cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24679935
title: Optimizing Refractive Outcomes of SMILE: Artificial Intelligence versus Conventional State-of-the-Art Nomograms

description: AI (artificial intelligence)-based methodologies have become established tools for researchers and physicians in the entire field of ophthalmology. However, the potential of AI to optimize the refractive outcome of keratorefractive surgery by means of machine learning (ML)-based nomograms has not been exhausted yet. In this study, we wanted to comprehensively compare state-of-the-art conventional nomograms for Small-Incision-Lenticule-Extraction (SMILE) with a novel ML-based nomogram regarding both their spherical and astigmatic predictability. A total of 1,342 eyes were analyzed for creation of three different nomograms based on a linear model (LM), a generalized additive mixed model (GAMM) and an artificial-neuronal-network (ANN), respectively. A total of 16 patient- and treatment-related features were included. Each model was trained by 895 eyes and validated by the remaining 447 eyes. Predictability was assessed by the difference between attempted and achieved change in spherical equivalent (SE) and the difference between target induced astigmatism (TIA) and surgically induced astigmatism (SIA). The root mean squared error (RMSE) of each model was computed as a measure of overall model performance. The RMSE of LM, GAMM and ANN were 0.355, 0.348 and 0.367 for the prediction of SE and 0.279, 0.278 and 0.290 for the astigmatic correction, respectively. By applying the created models, the theoretical yield of eyes within ±0.50 D of SE from target refraction improved from 82 to 83% (LM), 84% (GAMM) and 83% (ANN), respectively. Astigmatic outcomes showed an improvement of eyes within ±0.50 D from TIA from 90 to 93% (LM), 93% (GAMM) and 92% (ANN), respectively. Subjective manifest refraction was the single most influential covariate in all models. Machine learning endorsed the validity of state-of-the-art linear and non-linear SMILE nomograms. However, improving the accuracy of subjective manifest refraction seems warranted for optimizing ±0.50 D SE predictability beyond an apparent methodological 90% limit.
DOI: 10.6084/m9.figshare.24679935.v1
title: Optimizing Refractive Outcomes of SMILE: Artificial Intelligence versus Conventional State-of-the-Art Nomograms

description: AI (artificial intelligence)-based methodologies have become established tools for researchers and physicians in the entire field of ophthalmology. However, the potential of AI to optimize the refractive outcome of keratorefractive surgery by means of machine learning (ML)-based nomograms has not been exhausted yet. In this study, we wanted to comprehensively compare state-of-the-art conventional nomograms for Small-Incision-Lenticule-Extraction (SMILE) with a novel ML-based nomogram regarding both their spherical and astigmatic predictability. A total of 1,342 eyes were analyzed for creation of three different nomograms based on a linear model (LM), a generalized additive mixed model (GAMM) and an artificial-neuronal-network (ANN), respectively. A total of 16 patient- and treatment-related features were included. Each model was trained by 895 eyes and validated by the remaining 447 eyes. Predictability was assessed by the difference between attempted and achieved change in spherical equivalent (SE) and the difference between target induced astigmatism (TIA) and surgically induced astigmatism (SIA). The root mean squared error (RMSE) of each model was computed as a measure of overall model performance. The RMSE of LM, GAMM and ANN were 0.355, 0.348 and 0.367 for the prediction of SE and 0.279, 0.278 and 0.290 for the astigmatic correction, respectively. By applying the created models, the theoretical yield of eyes within ±0.50 D of SE from target refraction improved from 82 to 83% (LM), 84% (GAMM) and 83% (ANN), respectively. Astigmatic outcomes showed an improvement of eyes within ±0.50 D from TIA from 90 to 93% (LM), 93% (GAMM) and 92% (ANN), respectively. Subjective manifest refraction was the single most influential covariate in all models. Machine learning endorsed the validity of state-of-the-art linear and non-linear SMILE nomograms. However, improving the accuracy of subjective manifest refraction seems warranted for optimizing ±0.50 D SE predictability beyond an apparent methodological 90% limit.
DOI: 10.6084/m9.figshare.24581390
title: Association between Oral Active-Matrix Metalloproteinase-8 Levels and Subretinal Fibrosis among Wet Age-Related Macular Degeneration Patients

