cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25809004
title: Research progress on the relationship between AURKA and tumorigenesis: the neglected nuclear function of AURKA

description: AURKA is a threonine or serine kinase that needs to be activated by TPX2, Bora and other factors. AURKA is located on chromosome 20 and is amplified or overexpressed in many human cancers, such as breast cancer. AURKA regulates some basic cellular processes, and this regulation is realized <i>via</i> the phosphorylation of downstream substrates. AURKA can function in either the cytoplasm or the nucleus. It can promote the transcription and expression of oncogenes together with other transcription factors in the nucleus, including FoxM1, C-Myc, and NF-κB. In addition, it also sustains carcinogenic signaling, such as N-Myc and Wnt signaling. This article will focus on the role of AURKA in the nucleus and its carcinogenic characteristics that are independent of its kinase activity to provide a theoretical explanation for mechanisms of resistance to kinase inhibitors and a reference for future research on targeted inhibitors. AURKA plays an important role in the control of the proliferation, invasion, cell cycle regulation and self-renewal of cancer stem cells. Small molecule kinase inhibitors targeting AURKA have been developed, but the overall response rate of patients in clinical trials is not ideal, prompting us to pay attention to the non-kinase activity of AURKA. This review focuses on the nuclear function of AURKA and its oncogenic properties independent of kinase activity, demonstrating that the nuclear substrate of AURKA and the remote allosteric site of the kinase may be targets of anticancer therapy.
DOI: 10.6084/m9.figshare.25809004.v1
title: Research progress on the relationship between AURKA and tumorigenesis: the neglected nuclear function of AURKA

description: AURKA is a threonine or serine kinase that needs to be activated by TPX2, Bora and other factors. AURKA is located on chromosome 20 and is amplified or overexpressed in many human cancers, such as breast cancer. AURKA regulates some basic cellular processes, and this regulation is realized <i>via</i> the phosphorylation of downstream substrates. AURKA can function in either the cytoplasm or the nucleus. It can promote the transcription and expression of oncogenes together with other transcription factors in the nucleus, including FoxM1, C-Myc, and NF-κB. In addition, it also sustains carcinogenic signaling, such as N-Myc and Wnt signaling. This article will focus on the role of AURKA in the nucleus and its carcinogenic characteristics that are independent of its kinase activity to provide a theoretical explanation for mechanisms of resistance to kinase inhibitors and a reference for future research on targeted inhibitors. AURKA plays an important role in the control of the proliferation, invasion, cell cycle regulation and self-renewal of cancer stem cells. Small molecule kinase inhibitors targeting AURKA have been developed, but the overall response rate of patients in clinical trials is not ideal, prompting us to pay attention to the non-kinase activity of AURKA. This review focuses on the nuclear function of AURKA and its oncogenic properties independent of kinase activity, demonstrating that the nuclear substrate of AURKA and the remote allosteric site of the kinase may be targets of anticancer therapy.
DOI: 10.6084/m9.figshare.26779921
title: Humoral immunity and safety of respiratory virus vaccines in systemic lupus erythematosus population: a meta-analysis based on twenty-five observational studies

description: Systemic lupus erythematosus (SLE), an extensive autoimmune disorder, compromises viral resistance and alters immune responses post respiratory virus vaccines. This study aims to assess immune response levels and safety in SLE patients following respiratory virus vaccines. Extensive searches, until 1 March 2024, were conducted using PubMed, EMBASE, and Cochrane Library. Outcomes, encompassing seroconversion rate (SCR), antibody and IgG titers, neutralizing antibodies, anti-spike antibodies, anti-receptor binding domain (RBD) IgG, and adverse events, were appraised. Sixteen articles, comprising 25 observational studies, were included. SLE patients exhibited lower SCR (OR = 0.42, 95%CI: 0.26 to 0.69), antibody titers (SMD=-2.84, 95%CI: −3.36 to −1.61), and neutralizing antibodies (OR = 0.27, 95%CI: 0.13 to 0.56) compared to the healthy population post respiratory virus vaccines. Notably, differences were statistically insignificant for anti-RBD IgG (OR = 1.75, 95%CI: 0.10 to 29.42), IgG titers (SMD=-2.54, 95%CI: −5.57 to −0.49), anti-spike antibodies (OR = 0.35, 95%CI: 0.08 to 1.53), injection site discomfort (OR = 1.03, 95%CI: 0.52 to 2.06), fatigue (OR = 1.23, 95%CI: 0.74 to 2.03), fever (OR = 1.02, 95%CI: 0.64 to 1.63), localized reactions (OR = 0.69, 95%CI: 0.37 to 1.30), systemic reactions (OR = 1.00, 95%CI: 0.59 to 1.69), allergic reactions (OR = 5.11, 95%CI: 0.24 to 107.10), self-reported vaccination-related adverse events (OR = 1.61, 95%CI: 0.56 to 4.63), and disease flares after vaccination (OR = 1.00, 95%CI: 0.14 to 7.28). Despite the reduced immune response and host protection in SLE patients post-Corona Virus Disease 2019 (COVID-19) and influenza vaccines compared to the healthy population, safety profiles are comparable. Therefore, it is recommended that SLE patients receive COVID-19 and influenza viral vaccines to fortify their resistance.
DOI: 10.6084/m9.figshare.26779921.v1
title: Humoral immunity and safety of respiratory virus vaccines in systemic lupus erythematosus population: a meta-analysis based on twenty-five observational studies

