Bioinformatics analysis based on crucial genes of endothelial cells in rheumatoid

Objectives: Synovial neovascularization is an early and remarkable event that promotes the development of rheumatoid arthritis (RA) synovial hyperplasia. This study aimed to find potential diagnostic markers and molecular therapeutic targets for RA at the mRNA molecular level.Method: We download the expression profile dataset GSE46687 from the gene expression ontology (GEO) microarray, and used R software to screen out the differentially expressed genes between the normal group and the disease group. Then we performed functional enrichment analysis, used the STRING database to construct a protein-protein interaction (PPI) network, and identify candidate crucial genes, infiltration of the immune cells and targeted molecular drug.Results: Rheumatoid arthritis datasets included 113 differentially expressed genes (DEGs) including 104 upregulated and 9 downregulated DEGs. The enrichment analysis of genes shows that the differential genes are mainly enriched in condensed chromosomes, ribosomal subunits, and oxidative phosphorylation. Through PPI network analysis, seven crucial genes were identified: RPS13, RPL34, RPS29, RPL35, SEC61G, RPL39L, and RPL37A. Finally, we find the potential compound drug for RA.Conclusion: Through this method, the pathogenesis of RA endothelial cells was further explained. It provided new therapeutic targets, but the relationship between these genes and RA needs further research to be validated in the future

Topology Architecture and Routing Algorithms of Octagon-Connected Torus Interconnection Network

Two important issues in the design of interconnection networks for massively parallel computers are scalability and small diameter. A new interconnection network topology, called octagon-connected torus (OCT), is proposed. The OCT network combines the small diameter of octagon topology and the scalability of torus topology. The OCT network has better properties, such as small diameter, regular, symmetry and the scalability. The nodes of the OCT network adopt the Johnson coding scheme which can make routing algorithms simple and efficient. Both unicasting and broadcasting routing algorithms are designed for the OCT network, and it is based on the Johnson coding scheme. A detailed analysis shows that the OCT network is a better interconnection network in the properties of topology and the performance of communication

Coronal Sources and In Situ Properties of the Solar Winds Sampled by ACE During 1999 - 2008

We identify the coronal sources of the solar winds sampled by the ACE spacecraft during 1999-2008, and examine the in situ solar wind properties as a function of wind sources. The standard two-step mapping technique is adopted to establish the photospheric footpoints of the magnetic flux tubes along which the ACE winds flow. The footpoints are then placed in the context of EIT 284~\AA\ images and photospheric magnetograms, allowing us to categorize the sources into four groups: coronal holes (CHs), active regions (ARs), the quiet Sun (QS), and "Undefined". This practice also enables us to establish the response to solar activity of the fractions occupied by each kind of solar winds, and of their speeds and O$^{7+}$/O$^{6+}$ ratios measured in situ. We find that during the maximum phase, the majority of ACE winds originate from ARs. During the declining phase, CHs and ARs are equally important contributors to the ACE solar winds. The QS contribution increases with decreasing solar activity, and maximizes in the minimum phase when QS appear to be the primary supplier of the ACE winds. With decreasing activity, the winds from all sources tend to become cooler, as represented by the increasingly low O$^{7+}$/O$^{6+}$ ratios. On the other hand, during each activity phase, the AR winds tend to be the slowest and associated with the highest O$^{7+}$/O$^{6+}$ ratios, and the CH winds correspond to the other extreme, with the QS winds lying in between. Applying the same analysis method to the slow winds only, here defined as the winds with speeds lower than 500 km s$^{-1}$, we find basically the same overall behavior, as far as the contributions of individual groups of sources are concerned. This statistical study indicates that QS regions are an important source of the solar wind during the minimum phase.Comment: 24 pages, 7 figures, accepted for publication in Solar Physic

Parallel Implementation of OpenVX Feature Extraction Functions in Programmable Processing Architecture