description: Periodontitis causes low-grade systemic inflammation and has been associated with elevated active-matrix metalloproteinase (aMMP-8) levels, blood-ocular barrier breakdown and a risk of wet age-related macular degeneration. To assess the association between aMMP-8 levels and macular status among patients with wet age-related macular degeneration (AMD). Patients on anti-VEGF treatment for wet AMD were enrolled for oral aMMP-8 rinse test in Mehiläinen Private Hospital, Helsinki, Finland. Macular status was examined from spectral-domain optical coherence tomography (SD-OCT) scans by a medical retina specialist and aMMP-8 levels were analyzed with chairside point-of-care oral rinse (PerioSafe®) test and real-time quantitated by a dentist using the ORALyzer®- reader with a 10 ng/ml cut-off for aMMP-8 activity. Elevated aMMP-8 levels were found in 10 out of 32 patients. Age, gender, anti-VEGF (bevacizumab or aflibercept) distribution, cumulative number of anti-VEGF injections and treatment interval were comparable between patients with aMMP-8 levels below and above the point-of-care level. Macular status differed in regard to aMMP-8 activity; among patients with aMMP-8 levels below the point-of-care subretinal fibrosis was found in 6 out of 22 eyes, whereas among patients with aMMP-8 levels above the point-of-care subretinal fibrosis was found in 8 out of 10 eyes (<i>p</i> = 0.005). Respectively, the mean thickness of subretinal fibrosis at fovea was 19.5 ± 44.1 and 92.3 ± 78.3 µm (<i>p</i> = 0.018). No differences were found in the presence and in the area of geographic atrophy, or fluid distribution, whereas thicknesses of serous pigment epithelial detachment (65.5 ± 99.5 and 12.9 ± 27.9 µm, <i>p</i> = 0.038) and neuroretina (204.2 ± 57.8 µm and 143.0 ± 43.7 µm, <i>p</i> = 0.006) were greater in the eyes of patients with physiological aMMP-8 levels compared to those with elevated aMMP-8 levels. Elevated aMMP-8 levels may account for subretinal fibrosis formation in wet AMD.
DOI: 10.6084/m9.figshare.24581390.v1
title: Association between Oral Active-Matrix Metalloproteinase-8 Levels and Subretinal Fibrosis among Wet Age-Related Macular Degeneration Patients

description: Periodontitis causes low-grade systemic inflammation and has been associated with elevated active-matrix metalloproteinase (aMMP-8) levels, blood-ocular barrier breakdown and a risk of wet age-related macular degeneration. To assess the association between aMMP-8 levels and macular status among patients with wet age-related macular degeneration (AMD). Patients on anti-VEGF treatment for wet AMD were enrolled for oral aMMP-8 rinse test in Mehiläinen Private Hospital, Helsinki, Finland. Macular status was examined from spectral-domain optical coherence tomography (SD-OCT) scans by a medical retina specialist and aMMP-8 levels were analyzed with chairside point-of-care oral rinse (PerioSafe®) test and real-time quantitated by a dentist using the ORALyzer®- reader with a 10 ng/ml cut-off for aMMP-8 activity. Elevated aMMP-8 levels were found in 10 out of 32 patients. Age, gender, anti-VEGF (bevacizumab or aflibercept) distribution, cumulative number of anti-VEGF injections and treatment interval were comparable between patients with aMMP-8 levels below and above the point-of-care level. Macular status differed in regard to aMMP-8 activity; among patients with aMMP-8 levels below the point-of-care subretinal fibrosis was found in 6 out of 22 eyes, whereas among patients with aMMP-8 levels above the point-of-care subretinal fibrosis was found in 8 out of 10 eyes (<i>p</i> = 0.005). Respectively, the mean thickness of subretinal fibrosis at fovea was 19.5 ± 44.1 and 92.3 ± 78.3 µm (<i>p</i> = 0.018). No differences were found in the presence and in the area of geographic atrophy, or fluid distribution, whereas thicknesses of serous pigment epithelial detachment (65.5 ± 99.5 and 12.9 ± 27.9 µm, <i>p</i> = 0.038) and neuroretina (204.2 ± 57.8 µm and 143.0 ± 43.7 µm, <i>p</i> = 0.006) were greater in the eyes of patients with physiological aMMP-8 levels compared to those with elevated aMMP-8 levels. Elevated aMMP-8 levels may account for subretinal fibrosis formation in wet AMD.
DOI: 10.6084/m9.figshare.20330223
title: Additional file 1 of Which one of LDL-C /HDL-C ratio and non-HDL-C can better predict the severity of coronary artery disease in STEMI patients

