cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22622627.v1
title: Additional file 6 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 6: Table S5. Location bias enrichment test in CEN5.
DOI: 10.6084/m9.figshare.14758243.v2
title: Flexible and Fast Spatial Return Level Estimation Via a Spatially Fused Penalty

description: Spatial extremes are common for climate data as the observations are usually referenced by geographic locations and dependent when they are nearby. An important goal of extremes modeling is to estimate the T-year return level. Among the methods suitable for modeling spatial extremes, perhaps the simplest and fastest approach is the spatial generalized extreme value (GEV) distribution and the spatial generalized Pareto distribution (GPD) that assume marginal independence and only account for dependence through the parameters. Despite the simplicity, simulations have shown that return level estimation using the spatial GEV and spatial GPD still provides satisfactory results compared to max-stable processes, which are asymptotically justified models capable of representing spatial dependence among extremes. However, the linear functions used to model the spatially varying coefficients are restrictive and may be violated. We propose a flexible and fast approach based on the spatial GEV and spatial GPD by introducing fused lasso and fused ridge penalty for parameter regularization. This enables improved return level estimation for large spatial extremes compared to the existing methods. Supplemental files for this article are available online.
DOI: 10.25402/fon.19476845.v1
title: Supplementary Material – Phase I/Ib Dose-Escalation Study of Avelumab in Chinese Patients With Advanced Solid Tumors

description: <b>Supplementary Table 1. Antitumor activity</b>
 
 
 
 




<br><br><br><br>Phase I/Ib Dose-Escalation Study of Avelumab in
Chinese Patients With Advanced Solid Tumors
DOI: 10.6084/m9.figshare.22622542.v1
title: Additional file 5 of A web tool for the global identification of pig breeds

description: Additional file 5: Table S4. Information on the breeds used in the reference dataset.
DOI: 10.6084/m9.figshare.22622564
title: Additional file 7 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 7: Table S6. Results from CRISPRqtl screen in B80-T5 cells. The Sceptre algorithm was used to identify gene expression changes following CRISPRi mediated targeting of 16 loci associated with increased BC risk.
DOI: 10.6084/m9.figshare.20001086.v1
title: Additional file 4 of Circ_0004087 interaction with SND1 promotes docetaxel resistance in prostate cancer by boosting the mitosis error correction mechanism

description: Additional file 4. RNA-binding proteins.
DOI: 10.6084/m9.figshare.22622630
title: Additional file 7 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 7: Table S6. Comparison annotation coverage and continuity in CHM13 centromeres for HiCAT and HORmon.
DOI: 10.6084/m9.figshare.22622567
title: Additional file 8 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 8: Table S7. Sequences of sgRNAs used in validation assays.
DOI: 10.6084/m9.figshare.22622567.v1
title: Additional file 8 of CRISPR screens identify gene targets at breast cancer risk loci

description: Additional file 8: Table S7. Sequences of sgRNAs used in validation assays.
DOI: 10.6084/m9.figshare.22622615.v1
title: Additional file 2 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 2: Table S1. Simulated validation in canonical datasets.
DOI: 10.6084/m9.figshare.22622624
title: Additional file 5 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 5: Table S4. Comparison between HiCAT and previous studies for HORs in human centromeres.
DOI: 10.6084/m9.figshare.22622633.v1
title: Additional file 8 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 8: Table S7. HiCAT HORs in Arabidopsis thaliana centromeres.
DOI: 10.5281/zenodo.10630160
title: Dataset related to the article "Identification of subclinical cardiac amyloidosis in aortic stenosis patients undergoing transaortic valve replacement using radiomic analysis of computed tomography myocardial texture"

description: This record contains raw data related to the article "Identification of subclinical cardiac amyloidosis in aortic stenosis patients undergoing transaortic valve replacement using radiomic analysis of computed tomography myocardial texture"

Background. Cardiac amyloidosis (CA) is an increasingly diagnosed disease sharing several phenotypical features with aortic stenosis (AS).

Purpose. As diagnosing the two diseases has crucial prognostic and therapeutic implications, this study aims to identify a set Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation of stable and discriminative radiomic features derived from cardiac computed tomography to differentiate them.

