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- 2019
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Journal article (peer-reviewed)
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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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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| 3. |
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| 4. |
- Björnsson, Bergthor, et al.
(author)
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Digital twins to personalize medicine
- 2020
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In: Genome Medicine. - : Springer Science and Business Media LLC. - 1756-994X. ; 12:1
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Research review (peer-reviewed)abstract
- Personalized medicine requires the integration and processing of vast amounts of data. Here, we propose a solution to this challenge that is based on constructing Digital Twins. These are high-resolution models of individual patients that are computationally treated with thousands of drugs to find the drug that is optimal for the patient.
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| 5. |
- Blockhuys, Stephanie, 1983, et al.
(author)
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X-radiation enhances the collagen type I strap formation and migration potentials of colon cancer cells
- 2016
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In: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 7:44, s. 71390-71399
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Journal article (peer-reviewed)abstract
- Rectal cancer treatment still fails with local and distant relapses of the disease. It is hypothesized that radiotherapy could stimulate cancer cell dissemination and metastasis. In this study, we evaluated the effect of X-radiation on collagen type I strap formation potential, i.e. matrix remodeling associated with mesenchymal cell migration, and behaviors of SW480, SW620, HCT116 p53(+/+) and HCT116 p53(-/-) colon cancer cells. We determined a radiation-induced increase in collagen type I strap formation and migration potentials of SW480 and HCT116 p53(+/+). Further studies with HCT116 p53(+/+), indicated that after X-radiation strap forming cells have an increased motility. More, we detected a decrease in adhesion potential and mature integrin beta 1 expression, but no change in non-muscle myosin II expression for HCT116 p53(+/+) after X-radiation. Integrin beta 1 neutralization resulted in a decreased cell adhesion and collagen type I strap formation in both sham and X-radiated conditions. Our study indicates collagen type I strap formation as a potential mechanism of colon cancer cells with increased migration potential after X-radiation, and suggests that other molecules than integrin beta 1 and non-muscle myosin II are responsible for the radiation-induced collagen type I strap formation potential of colon cancer cells. This work encourages further molecular investigation of radiation-induced migration to improve rectal cancer treatment outcome.
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| 6. |
- Chen, Mo, et al.
(author)
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Energy-Efficient and Safe-Separation Operation for Successive Trains
- 2023
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In: IEEE Conference on Intelligent Transportation Systems, Proceedings, ITSC. - 2153-0017 .- 2153-0009. ; , s. 845-851
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Conference paper (peer-reviewed)abstract
- Energy-efficient and safe-separation during train operation is of great significance for urban rail transit systems, particularly on lines with high traffic density. This paper integrates the two issues and proposes a general cooperative operation method for successive trains with no limit on the number of trains. The cooperation problem is formulated as an optimal control problem and then solved as a nonlinear program. By simultaneously optimizing the speed profiles of each train, the total traction energy of the multi-train system can be minimized, ensuring safety by imposing dynamic time headway constraints among adjacent trains throughout the entire distance horizon. Moreover, a dynamic programming method is developed for comparative study, to verify the effectiveness of the proposed method.
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| 7. |
- Chen, Yun, 1966, et al.
(author)
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Neonatal losartan treatment suppresses renal expression of molecules involved in cell-cell and cell-matrix interactions
- 2004
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In: Journal of the American Society of Nephrology. - : Lippincott Williams & Wilkins. - 1046-6673 .- 1533-3450. ; 15:5, s. 1232-43
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Journal article (peer-reviewed)abstract
- Lack of neonatal angiotensin II type 1 receptor (AT(1)) stimulation produces renal abnormalities characterized by papillary atrophy and impaired urinary concentrating ability, but the mechanisms involved are still unclear. DNA microarray was used to identify genes that are differentially expressed in renal medulla in response to neonatal treatment with AT(1) receptor antagonist losartan (30 mg/kg per d), which commenced within 24 h after birth. The data showed that losartan treatment for 48 h downregulated 68 genes, approximately 30% of which encode various components of cytoskeleton and cytoskeleton-associated proteins, extracellular matrix, and enzymes involved in extracellular matrix maturation or turnover. With the use of immunohistochemistry and Western immunoblot, the microarray data were confirmed and it was demonstrated that losartan suppressed renal expression of syndecan 2, alpha-smooth muscle actin, MHC class II, and leukocyte type 12-lipoxygenase by day 4. In addition, losartan inhibited medullary expression of integrin alpha6 and caused relocalization of integrins alpha6 and alpha3. Moreover, losartan inhibited cell proliferation in medullary tubules by day 9, as detected by Ki-67 immunostaining. This study provides new data supporting the contention that a lack of AT(1) receptor stimulation results in abnormal matrix assembly, disturbed cell-cell and cell-matrix interactions, and subsequent abnormal tubular maturation. Moreover, regulation of the expression of leukocyte type 12-lipoxygenase and alpha-smooth muscle actin by the renin-angiotensin system in the immature kidney adds new knowledge toward the understanding of renal vascular development.