description: Additional file 1. Research data.
DOI: 10.6084/m9.figshare.20330223.v1
title: Additional file 1 of Which one of LDL-C /HDL-C ratio and non-HDL-C can better predict the severity of coronary artery disease in STEMI patients

description: Additional file 1. Research data.
DOI: 10.6084/m9.figshare.20330176
title: Additional file 1 of Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage

description: Additional file 1: Supplementary Table S1. Maize ear traits analysis of lx9801 and lx9801hlEW2b in two environments. Supplementary Table S2. Comparison of inflorescence meristems size between lx9801, lx9801hlEW2b, Zheng58, HY and CK with immature ears. Supplementary Table S3. Distribution of gene expression levels in each sample. Supplementary Table S4. Differentially expressed genes between HY and CK hybrids. Supplementary Table S5. GO enriched terms of additive expressed genes in the Zheng58 × lx9801hlEW2bhybrid. Supplementary Table S6. GO enriched terms of additive expressed genes in the Zheng58 × lx9801 hybrid. Supplementary Table S7. GO enriched terms of non-additive expressed genes in the Zheng58 × lx9801hlEW2b hybrid. Supplementary Table S8. GO enriched terms of non-additive expressed genes in the Zheng58 × lx9801 hybrid. Supplementary Table S9. Maker DEGs with ASE expression pattern in HY hybrid involved in regulation of ear development. Supplementary Table S10. Maker DEGs with ASE expression pattern in both HY and CK hybrids involved in regulation of ear development. Supplementary Table S11. Maker DEGs with ASE expression pattern in CK hybrid involved in regulation of ear development. Supplementary Table S12. Maker DEGs with additive expression pattern in HY hybrid involved in regulation of ear development. Supplementary Table S13. Maker DEGs with additive expression pattern in CK hybrid involved in regulation of ear development. Supplementary Table S14. Maker DEGs with non-additive expression pattern in HY hybrid involved in regulation of ear development. Supplementary Table S15. Maker DEGs with non-additive expression pattern in CK hybrid involved in regulation of ear development.
DOI: 10.6084/m9.figshare.20330176.v1
title: Additional file 1 of Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage

description: Additional file 1: Supplementary Table S1. Maize ear traits analysis of lx9801 and lx9801hlEW2b in two environments. Supplementary Table S2. Comparison of inflorescence meristems size between lx9801, lx9801hlEW2b, Zheng58, HY and CK with immature ears. Supplementary Table S3. Distribution of gene expression levels in each sample. Supplementary Table S4. Differentially expressed genes between HY and CK hybrids. Supplementary Table S5. GO enriched terms of additive expressed genes in the Zheng58 × lx9801hlEW2bhybrid. Supplementary Table S6. GO enriched terms of additive expressed genes in the Zheng58 × lx9801 hybrid. Supplementary Table S7. GO enriched terms of non-additive expressed genes in the Zheng58 × lx9801hlEW2b hybrid. Supplementary Table S8. GO enriched terms of non-additive expressed genes in the Zheng58 × lx9801 hybrid. Supplementary Table S9. Maker DEGs with ASE expression pattern in HY hybrid involved in regulation of ear development. Supplementary Table S10. Maker DEGs with ASE expression pattern in both HY and CK hybrids involved in regulation of ear development. Supplementary Table S11. Maker DEGs with ASE expression pattern in CK hybrid involved in regulation of ear development. Supplementary Table S12. Maker DEGs with additive expression pattern in HY hybrid involved in regulation of ear development. Supplementary Table S13. Maker DEGs with additive expression pattern in CK hybrid involved in regulation of ear development. Supplementary Table S14. Maker DEGs with non-additive expression pattern in HY hybrid involved in regulation of ear development. Supplementary Table S15. Maker DEGs with non-additive expression pattern in CK hybrid involved in regulation of ear development.
DOI: 10.5281/zenodo.10304174
title: NSG-adapted reference genome - TRACERx PDX study

description: NSG-adapted mouse reference genome and scripts to reproduce the results from whole-genome sequencing data derived from the tail of a male NOD SCID gamma (NSG) mouse (Mus musculus). The mouse was purchased from Charles River and had carried a subcutaneous human non-small cell lung cancer xenograft.

The raw whole-genome sequencing data are available on ENA under accession number PRJEB65917 (https://www.ebi.ac.uk/ena/browser/view/PRJEB65917).

