| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
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| 3. |
- Kristanl, Matej, et al.
(författare)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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Ingår i: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 4. |
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| 5. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 6. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 7. |
- Dai, Qile, et al.
(författare)
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OTTERS: a powerful TWAS framework leveraging summary-level reference data
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level reference eQTL datasets. The development of TWAS methods that can harness summary-level reference data is valuable to enable TWAS in broader settings and enhance power due to increased reference sample size. Thus, we develop a TWAS framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) that adapts multiple polygenic risk score (PRS) methods to estimate eQTL weights from summary-level eQTL reference data and conducts an omnibus TWAS. We show that OTTERS is a practical and powerful TWAS tool by both simulations and application studies.
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| 8. |
- Maimaiti, Nazhakaiti, et al.
(författare)
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Cervical musculoskeletal disorders and their relationships with personal and work-related factors among electronic assembly workers
- 2019
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Ingår i: Journal of Safety Research. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0022-4375 .- 1879-1247. ; 71, s. 79-85
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Electronics assembly workers are reported to have a high prevalence of musculoskeletal disorders (MSDs). This study investigated the prevalence of cervical MSDs and the complex relationships between cervical MSDs and individual, physical, psychosocial factors among electronics assembly workers. Methods: In this cross-sectional survey, self-administered questionnaires from 700 workers in electronics manufacturing workshops were analysed. Information concerning musculoskeletal symptoms, personal and work-related factors was collected. Finally, the prevalence of cervical MSDs was computed for different subgroups, and the relationships with different factors were analyzed using logistic regression and structural equation modeling (SEM). Results: The total 12 month prevalence of cervical MSDs among the survey population was 29.4%. Variables of gender, job tenure, twisting head frequently, neck flexion/extension for long time and work required to be done quickly showed significant associations with MSDs in a multivariate logistic regression (P < 0.05). The SEM analysis showed moderate and significant correlations between postural load (gamma = 0.279), gender (gamma = 0.233) and cervical MSDs, while there were weak but significant correlations between vibration (gamma = 0.024), work stress (gamma = 0.126), job tenure (gamma = 0.024) and cervical MSDs. Both work stress and vibration affected the MSDs indirectly through postural load. Conclusions: The logistic regression results support previous general epidemiological MSD studies, and indicates that individual, physical, and psychosocial factors are related to cervical MSDs. The SEM provides a better approximation of the complexity of the relationship between risk factors and cervical MSDs. Improving awkward postures may be effective ways to control the influence of occupational stressors or vibration on MSDs. Practical Applications: The study is to improve prevention of MSDs among electronics assembly workers and promote their occupational health.
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| 9. |
- Zhang, Ting, et al.
(författare)
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Home health care routing and scheduling in densely populated communities considering complex human behaviours
- 2023
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Ingår i: Computers & industrial engineering. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0360-8352 .- 1879-0550. ; 182
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Tidskriftsartikel (refereegranskat)abstract
- This study focuses on the home health care routing problem (HHCRP) in the scenario of high population density areas where many elders live closely together. This study considers two main objectives. The first is to reduce travel and wait times for nurses or elders. The second concerns socially related objectives in scheduling problems, such as quality of life and empowerment, by considering assumptions related to the acquaintanceship and mutual preferences of nurses and elders. This study models the effects of mutual preferences and acquain-tanceship on service time in HHCRP. We use the Markov decision process and chance-constrained programming (CCP) to model the system to conserve the sequential service provision parameters and better represent the influence of stochastic service times. Because traditional deterministic algorithms cannot solve such a model, we apply a model-free reinforcement learning algorithm, Q-learning (QL), as well as the ant colony optimisation (ACO) algorithm. Thus, we tackle this problem by developing a model and algorithm to solve complex, large-scale systems. This studys theoretical and practical contributions are verified by feedback from researchers and practitioners.
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| 10. |
- Baresel, Christian, et al.
(författare)
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Direct GHG emissions from a pilot scale MBR-process treating municipal wastewater
- 2022
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Ingår i: Advances in Climate Change Research. - : Elsevier BV. - 1674-9278 .- 2524-1761. ; 13:1, s. 138-145
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Tidskriftsartikel (refereegranskat)abstract
- To evaluate direct greenhouse gas emissions from Membrane Biological Reactor (MBR), measurements of nitrous oxide (N2O) and methane (CH4) were made at a pilot-scale MBR treating municipal wastewater Measurements were conducted during two campaigns with some changes in processes, i.e. introducing a pre-aeration tank in the second measurement, different distributions of aeration in the treatment line, not the same wastewater inflow rate, two types of ultrafiltration membrane. It was found that about 0.004% and 0.07% of the total ammonium loads were emitted as N2O, CH4 emissions were 0.026% and 0.12% of incoming TOC (0.008% and 0.04% of incoming COD) in 2014 and 2018. The obtained N2O emission values were relatively low.The study suggested that a high aeration at the beginning of the treatment line may result in significantly high emissions of both N2O and CH4. A significant change in aeration in the membrane ultrafiltration tank did not have the same impact. The MBR process is known for high quality effluent but have been questioned due to its higher carbon footprint due to energy consumption. This study gave a reference case about direct GHG emissions from MBR process and provide information for the further evaluation of MBR processes.
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