| 1. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 2. |
- Luo, Yifei, et al.
(författare)
-
Technology Roadmap for Flexible Sensors
- 2023
-
Ingår i: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
-
Forskningsöversikt (refereegranskat)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
|
|
| 3. |
- Osoegawa, Kazutoyo, et al.
(författare)
-
Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop
- 2019
-
Ingår i: Human Immunology. - : ELSEVIER SCIENCE INC. - 0198-8859 .- 1879-1166. ; 80:4, s. 228-236
-
Tidskriftsartikel (refereegranskat)abstract
- The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and software in use prior to the workshop. The organizers sent 50 cell lines to each of the 15 groups, scored the 15 independently generated sets of NGS HLA genotyping data, and generated "consensus" HLA genotypes for each of the 50 cell lines. Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score of 95% concordance at the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 loci satisfied the requirements to submit NGS HLA typing data for the 17th IHIW projects. Together, these PS and PT efforts constituted the 17th IHIW Quality Control project. Overall PT concordance rates for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5 were 98.1%, 97.0% and 98.1%, 99.0%, 98.6%, 98.8%, 97.6%, 96.0%, 99.1%, 90.0% and 91.7%, respectively. Across all loci, the majority of the discordance was due to allele dropout. The high cost of NGS HLA genotyping per experiment likely prevented the retyping of initially failed HLA loci. Despite the high HLA genotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software.
|
|
| 4. |
- Yin, Feng, et al.
(författare)
-
Fundamental Bounds on Position Estimation Using Proximity Reports
- 2016
-
Konferensbidrag (refereegranskat)abstract
- There is a big trend nowadays toward indoor proximity report based positioning. A binary valued proximity report can be obtained opportunistically through event-triggering, leading to significantly reduced signaling overhead for wireless communications. In this paper, we aim to derive two types of fundamental lower bound, namely the Cram´er-Rao bound and the Barankin bound, on the mean-square-error of any proximity report based position estimator. Using the maximum-likelihood estimator as a representative example, we show that the Barankin bound is potentially much tighter than the Cram´er-Rao bound and conclude that the Barankin bound ought be better suited for benchmarking any proximity report based position estimator.
|
|
| 5. |
- Yin, Feng, et al.
(författare)
-
Proximity Report Triggering Threshold Optimization for Network-Based Indoor Positioning
- 2015
-
Konferensbidrag (refereegranskat)abstract
- Driven by the promising beaconing techniques, this paper presents a general received-signal-strength (RSS) threshold optimization procedure for proximity reports to support networkbased indoor positioning. The desired RSS threshold is found through optimizing a metric function (for instance the localization root-mean-square-error) in terms of both the deployment information and the RSS modeling in consideration of an evaluation area. The resulting RSS threshold provides a trade-off between triggering many but less informative proximity reports with a low threshold, and triggering few but very informative proximity reports with a high threshold, and thus enables enhanced performance for some low-cost and low-complex proximity based positioning algorithms. The proposed framework is also validated with real RSS measurements collected in an office area with deployed bluetooth low-energy (BLE) beacons.
|
|
| 6. |
- Yin, Feng, 1984-, et al.
(författare)
-
Received-Signal-Strength Threshold Optimization Using Gaussian Processes
- 2017
-
Ingår i: IEEE Transactions on Signal Processing. - : Institute of Electrical and Electronics Engineers (IEEE). - 1053-587X .- 1941-0476. ; 65:8, s. 2164-2177
-
Tidskriftsartikel (refereegranskat)abstract
- There is a big trend nowadays to use event-triggered proximity report for indoor positioning. This paper presents a generic received-signal-strength (RSS) threshold optimization framework for generating informative proximity reports. The proposed framework contains five main building blocks, namely the deployment information, RSS model, positioning metric selection, optimization process and management. Among others, we focus on Gaussian process regression (GPR)-based RSS models and positioning metric computation. The optimal RSS threshold is found through minimizing the best achievable localization root-mean-square-error formulated with the aid of fundamental lower bound analysis. Computational complexity is compared for different RSS models and different fundamental lower bounds. The resulting optimal RSS threshold enables enhanced performance of new fashioned low-cost and low-complex proximity report-based positioning algorithms. The proposed framework is validated with real measurements collected in an office area where bluetooth-low-energy (BLE) beacons are deployed.
|
|
| 7. |
- Zhao, Yuxin, 1986-, et al.