description: Systemic lupus erythematosus (SLE), an extensive autoimmune disorder, compromises viral resistance and alters immune responses post respiratory virus vaccines. This study aims to assess immune response levels and safety in SLE patients following respiratory virus vaccines. Extensive searches, until 1 March 2024, were conducted using PubMed, EMBASE, and Cochrane Library. Outcomes, encompassing seroconversion rate (SCR), antibody and IgG titers, neutralizing antibodies, anti-spike antibodies, anti-receptor binding domain (RBD) IgG, and adverse events, were appraised. Sixteen articles, comprising 25 observational studies, were included. SLE patients exhibited lower SCR (OR = 0.42, 95%CI: 0.26 to 0.69), antibody titers (SMD=-2.84, 95%CI: −3.36 to −1.61), and neutralizing antibodies (OR = 0.27, 95%CI: 0.13 to 0.56) compared to the healthy population post respiratory virus vaccines. Notably, differences were statistically insignificant for anti-RBD IgG (OR = 1.75, 95%CI: 0.10 to 29.42), IgG titers (SMD=-2.54, 95%CI: −5.57 to −0.49), anti-spike antibodies (OR = 0.35, 95%CI: 0.08 to 1.53), injection site discomfort (OR = 1.03, 95%CI: 0.52 to 2.06), fatigue (OR = 1.23, 95%CI: 0.74 to 2.03), fever (OR = 1.02, 95%CI: 0.64 to 1.63), localized reactions (OR = 0.69, 95%CI: 0.37 to 1.30), systemic reactions (OR = 1.00, 95%CI: 0.59 to 1.69), allergic reactions (OR = 5.11, 95%CI: 0.24 to 107.10), self-reported vaccination-related adverse events (OR = 1.61, 95%CI: 0.56 to 4.63), and disease flares after vaccination (OR = 1.00, 95%CI: 0.14 to 7.28). Despite the reduced immune response and host protection in SLE patients post-Corona Virus Disease 2019 (COVID-19) and influenza vaccines compared to the healthy population, safety profiles are comparable. Therefore, it is recommended that SLE patients receive COVID-19 and influenza viral vaccines to fortify their resistance.
DOI: 10.6084/m9.figshare.27655581
title: Integrating transcriptomic data and digital pathology for NRG-based prediction of prognosis and therapy response in gastric cancer

description: Cancer is characterized by its ability to resist cell death, and emerging evidence suggests a potential correlation between non-apoptotic regulated cell death (RCD), tumor progression, and therapy response. However, the prognostic significance of non-apoptotic RCD-related genes (NRGs) and their relationships with immune response in gastric cancer (GC) remain unclear. In this study, RNA-seq gene expression and clinical information of GC patients were acquired from The Cancer Genome Atlas and the Gene Expression Omnibus databases. Cox and LASSO regression analyses were used to construct the NRG signature. Moreover, we developed a deep learning model based on ResNet50 to predict the NRG signature from digital pathology slides. The expression of signature hub genes was validated using real-time quantitative PCR and single-cell RNA sequencing data. We identified 13 NRGs as signature genes for predicting the prognosis of patients with GC. The high-risk group, characterized by higher NRG scores, demonstrated a shorter overall survival rate, increased immunosuppressive cell infiltration, and immune dysfunction. Moreover, associations were observed between the NRG signature and chemotherapeutic drug responsiveness, as well as immunotherapy effectiveness in GC patients. Furthermore, the deep learning model effectively stratified GC patients based on the NRG signature by leveraging morphological variances, showing promising results for the classification of GC patients. Validation experiments demonstrated that the expression level of SERPINE1 was significantly upregulated in GC, while the expression levels of GPX3 and APOD were significantly downregulated. The NRG signature and its deep learning model have significant clinical implications, highlighting the importance of individualized treatment strategies based on GC subtyping. These findings provide valuable insights for guiding clinical decision-making and treatment approaches for GC.
DOI: 10.6084/m9.figshare.27655581.v1
title: Integrating transcriptomic data and digital pathology for NRG-based prediction of prognosis and therapy response in gastric cancer

