Abstract Understanding user perceptions of interacting with the virtual world is one of the research focuses in recent years, given the rapid proliferation of virtual reality (VR) and driven to establish the metaverse. Users can generate a familiar connection between their bodies and the virtual world by being embodied in virtual hands, and hand representations can induce users’ embodiment in VR. The sense of embodiment represents the cognitive awareness of one's manifestation and includes three subcomponents: the sense of body ownership, agency and self-location. There is insufficient evidence in the literature about the effects of hand designs on the embodiment, especially based on studying its three subcomponents. This study investigates how virtual hand designs with five realism levels influence the three subcomponents of embodiment in VR. This research employs a self-report questionnaire commonly used in the literature to assess embodiment and evaluates agency and self-location by introducing implicit methods (intentional binding and proprioceptive measurement) derived from psychology. Besides, the objective data of eye tracking is used to explore the connection between embodiment and hand designs, and classifying participants’ eye tracking data to help analyze the link between embodiment and user attention. Overall, this research makes a major contribution through a systematic exploration of users’ embodied experience in VR and offers important evidence of the effects of virtual hand designs on body ownership, agency, and self-location, respectively. In addition, this study provides a valuable reference for further investigation of embodiment through implicit and objective methods, and practical design recommendations for virtual hand design in VR applications. 

Understanding the effects of hand design on embodiment in virtual reality

Abstract Understanding user perceptions of interacting with the virtual world is one of the research focuses in recent years, given the rapid proliferation of virtual reality (VR) and driven to establish the metaverse. Users can generate a familiar connection between their bodies and the virtual world by being embodied in virtual hands, and hand representations can induce users’ embodiment in VR. The sense of embodiment represents the cognitive awareness of one's manifestation and includes three subcomponents: the sense of body ownership, agency and self-location. There is insufficient evidence in the literature about the effects of hand designs on the embodiment, especially based on studying its three subcomponents. This study investigates how virtual hand designs with five realism levels influence the three subcomponents of embodiment in VR. This research employs a self-report questionnaire commonly used in the literature to assess embodiment and evaluates agency and self-location by introducing implicit methods (intentional binding and proprioceptive measurement) derived from psychology. Besides, the objective data of eye tracking is used to explore the connection between embodiment and hand designs, and classifying participants’ eye tracking data to help analyze the link between embodiment and user attention. Overall, this research makes a major contribution through a systematic exploration of users’ embodied experience in VR and offers important evidence of the effects of virtual hand designs on body ownership, agency, and self-location, respectively. In addition, this study provides a valuable reference for further investigation of embodiment through implicit and objective methods, and practical design recommendations for virtual hand design in VR applications.

Abstract Computer-aided design (CAD) plays an essential role in creative idea generation on 2D screens during the design process. In most CAD scenarios, virtual object translation is an essential operation, and it is commonly used when designers simulate their innovative solutions. The degrees of freedom (DoF) of virtual object translation modes have been found to directly impact users’ task performance and psychological aspects in simulated environments. Little is known in the existing literature about the sense of agency (SoA), which is a critical psychological aspect emphasizing the feeling of control, in translation modes on 2D screens during the design process. Hence, this study aims to assess users’ SoA in virtual object translation modes on mouse-based, touch-based, and handheld augmented reality (AR) interfaces through subjective and objective measures, such as self-report, task performance, and electroencephalogram (EEG) data. Based on our findings in this study, users perceived a greater feeling of control in 1DoF translation mode, which may help them come up with more creative ideas, than in 3DoF translation mode in the design process; additionally, the handheld AR interface offers less control feel, which may have a negative impact on design quality and creativity, as compared with mouse- and touch-based interfaces. This research contributes to the current literature by analyzing the association between virtual object translation modes and SoA, as well as the relationship between different 2D interfaces and SoA in CAD. As a result of these findings, we propose several design considerations for virtual object translation on 2D screens, which may enable designers to perceive a desirable feeling of control during the design process. 

