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Krishna, S., Kiselev, A., Kristoffersson, A., Repsilber, D. & Loutfi, A. (2019). A Novel Method for Estimating Distances from a Robot to Humans Using Egocentric RGB Camera. Sensors, 19(14), Article ID E3142.
Open this publication in new window or tab >>A Novel Method for Estimating Distances from a Robot to Humans Using Egocentric RGB Camera
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2019 (English)In: Sensors, ISSN 1424-8220, E-ISSN 1424-8220, Vol. 19, no 14, article id E3142Article in journal (Refereed) Published
Abstract [en]

Estimating distances between people and robots plays a crucial role in understanding social Human-Robot Interaction (HRI) from an egocentric view. It is a key step if robots should engage in social interactions, and to collaborate with people as part of human-robot teams. For distance estimation between a person and a robot, different sensors can be employed, and the number of challenges to be addressed by the distance estimation methods rise with the simplicity of the technology of a sensor. In the case of estimating distances using individual images from a single camera in a egocentric position, it is often required that individuals in the scene are facing the camera, do not occlude each other, and are fairly visible so specific facial or body features can be identified. In this paper, we propose a novel method for estimating distances between a robot and people using single images from a single egocentric camera. The method is based on previously proven 2D pose estimation, which allows partial occlusions, cluttered background, and relatively low resolution. The method estimates distance with respect to the camera based on the Euclidean distance between ear and torso of people in the image plane. Ear and torso characteristic points has been selected based on their relatively high visibility regardless of a person orientation and a certain degree of uniformity with regard to the age and gender. Experimental validation demonstrates effectiveness of the proposed method.

Place, publisher, year, edition, pages
MDPI, 2019
Keywords
Human–Robot Interaction, distance estimation, single RGB image, social interaction
National Category
Computer Vision and Robotics (Autonomous Systems)
Identifiers
urn:nbn:se:oru:diva-75583 (URN)10.3390/s19143142 (DOI)000479160300109 ()31319523 (PubMedID)2-s2.0-85070083052 (Scopus ID)
Note

Funding Agency:

Örebro University

Available from: 2019-08-16 Created: 2019-08-16 Last updated: 2019-11-15Bibliographically approved
Holster, S., Hooiveld, G. J., Repsilber, D., de Vos, W., Brummer, R. J. & König, J. (2019). Allogenic Faecal Microbiota Transfer Induces Immune-Related Gene Sets in the Colon Mucosa of Patients with Irritable Bowel Syndrome. Biomolecules, 9(10), Article ID 586.
Open this publication in new window or tab >>Allogenic Faecal Microbiota Transfer Induces Immune-Related Gene Sets in the Colon Mucosa of Patients with Irritable Bowel Syndrome
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2019 (English)In: Biomolecules, E-ISSN 2218-273X, Vol. 9, no 10, article id 586Article in journal (Refereed) Published
Abstract [en]

Faecal microbiota transfer (FMT) consists of the introduction of new microbial communities into the intestine of a patient, with the aim of restoring a disturbed gut microbiota. Even though it is used as a potential treatment for various diseases, it is unknown how the host mucosa responds to FMT. This study aims to investigate the colonic mucosa gene expression response to allogenic (from a donor) or autologous (own) FMT in patients with irritable bowel syndrome (IBS). In a recently conducted randomised, double-blinded, controlled clinical study, 17 IBS patients were treated with FMT by colonoscopy. RNA was isolated from colonic biopsies collected by sigmoidoscopy at baseline, as well as two weeks and eight weeks after FMT. In patients treated with allogenic FMT, predominantly immune response-related gene sets were induced, with the strongest response two weeks after the FMT. In patients treated with autologous FMT, predominantly metabolism-related gene sets were affected. Furthermore, several microbiota genera showed correlations with immune-related gene sets, with different correlations found after allogenic compared to autologous FMT. This study shows that the microbe–host response is influenced by FMT on the mucosal gene expression level, and that there are clear differences in response to allogenic compared to autologous FMT.

