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1.	Dunstan, R. H., et al. (author) Diverse characteristics of the urinary excretion of amino acids in humans and the use of amino acid supplementation to reduce fatigue and sub-health in adults 2017 In: Nutrition Journal. - : Springer Science and Business Media LLC. - 1475-2891. ; 16:19 Journal article (peer-reviewed)abstract Background: The excretion of amino acids in urine represents an important avenue for the loss of key nutrients. Some amino acids such as glycine and histidine are lost in higher abundance than others. These two amino acids perform important physiological functions and are required for the synthesis of key proteins such as haemoglobin and collagen. Methods: Stage 1 of this study involved healthy subjects(n = 151) who provided first of the morning urine samples and completed symptom questionnaires. Urine was analysed for amino acid composition by gas chromatography. Stage 2 involved a subset of the initial cohort (n = 37) who completed a 30 day trial of an amino acid supplement and subsequent symptom profile evaluation. Results: Analyses of urinary amino acid profiles revealed that three groups could be objectively defined from the 151 participants using k-means clustering. The amino acid profiles were significantly different between each of the clusters (Wilks' Lambda = 0.13, p < 0.0001). Cluster 1 had the highest loss of amino acids with histidine being the most abundant component. Cluster 2 had glycine present as the most abundant urinary amino acid and cluster 3 had equivalent abundances of glycine and histidine. Strong associations were observed between urinary proline concentrations and fatigue/pain scores (r =.56 to.83) for females in cluster 1, with several other differential sets of associations observed for the other clusters. Conclusions: Different phenotypic subsets exist in the population based on amino acid excretion characteristics found in urine. Provision of the supplement resulted in significant improvements in reported fatigue and sleep for 81% of the trial cohort with all females reporting improvements in fatigue.
2.	Dunstan, R. H., et al. (author) Sex differences in amino acids lost via sweating could lead to differential susceptibilities to disturbances in nitrogen balance and collagen turnover 2017 In: Amino Acids. - : Springer Science and Business Media LLC. - 0939-4451 .- 1438-2199. ; 49:8, s. 1337-1345 Journal article (peer-reviewed)abstract Fluid collected during sweating is enriched with amino acids derived from the skin's natural moisturising factors and has been termed "faux" sweat. Little is known about sex differences in sweat amino acid composition or whether faux sweat amino acid losses affect nitrogen balance. Faux sweat collected by healthy adults (n = 47) after exercise, and at rest by chronic fatigue patients, was analysed for amino acid composition. Healthy females had higher total amino acid concentrations in sweat (10.5 +/- 1.2 mM) compared with healthy males (6.9 +/- 0.9 mM). Females had higher levels of 13 amino acids in sweat including serine, alanine and glycine. Higher hydroxyproline and proline levels suggested greater collagen turnover in females. Modelling indicated that with conservative levels of exercise, amino acid losses in females via faux sweat were triple than those predicted for urine, whereas in males they were double. It was concluded that females were more susceptible to key amino acid loss during exercise and/or hot conditions. Females reporting chronic fatigue had higher levels of methionine in faux sweat than healthy females. Males reporting chronic fatigue had higher levels of numerous amino acids in faux sweat compared to healthy males. Higher amino acid loss in faux sweat associated with chronic fatigue could contribute to a hypometabolic state. Depending on activity levels, climatic conditions and gender, amino acid losses in sweat and skin leachate could influence daily protein turnover where periods of continuously high turnover could lead to a negative net nitrogen balance.
3.	Eriksson, Lennart, et al. (author) Editorial 2007 In: Journal of Chemometrics. - : John Wiley & Sons, Ltd. - 0886-9383 .- 1099-128X. ; 21:10-11, s. 397- Journal article (pop. science, debate, etc.)abstract
4.	Eriksson, Lennart, et al. (author) Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm) 2004 In: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 380:3, s. 419-29 Journal article (peer-reviewed)abstract This article describes the applicability of multivariate projection techniques, such as principal-component analysis (PCA) and partial least-squares (PLS) projections to latent structures, to the large-volume high-density data structures obtained within genomics, proteomics, and metabonomics. PCA and PLS, and their extensions, derive their usefulness from their ability to analyze data with many, noisy, collinear, and even incomplete variables in both X and Y. Three examples are used as illustrations: the first example is a genomics data set and involves modeling of microarray data of cell cycle-regulated genes in the microorganism Saccharomyces cerevisiae. The second example contains NMR-metabonomics data, measured on urine samples of male rats treated with either of the drugs chloroquine or amiodarone. The third and last data set describes sequence-function classification studies in a set of G-protein-coupled receptors using hierarchical PCA.
