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  • 1.
    Ahlgren, Joakim
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Department of Biochemistry and Organic Chemistry, Organic Chemistry I. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry.
    Reitzel, Kasper
    Danielsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Department of Biochemistry and Organic Chemistry, Organic Chemistry I. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry.
    Gogoll, Adolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Department of Biochemistry and Organic Chemistry, Organic Chemistry I. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Rydin, Emil
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Department of Biochemistry and Organic Chemistry, Organic Chemistry I. Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Biogenic phosphorus in oligotropic mountain lake sediments: Differences in composition measured with NMR spectroscopy2006In: Water Research, no 40, p. 3705-3712Article in journal (Refereed)
  • 2.
    Bergström, Sara K.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Goiny, Michel
    Danielsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Ungerstedt, Urban
    Andersson, Marit
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Markides, Karin E.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Screening of microdialysates taken before and after induced liver damage; on-line solid phase extraction-electrospray ionization-mass spectrometry2006In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1120, no 1-2, p. 21-26Article in journal (Refereed)
    Abstract [en]

    A novel method is described to follow known and unknown compounds in biological processes using microdialysis sampling and mass spectrometric detection. By implementation of internal standard, desalting/enrichment for the sample work-up, and multivariate data analysis, this methodology is a basis for future applications in early diagnosis of diseases and organ damage, as a complement to the routinely used clinical methods for biological samples. The present study includes screening without specific target analytes, of samples collected by microdialysis from liver of anaesthetized rats before and after local damage to this organ. Sample series were classified by principal component analysis, and the stimulation was identified in the chemical patterns produced by the presented analytical tool.

  • 3.
    Danielsson, Rolf
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Allard, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Sjöberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Exploring liquid chromatography-mass spectrometry fingerprints of urine samples from patients with prostate or urinary bladder cancer2011In: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 108, no 1, p. 33-48Article in journal (Refereed)
    Abstract [en]

    Data processing and analysis have become true rate and success limiting factors for molecular research where a large number of samples of high complexity are included in the data set. In general rather complicated methodologies are needed for the combination and comparison of information as obtained from selected analytical platforms. Although commercial as well as freely accessible software for high-throughput data processing are available for most platforms, tailored in-house solutions for data management and analysis can provide the versatility and transparency eligible for e.g. method development and pilot studies. This paper describes a procedure for exploring metabolic fingerprints in urine samples from prostate and bladder cancer patients with a set of in-house developed Matlab tools. In spite of the immense amount of data produced by the LC-MS platform, in this study more than 1010 data points, it is shown that the data processing tasks can be handled with reasonable computer resources. The preprocessing steps include baseline subtraction and noise reduction, followed by an initial time alignment. In the data analysis the fingerprints are treated as 2-D images, i.e. pixel by pixel, in contrast to the more common list-based approach after peak or feature detection. Although the latter approach greatly reduces the data complexity, it also involves a critical step that may obscure essential information due to undetected or misaligned peaks. The effects of remaining time shifts after the initial alignment are reduced by a binning and [‘]blurring’ procedure prior to the comparative multivariate and univariate data analyses. Other factors than cancer assignment were taken into account by ANOVA applied to the PCA scores as well as to the individual variables (pixels). It was found that the analytical day-to-day variations in our study had a large confounding effect on the cancer related differences, which emphasizes the role of proper normalization and/or experimental design. While PCA could not establish significant cancer related patterns, the pixel-wise univariate analysis could provide a list of about a hundred [‘]hotspots’ indicating possible biomarkers. This was also the limited goal for this study, with focus on the exploration of a really huge and complex data set. True biomarker identification, however, needs thorough validation and verification in separate patient sets.

