cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8105714.v1
title: Additional file 7: of Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence

description: KEGG enrichment of candidate target genes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8105702.v1
title: Additional file 5: of Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence

description: List of miRNA member in each family in Korla fragrant pear. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8105729
title: Additional file 9: of Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence

description: DEGs KEGG enriched TOP20. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.22261541
title: Pruning and thresholding approach for methylation risk scores in multi-ancestry populations

description: Recent efforts have focused on developing methylation risk scores (MRS), a weighted sum of the individual’s DNA methylation (DNAm) values of pre-selected CpG sites. Most of the current MRS approaches that utilize Epigenome-wide association studies (EWAS) summary statistics only include genome-wide significant CpG sites and do not consider co-methylation. New methods that relax the p-value threshold to include more CpG sites and account for the inter-correlation of DNAm might improve the predictive performance of MRS. We paired informed co-methylation pruning with P-value thresholding to generate pruning and thresholding (P+T) MRS and evaluated its performance among multi-ancestry populations. Through simulation studies and real data analyses, we demonstrated that pruning provides an improvement over simple thresholding methods for prediction of phenotypes. We demonstrated that European-derived summary statistics can be used to develop P+T MRS among other populations such as African populations. However, the prediction accuracy of P+T MRS may differ across multi-ancestry population due to environmental/cultural/social differences.
DOI: 10.6084/m9.figshare.22261541.v1
title: Pruning and thresholding approach for methylation risk scores in multi-ancestry populations

description: Recent efforts have focused on developing methylation risk scores (MRS), a weighted sum of the individual’s DNA methylation (DNAm) values of pre-selected CpG sites. Most of the current MRS approaches that utilize Epigenome-wide association studies (EWAS) summary statistics only include genome-wide significant CpG sites and do not consider co-methylation. New methods that relax the p-value threshold to include more CpG sites and account for the inter-correlation of DNAm might improve the predictive performance of MRS. We paired informed co-methylation pruning with P-value thresholding to generate pruning and thresholding (P+T) MRS and evaluated its performance among multi-ancestry populations. Through simulation studies and real data analyses, we demonstrated that pruning provides an improvement over simple thresholding methods for prediction of phenotypes. We demonstrated that European-derived summary statistics can be used to develop P+T MRS among other populations such as African populations. However, the prediction accuracy of P+T MRS may differ across multi-ancestry population due to environmental/cultural/social differences.
DOI: 10.5281/zenodo.7677600
title: Database of Residual Stress Measurements on Hot-rolled Wide Flange Steel Cross Sections

description: Data_info.csv: Database of 'Residual Stress Measurements on Hot-rolled Wide Flange Steel Cross Sections' including cross-sectional and material characteristics as well as information relevant to ploting the residual stress distributions. Distributions.zip: Residual stress distributions for the web and the flanges. To be unziped and positioned at the same location with the 'Data_info.csv', 'Processor.m' and 'QP_Coefficients' folder. Processor.m: MATLAB code that plots the residual stress distributions of a selected research work. QP_Coefficients.zip: Coefficients of a proposed optimization method to fit the measured residual stresses in the web and the flanges. To be unziped and positioned at the same location with the 'Data_info.csv', 'Processor.m' and 'Distributions' folder.
description: {"references": ["Skiadopoulos A, Sousa A de C e, Lignos DG. Proposed residual stress model for hot-rolled wide flange steel cross sections. Proceedings 10th European Conference on Steel and Composite Structures, vol. 6, Amsterdam, Netherlands: Ernst & Sohn; 2023. DOI: https://doi.org/10.1002/cepa.2736.", "Skiadopoulos A, de Castro e Sousa A, Lignos DG. Experiments and proposed model for residual stresses in hot-rolled wide flange shapes. Journal of Constructional Steel Research 2023; 210: 108069. DOI: 10.1016/j.jcsr.2023.108069."]}
DOI: 10.6084/m9.figshare.25219709
title: Supplementary Material for: Bilateral Cryptococcal Choroiditis in a Human Immunodeficiency Virus-Infected Patient: A Case Report