Aiming at the mass computing and slow speed of serial structure calculation of digital image processing, parallel implementation of underlying feature extraction kernel functions in the latest open source OpenVX specification 1.3 is completed, and the verification is carried out with the self-designed OpenVX programmable parallel processor. In the underlying feature extraction of the image, the basic pixel processing function Color Convert, the local image processing functions Gaussian Filter and Median Filter of OpenVX specification 1.3 are selected for filtering and smoothing. Harris Corners and Canny Edge Detector are selected for feature extraction. By dividing the complex nodes with large amount of computation into several simple nodes, different graph execution models are constructed and mapped on the OpenVX parallel processor to realize image edge detection and feature point extraction respectively. Verilog is used to design the hardware circuit, and the FPGA chip xcvu440-flga-2892-2-e of Xilinx has comprehensively verified that, compared with the serial mapping structure, the parallel acceleration ratio of the selected kernel function on the OpenVX programmable parallel processor can be up to 14.269. Experimental results show that the kernel functions in OpenVX specification 1.3, especially the complex kernel functions, can achieve expected acceleration effect in this parallel processing structure, and the speedup ratio of parallel and serial structures increases linearly

Sources of quasi-periodic propagating disturbances above a solar polar coronal hole

Quasi-periodic propagating disturbances (PDs) are ubiquitous in polar coronal holes on the Sun. It remains unclear as to what generates PDs. In this work, we investigate how the PDs are generated in the solar atmosphere by analyzing a fourhour dataset taken by the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO). We find convincing evidence that spicular activities in the solar transition region as seen in the AIA 304 {\AA} passband are responsible for PDs in the corona as revealed in the AIA 171 {\AA} images. We conclude that spicules are an important source that triggers coronal PDs.Comment: Accepted for publication in ApJ

Parallel Architecture Design for OpenVX Kernel Image Processing Functions

Although the traditional programmable processors are highly flexible, their processing speed and perfor-mance are inferior to the application specific integrated circuit (ASIC). Image processing is often a diverse, intensive and repetitive operation, so the processor must balance speed, performance and flexibility. OpenVX is an open source standard for preprocessing or auxiliary processing of image processing, graph computing and deep learning applications. Aiming at the kernel visual function library of OpenVX 1.3 standard, this paper designs and implements a programmable and extensible OpenVX parallel processor. The architecture adopts an application specific instruction processor (ASIP). After analyzing and comparing the topological characteristics of various interconnection networks, the backbone of the ASIP chooses the hierarchically cross-connected Mesh+ (HCCM+) with outstanding performance, and processing element (PE) is set at network nodes. PE array is constructed to support dynamic configuration, and a parallel processor is designed to realize programmable image processing based on efficient routing and com-munication. The proposed architecture is suitable for data parallel computing and emerging graph computing. The two computing modes can be configured separately or mixed. The kernel visual function and graph computing model are mapped to the parallel processor respectively to verify the two modes and compare the image processing speed under different PE numbers. The results show that OpenVX parallel processor can complete the mapping and linear speedup of kernel functions and high complexity graph calculation model. The average speedup of scheduling 16 PEs to various functions is approximately 15.0375. When implemented on an FPGA board with a 20 nm XCVU440 device, the prototype can run at a frequency of 125 MHz

LLM-Adapters: An Adapter Family for Parameter-Efficient Fine-Tuning of Large Language Models

