Johan Trygg | Umeå University (original) (raw)

Papers by Johan Trygg

Open Forum Infectious Diseases, 2015

Background. Accuracy in malaria diagnosis and staging is vital to reduce mortality and post infec... more Background. Accuracy in malaria diagnosis and staging is vital to reduce mortality and post infectious sequelae. In this study, we present a metabolomics approach to diagnostic staging of malaria infection, specifically Plasmodium falciparum infection in children.

PLOS ONE, 2015

Hierarchical modelling was applied in order to identify the organs that contribute to the levels ... more Hierarchical modelling was applied in order to identify the organs that contribute to the levels of metabolites in plasma. Plasma and organ samples from gut, kidney, liver, muscle and pancreas were obtained from mice. The samples were analysed using gas chromatography time-of-flight mass spectrometry (GC TOF-MS) at the Swedish Metabolomics centre, Umeå University, Sweden. The multivariate analysis was performed by means of principal component analysis (PCA) and orthogonal projections to latent structures (OPLS). The main goal of this study was to investigate how each organ contributes to the metabolic plasma profile. This was performed using hierarchical modelling. Each organ was found to have a unique metabolic profile. The hierarchical modelling showed that the gut, kidney and liver demonstrated the greatest contribution to the metabolic pattern of plasma. For example, we found that metabolites were absorbed in the gut and transported to the plasma. The kidneys excrete branched chain amino acids (BCAAs) and fatty acids are transported in the plasma to the muscles and liver. Lactic acid was also found to be transported from the pancreas to plasma. The results indicated that hierarchical modelling can be utilized to identify the organ contribution of unknown metabolites to the metabolic profile of plasma.

Batch Effects and Noise in Microarray Experiments, 2009

Pre-processing plays a vital role in cDNA-microarray data analysis. Without proper preprocessing ... more Pre-processing plays a vital role in cDNA-microarray data analysis. Without proper preprocessing it is likely that the biological conclusions will be misleading. However, there are many alternatives and in order to choose a proper pre-processing procedure it is necessary to understand the effect of different methods. This chapter discusses several pre-processing steps, including image analysis, background correction, normalization, and filtering. Spike-in data are used to illustrate how different procedures affect the analytical ability to detect differentially expressed genes and estimate their regulation. The result shows that pre-processing has a major impact on both the experiment's sensitivity and its bias. However, general recommendations are hard to give, since pre-processing consists of several actions that are highly dependent on each other. Furthermore, it is likely that pre-processing have a major impact on downstream analysis, such as clustering and classification, and pre-processing methods should be developed and evaluated with this in mind.

Springer Proceedings in Mathematics & Statistics, 2013

ABSTRACT OnPLS was recently proposed as a general extension of O2PLS for applications in multiblo... more ABSTRACT OnPLS was recently proposed as a general extension of O2PLS for applications in multiblock and path model analysis. OnPLS is very similar to O2PLS in the case with two matrices, but generalizes symmetrically to cases with more than two matrices without giving preference to any matrix. OnPLS extracts a minimal number of globally joint components that exhibit maximal covariance and correlation. A number of locally joint components are also extracted. These are shared between some matrices, but not between all. These components are also maximally covarying with maximal correlation. The variation that remains after the joint and locally joint variation has been extracted is unique to a particular matrix. This unique variation is orthogonal to all other matrices and captures phenomena specific in its matrix. The method’s utility has been demonstrated by its application to synthetic datasets with very good results in terms of its ability to decompose the matrices. It has been shown that OnPLS affords a reduced number of globally joint components and increased intercorrelations of scores, and that it greatly facilitates interpretation of the models. Preliminary results in the application on real data has also given positive results. The results are similar to previous results using other multiblock and path model methods, but afford an increased interpretability because of the locally joint and unique components.

International journal of pharmaceutics, Jan 10, 2015

Near-infrared chemical imaging (NIR-CI) is an attractive technique within the pharmaceutical indu... more Near-infrared chemical imaging (NIR-CI) is an attractive technique within the pharmaceutical industry, where tools are continuously in demand to assess the quality of the intermediate and final products. The present paper demonstrates how NIR-CI in combination with multivariate methods was utilized to spatially map physical properties and content of roll compacted ribbons and tablets. Additionally, extracted textural parameters from tablet images were correlated to the design parameters of the roll compaction process as well as to the physical properties of the granules. The results established the use of NIR-CI as a complementary nondestructive tool to determine the ribbon density and map the density distribution across the width and along the length of the ribbons. For the tablets, the compaction pressure developed during compression increased with the lateral distance from the center. Therefore, NIR-CI can be an effective tool to provide information about the spatial distribution...

Physiotherapy, 2015

To compare mechanical activity (deformation and deformation rate) of the dorsal neck muscles betw... more To compare mechanical activity (deformation and deformation rate) of the dorsal neck muscles between individuals with longstanding symptoms after anterior cervical decompression and fusion (ACDF) surgery and healthy controls. Preliminary cross-sectional study. Neurosurgery clinic. Ten individuals {mean age 60 [standard deviation (SD) 7.1]} who had undergone ACDF surgery 10 to 13 years previously and 10 healthy age- and sex-matched controls. Mechanical activity of the different layers of dorsal neck muscles, measured at the C4 segment using ultrasonography (speckle tracking analysis) during a standardised, resisted cervical extension task. A significant group×muscle interaction was found for muscle deformation (P<0.03) but not for deformation rate (P>0.79). The ACDF group showed significantly less deformation of the semispinalis capitis muscle during the extension task compared with the control group [mean 3.12 (SD 2.06) and 6.64 (SD 4.17), respectively; mean difference 3.34 (9...

