| 1. |
- Nilsson, Hans, et al.
(författare)
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Birth of a comet magnetosphere : A spring of water ions
- 2015
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 347:6220
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Tidskriftsartikel (refereegranskat)abstract
- The Rosetta mission shall accompany comet 67P/Churyumov-Gerasimenko from a heliocentric distance of >3.6 astronomical units through perihelion passage at 1.25 astronomical units, spanning low and maximum activity levels. Initially, the solar wind permeates the thin comet atmosphere formed from sublimation, until the size and plasma pressure of the ionized atmosphere define its boundaries: A magnetosphere is born. Using the Rosetta Plasma Consortium ion composition analyzer, we trace the evolution from the first detection of water ions to when the atmosphere begins repelling the solar wind (~3.3 astronomical units), and we report the spatial structure of this early interaction. The near-comet water population comprises accelerated ions (
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| 2. |
- Alvez, Maria Bueno, et al.
(författare)
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Next generation pan-cancer blood proteome profiling using proximity extension assay
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.
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| 3. |
- Ameur, Adam, et al.
(författare)
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SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
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Ingår i: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
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Tidskriftsartikel (refereegranskat)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
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| 4. |
- de Vries, Wim; Forsius, Martin; Lorenz, Martin; Lundin, Lars; Haußmann, Thomas; Augustin, Sabine; Ferretti, Marco; Kleemola, Sirpa; Vel, Evert,
(författare)
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Cause-effect Relationships of Forest Ecosystems
- 2002
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- For more than 20 years the Convention on Long-range Transboundary Air Pollution (CLRTAP) has been striving to control air pollutant emission in Europe and North America. Its Working Group onEffects (WGE) has been responsible for the scientific underpinning. The International CooperativeProgrammes (ICPs) identify air pollution effects on the environment through monitoring, modellingand scientific review. The scientific network of the ICPs and the monitoring and modelling resultshave been promoting the development of the Convention and are an essential component for itssuccess in the future.The International Cooperative Programme on Assessment and Monitoring of Air Pollution Effectson Forests (ICP Forests) collects in close cooperation with the European Commission data anddetermines cause effect relationships of changes in forests due to air pollution and other stresses bymeans of monitoring both at the large scale and at the scale of ecosystems. The International CooperativeProgramme on Integrated Monitoring of Air Pollution Effects on Ecosystems (ICP IM)determines and predicts the state of ecosystems or catchments and their changes from a long-termperspective with respect to the regional variation and impact of air pollutants.Both ICPs have been co-operating closely for a number of years now although the objects understudy are different at first sight. ICP IM is focusing on catchments in undisturbed ecosystems whileICP Forests monitors forest ecosystems which are managed regularly. As most ICP IM sites arewithin forest areas and as many countries have linked their plots of both programmes within onemonitoring system, it is common agreement to intensify the co-operation. One result of this intensiveco-operation is the harmonisation of assessment methods. As the next level of cooperation, thisreport reviews the outstanding data and information gathered by both programmes and presents forvarious areas of research the main findings. In addition results and information were contributed bya large number of participating countries. All support received from the countries in the preparationof the report is gratefully acknowledged.It is expected that this report will intensify the co-operation between the National Focal Centres(NFCs) in all participating countries and help to intensify the work in those areas which will be ofhighest priority for the two programmes in future.
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| 5. |
- Gad, Helge, et al.
(författare)
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MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool
- 2014
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 508:7495, s. 215-221
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Tidskriftsartikel (refereegranskat)abstract
- Cancers have dysfunctional redox regulation resulting in reactive oxygen species production, damaging both DNA and free dNTPs. The MTH1 protein sanitizes oxidized dNTP pools to prevent incorporation of damaged bases during DNA replication. Although MTH1 is non-essential in normal cells, we show that cancer cells require MTH1 activity to avoid incorporation of oxidized dNTPs, resulting in DNA damage and cell death. We validate MTH1 as an anticancer target in vivo and describe small molecules TH287 and TH588 as first-in-class nudix hydrolase family inhibitors that potently and selectively engage and inhibit the MTH1 protein in cells. Protein co-crystal structures demonstrate that the inhibitors bindin the active site of MTH1. The inhibitors cause incorporation of oxidized dNTPs in cancer cells, leading to DNA damage, cytotoxicity and therapeutic responses in patient-derived mouse xenografts. This study exemplifies the non-oncogene addiction concept for anticancer treatment and validates MTH1 as being cancer phenotypic lethal.
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| 6. |
- Holmström, Oscar, et al.
