| 1. |
- Ba, Alexandre, et al.
(författare)
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Inter-laboratory comparison of channelized hotelling observer computation
- 2018
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Ingår i: Medical Physics. - : Wiley. - 0094-2405 .- 2473-4209. ; 45:7, s. 3019-3030
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The task-based assessment of image quality using model observers is increasingly used for the assessment of different imaging modalities. However, the performance computation of model observers needs standardization as well as a well-established trust in its implementation methodology and uncertainty estimation. The purpose of this work was to determine the degree of equivalence of the channelized Hotelling observer performance and uncertainty estimation using an intercomparison exercise. Materials and Methods: Image samples to estimate model observer performance for detection tasks were generated from two-dimensional CT image slices of a uniform water phantom. A common set of images was sent to participating laboratories to perform and document the following tasks: (a) estimate the detectability index of a well-defined CHO and its uncertainty in three conditions involving different sized targets all at the same dose, and (b) apply this CHO to an image set where ground truth was unknown to participants (lower image dose). In addition, and on an optional basis, we asked the participating laboratories to (c) estimate the performance of real human observers from a psychophysical experiment of their choice. Each of the 13 participating laboratories was confidentially assigned a participant number and image sets could be downloaded through a secure server. Results were distributed with each participant recognizable by its number and then each laboratory was able to modify their results with justification as model observer calculation are not yet a routine and potentially error prone. Results: Detectability index increased with signal size for all participants and was very consistent for 6 mm sized target while showing higher variability for 8 and 10 mm sized target. There was one order of magnitude between the lowest and the largest uncertainty estimation. Conclusions: This intercomparison helped define the state of the art of model observer performance computation and with thirteen participants, reflects openness and trust within the medical imaging community. The performance of a CHO with explicitly defined channels and a relatively large number of test images was consistently estimated by all participants. In contrast, the paper demonstrates that there is no agreement on estimating the variance of detectability in the training and testing setting.
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| 2. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 3. |
- Fang, Jun, et al.
(författare)
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Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148
- 2017
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Genome wide association studies (GWAS) have mapped multiple independent cancer susceptibility loci to chr5p15.33. Here, we show that fine-mapping of pancreatic and testicular cancer GWAS within one of these loci (Region 2 in CLPTM1L) focuses the signal to nine highly correlated SNPs. Of these, rs36115365-C associated with increased pancreatic and testicular but decreased lung cancer and melanoma risk, and exhibited preferred protein-binding and enhanced regulatory activity. Transcriptional gene silencing of this regulatory element repressed TERT expression in an allele-specific manner. Proteomic analysis identifies allele-preferred binding of Zinc finger protein 148 (ZNF148) to rs36115365-C, further supported by binding of purified recombinant ZNF148. Knockdown of ZNF148 results in reduced TERT expression, telomerase activity and telomere length. Our results indicate that the association with chr5p15.33-Region 2 may be explained by rs36115365, a variant influencing TERT expression via ZNF148 in a manner consistent with elevated TERT in carriers of the C allele.
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| 4. |
- Clabbers, Max T. B., et al.
(författare)
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MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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| 5. |
- Corpolongo, A., et al.
(författare)
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SHERLOC Raman Mineral Class Detections of the Mars 2020 Crater Floor Campaign
- 2023
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Ingår i: Journal of Geophysical Research - Planets. - : John Wiley and Sons Inc. - 2169-9097 .- 2169-9100. ; 128:3
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Tidskriftsartikel (refereegranskat)abstract
- The goals of NASA's Mars 2020 mission include searching for evidence of ancient life on Mars, studying the geology of Jezero crater, understanding Mars' current and past climate, and preparing for human exploration of Mars. During the mission's first science campaign, the Perseverance rover's SHERLOC deep UV Raman and fluorescence instrument collected microscale, two-dimensional Raman and fluorescence images on 10 natural (unabraded) and abraded targets on two different Jezero crater floor units: Séítah and Máaz. We report SHERLOC Raman measurements collected during the Crater Floor Campaign and discuss their implications regarding the origin and history of Séítah and Máaz. The data support the conclusion that Séítah and Máaz are mineralogically distinct igneous units with complex aqueous alteration histories and suggest that the Jezero crater floor once hosted an environment capable of supporting microbial life and preserving evidence of that life, if it existed.
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| 6. |
- Hagenblad, Jenny, et al.
