| 1. |
- Ahlinder, Jon, et al.
(författare)
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Chemometrics comes to court: evidence evaluation of chem–bio threat agent attacks
- 2015
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Ingår i: Journal of Chemometrics. - : John Wiley & Sons. - 0886-9383 .- 1099-128X. ; 29:5, s. 267-276
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Tidskriftsartikel (refereegranskat)abstract
- Forensic statistics is a well-established scientific field whose purpose is to statistically analyze evidence in order to support legal decisions. It traditionally relies on methods that assume small numbers of independent variables and multiple samples. Unfortunately, such methods are less applicable when dealing with highly correlated multivariate data sets such as those generated by emerging high throughput analytical technologies. Chemometrics is a field that has a wealth of methods for the analysis of such complex data sets, so it would be desirable to combine the two fields in order to identify best practices for forensic statistics in the future. This paper provides a brief introduction to forensic statistics and describes how chemometrics could be integrated with its established methods to improve the evaluation of evidence in court.The paper describes how statistics and chemometrics can be integrated, by analyzing a previous know forensic data set composed of bacterial communities from fingerprints. The presented strategy can be applied in cases where chemical and biological threat agents have been illegally disposed.
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| 2. |
- Amiri, Saeid, et al.
(författare)
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Assessing the coefficient of variations of chemical data using bootstrap method
- 2011
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Ingår i: Journal of Chemometrics. - : Wiley. - 0886-9383 .- 1099-128X. ; 25:6, s. 295-300
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Andersson, Carin, et al.
(författare)
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A chemometrical approach to study interactions between ethynylestradiol and an AhR-agonist in stickleback (Gasterosteus aculeatus)
- 2010
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Ingår i: Journal of Chemometrics. - : Wiley. - 0886-9383 .- 1099-128X. ; 24:11-12, s. 768-778
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 4. |
- Andersson, C David, et al.
(författare)
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Multivariate assessment of virtual screening experiments
- 2010
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Ingår i: Journal of Chemometrics. - : John Wiley & Sons, Ltd. - 0886-9383 .- 1099-128X. ; 24:11-12, s. 757-767
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Tidskriftsartikel (refereegranskat)abstract
- Discovering molecules with a desired biological function is one of the great challenges in drug research. To discover new lead molecules, virtual screens (VS) are often conducted, in which databases of molecules are screened for potential binders to a specific protein, using molecular docking. The choice of docking software and parameter settings within the software can significantly influence the outcome of a VS. In this study, we have applied chemometric methods such as design of experiments, principal component analysis and partial least-square projections to latent structure (PLS) to simulated VS experiments to find and compare suitable conditions for performing VS against six protein targets selected from the DUD databases. The docking parameters in FRED, and scoring functions in both FRED and GOLD docking software, were varied according to a statistical experimental design and a PLS model was calculated to correlate the experimental setup to the VS outcome. The study revealed that the choice of scoring function has the greatest influence on VS outcome, and that other parameters have varying influence, depending on the protein target. We also found that substantial bias can be introduced by the lack of variation of molecular properties in the databases used in the screening. Our results provide indications that docking experiments could be tailored to the protein target in order to obtain satisfactory VS results.
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| 5. |
- Andersson, Per M, et al.
(författare)
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Strategies for subset selection of parts of an in-house chemical library
- 2001
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Ingår i: Journal of Chemometrics. - : Wiley. - 0886-9383. ; 15:4, s. 353-69
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Tidskriftsartikel (refereegranskat)abstract
- When a company decides to perform biological testing of their in-house library, i.e. compounds which have been synthesized or purchased over the years, it is usually not feasible or desirable to test all of them using e.g. high-throughput screening (HTS). The limitation is the usually high number of compounds to test (104-106) leading to practical limitations and high costs in terms of both material costs and disposal considerations. Therefore it is often desirable to make a selection of which compounds to include in the biological testing. A challenge is how to make this selection in order to cover the structural space of the in-house library as well as possible. Here we present and discuss different selection strategies based mainly on statistical molecular design (SMD). These methods require different prior information about the compounds under investigation, e.g. characterization of the chemical structure, affinity/biological activity data or neither of these. Which method to be used is largely problem-dependent, i.e. the composition and origin of the library, and hence the structural space, are of great importance. Chemical and biological knowledge about the system under investigation should as far as possible be considered when making the final decision on which method to apply.
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| 6. |
- Andersson, Patrik, et al.
