| 1. |
- Ameur, Adam, et al.
(författare)
-
SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
-
Ingår i: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
-
Tidskriftsartikel (refereegranskat)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
|
|
| 2. |
- Holmström, Oscar, et al.
(författare)
-
A novel deep learning-based point-of-care diagnostic method for detecting Plasmodium falciparum with fluorescence digital microscopy.
- 2020
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:11
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Malaria remains a major global health problem with a need for improved field-usable diagnostic tests. We have developed a portable, low-cost digital microscope scanner, capable of both brightfield and fluorescence imaging. Here, we used the instrument to digitize blood smears, and applied deep learning (DL) algorithms to detect Plasmodium falciparum parasites.METHODS: Thin blood smears (n = 125) were collected from patients with microscopy-confirmed P. falciparum infections in rural Tanzania, prior to and after initiation of artemisinin-based combination therapy. The samples were stained using the 4',6-diamidino-2-phenylindole fluorogen and digitized using the prototype microscope scanner. Two DL algorithms were trained to detect malaria parasites in the samples, and results compared to the visual assessment of both the digitized samples, and the Giemsa-stained thick smears.RESULTS: Detection of P. falciparum parasites in the digitized thin blood smears was possible both by visual assessment and by DL-based analysis with a strong correlation in results (r = 0.99, p < 0.01). A moderately strong correlation was observed between the DL-based thin smear analysis and the visual thick smear-analysis (r = 0.74, p < 0.01). Low levels of parasites were detected by DL-based analysis on day three following treatment initiation, but a small number of fluorescent signals were detected also in microscopy-negative samples.CONCLUSION: Quantification of P. falciparum parasites in DAPI-stained thin smears is feasible using DL-supported, point-of-care digital microscopy, with a high correlation to visual assessment of samples. Fluorescent signals from artefacts in samples with low infection levels represented the main challenge for the digital analysis, thus highlighting the importance of minimizing sample contaminations. The proposed method could support malaria diagnostics and monitoring of treatment response through automated quantification of parasitaemia and is likely to be applicable also for diagnostics of other Plasmodium species and other infectious diseases.
|
|
| 3. |
- Holmström, Oscar, et al.
(författare)
-
Point-of-care mobile digital microscopy and deep learning for the detection of soil-transmitted helminths and Schistosoma haematobium
- 2017
-
Ingår i: Global Health Action. - : Informa UK Limited. - 1654-9716 .- 1654-9880. ; 10:sup3
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Microscopy remains the gold standard in the diagnosis of neglected tropical diseases. As resource limited, rural areas often lack laboratory equipment and trained personnel, new diagnostic techniques are needed. Low-cost, point-of-care imaging devices show potential in the diagnosis of these diseases. Novel, digital image analysis algorithms can be utilized to automate sample analysis.OBJECTIVE: Evaluation of the imaging performance of a miniature digital microscopy scanner for the diagnosis of soil-transmitted helminths and Schistosoma haematobium, and training of a deep learning-based image analysis algorithm for automated detection of soil-transmitted helminths in the captured images.METHODS: A total of 13 iodine-stained stool samples containing Ascaris lumbricoides, Trichuris trichiura and hookworm eggs and 4 urine samples containing Schistosoma haematobium were digitized using a reference whole slide-scanner and the mobile microscopy scanner. Parasites in the images were identified by visual examination and by analysis with a deep learning-based image analysis algorithm in the stool samples. Results were compared between the digital and visual analysis of the images showing helminth eggs.RESULTS: Parasite identification by visual analysis of digital slides captured with the mobile microscope was feasible for all analyzed parasites. Although the spatial resolution of the reference slide-scanner is higher, the resolution of the mobile microscope is sufficient for reliable identification and classification of all parasites studied. Digital image analysis of stool sample images captured with the mobile microscope showed high sensitivity for detection of all helminths studied (range of sensitivity = 83.3-100%) in the test set (n = 217) of manually labeled helminth eggs.CONCLUSIONS: In this proof-of-concept study, the imaging performance of a mobile, digital microscope was sufficient for visual detection of soil-transmitted helminths and Schistosoma haematobium. Furthermore, we show that deep learning-based image analysis can be utilized for the automated detection and classification of helminths in the captured images.
|
|
| 4. |
- Langner, Taro, et al.