5.	Gottfries, Johan, et al. (author) On the impact of uncorrelated variation in regression mathematics 2008 In: Journal of Chemometrics. - : Wiley. - 0886-9383 .- 1099-128X. ; 22:11-12, s. 565-70 Journal article (peer-reviewed)abstract The objective of the present study is to investigate if, and if so, how uncorrelated variation relates to regression mathematics as exemplified by partial least squares (PLS) methodology. In contrast to previous methods, orthogonal partial least squares (OPLS) method requires a multi-focus, in the sense that in parallel to calculation of correlation it requires an analysis of orthogonal variation, i.e. the uncorrelated structure in a comprehensive way. Subsequent to the estimation of the correlation is the remaining orthogonal variation, i.e. uncorrelated data, divided into uncorrelated structure and stochastic noise by the OPLS component. Thus, it appears obvious that it is of interest to understand how the uncorrelated variation can influence the interpretation of the regression model. We have scrutinized three examples that pinpoint additional value from OPLS regarding the modelling of the orthogonal, i.e. uncorrelated, variation in regression mathematics. In agreement with the results, we conclude that uncorrelated variations do impact interpretations of regression analyses output and provides not only opportunities by OPLS but also an obligation for the user to maximize benefit from OPLS.
6.	Lundstedt, Torbjörn, et al. (author) Editorial 2006 In: Journal of Chemometrics. - : John Wiley & Sons, Ltd. - 0886-9383 .- 1099-128X. ; 20:8-10, s. 323-324 Journal article (pop. science, debate, etc.)
7.	Pinto, Rui Climaco, et al. (author) Advantages of orthogonal inspection in chemometrics 2012 In: Journal of Chemometrics. - : Wiley. - 0886-9383 .- 1099-128X. ; 26:6, s. 231-235 Journal article (peer-reviewed)abstract The demand for chemometrics tools and concepts to study complex problems in modern biology and medicine has prompted chemometricians to shift their focus away from a traditional emphasis on model predictive capacity toward optimizing information exchange via model interpretation for biological validation. The interpretation of projection-based latent variable models is not straightforward because of its confounding of different systematic variations in the model components. Over the last 15?years, this has spurred the development of orthogonal-based methods that are capable of separating the correlated variation (to Y) from the noncorrelated (orthogonal to Y) variations in a single model. Here, we aim to provide a conceptual explanation of the advantages of orthogonal variation inspection in the context of Partial Least Squares (PLS) in multivariate classification and calibration. We propose that by inspecting the orthogonal variation, both model interpretation and information quality are improved by enhancement of the resulting level of knowledge. Although the predictive capacity of PLS using orthogonal methods may be identical to that of PLS alone, the combined result can be superior when it comes to the model interpretation. By discussing theory and examples, several new advantages revealed by inspection of orthogonal variation are highlighted. Copyright (c) 2012 John Wiley & Sons, Ltd.
8.	Stenlund, Hans, et al. (author) Unlocking Interpretation in Near Infrared Multivariate Calibrations by Orthogonal Partial Least Squares 2009 In: Analytical Chemistry. ; 81:1, s. 203-9 Journal article (peer-reviewed)abstract Near infrared spectroscopy (NIR) was developed primarily for applications such as the quantitative determination of nutrients in the agricultural and food industries. Examples include the determination of water, protein, and fat within complex samples such as grain and milk. Because of its useful properties, NIR analysis has spread to other areas such as chemistry and pharmaceutical production. NIR spectra consist of infrared overtones and combinations thereof, making interpretation of the results complicated. It can be very difficult to assign peaks to known constituents in the sample. Thus, multivariate analysis (MVA) has been crucial in translating spectral data into information, mainly for predictive purposes. Orthogonal partial least squares (OPLS), a new MVA method, has prediction and modeling properties similar to those of other MVA techniques, e.g., partial least squares (PLS), a method with a long history of use for the analysis of NIR data. OPLS provides an intrinsic algorithmic improvement for the interpretation of NIR data. In this report, four sets of NIR data were analyzed to demonstrate the improved interpretation provided by OPLS. The first two sets included simulated data to demonstrate the overall principles; the third set comprised a statistically replicated design of experiments (DoE), to demonstrate how instrumental difference could be accurately visualized and correctly attributed to Wood’s anomaly phenomena; the fourth set was chosen to challenge the MVA by using data relating to powder mixing, a crucial step in the pharmaceutical industry prior to tabletting. Improved interpretation by OPLS was demonstrated for all four examples, as compared to alternative MVA approaches. It is expected that OPLS will be used mostly in applications where improved interpretation is crucial; one such area is process analytical technology (PAT). PAT involves fewer independent samples, i.e., batches, than would be associated with agricultural applications; in addition, the Food and Drug Administration (FDA) demands “process understanding” in PAT. Both these issues make OPLS the ideal tool for a multitude of NIR calibrations. In conclusion, OPLS leads to better interpretation of spectrometry data (e.g., NIR) and improved understanding facilitates cross-scientific communication. Such improved knowledge will decrease risk, with respect to both accuracy and precision, when using NIR for PAT applications.
