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1.
  • Nowak-Sliwinska, Patrycja, et al. (author)
  • Consensus guidelines for the use and interpretation of angiogenesis assays
  • 2018
  • In: Angiogenesis. - : Springer. - 0969-6970 .- 1573-7209. ; 21:3, s. 425-532
  • Research review (peer-reviewed)abstract
    • The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference.
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2.
  • Chown, Ryan, et al. (author)
  • PDRs4All: IV. An embarrassment of riches: Aromatic infrared bands in the Orion Bar
  • 2024
  • In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 685
  • Journal article (peer-reviewed)abstract
    • Context. Mid-infrared observations of photodissociation regions (PDRs) are dominated by strong emission features called aromatic infrared bands (AIBs). The most prominent AIBs are found at 3.3, 6.2, 7.7, 8.6, and 11.2 µm. The most sensitive, highest-resolution infrared spectral imaging data ever taken of the prototypical PDR, the Orion Bar, have been captured by JWST. These high-quality data allow for an unprecedentedly detailed view of AIBs. Aims. We provide an inventory of the AIBs found in the Orion Bar, along with mid-IR template spectra from five distinct regions in the Bar: the molecular PDR (i.e. the three H2 dissociation fronts), the atomic PDR, and the H II region. Methods. We used JWST NIRSpec IFU and MIRI MRS observations of the Orion Bar from the JWST Early Release Science Program, PDRs4All (ID: 1288). We extracted five template spectra to represent the morphology and environment of the Orion Bar PDR. We investigated and characterised the AIBs in these template spectra. We describe the variations among them here. Results. The superb sensitivity and the spectral and spatial resolution of these JWST observations reveal many details of the AIB emission and enable an improved characterization of their detailed profile shapes and sub-components. The Orion Bar spectra are dominated by the well-known AIBs at 3.3, 6.2, 7.7, 8.6, 11.2, and 12.7 µm with well-defined profiles. In addition, the spectra display a wealth of weaker features and sub-components. The widths of many AIBs show clear and systematic variations, being narrowest in the atomic PDR template, but showing a clear broadening in the H II region template while the broadest bands are found in the three dissociation front templates. In addition, the relative strengths of AIB (sub-)components vary among the template spectra as well. All AIB profiles are characteristic of class A sources as designated by Peeters (2022, A&A, 390, 1089), except for the 11.2 µm AIB profile deep in the molecular zone, which belongs to class B11.2. Furthermore, the observations show that the sub-components that contribute to the 5.75, 7.7, and 11.2 µm AIBs become much weaker in the PDR surface layers. We attribute this to the presence of small, more labile carriers in the deeper PDR layers that are photolysed away in the harsh radiation field near the surface. The 3.3/11.2 AIB intensity ratio decreases by about 40% between the dissociation fronts and the H II region, indicating a shift in the polycyclic aromatic hydrocarbon (PAH) size distribution to larger PAHs in the PDR surface layers, also likely due to the effects of photochemistry. The observed broadening of the bands in the molecular PDR is consistent with an enhanced importance of smaller PAHs since smaller PAHs attain a higher internal excitation energy at a fixed photon energy. Conclusions. Spectral-imaging observations of the Orion Bar using JWST yield key insights into the photochemical evolution of PAHs, such as the evolution responsible for the shift of 11.2 µm AIB emission from class B11.2 in the molecular PDR to class A11.2 in the PDR surface layers. This photochemical evolution is driven by the increased importance of FUV processing in the PDR surface layers, resulting in a “weeding out” of the weakest links of the PAH family in these layers. For now, these JWST observations are consistent with a model in which the underlying PAH family is composed of a few species: the so-called ‘grandPAHs’.
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3.
