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Obudulu, O., Mähler, N., Skotare, T., Bygdell, J., Abreu, I. N., Ahnlund, M., . . . Tuominen, H. (2018). A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees. BMC Genomics, 19, Article ID 11.
Open this publication in new window or tab >>A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees
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2018 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 11Article in journal (Refereed) Published
Abstract [en]

Background: Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32–38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3;Potri.019G104000).

Results: The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with a tendency towards increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. Multivariate OnPLS (orthogonal projections to latent structures) modeling of five different omics datasets (the transcriptome, proteome, GC-MS metabolome, LC-MS metabolome and pyrolysis-GC/MS metabolome) collected from the secondary xylem tissues of the stem revealed systemic variation in the different variables in the transgenic lines, including changes that correlated with the changes in the secondary cell wall composition. The OnPLS model also identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis.

Conclusions: Populus SCAMP proteins were shown to influence accumulation of secondary cell wall components, including polysaccharides and phenolic compounds, in the woody tissues of Populus tree stems. Our multi-omics analyses combined with the OnPLS modelling suggest that this function is mediated by changes in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues.

Place, publisher, year, edition, pages
Springer Publishing Company, 2018
Keywords
Secretory Carrier-Associated Membrane Protein (SCAMP), Populus, Wood chemistry, Wood density, Biomass, Bioprocessing, Cork, Multi-omics
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-143890 (URN)10.1186/s12864-017-4411-1 (DOI)000419232000004 ()
Funder
Swedish Research Council Formas, 232-2009-1698
Available from: 2018-01-12 Created: 2018-01-12 Last updated: 2018-08-06Bibliographically approved
Rahnama, L., Peterson, G., Kazemnejad, A., Trygg, J. & Peolsson, A. (2018). Alterations in the Mechanical Response of Deep Dorsal Neck Muscles in Individuals Experiencing Whiplash-Associated Disorders Compared to Healthy Controls: An Ultrasound Study. American Journal of Physical Medicine & Rehabilitation, 97(2), 75-82
Open this publication in new window or tab >>Alterations in the Mechanical Response of Deep Dorsal Neck Muscles in Individuals Experiencing Whiplash-Associated Disorders Compared to Healthy Controls: An Ultrasound Study
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2018 (English)In: American Journal of Physical Medicine & Rehabilitation, ISSN 0894-9115, E-ISSN 1537-7385, Vol. 97, no 2, p. 75-82Article in journal (Refereed) Published
Abstract [en]

Objective: The aim of this study was to investigate and compare the mechanical responses of dorsal neck muscles in individuals with whiplash-associated disorders (WAD) versus healthy individuals.

Design: This study included 36 individuals with WAD (26 women and 10 men) and 36 healthy controls (26 women and 10 men). Ultrasound imaging with speckle tracking was used to measure deformation and deformation rate in five dorsal neck muscles during a neck extension task.

Results: Compared with controls, individuals with WAD showed higher deformations of the semispinalis cervicis (P = 0.02) and multifidus (P = 0.002) muscles and higher deformation rates (P = 0.03 and 0.0001, respectively). Among individuals with WAD, multifidus deformation and deformation rate were significantly associated with pain, disability, and fatigue (r = 0.31-0.46, P = 0.0001-0.01).

Conclusions: These findings indicate that the mechanical responses of the deep dorsal neck muscles differ between individuals with WAD and healthy controls, possibly reflecting that these muscles use altered strategies while performing a neck extension task. This finding provides new insight into neck muscles pathology in patients with chronic WAD and may help improve rehabilitation programs.

Place, publisher, year, edition, pages
LIPPINCOTT WILLIAMS & WILKINS, 2018
Keywords
Whiplash Injury, Neck Muscle, Cervical Spine, Ultrasonography
National Category
Physiotherapy
Identifiers
urn:nbn:se:umu:diva-144947 (URN)10.1097/PHM.0000000000000845 (DOI)000423729500004 ()29016400 (PubMedID)
Available from: 2018-02-23 Created: 2018-02-23 Last updated: 2018-06-09Bibliographically approved
Torell, F., Bennet, K., Cereghini, S., Fabre, M., Rännar, S., Lundstedt-Enkel, K., . . . Lundstedt, T. (2018). Metabolic Profiling of Multiorgan Samples: Evaluation of MODY5/RCAD Mutant Mice. Journal of Proteome Research, 17(7), 2293-2306
Open this publication in new window or tab >>Metabolic Profiling of Multiorgan Samples: Evaluation of MODY5/RCAD Mutant Mice
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2018 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 17, no 7, p. 2293-2306Article in journal (Refereed) Published
Abstract [en]

