cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21581826
title: Supplementary Material for: Genomically stable gastric cancer characterized by hypomethylation in Wnt signal cascade

description: Introduction Gastric cancer is divided into four subtypes by their molecular features linked with genetic alterations, e.g., Epstein-Barr virus (EBV), microsatellite instability-high (MSI-high), chromosomal instability (CIN), and genomically stable (GS), called as TCGA classification. In this study, we tried to clarify the epigenetic features of the four GC subtypes according to aberrant methylation status in 23 loci. Methods A total of 98 gastric cancers and their normal gastric mucosa samples were included in this study. We divided gastric cancers into TCGA subtypes which were determined in line with MSI-high, EBV, CIN, to GS by their molecular features. The 13 loci of polymorphic microsatellite sequences were used to determine loss of heterogeneity (LOH) for the detection of CIN. The MSI status was determined by three mononucleotide repeat markers. Infection of EBV was determined by recovering EBV BNRF1 sequence from genomic DNA collected from gastric cancers. Methylation status of 23 loci was investigated by the combined bisulfite restriction analysis (COBRA). Status of other findings, e.g., KRAS mutations, HER2 expression status and infection of helicobacter pylori were confirmed. Results Gastric cancers were divided into MSI (13%), EBV (7%), CIN (53%), and GS (27%). By histological classification, poorly differentiated adenocarcinoma (por) was more in tumors categorized in MSI-high, and GS and signet-ring cell carcinoma (sig) was more in GS. Among the 23 loci investigated their methylation status, 18 loci were significantly hypermethylated in caner tissues. A unsupervised clustering divided gastric cancers into two clusters, and revealed that most GS tumors clustered together in a cluster that exhibited lower methylation levels, distinct from the other subtypes. The inter-variable clustering revealed that a cluster contained the three loci (SFRP2-region 1/2 and APC) belonging to the Wnt signal cascade (Wnt-associated loci). The mean methylation score of Wnt-associated loci was the lowest in GS tumors (MSI-high: 2.7 [95% confidence interval (CI), 2.3-2.9]; EBV:2.1[1.2-3.1]; CIN: 2.4 [2.2-2.7]; GS: 1.3 [0.8-0.7]). In contrast, the mean methylation score of the other 15 loci was significantly higher in MSI-high, while that in GS was as same as that in EBV or CIN (MSI- high: 10.4 [8.3-12.4]; EBV:5.7 [1.7-9.7]; CIN: 4.4 [3.6-5.1]; GS: 3.4 [2.2-4.6]). Additionally, the lower methylation score of Wnt-associated loci was observed only in sig tumors. Conclusions GS subtype tumors have the potential to possess distinct signatures in DNA hypomethylation profiles in Wnt signaling pathway, especially in signet-ring cell carcinoma.
DOI: 10.6084/m9.figshare.21581826.v1
title: Supplementary Material for: Genomically stable gastric cancer characterized by hypomethylation in Wnt signal cascade