description: <b><i>Introduction:</i></b> In this case report, we present a rare case of bilateral cryptococcal choroiditis following a diagnosis of meningitis in a 38-year-old woman with HIV. <b><i>Case Presentation:</i></b> A Colombian woman, newly diagnosed with HIV, presented with respiratory distress followed by meningeal syndrome. Further evaluation revealed cryptococcal meningitis caused by <i>Cryptococcus neoformans</i>, confirmed through cerebrospinal fluid analysis and brain magnetic resonance imaging. The patient reported mild blurred vision, prompting an ophthalmic examination that included indocyanine green angiography. The findings revealed signs of HIV retinopathy and multifocal choroidal lesions in both eyes, suggestive of choroidal cryptococcosis. Treatment involved intravenous administration of amphotericin B and flucytosine, followed by oral fluconazole. Subsequently, the choroidal lesions gradually regressed, and regular monitoring demonstrated no signs of recurrence. <b><i>Conclusion:</i></b> Cryptococcal choroiditis, though exceptionally rare, can occur in HIV-positive patients with disseminated cryptococcosis. Ophthalmologists should maintain a high index of suspicion for opportunistic infections, even in the absence of pronounced ocular symptoms, particularly in immunocompromised individuals. Early diagnosis and appropriate treatment are crucial for achieving favorable outcomes in such cases.
DOI: 10.6084/m9.figshare.25219709.v1
title: Supplementary Material for: Bilateral Cryptococcal Choroiditis in a Human Immunodeficiency Virus-Infected Patient: A Case Report

description: <b><i>Introduction:</i></b> In this case report, we present a rare case of bilateral cryptococcal choroiditis following a diagnosis of meningitis in a 38-year-old woman with HIV. <b><i>Case Presentation:</i></b> A Colombian woman, newly diagnosed with HIV, presented with respiratory distress followed by meningeal syndrome. Further evaluation revealed cryptococcal meningitis caused by <i>Cryptococcus neoformans</i>, confirmed through cerebrospinal fluid analysis and brain magnetic resonance imaging. The patient reported mild blurred vision, prompting an ophthalmic examination that included indocyanine green angiography. The findings revealed signs of HIV retinopathy and multifocal choroidal lesions in both eyes, suggestive of choroidal cryptococcosis. Treatment involved intravenous administration of amphotericin B and flucytosine, followed by oral fluconazole. Subsequently, the choroidal lesions gradually regressed, and regular monitoring demonstrated no signs of recurrence. <b><i>Conclusion:</i></b> Cryptococcal choroiditis, though exceptionally rare, can occur in HIV-positive patients with disseminated cryptococcosis. Ophthalmologists should maintain a high index of suspicion for opportunistic infections, even in the absence of pronounced ocular symptoms, particularly in immunocompromised individuals. Early diagnosis and appropriate treatment are crucial for achieving favorable outcomes in such cases.
DOI: 10.6084/m9.figshare.25219712
title: Supplementary Material for: Experience and Lessons Learned in the Treatment of Transforming Small Cell Neuroendocrine Carcinoma of the Prostate: A Case Report and Literature Review

