umu.sePublications
Change search
Link to record
Permanent link

Direct link
BETA
Nilsson, David
Publications (10 of 21) Show all publications
Skotare, T., Nilsson, D., Xiong, S., Geladi, P. & Trygg, J. (2019). Joint and unique multiblock analysis for integration and calibration transfer of NIR instruments. Analytical Chemistry, 91(5), 3516-3524
Open this publication in new window or tab >>Joint and unique multiblock analysis for integration and calibration transfer of NIR instruments
Show others...
2019 (English)In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 91, no 5, p. 3516-3524Article in journal (Refereed) Published
Abstract [en]

In the present paper, we introduce an end-to-end workflow called joint and unique multiblock analysis (JUMBA), which allows multiple sources of data to be analyzed simultaneously to better understand how they complement each other. In near-infrared (NIR) spectroscopy, calibration models between NIR spectra and responses are used to replace wet-chemistry methods, and the models tend to be instrument-specific. Calibration-transfer techniques are used for standardization of NIR-instrumentation, enabling the use of one model on several instruments. The current paper investigates both the similarities and differences among a variety of NIR instruments using JUMBA. We demonstrate JUMBA on both a previously unpublished data set in which five NIR instruments measured mushroom substrate and a publicly available data set measured on corn samples. We found that NIR spectra from different instrumentation largely shared the same underlying structures, an insight we took advantage of to perform calibration transfer. The proposed JUMBA transfer displayed excellent calibration-transfer performance across the two analyzed data sets and outperformed existing methods in terms of both prediction accuracy and stability. When applied to a multi-instrument environment, JUMBA transfer can integrate all instruments in the same model and will ensure higher consistency among them compared with existing calibration-transfer methods.

Place, publisher, year, edition, pages
Washington: American Chemical Society (ACS), 2019
Keywords
near-infrared spectroscopy, spent mushroom compost, multivariate calibration, water-content, standardization, regression, vegetation, models, ONPLS
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:umu:diva-156707 (URN)10.1021/acs.analchem.8b05188 (DOI)000460709200047 ()30758178 (PubMedID)2-s2.0-85062418105 (Scopus ID)
Projects
Bio4Energy
Available from: 2019-02-25 Created: 2019-02-25 Last updated: 2019-09-06Bibliographically approved
Peterson, G., O'Leary, S., Nilsson, D., Moodie, K., Tucker, K., Trygg, J. & Peolsson, A. (2019). Ultrasound imaging of dorsal neck muscles with speckle tracking analyses: the relationship between muscle deformation and force. Scientific Reports, 9, Article ID 13688.
Open this publication in new window or tab >>Ultrasound imaging of dorsal neck muscles with speckle tracking analyses: the relationship between muscle deformation and force
Show others...
2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 13688Article in journal (Refereed) Published
Abstract [en]

The development of methods of non-invasive measurement of neck muscle function remains a priority in the clinical sciences. In this study, dorsal neck muscle deformation vs time curves (deformation area) were evaluated against incremental force, recorded from non-invasive real-time ultrasound measurement. The results revealed subject-specific moderate to strong linear or non-linear relationships between deformation and force. Test-retest variability showed strong reliability for all five neck muscles summed together and fair to good reliability for the five muscles evaluated separately. Multivariate statistics were used to analyse the interactions between the dorsal neck muscles during different percentages of maximal voluntary contraction (MVC). Low force (10-20% MVC) was related to muscle shortening; higher force (40-80% MVC) showed combination of shortening and elongation deformation in the muscle interactions. The muscle interactions during isometric MVC test were subject-specific, with different combinations and deformations of the five neck muscles. Force >= 40% MVC were associated with a forward movement of the cervical spine that affected the ultrasound measurement of the dorsal neck muscles. Ultrasound with speckle-tracking analyses may be best used to detect low levels (<40% MVC) of neck muscle activity.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019
National Category
Physiotherapy
Identifiers
urn:nbn:se:umu:diva-164049 (URN)10.1038/s41598-019-49916-1 (DOI)000487216300008 ()31548564 (PubMedID)
Available from: 2019-10-15 Created: 2019-10-15 Last updated: 2019-10-15Bibliographically 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
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
Show others...
2018 (English)In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128XArticle in journal (Refereed) In press
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)2-s2.0-85051048496 (Scopus ID)
Conference
2018/10/09
Funder
eSSENCE - An eScience CollaborationSwedish Research Council, 2016‐04376
Available from: 2018-10-09 Created: 2018-10-09 Last updated: 2019-04-25Bibliographically 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
Show others...
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
Brynolfsson, P., Nilsson, D., Torheim, T., Asklund, T., Thellenberg Karlsson, C., Trygg, J., . . . Garpebring, A. (2017). Haralick texture features from apparent diffusion coefficient (ADC) MRI images depend on imaging and pre-processing parameters. Scientific Reports, 7, Article ID 4041.
Open this publication in new window or tab >>Haralick texture features from apparent diffusion coefficient (ADC) MRI images depend on imaging and pre-processing parameters
Show others...
2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 4041Article in journal (Refereed) Published
Abstract [en]

