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| 2. |
- Lynch, I, et al.
(författare)
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Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?
- 2020
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Ingår i: Nanomaterials (Basel, Switzerland). - : MDPI AG. - 2079-4991. ; 10:12
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Tidskriftsartikel (refereegranskat)abstract
- Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analyzed issues involved in developing an InChI for NMs (NInChI). The layers needed to capture NM structures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a “nano” extension to the InChI standard.
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| 4. |
- Falandysz, J, et al.
(författare)
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Multivariate analysis of the bioaccumulation of polychlorinated biphenyls (PCBs) in the marine pelagic food web from the southern part of the Baltic Sea, Poland
- 2002
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Ingår i: Journal of Environmental Monitoring. - : Royal Society of Chemistry (RSC). - 1464-0325 .- 1464-0333. ; 4:6, s. 929-941
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Tidskriftsartikel (refereegranskat)abstract
- The concentration, pattern, bioaccumulation and biomagnification features of many chlorobiphenyl congeners, including non- and mono-ortho chlorine substituted members have been determined in a pelagic food chain including mixed phyto- and zooplankton-1 herring (Clupea harengus), harbour porpoise (Phocoena phocoena) and black cormorants (Phalacrocorax carbo sinensis) collected from the southern part of the Baltic, Proper. TCDD (tetrachlorodibenzo-p-dioxin) toxic equivalents (TEQs) in plankton, herring, harbour porpoise and cormorants. were 0.42, 5.3, 79 and 2700 pg g(-1) lipid weight, respectively. Concentrations of total, polychlorinated biphehyls (PCBs) in plankton, herring harbour porpoise and cormorants were 1.9, 120, 8700 and 2100 ng g(-1) wet weight (210, 1300, 10000 and 42000 ng g(-1) lipid weight) respectively. Herring, harbour porpoise and black cormorant apparently bioaccumulate many PCBs found in their food, and the values of the bioaccumulation factor's (BAFs) for PCBs were approximately 10 in herring, 35 in harbour porpoise and up to 300 in breast muscle of, cormorants. Harbour porpoise clearly is able to metabolize. the most toxic, non-ortho PCBs (no. 77, 126 and 169) and a few mono-ortho PCBs (no. 114, 123 and 156), while all non- and mono-ortho PCBs are bioaccumulated by herring. Penta-, hexa- and hepta-CBs were the dominant homologue classes both in the muscle tissue and liver. PCB congeners nos. 201, 209, 172/192, 194 and 195 were characterized by the largest.. BAFs (between 100 and 300). Principal component analysis has been used to analyse the interdependences. and differences in the CB congener accumulation patterns between the, components of the investigated pelagic food web.
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| 5. |
- Falandysz, J, et al.
(författare)
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Polychlorinated biphenyls (PCBs) and their congener-specific accumulation in edible fish from the Gulf of Gdask, Baltic Sea
- 2002
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Ingår i: Food Additives & Contaminants. - : Informa UK Limited. - 0265-203X. ; 19:8, s. 779-95
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Tidskriftsartikel (refereegranskat)abstract
- Concentrations and composition profiles of polychlorinated biphenyls (PCBs) were investigated in composite samples of 10 species of edible fish from the Gulf of Gda sk, in the southern part of the Baltic Sea, Poland, to understand the status of contamination and possible human exposure risk. Apart from the total PCBs, planar non-ortho (IUPAC nos 77, 126, 169) and mono-ortho (nos 105, 114, 118, 123, 156, 157, 167, 189) chlorobiphenyls were also quantified and their dioxin-like toxicity assessed. The absolute total PCB concentrations in fish ranged from 43 to 490 ng g-1 wet wt (910-11000 ng g-1 lipids), while of TCDD TEQs of planar members were from 0.15 to 3.1 pg g-1 wet wt (8.1-81 pg g-1 lipids). The penta- and hexa-CBs usually comprised 70-80% of the total PCBs and were followed by hepta-, tetra- and tri-CBs, and for a specific site tri- and tetra-CBs comprised as much as 22%. Among the individual CB congeners, nos 118, 153 (+132) and 138 (+160 +163 +164) were the most abundant, while no. 110 comprised between 6.8 and 9.3% of the total PCBs in some species. Principal component analysis (PCA) was applied to examine the interdependences among CB congeners in the factor space. The PCA model and cluster analyses were further used to examine site- and species-specific differences and similarities of PCB composition, and the results are discussed. An assessed daily intake rate of TCDD TEQ of planar PCBs with the fishmeal of the Gulf of Gda sk in the 1990s was between 78 and 96 pg per capita or between 1.3 and 1.6 pg kg-1 body weight.