In the present study, we performed a metabolomics analysis to evaluate a MODY5/RCAD mouse mutant line as a potential model for HNF1B-associated diseases. Gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) of gut, kidney, liver, muscle, pancreas, and plasma samples uncovered the tissue specific metabolite distribution. Orthogonal projections to latent structures discriminant analysis (OPLS-DA) was used to identify the differences between MODY5/RCAD and wild-type mice in each of the tissues. The differences included, for example, increased levels of amino acids in the kidneys and reduced levels of fatty acids in the muscles of the MODY5/RCAD mice. Interestingly, campesterol was found in higher concentrations in the MODY5/RCAD mice, with a four-fold and three-fold increase in kidneys and pancreas, respectively. As expected, the MODY5/RCAD mice displayed signs of impaired renal function in addition to disturbed liver lipid metabolism, with increased lipid and fatty acid accumulation in the liver. From a metabolomics perspective, the MODY5/RCAD model was proven to display a metabolic pattern similar to what would be suspected in HNF1B-associated diseases. These findings were in line with the presumed outcome of the mutation based on the different anatomy and function of the tissues as well as the effect of the mutation on development.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2018
Keywords
HNF1B-associated diseases, metabolomics, OPLS-DA, multiorgan samples, MODY5, RCAD, mouse model
National Category
Endocrinology and Diabetes
Identifiers
urn:nbn:se:umu:diva-150378 (URN)10.1021/acs.jproteome.7b00821 (DOI)000438469900004 ()29873499 (PubMedID)2-s2.0-85048373012 (Scopus ID)
Available from: 2018-08-08 Created: 2018-08-08 Last updated: 2018-08-08Bibliographically approved
Sjögren, R., Stridh, K., Skotare, T. & Trygg, J. (2018). Multivariate patent analysis: using chemometrics to analyze collections of chemical and pharmaceutical patents. Paper presented at 2018/10/09. Journal of Chemometrics, Article ID e3041.
Open this publication in new window or tab >>Multivariate patent analysis: using chemometrics to analyze collections of chemical and pharmaceutical patents
2018 (English)In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, article id e3041Article in journal (Refereed) Published
Abstract [en]

Abstract Patents are an important source of technological knowledge, but the amount of existing patents is vast and quickly growing. This makes development of tools and methodologies for quickly revealing patterns in patent collections important. In this paper, we describe how structured chemometric principles of multivariate data analysis can be applied in the context of text analysis in a novel combination with common machine learning preprocessing methodologies. We demonstrate our methodology in 2 case studies. Using principal component analysis (PCA) on a collection of 12338 patent abstracts from 25 companies in big pharma revealed sub-fields which the companies are active in. Using PCA on a smaller collection of patents retrieved by searching for a specific term proved useful to quickly understand how patent classifications relate to the search term. By using orthogonal projections to latent structures (O-PLS) on patent classification schemes, we were able to separate patents on a more detailed level than using PCA. Lastly, we performed multi-block modeling using OnPLS on bag-of-words representations of abstracts, claims, and detailed descriptions, respectively, showing that semantic variation relating to patent classification is consistent across multiple text blocks, represented as globally joint variation. We conclude that using machine learning to transform unstructured data into structured data provide a good preprocessing tool for subsequent chemometric multivariate data analysis and provides an easily interpretable and novel workflow to understand large collections of patents. We demonstrate this on collections of chemical and pharmaceutical patents.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
Keywords
text analytics, OnPLS, principal component analysis, orthogonal projections to latent structures, feature engineering
National Category
Other Chemistry Topics
Identifiers
urn:nbn:se:umu:diva-152511 (URN)10.1002/cem.3041 (DOI)
Conference
2018/10/09
Funder
Swedish Research Council, 2016‐04376eSSENCE - An eScience CollaborationThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2018-10-09 Created: 2018-10-09 Last updated: 2018-11-06Bibliographically approved
Peterson, G., Nilsson, D., Trygg, J. & Peolsson, A. (2018). Neck-specific exercise improves impaired interactions between ventral neck muscles in chronic whiplash: A randomized controlled ultrasound study. Scientific Reports, 8, Article ID 9649.
Open this publication in new window or tab >>Neck-specific exercise improves impaired interactions between ventral neck muscles in chronic whiplash: A randomized controlled ultrasound study
2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 9649Article in journal (Refereed) Published
Abstract [en]