9.	Svelander, Cecilia, 1980, et al. (author) Postprandial lipid and insulin responses among healthy, overweight men to mixed meals served with baked herring, pickled herring or baked, minced beef 2015 In: European Journal of Nutrition. - : Springer Science and Business Media LLC. - 1436-6207 .- 1436-6215. ; 54:6, s. 945-958 Journal article (peer-reviewed)abstract PURPOSE: The aim was to compare postprandial lipid, insulin and vitamin D responses after consumption of three otherwise identical meals served either with baked herring, pickled herring or with baked, minced beef. METHODS: Seventeen healthy, overweight men (mean age 58 years, BMI 26.4-29.5 kg/m2) consumed standardized lunches together with baked herring, pickled herring or baked, minced beef on three occasions in a crossover design. Blood samples were taken just before and up to 7 h after the meal. The postprandial response was measured as serum concentrations of triglycerides (TG), total cholesterol and lipoproteins (LDL, HDL and VLDL), insulin, 25-OH vitamin D and plasma fatty acid composition. RESULTS: There was no difference in postprandial lipid responses between the two herring meals, whereas a slower TG clearance was observed after the baked, minced beef meal. The 150 g servings of baked and pickled herring provided 3.3 and 2.8 g of long-chain n-3 polyunsaturated fatty acids (LC n-3 PUFA), respectively, which was reflected in a substantial postprandial increase in plasma LC n-3 PUFA levels. The pickled herring contained 22 % sugar and consequently gave a higher insulin response compared with the other two meals. CONCLUSIONS: Both pickled and baked herring are good sources of LC n-3 PUFA in the diet, but the presence of sugar in pickled herring should be taken into consideration, especially if large amounts are consumed. The faster postprandial TG clearance after a meal with baked herring compared with baked beef supports previous studies on the beneficial effects of herring on cardiovascular health.
10.	Wiklund, Susanne, et al. (author) Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models 2008 In: Analytical Chemistry. - Columbus, OH : American Chemical Society. - 0003-2700 .- 1520-6882. ; 80:1, s. 115-22 Journal article (peer-reviewed)abstract Metabolomics studies generate increasingly complex data tables, which are hard to summarize and visualize without appropriate tools. The use of chemometrics tools, e.g., principal component analysis (PCA), partial least-squares to latent structures (PLS), and orthogonal PLS (OPLS), is therefore of great importance as these include efficient, validated, and robust methods for modeling information-rich chemical and biological data. Here the S-plot is proposed as a tool for visualization and interpretation of multivariate classification models, e.g., OPLS discriminate analysis, having two or more classes. The S-plot visualizes both the covariance and correlation between the metabolites and the modeled class designation. Thereby the S-plot helps identifying statistically significant and potentially biochemically significant metabolites, based both on contributions to the model and their reliability. An extension of the S-plot, the SUS-plot (shared and unique structure), is applied to compare the outcome of multiple classification models compared to a common reference, e.g., control. The used example is a gas chromatography coupled mass spectroscopy based metabolomics study in plant biology where two different transgenic poplar lines are compared to wild type. By using OPLS, an improved visualization and discrimination of interesting metabolites could be demonstrated.
11.	Alreshidi, M. M., et al. (author) Amino acids and proteomic acclimation of Staphylococcus aureus when incubated in a defined minimal medium supplemented with 5% sodium chloride 2019 In: Microbiologyopen. - : Wiley. - 2045-8827. ; 8:6 Journal article (peer-reviewed)abstract Staphylococcus aureus is a versatile bacterium that can adapt to survive and grow in a wide range of salt concentrations. This study investigated whether the cells could mount a response to survive a challenge of 5% NaCl in a minimal incubation medium that would not support cell replication. Cells were grown in liquid culture, washed and then incubated for 90 min at 37 degrees C in a medium that contained only glycine and glucose as substrates in PBS plus trace elements. The control cells were compared with a treatment group which was incubated with an additional 5% NaCl. Significantly more glycine was taken up by the cells exposed to 5% NaCl compared with control cells, and both groups consumed 99% of the glucose supplied. The NaCl treated cells had significantly higher cytoplasmic levels of proline and glutamic acid as well as lower levels of alanine and methionine compared with the controls (p < 0.05). The levels of the two major cytoplasmic amino acids, aspartic acid and glycine, remained constant in control and treated cells. Proteomic analyses revealed that 10 proteins showed differential responses between the control and treatment groups. The reductions in proteins were primarily associated with processes of protein biosynthesis, pathogenicity, and cell adhesion. Since cell numbers remained constant during the incubation period in minimal medium, it was concluded that there was no cell division to support population growth. The results provided evidence that the cells in the minimal medium exposed to the NaCl treatment underwent in situ homeostatic changes to adjust to the new environmental conditions. It was proposed that this represented a phenotypic shift to form cells akin to small colony variants, with lower metabolic rates and lower levels of key proteins associated with pathogenicity.