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| 6. |
- Falandysz, J, et al.
(författare)
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Polychlorinated biphenyls (PCBs) in black cormorants breeding at the coast of the Gulf of Gdansk, Baltic Sea
- 2003
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Ingår i: Fresenius Environmental Bulletin: Special Issue: Sp. Iss. SI. ; 12:2, s. 127-42
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Tidskriftsartikel (refereegranskat)abstract
- Concentrations, composition profiles and biomagnification of polychlorinated biphenyls non-ortho (IUPAC nos 77, 126, 169), mono-ortho (105, 114, 118, 123, 156, 157, 167, 189) and total PCBs were investigated in black cormorants (Phalacrocorax carbo sinensis) breeding at the coast of the Gulf of Gdansk, Baltic Sea. Total PCB concentrations in birds were in the range from 750 to 5200 ng/g wet wt ( from 19000 to 110000 ng/g lipid wt) in the breast muscles and from 440 to 4200 ng/g, wet wt (13000 to 69000 ng/g lipid wt) in liver. Penta-, hexa and hepta-CBs were dominating homologue classes both in the muscle tissue and liver. PCB congeners nos. 201, 209, 172/192. 194 and 195 were characterized by the greatest bioaccumulation factors (between 100 and 300). Principal Component Analysis (PCA) has been used to analyse accumulation pattern and interdependences among CB congeners.
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| 7. |
- Federico, A, et al.
(författare)
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Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data
- 2020
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Ingår i: Nanomaterials (Basel, Switzerland). - : MDPI AG. - 2079-4991. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Preprocessing of transcriptomics data plays a pivotal role in the development of toxicogenomics-driven tools for chemical toxicity assessment. The generation and exploitation of large volumes of molecular profiles, following an appropriate experimental design, allows the employment of toxicogenomics (TGx) approaches for a thorough characterisation of the mechanism of action (MOA) of different compounds. To date, a plethora of data preprocessing methodologies have been suggested. However, in most cases, building the optimal analytical workflow is not straightforward. A careful selection of the right tools must be carried out, since it will affect the downstream analyses and modelling approaches. Transcriptomics data preprocessing spans across multiple steps such as quality check, filtering, normalization, batch effect detection and correction. Currently, there is a lack of standard guidelines for data preprocessing in the TGx field. Defining the optimal tools and procedures to be employed in the transcriptomics data preprocessing will lead to the generation of homogeneous and unbiased data, allowing the development of more reliable, robust and accurate predictive models. In this review, we outline methods for the preprocessing of three main transcriptomic technologies including microarray, bulk RNA-Sequencing (RNA-Seq), and single cell RNA-Sequencing (scRNA-Seq). Moreover, we discuss the most common methods for the identification of differentially expressed genes and to perform a functional enrichment analysis. This review is the second part of a three-article series on Transcriptomics in Toxicogenomics.
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| 9. |
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| 10. |
- Jeliazkova, N, et al.
(författare)
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Towards FAIR nanosafety data
- 2021
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Ingår i: Nature nanotechnology. - : Springer Science and Business Media LLC. - 1748-3395 .- 1748-3387. ; 16:86, s. 644-
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Tidskriftsartikel (refereegranskat)
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