Methods: Forty-two patients were included in the study. For each patient, 107 radiomics features were evaluated by means of geometrical transformations (translations) to the region of interests (ROIs) and intra class correlation coefficient (ICC) computation. A stratified 7-fold cross (k=7) validation was performed to split data into learning, validation and test set. Three features selection methods (Wilcoxon signed rank-based method and/or LASSO regression) and five machine learning classifiers.

Results: Ninety radiomic features satisfied robustness criteria and 10 were kept after feature selection. The best results were obtained using logistic regression classifier combined with Wilcoxon signed rank and LASSO regression, obtaining an accuracy of 95 ± 7% and sensitivity and specificity equal to 95 ± 12% in the test set. 

Conclusions: the application of radiomics shows promising results in distinguishing left ventricle hypertrophy caused by CA from AS and might be used as a non-invasive tool able to support clinical decision making.
DOI: 10.5281/zenodo.10630161
title: Dataset related to the article "Identification of subclinical cardiac amyloidosis in aortic stenosis patients undergoing transaortic valve replacement using radiomic analysis of computed tomography myocardial texture"

description: This record contains raw data related to the article "Identification of subclinical cardiac amyloidosis in aortic stenosis patients undergoing transaortic valve replacement using radiomic analysis of computed tomography myocardial texture"

Background. Cardiac amyloidosis (CA) is an increasingly diagnosed disease sharing several phenotypical features with aortic stenosis (AS).

Purpose. As diagnosing the two diseases has crucial prognostic and therapeutic implications, this study aims to identify a set Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation of stable and discriminative radiomic features derived from cardiac computed tomography to differentiate them.

Methods: Forty-two patients were included in the study. For each patient, 107 radiomics features were evaluated by means of geometrical transformations (translations) to the region of interests (ROIs) and intra class correlation coefficient (ICC) computation. A stratified 7-fold cross (k=7) validation was performed to split data into learning, validation and test set. Three features selection methods (Wilcoxon signed rank-based method and/or LASSO regression) and five machine learning classifiers.

Results: Ninety radiomic features satisfied robustness criteria and 10 were kept after feature selection. The best results were obtained using logistic regression classifier combined with Wilcoxon signed rank and LASSO regression, obtaining an accuracy of 95 ± 7% and sensitivity and specificity equal to 95 ± 12% in the test set. 

Conclusions: the application of radiomics shows promising results in distinguishing left ventricle hypertrophy caused by CA from AS and might be used as a non-invasive tool able to support clinical decision making.
DOI: 10.6084/m9.figshare.22622621.v1
title: Additional file 4 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 4: Table S3. Centromere regions in human and Arabidopsis thaliana.
DOI: 10.6084/m9.figshare.22622636
title: Additional file 9 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 9: Table S8. Runtime for HiCAT in human and Arabidopsis thaliana.
DOI: 10.6084/m9.figshare.20001333.v1
title: A novel ribosomal protein S6 kinase 2 inhibitor attenuates the malignant phenotype of cutaneous malignant melanoma cells by inducing cell cycle arrest and apoptosis

description: Malignant melanoma (MM) is a highly life-threatening tumor causing the majority of the cutaneous cancer-related deaths. Previously, ribosomal protein S6 kinase 2 (RSK2), the downstream effector of the MAPK pathway, represents a therapeutic target in melanoma. AE007 is discovered as a targeted RSK2 inhibitor, and subsequent results showed that AE007 inhibits RSK2 by directly binding to its protein kinase domain. AE007 causes cell cycle arrest and cellular apoptosis, thereby dramatically inhibiting proliferation, migration, and invasion of melanoma cells. Nevertheless, melanocytes and keratinocytes are not affected by this compound. In addition, suppression of RSK2 abrogates the inhibitory effect of AE007 on melanoma cell proliferation. AE007 treatment significantly inhibits the expression of Cyclin D1, Cyclin B1, CDK2, and Bcl-2, while raises the cleavage of PARP. Moreover, RNA sequencing results show that AE007 treatment can affect the genes expression profile, including the expression of cell cycle and DNA replication genes. In conclusion, AE007 is a promising melanoma therapeutic agent by targeting RSK2.
DOI: 10.6084/m9.figshare.13711807
title: The ballast effect controls the settling of autochthonous organic carbon in karst reservoirs