  • Habart, Emilie, et al. (author)
  • PDRs4All II. JWST’s NIR and MIR imaging view of the Orion Nebula
  • 2024
  • In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 685
  • Journal article (peer-reviewed)abstract
    • Context. The James Webb Space Telescope (JWST) has captured the most detailed and sharpest infrared (IR) images ever taken of the inner region of the Orion Nebula, the nearest massive star formation region, and a prototypical highly irradiated dense photo-dissociation region (PDR). Aims. We investigate the fundamental interaction of far-ultraviolet (FUV) photons with molecular clouds. The transitions across the ionization front (IF), dissociation front (DF), and the molecular cloud are studied at high-angular resolution. These transitions are relevant to understanding the effects of radiative feedback from massive stars and the dominant physical and chemical processes that lead to the IR emission that JWST will detect in many Galactic and extragalactic environments. Methods. We utilized NIRCam and MIRI to obtain sub-arcsecond images over ∼150′′ and 42′′ in key gas phase lines (e.g., Pa α, Br α, [FeII] 1.64 µm, H2 1–0 S(1) 2.12 µm, 0–0 S(9) 4.69 µm), aromatic and aliphatic infrared bands (aromatic infrared bands at 3.3–3.4 µm, 7.7, and 11.3 µm), dust emission, and scattered light. Their emission are powerful tracers of the IF and DF, FUV radiation field and density distribution. Using NIRSpec observations the fractional contributions of lines, AIBs, and continuum emission to our NIRCam images were estimated. A very good agreement is found for the distribution and intensity of lines and AIBs between the NIRCam and NIRSpec observations. Results. Due to the proximity of the Orion Nebula and the unprecedented angular resolution of JWST, these data reveal that the molecular cloud borders are hyper structured at small angular scales of ∼0.1–1′′ (∼0.0002–0.002 pc or ∼40–400 au at 414 pc). A diverse set of features are observed such as ridges, waves, globules and photoevaporated protoplanetary disks. At the PDR atomic to molecular transition, several bright features are detected that are associated with the highly irradiated surroundings of the dense molecular condensations and embedded young star. Toward the Orion Bar PDR, a highly sculpted interface is detected with sharp edges and density increases near the IF and DF. This was predicted by previous modeling studies, but the fronts were unresolved in most tracers. The spatial distribution of the AIBs reveals that the PDR edge is steep and is followed by an extensive warm atomic layer up to the DF with multiple ridges. A complex, structured, and folded H0/H2 DF surface was traced by the H2 lines. This dataset was used to revisit the commonly adopted 2D PDR structure of the Orion Bar as our observations show that a 3D “terraced” geometry is required to explain the JWST observations. JWST provides us with a complete view of the PDR, all the way from the PDR edge to the substructured dense region, and this allowed us to determine, in detail, where the emission of the atomic and molecular lines, aromatic bands, and dust originate. Conclusions. This study offers an unprecedented dataset to benchmark and transform PDR physico-chemical and dynamical models for the JWST era. A fundamental step forward in our understanding of the interaction of FUV photons with molecular clouds and the role of FUV irradiation along the star formation sequence is provided.
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4.
  • Peeters, Els, et al. (author)
  • PDRs4All: III. JWST's NIR spectroscopic view of the Orion Bar
  • 2024
  • In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 685
  • Journal article (peer-reviewed)abstract
    • Context. JWST has taken the sharpest and most sensitive infrared (IR) spectral imaging observations ever of the Orion Bar photodis-sociation region (PDR), which is part of the nearest massive star-forming region the Orion Nebula, and often considered to be the 'prototypical'strongly illuminated PDR. Aims. We investigate the impact of radiative feedback from massive stars on their natal cloud and focus on the transition from the H II region to the atomic PDR -crossing the ionisation front (IF) -, and the subsequent transition to the molecular PDR -crossing the dissociation front (DF). Given the prevalence of PDRs in the interstellar medium and their dominant contribution to IR radiation, understanding the response of the PDR gas to far-ultraviolet (FUV) photons and the associated physical and chemical processes is fundamental to our understanding of star and planet formation and for the interpretation of any unresolved PDR as seen by JWST. Methods. We used high-resolution near-IR integral field spectroscopic data from NIRSpec on JWST to observe the Orion Bar PDR as part of the PDRs4All JWST Early Release Science programme. We constructed a 3″ × 25″ spatio-spectral mosaic covering 0.97-5.27 μm at a spectral resolution R of ~2700 and an angular resolution of 0.075″-0.173″. To study the properties of key regions captured in this mosaic, we extracted five template spectra in apertures centred on the three H2 dissociation fronts, the atomic PDR, and the H II region. This wealth of detailed spatial-spectral information was analysed in terms of variations in the physical conditions-incident UV field, density, and temperature -of the PDR gas. Results. The NIRSpec data reveal a forest of lines including, but not limited to, He I, H I, and C I recombination lines; ionic lines (e.g. Fe III and Fe II); O I and N I fluorescence lines; aromatic infrared bands (AIBs, including aromatic CH, aliphatic CH, and their CD counterparts); pure rotational and ro-vibrational lines from H2; and ro-vibrational lines from HD, CO, and CH+, with most of them having been detected for the first time towards a PDR. Their spatial distribution resolves the H and He ionisation structure in the Huygens region, gives insight into the geometry of the Bar, and confirms the large-scale stratification of PDRs. In addition, we observed numerous smaller-scale structures whose typical size decreases with distance from θ1 Ori C and IR lines from C I, if solely arising from radiative recombination and cascade, reveal very high gas temperatures (a few 1000 K) consistent with the hot irradiated surface of small-scale dense clumps inside the PDR. The morphology of the Bar, in particular that of the H2 lines, reveals multiple prominent filaments that exhibit different characteristics. This leaves the impression of a 'terraced'transition from the predominantly atomic surface region to the CO-rich molecular zone deeper in. We attribute the different characteristics of the H2 filaments to their varying depth into the PDR and, in some cases, not reaching the C+/C/CO transition. These observations thus reveal what local conditions are required to drive the physical and chemical processes needed to explain the different characteristics of the DFs and the photochemical evolution of the AIB carriers. Conclusions. This study showcases the discovery space created by JWST to further our understanding of the impact radiation from young stars has on their natal molecular cloud and proto-planetary disk, which touches on star and planet formation as well as galaxy evolution.