(författare)
-
Cramér–Rao Bounds for Filtering Based on Gaussian Process State-Space Models
- 2019
-
Ingår i: IEEE Transactions on Signal Processing. - : Institute of Electrical and Electronics Engineers (IEEE). - 1053-587X .- 1941-0476. ; 67:23, s. 5936-5951
-
Tidskriftsartikel (refereegranskat)abstract
- Posterior Cramér-Rao bounds (CRBs) are derived for the estimation performance of three Gaussian process-based state-space models. The parametric CRB is derived for the case with a parametric state transition and a Gaussian process-based measurement model. We illustrate the theory with a target tracking example and derive both parametric and posterior filtering CRBs for this specific application. Finally, the theory is illustrated with a positioning problem, with experimental data from an office environment where the obtained estimation performance is compared to the derived CRBs.
|
|
| 8. |
- Zhao, Yuxin, 1986-, et al.
(författare)
-
Gaussian Process for Propagation modeling and Proximity Reports Based Indoor Positioning
- 2016
-
Ingår i: 2016 IEEE 83rd Vehicular Technology Conference (VTC Spring). - : IEEE. - 9781509016983 ; , s. 1-5
-
Konferensbidrag (refereegranskat)abstract
- The commercial interest in proximity services is increasing. Application examples include location-based information and advertisements, logistics, social networking, file sharing, etc. In this paper, we consider network-based positioning based on times series of proximity reports from a mobile device, either only a proximity indicator, or a vector of RSS from observed nodes. Such positioning corresponds to a latent and nonlinear observation model. To address these problems, we combine two powerful tools, namely particle filtering and Gaussian process regression (GPR) for radio signal propagation modeling. The latter also provides some insights into the spatial correlation of the radio propagation in the considered area. Radio propagation modeling and positioning performance are evaluated in a typical office area with Bluetooth-Low-Energy (BLE) beacons deployed for proximity detection and reports. Results show that the positioning accuracy can be improved by using GPR.
|
|
| 9. |
- Zhao, Yuxin, 1986-, et al.
(författare)
-
Gaussian Processes for Flow Modeling and Prediction of Positioned Trajectories Evaluated with Sports Data
- 2016
-
Ingår i: 19th International Conference on Information Fusion (FUSION), 2016. - : Institute of Electrical and Electronics Engineers (IEEE). - 9780996452748 - 9781509020126 ; , s. 1461-1468
-
Konferensbidrag (refereegranskat)abstract
- Kernel-based machine learning methods are gaining increasing interest in flow modeling and prediction in recent years. Gaussian process (GP) is one example of such kernelbased methods, which can provide very good performance for nonlinear problems. In this work, we apply GP regression to flow modeling and prediction of athletes in ski races, but the proposed framework can be generally applied to other use cases with device trajectories of positioned data. Some specific aspects can be addressed when the data is periodic, like in sports where the event is split up over multiple laps along a specific track. Flow models of both the individual skier and a cluster of skiers are derived and analyzed. Performance has been evaluated using data from the Falun Nordic World Ski Championships 2015, in particular the Men’s cross country 4 × 10 km relay. The results show that the flow models vary spatially for different skiers and clusters. We further demonstrate that GP regression provides powerful and accurate models for flow prediction.
|
|
| 10. |
- Zhao, Yuxin, 1986-, et al.
(författare)
-
Particle Filtering for Positioning Based on Proximity Reports
- 2015
-
Konferensbidrag (refereegranskat)abstract
- The commercial interest in proximity services is increasing. Application examples include location-based information and advertisements, logistics, social networking, file sharing, etc. In this paper, we consider positioning of devices based on time series proximity reports from a mobile device to a network node. This corresponds to nonlinear measurements with respect to the device position in relation to the network nodes. Therefore, particle filtering is applicable for positioning. Positioning performance is evaluated in a typical office area with Bluetooth-low-energy beacons deployed for proximity detection and report. Accuracy is concluded to vary spatially over the office floor, and in relation to the beacon deployment density.
|
|
| 11. |
- Zhao, Yuxin, 1986-, et al.
(författare)
-
Sequential Monte Carlo Methods and Theoretical Bounds for Proximity Report Based Indoor Positioning
- 2018
-
Ingår i: IEEE Transactions on Vehicular Technology. - : Institute of Electrical and Electronics Engineers (IEEE). - 0018-9545 .- 1939-9359. ; 67:6, s. 5372-5386
-
Tidskriftsartikel (refereegranskat)abstract
- The commercial interest in proximity services is increasing. Application examples include location-based information and advertisements, logistics, social networking, file sharing, etc. In this paper, we consider positioning of devices based on a time series of proximity reports from a mobile device to a network node. This corresponds to nonlinear measurements with respect to the device position in relation to the network nodes. Motion model will be needed together with the measurements to determine the position of the device. Therefore, sequential Monte Carlo methods, namely particle filtering and smoothing, are applicable for positioning. Positioning performance is evaluated in a typical office area with Bluetooth-low-energy beacons deployed for proximity detection and report, and is further compared to parametric Cramér-Rao lower bounds. Finally, the position accuracy is also evaluated with real experimental data.
|
|