The original manuscript describing this sample is available here.
DOI: 10.5281/zenodo.10304175
title: NSG-adapted reference genome - TRACERx PDX study

description: NSG-adapted mouse reference genome and scripts to reproduce the results from whole-genome sequencing data derived from the tail of a male NOD SCID gamma (NSG) mouse (Mus musculus). The mouse was purchased from Charles River and had carried a subcutaneous human non-small cell lung cancer xenograft.

The raw whole-genome sequencing data are available on ENA under accession number PRJEB65917 (https://www.ebi.ac.uk/ena/browser/view/PRJEB65917).

The original manuscript describing this sample is available here.
DOI: 10.6084/m9.figshare.7223231
title: STR Data-Uyghur.xlsx

description: The complex topography of Xinjiang Uyghur Autonomous Region of China with three
major mountains and two basins has hindered large-scale human migrations,
admixture and assimilation. Essentially, the specific history and population structure of Uyghurs in
Xinjiang has remained a matter of contention for a long time. Here, we explored
the genetic history of the Uyghurs (n=546) from 5 geographical regions using 27 Y-STR markers.Population
structure analysis supported the Uyghurs were genetically closer to Central
Asian than other populations. We also observed slight difference between
northern Xinjiang and southern Xinjiang. We unveiled a more
complex genetic structure and ancestral admixture history
of Uyghurs, which suggested early human
activities happening in Xinjiang.
 <br>
DOI: 10.6084/m9.figshare.20330257
title: Additional file 4 of DNA methylation subtypes guiding prognostic assessment and linking to responses the DNA methyltransferase inhibitor SGI-110 in urothelial carcinoma

description: Additional file 4. Summary of clinical information in three cohorts.
DOI: 10.6084/m9.figshare.20330254.v1
title: Additional file 3 of DNA methylation subtypes guiding prognostic assessment and linking to responses the DNA methyltransferase inhibitor SGI-110 in urothelial carcinoma

description: Additional file 3. Summary of the regions of methylation classification in three cohorts.
DOI: 10.34740/kaggle/dsv/7685102
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.6084/m9.figshare.20330251.v1
title: Additional file 2 of DNA methylation subtypes guiding prognostic assessment and linking to responses the DNA methyltransferase inhibitor SGI-110 in urothelial carcinoma

description: Additional file 2. Summary of sequencing information in samples.
DOI: 10.6084/m9.figshare.20330251
title: Additional file 2 of DNA methylation subtypes guiding prognostic assessment and linking to responses the DNA methyltransferase inhibitor SGI-110 in urothelial carcinoma

description: Additional file 2. Summary of sequencing information in samples.
DOI: 10.6084/m9.figshare.8796140.v2
title: Epigenome-wide association study of DNA methylation and microRNA expression highlights novel pathways for human complex traits

description: DNA methylation (DNAm) and microRNAs (miRNAs) have been implicated in a wide-range of human diseases. While often studied in isolation, DNAm and miRNAs are not independent. We analyzed associations of expression of 283 miRNAs with DNAm at &gt;400K CpG sites in whole blood obtained from 3565 individuals and identified 227 CpGs at which differential methylation was associated with the expression of 40 nearby miRNAs (<i>cis</i>-miR-eQTMs) at FDR&lt;0.01, including 91 independent CpG sites at <i>r<sup>2</sup></i> &lt; 0.2. <i>cis-</i>miR-eQTMs were enriched for CpGs in promoter and polycomb-repressed state regions, and 60% were inversely associated with miRNA expression. Bidirectional Mendelian randomization (MR) analysis further identified 58 <i>cis</i>-miR-eQTMCpG-miRNA pairs where DNAm changes appeared to drive miRNA expression changes and opposite directional effects were unlikely. Integration of genetic variants in joint analyses revealed an average partial between <i>cis-</i>miR-eQTM CpGs and miRNAs of 2% after conditioning on site-specific genetic variation, suggesting that DNAm is an important epigenetic regulator of miRNA expression. Finally, two-step MR analysis was performed to identify putatively causal CpGs driving miRNA expression in relation to human complex traits. We found that an imprinted region on 14q32 that was previously identified in relation to age at menarche is enriched with <i>cis-</i>miR-eQTMs. Nine CpGs and three miRNAs at this locus tested causal for age at menarche, reflecting novel epigenetic-driven molecular pathways underlying this complex trait. Our study sheds light on the joint genetic and epigenetic regulation of miRNA expression and provides insights into the relations of miRNAs to their targets and to complex phenotypes.
DOI: 10.6084/m9.figshare.11417589
title: The effect of dipeptidyl peptidase-4 inhibitor and glucagon-like peptide-1 receptor agonist in gestational diabetes mellitus: a systematic review