Place, publisher, year, edition, pages
MDPI, 2019
Keywords
Faecal microbiota transfer, Faecal microbiota transplantation, irritable bowel syndrome, gene expression, gut microbiota, host-microbe interaction
National Category
Medical and Health Sciences Gastroenterology and Hepatology
Research subject
Medicine
Identifiers
urn:nbn:se:oru:diva-77171 (URN)10.3390/biom9100586 (DOI)31597320 (PubMedID)
Available from: 2019-10-10 Created: 2019-10-10 Last updated: 2019-10-21Bibliographically approved
Edebol-Carlman, H., Rode, J., König, J., Hutchinson, A., Repsilber, D., Kiselev, A., . . . Brummer, R. J. (2019). Evaluating the effects of probiotic intake on brain activity during an emotional attention task and blood markers related to stress in healthy subjects. In: : . Paper presented at Mind, Mood & Microbes, 2nd International Conference on Microbiota-Gut-Brain Axis, Amsterdam, The Netherlands, 17-18 January, 2019.
Open this publication in new window or tab >>Evaluating the effects of probiotic intake on brain activity during an emotional attention task and blood markers related to stress in healthy subjects
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2019 (English)Conference paper, Oral presentation with published abstract (Refereed)
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:oru:diva-73848 (URN)
Conference
Mind, Mood & Microbes, 2nd International Conference on Microbiota-Gut-Brain Axis, Amsterdam, The Netherlands, 17-18 January, 2019
Available from: 2019-04-17 Created: 2019-04-17 Last updated: 2019-04-17Bibliographically approved
Rajan, S. K., Lindqvist, C. M., Brummer, R. J., Schoultz, I. & Repsilber, D. (2019). Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method. PLoS ONE, 14(9), Article ID e0222171.
Open this publication in new window or tab >>Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method
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2019 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, no 9, article id e0222171Article in journal (Refereed) Published
Abstract [en]

The human gut microbiota is well established as an important factor in health and disease. Fecal sample microbiota are often analyzed as a proxy for gut microbiota, and characterized with respect to their composition profiles. Modern approaches employ whole genome shotgun next-generation sequencing as the basis for these analyses. Sequencing depth as well as choice of next-generation sequencing data analysis method constitute two main interacting methodological factors for such an approach. In this study, we used 200 million sequence read pairs from one fecal sample for comparing different taxonomy classification methods, using default and custom-made reference databases, at different sequencing depths. A mock community data set with known composition was used for validating the classification methods. Results suggest that sequencing beyond 60 million read pairs does not seem to improve classification. The phylogeny prediction pattern, when using the default databases and the consensus database, appeared to be similar for all three methods. Moreover, these methods predicted rather different species. We conclude that the choice of sequencing depth and classification method has important implications for taxonomy composition prediction. A multi-method-consensus approach for robust gut microbiota NGS analysis is recommended.

Place, publisher, year, edition, pages
PLOS, 2019
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:oru:diva-76641 (URN)10.1371/journal.pone.0222171 (DOI)31527871 (PubMedID)
Available from: 2019-09-24 Created: 2019-09-24 Last updated: 2019-09-24Bibliographically approved
Djekic, D., Pinto, R., Repsilber, D., Hyötyläinen, T. & Henein, M. (2019). Serum untargeted lipidomic profiling reveals dysfunction of phospholipid metabolism in subclinical coronary artery disease. Vascular Health and Risk Management, 15, 123-135
Open this publication in new window or tab >>Serum untargeted lipidomic profiling reveals dysfunction of phospholipid metabolism in subclinical coronary artery disease
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2019 (English)In: Vascular Health and Risk Management, ISSN 1176-6344, E-ISSN 1178-2048, Vol. 15, p. 123-135Article in journal (Refereed) Published
Abstract [en]

Purpose: Disturbed metabolism of cholesterol and triacylglycerols (TGs) carries increased risk for coronary artery calcification (CAC). However, the exact relationship between individual lipid species and CAC remains unclear. The aim of this study was to identify disturbances in lipid profiles involved in the calcification process, in an attempt to propose potential biomarker candidates.

Patients and methods: We studied 70 patients at intermediate risk for coronary artery disease who had undergone coronary calcification assessment using computed tomography and Agatston coronary artery calcium score (CACS). Patients were divided into three groups: with no coronary calcification (NCC; CACS: 0; n=26), mild coronary calcification (MCC; CACS: 1-250; n=27), or severe coronary calcification (SCC; CACS: >250; n=17). Patients' serum samples were analyzed using liquid chromatography-mass spectrometry in an untargeted lipidomics approach.

