Function annotation of hepatic retinoid x receptor α based on genome-wide DNA binding and transcriptome profiling.

BackgroundRetinoid x receptor α (RXRα) is abundantly expressed in the liver and is essential for the function of other nuclear receptors. Using chromatin immunoprecipitation sequencing and mRNA profiling data generated from wild type and RXRα-null mouse livers, the current study identifies the bona-fide hepatic RXRα targets and biological pathways. In addition, based on binding and motif analysis, the molecular mechanism by which RXRα regulates hepatic genes is elucidated in a high-throughput manner.Principal findingsClose to 80% of hepatic expressed genes were bound by RXRα, while 16% were expressed in an RXRα-dependent manner. Motif analysis predicted direct repeat with a spacer of one nucleotide as the most prevalent RXRα binding site. Many of the 500 strongest binding motifs overlapped with the binding motif of specific protein 1. Biological functional analysis of RXRα-dependent genes revealed that hepatic RXRα deficiency mainly resulted in up-regulation of steroid and cholesterol biosynthesis-related genes and down-regulation of translation- as well as anti-apoptosis-related genes. Furthermore, RXRα bound to many genes that encode nuclear receptors and their cofactors suggesting the central role of RXRα in regulating nuclear receptor-mediated pathways.ConclusionsThis study establishes the relationship between RXRα DNA binding and hepatic gene expression. RXRα binds extensively to the mouse genome. However, DNA binding does not necessarily affect the basal mRNA level. In addition to metabolism, RXRα dictates the expression of genes that regulate RNA processing, translation, and protein folding illustrating the novel roles of hepatic RXRα in post-transcriptional regulation

Powder Compaction Simulation

Powders are one of most manipulated materials in many industries such as food, pharmaceutical, energy and metallurgical industries. An important process for the powders is the compaction into solids with small porosity or high relative density. However, powders exhibit complex behavior during this process. After rearrangement and jamming of the powder bed, many types of deformation mechanisms dominate the compaction of granular materials, including elastic and plastic deformation of each individual particle. Therefore, having a better understanding of macroscale and microscale properties of powder beds and single particles during the compaction process is necessary. In addition, to reduce cost and time for experimental efforts, it is important to have modeling and simulation capabilities for the powder compaction process. This study creates a new version of an existing powder compaction simulation nanoHUB tool. This version includes more features, such as single elastic and plastic particle deformation and microstructure evolution during the compaction of plastic powder beds. Using the solver developed by Dr. Marcial Gonzalez [1, 2], this nanoHUB tool is able to simulate binary mixtures of monodispersed systems of both plastic and elastic particles. Also, it generates the pressure-deformation relationship for a single particle when it is compressed between rigid plates. [1] Gonzalez M. and Cuitiño, A.M., “A nonlocal contact formulation for confined granular systems”, Journal of the Mechanics and Physics of Solids, 60, 333–350, 2012. [2] Gonzalez M. and Cuitiño A.M., “Microstructure evolution of compressible granular system

Competitive Advantage Attacks to Decentralized Federated Learning

Decentralized federated learning (DFL) enables clients (e.g., hospitals and banks) to jointly train machine learning models without a central orchestration server. In each global training round, each client trains a local model on its own training data and then they exchange local models for aggregation. In this work, we propose SelfishAttack, a new family of attacks to DFL. In SelfishAttack, a set of selfish clients aim to achieve competitive advantages over the remaining non-selfish ones, i.e., the final learnt local models of the selfish clients are more accurate than those of the non-selfish ones. Towards this goal, the selfish clients send carefully crafted local models to each remaining non-selfish one in each global training round. We formulate finding such local models as an optimization problem and propose methods to solve it when DFL uses different aggregation rules. Theoretically, we show that our methods find the optimal solutions to the optimization problem. Empirically, we show that SelfishAttack successfully increases the accuracy gap (i.e., competitive advantage) between the final learnt local models of selfish clients and those of non-selfish ones. Moreover, SelfishAttack achieves larger accuracy gaps than poisoning attacks when extended to increase competitive advantages

