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  • 1.
    Amiri, Saeid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Zwanzig, Silvelyn
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Assessing the coefficient of variations of chemical data using bootstrap method2011In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 25, no 6, p. 295-300Article in journal (Refereed)
    Abstract [en]

    The coefficient of variation is frequently used in the comparison and precision of results with different scales. This work examines the comparison of the coefficient of variation without any assumptions about the underlying distribution. A family of tests based on the bootstrap method is proposed, and its properties are illustrated using Monte Carlo simulations. The proposed method is applied to chemical experiments with iid and non-iid observations.

  • 2.
    Andersson, Carin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Environmental Toxicology.
    Lundstedt-Enkel, Katrin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Environmental Toxicology.
    Katsiadaki, Ioanna
    Holt, William V
    Van Look, Katrien J W
    Örberg, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Environmental Toxicology.
    A chemometrical approach to study interactions between ethynylestradiol and an AhR-agonist in stickleback (Gasterosteus aculeatus)2010In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 24, no 11-12, p. 768-778Article in journal (Refereed)
    Abstract [en]

    Quantifiable responses in fish, such as induction of certain proteins, can be used as indicators of chemical contamination of waterways. In order to evaluate differences in ethoxyresorufin-O-deethylase (EROD) induction capacity of the gill and the liver and effects on organs and biomarker proteins, e.g. gill and liver EROD, hepatosomatic index (HSI), nephrosomatic index (NSI), gonadosomatic index (GSI), spiggin, vitellogenin and sperm motility were analysed in male three-spined sticklebacks (Gasterosteus aculeatus) exposed for 21 days to β-naphthoflavone (βNF) alone (Exp 1) or in combination with 17α-ethynylestradiol (EE2) (Exp 2). The sperm motility variables were studied using computer-assisted sperm analysis (CASA).

    Exp 1: Gill EROD activity was significantly induced in fish exposed to ≥1.2 µg/l and hepatic EROD activity in fish exposed to ≥6 µg/l. No significant effect of ßNF on the production of spiggin or vitellogenin or on sperm variables was found.

    Exp 2: A significant additative effect of EE2 + βNF was shown for gill EROD. A significant antagonistic effect of the two compounds was found on NSI where an increased EE2 concentration led to an increase in NSI while an increased concentration of βNF led to a decreased NSI. Interestingly, the results showed that exposure to intermediate concentrations of EE2 and ßNF led to a significant increase in the sperm variables. In the aquatic environment mixtures of numerous chemicals with oestrogenic activity are present, so if the capacity to induce gill EROD activity is a general property of oestrogen-acting chemicals, our findings are important.

  • 3.
    Lundstedt-Enkel, Katrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Environmental Toxicology.
    Karlsson, Daniel
    Darnerud, Per Ola
    Interaction study with rats given two flame retardants: polybrominated diphenyl ethers (Bromkal 70-5 DE) and chlorinated paraffins (Cereclor 70L)2010In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 24, no 11-12, p. 710-718Article in journal (Refereed)
    Abstract [en]

    This study explored possible interaction effects on animal liver microsomal enzymes and thyroid hormones of two flame retardants: Bromkal 70-5 DE, a mixture of polybrominated diphenyl ethers (hereafter called PBDE); and Cereclor 70L, a mixture of chlorinated paraffins (hereafter called CP). Female Sprague-Dawley rats were exposed to these compounds in dose ranges of 1.3–18.7 mg/kg bw/day (PBDE) and 1–55 mg/kg bw/day (CP), by gavage for 14 days. Biological responses were measured on liver somatic index (LSI) and hepatic enzyme activity of (a) ethoxyresorufin-O-deethylase (EROD) (indicating CYP1A1 activity), (b) pentoxyresorufin-O-depentylase (PROD) (indicating CYP2B activity) and (c) the phase II conjugation enzyme uridine diphosphoglucuronosyl transferase (UDP-GT). The levels of total and free thyroxine hormone in rat plasma (TT4 and FT4, respectively) were also measured. In the experimental work, a Doehlert uniform shell design was used in order to select the combination of concentrations of PBDE and CP administered to the rats. Eight different combinations were used, including a control. The measured responses were modelled with multiple linear regression (MLR), giving response surface plots. The results showed strong synergism between the two flame retardants at one particular exposure combination, resulting in increased hepatic microsomal enzyme responses and decreased serum T4 concentrations. Notably, the exposure combination causing the most marked effects represented intermediate doses of both substances. The mechanisms behind the observed effects are unknown, but may involve induction or inhibition of enzyme systems.