Results: We identified 103 lipids within the glycerolipid, glycerophospholipid, sphingolipid, and sterol lipid classes. After false discovery rate correction, phosphatidylcholine (PC)(16:0/20:4) in higher levels and PC(18:2/18:2), PC(36:3), and phosphatidylethanolamine(20:0/18:2) in lower levels were identified as correlates with SCC compared to NCC. There were no significant differences in the levels of individual TGs between the three groups; however, clustering the lipid profiles showed a trend for higher levels of saturated and monounsaturated TGs in SCC compared to NCC. There was also a trend for lower TG (49:2), TG(51:1), TG(54:5), and TG(56:8) levels in SCC compared to MCC.

Conclusion: In this study we investigated the lipidome of patients with coronary calcification. Our results suggest that the calcification process may be associated with dysfunction in autophagy. The lipidomic biomarkers revealed in this study may aid in better assessment of patients with subclinical coronary artery disease.

Place, publisher, year, edition, pages
DOVE Medical Press Ltd., 2019
Keywords
coronary artery calcification, coronary artery calcium score, lipidomics, triacylglycerol, lipids, atherosclerosis, autophagy
National Category
Cardiac and Cardiovascular Systems
Identifiers
urn:nbn:se:oru:diva-74648 (URN)10.2147/VHRM.S202344 (DOI)000468547500001 ()
Funder
Swedish Heart Lung Foundation
Available from: 2019-06-10 Created: 2019-06-10 Last updated: 2019-06-10Bibliographically approved
Drobin, K., Assadi, G., Hong, M.-G., Andersson, E., Fredolini, C., Forsström, B., . . . Halfvarson, J. (2019). Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci. Inflammatory Bowel Diseases, 25(2), 306-316
Open this publication in new window or tab >>Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci
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2019 (English)In: Inflammatory Bowel Diseases, ISSN 1078-0998, E-ISSN 1536-4844, Vol. 25, no 2, p. 306-316Article in journal (Refereed) Published
Abstract [en]

Background: Few studies have investigated the blood proteome of inflammatory bowel disease (IBD). We characterized the serum abundance of proteins encoded at 163 known IBD risk loci and tested these proteins for their biomarker discovery potential.

Methods: Based on the Human Protein Atlas (HPA) antibody availability, 218 proteins from genes mapping at 163 IBD risk loci were selected. Targeted serum protein profiles from 49 Crohn's disease (CD) patients, 51 ulcerative colitis (UC) patients, and 50 sex- and age-matched healthy individuals were obtained using multiplexed antibody suspension bead array assays. Differences in relative serum abundance levels between disease groups and controls were examined. Replication was attempted for CD-UC comparisons (including disease subtypes) by including 64 additional patients (33 CD and 31 UC). Antibodies targeting a potentially novel risk protein were validated by paired antibodies, Western blot, immuno-capture mass spectrometry, and epitope mapping.

Results: By univariate analysis, 13 proteins mostly related to neutrophil, T-cell, and B-cell activation and function were differentially expressed in IBD patients vs healthy controls, 3 in CD patients vs healthy controls and 2 in UC patients vs healthy controls (q < 0.01). Multivariate analyses further differentiated disease groups from healthy controls and CD subtypes from UC (P < 0.05). Extended characterization of an antibody targeting a novel, discriminative serum marker, the laccase (multicopper oxidoreductase) domain containing 1 (LACC1) protein, provided evidence for antibody on-target specificity.

Conclusions: Using affinity proteomics, we identified a set of IBD-associated serum proteins encoded at IBD risk loci. These candidate proteins hold the potential to be exploited as diagnostic biomarkers of IBD.

Place, publisher, year, edition, pages
Oxford University Press, 2019
Keywords
inflammatory bowel disease, affinity proteomics, LACC1
National Category
Gastroenterology and Hepatology Immunology in the medical area
Identifiers
urn:nbn:se:oru:diva-69892 (URN)10.1093/ibd/izy326 (DOI)000462580900020 ()30358838 (PubMedID)2-s2.0-85059799081 (Scopus ID)
Funder
Swedish Research Council, 2013-3862 2011-2764Knut and Alice Wallenberg FoundationKnowledge Foundation
Note

Funding Agencies:

AstraZeneca (Translational Research Program "Post-genomic applications in IBD: exploitation of genetic information toward improved diagnosis and therapy")

Örebro University Hospital Research Foundation  

Swedish Government (CancerUU)  

Science for Life Laboratory Stockholm  

KTH Center for Applied Precision Medicine (KCAP) - Erling-Persson Family Foundation