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| 8. |
- Fan, Qunping, 1989, et al.
(author)
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High-performance all-polymer solar cells enabled by a novel low bandgap non-fully conjugated polymer acceptor
- 2021
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In: Science in China Series B. - : Springer Nature. - 1674-7291 .- 1869-1870. ; 64, s. 1380-1388
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Journal article (peer-reviewed)abstract
- Anon-fully conjugated polymer as a new class of acceptor materials has shown some advantages over its small molecular counterpart when used in photoactive layers for all-polymer solar cells (all-PSCs), despite a low power conversion efficiency (PCE) caused by its narrow absorption spectra. Herein, a novel non-fully conjugated polymer acceptor PFY-2TS with a low bandgap of similar to 1.40 eV was developed, via polymerizing a large pi-fused small molecule acceptor (SMA) building block (namely YBO) with a non-conjugated thioalkyl linkage. Compared with its precursor YBO, PFY-2TS retains a similar low bandgap but a higher LUMO level. Moreover, compared with the structural analog of YBO-based fully conjugated polymer acceptor PFY-DTC, PFY-2TS shows similar absorption spectrum and electron mobility, but significantly different molecular crystallinity and aggregation properties, which results in optimal blend morphology with a polymer donor PBDB-T and better device physical processes in all-PSCs. As a result, PFY-2TS-based all-PSCs achieved a PCE of 12.31% with a small energy loss of 0.56 eV enabled by the reduced non-radiative energy loss (0.24 eV), which is better than that of 11.08% for the PFY-DTC-based ones. Our work clearly demonstrated that non-fully conjugated polymers as a new class of acceptor materials are very promising for the development of high-performance all-PSCs.
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| 9. |
- Xiao, Zhuang, et al.
(author)
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Eco-Driving for Metro Trains: A Computationally Efficient Approach Using Convex Programming
- 2023
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In: IEEE Transactions on Vehicular Technology. - 0018-9545 .- 1939-9359. ; 72:8, s. 10063-10076
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Journal article (peer-reviewed)abstract
- Eco-driving for trains has traditionally focused on minimizing mechanical energy consumption at wheels, while completely ignoring traction chain losses that are rather significant. This paper presents a computationally efficient approach to minimize the total electrical energy consumption from traction substations (TS). After a nonlinear and non-convex program is formulated in time domain, a nonlinear and non-convex program is formulated in space domain to overcome the drawbacks of the model in time domain. By convex modeling steps, the non-convex program in space domain is reformulated as a convex program that can be efficiently solved. To further reduce computational effort, a real-time iteration sequential quadratic programming (SQP) algorithm is proposed to solve the convex program in a model predictive control framework. Numerical results indicate that the proposed SQP method yields a near-optimal solution with high computational efficiency. Compared to a traditional mechanical energy consumption model, a TS-to-traction energy efficiency can be improved.
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| 10. |
- Xiao, Zhuang, et al.
(author)
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Energy-efficient predictive control for trams incorporating disjunctive time constraints from traffic lights
- 2023
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In: Transportation Research, Part C: Emerging Technologies. - 0968-090X. ; 151
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Journal article (peer-reviewed)abstract
- Tram operations are often blocked by traffic lights, leading to frequent decelerations and re-accelerations that increase operational energy consumption. This paper focuses on tram energy-efficient control problem incorporating time constraints from traffic lights that have multiple feasible green time windows (GTWs). We formulate the problem as a mixed-integer nonlinear program (MINLP), where binary variables are assigned to model disjunctive time constraints of the GTWs. To address computational challenge of solving the MINLP, we reformulate it as a tractable nonlinear program (NLP). Specifically, an equivalent NLP is first presented by replacing the integrality constraint with nonlinear constraints, and then the nonlinear constraints are relaxed and penalized into cost functions. To recover a solution of the MINLP, we propose a computationally efficient sequential quadratic programming algorithm in a shrinking horizon model predictive control framework, which updates the penalty parameter and quadratic programming subproblems in parallel. The solution obtained from the subproblem is feasible in each iteration, and convergence of the feasibility iterations can be enforced by the updated penalty. The performance of the proposed approach is investigated on different scenarios using real-life tram data. Results show that the method is able to generate energy-efficient driving trajectories in a dynamic environment, while crossing traffic lights in effective GTWs without unnecessary decelerations and re-accelerations.
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