(författare)
-
Kidney segmentation in neck-to-knee body MRI of 40,000 UK Biobank participants
- 2020
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- The UK Biobank is collecting extensive data on health-related characteristics of over half a million volunteers. The biological samples of blood and urine can provide valuable insight on kidney function, with important links to cardiovascular and metabolic health. Further information on kidney anatomy could be obtained by medical imaging. In contrast to the brain, heart, liver, and pancreas, no dedicated Magnetic Resonance Imaging (MRI) is planned for the kidneys. An image-based assessment is nonetheless feasible in the neck-to-knee body MRI intended for abdominal body composition analysis, which also covers the kidneys. In this work, a pipeline for automated segmentation of parenchymal kidney volume in UK Biobank neck-to-knee body MRI is proposed. The underlying neural network reaches a relative error of 3.8%, with Dice score 0.956 in validation on 64 subjects, close to the 2.6% and Dice score 0.962 for repeated segmentation by one human operator. The released MRI of about 40,000 subjects can be processed within one day, yielding volume measurements of left and right kidney. Algorithmic quality ratings enabled the exclusion of outliers and potential failure cases. The resulting measurements can be studied and shared for large-scale investigation of associations and longitudinal changes in parenchymal kidney volume.
|
|
| 5. |
- Lundin, Johan, et al.
(författare)
-
Diagnosis of soil-transmitted helminth infections with digital mobile microscopy and artificial intelligence in a resource-limited setting
- 2024
-
Ingår i: PLoS Neglected Tropical Diseases. - : Public Library of Science (PLoS). - 1935-2727 .- 1935-2735. ; 18:4
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Infections caused by soil-transmitted helminths (STHs) are the most prevalent neglected tropical diseases and result in a major disease burden in low- and middle-income countries, especially in school-aged children. Improved diagnostic methods, especially for light intensity infections, are needed for efficient, control and elimination of STHs as a public health problem, as well as STH management. Image-based artificial intelligence (AI) has shown promise for STH detection in digitized stool samples. However, the diagnostic accuracy of AI-based analysis of entire microscope slides, so called whole-slide images (WSI), has previously not been evaluated on a sample-level in primary healthcare settings in STH endemic countries.Methodology/Principal findings: Stool samples (n = 1,335) were collected during 2020 from children attending primary schools in Kwale County, Kenya, prepared according to the Kato-Katz method at a local primary healthcare laboratory and digitized with a portable whole-slide microscopy scanner and uploaded via mobile networks to a cloud environment. The digital samples of adequate quality (n = 1,180) were split into a training (n = 388) and test set (n = 792) and a deep-learning system (DLS) developed for detection of STHs. The DLS findings were compared with expert manual microscopy and additional visual assessment of the digital samples in slides with discordant results between the methods. Manual microscopy detected 15 (1.9%) Ascaris lumbricoides, 172 (21.7%) Tricuris trichiura and 140 (17.7%) hookworm (Ancylostoma duodenale or Necator americanus) infections in the test set. Importantly, more than 90% of all STH positive cases represented light intensity infections. With manual microscopy as the reference standard, the sensitivity of the DLS as the index test for detection of A. lumbricoides, T. trichiura and hookworm was 80%, 92% and 76%, respectively. The corresponding specificity was 98%, 90% and 95%. Notably, in 79 samples (10%) classified as negative by manual microscopy for a specific species, STH eggs were detected by the DLS and confirmed correct by visual inspection of the digital samples.Conclusions/Significance: Analysis of digitally scanned stool samples with the DLS provided high diagnostic accuracy for detection of STHs. Importantly, a substantial number of light intensity infections were missed by manual microscopy but detected by the DLS. Thus, analysis of WSIs with image-based AI may provide a future tool for improved detection of STHs in a primary healthcare setting, which in turn could facilitate monitoring and evaluation of control programs.
|
|
| 6. |
- Otten, Julia, 1973-, et al.
(författare)
-
Benefits of a Paleolithic diet with and without supervised exercise on fat mass, insulin sensitivity, and glycemic control : a randomized controlled trial in individuals with type 2 diabetes
- 2017
-
Ingår i: Diabetes/Metabolism Research Reviews. - : Wiley. - 1520-7552 .- 1520-7560. ; 33:1
-
Tidskriftsartikel (refereegranskat)abstract
- BackgroundMeans to reduce future risk for cardiovascular disease in subjects with type 2 diabetes are urgently needed.MethodsThirty-two patients with type 2 diabetes (age 59 ± 8 years) followed a Paleolithic diet for 12 weeks. Participants were randomized to either standard care exercise recommendations (PD) or 1-h supervised exercise sessions (aerobic exercise and resistance training) three times per week (PD-EX).ResultsFor the within group analyses, fat mass decreased by 5.7 kg (IQR: −6.6, −4.1; p < 0.001) in the PD group and by 6.7 kg (−8.2, −5.3; p < 0.001) in the PD-EX group. Insulin sensitivity (HOMA-IR) improved by 45% in the PD (p < 0.001) and PD-EX (p < 0.001) groups. HbA1c decreased by 0.9% (−1.2, −0.6; p < 0.001) in the PD group and 1.1% (−1.7, −0.7; p < 0.01) in the PD-EX group. Leptin decreased by 62% (p < 0.001) in the PD group and 42% (p < 0.001) in the PD-EX group. Maximum oxygen uptake increased by 0.2 L/min (0.0, 0.3) in the PD-EX group, and remained unchanged in the PD group (p < 0.01 for the difference between intervention groups). Male participants decreased lean mass by 2.6 kg (−3.6, −1.3) in the PD group and by 1.2 kg (−1.3, 1.0) in the PD-EX group (p < 0.05 for the difference between intervention groups).ConclusionsA Paleolithic diet improves fat mass and metabolic balance including insulin sensitivity, glycemic control, and leptin in subjects with type 2 diabetes. Supervised exercise training may not enhance the effects on these outcomes, but preserves lean mass in men and increases cardiovascular fitness.
|
|
| 7. |
|
|
| 8. |
- Tinghög, Petter, et al.