12.	Alreshidi, M. M., et al. (author) Changes in the Cytoplasmic Composition of Amino Acids and Proteins Observed in Staphylococcus aureus during Growth under Variable Growth Conditions Representative of the Human Wound Site 2016 In: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 11:7 Journal article (peer-reviewed)abstract Staphylococcus aureus is an opportunistic pathogen responsible for a high proportion of nosocomial infections. This study was conducted to assess the bacterial responses in the cytoplasmic composition of amino acids and ribosomal proteins under various environmental conditions designed to mimic those on the human skin or within a wound site: pH6-8, temperature 35-37 degrees C, and additional 0-5% NaCl. It was found that each set of environmental conditions elicited substantial adjustments in cytoplasmic levels of glutamic acid, aspartic acid, proline, alanine and glycine (P < 0.05). These alterations generated characteristic amino acid profiles assessed by principle component analysis (PCA). Substantial alterations in cytoplasmic amino acid and protein composition occurred during growth under conditions of higher salinity stress implemented via additional levels of NaCl in the growth medium. The cells responded to additional NaCl at pH 6 by reducing levels of ribosomal proteins, whereas at pH 8 there was an upregulation of ribosomal proteins compared with the reference control. The levels of two ribosomal proteins, L32 and S19, remained constant across all experimental conditions. The data supported the hypothesis that the bacterium was continually responding to the dynamic environment by modifying the proteome and optimising metabolic homeostasis.
13.	Alreshidi, M. M., et al. (author) Metabolomic and proteomic responses of Staphylococcus aureus to prolonged cold stress 2015 In: Journal of Proteomics. - : Elsevier BV. - 1874-3919. ; 121, s. 44-55 Journal article (peer-reviewed)abstract The high pathogenicity of Staphylococcus aureus is thought to be due to its extraordinary capacity to rapidly adapt to changes in environmental conditions. This study was carried out to investigate whether the cytoplasmic profiles of metabolites and proteins of Staphylococcus aureus were altered in response to prolonged exposure to cold stress. Metabolic profiling and proteomics were used to characterise alterations in cytoplasmic proteins and metabolites in cells from the mid-exponential phase of growth under ideal conditions at 37 degrees C and compared with equivalent cells exposed to prolonged cold stress for 2 weeks at 4 degrees C. Principle component analysis (PCA) of the metabolomic and proteomic data indicated that, at the mid-exponential phase of growth, prolonged cold stress conditions generated cells with different metabolite and protein profiles compared with those grown at 37 degrees C. Nine ribosomal proteins and citric acid were substantially elevated in the cytoplasmic fractions from the cells adapted to cold-stress but most amino acids showed a reduction in their concentration in cold-stressed samples. The data provided strong evidence supporting the hypothesis that specific changes in metabolic homeostasis and protein composition were critical to the adaptive processes required for survival under cold stress. Work in our laboratory has shown that prolonged exposure of Staphylococcus aureus to cold stress can result in the formation of small colony variants (SCVs) associated with significant alterations in the cell wall composition [8]. Further studies revealed that Staphylococcus aureus altered cell size and cell wall thickness in response to exposure to cold temperatures, alterations in pH and exposure to antibiotics [10]. The current study has utilised the prolonged exposure to cold stress as a model system to explore changes in the proteome and associated metabolic homeostasis following environmental challenges. The study provides an improved understanding of how Staphylococcus aureus adapts to the changing environment whilst in transition between human hosts. The results indicated an unexpected production of 9 ribosomal proteins and citric acid in response to cold stress suggesting specific survival roles for these proteins and citric acid as an adaptation mechanism for empowering survival under these conditions. Crown Copyright (C) 2015 Published by Elsevier B.V. All rights reserved.