Evaluating the feeling of control in virtual object translation on 2D interfaces

Cryptocurrency, as a typical application scene of blockchain, has attracted broad interests from both industrial and academic communities. With its rapid development, the cryptocurrency transaction network embedding (CTNE) has become a hot topic. It embeds transaction nodes into low-dimensional feature space while effectively maintaining a network structure, thereby discovering desired patterns demonstrating involved users' normal and abnormal behaviors. Based on a wide investigation into the state-of-the-art CTNE, this survey has made the following efforts: 1) categorizing recent progress of CTNE methods, 2) summarizing the publicly available cryptocurrency transaction network datasets, 3) evaluating several widely-adopted methods to show their performance in several typical evaluation protocols, and 4) discussing the future trends of CTNE. By doing so, it strives to provide a systematic and comprehensive overview of existing CTNE methods from static to dynamic perspectives, thereby promoting further research into this emerging and important field.

Cryptocurrency Transaction Network Embedding From Static and Dynamic Perspectives: An Overview

Abstract Computer-aided design (CAD) plays an essential role in creative idea generation on 2D screens during the design process. In most CAD scenarios, virtual object translation is an essential operation, and it is commonly used when designers simulate their innovative solutions. The degrees of freedom (DoF) of virtual object translation modes have been found to directly impact users’ task performance and psychological aspects in simulated environments. Little is known in the existing literature about the sense of agency (SoA), which is a critical psychological aspect emphasizing the feeling of control, in translation modes on 2D screens during the design process. Hence, this study aims to assess users’ SoA in virtual object translation modes on mouse-based, touch-based, and handheld augmented reality (AR) interfaces through subjective and objective measures, such as self-report, task performance, and electroencephalogram (EEG) data. Based on our findings in this study, users perceived a greater feeling of control in 1DoF translation mode, which may help them come up with more creative ideas, than in 3DoF translation mode in the design process; additionally, the handheld AR interface offers less control feel, which may have a negative impact on design quality and creativity, as compared with mouse- and touch-based interfaces. This research contributes to the current literature by analyzing the association between virtual object translation modes and SoA, as well as the relationship between different 2D interfaces and SoA in CAD. As a result of these findings, we propose several design considerations for virtual object translation on 2D screens, which may enable designers to perceive a desirable feeling of control during the design process.

Survey/review study
Deep Common Spatial Pattern Based Motor Imagery Classification with Improved Objective Function

Nanxi Yu 1,2, Rui Yang 1, and Mengjie Huang 1,*


1 School of Electrical Engineering, Electronics & Computer Science, University of Liverpool, Liverpool, L69 3BX, United Kingdom
2 Department of Biostatistics, Graduate School of Arts and Sciences, Yale University, New Haven, CT 06511, United States
* Correspondence: Mengjie.Huang@liverpool.ac.uk
 
 
Received: 12 October 2022
Accepted: 28 November 2022
Published: 22 December 2022
 

Abstract: Common spatial pattern (CSP) technique has been very popular in terms of electroencephalogram (EEG) features extraction in motor imagery (MI)-based brain-computer interface (BCI). Through the simultaneous diagonalization of the covariance matrices, CSP intends to transform data into another mapping with data of different categories having maximal differences in their measures of dispersion. This paper shows the objective function realized by original CSP method could be inaccurate by regularizing the estimated spatial covariance matrix from EEG data by trace, leading to some flaws in the features to be extracted. In order to deal with this problem, a novel deep CSP (DCSP) model with optimal objective function is proposed in this paper. The benefits of the proposed DCSP method over original CSP method are verified with experiments on two EEG based MI datasets where the classification accuracy is effectively improved.

/pdf/deep-common-spatial-pattern-based-motor-imagery-m1vdryma.pdf

Deep Common Spatial Pattern based Motor Imagery Classification with Improved Objective Function

DNA double‐strand breaks can seriously damage the genetic information that organisms depend on for survival and reproduction. Therefore, cells require a robust DNA damage response mechanism to repair the damaged DNA. Homologous recombination (HR) allows error‐free repair, which is key to maintaining genomic integrity. Long non‐coding RNAs (lncRNAs) are RNA molecules that are longer than 200 nucleotides. In recent years, a number of studies have found that lncRNAs can act as regulators of gene expression and DNA damage response mechanisms, including HR repair. Moreover, they have significant effects on the occurrence, development, invasion and metastasis of tumor cells, as well as the sensitivity of tumors to radiotherapy and chemotherapy. These studies have therefore begun to expose the great potential of lncRNAs for clinical applications. In this review, we focus on the regulatory roles of lncRNAs in HR repair.