description: Data for the manuscript of "The ballast effect controls the settling of autochthonous organic carbon in karst reservoirs"
DOI: 10.6084/m9.figshare.22622651
title: Additional file 1 of Verification of prognostic expression biomarkers is improved by examining enriched leukemic blasts rather than mononuclear cells from acute myeloid leukemia patients

description: Additional file 1: Supplemental Methods. Supplemental Figure 1. Genomic landscape of mutations in various cohorts of patients used for the study. Supplemental Figure 2. Quality Control Assessments of RNAseq Data. Supplemental Figure 3. Principal Component (PC) Analyses of QC Data. Supplemental Figure 4. QQ plots of observed and expected results. Supplemental Figure 5. LSC17 score applied to RNAseq data from bulk MNCs and VLBsCD34+. Supplemental Table 1. Genetic Sequencing Data. Supplemental Table 2. RNA Sequencing Data. Supplemental Table 3. QRT-PCR Assays. Supplemental Table 4. Characteristics of included and excluded patients. Supplemental Table 5. Comparisons to assess the impact of batch, instrument, and tissue source on transcript profiles. Supplemental Table 6. Expression changes associated with patient characteristics. Supplemental Table 7. Pathways associated with DEGs and patient characteristics. Supplemental Table 8. Expression changes and pathways associated with clinical outcomes. Supplemental Table 9. Prognostic significance of LSC17 in RNA from MNCs and VLBsCD34+ from the discovery cohort.
DOI: 10.6084/m9.figshare.13711943
title: CD36 and LC3B initiated autophagy in B cells regulates the humoral immune response

description: Scavenger receptors are pattern recognition receptors that recognize both foreign and self-ligands, and initiate different mechanisms of cellular activation, often as co-receptors. The function of scavenger receptor CD36 in the immune system has mostly been studied in macrophages but it is also highly expressed by innate type B cells where its function is less explored. Here we report that CD36 is involved in macro-autophagy/autophagy in B cells, and in its absence, the humoral immune response is impaired. We found that CD36-deficient B cells exhibit a significantly reduced plasma cell formation, proliferation, mitochondrial mobilization and oxidative phosphorylation. These changes were accompanied by impaired initiation of autophagy, and we found that CD36 regulated autophagy and colocalized with autophagosome membrane protein MAP1LC3/LC3 (microtubule-associated protein 1 light chain 3). When we investigated T-cell-dependent immune responses, we found that mice with CD36 deficiency, specifically in B cells, exhibited attenuated germinal center responses, class switching, and antibody production as well as autophagosome formation. These findings establish a critical role for CD36 in B cell responses and may also contribute to our understanding of CD36-mediated autophagy in other cells as well as in B cell lymphomas that have been shown to express the receptor. <b>Abbreviations:</b> AICDA/AID: activation-induced cytidine deaminase; ATG5: autophagy related 5; ATP: adenosine triphosphate; BCR: B-cell receptor; CPG: unmethylated cytosine-guanosine; CQ: chloroquine; DC: dendritic cells; FOB: follicular B cells; GC: germinal center; Ig: immunoglobulin; LPS: lipopolysaccharide; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MFI: mean fluorescence intensity; MZB: marginal zone B cells; NP-CGG: 4-hydroxy-3-nitrophenylacetyl-chicken gamma globulin; OCR: oxygen consumption rate; oxLDL: oxidized low-density lipoprotein; PC: plasma cells; Rapa: rapamycin; SQSTM1/p62: sequestosome 1; SRBC: sheep red blood cells; Tfh: follicular helper T cells; TLR: toll-like receptor.
DOI: 10.6084/m9.figshare.22622594
title: Additional file 5 of Analysis of serum reproductive hormones and ovarian genes in pubertal female goats

description: Additional file 5: Table S4. KEGG analysis of DEGs.
DOI: 10.6084/m9.figshare.20001333
title: A novel ribosomal protein S6 kinase 2 inhibitor attenuates the malignant phenotype of cutaneous malignant melanoma cells by inducing cell cycle arrest and apoptosis