In recent years, texture analysis of medical images has become increasingly popular in studies investigating diagnosis, classification and treatment response assessment of cancerous disease. Despite numerous applications in oncology and medical imaging in general, there is no consensus regarding texture analysis workflow, or reporting of parameter settings crucial for replication of results. The aim of this study was to assess how sensitive Haralick texture features of apparent diffusion coefficient (ADC) MR images are to changes in five parameters related to image acquisition and pre-processing: noise, resolution, how the ADC map is constructed, the choice of quantization method, and the number of gray levels in the quantized image. We found that noise, resolution, choice of quantization method and the number of gray levels in the quantized images had a significant influence on most texture features, and that the effect size varied between different features. Different methods for constructing the ADC maps did not have an impact on any texture feature. Based on our results, we recommend using images with similar resolutions and noise levels, using one quantization method, and the same number of gray levels in all quantized images, to make meaningful comparisons of texture feature results between different subjects.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:umu:diva-134993 (URN)10.1038/s41598-017-04151-4 (DOI)000403874900024 ()28642480 (PubMedID)
Note

Originally included in thesis in manuscript form.

Available from: 2017-05-15 Created: 2017-05-15 Last updated: 2018-06-09Bibliographically approved
Peolsson, A., Peterson, G., Trygg, J. & Nilsson, D. (2016). Altered mechanical deformation of the trapezius and multifidus muscles registered with ultrasonography in women with chronic whiplash-associated disorders. Paper presented at 2016/12/19. Manual Therapy, 25, e58
Open this publication in new window or tab >>Altered mechanical deformation of the trapezius and multifidus muscles registered with ultrasonography in women with chronic whiplash-associated disorders
2016 (English)In: Manual Therapy, ISSN 1356-689X, E-ISSN 1532-2769, Vol. 25, p. e58-Article in journal (Refereed) Published
Abstract [en]

Background: The deformation and deformation rate of the dorsal neck muscle layers in individuals with chronic whiplash associated disorders (WAD) is rarely evaluated, and the mechanical behaviour during dynamic neck extension remains to be investigated.

Purpose: To compare the deformation and deformation rate of dorsal neck muscles (trapezius, splenius capitis, semispinalis capitis and cervicis, and multifidus) in women with chronic WAD compared with healthy controls during a dynamic resisted neck extension.

Methods: Nine women with chronic grade 2 and 3 WAD (mean age 38 years, standard deviation [SD] 11.3) and nine age- and gender-matched healthy controls (mean age 38 years, SD 11.6) participated in this cross-sectional, controlled study. Ultrasonography movies and post-process speckle tracking were used to investigate real-time mechanical dorsal neck muscle behaviour at the C4 segmental level during a low-loaded dynamic standardized neck extension. Deformation (longitudinal shortening and elongation) and deformation rate (speed of deformation) were calculated during the entire exercise sequence.

Results: There were significant differences between the WAD and control groups in total deformation for the trapezius (p < 0.04) and multifidus (p < 0.03). The WAD group showed more shortening in the deformation pattern during the concentric contraction phase in the trapezius muscle, and during both the concentric and eccentric phase in the multifidus muscle compared to healthy controls. There were no other significant differences between groups either in deformation or deformation rate.

Conclusion: There were altered mechanical deformations of the trapezius and multifidus muscles, with preliminary evidence for overuse in individuals with WAD compared to healthy controls. The findings must be interpreted with caution due to the small sample size.

Implications: An ultrasound investigation made it possible to non-invasively capture multi-layered muscles in real time, adding new information of value for clinical practice of patients with WAD, which may impact future rehabilitation.

Keywords
Whiplash injury, Neck muscles, Ultrasonography
National Category
Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-128918 (URN)10.1016/j.math.2016.05.081 (DOI)
Conference
2016/12/19
Available from: 2016-12-19 Created: 2016-12-19 Last updated: 2018-06-09Bibliographically approved
Peterson, G., Nilsson, D., Peterson, S., Dedering, Å., Trygg, J., Wallman, T. & Peolsson, A. (2016). Changes in dorsal neck muscle function in individuals with chronic whiplash-associated disorders: a real-time ultrasound case-control study. Ultrasound in Medicine and Biology, 42(5), 1090-1102
Open this publication in new window or tab >>Changes in dorsal neck muscle function in individuals with chronic whiplash-associated disorders: a real-time ultrasound case-control study
Show others...
2016 (English)In: Ultrasound in Medicine and Biology, ISSN 0301-5629, E-ISSN 1879-291X, Vol. 42, no 5, p. 1090-1102Article in journal (Refereed) Published
Abstract [en]

Impaired neck muscle function leads to disability in individuals with chronic whiplash-associated disorder (WAD), but diagnostic tools are lacking. In this study, deformations and deformation rates were investigated in five dorsal neck muscles during 10 arm elevations by ultrasonography with speckle tracking analyses. Forty individuals with chronic WAD (28 women and 12 men, mean age = 37 y) and 40 healthy controls matched for age and sex were included. The WAD group had higher deformation rates in the multifidus muscle during the first (p < 0.04) and 10th (only women, p < 0.01) arm elevations compared with the control group. Linear relationships between the neck muscles for deformation rate (controls: R-2 = 0.24-0.82, WAD: R-2 = 0.05-0.74) and deformation of the deepest muscles (controls: R-2 = 0.61-0.32, WAD: R-2 = 0.15-0.01) were stronger for women in the control group versus women with WAD, indicating there is altered interplay between dorsal neck muscles in chronic WAD. 