The role and mechanism of long non‐coding RNAs in homologous recombination repair of radiation‐induced DNA damage

BACKGROUND
DNA-damaging agents, including radiation and platinum-based chemotherapy, are indispensable treatments for non-small cell lung cancer (NSCLC) patients. However, cancer cells tend to be resistant to both radiation and chemotherapy, thus resulting in treatment failure or recurrence. The purpose of this study was to explore the effect and mechanism of long non-coding RNA (lncRNA) PANDAR (promoter of CDKN1A antisense DNA damage-activated RNA) on NSCLC sensitivity to radiation and chemotherapy.


METHODS
Cell counting kit (CCK-8), colony formation and flow cytometry were respectively performed to determine the cell cycle and apoptosis of NSCLC cells treated with γ-ray radiation and cisplatin. The extent of DNA damage was evaluated using a comet assay and immunofluorescence staining against γH2AX. In addition, we explored the role of PANDAR in DNA damage response pathways through western blot analysis. Finally, a nude mouse subcutaneous xenograft model was established to assess the sensitivity to radiation and chemotherapy in vivo.


RESULTS
In cell experiments, PANDAR knockdown can increase the sensitivity of NSCLC cells to radiation and cisplatin. The CCK-8 results showed that cell viability was significantly increased in the overexpression group after radiation and cisplatin treatments. The overexpression group also showed more colonies, less apoptosis and DNA damage, and G2/M phase arrest was aggravated to provide the time necessary for DNA repair. Contrary to PANDAR overexpression, the trends were reversed in the PANDAR knockdown group. Furthermore, PANDAR knockdown inhibited radiation and cisplatin-activated phosphorylation levels of ATR and CHK1 in NSCLC cells. Finally, our in vivo model showed that targeting PANDAR significantly sensitized NSCLC to radiation and cisplatin.


CONCLUSION
Our study showed that PANDAR knockdown promoted sensitivity to radiation and cisplatin in NSCLC by regulating the ATR/CHK1 pathway, thus providing a novel understanding as well as a therapeutic target for NSCLC treatment. In NSCLC cells, lncRNA PANDAR negatively regulates sensitivity to radiation and cisplatin. PANDAR can promote the repair of radiation and cisplatin-induced DNA damage and activation of the G2/M checkpoint through the ATR/CHK1 pathway. PANDAR knockdown results in defects in DNA damage repair accompanied by more cell apoptosis.

Long non-coding RNA PANDAR promoted radiation and cisplatin-induced DNA damage repair through ATR/CHK1 in NSCLC.

Many current microRNA (miRNA) expression datasets for renal cell carcinoma (RCC) often show inconsistent analysis results, so a shift to comprehensive analysis of multiple datasets can effectively accelerate molecular screening for precision medicine and translational medicine research. MicroRNA (miR)-188-5p is a clinically noteworthy miRNA whose aberrant expression was previously observed in a variety of cancers, but its role in RCC is unclear. In this study, we undertook a comprehensive analysis of four RCC miRNA expression datasets and validated the results using The Cancer Genome Atlas (TCGA) dataset and a cohort of collected clinical samples. Fifteen miRNAs were identified as potential diagnostic markers by the analysis of four RCC miRNAs datasets. Analysis of the TCGA kidney renal clear cell carcinoma dataset showed significantly shorter survival in RCC patients with reduced miR-188-5p expression levels, and our collection of RCC clinical samples showed low miR-188-5p expression in the tumors. Overexpression of miR-188-5p in Caki-1 and 786-O cells inhibited cell growth, colony formation, invasion, and migration. In contrast, miR-188-5p inhibitors reversed these cell phenotypes. We identified a binding site for miR-188-5p in the 3'-UTR region of myristoylated alanine-rich C-kinase substrate (MARCKS) mRNA and demonstrated an interaction between these two molecules. Quantitative RT-PCR and western blot analysis revealed that miR-188-5p could regulate the AKT/mTOR signaling pathway through MARCKS. Mouse transplantation tumor assay indicated that miR-188-5p reduced the tumorigenicity of RCC in vivo. MicroRNA-188-5p could be a valuable new molecule for RCC diagnosis and prognosis.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cas.15832