PloS one, 2013

Conflicting findings in both interventional and observational studies have resulted in a lack of ... more Conflicting findings in both interventional and observational studies have resulted in a lack of consensus on the benefits of ω3 fatty acids in reducing disease risk. This may be due to individual variability in response. We used a multi-platform lipidomic approach to investigate both the consistent and inconsistent responses of individuals comprehensively to a defined ω3 intervention. The lipidomic profile including fatty acids, lipid classes, lipoprotein distribution, and oxylipins was examined multi- and uni-variately in 12 healthy subjects pre vs. post six weeks of ω3 fatty acids (1.9 g/d eicosapentaenoic acid [EPA] and 1.5 g/d docosahexaenoic acid [DHA]). Total lipidomic and oxylipin profiles were significantly different pre vs. post treatment across all subjects (p=0.00007 and p=0.00002 respectively). There was a strong correlation between oxylipin profiles and EPA and DHA incorporated into different lipid classes (r(2)=0.93). However, strikingly divergent responses among indi...

International journal of pharmaceutics, Jan 15, 2013

Roll compaction is a continuous process for solid dosage form manufacturing increasingly popular ... more Roll compaction is a continuous process for solid dosage form manufacturing increasingly popular within pharmaceutical industry. Although roll compaction has become an established technique for dry granulation, the influence of material properties is still not fully understood. In this study, a quality by design (QbD) approach was utilized, not only to understand the influence of different qualities of mannitol and dicalcium phosphate (DCP), but also to predict critical quality attributes of the drug product based solely on the material properties of that filler. By describing each filler quality in terms of several representative physical properties, orthogonal projections to latent structures (OPLS) was used to understand and predict how those properties affected drug product intermediates as well as critical quality attributes of the final drug product. These models were then validated by predicting product attributes for filler qualities not used in the model construction. The r...

International journal of pharmaceutics, Jan 15, 2011

Roll compaction is gaining importance in pharmaceutical industry for the dry granulation of heat ... more Roll compaction is gaining importance in pharmaceutical industry for the dry granulation of heat or moisture sensitive powder blends with poor flowing properties prior to tabletting. We studied the influence of microcrystalline cellulose (MCC) properties on the roll compaction process and the consecutive steps in tablet manufacturing. Four dissimilar MCC grades, selected by subjecting their physical characteristics to principal components analysis, and three speed ratios, i.e. the ratio of the feed screw speed and the roll speed of the roll compactor, were included in a full factorial design. Orthogonal projection to latent structures was then used to model the properties of the resulting roll compacted products (ribbons, granules and tablets) as a function of the physical MCC properties and the speed ratio. This modified version of partial least squares regression separates variation in the design correlated to the considered response from the variation orthogonal to that response....

Genome Announcements, 2015

We present the complete genome sequence of Francisella guangzhouensis strain 08HL01032(T), which ... more We present the complete genome sequence of Francisella guangzhouensis strain 08HL01032(T), which consists of one chromosome (1,658,482 bp) and one plasmid (3,045 bp) with G+C contents of 32.0% and 28.7%, respectively.

Journal of rehabilitation medicine, 2014

To evaluate the capacity of the ultrasound-based method of speckle tracking analysis to detect ch... more To evaluate the capacity of the ultrasound-based method of speckle tracking analysis to detect changes in multilayered dorsal neck muscle activity induced by performing a lifting task. Twenty-one healthy individuals. Participants performed a loaded lifting task in 3 different postural orientations of the neck (neutral, flexed and forward head posture). Ultrasound images were recorded and speckle tracking analysis was used to quantify muscle deformation and deformation rate over 3 equal time-periods during the lifting sequence (rest, mid-lift and end-lift). Significant main effects of postural orientation for the deformation measure (p < 0.05) and time for the deformation rate measure (p < 0.05) were observed in all dorsal muscles examined. Significant time by postural interactions for the deformation measure were observed in the trapezius, semispinalis cervicis and multifidus (p < 0.05) and in the semispinalis cervicis (p < 0.05) for the deformation rate measure. Speckle...

International Journal of Pharmaceutics, 2015

In this study, the roll compaction of an intermediate drug load formulation was performed using h... more In this study, the roll compaction of an intermediate drug load formulation was performed using horizontally and vertically force fed roll compactors. The horizontally fed roll compactor was equipped with an instrumented roll technology allowing the direct measurement of normal stress at the roll surface, while the vertically fed roll compactor was equipped with a force gauge between the roll axes. Furthermore, characterization of ribbons, granules and tablets was also performed. Ribbon porosity was primarily found to be a function of normal stress, exhibiting a quadratic relationship thereof. A similar quadratic relationship was also observed between roll force and ribbon porosity of the vertically fed roll compactor. The predicted peak pressure (Pmax) using the Johanson model was found to be higher than the measured normal stress, however, the predicted Pmax correlated well with the ribbon relative density/porosity and the majority of downstream properties of granules and tablets, demonstrating its use as a scale-independent parameter. A latent variable model was developed for both the horizontal and vertical fed roll compactors to express ribbon porosity as a function of geometric and process parameters. The model validation, performed with new data, resulted in overall good predictions. This study successfully demonstrated the scale up/transfer between two different roll compactors and revealed that the combined use of design of experiments, latent variable models and in silico predictions result in better understanding of the critical process parameters in roll compaction.

Manual Therapy, 2014

Previous studies have shown altered neck muscle function in individuals with chronic whiplash ass... more 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 ¼ 0.14e0.70); to the tenth arm elevation (R 2 ¼ 0.51e0.71). 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 ¼ 0.13e0.57). 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.