| 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. |
- 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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| 3. |
- Ren, Luyao, et al.
(författare)
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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| 4. |
- Zhang, Kaicheng, et al.
(författare)
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SN 2014J in M82 : new insights on the spectral diversity of Type Ia supernovae
- 2018
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 481:1, s. 878-893
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Tidskriftsartikel (refereegranskat)abstract
- We present extensive spectroscopic observations for one of the closest Type Ia supernovae (SNe Ia), SN 2014J discovered in M82, ranging from 10.4 d before to 473.2 d after B-band maximum light. The diffuse interstellar band features detected in a high-resolution spectrum allow an estimate of line-of-sight extinction as A(v) similar to 1.9 +/- 0.6 mag. Spectroscopically, SN 2014J can be put into the high-velocity (HV) subgroup in Wang's classification with a velocity of Si II lambda 6355 at maximum light of upsilon(0) = 1.22 +/- 0.01 x 10(4) km s(-1) but has a low velocity gradient (LVG, following Benetti's classification) of (v) over bar = 41 +/- 2 km s(-1) d(-1), which is inconsistent with the trend that HV SNe Ia generally have larger velocity gradients. We find that the HV SNe Ia with LVGs tend to have relatively stronger Si III (at similar to 4400 angstrom) absorptions in early spectra, larger ratios of S II lambda 5468 to S II lambda 5640, and weaker Si II 5972 absorptions compared to their counterparts with similar velocities but high velocity gradients. This shows that the HV+ LVG subgroup of SNe Ia may have intrinsically higher photospheric temperature, which indicates that their progenitors may experience more complete burning in the explosions relative to the typical HV SNe Ia.
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| 5. |
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| 6. |
- He, Yuan, et al.
(författare)
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Acoustic Localization System for Precise Drone Landing
- 2024
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Ingår i: IEEE Transactions on Mobile Computing. ; 23:5, s. 4126-4144
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Tidskriftsartikel (refereegranskat)abstract
- We present MicNest: an acoustic localization system enabling precise drone landing. In MicNest, multiple microphones are deployed on a landing platform in carefully devised configurations. The drone carries a speaker transmitting purposefully-designed acoustic pulses. The drone may be localized as long as the pulses are correctly detected. Doing so is challenging: i) because of limited transmission power, propagation attenuation, background noise, and propeller interference, the Signal-to-Noise Ratio (SNR) of received pulses is intrinsically low; ii) the pulses experience non-linear Doppler distortion due to the physical drone dynamics; iii) as location information is used during landing, the processing latency must be reduced to effectively feed the flight control loop. To tackle these issues, we design a novel pulse detector, Matched Filter Tree (MFT), whose idea is to convert pulse detection to a tree search problem. We further present three practical methods to accelerate tree search jointly. Our experiments show that MicNest can localize a drone 120 m away with 0.53% relative localization error at 20 Hz location update frequency. For navigating drone landing, MicNest can achieve a success rate of 94 %. The average landing error (distance between landing point and target point) is only 4.3 cm.
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| 7. |
- Hering, Alessa, et al.
(författare)
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Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning
- 2023
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Ingår i: IEEE Transactions on Medical Imaging. - : Institute of Electrical and Electronics Engineers (IEEE). - 0278-0062 .- 1558-254X. ; 42:3, s. 697-712
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Tidskriftsartikel (refereegranskat)abstract
- Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https:// learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods.
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| 8. |
- Wang, Weiguo, et al.
(författare)
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Acoustic localization of drones in precise landing : The research and practice with micnest
- 2023
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Ingår i: GetMobile. - : Association for Computing Machinery (ACM). - 2375-0529 .- 2375-0537. ; 27:3, s. 27-32
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Delivery drones have the potential to revolutionize transportation and distribution of goods. With their autonomous navigation capabilities, they offer an efficient solution to bypass the challenges posed by complex urban traffic and enable instant package delivery. Many industrial firms are actively exploring the commercial feasibility of instant drone deliveries. Meituan, one of the largest companies in this area, devised a systematic approach to instant delivery using drones. The process begins with loading the package onto the drone, which then takes off, ascends to cruising altitude, and sets a direct course towards the designated destination. Typically, this destination is a Meituan-operated self-collection station located near the customer.
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| 9. |
- Wang, Weiguo, et al.
(författare)
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MicNest : Long-Range Instant Acoustic Localization of Drones in Precise Landing
- 2022
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Ingår i: SenSys '22. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450398862 ; , s. 504-517
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Konferensbidrag (refereegranskat)abstract
- We present MicNest: an acoustic localization system enabling precise landing of aerial drones. Drone landing is a crucial step in a drone's operation, especially as high-bandwidth wireless networks, such as 5G, enable beyond-line-of-sight operation in a shared airspace and applications such as instant asset delivery with drones gain traction. In MicNest, multiple microphones are deployed on a landing platform in carefully devised configurations. The drone carries a speaker transmitting purposefully-designed acoustic pulses. The drone may be localized as long as the pulses are correctly detected. Doing so is challenging: i) because of limited transmission power, propagation attenuation, background noise, and propeller interference, the Signal-to-Noise Ratio (SNR) of received pulses is intrinsically low; ii) the pulses experience non-linear Doppler distortion due to the physical drone dynamics while airborne; iii) as location information is to be used during landing, the processing latency must be reduced to effectively feed the flight control loop. To tackle these issues, we design a novel pulse detector, Matched Filter Tree (MFT), whose idea is to convert pulse detection to a tree search problem. We further present three practical methods to accelerate tree search jointly. Our real-world experiments show that MicNest is able to localize a drone 120 m away with 0.53% relative localization error at 20 Hz location update frequency.
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| 10. |
- Cao, Shan, et al.
(författare)
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L-arginine metabolism inhibits arthritis and inflammatory bone loss
- 2024
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ PUBLISHING GROUP. - 0003-4967 .- 1468-2060. ; 83, s. 72-87
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Tidskriftsartikel (refereegranskat)abstract
- ObjectivesTo investigate the effect of the L-arginine metabolism on arthritis and inflammation-mediated bone loss.MethodsL-arginine was applied to three arthritis models (collagen-induced arthritis, serum-induced arthritis and human TNF transgenic mice). Inflammation was assessed clinically and histologically, while bone changes were quantified by mu CT and histomorphometry. In vitro, effects of L-arginine on osteoclast differentiation were analysed by RNA-seq and mass spectrometry (MS). Seahorse, Single Cell ENergetIc metabolism by profilIng Translation inHibition and transmission electron microscopy were used for detecting metabolic changes in osteoclasts. Moreover, arginine-associated metabolites were measured in the serum of rheumatoid arthritis (RA) and pre-RA patients.ResultsL-arginine inhibited arthritis and bone loss in all three models and directly blocked TNF alpha-induced murine and human osteoclastogenesis. RNA-seq and MS analyses indicated that L-arginine switched glycolysis to oxidative phosphorylation in inflammatory osteoclasts leading to increased ATP production, purine metabolism and elevated inosine and hypoxanthine levels. Adenosine deaminase inhibitors blocking inosine and hypoxanthine production abolished the inhibition of L-arginine on osteoclastogenesis in vitro and in vivo. Altered arginine levels were also found in RA and pre-RA patients.ConclusionOur study demonstrated that L-arginine ameliorates arthritis and bone erosion through metabolic reprogramming and perturbation of purine metabolism in osteoclasts.
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