description: <b><i>Introduction:</i></b> Small cell neuroendocrine carcinoma of the prostate (SCNECP) is a rare and highly malignant tumor that commonly transforms into conventional prostate adenocarcinoma (CPAC). Most of SCNECP cases cannot be detected and diagnosed early, and SCNECP is often diagnosed when there is liver and lung metastasis. Therefore, the early detection of the process from CPAC to SCNECP is crucial. <b><i>Case Report:</i></b> We present a case of a 73-year-old man who was initially admitted to our hospital with metastatic CPAC. He was administered goserelin acetate 3.6 mg combined with bicalutamide tablets (50 mg) once daily for endocrine therapy and docetaxel (100 mg) combined with prednisone (5 mg) twice a day. After treatment, the prostate-specific antigen (PSA) level decreased significantly, but the CEA, CA199, and CA125 levels began to increase progressively after a short decline. However, no solid tumor recurrence was observed in multiple reexaminations. It was not until 9 months after the elevation of tumor markers that multiple metastatic lesions appeared in the liver, which finally confirmed the diagnosis of metastatic SCNECP. After chemotherapy with etoposide 360 mg combined with carboplatin 200 mg, the tumor size was significantly reduced, and tumor markers decreased. However, the remission time was only 3 months. The patient’s liver metastases continued to grow, and CEA, CA199, and CA125 levels continued to increase. <b><i>Conclusion:</i></b> During CPAC treatment, PSA levels continued to decrease, whereas CEA, CA199, and CA125 levels continued to increase. This suggests the possibility of the transformation of CPAC into SCNECP.
DOI: 10.6084/m9.figshare.22261543.v1
title: NAT10 mediated mRNA acetylation modification patterns associated with colon cancer progression and microsatellite status

description: N4-acetylcytidine (ac4C) is one type of RNA modification found in eukaryotes. RNA acetylation modifications are gradually expanding in oncology. However, the role of RNA acetylation modifications in colorectal cancer and its association with colorectal cancer microsatellite status remain unclear. Using public databases and in vitro experiments, we verified the expression and biological function of NAT10, as the key RNA acetylation modification enzyme, in colorectal cancer. The results showed that NAT10 was highly expressed in colorectal cancer, and significantly promoted colorectal cancer cell proliferation. NAT10 was also involved in several aspects of cell homoeostasis such as ion transport, calcium-dependent phospholipid binding, and RNA stability. NAT10 expression positively correlated with immune infiltration in colorectal cancer. We further constructed a risk regression model for mRNA acetylation in colorectal cancer using acetylation-related differential genes. We found that tumour immune infiltration, microsatellite instability (MSI) proportion, tumour immune mutation burden, and patient response to immunotherapy were positively correlated with risk scores. For the first time, our study showed that the level of mRNA acetylation modification level is elevated in colorectal cancer and positively correlates with immune infiltration and microsatellite status of patients. Based on our findings, NAT10 may be a new target for colorectal cancer treatment.
DOI: 10.6084/m9.figshare.22261543
title: NAT10 mediated mRNA acetylation modification patterns associated with colon cancer progression and microsatellite status

description: N4-acetylcytidine (ac4C) is one type of RNA modification found in eukaryotes. RNA acetylation modifications are gradually expanding in oncology. However, the role of RNA acetylation modifications in colorectal cancer and its association with colorectal cancer microsatellite status remain unclear. Using public databases and in vitro experiments, we verified the expression and biological function of NAT10, as the key RNA acetylation modification enzyme, in colorectal cancer. The results showed that NAT10 was highly expressed in colorectal cancer, and significantly promoted colorectal cancer cell proliferation. NAT10 was also involved in several aspects of cell homoeostasis such as ion transport, calcium-dependent phospholipid binding, and RNA stability. NAT10 expression positively correlated with immune infiltration in colorectal cancer. We further constructed a risk regression model for mRNA acetylation in colorectal cancer using acetylation-related differential genes. We found that tumour immune infiltration, microsatellite instability (MSI) proportion, tumour immune mutation burden, and patient response to immunotherapy were positively correlated with risk scores. For the first time, our study showed that the level of mRNA acetylation modification level is elevated in colorectal cancer and positively correlates with immune infiltration and microsatellite status of patients. Based on our findings, NAT10 may be a new target for colorectal cancer treatment.
DOI: 10.6084/m9.figshare.8105711
title: Additional file 6: of Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence

description: Potential target genes of DEMs predicted by psRNATarget. (XLSX 1488 kb)
DOI: 10.6084/m9.figshare.8105789
title: MOESM1 of H/ACA box small nucleolar RNA 7B acts as an oncogene and a potential prognostic biomarker in breast cancer