(författare)
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Ultraviolet absorption characteristics and calculated semi-empirical parameters as chemical descriptors in multivariate modelling of polychlorinated biphenyls
- 1996
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Ingår i: Journal of Chemometrics. - 0886-9383 .- 1099-128X. ; 10:2, s. 171-185
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Tidskriftsartikel (refereegranskat)abstract
- The structural variation within the polychlorinated biphenyls (PCBs) was characterized by using principal component analysis (PCA). A multivariate model was evolved from 52 physicochemical descriptors including measured ultraviolet (UV) absorption spectra, calculated semiempirical parameters (AM1) and properties captured from the literature. Parameters calculated by using the AM1-Hamiltonian were e.g. heat of formation, dipole moments, ionization potential and the barrier of internal rotation. The UV spectra were measured and digitized in the range 200-300 nm. The multivariate model revealed that most of the information within the set of physicochemical parameters was related to molecular size. Descriptors depending on size were e.g. GC retention times, partition coefficients and a subset of semiempirically derived energy terms. Important also were parameters reflecting differences in substitution patterns and related to electronic and steric properties, such as UV absorption in the wavelength region 245-300 nm, the barrier of internal rotation and the ionization potential. The developed model describes the large variation in physicochemical characteristics within the PCBs. The importance of a broad chemical characterization is illustrated by a quantitative structure-activity relationship (QSAR) for the potency of inhibition of intercellular communication for 27 structurally diverse tetra- to heptachlorinated PCBs.
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| 7. |
- Antti, Henrik, et al.
(författare)
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Batch statistical processing of 1H NMR-derived urinary spectral data
- 2002
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Ingår i: Journal of Chemometrics: Special Issue: Proceedings of the 7th Scandinavian Symposium on Chemometrics. Issue Edited by Lars Nørgaard. - : Wiley. ; 16:8-10, s. 461-8
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Tidskriftsartikel (refereegranskat)abstract
- Multivariate statistical batch processing (BP) analysis of 1H nuclear magnetic resonance (NMR) urine spectra was employed to establish time-dependent metabolic variations in animals treated with the model hepatotoxin hydrazine. Hydrazine was administered orally to rats (at 90 mg kg-1), and urine samples were collected from dosed rats and matched control animals (n = 5 per group) at time points up to 168 h post-dose. Urine samples were analysed via 1H NMR spectroscopy and partial least squares-based batch processing analysis, treating each rat as an individual batch comprising a series of timed urine samples. A model defining the mean urine profile was established for the control group, and samples obtained from hydrazine-treated animals were assessed using this model. Time-dependent deviations from the control model were evident in all hydrazine-treated animals, and hepatotoxicity was manifested by increased urinary excretion of taurine, creatine, 2-aminoadipate, citrulline and -alanine together with depletion of urinary levels of citrate, succinate and hippurate. The experiment was repeated at six different pharmaceutical centres in order to assess the robustness of the technology and to establish the natural variability in the data. Results were consistent across the data for all centres. BP plots showed a characteristic pattern for each toxin, allowing the time points at which there were maximum metabolic differences to be determined and providing a means of visualizing the net toxin-induced metabolic movement of urinary metabolism. BP may prove to be a powerful metabonomic tool in defining time-dependent metabolic consequences of toxicity and is an efficient means of visualizing inter-animal variations in response as well as defining multivariate statistical limits of normality in terms of biofluid composition.
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| 8. |
- Artursson, Tom, et al.
(författare)
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Drift correction for gas sensors using multivariate methods
- 2000
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Ingår i: Journal of Chemometrics. - 0886-9383 .- 1099-128X. ; 14:5-6, s. 711-723
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Tidskriftsartikel (refereegranskat)abstract
- Drift is one of the most serious impairments afflicting gas sensors. It can be seen as a gradual change in the sensor response over a long period of time when the external conditions an constant. This paper presents a new simple drift counteraction method based on PCA and PLS. The basic idea is to remove the drift direction component from the measurements. The direction of the drift, p, is calculated from measurements for a reference gas. Projecting the sample gas measurements on this vector gives the score vector t. The drift component tp(T) can then he removed from the sample gas data, which we call component correction (CC). The method is tested on a data set based on a reduced factorial design with four gases and a concentration gradient of hydrogen. It is found that the method works efficiently for both cases. Copyright (C) 2000 John Wiley & Sons, Ltd.
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| 9. |
- Axrup, L, et al.
(författare)
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Using miniature diode array NIR spectrometers for analysing wood chips and bark samples in motion
- 2000
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Ingår i: JOURNAL OF CHEMOMETRICS. - : JOHN WILEY & SONS LTD. - 0886-9383. ; 14:5-6, s. 561-572
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Tidskriftsartikel (refereegranskat)abstract
- The chemical and physical properties of the wood chips entering the Kraft pulping process are of high interest for many different reasons. The most important one is the possibility to establish an effective and dynamic forward process control. The same is
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| 10. |
- Berglund, Anders, 1970-, et al.
(författare)
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The GIFI approach to non-linear PLS modeling
- 2001
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Ingår i: Journal of Chemometrics. - : Wiley Inter Science. - 0886-9383 .- 1099-128X. ; 15:4, s. 321-36
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Tidskriftsartikel (refereegranskat)abstract
- The GIFI approach to non-linear modeling involves the transformation of quantitative variables to a set of 1/0 dummies in a similar manner to the way qualitative variables are coded. This is followed by analyzing the sets of 1/0 dummies by principal component analysis, multiple regression or, as discussed here, PLS. The patterns of the resulting coefficients indicate the nature of the non-linearities in the data. Here the potential uses and limitations of PLS regression, in combination with four variants of GIFI coding, are investigated using both simulated and empirical data sets.
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