  • 4.
    Danielsson, Rolf
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry, Analytical Chemistry.
    Bäckström, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry, Analytical Chemistry.
    Ullsten, Sara
    Rapid multivariate analysis of LC/GC/CE data (single or multiple channel detection) without prior peak alignment2006In: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 84, no 1-2, p. 33-39Article in journal (Refereed)
    Abstract [en]

    One- or two-dimensional data obtained with LC/GC/CE and single or multiple channel detection (MS, UV/VIS) are often used as 'fingerprints' in order to characterize complex samples. The relation between samples is then explored by multivariate data analysis (PCA, hierarchical clustering), but inevitable more or less random variation in separation conditions obstructs the analysis. Several methods for peak alignment have been developed, with more or less increase of time and efforts for computations. In this work another approach is presented, based on a correlation measure less sensitive for variations in retention/migration time. The merits of the method as a fast initial data exploration tool are demonstrated for a case study of urine profiling with CE/MS.

  • 5. Daszykowski, M.
    et al.
    Danielsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Walczak, B.
    No-alignment-strategies for exploring a set of two-way data tables obtained from capillary electrophoresis-mass spectrometry2008In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1192, no 1, p. 157-165Article in journal (Refereed)
    Abstract [en]

    Hyphenated techniques such as capillary electrophoresis-mass spectrometry (CE-MS) or high-performance liquid chromatography with diode array detection (HPLC-DAD), etc., are known to produce a huge amount of data since each sample is characterized by a two-way data table. In this paper different ways of obtaining sample-related information from a set of such tables are discussed. Working with original data requires alignment techniques due to time shifts caused by unavoidable variations in separation conditions. Other pre-processing techniques have been suggested to facilitate comparison among samples without prior peak alignment, for example, 'binning' and/or 'blurring' the data along the time dimension. All these techniques, however, require optimization of some parameters, and in this paper an alternative parameter-free method is proposed. The individual data tables (X) are represented as Gram matrices (XXT), where the summation is taken over the time dimension. Hence the possible variations in time scale are eliminated, while the time information is at least partly preserved by the correlation structure between the detection channels. For comparison among samples, a similarity matrix is constructed and explored by principal component analysis and hierarchical clustering. The Gram matrix approach was tested and compared to some other methods using 'binned' and 'blurred' data for a data set with CE-MS runs on urine samples. In addition to data exploration by principal component analysis and hierarchical clustering, a discriminant partial least squares model was constructed to discriminate between the samples that were taken with and without the prior intake of a drug. The result showed that the proposed method is at least as good as the others with respect to cluster identification and class prediction. A distinct advantage is that there is no need for parameter optimization, while a potential drawback is the large size of the Gram matrices for data with high mass resolution.

  • 6. Frank, Adrian
    et al.
    Danielsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Chemistry. Analytisk kemi.
    Selenius, Olle
    Comparison of two monitoring systems for Cu and Mo in the Swedish environment2004In: Science of the Total Environment, no 330, p. 131-143Article in journal (Refereed)
    Abstract [en]

    Bio-geochemical samples (BGS) are roots of certain aquatic plants and mosses suitable for monitoring elements dissolved in stream water. The moose, a wild ruminant living in most parts of Sweden, represents higher trophic level and another manifestation of bioavailability. By analyzing BGS (n=33 600) and moose liver (n=2400), a systematic survey has been performedin the terrestrial environment of Sweden. Cu and Mo are essential elements for life, and their presence is especially important for the Cu-dependent processes in ruminants. The availability of Cu and Mo as monitored in BGS and moose was visualized in the form of maps and subjected to further statistical analysis. The medians, with lower and upper quartiles indicated as intervals, for the country as a whole were: moose liver, Cu=34 (20-59), Mo=0.82 (0.58-1.06) mg kg -1 wet weight; BGS, Cu=50 (35-77), Mo=9.0 (5.3-18.0) mg kg -1 dry weight. The ranges of medians for the 22 Swedish counties were: moose liver, Cu=(20-62), Mo=(0.54-1.18) mg kg -1 wet weight; BGS, Cu=(28-115), Mo=(5-47) mg kg -1 dry weight. The relationships between the counties and the connections between the monitoring variables were elucidated by principal component analysis (PCA). It was demonstrated that two monitoring systems could give divergent results. An unexpectedly strong negative correlation was found between the county medians for Cu in BGS and moose liver. A possible explanation, based on the interaction between Cu and Mo in moose, could not be verified.