Keywords
Whiplash injury, Ultrasonography, Neck muscles, Spine
National Category
Health Sciences
Identifiers
urn:nbn:se:umu:diva-120620 (URN)10.1016/j.ultrasmedbio.2015.12.022 (DOI)000373385300008 ()26921149 (PubMedID)
Available from: 2016-08-16 Created: 2016-05-18 Last updated: 2018-06-07Bibliographically approved
Peolsson, A., Peterson, G., Trygg, J. & Nilsson, D. (2016). Multivariate analysis of ultrasound-recorded dorsal strain sequences: Investigation of dynamic neck extensions in women with chronic whiplash associated disorders. Scientific Reports, 6, Article ID 30415.
Open this publication in new window or tab >>Multivariate analysis of ultrasound-recorded dorsal strain sequences: Investigation of dynamic neck extensions in women with chronic whiplash associated disorders
2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 30415Article in journal (Refereed) Published
Abstract [en]

Whiplash Associated Disorders (WAD) refers to the multifaceted and chronic burden that is common after a whiplash injury. Tools to assist in the diagnosis of WAD and an increased understanding of neck muscle behaviour are needed. We examined the multilayer dorsal neck muscle behaviour in nine women with chronic WAD versus healthy controls during the entire sequence of a dynamic low-loaded neck extension exercise, which was recorded using real-time ultrasound movies with high frame rates. Principal component analysis and orthogonal partial least squares were used to analyse mechanical muscle strain (deformation in elongation and shortening). The WAD group showed more shortening during the neck extension phase in the trapezius muscle and during both the neck extension and the return to neutral phase in the multifidus muscle. For the first time, a novel non-invasive method is presented that is capable of detecting altered dorsal muscle strain in women with WAD during an entire exercise sequence. This method may be a breakthrough for the future diagnosis and treatment of WAD.

National Category
Medical Image Processing
Identifiers
urn:nbn:se:umu:diva-125578 (URN)10.1038/srep30415 (DOI)000380660500001 ()27484361 (PubMedID)
External cooperation:
Available from: 2016-09-14 Created: 2016-09-13 Last updated: 2018-06-07Bibliographically approved
Peterson, G., Dedering, Å., Andersson, E., Nilsson, D., Trygg, J., Peolsson, M., . . . Peolsson, A. (2015). Altered ventral neck muscle deformation for individuals with whiplash associated disorder compared to healthy controls: A case-control ultrasound study. Manual Therapy, 20(2), 319-327
Open this publication in new window or tab >>Altered ventral neck muscle deformation for individuals with whiplash associated disorder compared to healthy controls: A case-control ultrasound study
Show others...
2015 (English)In: Manual Therapy, ISSN 1356-689X, E-ISSN 1532-2769, Vol. 20, no 2, p. 319-327Article in journal (Refereed) Published
Abstract [en]

Previous studies have shown altered neck muscle function in individuals with chronic whiplash associated disorder (WAD). However, we lack real-time investigations with non-invasive methods that can distinguish between the different ventral neck muscle layers. This study investigated deformations and deformation rates in the sternocleidomastoid (SCM), longus capitis (Lcap), and longus colli (Lco) muscles with real-time ultrasonography. Twenty-six individuals with WAD were compared with 26 controls, matched for age and sex. Ultrasound imaging of the SCM, Lcap, and Lco were recorded during 10 repetitive arm elevations. The first and tenth arm elevations were post-process analyzed with speckle tracking. There were few significant differences in the deformations or deformation rates in the SCM, Lcap, and Lco between the WAD and control group. In controls, deformations and deformation rates showed linear positive relationships between SCM/Lcap, SCM/Lco, and Lcap/Lco which increased from the first arm elevation (R-2 = 0.14-0.70); to the tenth arm elevation (R-2 = 0.51-0.71). The WAD group showed similar or weaker linear relationship (R-2 < 0.19) during the tenth compared to the first (R-2 < 0.44) arm elevation except for deformations in Lcap/Lco (R-2 = 0.13-0.57). This result indicated that deformations and deformation rates in one muscle were correlated by similar deformations and deformation rates in other neck muscles in the control group, but this interplay between muscles was not found in the WAD group. (C) 2014 Elsevier Ltd. All rights reserved.

Place, publisher, year, edition, pages
Elsevier, 2015
Keywords
Whiplash injury, Ultrasonography, Neck muscles
National Category
Public Health, Global Health, Social Medicine and Epidemiology
Identifiers
urn:nbn:se:umu:diva-103160 (URN)10.1016/j.math.2014.10.006 (DOI)000352769200013 ()25454684 (PubMedID)
Available from: 2015-05-29 Created: 2015-05-18 Last updated: 2018-06-07Bibliographically approved
Organisations

Search in DiVA

Show all publications