Optical limiting using Laguerre-Gaussian beams

We demonstrate optical limiting using the self-lensing effect of a higher-order Laguerre-Gaussian beam in a thin dye-doped polymer sample, which we find is consistent with our model using Gaussian decomposition. The peak phase shift in the sample required for limiting is smaller than for a fundamental Gaussian beam with the added flexibility that the nonlinear medium can be placed either in front of or behind the beam focus.Comment: 3 pages, 4 figure

Contrast and Clustering: Learning Neighborhood Pair Representation for Source-free Domain Adaptation

Unsupervised domain adaptation uses source data from different distributions to solve the problem of classifying data from unlabeled target domains. However, conventional methods require access to source data, which often raise concerns about data privacy. In this paper, we consider a more practical but challenging setting where the source domain data is unavailable and the target domain data is unlabeled. Specifically, we address the domain discrepancy problem from the perspective of contrastive learning. The key idea of our work is to learn a domain-invariant feature by 1) performing clustering directly in the original feature space with nearest neighbors; 2) constructing truly hard negative pairs by extended neighbors without introducing additional computational complexity; and 3) combining noise-contrastive estimation theory to gain computational advantage. We conduct careful ablation studies and extensive experiments on three common benchmarks: VisDA, Office-Home, and Office-31. The results demonstrate the superiority of our methods compared with other state-of-the-art works.Comment: Journal article

Function Annotation of Hepatic Retinoid x Receptor α Based on Genome-Wide DNA Binding and Transcriptome Profiling

Background Retinoid x receptor α (RXRα) is abundantly expressed in the liver and is essential for the function of other nuclear receptors. Using chromatin immunoprecipitation sequencing and mRNA profiling data generated from wild type and RXRα-null mouse livers, the current study identifies the bona-fide hepatic RXRα targets and biological pathways. In addition, based on binding and motif analysis, the molecular mechanism by which RXRα regulates hepatic genes is elucidated in a high-throughput manner. Principal Findings Close to 80% of hepatic expressed genes were bound by RXRα, while 16% were expressed in an RXRα-dependent manner. Motif analysis predicted direct repeat with a spacer of one nucleotide as the most prevalent RXRα binding site. Many of the 500 strongest binding motifs overlapped with the binding motif of specific protein 1. Biological functional analysis of RXRα-dependent genes revealed that hepatic RXRα deficiency mainly resulted in up-regulation of steroid and cholesterol biosynthesis-related genes and down-regulation of translation- as well as anti-apoptosis-related genes. Furthermore, RXRα bound to many genes that encode nuclear receptors and their cofactors suggesting the central role of RXRα in regulating nuclear receptor-mediated pathways. Conclusions This study establishes the relationship between RXRα DNA binding and hepatic gene expression. RXRα binds extensively to the mouse genome. However, DNA binding does not necessarily affect the basal mRNA level. In addition to metabolism, RXRα dictates the expression of genes that regulate RNA processing, translation, and protein folding illustrating the novel roles of hepatic RXRα in post-transcriptional regulation.This work was supported by the National Institutes of Health (DK092100 and CA053596 to YYW). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

ContiFormer: Continuous-Time Transformer for Irregular Time Series Modeling

Modeling continuous-time dynamics on irregular time series is critical to account for data evolution and correlations that occur continuously. Traditional methods including recurrent neural networks or Transformer models leverage inductive bias via powerful neural architectures to capture complex patterns. However, due to their discrete characteristic, they have limitations in generalizing to continuous-time data paradigms. Though neural ordinary differential equations (Neural ODEs) and their variants have shown promising results in dealing with irregular time series, they often fail to capture the intricate correlations within these sequences. It is challenging yet demanding to concurrently model the relationship between input data points and capture the dynamic changes of the continuous-time system. To tackle this problem, we propose ContiFormer that extends the relation modeling of vanilla Transformer to the continuous-time domain, which explicitly incorporates the modeling abilities of continuous dynamics of Neural ODEs with the attention mechanism of Transformers. We mathematically characterize the expressive power of ContiFormer and illustrate that, by curated designs of function hypothesis, many Transformer variants specialized in irregular time series modeling can be covered as a special case of ContiFormer. A wide range of experiments on both synthetic and real-world datasets have illustrated the superior modeling capacities and prediction performance of ContiFormer on irregular time series data. The project link is https://seqml.github.io/contiformer/.Comment: Neurips 2023 Poste