description: Additional file 1. knockdown oligos used in the article.
DOI: 10.6084/m9.figshare.8105789.v1
title: MOESM1 of H/ACA box small nucleolar RNA 7B acts as an oncogene and a potential prognostic biomarker in breast cancer

description: Additional file 1. knockdown oligos used in the article.
DOI: 10.6084/m9.figshare.21213050
title: Paul Auster and August Brill’s solitary rooms: the spatiality of solitude

description: Abstract: For Paul Auster, a room is in essence “the substance of solitude itself”, a spatially defined solitude. In this respect, the phenomenon has transcended its physical limitations and assumed existential and philosophical significance. In his writings, a room is first and foremost an architectural space that a solitary writer occupies. Besides, it is metaphorized as the mind that is the room - an intellectually constructed space; and lastly, it is a place narrated in his stories where his characters meditate and compose, a space that exists in words. This paper studies Auster’s life writings and one of his fictions, Man in the Dark, to present the complexity of the three forms of solitary rooms and their mutual inclusion in intersubjective solitude.
DOI: 10.6084/m9.figshare.21213050.v1
title: Paul Auster and August Brill’s solitary rooms: the spatiality of solitude

description: Abstract: For Paul Auster, a room is in essence “the substance of solitude itself”, a spatially defined solitude. In this respect, the phenomenon has transcended its physical limitations and assumed existential and philosophical significance. In his writings, a room is first and foremost an architectural space that a solitary writer occupies. Besides, it is metaphorized as the mind that is the room - an intellectually constructed space; and lastly, it is a place narrated in his stories where his characters meditate and compose, a space that exists in words. This paper studies Auster’s life writings and one of his fictions, Man in the Dark, to present the complexity of the three forms of solitary rooms and their mutual inclusion in intersubjective solitude.
DOI: 10.6084/m9.figshare.8105963.v1
title: Additional file 1: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S1. Phenotypic data of all samples. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.21499230
title: Genomes, fossils and the concurrent rise of modern birds and angiosperms in Late Cretaceous

description: The dataset includes a total of 5756 CDS, 4871 introns, 2384 intergenic markers, and 12449 CNEEs generated from the genomes of 124 species of neognaths and paleognaths. It also includes the species trees derived from intron, intergenic, and CDS markers.
DOI: 10.6084/m9.figshare.21202033.v1
title: Additional file 2 of Profiles of transcriptome and metabolic pathways after hypobaric hypoxia exposure

description: Additional file 2.
DOI: 10.6084/m9.figshare.8105981
title: Additional file 4: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S4. Number of elite alleles contained in each recombinant inbred line. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8105975.v1
title: Additional file 3: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S3. Details of phenotypic difference between two alleles of each loci. a, phenotype of 0 allele minus that of 2 allele. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.8105996.v1
title: Additional file 6: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S5. Annotated function of differentially expressed genes identified from the stable loci. a FPKM, fragments per kilo base of exon per million fragments mapped. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.21202030
title: Additional file 1 of Profiles of transcriptome and metabolic pathways after hypobaric hypoxia exposure

description: Additional file 1.
DOI: 10.6084/m9.figshare.21213138.v1
title: Monk, official and Gentry: multiple writings of Jingshan annals and the regional sight of the late ming Buddhist revival

description: Abstract: When discussing the revival of Buddhism in the late Ming Dynasty, scholars lack the study of rich local records, specific regions and typical cases. Jingshan temple in Hangzhou provides such a sample. An outstanding manifestation of Jingshan Temple in the late Ming Dynasty is the emergency of a whole bunch of annals. Different groups such as monks, magistrates, and gentry all participated in the writing of the history of Jingshan diachronically in the same space. Different versions of Jingshan Annals reveal the interweaving of historical events, trends of the times, and the wishes of various groups in distinct regions, shedding light on the development that Buddhist historical records began to involve other classics outside Buddhism instead of only focusing on Buddhist sutras. This process manifests that the revival of Buddhism in the late Ming Dynasty is also a diachronic active state achieved by the people’s activities with different purposes in a specific area.
DOI: 10.6084/m9.figshare.21202030.v1
title: Additional file 1 of Profiles of transcriptome and metabolic pathways after hypobaric hypoxia exposure