  • 7. Frank, Adrian
    et al.
    McPartlin, Joe
    Danielsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Chemistry. Analytisk kemi.
    Nova Scotia moose mystery - a moose sickness related to cobalt- and vitamin B12 deficiency2004In: The Science of the Total Environment, no 318, p. 89-100Article in journal (Refereed)
    Abstract [en]

    A wasting, debilitating disease with uncertain aetiology, affecting moose (Alces alces americana) in Eastern North America has been reported repeatedly ever since the 1910s. Despite the intensive studies during 1930-1960s the cause of the sickness could not be established. In the 1960s a parasitic nematode (Parelaphostrongylus tenuis) was reported as constituting a probable explanation for the sickness, although several clinical and pathological signs remained unexplained. In Sweden, a moose disease with similar signs, has been shown to be caused by molybdenosis resulting from a nutritional imbalance. The findings of this investigation were applied in Nova Scotia to determine trace element concentrations in tissues from indigenous moose. Co deficiency was found in about half of the cases and the investigation was complemented by determining the vitamin B12 level, which proved nutritional Co/vitamin B12 deficiency, further verified by an increased MMA (methylmalonic acid) level in plasma. Deficiencies were found mainly in the Tobeatic and Cape Breton Highland regions. No indications of molybdenosis or other trace element disturbances were found in Nova Scotia. Otherwise, extremely high Cd levels (148 mg Cd/kg kidney wet wt., maximum) were found, though probably not contributing to the moose sickness. The Cd burden of moose on mainland Nova Scotia was more than 50% higher than that of moose in Huntville and Alonquin (Ontario, Canada) and five- to six-fold is higher than the highest Cd levels found in Sweden. To counteract the bio-geochemical effects of Co deficiency in the moose environment, provision of Co-containing salt licks is suggested.

  • 8. Fuevesi, J.
    et al.
    Danielsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Bencsik, K.
    Hanrieder, Jörg
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Zsiros, V.
    Rajda, C.
    Hakansson, P.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Vecsei, L.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Cerebrospinal fluid proteome analysis reveals differentially abundant proteins in multiple sclerosis2014In: Multiple Sclerosis, ISSN 1352-4585, E-ISSN 1477-0970, Vol. 20, p. 180-181Article in journal (Refereed)
  • 9.
    Isaac, Giorgis
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Analytisk kemi.
    Fredriksson, Anders
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology.
    Danielsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Analytisk kemi.
    Eriksson, Per
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology.
    Bergquist, Jonas
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Analytisk kemi.
    Brain lipid composition in postnatal iron-induced motor behavior alterations following chronic neuroleptic administration in mice2006In: FEBS Journal, no 273, p. 2232-2243Article in journal (Refereed)
  • 10.
    Johannesson, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Olsson, Louise
    Bäckström, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Wetterhall, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Danielsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Screening for biomarkers in plasma from patients with gangrenous phlegmonous appendicitis using CE and CEC in combination with MS2007In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 28, no 9, p. 1435-1443Article in journal (Refereed)
    Abstract [en]

    Today a high degree of "false" appendicitis diagnoses are occurring. In this study, a screening experiment of biomarkers of two different kinds of appendicitis, gangrenous and phlegmonous, were conducted with CE and CEC coupled to MS. Plasma samples were obtained from patients pre- and post-surgery. A large amount of data was generated to be able to compare them, and chemometrics tools were utilized to visualize the differences. Indicative patterns were found for both pre- and post-surgery of the two types of inflammation as well as between them. The divergences were traced back to the MS peaks obtained in the CE- and CEC-MS setups as possible biomarkers for the two forms of appendicitis.

  • 11. Lundstrom, US
    et al.
    Nyberg, L
    Danielsson, R
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    van, Hees PAW
    Andersson, Madelen
    Forest soil acidification: Monitoring on the regional scale, Varmland, Sweden1998In: Ambio, ISSN 0044-7447, Vol. 27, no 7, p. 551-556Article in journal (Refereed)
    Abstract [en]

    A forest soil survey was performed at 180 sites in the county of Varmland in mid-western Sweden. The survey included field observations, the total composition of the soil, the composition of the exchangeable pool and the soil solution at four depths. The southwestern part of Varmland was affected by soil acidification while no indications of soil acidification were found in the north. Evaluation of the data with principal component analysis (PCA) showed that the dominating variables, giving the same spatial distribution as the atmospheric deposition, were those of the soil solution composition and especially the concentration of total Al, inorganic Al and pH in the B-horizon. The composition of the exchangeable pool was less indicative of acidification. Sampling of soil solution in large surveys is possible by the centrifuge drainage technique.