Chronic pain and disability is common in whiplash-associated disorders (WAD), leading to personal suffering, sick leave, and social cost. The cervical spine is heavily dependent on muscular support and whiplash injury can cause damage to the neck muscles, but diagnostic tools to measure neck muscle impairment and evaluate exercise interventions are lacking. Therefore, the present study investigated ventral neck muscle interactions in 26 individuals with chronic WAD randomized to neck-specific exercise (NSE) or remaining on a waiting list (WL) in 3 months. We performed real-time, non-invasive ultrasound measurements with speckle tracking analysis and calculated the deformation area and deformation rate in three ventral neck muscles. Multivariate statistics were used to analyse interactions between the muscles. After 3 months of NSE, significant improvements were observed in neck muscle interactions and pain intensity in the NSE group compared to the WL group. Thus, this study demonstrates that non-invasive ultrasound can be a diagnostic tool for muscle impairment and used to evaluate exercise interventions in WAD and stands to make a breakthrough for better management in chronic WAD.

Place, publisher, year, edition, pages
Nature Publishing Group, 2018
National Category
Physiotherapy
Identifiers
urn:nbn:se:umu:diva-150773 (URN)10.1038/s41598-018-27685-7 (DOI)000436078500012 ()29941911 (PubMedID)
Available from: 2018-08-31 Created: 2018-08-31 Last updated: 2018-08-31Bibliographically approved
Surowiec, I., Johansson, E., Stenlund, H., Rantapää-Dahlqvist, S., Bergström, S., Normark, J. & Trygg, J. (2018). Quantification of run order effect on chromatography: mass spectrometry profiling data. Journal of Chromatography A, 1568, 229-234
Open this publication in new window or tab >>Quantification of run order effect on chromatography: mass spectrometry profiling data
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2018 (English)In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1568, p. 229-234Article in journal (Refereed) Published
Abstract [en]

Chromatographic systems coupled with mass spectrometry detection are widely used in biological studies investigating how levels of biomolecules respond to different internal and external stimuli. Such changes are normally expected to be of low magnitude and therefore all experimental factors that can influence the analysis need to be understood and minimized. Run order effect is commonly observed and constitutes a major challenge in chromatography-mass spectrometry based profiling studies that needs to be addressed before the biological evaluation of measured data is made. So far there is no established consensus, metric or method that quickly estimates the size of this effect. In this paper we demonstrate how orthogonal projections to latent structures (OPLS®) can be used for objective quantification of the run order effect in profiling studies. The quantification metric is expressed as the amount of variation in the experimental data that is correlated to the run order. One of the primary advantages with this approach is that it provides a fast way of quantifying run-order effect for all detected features, not only internal standards. Results obtained from quantification of run order effect as provided by the OPLS can be used in the evaluation of data normalization, support the optimization of analytical protocols and identification of compounds highly influenced by instrumental drift. The application of OPLS for quantification of run order is demonstrated on experimental data from plasma profiling performed on three analytical platforms: GCMS metabolomics, LCMS metabolomics and LCMS lipidomics.

Keywords
Run order effect quantification, Mass spectrometry profiling, OPLS, Instrumental drift
National Category
Rheumatology and Autoimmunity
Identifiers
urn:nbn:se:umu:diva-150428 (URN)10.1016/j.chroma.2018.07.019 (DOI)000443669600025 ()2-s2.0-85049727571 (Scopus ID)
Available from: 2018-08-07 Created: 2018-08-07 Last updated: 2018-11-05Bibliographically approved
Skotare, T., Sjögren, R., Surowiec, I., Nilsson, D. & Trygg, J. (2018). Visualization of descriptive multiblock analysis. Paper presented at 2018/10/09. Journal of Chemometrics
Open this publication in new window or tab >>Visualization of descriptive multiblock analysis
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2018 (English)In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128XArticle in journal (Refereed) Published
Abstract [en]

