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- Dornelas, M., et al.
(författare)
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BioTIME: A database of biodiversity time series for the Anthropocene
- 2018
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 27:7, s. 760-786
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km(2) (158 cm(2)) to 100 km(2) (1,000,000,000,000 cm(2)). Time period and grainBio: TIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.
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- Pagano, G., et al.
(författare)
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Fanconi anaemia proteins : Major roles in cell protection against oxidative damage
- 2003
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Ingår i: Bioessays. - : Wiley. - 0265-9247 .- 1521-1878. ; 25:6, s. 589-595
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Forskningsöversikt (refereegranskat)abstract
- Fanconi anaemia (FA) is a cancer-prone genetic disorder that is characterised by cytogenetic instability and redox abnormalities. Although rare subtypes of FA (B, D1 and D2) have been implicated in DNA repair through links with BRCA1 and BRCA2, such a role has yet to be demonstrated for gene products of the common subtypes. Instead, these products have been strongly implicated in xenobiotic metabolism and redox homeostasis through interactions of FANCC with cytochrome P-450 reductase and with glutathione S-transferase, and of FANCG with cytochrome P-450 2E1, as well as redox-dependent signalling through an interaction between FANCA and Akt kinase. We hypothesise that FA proteins act directly (via FANCC and FANCG) and indirectly (via FANCA, BRCA2 and FANCD2) with the machinery of cellular defence to modulate oxidative stress. The latter interactions may co-ordinate the link between the response to DNA damage and oxidative stress parameters (3, 6-12). © 2003 Wiley Periodicals, Inc.
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- Obon-Santacana, M, et al.
(författare)
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Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes
- 2022
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 14:17
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Tidskriftsartikel (refereegranskat)abstract
- The gut microbiome is a potential modifiable risk factor for colorectal cancer (CRC). We re-analyzed all eight previously published stool sequencing data and conducted an MWAS meta-analysis. We used cross-validated LASSO predictive models to identify a microbiome signature for predicting the risk of CRC and precancerous lesions. These models were validated in a new study, Colorectal Cancer Screening (COLSCREEN), including 156 participants that were recruited in a CRC screening context. The MWAS meta-analysis identified 95 bacterial species that were statistically significantly associated with CRC (FDR < 0.05). The LASSO CRC predictive model obtained an area under the receiver operating characteristic curve (aROC) of 0.81 (95%CI: 0.78–0.83) and the validation in the COLSCREEN dataset was 0.75 (95%CI: 0.66–0.84). This model selected a total of 32 species. The aROC of this CRC-trained model to predict precancerous lesions was 0.52 (95%CI: 0.41–0.63). We have identified a signature of 32 bacterial species that have a good predictive accuracy to identify CRC but not precancerous lesions, suggesting that the identified microbes that were enriched or depleted in CRC are merely a consequence of the tumor. Further studies should focus on CRC as well as precancerous lesions with the intent to implement a microbiome signature in CRC screening programs.
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- Quentin, Audrey G, et al.
(författare)
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Non-structural carbohydrates in woody plants compared among laboratories.
- 2015
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Ingår i: Tree physiology. - : Oxford University Press (OUP). - 1758-4469 .- 0829-318X. ; 35:11, s. 1146-1165
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Tidskriftsartikel (refereegranskat)abstract
- Non-structural carbohydrates (NSC) in plant tissue are frequently quantified to make inferences about plant responses to environmental conditions. Laboratories publishing estimates of NSC of woody plants use many different methods to evaluate NSC. We asked whether NSC estimates in the recent literature could be quantitatively compared among studies. We also asked whether any differences among laboratories were related to the extraction and quantification methods used to determine starch and sugar concentrations. These questions were addressed by sending sub-samples collected from five woody plant tissues, which varied in NSC content and chemical composition, to 29 laboratories. Each laboratory analyzed the samples with their laboratory-specific protocols, based on recent publications, to determine concentrations of soluble sugars, starch and their sum, total NSC. Laboratory estimates differed substantially for all samples. For example, estimates for Eucalyptus globulus leaves (EGL) varied from 23 to 116 (mean = 56) mg g(-1) for soluble sugars, 6-533 (mean = 94) mg g(-1) for starch and 53-649 (mean = 153) mg g(-1) for total NSC. Mixed model analysis of variance showed that much of the variability among laboratories was unrelated to the categories we used for extraction and quantification methods (method category R(2) = 0.05-0.12 for soluble sugars, 0.10-0.33 for starch and 0.01-0.09 for total NSC). For EGL, the difference between the highest and lowest least squares means for categories in the mixed model analysis was 33 mg g(-1) for total NSC, compared with the range of laboratory estimates of 596 mg g(-1). Laboratories were reasonably consistent in their ranks of estimates among tissues for starch (r = 0.41-0.91), but less so for total NSC (r = 0.45-0.84) and soluble sugars (r = 0.11-0.83). Our results show that NSC estimates for woody plant tissues cannot be compared among laboratories. The relative changes in NSC between treatments measured within a laboratory may be comparable within and between laboratories, especially for starch. To obtain comparable NSC estimates, we suggest that users can either adopt the reference method given in this publication, or report estimates for a portion of samples using the reference method, and report estimates for a standard reference material. Researchers interested in NSC estimates should work to identify and adopt standard methods.
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- Mas-Lloret, J, et al.
(författare)
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Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample
- 2020
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 7:1, s. 92-
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Tidskriftsartikel (refereegranskat)abstract
- The gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300 k reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis.
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- Mitra, Mainak, et al.