description: Gestational diabetes mellitus (GDM) is the most common complication in pregnancy and affects 13% pregnant women around the world. GDM has both short-term and long-term negative effect on mother and offspring. Dipeptidyl peptidase-4 (DPP-4) inhibitor and glucagon-like peptide-1 receptor agonist (GLP-1 Ra) have shown many extra-benefits in diabetes patients, and may be a promising choice to GDM. Here, we conducted a systematic review of randomized controlled trials to investigate the effect of DPP-4 inhibitor and GLP-1 Ra in GDM. This project was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta Analyses (PRISMA) statement. We searched PubMed, EMBASE and Cochrane library up to November 8 2019 for eligible trials. A total of 982 records were identified and 4 trials (516 participants) met the criteria in the end. The results suggested that DPP-4 inhibitor and GLP-1 Ra can reduce the rate of developing postpartum diabetes, help to normalization of blood glucose and improve insulin resistance and β-cell function. Although the treatments showed beneficial effects in GDM patients, but the present data could not prove it use in GDM. Further clinical trials will be needed.
DOI: 10.6084/m9.figshare.11417589.v1
title: The effect of dipeptidyl peptidase-4 inhibitor and glucagon-like peptide-1 receptor agonist in gestational diabetes mellitus: a systematic review

description: Gestational diabetes mellitus (GDM) is the most common complication in pregnancy and affects 13% pregnant women around the world. GDM has both short-term and long-term negative effect on mother and offspring. Dipeptidyl peptidase-4 (DPP-4) inhibitor and glucagon-like peptide-1 receptor agonist (GLP-1 Ra) have shown many extra-benefits in diabetes patients, and may be a promising choice to GDM. Here, we conducted a systematic review of randomized controlled trials to investigate the effect of DPP-4 inhibitor and GLP-1 Ra in GDM. This project was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta Analyses (PRISMA) statement. We searched PubMed, EMBASE and Cochrane library up to November 8 2019 for eligible trials. A total of 982 records were identified and 4 trials (516 participants) met the criteria in the end. The results suggested that DPP-4 inhibitor and GLP-1 Ra can reduce the rate of developing postpartum diabetes, help to normalization of blood glucose and improve insulin resistance and β-cell function. Although the treatments showed beneficial effects in GDM patients, but the present data could not prove it use in GDM. Further clinical trials will be needed.
DOI: 10.6084/m9.figshare.15087370
title: Additional file 1 of Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression

description: Additional file 1: Overall survival of gastric cancer in five cohorts, CAF stratified by MCPCOUNTER, XCELL, EPIC respectively.
DOI: 10.6084/m9.figshare.15087379
title: Additional file 4 of Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression

description: Additional file 4: TGF-beta pathway, Hedgehog pathway and RTKs ligands list.
DOI: 10.6084/m9.figshare.15087376
title: Additional file 3 of Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression

description: Additional file 3: GSEA results in GSE62254 cohort.
DOI: 10.6084/m9.figshare.15087379.v1
title: Additional file 4 of Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression

description: Additional file 4: TGF-beta pathway, Hedgehog pathway and RTKs ligands list.
DOI: 10.6084/m9.figshare.15087370.v1
title: Additional file 1 of Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression

description: Additional file 1: Overall survival of gastric cancer in five cohorts, CAF stratified by MCPCOUNTER, XCELL, EPIC respectively.
DOI: 10.6084/m9.figshare.15087373.v1
title: Additional file 2 of Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression

description: Additional file 2: GSEA results in entire TCGA cohort, MSI, CIN and GS subtype.
DOI: 10.6084/m9.figshare.20330254
title: Additional file 3 of DNA methylation subtypes guiding prognostic assessment and linking to responses the DNA methyltransferase inhibitor SGI-110 in urothelial carcinoma

description: Additional file 3. Summary of the regions of methylation classification in three cohorts.
DOI: 10.6084/m9.figshare.20330257.v1
title: Additional file 4 of DNA methylation subtypes guiding prognostic assessment and linking to responses the DNA methyltransferase inhibitor SGI-110 in urothelial carcinoma

description: Additional file 4. Summary of clinical information in three cohorts.
DOI: 10.6084/m9.figshare.15087373
title: Additional file 2 of Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression

description: Additional file 2: GSEA results in entire TCGA cohort, MSI, CIN and GS subtype.