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5.
  • Nijkamp, J. F., et al. (author)
  • De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
  • 2012
  • In: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 11, s. Article Number: 36-
  • Journal article (peer-reviewed)abstract
    • Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN. PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN. PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN. PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN. PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.
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6.
  • Rocha, W. R.M., et al. (author)
  • JWST Observations of Young protoStars (JOYS+): Detecting icy complex organic molecules and ions: I. CH4, SO2, HCOO, OCN, H2CO, HCOOH, CH3CH2OH, CH3CHO, CH3OCHO, and CH3COOH
  • 2024
  • In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 683
  • Journal article (peer-reviewed)abstract
    • Context. Complex organic molecules (COMs) are ubiquitously detected in the gas phase and thought to be mostly formed on icy grains. Nevertheless, there have not been any unambiguous detections of COMs larger than CH3OH in ices reported thus far. Exploring this matter in greater detail has now become possible with the unprecedented possibilities offered by the James Webb Space Telescope (JWST) within the infrared (IR) spectral range with its very high sensitivity and spectral resolution in the critical 5 10 μm range, the fingerprint region of oxygen-bearing COMs. Aims. In the JWST Observations of Young protoStars (JOYS+) program, more than 30 protostars are undergoing observation with the Medium Resolution Spectrograph (MRS) of the Mid-IR Instrument (MIRI). The goal of this study is to comprehensively explore the COMs ice signatures in one low- and one high-mass protostar: NGC 1333 IRAS 2A and IRAS 23385+6053, respectively. Methods. We performed global continuum and silicate subtractions of the MIRI-MRS spectra, followed by a local continuum subtraction in optical depth scale in the range around 6.8 and 8.6 μm, the ice COM fingerprint region. We explored different choices for the local continuum and silicate subtraction. Next, we fit the observational data with a large sample of available IR laboratory ice spectra. We used the ENIIGMA fitting tool, a genetic algorithm-based code that not only finds the best fit between the lab data and the observations, but also performs a statistical analysis of the solutions, such as deriving the confidence intervals and quantifying fit degeneracy. Results. We report the best fits for the spectral ranges between 6.8 and 8.6 μm in NGC 1333 IRAS 2A and IRAS 23385+6053, originating from simple molecules and COMs, as well as negative ions. Overall, we find that ten chemical species are needed to reproduce the astronomical data. The strongest feature in this range (7.7 μm) is dominated by CH4, with contributions from SO2 and OCN. Our results indicate that the 7.2 and 7.4 μm bands are mostly dominated by HCOO. We also find statistically robust detections of COMs based on multiple bands, most notably, CH3CHO, CH3CH2OH, and CH3OCHO. We also report a likely detection of CH3COOH. Based on the ice column density ratios between CH3CH2OH and CH3CHO of NGC 1333 IRAS 2A and IRAS 23385+6053, we find compelling evidence that these COMs are formed on icy grains. Finally, the derived ice abundances for NGC 1333 IRAS 2A correlate well with those in comet 67P/GC within a factor of 5. Conclusions. Based on the high-quality JWST (MIRI-MRS) spectra, we conclude that COMs are present in interstellar ices, thus providing additional proof for the solid-state origin of these species in star-forming regions. In addition, the good correlation between the ice abundances in comet 67P and NGC 1333 IRAS 2A is fully in line with the idea that cometary COMs may be inherited from the early protostellar phases to a significant extent.
