Subclass-balancing Contrastive Learning for Long-tailed Recognition

Long-tailed recognition with imbalanced class distribution naturally emerges in practical machine learning applications. Existing methods such as data reweighing, resampling, and supervised contrastive learning enforce the class balance with a price of introducing imbalance between instances of head class and tail class, which may ignore the underlying rich semantic substructures of the former and exaggerate the biases in the latter. We overcome these drawbacks by a novel ``subclass-balancing contrastive learning (SBCL)'' approach that clusters each head class into multiple subclasses of similar sizes as the tail classes and enforce representations to capture the two-layer class hierarchy between the original classes and their subclasses. Since the clustering is conducted in the representation space and updated during the course of training, the subclass labels preserve the semantic substructures of head classes. Meanwhile, it does not overemphasize tail class samples, so each individual instance contribute to the representation learning equally. Hence, our method achieves both the instance- and subclass-balance, while the original class labels are also learned through contrastive learning among subclasses from different classes. We evaluate SBCL over a list of long-tailed benchmark datasets and it achieves the state-of-the-art performance. In addition, we present extensive analyses and ablation studies of SBCL to verify its advantages

The Role of XPG in Processing (CAG)n/(CTG)n DNA Hairpins

BACKGROUND: During DNA replication or repair, disease-associated (CAG)n/(CTG)n expansion can result from formation of hairpin structures in the repeat tract of the newly synthesized or nicked DNA strand. Recent studies identified a nick-directed (CAG)n/(CTG)n hairpin repair (HPR) system that removes (CAG)n/(CTG)n hairpins from human cells via endonucleolytic incisions. Because the process is highly similar to the mechanism by which XPG and XPF endonucleases remove bulky DNA lesions during nucleotide excision repair, we assessed the potential role of XPG in conducting (CAG)n/(CTG)n HPR. RESULTS: To determine if the XPG endonuclease is involved in (CAG)n/(CTG)n hairpin removal, two XPG-deficient cell lines (GM16024 and AG08802) were examined for their ability to process (CAG)n/(CTG)n hairpins in vitro. We demonstrated that the GM16024 cell line processes all hairpin substrates as efficiently as HeLa cells, and that the AG08802 cell line is partially defective in HPR. Analysis of repair intermediates revealed that nuclear extracts from both XPG-deficient lines remove CAG/CTG hairpins via incisions, but the incision products are distinct from those generated in HeLa extracts. We also show that purified recombinant XPG protein greatly stimulates HPR in XPG-deficient extracts by promoting an incision 5\u27 to the hairpin. CONCLUSIONS: Our results strongly suggest that 1) human cells possess multiple pathways to remove (CAG)n/(CTG)n hairpins located in newly synthesized (or nicked) DNA strand; and 2) XPG, although not essential for (CAG)n/(CTG)n hairpin removal, stimulates HPR by facilitating a 5\u27 incision to the hairpin. This study reveals a novel role for XPG in genome-maintenance and implicates XPG in diseases caused by trinucleotide repeat expansion

Genome-Wide Mendelian Randomization Identifies Putatively Causal Gut Microbiota For Multiple Peptic Ulcer Diseases

OBJECTIVE: The pathogenesis of peptic ulcer diseases (PUDs) involves multiple factors, and the contribution of gut microbiota to this process remains unclear. While previous studies have associated gut microbiota with peptic ulcers, the precise nature of the relationship, whether causal or influenced by biases, requires further elucidation. DESIGN: The largest meta-analysis of genome-wide association studies was conducted by the MiBioGen consortium, which provided the summary statistics of gut microbiota for implementation in the Mendelian randomization (MR) analysis. Summary statistics for five types of PUDs were compiled using the FinnGen Consortium R8 release data. Various statistical techniques, including inverse variance weighting (IVW), MR-Egger, weighted median (WM), weighted mode, and simple mode, were employed to assess the causal relationships between gut microbiota and these five PUDs. RESULT: In the intestinal microbiome of 119 known genera, we found a total of 14 causal associations with various locations of PUDs and reported the potential pathogenic bacteria of CONCLUSION: In this study, the pathogenic bacterial genera in the gut microbiota that promote the occurrence of PUDs were found to be causally related. There are multiple correlations between intestinal flora and PUDs, overlapping PUDs have overlapping associated genera. The variance in ulcer-related bacterial genera across different locations underscores the potential influence of anatomical locations and physiological functions

Elucidating the Synergic Effect in Nanoscale MoS\u3csub\u3e2\u3c/sub\u3e/TiO\u3csub\u3e2\u3c/sub\u3e Heterointerface for Na-Ion Storage