Available from: 2018-11-06 Created: 2018-11-06 Last updated: 2019-06-19Bibliographically approved
Holster, S., Lindqvist, C. M., Repsilber, D., Salonen, A., de Vos, W., König, J. & Brummer, R. J. (2019). The Effect of Allogenic Versus Autologous Fecal Microbiota Transfer on Symptoms, Visceral Perception and Fecal and Mucosal Microbiota in Irritable Bowel Syndrome: A Randomized Controlled Study. Clinical and Translational Gastroenterology, 10(4), Article ID e00034.
Open this publication in new window or tab >>The Effect of Allogenic Versus Autologous Fecal Microbiota Transfer on Symptoms, Visceral Perception and Fecal and Mucosal Microbiota in Irritable Bowel Syndrome: A Randomized Controlled Study
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2019 (English)In: Clinical and Translational Gastroenterology, ISSN 2155-384X, E-ISSN 2155-384X, Vol. 10, no 4, article id e00034Article in journal (Refereed) Published
Abstract [en]

OBJECTIVES: Fecal microbiota transfer (FMT) is suggested as a potential treatment for patients with irritable bowel syndrome (IBS). We aimed to study the effect of allogenic and autologous FMT on IBS symptoms, visceral sensitivity, and compositional changes in fecal and mucosa-adherent microbiota.

METHODS: Seventeen patients with IBS were randomized either to receive fecal material from a healthy donor (allogenic) or to receive their own fecal material (autologous). The fecal material was administered into the cecum by whole colonoscopy after bowel cleansing.

RESULTS: No significant differences were found between the allogenic and the autologous FMT regarding symptom scores. However, symptom scores of patients receiving allogenic fecal material significantly decreased after FMT compared with baseline (P 5 0.02), which was not the case in the autologous group (P50.16). Visceral sensitivity was not affected except for a small beneficial effect on urge scores in the autologous group (P < 0.05). While both fecal and mucosa-adherent microbiota of some patients shifted to their respective donor’s fecal microbiota, some patients showed no relevant microbial changes after allogenic FMT. Large compositional shifts in fecal and mucosa-adherent microbiota also occurred in the autologous group.

CONCLUSIONS: This study showed that a single FMT by colonoscopy may have beneficial effects in IBS; however, the allogenic fecal material was not superior to the autologous fecal material. This suggests that bowel cleansing prior to the colonoscopy and/or processing of the fecal material as part of the FMT routine contribute to symptoms and gut microbiota composition changes in IBS.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019
National Category
Gastroenterology and Hepatology
Research subject
Medicine
Identifiers
urn:nbn:se:oru:diva-74035 (URN)10.14309/ctg.0000000000000034 (DOI)000466787000001 ()31009405 (PubMedID)
Funder
Swedish Nutrition Foundation (SNF)
Note

Funding Agencies:

SIAM Gravitation Grant  024.002.002 

Spinoza 2008 Award of the Netherlands Organization for Scientific Research (NWO) 

Available from: 2019-05-06 Created: 2019-05-06 Last updated: 2019-06-19Bibliographically approved
Ganda Mall, J.-P., Östlund-Lagerström, L., Lindqvist, C. M., Algilani, S., Rasoal, D., Repsilber, D., . . . Schoultz, I. (2018). Are self-reported gastrointestinal symptoms among older adults associated with increased intestinal permeability and psychological distress?. BMC Geriatrics, 18(1), Article ID 75.
Open this publication in new window or tab >>Are self-reported gastrointestinal symptoms among older adults associated with increased intestinal permeability and psychological distress?
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2018 (English)In: BMC Geriatrics, ISSN 1471-2318, E-ISSN 1471-2318, Vol. 18, no 1, article id 75Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Despite the substantial number of older adults suffering from gastrointestinal (GI) symptoms little is known regarding the character of these complaints and whether they are associated with an altered intestinal barrier function and psychological distress. Our aim was to explore the relationship between self-reported gut health, intestinal permeability and psychological distress among older adults.

METHODS: Three study populations were included: 1) older adults with GI symptoms (n = 24), 2) a group of older adults representing the general elderly population in Sweden (n = 22) and 3) senior orienteering athletes as a potential model of healthy ageing (n = 27). Questionnaire data on gut-health, psychological distress and level of physical activity were collected. Intestinal permeability was measured by quantifying zonulin in plasma. The level of systemic and local inflammation was monitored by measuring C-reactive protein (CRP), hydrogen peroxide in plasma and calprotectin in stool samples. The relationship between biomarkers and questionnaire data in the different study populations was illustrated using a Principal Component Analysis (PCA).

