Electron cryo-tomography allows for high-resolution imaging of stereocilia in their native state. Because their actin filaments have a higher degree of order, we imaged stereocilia from mice lacking the actin crosslinker plastin 1 (PLS1). We found that while stereocilia actin filaments run 13 nm apart in parallel for long distances, there were gaps of significant size that were stochastically distributed throughout the actin core. Actin crosslinkers were distributed through the stereocilium, but did not occupy all possible binding sites. At stereocilia tips, protein density extended beyond actin filaments, especially on the side of the tip where a tip link should anchor. Along the shaft, repeating density was observed that corresponds to actin-to-membrane connectors. In the taper region, most actin filaments terminated near the plasma membrane. The remaining filaments twisted together to make a tighter bundle than was present in the shaft region; the spacing between them decreased from 13 nm to 9 nm. Our models illustrate detailed features of distinct structural domains that are present within the stereocilium.
Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin bundles, traditional approaches to filament detection and tracing have failed in these cases. In this study, we introduce BundleTrac, an effective method to trace hundreds of filaments in a bundle. A comparison between BundleTrac and manually tracing the actin filaments in a stereocilium showed that BundleTrac accurately built 326 of 330 filaments (98.8%), with an overall cross-distance of 1.3 voxels for the 330 filaments. BundleTrac is an effective semi-automatic modeling approach in which a seed point is provided for each filament and the rest of the filament is computationally identified. We also demonstrate the potential of a denoising method that uses a polynomial regression to address the resolution and high-noise anisotropic environment of the density map.
Sentiment analysis research in low-resource languages such as Bengali is still unexplored due to the scarcity of annotated data and the lack of text processing tools. Therefore, in this work, we focus on generating resources and showing the applicability of the crosslingual sentiment analysis approach in Bengali. For benchmarking, we created and annotated a comprehensive corpus of around 12000 Bengali reviews. To address the lack of standard text-processing tools in Bengali, we leverage resources from English utilizing machine translation. We determine the performance of supervised machine learning (ML) classifiers in machine-translated English corpus and compare it with the original Bengali corpus. Besides, we examine sentiment preservation in the machine-translated corpus utilizing Cohen's Kappa and Gwet's AC1. To circumvent the laborious data labeling process, we explore lexicon-based methods and study the applicability of utilizing cross-domain labeled data from the resource-rich language. We find that supervised ML classifiers show comparable performances in Bengali and machinetranslated English corpus. By utilizing labeled data, they achieve 15%-20% higher F1 scores compared to both lexicon-based and transfer learning-based methods. Besides, we observe that machine translation does not alter the sentiment polarity of the review for most of the cases. Our experimental results demonstrate that the machine translation based crosslingual approach can be an effective way for sentiment classification in Bengali.
Introduction Method Cryo-electron microscopy (cryo-EM) density maps at medium resolution (5-10 Å) reveal secondary structural features such as α-helices and β-sheets. However, they lack the side chain details that would enable a direct structure determination. Among the more than 800 entries in the Electron Microscopy Data Bank (EMDB) of medium-resolution density maps that are associated with atomic models, a wide variety of similarities exist between maps and models. To validate such atomic models and to classify structural features, a local similarity criterion, the F 1 score, is proposed and evaluated in this study. The F 1 score is normalized
Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2–4 Å resolutions. The results show that the normalized probability density function of block lengths is similar between the X-ray data set and the cryo-EM data set for most of the residue types, but differences were observed for ARG, GLU, ILE, LYS, PHE, TRP, and TYR for which conformations with certain shorter block lengths are more likely to be observed in the cryo-EM set with 2–4 Å resolutions.
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