Interface engineering in electrode materials is an attractive strategy for enhancing charge storage, enabling fast kinetics, and improving cycling stability for energy storage systems. Nevertheless, the performance improvement is usually ambiguously ascribed to the “synergetic effect”, the fundamental understanding toward the effect of the interface at molecular level in composite materials remains elusive. In this work, a well-defined nanoscale MoS2/TiO2 interface is rationally designed by immobilizing TiO2 nanocrystals on MoS2 nanosheets. The role of heterostructure interface between TiO2 and MoS2 by operando synchrotron X-ray diffraction (sXRD), solid-state nuclear magnetic resonance, and density functional theory calculations is investigated. It is found that the existence of a hetero-interfacial electric field can promote charge transfer kinetics. Based on operando sXRD, it is revealed that the heterostructure follows a solid-solution reaction mechanism with small volume changes during cycling. As such, the electrode demonstrates ultrafast Na+ ions storage of 300 mAh g−1 at 10 A g−1 and excellent reversible capacity of 540 mAh g−1 at 0.2 A g−1. This work provides significant insights into understanding of heterostructure interface at molecular level, which suggests new strategies for creating unconventional nanocomposite electrode materials for energy storage systems

B-Cell Receptor-Associated Protein 31 Regulates the Expression of Valosin-Containing Protein Through Elf2

Background/Aims: B-cell receptor-associated protein 31 (Bap31) is an evolutionarily conserved, ubiquitously expressed, polytopic integral membrane protein in the endoplasmic reticulum (ER) that is involved in the regulation of apoptosis, protein transport and degradation. Patients with Bap31 mutations exhibit symptoms similar to those exhibited by patients with central nervous system (CNS) diseases, such as deafness, dystonia, and intellectual disability. The present study aimed to investigate the function of Bap31 in CNS diseases by identifying a CNS disease-related gene regulated by Bap31 and exploring the underlying molecular mechanism. Methods: ShRNA-Bap31 and siRNA-Bap31 were used to knockdown Bap31 in N2a cells, and real-time PCR was performed to detect the mRNA levels of genes involved in CNS diseases. Western blot analyses were used to examine the protein levels of the candidate gene (valosin-containing protein, VCP) both in vivo and in vitro. The functions of Bap31 and VCP in mediating the degradation of the hyper-unstable mutant of cystic fibrosis trans-membrane conductance regulator (CFTRΔF508) were studied. Moreover, real-time PCR, Western blot and dual luciferase reporter analyses were conducted to investigate the molecular mechanism by which Bap31 regulates the expression levels of VCP. Results: VCP was identified as a candidate gene based on its differential expression in N2a cells following both shRNA- and siRNA-mediated knockdown of Bap31. Both the mRNA and protein levels of VCP were regulated by Bap31 in vivo and in vitro. In the ER-associated degradation (ERAD) pathway, Bap31 also regulated VCP expression and caused differences in the binding quantities of CFTRΔF508 and VCP. Furthermore, a transcription factor of VCP (E74-like factor 2, Elf2) was regulated by Bap31, and Elf2 mediated the changes in VCP transcription and expression in cells with altered Bap31 expression. Conclusion: These results indicate that Bap31 regulates the expression of VCP possibly via Elf2 and support the potential molecular function of Bap31 in CNS diseases

Human-in-the-Loop Schema Induction

Schema induction builds a graph representation explaining how events unfold in a scenario. Existing approaches have been based on information retrieval (IR) and information extraction(IE), often with limited human curation. We demonstrate a human-in-the-loop schema induction system powered by GPT-3. We first describe the different modules of our system, including prompting to generate schematic elements, manual edit of those elements, and conversion of those into a schema graph. By qualitatively comparing our system to previous ones, we show that our system not only transfers to new domains more easily than previous approaches, but also reduces efforts of human curation thanks to our interactive interface.Comment: 10 pages, ACL2023 demo trac

Genome-wide Mendelian randomization identifies putatively causal gut microbiota for multiple peptic ulcer diseases

ObjectiveThe pathogenesis of peptic ulcer diseases (PUDs) involves multiple factors, and the contribution of gut microbiota to this process remains unclear. While previous studies have associated gut microbiota with peptic ulcers, the precise nature of the relationship, whether causal or influenced by biases, requires further elucidation.DesignThe largest meta-analysis of genome-wide association studies was conducted by the MiBioGen consortium, which provided the summary statistics of gut microbiota for implementation in the Mendelian randomization (MR) analysis. Summary statistics for five types of PUDs were compiled using the FinnGen Consortium R8 release data. Various statistical techniques, including inverse variance weighting (IVW), MR-Egger, weighted median (WM), weighted mode, and simple mode, were employed to assess the causal relationships between gut microbiota and these five PUDs.ResultIn the intestinal microbiome of 119 known genera, we found a total of 14 causal associations with various locations of PUDs and reported the potential pathogenic bacteria of Bilophila et al. Among them, four had causal relationships with esophageal ulcer, one with gastric ulcer, three with gastroduodenal ulcer, four with duodenal ulcer, and two with gastrojejunal ulcer.ConclusionIn this study, the pathogenic bacterial genera in the gut microbiota that promote the occurrence of PUDs were found to be causally related. There are multiple correlations between intestinal flora and PUDs, overlapping PUDs have overlapping associated genera. The variance in ulcer-related bacterial genera across different locations underscores the potential influence of anatomical locations and physiological functions