14.	Alreshidi, M. M., et al. (author) The Uptake and Release of Amino Acids by Staphylococcus aureus at Mid-Exponential and Stationary Phases and Their Corresponding Responses to Changes in Temperature, pH and Osmolality 2020 In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 10 Journal article (peer-reviewed)abstract Staphylococcus aureus is an important pathogen that is associated with nosocomial infections, as well as food poisoning. This bacterium is resistant to antimicrobial agents and can survive in a wide range of environmental conditions. The aim of this study was to measure the uptake and release of amino acids by S. aureus at mid-exponential and stationary phases of growth following exposure to a combination of conditions including variations in temperature, pH and NaCl. Bacterial cells were grown up to mid-exponential and stationary phases in tryptic soy broth (TSB), where the supernatants were collected for analyses of amino acids to determine the uptake and release characteristics. The uptake/release of amino acids was estimated by subtracting the initial levels of the free amino acids in the media from those measured at mid-exponential and stationary phases of growth. When cells were grown at ideal conditions, the analyses revealed that significant uptake of amino acids had occurred by stationary phase compared with the mid-exponential phase. A substantial release of valine and tyrosine into the external media was observed by cells at stationary phase. At both phases, the uptake and release patterns were significantly different between cells grown under ideal control conditions, when compared with those grown under various combinations of sub-optimal environmental conditions. The analyses of the supernatants harvested from controls and treatment groups at exponential phase indicated that the total uptake of amino acids was reduced approximately five times by cells grown with addition of 2.5% NaCl or with pH6 at 35 degrees C, and 2-fold by cells grown at pH8 at 35 degrees C. However, the final quantities of amino acids taken up by cells grown to stationary phase did not significantly alter between control and treated samples. Valine was found to be the most abundant amino acid that was significantly released into the media at stationary phase by both control and treated samples. It was evident that diverse environmental conditions resulted in differential patterns of amino acid uptake and release during adaptation to designated conditions.
15.	Backlund, Anders, 1965-, et al. (author) Chemography and Phylogeny : navigating chemical and evolutionary space 2006 In: Planta Medica. - : Georg Thieme Verlag KG. - 0032-0943 .- 1439-0221. ; 72:11, s. 972-972 Journal article (other academic/artistic)
16.	Corbo, Vesna (author) 1. Dynamic Demand Adjustment and Exchange Rate Volatility. 2. The Replacement Ratio, Unemployment and Wage Setting 2012 Licentiate thesis (other academic/artistic)
17.	Crompton, M. J., et al. (author) Small changes in environmental parameters lead to alterations in antibiotic resistance, cell morphology and membrane fatty acid composition in Staphylococcus lugdunensis 2014 In: PLoS ONE. - : Public Library of Science. - 1932-6203. ; 9:4 Journal article (peer-reviewed)abstract Staphylococcus lugdunensis has emerged as a major cause of community-acquired and nosocomial infections. This bacterium can rapidly adapt to changing environmental conditions to survive and capitalize on opportunities to colonize and infect through wound surfaces. It was proposed that S. lugdunensis would have underlying alterations in metabolic homeostasis to provide the necessary levels of adaptive protection. The aims of this project were to examine the impacts of subtle variations in environmental conditions on growth characteristics, cell size and membrane fatty acid composition in S. lugdunensis. Liquid broth cultures of S. lugdunensis were grown under varying combinations of pH (6-8), temperature (35-39°C) and osmotic pressure (0-5% sodium chloride w/w) to reflect potential ranges of conditions encountered during transition from skin surfaces to invasion of wound sites. The cells were harvested at the mid-exponential phase of growth and assessed for antibiotic minimal inhibitory concentration (MIC), generation time, formation of small colony variants, cell size (by scanning electron microscopy) and membrane fatty acid composition. Stress regimes with elevated NaCl concentrations resulted in significantly higher antibiotic resistance (MIC) and three of the combinations with 5% NaCl had increased generation times (P<0.05). It was found that all ten experimental growth regimes, including the control and centroid cultures, yielded significantly different profiles of plasma membrane fatty acid composition (P<0.0001). Alterations in cell size (P<0.01) were also observed under the range of conditions with the most substantial reduction occurring when cells were grown at 39°C, pH 8 (514±52 nm, mean ± Standard Deviation) compared with cells grown under control conditions at 37°C with pH 7 (702±76 nm, P<0.01). It was concluded that S. lugdunensis responded to slight changes in environmental conditions by altering plasma membrane fatty acid composition, growth rates and morphology to achieve optimal adaptations for survival in changing environments. © 2014 Crompton et al.