description: Malignant melanoma (MM) is a highly life-threatening tumor causing the majority of the cutaneous cancer-related deaths. Previously, ribosomal protein S6 kinase 2 (RSK2), the downstream effector of the MAPK pathway, represents a therapeutic target in melanoma. AE007 is discovered as a targeted RSK2 inhibitor, and subsequent results showed that AE007 inhibits RSK2 by directly binding to its protein kinase domain. AE007 causes cell cycle arrest and cellular apoptosis, thereby dramatically inhibiting proliferation, migration, and invasion of melanoma cells. Nevertheless, melanocytes and keratinocytes are not affected by this compound. In addition, suppression of RSK2 abrogates the inhibitory effect of AE007 on melanoma cell proliferation. AE007 treatment significantly inhibits the expression of Cyclin D1, Cyclin B1, CDK2, and Bcl-2, while raises the cleavage of PARP. Moreover, RNA sequencing results show that AE007 treatment can affect the genes expression profile, including the expression of cell cycle and DNA replication genes. In conclusion, AE007 is a promising melanoma therapeutic agent by targeting RSK2.
DOI: 10.6084/m9.figshare.22622591
title: Additional file 4 of Analysis of serum reproductive hormones and ovarian genes in pubertal female goats

description: Additional file 4: Table S3. GO analysis of DEGs.
DOI: 10.6084/m9.figshare.22622618
title: Additional file 3 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 3: Table S2. Simulated validation in local nested HOR(LN-HOR) datasets.
DOI: 10.6084/m9.figshare.20001305.v1
title: N6-methyladenine- induced LINC00667 promoted breast cancer progression through m6A/KIAA1429 positive feedback loop

description: Increasing evidence supports that N<sup>6</sup>-methyladenine (m<sup>6</sup>A) and long noncoding RNAs (lncRNAs) both act as master regulators involved in breast cancer (BC) tumorigenesis at epigenetic modification level. Here, our research tries to unveil the interaction of m<sup>6</sup>A and lncRNAs on BC progression and explore the underlying regulatory mechanism. In the current study, we found that LINC00667 was m<sup>6</sup>A-modified lncRNA, which was up-regulated upon the overexpression of KIAA1429. The high expression of LINC00667 was correlated with the prognosis of BC patients. Bio-functional assays indicated that LINC00667 promoted the proliferation and migration of BC cells. Mechanistic assays illustrated that KIAA1429 targeted the m<sup>6</sup>A modification site of LINC00667 and enhanced its mRNA stability. Moreover, LINC00667 positively regulated the KIAA1429 via sponging miR-556-5p, forming a KIAA1429/m<sup>6</sup>A/LINC00667/miR-556-5p feedback loop. Collectively, the central findings of our study suggest that KIAA1429-induced LINC00667 exerted its functions as an oncogene in BC progression through m<sup>6</sup>A-dependent feedback loop.
DOI: 10.6084/m9.figshare.20001308.v1
title: A high level of the long non-coding RNA <i>MCF2L-AS1</i> is associated with poor prognosis in breast cancer and <i>MCF2L-AS1</i> activates YAP transcriptional activity to enhance breast cancer proliferation and metastasis

description: Breast cancer (BC) is one of the most prevalent gynecologic malignant tumors with a poor prognosis and the second leading cause of cancer-related deaths in women worldwide. In recent years, it has been shown that long non-coding RNA (lncRNA) plays an important role in the development of breast cancer (BC). An antisense lncRNA from the MCF2 cell line (MCF2L-AS1) has been discovered recently and has been shown to function in a variety of malignancies. However, its function as a regulator of BC development has yet to be determined. Herein, the bioinformatics study analysis showed that MCF2L-AS1 was frequently highly expressed in BC tumors, and this overexpression was associated with worse patient outcomes. BC cells’ proliferation, migration, and invasion are inhibited when MCF2L-AS1 is silenced, whereas the inverse is evident when MCF2L-AS1 is overexpressed. It was also observed that MCF2L-AS1 knockdown decreased carcinogenesis in xenograft tumor models. Furthermore, we discovered that MCF2L-AS1 could bind to and improve the transcription activity of the yes-associated protein (YAP). However, following YAP knockdown, this lncRNA’s ability to drive BC malignancy was considerably reduced. In conclusion, MCF2L-AS1 may represent a potential predictive biomarker in BC patients, as well as a key regulator of BC cell proliferation. It works through positive feedback processes involving direct YAP binding and subsequent modulation of intracellular gene expression. Our findings add to our understanding of MCF2L-AS1 regulation and its potential as a therapeutic target in patients with this fatal cancer type.
DOI: 10.6084/m9.figshare.22622618.v1
title: Additional file 3 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 3: Table S2. Simulated validation in local nested HOR(LN-HOR) datasets.
DOI: 10.6084/m9.figshare.22622630.v1
title: Additional file 7 of HiCAT: a tool for automatic annotation of centromere structure