Integrated analysis identifies microRNA-188-5p as a suppressor of AKT/mTOR pathway in renal cancer.

Abstract Background Radiotherapy is an important treatment for lung cancer, mainly by triggering DNA double-strand breaks to induce cell death. Blocking DNA damage repair can increase the radiosensitivity of tumor cells. Recent studies have identified long noncoding RNAs as key regulators in DNA damage repair. The lncRNA ANRIL was previously shown to be involved in homologous recombination (HR) repair, but its specific mechanism has not been fully elucidated. Methods The downstream interacting miRNAs of ANRIL were predicted according to miRanda software. Fluorescence quantitative PCR was used to detect the expression levels of ANRIL and candidate miRNAs. Clone formation experiment and cell viability assays detect cell viability after ionizing radiation. Apoptosis assay was used to detect the apoptosis of cells after 8 h of ionizing radiation. Western blot analysis and immunofluorescence assays verified the protein expression levels of the downstream target molecule PARP1 of miR-7-5p and key molecules in the HR pathway. Fluorescent reporter gene experiments were used to verify the interaction between ANRIL and miR-7-5p and between miR-7-5p and PARP1. Results Bioinformatics analysis and qPCR validation suggested that miR-7-5p might be a downstream molecule of ANRIL. The expression of miR-7-5p was up-regulated after knockdown of ANRIL, and the expression of miR-7-5p was down-regulated after overexpression of ANRIL. Meanwhile, there was a negative correlation between ANRIL and miR-7-5p expression changes before and after ionizing radiation. The luciferase reporter gene assay confirmed the existence of ANRIL binding site with miR-7-5p, and found that transfection of miR-7-5p inhibitor can reduce the radiation sensitivity of ANRIL-KD cells. A downstream target molecule of miR-7-5p related to HR repair, PARP1, was screened through website prediction. Subsequently, it was confirmed by Western blot and luciferase reporter assays that miR-7-5p could down-regulate the expression of PARP1, and there was a miR-7-5p binding site on the 3'UTR of PARP1 mRNA. This suggests that ANRIL may act as a competitive endogenous RNA to bind miR-7-5p and upregulate the expression of PARP1. Western blot and immunofluorescence staining were used to detect the expression changes of HR repair factors in ANRIL-KD cells after ionizing radiation, and it was found that knockdown of ANRIL can inhibit the expression of PARP1, BRCA1 and Rad51, hinder radiation-induced HR repair, and eventually result in resensitizing ANRIL-KD cells to ionizing radiation. Conclusions Our findings provide evidence that ANRIL targets the miR-7-5p/PARP1 axis to exert its regulatory effect on HR repair, suggesting that altering ANRIL expression may be a promising strategy to overcome radiation resistance. 

/pdf/lncrna-anril-promotes-hr-repair-through-regulating-parp1-1elshw78.pdf

Nanxi Yu

Papers

Deep Common Spatial Pattern based Motor Imagery Classification with Improved Objective Function

The role and mechanism of long non‐coding RNAs in homologous recombination repair of radiation‐induced DNA damage

Long non-coding RNA PANDAR promoted radiation and cisplatin-induced DNA damage repair through ATR/CHK1 in NSCLC.

Integrated analysis identifies microRNA-188-5p as a suppressor of AKT/mTOR pathway in renal cancer.

LncRNA ANRIL promotes HR repair through regulating PARP1 expression by sponging miR-7-5p in lung cancer