  • 12.
    Petersson, Erik
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Analytisk kemi.
    Rosén, Johan
    Turner, Charlotta
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Analytisk kemi.
    Danielsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Analytisk kemi.
    Hellenäs, Karl-Erik
    Critical factors and pitfalls affecting the extraction of acrylamide from foods: An optimisation study2006In: Analytica Chimica Acta, no 557, p. 287-295Article in journal (Refereed)
  • 13. Simonsson, Magnus
    et al.
    Kaiser, Klaus
    Danielsson, Rolf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Chemistry. Analytisk kemi.
    Andreux, Francis
    Ranger, Jacques
    Estimating nitrate, dissolved organic carbon and DOC fractions in forest floor leachates using ultraviolet absorbance spectra and multivariate analysis2005In: Geoderma, no 124, p. 157-168Article in journal (Refereed)
    Abstract [en]

    Multivariate regressions on ultraviolet (UV) absorbance (210-300 nm) data were tested as a potential tool to estimate concentrations of total dissolved organic carbon (DOC), DOC in the XAD-8-adsorbable (hydrophobic) fraction (HoDOC), and dissolved nitrate (NO3-N) in forest floor leachates. Partial least square (PLS) regressions were established for 20 zero-tension lysimeter solutions sampled in plots of coniferous and deciduous forest stands from May 2002 to January 2003. These regressions were validated against data from 24 other zero-tension solutions sampled in the same stands. The root mean square error of prediction (RMSEP) was 2.0 mg/l for DOC and 1.6 mg/l for HoDOC. These errors were 39% (DOC) and 20% (HoDOC) smaller than the errors obtained with regressions using only absorbance at 280 nm. For NO3-N, RMSEP was 0.12 mg/l (estimation by single wavelength regression is not possible). DOC and HoDOC covaried strongly and could not be estimated independently based on absorbances; HoDOC varied only between 61% and 81% of the DOC. Partly for this reason, an attempt to estimate the HoDOC/DOC ratio based on specific absorbance spectra (absorbance units per mg/l of total DOC) was little successful. Partly, however, this problem resulted from the fact that both HoDOC amd HiDOC fractions had a considerable UV absorptivity, which was not consistent between samples.

  • 14. Torelm, I
    et al.
    Danielsson, R
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Chemistry.
    Variations in Major Nutrients and Minerals in Swedish Foods. Multicenter, Multiseasonal, Multichain Study1998In: Journal of Food Composition and Analysis, ISSN 0889-1575, Vol. 11, p. 11-31Article in journal (Refereed)
  • 15.
    Vallin, Örjan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Lindberg, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Danielsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Thornell, Greger
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Microsystems Technology.
    Polishing of quartz by rapid etching in ammonium bifluoride2007In: IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, ISSN 0885-3010, E-ISSN 1525-8955, Vol. 54, no 7, p. 1454-1462Article in journal (Refereed)
    Abstract [en]

    The etch rate and surface roughness of polished and lapped AT-cut quartz subjected to hot (90, 110, and 130 degrees C), concentrated (50, 65, 80 wt %) ammonium bi-fluoride have been investigated. Having used principal component analysis to verify experimental solidity and analyze data, we claim with confidence that this parameter space does not, as elsewhere stated, allow for a polishing effect or even a preserving setting. Etch rates were found to correlate well, and possibly logarithmically, with temperature except for the hottest etching applied to lapped material. Roughness as a function of temperature and concentration behaved well for the lapped material, but lacked systematic variation in the case of the polished material. At the lowest temperature, concentration had no effect on etch rate or roughness. Future efforts are targeted at temperatures and concentrations closer to the solubility limit.

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