RESULTS: Older adults with GI symptoms displayed significantly higher levels of both zonulin and psychological distress than both general older adults and senior orienteering athletes. The PCA analysis revealed a separation between senior orienteering athletes and older adults with GI symptoms and showed an association between GI symptoms, psychological distress and zonulin.

CONCLUSIONS: Older adults with GI symptoms express increased plasma levels of zonulin, which might reflect an augmented intestinal permeability. In addition, this group suffer from higher psychological distress compared to general older adults and senior orienteering athletes. This relationship was further confirmed by a PCA plot, which illustrated an association between GI symptoms, psychological distress and intestinal permeability.

Place, publisher, year, edition, pages
BioMed Central, 2018
Keywords
Older adults; Gastrointestinal symptoms; Intestinal barrier function; Psychological distress
National Category
Geriatrics
Identifiers
urn:nbn:se:oru:diva-66053 (URN)10.1186/s12877-018-0767-6 (DOI)000428260300001 ()29554871 (PubMedID)2-s2.0-85044174344 (Scopus ID)
Funder
Knowledge Foundation, 20110225
Note

Funding Agencies:

Bo Rydins stiftelse  F0514 

Faculty of Medicine and Health at Örebro University  

Diarrheal Disease Research Centre, Linköping University  

Available from: 2018-03-27 Created: 2018-03-27 Last updated: 2018-08-20Bibliographically approved
Rush, S. & Repsilber, D. (2018). Capturing context-specific regulation in molecular interaction networks. BMC Bioinformatics, 19(1), Article ID 539.
Open this publication in new window or tab >>Capturing context-specific regulation in molecular interaction networks
2018 (English)In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 19, no 1, article id 539Article in journal (Refereed) Published
Abstract [en]

Background: Molecular profiles change in response to perturbations. These changes are coordinated into functional modules via regulatory interactions. The genes and their products within a functional module are expected to be differentially expressed in a manner coherent with their regulatory network. This perspective presents a promising approach to increase precision in detecting differential signals as well as for describing differential regulatory signals within the framework of a priori knowledge about the underlying network, and so from a mechanistic point of view.

Results: We present Coherent Network Expression (CoNE), an effective procedure for identifying differentially activated functional modules in molecular interaction networks. Differential gene expression is chosen as example, and differential signals coherent with the regulatory nature of the network are identified. We apply our procedure to systematically simulated data, comparing its performance to alternative methods. We then take the example case of a transcription regulatory network in the context of particle-induced pulmonary inflammation, recapitulating and proposing additional candidates to previously obtained results. CoNE is conveniently implemented in an R-package along with simulation utilities.

Conclusion: Combining coherent interactions with error control on differential gene expression results in uniformly greater specificity in inference than error control alone, ensuring that captured functional modules constitute real findings.

Place, publisher, year, edition, pages
BioMed Central, 2018
Keywords
Activated subnetwork, Coherent differential expression, Differential regulation, Error control, Functional module, Molecular network
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:oru:diva-65214 (URN)10.1186/s12859-018-2513-7 (DOI)000454209300003 ()30577761 (PubMedID)2-s2.0-85058920164 (Scopus ID)
Funder
Knowledge Foundation, 20110225
Available from: 2018-02-24 Created: 2018-02-24 Last updated: 2019-01-11Bibliographically approved
Björkqvist, O., Repsilber, D., Seifert, M., Engstrand, L., Rangel, I. & Halfvarson, J. (2018). Increasing abundance of faecalibacterium prausnitzii is associated with decreased intestinal inflammation in Crohn's disease: A longitudinal study. Journal of Crohn's & Colitis, 12(Suppl. 1), S468-S469
Open this publication in new window or tab >>Increasing abundance of faecalibacterium prausnitzii is associated with decreased intestinal inflammation in Crohn's disease: A longitudinal study
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2018 (English)In: Journal of Crohn's & Colitis, ISSN 1873-9946, E-ISSN 1876-4479, Vol. 12, no Suppl. 1, p. S468-S469Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
Oxford University Press, 2018
National Category
Gastroenterology and Hepatology
Identifiers
urn:nbn:se:oru:diva-66747 (URN)000427318902090 ()
Available from: 2018-04-26 Created: 2018-04-26 Last updated: 2018-08-31Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7173-5579

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