  • 4.
    Lundstedt-Enkel, Katrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology.
    Lek, Per M.
    Lundstedt, Torbjörn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Örberg, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology.
    QSBMR - Quantitative Structure Biomagnification Relationships: Physicochemical and Structural Descriptors Important for the Biomagnification of Organochlorines and Brominated Flame Retardants2006In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 20, no 8-10, p. 392-401Article in journal (Refereed)
    Abstract [en]

    The aim of this project is to establish models to predict the biomagnification of contaminants present in Baltic Sea biota. In this paper a quantitative model that we term QSBMR-Quantitative Structure Biomagnification Relationships is presented. This model describes the relationship between the biomagnification factors (BMFs) for several organochlorines (OCs) and brominated flame retardants (BFRs), for example, polychlorinated biphenyls (PCBs), polybrominated diphenylethers (PBDEs) and hexabromocyclododecane (HBCD), and their descriptors, for example, physico-chemical properties and structural descriptors. The concentrations of contaminants in herring (Clupea harengus) muscle and guillemot (Uria aalge) egg from the Baltic Sea were used. The BMFs were calculated with the randomly sampled ratios (RSR) method that denotes the BMFs with a measure of the variation. In order to describe the physico-chemical properties and chemical structures, approximately 100 descriptors for the contaminants were generated: (a), by using the software (TSAR); (b) finding log Kow values from the literature, and (c) creating binary fingerprint variables that described the position of the chlorine and bromine for the respective PCB and PBDE molecules. Partial least squares (PLS) regression was used to model the relationship between the contaminants' BMF and the descriptors and the resulting QSBMR revealed that more than 20 descriptors in combination were important for the biomagnification of OCs and BFRs between herring and guillemot. The model including all contaminants (R2X=0.73, R2Y=0.87 and Q2=0.63, three components) explained approximately as much of the variation as the model with the PCBs alone (R2X=0.83, R2Y=0.87 and Q2=0.58, two components). The model with the BFRs alone (R2X=0.68, R2Y=0.88 and Q2 = 0.41, two components) had a slightly lower Q2 than the model including all contaminants. For validation, a training set of seven contaminants was selected by multivariate design (MVD) and a model was established. This model was then used to predict the BMFs of the test set (seven contaminants not included in the model). The resulting R2 for the regression Observed BMF versus Predicted BMF was high (0.65). The good models showed that descriptors important for the biomagnification of OCs and BFRs had been used. These types of models will be useful for in silico predictions of the biomagnification of new, not yet investigated, compounds as an aid in risk assessments.

  • 5.
    Muthas, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Lek, Per M.
    Nurbo, Johanna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Karlén, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Lundstedt, Torbjörn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Focused hierarchical design of peptide libraries - follow the lead2007In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 21, no 10-11, p. 486-495Article in journal (Refereed)
    Abstract [en]

    A novel design strategy based on the hierarchical design of experiments (HDoE) method named focused hierarchical design of experiments (FHDoE) is presented. FHDoE combine two design layers and use focused substitutions to increase the probability of obtaining active peptides when designing libraries through a selection of compounds biased towards a lead structure. Increasing the number of peptides with measurable activity will increase the information gained and the likelihood of constructing good quantitative structure-activity relationship (QSAR) models. The utility of the novel design method is verified using two different approaches. First, a library designed with the novel FHDoE method was compared with libraries generated from classical positional scanning techniques (e.g., alanine scan) as well as with general and centered minimum analog peptide sets (MAPS) libraries by using an example found in the literature. Secondly, the same design strategies were applied to a dataset of 58 angiotensin converting enzyme (ACE) dipeptide inhibitors. QSAR models were generated from designed sublibraries and the activities of the remaining compounds were predicted. These two examples show that the use of FHDoE renders peptide libraries close in physicochemical space to the native ligand, yielding a more thorough screening of the area of interest as compared to the classical positional scans and fractional factorial design (FFD). It is also shown that an FHDoE library of six dipeptides could produce a QSAR model that better described the requisites of high activity ACE inhibitors than could QSAR models built from either a nine-dipeptide library designed with MAPS or a 58-dipeptide library.

  • 6.
    Pedersen, Finn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis.
    Bengtsson, Ewert
    Nordin, Bo
    An extended strategy for exploratory multivariate image analysis including noise considerations1995In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 9, no 5, p. 389-409Article in journal (Refereed)
1 - 6 of 6
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