The success of large language models (LLMs), like GPT-4 and ChatGPT, has led to the development of numerous cost-effective and accessible alternatives that are created by finetuning open-access LLMs with task-specific data (e.g., ChatDoctor) or instruction data (e.g., Alpaca). Among the various fine-tuning methods, adapter-based parameter-efficient fine-tuning (PEFT) is undoubtedly one of the most attractive topics, as it only requires fine-tuning a few external parameters instead of the entire LLMs while achieving comparable or even better performance. To enable further research on PEFT methods of LLMs, this paper presents LLM-Adapters, an easy-to-use framework that integrates various adapters into LLMs and can execute these adapter-based PEFT methods of LLMs for different tasks. The framework includes state-of-the-art open-access LLMs such as LLaMA, BLOOM, and GPT-J, as well as widely used adapters such as Series adapters, Parallel adapter, Prompt-based learning and Reparametrization-based methods. Moreover, we conduct extensive empirical studies on the impact of adapter types, placement locations, and hyper-parameters to the best design for each adapter-based methods. We evaluate the effectiveness of the adapters on fourteen datasets from two different reasoning tasks, Arithmetic Reasoning and Commonsense Reasoning. The results demonstrate that using adapter-based PEFT in smaller-scale LLMs (7B) with few extra trainable parameters yields comparable, and in some cases superior, performance to powerful LLMs (175B) in zero-shot inference on both reasoning tasks.Comment: EMNLP 2023. The code of our framework can be found at https://github.com/AGI-Edgerunners/LLM-Adapters. We will keep all of the code open-source and continue to update the framework with new adapters, LLMs, and task

Nitidine Chloride Alleviates Inflammation and Cellular Senescence in Murine Osteoarthritis Through Scavenging ROS

Osteoarthritis (OA) is one of the most common chronic musculoskeletal disorder worldwide, representing a major source of disability, pain and socioeconomic burden. Yet the effective pharmaceutical treatments applied in the clinical works are merely symptomatic management with uncertainty around their long-term safety and efficacy, namely no drugs currently are capable of modulating the biological progression of OA. Here, we identified the potent anti-inflammatory as well as anti-oxidative properties of Nitidine Chloride (NitC), a bioactive phytochemical alkaloid extracted from natural herbs, in IL-1β-treated rat articular chondrocytes (RACs), LPS-stimulated RAW 264.7 and rat osteoarthritic models in vivo. We demonstrated NitC remarkably inhibited the production of inflammatory mediators including COX2 and iNOS, suppressed the activation of MAPK and NF-κB cell signaling pathway and reduced the expression of extracellular matrix (ECM) degrading enzymes including MMP3, MMP9 and MMP13 in IL-1β-treated RACs. Several emerging bioinformatics tools were performed to predict the underlying mechanism, the result of which indicated the potential reactive oxygen species (ROS) clearance potential of NitC. Further, NitC exhibited its anti-oxidative potential through ameliorating cellular senescence in IL-1β-treated RACs and decreasing NLRP3 inflammasomes activation in LPS-stimulated RAW 264.7 via scavenging ROS. Additionally, X-ray, micro-CT and other experiments in vivo demonstrated that intra-articular injection of NitC significantly alleviated the cartilage erosion, ECM degradation and subchondral alterations in OA progression. In conclusion, the present study reported the potent anti-inflammatory and anti-oxidative potential of NitC in OA biological process, providing a promising therapeutic agent for OA management

MOF-Derived Robust and Synergetic Acid Sites Inducing C-N Bond Disruption for Energy-Efficient CO₂Desorption

Amine-based scrubbing technique is recognized as a promising method of capturing CO2 to alleviate climate change. However, the less stability and poor acidity of solid acid catalysts (SACs) limit their potential to further improve amine regeneration activity and reduce the energy penalty. To address these challenges, here, we introduce two-dimensional (2D) cobalt-nitrogen-doped carbon nanoflakes (Co-N-C NSs) driven by a layered metal-organic framework that work as SACs. The designed 2D Co-N-C SACs can exhibit promising stability, superhydrophilic surface, and acidity. Such 2D structure also contains well-confined Co-N4 Lewis acid sites and -OH Brønsted acid sites to have a synergetic effect on C-N bond disruption and significantly increase CO2 desorption rate by 281% and reduce the reaction temperatures to 88 °C, minimizing water evaporation by 20.3% and subsequent regeneration energy penalty by 71.7% compared to the noncatalysis.</p