| 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. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 4. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 5. |
- Juang, Yu-Pu, et al.
(författare)
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Synthesis, distribution analysis and mechanism studies of N-acyl glucosamine-bearing oleanolic saponins
- 2020
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Ingår i: Bioorganic chemistry (Print). - : Elsevier. - 0045-2068. ; 99, s. 103835-
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Tidskriftsartikel (refereegranskat)abstract
- A series of N-acyl glucosamine-bearingtriterpenoidsaponins has been synthesized with cytotoxic activities evaluated against HL-60, PC-3, HCT-116, and CT-26 tumor cells. Saponins incorporated anoleanolic acid (OA) triterpenoidal core exhibited the highest cytotoxic activity. To study the influence of the lengths of acyl-carbon chain onN-position of glucosamine, cells were treated with28-propargylamides and then reacted with an azido-fluorogenic probe under CuAACclickreactions to visualize the intact distributions of these compounds by confocal microscopy and flow cytometry; it was found that cytotoxic-active compounds (30–32) located in the cytosol and inactivecompounds bearing longer carbon chains (33–35) were impenetrable across cell membranes.Our study demonstrated the defined lipophilic acyl-carbon chain length can precisely regulate thecytotoxic activityof saponins, which is useful for the future development of cytotoxic agents.Furthermore, using quantitative proteomics and immunolabeling,the mechanism ofcytotoxicity induced by the synthetic saponin after membrane penetration could be a result of activation of death receptor pathway and inhibition of PI3K/Akt/mTOR pathway.
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| 6. |
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| 7. |
- Fernández Schrunder, Alejandro, 1993-, et al.
(författare)
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A Bioimpedance Spectroscopy Interface for EIM Based on IF-Sampling and Pseudo 2-Path SC Bandpass ΔΣ ADC
- 2024
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Ingår i: IEEE Transactions on Biomedical Circuits and Systems. - : Institute of Electrical and Electronics Engineers (IEEE). - 1932-4545 .- 1940-9990. ; , s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents a low-noise bioimpedance (bio-Z) spectroscopy interface for electrical impedance myography (EIM) over the 1 kHz to 2 MHz frequency range. The proposed interface employs a sinusoidal signal generator based on direct-digital-synthesis (DDS) to improve the accuracy of the bio-Z reading, and a quadrature low-intermediate frequency (IF) readout to achieve a good noise-to-power efficiency and the required data throughput to detect muscle contractions. The readout is able to measure baseline and time-varying bio-Z by employing robust and power-efficient low-gain IAs and sixth-order single-bit bandpass (BP) ΔΣ ADCs. The proposed bio-Z spectroscopy interface is implemented in a 180 nm CMOS process, consumes 344.3 - 479.3 μ W, and occupies 5.4 mm 2 area. Measurement results show 0.7 mΩ/√Hz sensitivity at 15.625 kHz, 105.8 dB SNR within 4 Hz bandwidth, and a 146.5 dB figure-of-merit. Additionally, recording of EIM in time and frequency domain during contractions of the bicep brachii muscle demonstrates the potential of the proposed bio-Z interface for wearable EIM systems.
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| 8. |
- Fernández Schrunder, Alejandro, 1993-, et al.
(författare)
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A Real-Time Muscle Fatigue Detection System Based on Multi-Frequency EIM and sEMG for Effective NMES
- 2024
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Ingår i: IEEE Sensors Journal. - : Institute of Electrical and Electronics Engineers (IEEE). - 1530-437X .- 1558-1748. ; , s. 1-1
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Tidskriftsartikel (refereegranskat)abstract
- Neuromuscular electrical stimulation (NMES) is a self-directed home based therapeutic tool in early rehabilitation for musculoskeletal (MSK) conditions. However, the effectiveness of traditional NMES is fundamentally constrained by muscle fatigue. To address this limitation, this work proposes a detection system, which simultaneously records multifrequency electrical impedance myography (EIM) and surface electromyography(sEMG) in real time for time-frequency analysis of muscle activation, contraction, and fatigue. To demonstrate the ability to monitor these muscle physiological states, two experiments involving weightless and weighted dynamic contractions of the biceps brachii muscle were performed. Results from these experiments show synchronous changes in sEMG and EIM spectra during contractions, and clear trends in sEMG’s mean power frequency (MPF) and EIM spectra with fatigue progression. Additionally, the configurable 4-channel NMES has been electrically evaluated for clinical use, demonstrating the feasibility of the proposed system for closed-loop stimulation. This work showcases the potential of sEMG and multi-frequency EIM to enhance the effectiveness of NMES for MSK conditions by capturing the behavior of distinct mechanisms of muscle fatigue.
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| 9. |
- Flötteröd, Gunnar, et al.
(författare)
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Behavioral calibration and analysis of a large-scale travel microsimulation
- 2012
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Ingår i: Networks and Spatial Economics. - : Springer Science and Business Media LLC. - 1566-113X .- 1572-9427. ; 12:4, s. 481-502
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Tidskriftsartikel (refereegranskat)abstract
- This article reports on the calibration and analysis of a fully disaggregate (agent-based) transport simulation for the metropolitan area of Zurich. The agent-based simulation goes beyond traditional transport models in that it equilibrates not only route choice but all-day travel behavior, including departure time choice and mode choice. Previous work has shown that the application of a novel calibration technique that adjusts all choice dimensions at once from traffic counts yields cross-validation results that are competitive with any state-of-the-art four-step model. While the previous study aims at a methodological illustration of the calibration method, this work focuses on the real-world scenario, and it elaborates on the usefulness of the obtained results for further demand analysis purposes.
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| 10. |
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