description: Additional file 7: Table S6. Comparison annotation coverage and continuity in CHM13 centromeres for HiCAT and HORmon.
DOI: 10.6084/m9.figshare.10041995
title: MOESM11 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 12. Supplementary document for Delaunay code.
DOI: 10.6084/m9.figshare.10041995.v1
title: MOESM11 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 12. Supplementary document for Delaunay code.
DOI: 10.6084/m9.figshare.10042004
title: MOESM14 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 15. Supplementary document for SVM code.
DOI: 10.6084/m9.figshare.10042004.v1
title: MOESM14 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 15. Supplementary document for SVM code.
DOI: 10.6084/m9.figshare.10042007
title: MOESM15 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 16. Supplementary document for RF code.
DOI: 10.6084/m9.figshare.10042007.v1
title: MOESM15 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 16. Supplementary document for RF code.
DOI: 10.6084/m9.figshare.10042013
title: MOESM2 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 2. Original data of leaf area and canopy height.
DOI: 10.6084/m9.figshare.10042013.v1
title: MOESM2 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 2. Original data of leaf area and canopy height.
DOI: 10.6084/m9.figshare.10042016
title: MOESM3 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 3. Original data of individual leaf traits.
DOI: 10.6084/m9.figshare.10042016.v1
title: MOESM3 of A high-throughput stereo-imaging system for quantifying rape leaf traits during the seedling stage

description: Additional file 3. Original data of individual leaf traits.
DOI: 10.5525/gla.researchdata.1502
title: The genomic underpinnings of head and body shape morphology across Arctic charr ecomorph pairs

description: Body shape data and genomic data for a set of Arctic charr (fish) from Scotland
DOI: 10.6084/m9.figshare.22622638
title: Additional file 2 of Neuroglobin plays as tumor suppressor by disrupting the stability of GPR35 in colorectal cancer

description: Additional file 2. Methyl target information and results.
DOI: 10.6084/m9.figshare.22622638.v1
title: Additional file 2 of Neuroglobin plays as tumor suppressor by disrupting the stability of GPR35 in colorectal cancer

description: Additional file 2. Methyl target information and results.
DOI: 10.6084/m9.figshare.20001305
title: N6-methyladenine- induced LINC00667 promoted breast cancer progression through m6A/KIAA1429 positive feedback loop

description: Increasing evidence supports that N<sup>6</sup>-methyladenine (m<sup>6</sup>A) and long noncoding RNAs (lncRNAs) both act as master regulators involved in breast cancer (BC) tumorigenesis at epigenetic modification level. Here, our research tries to unveil the interaction of m<sup>6</sup>A and lncRNAs on BC progression and explore the underlying regulatory mechanism. In the current study, we found that LINC00667 was m<sup>6</sup>A-modified lncRNA, which was up-regulated upon the overexpression of KIAA1429. The high expression of LINC00667 was correlated with the prognosis of BC patients. Bio-functional assays indicated that LINC00667 promoted the proliferation and migration of BC cells. Mechanistic assays illustrated that KIAA1429 targeted the m<sup>6</sup>A modification site of LINC00667 and enhanced its mRNA stability. Moreover, LINC00667 positively regulated the KIAA1429 via sponging miR-556-5p, forming a KIAA1429/m<sup>6</sup>A/LINC00667/miR-556-5p feedback loop. Collectively, the central findings of our study suggest that KIAA1429-induced LINC00667 exerted its functions as an oncogene in BC progression through m<sup>6</sup>A-dependent feedback loop.