The Protein Information Resource (PIR) is an integrated public resource of protein informatics. To facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors, PIR has extended its superfamily concept and developed the SuperFamily (PIRSF) classification system. Based on the evolutionary relationships of whole proteins, this classification system allows annotation of both specific biological and generic biochemical functions. The system adopts a network structure for protein classification from superfamily to subfamily levels. Protein family members are homologous (sharing common ancestry) and homeomorphic (sharing full-length sequence similarity with common domain architecture). The PIRSF database consists of two data sets, preliminary clusters and curated families. The curated families include family name, protein membership, parent-child relationship, domain architecture, and optional description and bibliography. PIRSF is accessible from the website at http://pir.georgetown.edu/pirsf/ for report retrieval and sequence classification. The report presents family annotation, membership statistics, cross-references to other databases, graphical display of domain architecture, and links to multiple sequence alignments and phylogenetic trees for curated families. PIRSF can be utilized to analyze phylogenetic profiles, to reveal functional convergence and divergence, and to identify interesting relationships between homeomorphic families, domains and structural classes.
NOD‐like receptor family protein 3 (NLRP3)‐mediated inflammasome activation promotes caspase‐1‐dependent production of interleukin‐1β (IL‐1β) and requires the adaptor protein ASC. Compared with the priming and activation mechanisms of the inflammasome signaling pathway, post‐translational ubiquitination/deubiquitination mechanisms controlling inflammasome activation have not been clearly addressed. We here demonstrate that the deubiquitinating enzyme USP50 binds to the ASC protein and subsequently regulates the inflammasome signaling pathway by deubiquitinating the lysine 63‐linked polyubiquitination of ASC. USP50 knockdown in human THP‐1 cells and mouse bone marrow‐derived macrophages shows a significant decrease in procaspase‐1 cleavage, resulting in a reduced secretion of IL‐1β and interleukin‐18 (IL‐18) upon treatment with NLRP3 stimuli and a reduction in ASC speck formation and oligomerization. Thus, we elucidate a novel regulatory mechanism of the inflammasome signaling pathway mediated by the USP50 deubiquitinating enzyme.
This paper proposes a recommender system to alleviate the coldstart problem that can estimate user preferences based on only a small number of items. To identify a user's preference in the cold state, existing recommender systems, such as Netflix, initially provide items to a user; we call those items evidence candidates.Recommendations are then made based on the items selected by the user. Previous recommendation studies have two limitations:(1) the users who consumed a few items have poor recommendations and (2) inadequate evidence candidates are used to identify user preferences. We propose a meta-learning-based recommender system called MeLU to overcome these two limitations. From metalearning, which can rapidly adopt new task with a few examples, MeLU can estimate new user's preferences with a few consumed items. In addition, we provide an evidence candidate selection strategy that determines distinguishing items for customized preference estimation. We validate MeLU with two benchmark datasets, and the proposed model reduces at least 5.92% mean absolute error than two comparative models on the datasets. We also conduct a user study experiment to verify the evidence selection strategy.
Sequential recommendation techniques provide users with product recommendations fitting their current preferences by handling dynamic user preferences over time. Previous studies have focused on modeling sequential dynamics without much regard to which of the best-selling products (i.e., head items) or niche products (i.e., tail items) should be recommended. We scrutinize the structural reason for why tail items are barely served in the current sequential recommendation model, which consists of an item-embedding layer, a sequence-modeling layer, and a recommendation layer. Well-designed sequence-modeling and recommendation layers are expected to naturally learn suitable item embeddings. However, tail items are likely to fall short of this expectation because the current model structure is not suitable for learning high-quality embeddings with insufficient data. Thus, tail items are rarely recommended. To eliminate this issue, we propose a framework called CITIES, which aims to enhance the quality of the tail-item embeddings by training an embedding-inference function using multiple contextual head items so that the recommendation performance improves for not only the tail items but also for the head items. Moreover, our framework can infer new-item embeddings without an additional learning process. Extensive experiments on two realworld datasets show that applying CITIES to the state-of-the-art methods improves recommendation performance for both tail and head items. We conduct an additional experiment to verify that CITIES can infer suitable new-item embeddings as well.
Recently, opinion summarization, which is the generation of a summary from multiple reviews, has been conducted in a self-supervised manner by considering a sampled review as a pseudo summary. However, non-text data such as image and metadata related to reviews have been considered less often. To use the abundant information contained in non-text data, we propose a self-supervised multimodal opinion summarization framework called Mul-timodalSum. Our framework obtains a representation of each modality using a separate encoder for each modality, and the text decoder generates a summary. To resolve the inherent heterogeneity of multimodal data, we propose a multimodal training pipeline. We first pretrain the text encoder-decoder based solely on text modality data. Subsequently, we pretrain the non-text modality encoders by considering the pretrained text decoder as a pivot for the homogeneous representation of multimodal data. Finally, to fuse multimodal representations, we train the entire framework in an end-to-end manner. We demonstrate the superiority of MultimodalSum by conducting experiments on Yelp and Amazon datasets.
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