18.	Dunstan, R H, et al. (author) Development of a complex amino acid supplement, Fatigue Reviva¿, for oral ingestion: initial evaluations of product concept and impact on symptoms of sub-health in a group of males 2013 In: Nutrition Journal. - 1475-2891. ; 12:115 Journal article (peer-reviewed)abstract Abstract Background A new dietary supplement, Fatigue Reviva™, has been recently developed to address issues related to amino acid depletion following illness or in conditions of sub-health where altered amino acid homeostasis has been associated with fatigue. Complex formulations of amino acids present significant challenges due to solubility and taste constraints. This initial study sets out to provide an initial appraisal of product palatability and to gather pilot evidence for efficacy. Methods Males reporting symptoms of sub-health were recruited on the basis of being free from any significant medical or psychological condition. Each participant took an amino acid based dietary supplement (Fatigue Reviva™) daily for 30 days. Comparisons were then made between pre- and post-supplement general health symptoms and urinary amino acid profiles. Results Seventeen men took part in the study. Following amino acid supplementation the total Chalder fatigue score improved significantly (mean ± SEM, 12.5 ± 0.9 versus 10.0 ± 1.0, P<0.03). When asked whether they thought that the supplement had improved their health, 65% of participants responded positively. A subgroup of participants reported gastrointestinal symptoms which were attributed to the supplement and which were believed to result from the component fructooligosaccharide. Analysis of urinary amino acids revealed significant alterations in the relative abundances of a number of amino acids after supplementation including an increase in valine, isoleucine and glutamic acid and reduced levels of glutamine and ornithine. Discriminant function analysis of the urinary amino acid data revealed significant differences between the pre- and post-supplement urine excretion profiles. Conclusions The results indicated that Fatigue Reviva™ was palatable and that 65% of the study group reported that they felt the product had improved their health. The product could provide an effective tool for the management of unexplained fatigue and symptoms of sub-health. Further product development may yield additional options for those patients susceptible to fructooligosaccharide.
19.	Dunstan, R. H., et al. (author) Sweat facilitated amino acid losses in male athletes during exercise at 32-34°C 2016 In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:12 Journal article (peer-reviewed)abstract Sweat contains amino acids and electrolytes derived from plasma and athletes can lose 1-2L of sweat per hour during exercise. Sweat may also contain contributions of amino acids as well as urea, sodium and potassium from the natural moisturizing factors (NMF) produced in the stratum corneum. In preliminary experiments, one participant was tested on three separate occasions to compare sweat composition with surface water washings from the same area of skin to assess contributions from NMF. Two participants performed a 40 minute self-paced cycle session with sweat collected from cleansed skin at regular intervals to assess the contributions to the sweat load from NMF over the period of exercise. The main study investigated sweat amino acid composition collected from nineteen male athletes following standardised endurance exercise regimes at 32-34°C and 20-30% RH. Plasma was also collected from ten of the athletes to compare sweat and plasma composition of amino acids. The amino acid profiles of the skin washings were similar to the sweat, suggesting that the NMF could contribute certain amino acids into sweat. Since the sweat collected from athletes contained some amino acid contributions from the skin, this fluid was subsequently referred to as "faux" sweat. Samples taken over 40 minutes of exercise showed that these contributions diminished over time and were minimal at 35 minutes. In the main study, the faux sweat samples collected from the athletes with minimal NMF contributions, were characterised by relatively high levels of serine, histidine, ornithine, glycine and alanine compared with the corresponding levels measured in the plasma. Aspartic acid was detected in faux sweat but not in the plasma. Glutamine and proline were lower in the faux sweat than plasma in all the athletes. Three phenotypic groups of athletes were defined based on faux sweat volumes and composition profiles of amino acids with varying relative abundances of histidine, serine, glycine and ornithine. It was concluded that for some individuals, faux sweat resulting from exercise at 32-34°C and 20-30% RH posed a potentially significant source of amino acid loss. © 2016 Dunstan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
20.	Dunstan, R. H., et al. (author) Sweat facilitated losses of amino acids in Standardbred horses and the application of supplementation strategies to maintain condition during training 2015 In: Comparative Exercise Physiology. - : Wageningen Academic Publishers. - 1755-2540 .- 1755-2559. ; 11:4, s. 201-212 Journal article (peer-reviewed)abstract Little is known about the amino acid composition of horse sweat, but significant fluid losses can occur during exercise with the potential to facilitate substantial nutrient losses. Sweat and plasma amino acid compositions for Standardbred horses were assessed to determine losses during a standardised training regime. Two cohorts of horses 2013 (n=5) and 2014 (n=6) were assessed to determine baseline levels of plasma and sweat amino acids. An amino acid supplement designed to counter losses in sweat during exercise was provided after morning exercise daily for 5 weeks (2013, n=5; 2014, n=4). After the supplementation period, blood and sweat samples were collected to assess amino acid composition changes. From baseline assessments of sweat in both cohorts, it was found that serine, glutamic acid, histidine and phenylalanine were present at up to 9 times the corresponding plasma concentrations and aspartic acid at 0-2.2 mu mol/l in plasma was measured at 154-262 mu mol/l in sweat. In contrast, glutamine, asparagine, methionine and cystine were conserved in the plasma by having lower concentrations in the sweat. The predominant plasma amino acids were glycine, glutamine, alanine, valine, serine, lysine and leucine. As the sweat amino acid profile did not simply reflect plasma composition, it was proposed that mechanisms exist to generate high concentrations of certain amino acids in sweat whilst selectively preventing the loss of others. The estimated amino acid load in 16 l of circulating plasma was 3.8-4.3 g and the calculated loss via sweat during high intensity exercise was 1.6-3.0 g. Following supplementation, total plasma amino acid levels from both cohorts increased from initial levels of 2,293 and 2,044 mu mol/l to post-supplementation levels of 2,674 and 2,663 mu mol/l respectively (P<0.05). It was concluded that the strategy of providing free amino acids immediately after exercise resulted in raising resting plasma amino acid levels.