Abstract Understanding and making the most of complex data collected from multiple sources is a challenging task. Data integration is the procedure of describing the main features in multiple data blocks, and several methods for multiblock analysis have been previously developed, including OnPLS and JIVE. One of the main challenges is how to visualize and interpret the results of multiblock analyses because of the increased model complexity and sheer size of data. In this paper, we present novel visualization tools that simplify interpretation and overview of multiblock analysis. We introduce a correlation matrix plot that provides an overview of the relationships between blocks found by multiblock models. We also present a multiblock scatter plot, a metadata correlation plot, and a variation distribution plot, that simplify the interpretation of multiblock models. We demonstrate our visualizations on an industrial case study in vibration spectroscopy (NIR, UV, and Raman datasets) as well as a multiomics integration study (transcript, metabolite, and protein datasets). We conclude that our visualizations provide useful tools to harness the complexity of multiblock analysis and enable better understanding of the investigated system.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
Keywords
data fusion, descriptive analytics, multiblock analysis, OnPLS, visualization
National Category
Other Chemistry Topics
Identifiers
urn:nbn:se:umu:diva-152512 (URN)10.1002/cem.3071 (DOI)
Conference
2018/10/09
Funder
eSSENCE - An eScience CollaborationSwedish Research Council, 2016‐04376
Available from: 2018-10-09 Created: 2018-10-09 Last updated: 2018-11-09Bibliographically approved
Galindo-Prieto, B., Trygg, J. & Geladi, P. (2017). A new approach for variable influence on projection (VIP) in O2PLS models. Chemometrics and Intelligent Laboratory Systems, 160, 110-124
Open this publication in new window or tab >>A new approach for variable influence on projection (VIP) in O2PLS models
2017 (English)In: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 160, p. 110-124Article in journal (Refereed) Published
Abstract [en]

A novel variable influence on projection approach for O2PLS® models, named VIPO2PLS, is presented in this paper. VIPO2PLS is a model-based method for judging the importance of variables. Its cornerstone is the 2-way formalism of the O2PLS models; i.e. the use of both predictive and orthogonal normalized loadings of the two modelled data matrices, and also a new weighting system based on the sum of squares of both data blocks (X, Y). The VIPO2PLS algorithm has been tested in one synthetic data set and two real cases, and the outcomes have been compared to the PLS-VIP, VIPOPLS, and i-PLS methods. The purpose is to achieve a sharper and enhanced model interpretation of O2PLS models by using the new VIPO2PLS method for assessing the importance of both X- and Y- variables.

Place, publisher, year, edition, pages
Elsevier, 2017
Keywords
Multi-block variable selection, O2PLS, VIP, Variable importance, Model interpretation, Multivariate calibration
National Category
Chemical Sciences Computer and Information Sciences
Identifiers
urn:nbn:se:umu:diva-128916 (URN)10.1016/j.chemolab.2016.11.005 (DOI)000392684100013 ()
Available from: 2016-12-19 Created: 2016-12-19 Last updated: 2018-06-09Bibliographically approved
Kuess, P., Andrzejewski, P., Nilsson, D., Georg, P., Knoth, J., Susani, M., . . . Nyholm, T. (2017). Association between pathology and texture features of multi parametric MRI of the prostate. Physics in Medicine and Biology, 62(19), 7833-7854
Open this publication in new window or tab >>Association between pathology and texture features of multi parametric MRI of the prostate
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2017 (English)In: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560, Vol. 62, no 19, p. 7833-7854Article in journal (Refereed) Published
Abstract [en]