description: Cancer is characterized by its ability to resist cell death, and emerging evidence suggests a potential correlation between non-apoptotic regulated cell death (RCD), tumor progression, and therapy response. However, the prognostic significance of non-apoptotic RCD-related genes (NRGs) and their relationships with immune response in gastric cancer (GC) remain unclear. In this study, RNA-seq gene expression and clinical information of GC patients were acquired from The Cancer Genome Atlas and the Gene Expression Omnibus databases. Cox and LASSO regression analyses were used to construct the NRG signature. Moreover, we developed a deep learning model based on ResNet50 to predict the NRG signature from digital pathology slides. The expression of signature hub genes was validated using real-time quantitative PCR and single-cell RNA sequencing data. We identified 13 NRGs as signature genes for predicting the prognosis of patients with GC. The high-risk group, characterized by higher NRG scores, demonstrated a shorter overall survival rate, increased immunosuppressive cell infiltration, and immune dysfunction. Moreover, associations were observed between the NRG signature and chemotherapeutic drug responsiveness, as well as immunotherapy effectiveness in GC patients. Furthermore, the deep learning model effectively stratified GC patients based on the NRG signature by leveraging morphological variances, showing promising results for the classification of GC patients. Validation experiments demonstrated that the expression level of SERPINE1 was significantly upregulated in GC, while the expression levels of GPX3 and APOD were significantly downregulated. The NRG signature and its deep learning model have significant clinical implications, highlighting the importance of individualized treatment strategies based on GC subtyping. These findings provide valuable insights for guiding clinical decision-making and treatment approaches for GC.
DOI: 10.6084/m9.figshare.26954481
title: Detection of genomic variants by genome sequencing in foetuses with central nervous system abnormalities

description: Clinical validity of genome sequencing (GS) (&gt;30×) has been preliminarily verified in the post-natal setting. This study is to investigate the potential utility of trio-GS as a prenatal test for diagnosis of central nervous system (CNS) anomalies. We performed trio-based GS on a prospective cohort of 17 foetuses with CNS abnormalities. Single nucleotide variation (SNV), small insertion and deletion (Indel), copy number variation (CNV), structural variant (SV), and regions with absence of heterozygosity (AOH) were analyzed and classified according to ACMG guidelines. Trio-GS identified diagnostic findings in 29.4% (5/17) of foetuses, with pathogenic variants found in <i>SON</i>, <i>L1CAM</i>, <i>KMT2D,</i> and <i>ASPM</i>. Corpus callosum (CC) and cavum septum pellucidum (CSP) abnormalities were the most frequent CNS abnormalities (47.1%, 8/17) with a diagnostic yield of 50%. A total of 29.4% (5/17) foetuses had variants of uncertain significance (VUS). Particularly, maternal uniparental disomy 16 and a <i>de novo</i> mosaic 4p12p11 duplication were simultaneously detected in one foetus with abnormal sulcus development. In addition, parentally inherited chromosomal inversions were identified in two foetuses. GS demonstrates its feasibility in providing genetic diagnosis for foetal CNS abnormalities and shows the potential to expand the application to foetuses with other ultrasound anomalies in prenatal diagnosis.
DOI: 10.6084/m9.figshare.26954481.v1
title: Detection of genomic variants by genome sequencing in foetuses with central nervous system abnormalities