(författare)
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The introduction history of Hordeum vulgare var. nudum (naked barley) into Fennoscandia
- 2024
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Ingår i: Vegetation History and Archaeobotany. - : SPRINGER. - 0939-6314 .- 1617-6278. ; 33:2, s. 237-245
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Tidskriftsartikel (refereegranskat)abstract
- Hordeum vulgare var. nudum (naked barley) is one of the oldest and most common cereals found from Neolithic Fennoscandia. After the Bronze Age, naked barley largely disappeared and was replaced by Hordeum vulgare var. vulgare (hulled barley) and other cereals. During the early 19th century, naked barley of Asian origins was reintroduced to Fennoscandia. In this study, we have genetically characterized samples of Fennoscandian landraces of naked barley which were preserved in gene banks and museum collections. The analyses show that the Fennoscandian naked barley can be split into three groups: First, naked two-row barley, with a likely origin in Asia; second, naked six-row barley, with a likely origin in the eastern Himalayas and introduced during the 19th century; third, naked six-row barley genetically related to the original Fennoscandian hulled barley. The results suggest that this last group represents the ancient form of naked barley, which was possibly introduced in the Neolithic. At that time both naked and hulled barleys were grown and enough gene flow probably occurred between these two subspecies to create a Fennoscandian barley that is genetically distinct, irrespective of whether it is hulled or naked. This hypothesis was further supported by genotyping of the Nud gene, which is responsible for the naked phenotype. All naked barleys which we studied contained the same mutation allele, nud1.a, thus showing that naked Fennoscandian barley arose by crossings between naked and hulled barley and not by new mutations of hulled barley.
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| 7. |
- Hagenblad, Jenny, et al.
(författare)
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Utilising ancient DNA to understand crop population dynamics across a millennium: A case study of archaeological barley (Hordeum vulgare L.) from Gran Canaria, Spain
- 2024
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Ingår i: Journal of Archaeological Science. - : ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD. - 0305-4403 .- 1095-9238. ; 167
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Tidskriftsartikel (refereegranskat)abstract
- Landraces are described as genetically diverse, dynamic populations of unimproved crops. However, studying the development of a landrace population over longer periods of time has rarely been done due to a lack of suitable archaeological materials. The indigenous grain silos of Gran Canaria provide a unique opportunity for genetically analysing multiple specimens from the same time period as well as sampling the same population at multiple time points. Here we report a genetic study of a landrace barley (Hordeum vulgare L.) sampled repeatedly over a period of 1400 years. We successfully enriched extracted aDNA for the barley exome using capture techniques and present sequencing data from ten archaeological and six extant samples. The results show that the landrace barley population of Gran Canaria has not undergone any dramatic genetic turnover or influx of new genetic material since the 7th century CE, but that the scale of cultivation seems to have varied. We detect smaller temporal changes of the genetic composition during the studied period and suggest that these changes reflect natural selection for adaptation to a changing climate and a dynamic agricultural society.
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| 8. |
- Holm-Alwmark, S., et al.
(författare)
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Stratigraphic Relationships in Jezero Crater, Mars : Constraints on the Timing of Fluvial-Lacustrine Activity From Orbital Observations
- 2021
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Ingår i: Journal of Geophysical Research: Planets. - 2169-9097. ; 126:7
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Tidskriftsartikel (refereegranskat)abstract
- On February 18, 2021 NASA's Perseverance rover landed in Jezero crater, located at the northwestern edge of the Isidis basin on Mars. The uppermost surface of the present-day crater floor is dominated by a distinct geologic assemblage previously referred to as the dark-toned floor. It consists of a smooth, dark-toned unit overlying and variably covering light-toned, roughly eroded deposits showing evidence of discrete layers. In this study, we investigated the stratigraphic relations between materials that comprise this assemblage, the main western delta deposit, as well as isolated mesas located east of the main delta body that potentially represent delta remnants. A more detailed classification and differentiation of crater floor units in Jezero and determination of their relative ages is vital for the understanding of the geologic evolution of the crater system, and determination of the potential timeline and environments of habitability. We have investigated unit contacts using topographic profiles and DEMs as well as the distribution of small craters and fractures on the youngest portions of the crater floor. Our results indicate that at least some of the deltaic deposition in Jezero postdates emplacement of the uppermost surface of the crater floor assemblage. The inferred age of the floor assemblage can therefore help to constrain the timing of the Jezero fluviolacustrine system, wherein at least some lake activity postdates the age of the uppermost crater floor. We present hypotheses that can be tested by Perseverance and can be used to advance our knowledge of the geologic evolution of the area.
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| 9. |
- Ryan, Rebecca A., et al.
(författare)
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Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene
- 2017
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Ingår i: Journal of Visualized Experiments. - : MyJove Corporation. - 1940-087X. ; :126
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Tidskriftsartikel (refereegranskat)abstract
- The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C-60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C-60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.
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