The role of multi-parametric (mp)MRI in the diagnosis and treatment of prostate cancer has increased considerably. An alternative to visual inspection of mpMRI is the evaluation using histogram-based (first order statistics) parameters and textural features (second order statistics). The aims of the present work were to investigate the relationship between benign and malignant sub-volumes of the prostate and textures obtained from mpMR images. The performance of tumor prediction was investigated based on the combination of histogram-based and textural parameters. Subsequently, the relative importance of mpMR images was assessed and the benefit of additional imaging analyzed. Finally, sub-structures based on the PI-RADS classification were investigated as potential regions to automatically detect maligned lesions. Twenty-five patients who received mpMRI prior to radical prostatectomy were included in the study. The imaging protocol included T2, DWI, and DCE. Delineation of tumor regions was performed based on pathological information. First and second order statistics were derived from each structure and for all image modalities. The resulting data were processed with multivariate analysis, using PCA (principal component analysis) and OPLS-DA (orthogonal partial least squares discriminant analysis) for separation of malignant and healthy tissue. PCA showed a clear difference between tumor and healthy regions in the peripheral zone for all investigated images. The predictive ability of the OPLS-DA models increased for all image modalities when first and second order statistics were combined. The predictive value reached a plateau after adding ADC and T2, and did not increase further with the addition of other image information. The present study indicates a distinct difference in the signatures between malign and benign prostate tissue. This is an absolute prerequisite for automatic tumor segmentation, but only the first step in that direction. For the specific identified signature, DCE did not add complementary information to T2 and ADC maps.

Keywords
textural features, mpMRI, prostate cancer, haralick texture features
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:umu:diva-142316 (URN)10.1088/1361-6560/aa884d (DOI)000425829000002 ()28837046 (PubMedID)
Available from: 2017-11-27 Created: 2017-11-27 Last updated: 2018-06-09Bibliographically approved
Checa, A., Idborg, H., Zandian, A., Sar, D. G., Surowiec, I., Trygg, J., . . . Wheelock, C. E. (2017). Dysregulations in circulating sphingolipids associate with disease activity indices in female patients with systemic lupus erythematosus: a cross-sectional study. Lupus, 26(10), 1023-1033
Open this publication in new window or tab >>Dysregulations in circulating sphingolipids associate with disease activity indices in female patients with systemic lupus erythematosus: a cross-sectional study
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2017 (English)In: Lupus, ISSN 0961-2033, E-ISSN 1477-0962, Vol. 26, no 10, p. 1023-1033Article in journal (Refereed) Published
Abstract [en]

Objective The objective of this study was to investigate the association of clinical and renal disease activity with circulating sphingolipids in patients with systemic lupus erythematosus.

Methods We used liquid chromatography tandem mass spectrometry to measure the levels of 27 sphingolipids in plasma from 107 female systemic lupus erythematosus patients and 23 controls selected using a design of experiment approach. We investigated the associations between sphingolipids and two disease activity indices, the Systemic Lupus Activity Measurement and the Systemic Lupus Erythematosus Disease Activity Index. Damage was scored according to the Systemic Lupus International Collaborating Clinics damage index. Renal activity was evaluated with the British Island Lupus Activity Group index. The effects of immunosuppressive treatment on sphingolipid levels were evaluated before and after treatment in 22 female systemic lupus erythematosus patients with active disease.

Results Circulating sphingolipids from the ceramide and hexosylceramide families were increased, and sphingoid bases were decreased, in systemic lupus erythematosus patients compared to controls. The ratio of C-16:0-ceramide to sphingosine-1-phosphate was the best discriminator between patients and controls, with an area under the receiver-operating curve of 0.77. The C-16:0-ceramide to sphingosine-1-phosphate ratio was associated with ongoing disease activity according to the Systemic Lupus Activity Measurement and the Systemic Lupus Erythematosus Disease Activity Index, but not with accumulated damage according to the Systemic Lupus International Collaborating Clinics Damage Index. Levels of C-16:0- and C-24:1-hexosylceramides were able to discriminate patients with current versus inactive/no renal involvement. All dysregulated sphingolipids were normalized after immunosuppressive treatment.

Conclusion We provide evidence that sphingolipids are dysregulated in systemic lupus erythematosus and associated with disease activity. This study demonstrates the utility of simultaneously targeting multiple components of a pathway to establish disease associations.

Place, publisher, year, edition, pages
SAGE PUBLICATIONS LTD, 2017
Keywords
Systemic lupus erythematosus, sphingolipids, disease activity
National Category
Rheumatology and Autoimmunity Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-139613 (URN)10.1177/0961203316686707 (DOI)000407822000002 ()28134039 (PubMedID)
Available from: 2017-10-09 Created: 2017-10-09 Last updated: 2018-06-09Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0003-3799-6094

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