(författare)
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Point-of-Care Digital Cytology With Artificial Intelligence for Cervical Cancer Screening in a Resource-Limited Setting
- 2021
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Ingår i: JAMA Network Open. - : American Medical Association (AMA). - 2574-3805. ; 4:3
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Tidskriftsartikel (refereegranskat)abstract
- Importance: Cervical cancer is highly preventable but remains a common and deadly cancer in areas without screening programs. The creation of a diagnostic system to digitize Papanicolaou test samples and analyze them using a cloud-based deep learning system (DLS) may provide needed cervical cancer screening to resource-limited areas.Objective: To determine whether artificial intelligence-supported digital microscopy diagnostics can be implemented in a resource-limited setting and used for analysis of Papanicolaou tests.Design, Setting, and Participants: In this diagnostic study, cervical smears from 740 HIV-positive women aged between 18 and 64 years were collected between September 1, 2018, and September 30, 2019. The smears were digitized with a portable slide scanner, uploaded to a cloud server using mobile networks, and used to train and validate a DLS for the detection of atypical cervical cells. This single-center study was conducted at a local health care center in rural Kenya.Exposures: Detection of squamous cell atypia in the digital samples by analysis with the DLS.Main Outcomes and Measures: The accuracy of the DLS in the detection of low- and high-grade squamous intraepithelial lesions in Papanicolaou test whole-slide images.Results: Papanicolaou test results from 740 HIV-positive women (mean [SD] age, 41.8 [10.3] years) were collected. The DLS was trained using 350 whole-slide images and validated on 361 whole-slide images (average size, 100 387 x 47 560 pixels). For detection of cervical cellular atypia, sensitivities were 95.7% (95% CI, 85.5%-99.5%) and 100% (95% CI, 82.4%-100%), and specificities were 84.7% (95% CI, 80.2%-88.5%) and 78.4% (95% CI, 73.6%-82.4%), compared with the pathologist assessment of digital and physical slides, respectively. Areas under the receiver operating characteristic curve were 0.94 and 0.96, respectively. Negative predictive values were high (99%-100%), and accuracy was high, particularly for the detection of high-grade lesions. Interrater agreement was substantial compared with the pathologist assessment of digital slides (kappa = 0.72) and fair compared with the assessment of glass slides (kappa = 0.36). No samples that were classified as high grade by manual sample analysis had false-negative assessments by the DLS.Conclusions and Relevance: In this study, digital microscopy with artificial intelligence was implemented at a rural clinic and used to detect atypical cervical smears with a high sensitivity compared with visual sample analysis.
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| 7. |
- Lundin, Johan, et al.
(författare)
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Diagnosis of soil-transmitted helminth infections with digital mobile microscopy and artificial intelligence in a resource-limited setting
- 2024
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Ingår i: PLoS Neglected Tropical Diseases. - : Public Library of Science (PLoS). - 1935-2727 .- 1935-2735. ; 18:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Infections caused by soil-transmitted helminths (STHs) are the most prevalent neglected tropical diseases and result in a major disease burden in low- and middle-income countries, especially in school-aged children. Improved diagnostic methods, especially for light intensity infections, are needed for efficient, control and elimination of STHs as a public health problem, as well as STH management. Image-based artificial intelligence (AI) has shown promise for STH detection in digitized stool samples. However, the diagnostic accuracy of AI-based analysis of entire microscope slides, so called whole-slide images (WSI), has previously not been evaluated on a sample-level in primary healthcare settings in STH endemic countries.Methodology/Principal findings: Stool samples (n = 1,335) were collected during 2020 from children attending primary schools in Kwale County, Kenya, prepared according to the Kato-Katz method at a local primary healthcare laboratory and digitized with a portable whole-slide microscopy scanner and uploaded via mobile networks to a cloud environment. The digital samples of adequate quality (n = 1,180) were split into a training (n = 388) and test set (n = 792) and a deep-learning system (DLS) developed for detection of STHs. The DLS findings were compared with expert manual microscopy and additional visual assessment of the digital samples in slides with discordant results between the methods. Manual microscopy detected 15 (1.9%) Ascaris lumbricoides, 172 (21.7%) Tricuris trichiura and 140 (17.7%) hookworm (Ancylostoma duodenale or Necator americanus) infections in the test set. Importantly, more than 90% of all STH positive cases represented light intensity infections. With manual microscopy as the reference standard, the sensitivity of the DLS as the index test for detection of A. lumbricoides, T. trichiura and hookworm was 80%, 92% and 76%, respectively. The corresponding specificity was 98%, 90% and 95%. Notably, in 79 samples (10%) classified as negative by manual microscopy for a specific species, STH eggs were detected by the DLS and confirmed correct by visual inspection of the digital samples.Conclusions/Significance: Analysis of digitally scanned stool samples with the DLS provided high diagnostic accuracy for detection of STHs. Importantly, a substantial number of light intensity infections were missed by manual microscopy but detected by the DLS. Thus, analysis of WSIs with image-based AI may provide a future tool for improved detection of STHs in a primary healthcare setting, which in turn could facilitate monitoring and evaluation of control programs.
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| 8. |
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| 9. |
- Abrego, Nerea, et al.
(författare)
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Airborne DNA reveals predictable spatial and seasonal dynamics of fungi
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 631, s. 835-842
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Tidskriftsartikel (refereegranskat)abstract
- Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5.
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| 10. |
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