description: Clinical validity of genome sequencing (GS) (&gt;30×) has been preliminarily verified in the post-natal setting. This study is to investigate the potential utility of trio-GS as a prenatal test for diagnosis of central nervous system (CNS) anomalies. We performed trio-based GS on a prospective cohort of 17 foetuses with CNS abnormalities. Single nucleotide variation (SNV), small insertion and deletion (Indel), copy number variation (CNV), structural variant (SV), and regions with absence of heterozygosity (AOH) were analyzed and classified according to ACMG guidelines. Trio-GS identified diagnostic findings in 29.4% (5/17) of foetuses, with pathogenic variants found in <i>SON</i>, <i>L1CAM</i>, <i>KMT2D,</i> and <i>ASPM</i>. Corpus callosum (CC) and cavum septum pellucidum (CSP) abnormalities were the most frequent CNS abnormalities (47.1%, 8/17) with a diagnostic yield of 50%. A total of 29.4% (5/17) foetuses had variants of uncertain significance (VUS). Particularly, maternal uniparental disomy 16 and a <i>de novo</i> mosaic 4p12p11 duplication were simultaneously detected in one foetus with abnormal sulcus development. In addition, parentally inherited chromosomal inversions were identified in two foetuses. GS demonstrates its feasibility in providing genetic diagnosis for foetal CNS abnormalities and shows the potential to expand the application to foetuses with other ultrasound anomalies in prenatal diagnosis.
DOI: 10.6084/m9.figshare.27289597
title: The Masquelet technique triggers the formation of a network involving LncRNA, circRNA, miRNA, and mRNA during bone repair

description: The ceRNA network, which is competitive endogenous RNA, uncovers a fresh mechanism of RNA interaction and holds significant importance in diverse biological processes. The aim of this study is to investigate the molecular process of induced membrane (IM) formation in bone defects using the Masquelet’s induced membrane technique (MIMT), in order to offer novel insights and a theoretical foundation for enhancing the treatment of bone defects with MIMT. In this work, we identified differentially expressed mRNAs (DEGs), lncRNAs (DELs), circRNAs (DECs), and miRNAs (DEMs). To explore the primary functions of the shared DEGs, we utilized Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Next, predictions were made for lncRNA-miRNA and miRNA-mRNA interactions, and the Cytoscape software was utilized to construct the regulatory network for ceRNA. By integrating GO and KEGG enrichment analysis, a total of 385 differentially expressed genes (DEGs) were discovered in the samples from the MIMT-treated group. Additionally, after re-annotating the probes and intersecting two sets of differently expressed miRNAs, 1304 differentially expressed lncRNAs (DELs) and 23 differentially expressed circRNAs (DECs) were identified. Furthermore, 13 differentially expressed miRNAs (DEMs) were obtained. Moreover, utilizing the anticipated objectives of DEMs, we acquired 1203 pairs of lncRNA-miRNA-mRNA interactors (comprising 24 lncRNAs, 10 miRNAs, and 115 mRNAs) and 250 pairs of circRNA-miRNA-mRNA interactions (comprising 7 circRNAs, 9 miRNAs, and 115 mRNAs). CEBPA, DGAT2, CDKN1A, PLIN2, and CIDEC were identified as the five hub proteins in the PPI network. LncRNA/circRNA-hsa-miR-671-5p could potentially regulate the primary central protein, CEBPA. In this study, we described the potential regulatory mechanism of the MIMT in treating bone defects. We proposed a new lncRNA–miRNA–mRNA ceRNA network that could help further explore the molecular mechanisms of bone repair.
DOI: 10.6084/m9.figshare.27289597.v1
title: The Masquelet technique triggers the formation of a network involving LncRNA, circRNA, miRNA, and mRNA during bone repair

description: The ceRNA network, which is competitive endogenous RNA, uncovers a fresh mechanism of RNA interaction and holds significant importance in diverse biological processes. The aim of this study is to investigate the molecular process of induced membrane (IM) formation in bone defects using the Masquelet’s induced membrane technique (MIMT), in order to offer novel insights and a theoretical foundation for enhancing the treatment of bone defects with MIMT. In this work, we identified differentially expressed mRNAs (DEGs), lncRNAs (DELs), circRNAs (DECs), and miRNAs (DEMs). To explore the primary functions of the shared DEGs, we utilized Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Next, predictions were made for lncRNA-miRNA and miRNA-mRNA interactions, and the Cytoscape software was utilized to construct the regulatory network for ceRNA. By integrating GO and KEGG enrichment analysis, a total of 385 differentially expressed genes (DEGs) were discovered in the samples from the MIMT-treated group. Additionally, after re-annotating the probes and intersecting two sets of differently expressed miRNAs, 1304 differentially expressed lncRNAs (DELs) and 23 differentially expressed circRNAs (DECs) were identified. Furthermore, 13 differentially expressed miRNAs (DEMs) were obtained. Moreover, utilizing the anticipated objectives of DEMs, we acquired 1203 pairs of lncRNA-miRNA-mRNA interactors (comprising 24 lncRNAs, 10 miRNAs, and 115 mRNAs) and 250 pairs of circRNA-miRNA-mRNA interactions (comprising 7 circRNAs, 9 miRNAs, and 115 mRNAs). CEBPA, DGAT2, CDKN1A, PLIN2, and CIDEC were identified as the five hub proteins in the PPI network. LncRNA/circRNA-hsa-miR-671-5p could potentially regulate the primary central protein, CEBPA. In this study, we described the potential regulatory mechanism of the MIMT in treating bone defects. We proposed a new lncRNA–miRNA–mRNA ceRNA network that could help further explore the molecular mechanisms of bone repair.
DOI: 10.6084/m9.figshare.27309116
title: Informing factors and outcomes of self-assessment practices in medical education: a systematic review

