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Selective autophagy is a conserved subcellular process that maintains the health of eukaryotic cells by targeting damaged or toxic cytoplasmic components to the vacuole/lysosome for degradation. A key player in the initiation of selective autophagy in S. Cerevisiae (baker’s yeast) is a large adapter protein called Atg11. Atg11 has multiple predicted coiled-coil domains and intrinsically disordered regions, is known to dimerize, and binds and organizes other essential components of the autophagosome formation machinery, including Atg1 and Atg9. We performed systematic directed mutagenesis on the coiled-coil 2 domain of Atg11 in order to map which residues were required for its structure and function. Using yeast-2-hybrid and coimmunoprecipitation, we found only three residues to be critical: I562, Y565, and I569. Mutation of any of these, but especially Y565, could interfere with Atg11 dimerization and block its interaction with Atg1 and Atg9, thereby inactivating selective autophagy.

In this paper, we introduce two new methods of mitigating decoder error propagation for low-latency sliding window decoding (SWD) of spatially coupled low-density parity-check (SC-LDPC) codes. Building on the recently introduced idea of check node (CN) doping of regular SC-LDPC codes, here we employ variable node (VN) doping to fix (set to a known value) a subset of variable nodes in the coupling chain. Both of these doping methods have the effect of allowing SWD to recover from error propagation, at a cost of a slight rate loss. Experimental results show that, similar to CN doping, VN doping improves performance by up to two orders of magnitude compared to un-doped SC-LDPC codes in the typical signal-to-noise ratio operating range. Further, compared to CN doping, VN doping has the advantage of not requiring any changes to the decoding process. In addition, a log-likelihood-ratio based window extension algorithm is proposed to reduce the effect of error propagation. Using this approach, we show that decoding latency can be reduced by up to a significant fraction without suffering any loss in performance.

In this paper, we introduce two new methods of mitigating decoder error propagation for low-latency sliding window decoding (SWD) of spatially coupled low density parity check (SC-LDPC) codes. Building on the recently introduced idea of check node (CN) doping of regular SC-LDPC codes, here we employ variable node (VN) doping to fix (set to a known value) a subset of variable nodes in the coupling chain. Both of these doping methods have the effect of allowing SWD to recover from error propagation, at a cost of a slight rate loss. Experimental results show that, similar to CN doping, VN doping improves performance by up to two orders of magnitude compared to undoped SC-LDPC codes in the typical signal-to-noise ratio operating range. Further, compared to CN doping, VN doping has the advantage of not requiring any changes to the decoding process.In addition, a log-likelihood-ratio based window extension algorithm is proposed to reduce the effect of error propagation. Using this approach, we show that decoding latency can be reduced by up to a significant fraction without suffering any loss in performance

Abstract In this paper we examine a low-energy solar energetic particle (SEP) event observed by IS⊙IS’s Energetic Particle Instrument-Low (EPI-Lo) inside 0.18 au on 2020 September 30. This small SEP event has a very interesting time profile and ion composition. Our results show that the maximum energy and peak in intensity are observed mainly along the open radial magnetic field. The event shows velocity dispersion, and strong particle anisotropies are observed throughout the event, showing that more particles are streaming outward from the Sun. We do not see a shock in the in situ plasma or magnetic field data throughout the event. Heavy ions, such as O and Fe, were detected in addition to protons and 4He, but without significant enhancements in 3He or energetic electrons. Our analysis shows that this event is associated with a slow streamer blowout coronal mass ejection (SBO-CME), and the signatures of this small CME event are consistent with those typical of larger CME events. The time–intensity profile of this event shows that the Parker Solar Probe encountered the western flank of the SBO-CME. The anisotropic and dispersive nature of this event in a shockless local plasma gives indications that these particles are most likelymore »accelerated remotely near the Sun by a weak shock or compression wave ahead of the SBO-CME. This event may represent direct observations of the source of the low-energy SEP seed particle population.« less

The phase problem in X-ray crystallography arises from the fact that only the intensities, and not the phases, of the diffracting electromagnetic waves are measured directly. Molecular replacement can often estimate the relative phases of reflections starting with those derived from a template structure, which is usually a previously solved structure of a similar protein. The key factor in the success of molecular replacement is finding a good template structure. When no good solved template exists, predicted structures based partially on templates can sometimes be used to generate models for molecular replacement, thereby extending the lower bound of structural and sequence similarity required for successful structure determination. Here, the effectiveness is examined of structures predicted by a state-of-the-art prediction algorithm, the Associative memory, Water-mediated, Structure and Energy Model Suite ( AWSEM-Suite ), which has been shown to perform well in predicting protein structures in CASP13 when there is no significant sequence similarity to a solved protein or only very low sequence similarity to known templates. The performance of AWSEM-Suite structures in molecular replacement is discussed and the results show that AWSEM-Suite performs well in providing useful phase information, often performing better than I-TASSER-MR and the previous algorithm AWSEM-Template .