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7.
  • Van Gelder, M. L., et al. (author)
  • JOYS+: Mid-infrared detection of gas-phase SO 2 emission in a low-mass protostar
  • 2024
  • In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 682
  • Journal article (peer-reviewed)abstract
    • Context. Thanks to the Mid-InfraRed Instrument (MIRI) on the James Webb Space Telescope (JWST), our ability to observe the star formation process in the infrared has greatly improved. Due to its unprecedented spatial and spectral resolution and sensitivity in the mid-infrared, JWST/MIRI can see through highly extincted protostellar envelopes and probe the warm inner regions. An abundant molecule in these warm inner regions is SO2, which is a common tracer of both outflow and accretion shocks as well as hot core chemistry. Aims. This paper presents the first mid-infrared detection of gaseous SO2 emission in an embedded low-mass protostellar system rich in complex molecules and aims to determine the physical origin of the SO2 emission. Methods. JWST/MIRI observations taken with the Medium Resolution Spectrometer (MRS) of the low-mass protostellar binary NGC 1333 IRAS 2A in the JWST Observations of Young protoStars (JOYS+) program are presented. The observations reveal emission from the SO2 ν3 asymmetric stretching mode at 7.35 µm. Using simple slab models and assuming local thermodynamic equilibrium (LTE), we derived the rotational temperature and total number of SO2 molecules. We then compared the results to those derived from high-angular-resolution SO2 data on the same scales (∼50−100 au) obtained with the Atacama Large Millimeter/submillimeter Array (ALMA). Results. The SO2 emission from the ν3 band is predominantly located on ∼50−100 au scales around the mid-infrared continuum peak of the main component of the binary, IRAS 2A1. A rotational temperature of 92 ± 8 K is derived from the ν3 lines. This is in good agreement with the rotational temperature derived from pure rotational lines in the vibrational ground state (i.e., ν = 0) with ALMA (104 ± 5 K), which are extended over similar scales. However, the emission of the ν3 lines in the MIRI-MRS spectrum is not in LTE given that the total number of molecules predicted by a LTE model is found to be a factor of 2 × 104 higher than what is derived for the ν = 0 state from the ALMA data. This difference can be explained by a vibrational temperature that is ∼100 K higher than the derived rotational temperature of the ν = 0 state: Tvib ∼ 200 K versus Trot = 104 ± 5 K. The brightness temperature derived from the continuum around the ν3 band (∼7.35 µm) of SO2 is ∼180 K, which confirms that the ν3 = 1 level is not collisionally populated but rather infrared-pumped by scattered radiation. This is also consistent with the non-detection of the ν2 bending mode at 18−20 µm. The similar rotational temperature derived from the MIRI-MRS and ALMA data implies that they are in fact tracing the same molecular gas. The inferred abundance of SO2 , determined using the LTE fit to the lines of the vibrational ground state in the ALMA data, is 1.0 ± 0.3 × 10−8 with respect to H2, which is on the lower side compared to interstellar and cometary ices (10−8−10−7). Conclusions. Given the rotational temperature, the extent of the emission (∼100 au in radius), and the narrow line widths in the ALMA data (∼3.5 km s−1), the SO2 in IRAS 2A likely originates from ice sublimation in the central hot core around the protostar rather than from an accretion shock at the disk–envelope boundary. Furthermore, this paper shows the importance of radiative pumping and of combining JWST observations with those from millimeter interferometers such as ALMA to probe the physics on disk scales and to infer molecular abundances.
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8.
  • Wright, Gillian, et al. (author)
  • The Mid-infrared Instrument for JWST and Its In-flight Performance
  • 2023
  • In: Publications of the Astronomical Society of the Pacific. - 0004-6280 .- 1538-3873. ; 135:1046
  • Journal article (peer-reviewed)abstract
    • The Mid-Infrared Instrument (MIRI) extends the reach of the James Webb Space Telescope (JWST) to 28.5 μm. It provides subarcsecond-resolution imaging, high sensitivity coronagraphy, and spectroscopy at resolutions of λ/Δλ ∼ 100-3500, with the high-resolution mode employing an integral field unit to provide spatial data cubes. The resulting broad suite of capabilities will enable huge advances in studies over this wavelength range. This overview describes the history of acquiring this capability for JWST. It discusses the basic attributes of the instrument optics, the detector arrays, and the cryocooler that keeps everything at approximately 7 K. It gives a short description of the data pipeline and of the instrument performance demonstrated during JWST commissioning. The bottom line is that the telescope and MIRI are both operating to the standards set by pre-launch predictions, and all of the MIRI capabilities are operating at, or even a bit better than, the level that had been expected. The paper is also designed to act as a roadmap to more detailed papers on different aspects of MIRI.