description: Self-assessment (SA) is increasingly recognized not only as an assessment method but also as a vital learning activity that enables learners to identify their strengths and limitations, fostering a crucial skill for lifelong learning. Despite its acknowledged significance, there remains a gap in understanding SA <i>for</i> and <i>as</i> learning, rather than merely <i>of</i> learning. This review, therefore, explores two primary questions: (1) What factors inform the implementation of medical students’ SA practices? (2) How does SA practices contribute to various educational outcomes? A systematic review was conducted across five databases, employing a combination of keywords pertinent to SA and medical education. Our selection criteria deliberately excluded articles that solely focused on the accuracy of SA or used SA exclusively as a measure for other outcome variables. As a result, 39 studies met our inclusion criteria and were analyzed for this review. Qualitative narrative synthesis was used to summarize the informing factors. Furthermore, Kirkpatrick’s model was employed to categorize and summarize the effects of SA activities across various educational outcome levels, including reactions, learning, and behavioral changes. Our review reveals that key factors influencing students’ SA includes feedback from various stakeholders, peer assessment, the format of SA, and both learner and teacher training. Among the 39 studies examined, the majority demonstrated positive effects of SA on aspects such as attitudes and skills. However, a minority found no significant associations, with these outcomes frequently linked to contextual variables and how SA was implemented. Our review does not focus on SA accuracy or its role as an assessment method; instead it delves into the role of SA as an integral learning practice. We explored its influencing factors and its impact across various outcomes. The findings indicate that for SA to effectively enhance student learning outcomes, it must be implemented with ample support, clear guidelines, and within contexts that encourage feedback and reflection.
DOI: 10.6084/m9.figshare.27309116.v1
title: Informing factors and outcomes of self-assessment practices in medical education: a systematic review

description: Self-assessment (SA) is increasingly recognized not only as an assessment method but also as a vital learning activity that enables learners to identify their strengths and limitations, fostering a crucial skill for lifelong learning. Despite its acknowledged significance, there remains a gap in understanding SA <i>for</i> and <i>as</i> learning, rather than merely <i>of</i> learning. This review, therefore, explores two primary questions: (1) What factors inform the implementation of medical students’ SA practices? (2) How does SA practices contribute to various educational outcomes? A systematic review was conducted across five databases, employing a combination of keywords pertinent to SA and medical education. Our selection criteria deliberately excluded articles that solely focused on the accuracy of SA or used SA exclusively as a measure for other outcome variables. As a result, 39 studies met our inclusion criteria and were analyzed for this review. Qualitative narrative synthesis was used to summarize the informing factors. Furthermore, Kirkpatrick’s model was employed to categorize and summarize the effects of SA activities across various educational outcome levels, including reactions, learning, and behavioral changes. Our review reveals that key factors influencing students’ SA includes feedback from various stakeholders, peer assessment, the format of SA, and both learner and teacher training. Among the 39 studies examined, the majority demonstrated positive effects of SA on aspects such as attitudes and skills. However, a minority found no significant associations, with these outcomes frequently linked to contextual variables and how SA was implemented. Our review does not focus on SA accuracy or its role as an assessment method; instead it delves into the role of SA as an integral learning practice. We explored its influencing factors and its impact across various outcomes. The findings indicate that for SA to effectively enhance student learning outcomes, it must be implemented with ample support, clear guidelines, and within contexts that encourage feedback and reflection.