21.	Elfaitouri, A, et al. (author) Murine Gammaretrovirus Group G3 Was Not Found in Swedish Patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Fibromyalgia 2011 In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:10 Journal article (peer-reviewed)abstract Background: The recent report of gammaretroviruses of probable murine origin in humans, called xenotropic murine retrovirus related virus (XMRV) and human murine leukemia virus related virus (HMRV), necessitated a bioinformatic search for this virus in genomes of the mouse and other vertebrates, and by PCR in humans. Results: Three major groups of murine endogenous gammaretroviruses were identified. The third group encompassed both exogenous and endogenous Murine Leukemia Viruses (MLVs), and most XMRV/HMRV sequences reported from patients suffering from myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Two sensitive real-time PCRs for this group were developed. The predicted and observed amplification range for these and three published XMRV/HMRV PCRs demonstrated conspicuous differences between some of them, partly explainable by a recombinatorial origin of XMRV. Three reverse transcription real-time PCRs (RTQPCRs), directed against conserved and not overlapping stretches of env, gag and integrase (INT) sequences of XMRV/HMRV were used on human samples. White blood cells from 78 patients suffering from ME/CFS, of which 30 patients also fulfilled the diagnostic criteria for fibromyalgia (ME/CFS/FM) and in 7 patients with fibromyalgia (FM) only, all from the Gothenburg area of Sweden. As controls we analyzed 168 sera from Uppsala blood donors. We controlled for presence and amplifiability of nucleic acid and for mouse DNA contamination. To score as positive, a sample had to react with several of the XMRV/HMRV PCRs. None of the samples gave PCR reactions which fulfilled the positivity criteria. Conclusions: XMRV/HMRV like proviruses occur in the third murine gammaretrovirus group, characterized here. PCRs developed by us, and others, approximately cover this group, except for the INT RTQPCR, which is rather strictly XMRV specific. Using such PCRs, XMRV/HMRV could not be detected in PBMC and plasma samples from Swedish patients suffering from ME/CFS/FM, and in sera from Swedish blood donors.
22.	Eriksson, Lennart, et al. (author) Time-resolved QSAR: an approach to PLS modelling of three-way biological data 2004 In: Chemometrics and Intelligent Laboratory Systems. - : Elsevier BV. - 0169-7439. ; 73:1, s. 73-84 Journal article (peer-reviewed)abstract This paper outlines a novel approach to the analysis of three-way Y-data in quantitative structure–activity relationship (QSAR) modelling. The new method represents a modification of an existing approach for multivariate modelling of batch process data. It is based on unfolding the three-way Y-matrix into a two-way matrix according to a sequential order of an external variable. In QSAR, time, pH, or temperature at which the biological data were gathered, are conceivably such external variables. Thus, unfolding can be done differently depending on the objective of the investigation, thereby shifting the focus of the QSAR analysis. The ensuing multivariate data analysis uses two levels of modelling. (1) On the lower (observation) level a projections to latent structures (PLS) model is developed between the unfolded biological data and the external variable. This model will identify compounds with biological data being sensitive to changes in the external variable (like time, pH, or temperature). (2) The scores of the lower level model are then re-arranged to enable the upper (QSAR) level model. In this model, a battery of structure descriptors (X) is related to the Y-matrix of scores of the lower level model. As an example, a series of 35 compounds and their anti-microbial activity towards the bacterial strain Escherichia coli CCM2260 is used. This biological activity has been determined at different times (2 to 10 h) and pH-values (pH 5.6 to 8.0).