(författare)
-
Prevalence of mental ill health, traumas and postmigration stress among refugees from Syria resettled in Sweden after 2011 : a population-based survey
- 2017
-
Ingår i: BMJ Open. - : BMJ Publishing Group Ltd. - 2044-6055. ; 7:12
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: To estimate the prevalence of and associations between anxiety, depression, post-traumatic stress disorder (PTSD), low subjective well-being (SWB), potential traumas and postmigration stress among refugees from Syria resettled in Sweden.DESIGN: A cross-sectional and population-based questionnaire study based on a known and complete sample frame. The survey included multiple measures of mental ill health and factors of particular relevance for refugees. Weighted analyses were conducted to calculate representative prevalence rates and associations. Associations were investigated through a series of logistic regression analyses. All analyses were supplemented with robust 95% CIs.SETTING: Sweden.PARTICIPANTS: A random sample of 1215 individuals (response rate 30.4%) from Syria aged 18-64 years that were granted residency in Sweden on grounds of asylum between 2011 and 2013.MAIN OUTCOME MEASURES: Anxiety, depression, PTSD and low SWB were assessed through Hopkins Symptom Checklist, Harvard Trauma Questionnaire and WHO-5 Well-being Index, using established cut-offs.RESULTS: A majority of the participants met the criteria for at least one of the studied types of mental ill health, and the comorbidity was high. Depression was the most the common type with 40.2% (95% CI 36.9% to 43.3%), followed by low SWB with 37.7% (95% CI 34.8% to 40.1%), anxiety with 31.8% (95% CI 29.2% to 34.7%) and PTSD with 29.9% (95% CI 27.2% to 32.6%). Refugee-related potentially traumatic events (PTEs) experienced before or during migration was common as was substantial levels of postmigration stress. Most types of refugee-related PTEs, especially being exposed to interpersonal violence, and postmigration stress were associated with increased risks for anxiety, depression, low SWB and PTSD.CONCLUSIONS: Mental ill health, in terms of anxiety, depression, low SWB and PTSD, are highly elevated and comorbid among refugees from Syria. Increased attention from multiple societal sectors to adequately support Syrian refugees' mental health needs, promoting recovery and reducing postmigration stress are needed.
|
|
| 9. |
- Vressner, Andreas, et al.
(författare)
-
Pressure oscillations during rapid HCCI combustion
- 2003
-
Ingår i: SAE Technical Paper. - 400 Commonwealth Drive, Warrendale, PA, United States : SAE International. - 0148-7191.
-
Konferensbidrag (refereegranskat)abstract
- This work has focused on studying the in-cylinder pressure fluctuations caused by rapid HCCI combustion and determine what they consist of. Inhomogeneous autoignition sets up pressure waves traversing the combustion chamber. These pressure waves induce high gas velocities which causes increased heat transfer to the walls or in worst case engine damage. In order to study the pressure fluctuations a number of pressure transducers were mounted in the combustion chamber. The multi transducer arrangement was such that six transducers were placed circumferentially, one placed near the centre and one at a slight offset in the combustion chamber. The fitting of six transducers circumferentially was enabled by a spacer design and the two top mounted transducers were fitted in a modified cylinder head. During testing a disc shaped combustion chamber was used. The results of the tests conducted were that the in-cylinder pressure experienced during rapid HCCI-combustion is inhomogeneous. Pressure oscillations were experienced which showed good accordance to vibration mode shapes and frequencies suggested by acoustic vibration theory. The pressure waves manifested largest intensities for the first vibration mode, a mode suggesting radial propagation of the pressure waves in the combustion chamber. Experiments showed that the direction of the pressure wave was random which hinted absence of hot spot ignition. Hot spots mean that some part of the combustion chamber is physically hotter than the rest which ignites adjacent mixture. There is no evidence available yet to demonstrate engine damage during rapid HCCI combustion. An explanation to this could be that the violent combustion reactions related to SI knock damage is not present in HCCI combustion due to the diluted mixtures. The local heat released will therefore be lower. Finally, engine tests using two other combustion chamber geometries were conducted. The results showed that altering the geometry of the combustion chamber affects the resulting frequency spectrum. The two geometries were hill- and a bowl shaped respectively. Analytical calculations on the bowl shape vibration frequencies indicate reasonably good accordance to experimental results.
|
|
| 10. |
|
|