(författare)
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Nonheme Fe(IV) Oxo Complexes of Two New Pentadentate Ligands and Their Hydrogen-Atom and Oxygen-Atom Transfer Reactions
- 2015
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 54:15, s. 7152-7164
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Tidskriftsartikel (refereegranskat)abstract
- Two new pentadentate {N5} donor ligands based on the N4Py (N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) framework have been synthesized, viz. [N-(1-methyl-2-benzimidazolyl)methyl-N-(2-pyridyl)methyl-N-(bis-2-pyridyl methyl)amine] (L1) and [N-bis(1-methyl-2-benzimidazolyl)methyl-N-(bis-2-pyridylmethyl)amine] (L2), where one or two pyridyl arms of N4Py have been replaced by corresponding (N-methyl)benzimidazolyl-containing arms. The complexes [FeII(CH3CN)(L)]2+ (L = L1 (1); L2 (2)) were synthesized, and reaction of these ferrous complexes with iodosylbenzene led to the formation of the ferryl complexes [FeIV(O)(L)]2+ (L = L1 (3); L2 (4)), which were characterized by UV–vis spectroscopy, high resolution mass spectrometry, and Mössbauer spectroscopy. Complexes 3 and 4 are relatively stable with half-lives at room temperature of 40 h (L = L1) and 2.5 h (L = L2). The redox potentials of 1 and 2, as well as the visible spectra of 3 and 4, indicate that the ligand field weakens as ligand pyridyl substituents are progressively substituted by (N-methyl)benzimidazolyl moieties. The reactivities of 3 and 4 in hydrogen-atom transfer (HAT) and oxygen-atom transfer (OAT) reactions show that both complexes exhibit enhanced reactivities when compared to the analogous N4Py complex ([FeIV(O)(N4Py)]2+), and that the normalized HAT rates increase by approximately 1 order of magnitude for each replacement of a pyridyl moiety; i.e., [FeIV(O)(L2)]2+ exhibits the highest rates. The second-order HAT rate constants can be directly related to the substrate C–H bond dissociation energies. Computational modeling of the HAT reactions indicates that the reaction proceeds via a high spin transition state.
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| 17. |
- Pintado, X., et al.
(författare)
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Shear strength and shear stiffness analysis of compacted Wyoming-type bentonite
- 2023
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Ingår i: Geomechanics for Energy and the Environment. - 2352-3808. ; 34
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Tidskriftsartikel (refereegranskat)abstract
- Wyoming-type bentonite is one of the materials to be used as part of the Engineered Barrier System (EBS) in deep geological disposal facilities for the safe disposal of spent nuclear fuel. In the KBS-3 type repository, the canisters containing the spent fuel assemblies are surrounded by bentonite buffer. Therefore, it is necessary to understand the bentonite behaviour in shearing conditions for the long-term performance assessment of the canisters. Bentonite shearing could arise, for example, due to potential post-glacial earthquakes. The deviatoric stress at failure and the shear modulus of a compacted Wyoming-type bentonite were measured using different shearing tests. Tests were carried out on unsaturated samples at three laboratories. The shearing tests on unsaturated samples were unconfined and triaxial compression tests, hollow cylinder tests and simple shear tests. Unconfined and triaxial compression tests were also carried out on saturated samples. The failure was quite ductile when tests were carried out with confining pressure. The samples were compacted at different dry densities and degrees of saturation and tested at different confining pressures and strain levels to study their influence on the shear properties. Shear strength and shear modulus were studied based on models that consider the double porosity structure of the bentonites. Previously published triaxial tests and resonant column test results were also included in this study. In combination with these models, several alternatives for the definition of the constitutive stress were checked for the case of bentonite. A novel, approach, involving the results of mercury intrusion porosimetry in estimating the constitutive stress, was introduced. The shear strength calculated by the models showed a good agreement with the measured values. In some cases, unrealistic large tensile stresses were predicted. Furthermore, the models can assess the tendency of the shear modulus as a function of the shear strain, degree of saturation and dry density.
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| 18. |
- Lind, Monica, et al.
(författare)
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Short-term exposure to dioxin impairs bone tissue in male rats
- 2009
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Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 75:5, s. 680-684
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Tidskriftsartikel (refereegranskat)abstract
- Chronic and sub-chronic studies in rats have previously shown that dioxin-like compounds impair the bone tissue homeostasis. In the present study, tibiae and serum were analyzed to study possible effects of short term dioxin exposure on rats. Two month old (ca. 200g) male rats were injected with 50microg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) kg(-1) bw and tibiae were excised 5d following the exposure. Bone composition, dimensions and strength were analyzed by pQCT and three-point bending test on tibiae. In addition, detailed bone composition was analyzed by optical emission spectroscopy (ICP-OES) and Fourier transform infrared spectrometry (FTIR). Analysis of the serum bone biomarkers procollagen type-I N-terminal propeptide (PINP) and carboxyterminal cross linking teleopeptide (CTX) were also performed. pQCT-results showed alterations in the metaphysis, with a significant decrease in trabecular bone cross-sectional area (-19%, p<0.05) and a significant increase in total bone mineral density (+7%, p<0.05) in TCDD-exposed rats. Analyses of the bones by ICP-OES and FTIR showed that bones from exposed rats had a higher relative proportion of crystalline phosphate (+13% for a1080 and +11% for a1113, p<0.05) and lower acid phosphate content (-22% for a1145, p<0.05), resembling the composition of more mature bones. Serum analysis showed that the bone formation marker PINP was decreased (-37%, p<0.05) and that the bone resorption marker CTX was increased (+14%, p<0.05) indicating a net loss of bone tissue. In conclusion, 5d of exposure to TCDD was sufficient to negatively affect bone tissue in male rats.
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