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- 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. |
- Liu, Xixi, 1995, et al.
(författare)
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Effortless Training of Joint Energy-Based Models with Sliced Score Matching
- 2022
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Ingår i: Proceedings - International Conference on Pattern Recognition. - 1051-4651. - 9781665490627 ; 2022-August, s. 2643-2649
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Konferensbidrag (refereegranskat)abstract
- Standard discriminative classifiers can be upgraded to joint energy-based models (JEMs) by combining the classification loss with a log-evidence loss. Hence, such models intrinsically allow detection of out-of-distribution (OOD) samples, and empirically also provide better-calibrated posteriors, i.e., prediction uncertainties. However, the training procedure suggested for JEMs (using stochastic gradient Langevin dynamics---or SGLD---to maximize the evidence) is reported to be brittle. In this work, we propose to utilize score matching---in particular sliced score matching---to obtain a stable training method for JEMs. We observe empirically that the combination of score matching with the standard classification loss leads to improved OOD detection and better-calibrated classifiers for otherwise identical DNN architectures. Additionally, we also analyze the impact of replacing the regular soft-max layer for classification with a gated soft-max one in order to improve the intrinsic transformation invariance and generalization ability.
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| 4. |
- Liu, Xixi, 1995, et al.
(författare)
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Joint Energy-based Model for Deep Probabilistic Regression
- 2022
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Ingår i: Proceedings - International Conference on Pattern Recognition. - 1051-4651. - 9781665490627 ; 2022-August, s. 2693-2699
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Konferensbidrag (refereegranskat)abstract
- It is desirable that a deep neural network trained on a regression task does not only achieve high prediction accuracy, but its prediction posteriors are also well-calibrated, especially in safety-critical settings. Recently, energy-based models specifically to enrich regression posteriors have been proposed and achieve state-of-art results in object detection tasks. However, applying these models at prediction time is not straightforward as the resulting inference methods require to minimize an underlying energy function. Furthermore, these methods empirically do not provide accurate prediction uncertainties. Inspired by recent joint energy-based models for classification, in this work we propose to utilize a joint energy model for regression tasks and describe architectural differences needed in this setting. Within this frame-work, we apply our methods to three computer vision regression tasks. We demonstrate that joint energy-based models for deep probabilistic regression improve the calibration property, do not require expensive inference, and yield competitive accuracy in terms of the mean absolute error (MAE).
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| 5. |
- Wang, Shih-Hao, et al.
(författare)
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TAROGE-M : radio antenna array on antarctic high mountain for detecting near-horizontal ultra-high energy air showers
- 2022
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The TAROGE-M radio observatory is a self-triggered antenna array on top of the similar to 2700m high Mt. Melbourne in Antarctica, designed to detect impulsive geomagnetic emission from extensive air showers induced by ultra-high energy (UHE) particles beyond 1017 eV, including cosmic rays, Earth-skimming tau neutrinos, and particularly, the "ANITA anomalous events" (AAE) from near and below the horizon. The six AAE discovered by the ANITA experiment have signal features similar to tau neutrinos but that hypothesis is in tension either with the interaction length predicted by Standard Model or with the flux limits set by other experiments. Their origin remains uncertain, requiring more experimental inputs for clarification. The detection concept of TAROGE-M takes advantage of a high altitude with synoptic view toward the horizon as an efficient signal collector, and the radio quietness as well as strong and near vertical geomagnetic field in Antarctica, enhancing the relative radio signal strength. This approach has a low energy threshold, high duty cycle, and is easy to extend for quickly enlarging statistics. Here we report experimental results from the first TAROGEM station deployed in January 2020, corresponding to approximately one month of livetime. The station consists of six receiving antennas operating at 180-450 MHz, and can reconstruct source directions of impulsive events with an angular resolution of similar to 0.3 ffi, calibrated in situ with a drone-borne pulser system. To demonstrate TAROGE-M's ability to detect UHE air showers, a search for cosmic ray signals in 25.3-days of data together with the detection simulation were conducted, resulting in seven identified candidates. The detected events have a mean reconstructed energy of 0.95+0.46 -0.31 EeV and zenith angles ranging from 25 ffi to 82 ffi, with both distributions agreeing with the simulations, indicating an energy threshold at about 0.3 EeV. The estimated cosmic ray flux at that energy is 1.2+0.7 -0.9x10(-16) eV(-1) km(-2) yr(-1) sr(-1), also consistent with results of other experiments. The TAROGE-M sensitivity to AAEs is approximated by the tau neutrino exposure with simulations, which suggests comparable sensitivity as ANITA's at around 1 EeV energy with a few station-years of operation. These first results verified the station design and performance in a polar and high-altitude environment, and are promising for further discovery of tau neutrinos and AAEs after an extension in the near future.
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