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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
- 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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| 5. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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| 7. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 8. |
- Gao, Shi Chao, et al.
(författare)
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Data-driven estimation of blood pressure using photoplethysmographic signals
- 2016
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Ingår i: Proceedings of EMBC-16, 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. - : IEEE. - 9781457702204
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Konferensbidrag (refereegranskat)abstract
- Noninvasive measurement of blood pressure by optical methods receives considerable interest, but the complexity of the measurement and the difficulty of adjusting parameters restrict applications. We develop a method for estimating the systolic and diastolic blood pressure using a single-point optical recording of a photoplethysmographic (PPG) signal. The estimation is data-driven, we use automated machine learning algorithms instead of mathematical models. Combining supervised learning with a discrete wavelet transform, the method is insensitive to minor irregularities in the PPG waveform, hence both pulse oximeters and smartphone cameras can record the signal. We evaluate the accuracy of the estimation on 78 samples from 65 subjects (40 male, 25 female, age 29±7) with no history of cardiovascular disease. The estimate for systolic blood pressure has a mean error 4.9±4.9 mm Hg, and 4.3±3.7 mm Hg for diastolic blood pressure when using the oximeter-obtained PPG. The same values are 5.1±4.3 mm Hg and 4.6±4.3 mm Hg when using the phone-obtained PPG, comparing with A&D UA-767PBT result as gold standard. The simplicity of the method encourages ambulatory measurement, and given the ease of sharing the measured data, we expect a shift to data-oriented approaches deriving insight from ubiquitous mobile devices that will yield more accurate machine learning models in monitoring blood pressure.
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| 9. |
- Jiang, Wen jun, et al.
(författare)
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Adaptive Thresholding with Inverted Triangular Area for Real-Time Detection of the Heart Rate from Photoplethysmogram Traces on a Smartphone
- 2014
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Konferensbidrag (refereegranskat)abstract
- Photoplethysmogram (PPG) signals acquired by smartphone cameras are weaker than those acquired by dedicated pulse oximeters. Furthermore, the signals have lower sampling rates, have notches in the waveform and are more severely affected by baseline drift, leading to specific morphological characteristics. This paper introduces a new feature, the inverted triangular area, to address these specific characteristics. The new feature enables real-time adaptive waveform detection using an algorithm of linear time complexity. It can also recognize notches in the waveform and it is inherently robust to baseline drift. An implementation of the algorithm on Android is available for free download. We collected data from 24 volunteers and compared our algorithm in peak detection with two competing algorithms designed for PPG signals, Incremental-Merge Segmentation (IMS) and Adaptive Thresholding (ADT). A sensitivity of 98.0 % and a positive predictive value of 98.8 % were obtained, which were 7.7 % higher than the IMS algorithm in sensitivity, and 8.3 % higher than the ADT algorithm in positive predictive value. The experimental results confirmed the applicability of the proposed method.
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| 10. |
- Jiang, Wen Jun, et al.
(författare)
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Real-time Quantifying Heart Beat Rate from Facial Video Recording on a Smart Phone using Kalman Filters
- 2014
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Konferensbidrag (refereegranskat)abstract
- Photoplethysmography (PPG) can be carried out through facial video recording by a smart phone camera in ambient light. The main challenge is to eliminate motion artifacts and ambient noise. We describe a real-time algorithm to quantify the heart beat rate from facial video recording captured by the camera of a smart phone. We extract the green channel from the video. Then we normalize it and use a Kalman filter with a particular structure to eliminate ambient noise. This filter also enhances the heart pulse component in the signal distorted by Gaussian noise and white noise. After that we employ a band-pass FIR filter to remove the remaining motion artifacts. This is followed by peak detection or Lomb periodogram to estimate heart rate. The algorithm has low computational overhead, low delay and high robustness, making it suitable for real-time interaction on a smart phone. Finally we describe an Android application based on this study.
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