23.	Gao, C. X., et al. (author) Exploration of multiple Sortase A protein conformations in virtual screening 2016 In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6:20413 Journal article (peer-reviewed)abstract Methicillin resistant Staphylococcus aureus (MRSA) has become a major health concern which has brought about an urgent need for new therapeutic agents. As the S. aureus Sortase A (SrtA) enzyme contributes to the adherence of the bacteria to the host cells, inhibition thereof by small molecules could be employed as potential antivirulence agents, also towards resistant strains. Albeit several virtual docking SrtA campaigns have been reported, no strongly inhibitatory non-covalent binders have as yet emerged therefrom. In order to better understand the binding modes of small molecules, and the effect of different receptor structures employed in the screening, we herein report on an exploratory study employing 10 known binders and 500 decoys on 100 SrtA structures generated from regular or steered molecular dynamics simulations on four different SrtA crystal/NMR structures. The results suggest a correlation between the protein structural flexibility and the virtual screening performance, and confirm the noted immobilization of the beta 6/beta 7 loop upon substrate binding. The NMR structures reported appear to perform slightly better than the Xray-crystal structures, but the binding modes fluctuate tremendously, and it might be suspected that the catalytic site is not necessarily the preferred site of binding for some of the reported active compounds.
24.	Gertow, J., et al. (author) Ceramides are associated with inflammatory processes in human mediastinal adipose tissue 2014 In: NMCD. Nutrition Metabolism and Cardiovascular Diseases. - : Elsevier BV. - 0939-4753 .- 1590-3729. ; 24:2, s. 124-131 Journal article (peer-reviewed)abstract Background and Aim: Ceramides are poorly characterized in human adipose tissue. The aim of this study was to investigate concentrations of different ceramide species in human subcutaneous and visceral adipose tissue depots and to determine associations between ceramides and global gene expression profiles. Methods and Results: Concentrations of six ceramide species were determined in plasma and in subcutaneous and mediastinal adipose tissue from 10 overweight subjects (BMI 29.4±4.9kg/m2). In the adipose tissue biopsies gene expression arrays were performed and relationships between ceramides and gene expression analyzed. Immunostaining of the two adipose tissue depots was performed in an independent group of 10 patients. Mediastinal adipose tissue contained significantly higher concentrations (p<0.05) of all six ceramide species than the subcutaneous depot. Of the six ceramides in plasma, concentrations of only two (Cer d18:1/18:0 and Cer d18:1/22:0) correlated significantly (p<0.05) with the corresponding species in mediastinal adipose tissue, but there were no significant correlations between ceramides in plasma and subcutaneous adipose tissue. Multivariate analysis identified significant correlations between the total ceramide concentration and global gene expression within mediastinal, but not subcutaneous adipose tissue, according to cross-validation. Gene ontology analysis of genes related to ceramides in the mediastinal depot revealed that genes positively correlated with ceramides were associated mainly with immune and inflammatory categories, while genes negatively correlated with ceramides were associated mainly with lipid and carbohydrate metabolism. Conclusions: Ceramides in human mediastinal adipose tissue may be involved in inflammation and lipid and carbohydrate metabolism. © 2013 Elsevier B.V.
25.	Gottfries, Johan, 1958 (author) Effect of low temperature on growth and ultra-structure of Staphylococcus spp. 2012 In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:1 Journal article (peer-reviewed)abstract The effect of temperature fluctuation is an important factor in bacterial growth especially for pathogens such as the staphylococci that have to remain viable during potentially harsh and prolonged transfer conditions between hosts. The aim of this study was to investigate the response of S. aureus, S. epidermidis, and S. lugdunensis when exposed to low temperature (4°C) for prolonged periods, and how this factor affected their subsequent growth, colony morphology, cellular ultra-structure, and amino acid composition in the non-cytoplasmic hydrolysate fraction. Clinical isolates were grown under optimal conditions and then subjected to 4°C conditions for a period of 8 wks. Cold-stressed and reference control samples were assessed under transmission electron microscopy (TEM) to identify potential ultra-structural changes. To determine changes in amino acid composition, cells were fractured to remove the lipid and cytoplasmic components and the remaining structural components were hydrolysed. Amino acid profiles for the hydrolysis fraction were then analysed for changes by using principal component analysis (PCA). Exposure of the three staphylococci to prolonged low temperature stress resulted in the formation of increasing proportions of small colony variant (SCV) phenotypes. TEM revealed that SCV cells had significantly thicker and more diffuse cell-walls than their corresponding WT samples for both S. aureus and S. epidermidis, but the changes were not significant for S. lugdunensis. Substantial species-specific alterations in the amino acid composition of the structural hydrolysate fraction were also observed in the cold-treated cells. The data indicated that the staphylococci responded over prolonged periods of cold-stress treatment by transforming into SCV populations. The observed ultra-structural and amino acid changes were proposed to represent response mechanisms for staphylococcal survival amidst hostile conditions, thus maintaining the viability of the species until favourable conditions arise again.

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