description: Additional file 1.
DOI: 10.6084/m9.figshare.21213138
title: Monk, official and Gentry: multiple writings of Jingshan annals and the regional sight of the late ming Buddhist revival

description: Abstract: When discussing the revival of Buddhism in the late Ming Dynasty, scholars lack the study of rich local records, specific regions and typical cases. Jingshan temple in Hangzhou provides such a sample. An outstanding manifestation of Jingshan Temple in the late Ming Dynasty is the emergency of a whole bunch of annals. Different groups such as monks, magistrates, and gentry all participated in the writing of the history of Jingshan diachronically in the same space. Different versions of Jingshan Annals reveal the interweaving of historical events, trends of the times, and the wishes of various groups in distinct regions, shedding light on the development that Buddhist historical records began to involve other classics outside Buddhism instead of only focusing on Buddhist sutras. This process manifests that the revival of Buddhism in the late Ming Dynasty is also a diachronic active state achieved by the people’s activities with different purposes in a specific area.
DOI: 10.6084/m9.figshare.8105993
title: Additional file 2: of Maternal dietary glycaemic change during gestation influences insulin-related gene methylation in the placental tissue: a genome-wide methylation analysis

description: Significant GO terms by enrichment analysis based on CpG sites from four selective genes related to insulin regulation. (XLS 4 kb)
DOI: 10.6084/m9.figshare.8105993.v1
title: Additional file 2: of Maternal dietary glycaemic change during gestation influences insulin-related gene methylation in the placental tissue: a genome-wide methylation analysis

description: Significant GO terms by enrichment analysis based on CpG sites from four selective genes related to insulin regulation. (XLS 4 kb)
DOI: 10.6084/m9.figshare.8105963
title: Additional file 1: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S1. Phenotypic data of all samples. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.8105966.v1
title: Additional file 2: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S2. Phenotypic correlation coefficients among the CL、CSA、CAD and CV across two cropping seasons in the YZX × 02428 RIL population. * and ** indicate significance levels at P &lt; 0.05 and P &lt; 0.01, respectively. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8105984
title: Additional file 1: of Maternal dietary glycaemic change during gestation influences insulin-related gene methylation in the placental tissue: a genome-wide methylation analysis

description: Significant DMRs and CpG sites based on the genome-wide differential methylation analysis (FDR-adjusted Pâ &lt;â 0.05) and annotation information. (XLSX 148 kb)
DOI: 10.6084/m9.figshare.8105984.v1
title: Additional file 1: of Maternal dietary glycaemic change during gestation influences insulin-related gene methylation in the placental tissue: a genome-wide methylation analysis

description: Significant DMRs and CpG sites based on the genome-wide differential methylation analysis (FDR-adjusted Pâ &lt;â 0.05) and annotation information. (XLSX 148 kb)
DOI: 10.6084/m9.figshare.8105999.v1
title: Additional file 7: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S6. Primers used for qRT-PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.12813478
title: Additional file 1 of Distinct promoter methylation patterns of LKB1 in the hamartomatous polyps of Peutz-Jeghers syndrome and its potential in gastrointestinal malignancy prediction

description: Additional file 1.
DOI: 10.6084/m9.figshare.21202035.v1
title: Additional file 2 of Mutational and transcriptional alterations and clinicopathological factors predict the prognosis of stage I hepatocellular carcinoma

description: Additional file 2: Table S2. The patient identifier for all subjects involved in this study. Description of data: A list of submitter id of all 163 patients.
DOI: 10.6084/m9.figshare.8105966
title: Additional file 2: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S2. Phenotypic correlation coefficients among the CL、CSA、CAD and CV across two cropping seasons in the YZX × 02428 RIL population. * and ** indicate significance levels at P &lt; 0.05 and P &lt; 0.01, respectively. (XLSX 10 kb)