studied non-breeding season.
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| 48. |
- Lévy, Romain, et al.
(författare)
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Human CARMIL2 deficiency underlies a broader immunological and clinical phenotype than CD28 deficiency.
- 2023
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Ingår i: The Journal of experimental medicine. - : Rockefeller University Press. - 1540-9538 .- 0022-1007. ; 220:2
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Tidskriftsartikel (refereegranskat)abstract
- Patients with inherited CARMIL2 or CD28 deficiency have defective T cell CD28 signaling, but their immunological and clinical phenotypes remain largely unknown. We show that only one of three CARMIL2 isoforms is produced and functional across leukocyte subsets. Tested mutant CARMIL2 alleles from 89 patients and 52 families impair canonical NF-κB but not AP-1 and NFAT activation in T cells stimulated via CD28. Like CD28-deficient patients, CARMIL2-deficient patients display recalcitrant warts and low blood counts of CD4+ and CD8+ memory T cells and CD4+ TREGs. Unlike CD28-deficient patients, they have low counts of NK cells and memory B cells, and their antibody responses are weak. CARMIL2 deficiency is fully penetrant by the age of 10 yr and is characterized by numerous infections, EBV+ smooth muscle tumors, and mucocutaneous inflammation, including inflammatory bowel disease. Patients with somatic reversions of a mutant allele in CD4+ T cells have milder phenotypes. Our study suggests that CARMIL2 governs immunological pathways beyond CD28.
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| 49. |
- Maccari, Maria Elena, et al.
(författare)
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Activated phosphoinositide 3-kinase δ syndrome: Update from the ESID Registry and comparison with other autoimmune-lymphoproliferative inborn errors of immunity.
- 2023
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Ingår i: The Journal of allergy and clinical immunology. - 1097-6825. ; 152:4
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Tidskriftsartikel (refereegranskat)abstract
- Activated phosphoinositide-3-kinase δ syndrome (APDS) is an inborn error of immunity (IEI) with infection susceptibility and immune dysregulation, clinically overlapping with other conditions. Management depends on disease evolution, but predictors of severe disease are lacking.This study sought to report the extended spectrum of disease manifestations in APDS1 versus APDS2; compare these to CTLA4 deficiency, NFKB1 deficiency, and STAT3 gain-of-function (GOF) disease; and identify predictors of severity in APDS.Data was collected from the ESID (European Society for Immunodeficiencies)-APDS registry and was compared with published cohorts of the other IEIs.The analysis of 170 patients with APDS outlines high penetrance and early onset of APDS compared to the other IEIs. The large clinical heterogeneity even in individuals with the same PIK3CD variant E1021K illustrates how poorly the genotype predicts the disease phenotype and course. The high clinical overlap between APDS and the other investigated IEIs suggests relevant pathophysiological convergence of the affected pathways. Preferentially affected organ systems indicate specific pathophysiology: bronchiectasis is typical of APDS1; interstitial lung disease and enteropathy are more common in STAT3 GOF and CTLA4 deficiency. Endocrinopathies are most frequent in STAT3 GOF, but growth impairment is also common, particularly in APDS2. Early clinical presentation is a risk factor for severe disease in APDS.APDS illustrates how a single genetic variant can result in a diverse autoimmune-lymphoproliferative phenotype. Overlap with other IEIs is substantial. Some specific features distinguish APDS1 from APDS2. Early onset is a risk factor for severe disease course calling for specific treatment studies in younger patients.
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| 50. |
- Martins, Gabriel G., et al.
(författare)
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Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts : a success story and key asset for analysts and life scientists
- 2021
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 10, s. 334-334
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Tidskriftsartikel (refereegranskat)abstract
- NEUBIAS, the European Network of Bioimage Analysts, was created in 2016 with the goal of improving the communication and the knowledge transfer among the various stakeholders involved in the acquisition, processing and analysis of biological image data, and to promote the establishment and recognition of the profession of Bioimage Analyst. One of the most successful initiatives of the NEUBIAS programme was its series of 15 training schools, which trained over 400 new Bioimage Analysts, coming from over 40 countries. Here we outline the rationale behind the innovative three-level program of the schools, the curriculum, the trainer recruitment and turnover strategy, the outcomes for the community and the career path of analysts, including some success stories. We discuss the future of the materials created during this programme and some of the new initiatives emanating from the community of NEUBIAS-trained analysts, such as the NEUBIAS Academy. Overall, we elaborate on how this training programme played a key role in collectively leveraging Bioimaging and Life Science research by bringing the latest innovations into structured, frequent and intensive training activities, and on why we believe this should become a model to further develop in Life Sciences.
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