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9.
  • Ray, T. P., et al. (author)
  • Outflows from the youngest stars are mostly molecular
  • 2023
  • In: Nature. - 0028-0836 .- 1476-4687. ; 622, s. 48-52
  • Journal article (peer-reviewed)abstract
    • The formation of stars and planets is accompanied not only by the build-up of matter, namely accretion, but also by its expulsion in the form of highly supersonic jets that can stretch for several parsecs1,2. As accretion and jet activity are correlated and because young stars acquire most of their mass rapidly early on, the most powerful jets are associated with the youngest protostars3. This period, however, coincides with the time when the protostar and its surroundings are hidden behind many magnitudes of visual extinction. Millimetre interferometers can probe this stage but only for the coolest components3. No information is provided on the hottest (greater than 1,000 K) constituents of the jet, that is, the atomic, ionized and high-temperature molecular gases that are thought to make up the jet's backbone. Detecting such a spine relies on observing in the infrared that can penetrate through the shroud of dust. Here we report near-infrared observations of Herbig-Haro 211 from the James Webb Space Telescope, an outflow from an analogue of our Sun when it was, at most, a few times 104 years old. These observations reveal copious emission from hot molecules, explaining the origin of the 'green fuzzies'4-7 discovered nearly two decades ago by the Spitzer Space Telescope8. This outflow is found to be propagating slowly in comparison to its more evolved counterparts and, surprisingly, almost no trace of atomic or ionized emission is seen, suggesting its spine is almost purely molecular. Near-infrared imagery and spectroscopy from JWST of the Herbig-Haro 211 system, an analogue of the young Sun, reveals supersonic jets of hot molecules that can explain the origin of the 'green fuzzies' phenomenon.
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10.
  • Tychoniec, Łukasz, et al. (author)
  • JWST Observations of Young protoStars (JOYS) Linked accretion and ejection in a Class I protobinary system
  • 2024
  • In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 687
  • Journal article (peer-reviewed)abstract
    • Context. Accretion and ejection dictate the outcomes of star and planet formation processes. The mid-infrared (MIR) wavelength range offers key tracers of processes that have been difficult to detect and spatially resolve in protostars until now. Aims. We aim to characterize the interplay between accretion and ejection in the low-mass Class I protobinary system TMC1, comprising two young stellar objects: TMC1-W and TMC1-E at a 85 au separation. Methods. Using the James Webb Space Telescope (JWST) Mid-Infrared Instrument (MIRI) observations in 5–28 µm range, we measured the intensities of emission lines of H2, atoms, and ions, for instance, the [Fe II] and [Ne II], and HI recombination lines. We analyzed the spatial distribution of the different species using the MIRI Medium Resolution Spectrometer (MRS) capabilities to spatially resolve emission at 0'.́2–0'.́7 scales. we compared these results with the corresponding Atacama Large Millimeter/submillimeter Array (ALMA) maps tracing cold gas and dust. Results. We detected H2 outflow coming from TMC1-E, with no significant H2 emission from TMC1-W. The H2 emission from TMC1-E outflow appears narrow and extends to wider opening angles with decreasing Eup from S(8) to S(1) rotational transitions, indicating the disk wind as its origin. The outflow from TMC1-E protostar shows spatially extended emission lines of [Ne II], [Ne III], [Ar II], and [Ar III], with their line ratios consistent with UV radiation as a source of ionization. With ALMA, we detected an accretion streamer infalling from >1000 au scales onto the TMC1-E component. The TMC1-W protostar powers a collimated jet, detected with [Fe II] and [Ni II], making it consistent with energetic flow. A much weaker ionized jet is observed from TMC1-E, and both jets appear strikingly parallel to each other, indicating that the disks are co-planar. TMC1-W is associated with strong emission from hydrogen recombination lines, tracing the accretion onto the young star. Conclusions. MIRI-MRS observations provide an unprecedented view of protostellar accretion and ejection processes on 20 au scales. Observations of a binary Class I protostellar system show that the two processes are clearly intertwined, with accretion from the envelope onto the disk influencing a wide-angle wind ejected on disk scales. Finally, the accretion from the protostellar disk onto the protostar is associated with the source launching a collimated high-velocity jet within the innermost regions of the disk.
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