description: Introduction Gastric cancer is divided into four subtypes by their molecular features linked with genetic alterations, e.g., Epstein-Barr virus (EBV), microsatellite instability-high (MSI-high), chromosomal instability (CIN), and genomically stable (GS), called as TCGA classification. In this study, we tried to clarify the epigenetic features of the four GC subtypes according to aberrant methylation status in 23 loci. Methods A total of 98 gastric cancers and their normal gastric mucosa samples were included in this study. We divided gastric cancers into TCGA subtypes which were determined in line with MSI-high, EBV, CIN, to GS by their molecular features. The 13 loci of polymorphic microsatellite sequences were used to determine loss of heterogeneity (LOH) for the detection of CIN. The MSI status was determined by three mononucleotide repeat markers. Infection of EBV was determined by recovering EBV BNRF1 sequence from genomic DNA collected from gastric cancers. Methylation status of 23 loci was investigated by the combined bisulfite restriction analysis (COBRA). Status of other findings, e.g., KRAS mutations, HER2 expression status and infection of helicobacter pylori were confirmed. Results Gastric cancers were divided into MSI (13%), EBV (7%), CIN (53%), and GS (27%). By histological classification, poorly differentiated adenocarcinoma (por) was more in tumors categorized in MSI-high, and GS and signet-ring cell carcinoma (sig) was more in GS. Among the 23 loci investigated their methylation status, 18 loci were significantly hypermethylated in caner tissues. A unsupervised clustering divided gastric cancers into two clusters, and revealed that most GS tumors clustered together in a cluster that exhibited lower methylation levels, distinct from the other subtypes. The inter-variable clustering revealed that a cluster contained the three loci (SFRP2-region 1/2 and APC) belonging to the Wnt signal cascade (Wnt-associated loci). The mean methylation score of Wnt-associated loci was the lowest in GS tumors (MSI-high: 2.7 [95% confidence interval (CI), 2.3-2.9]; EBV:2.1[1.2-3.1]; CIN: 2.4 [2.2-2.7]; GS: 1.3 [0.8-0.7]). In contrast, the mean methylation score of the other 15 loci was significantly higher in MSI-high, while that in GS was as same as that in EBV or CIN (MSI- high: 10.4 [8.3-12.4]; EBV:5.7 [1.7-9.7]; CIN: 4.4 [3.6-5.1]; GS: 3.4 [2.2-4.6]). Additionally, the lower methylation score of Wnt-associated loci was observed only in sig tumors. Conclusions GS subtype tumors have the potential to possess distinct signatures in DNA hypomethylation profiles in Wnt signaling pathway, especially in signet-ring cell carcinoma.
DOI: 10.15129/2b2b4637-2bbc-4c57-9acf-79512d4ba63e
title: Data for: "Silica Coated Colloidal Semiconductor Quantum Dot Supracrystal Microlasers"

description: This data relates to the conference paper and will be made public on the day of the conference, 13 November 2022. A novel approach for silica-coated colloidal quantum dot supracrystal microsphere lasers is demonstrated. These lasers consist of an assembly of red-emitting CdSxSe1-x/ZnS quantum dots that act as both the gain medium and the optical cavity, and have great potential for biosensing, bioimaging, and integrated photonics.
DOI: 10.34740/kaggle/dsv/4536214
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.34740/kaggle/dsv/4536233
title: 2021 World Population (updated daily)
DOI: 10.5281/zenodo.7108816
title: Subtitled speech: Phenomenology of tickertape synesthesia

description: Instropective description of ticker-tape synesthesia, and description of their perception when listening to noises, pseudowords and other stimuli. Here are included: the dataset of questionnaire answers, the audio stimuli (noises, including humann, animal and noises), and the english version of the questionnaire.
DOI: 10.5281/zenodo.7108817
title: Subtitled speech: Phenomenology of tickertape synesthesia

description: Instropective description of ticker-tape synesthesia, and description of their perception when listening to noises, pseudowords and other stimuli.
DOI: 10.5281/zenodo.7334319
title: Subtitled speech: Phenomenology of tickertape synesthesia

description: Instropective description of ticker-tape synesthesia, and description of their perception when listening to noises, pseudowords and other stimuli. Here are included: the dataset of questionnaire answers, the audio stimuli (noises, including humann, animal and noises), and the english version of the questionnaire.
DOI: 10.5281/zenodo.7196777
title: CN-N (version 1): a crop-specific, 1 km-resolution nitrogen rate data product in China over 2004–2016

description: CN-N version 1: A dataset of crop-specific, 1 km resolution nitrogen rate for rice, wheat and maize in China over 2004-2016
DOI: 10.5281/zenodo.7196776
title: CN-N (version 1): a crop-specific, 1 km-resolution nitrogen rate data product in China over 2004–2016

description: CN-N version 1: A dataset of crop-specific, 1 km resolution nitrogen rate for rice, wheat and maize in China over 2004-2016
DOI: 10.6084/m9.figshare.21581847
title: Supplementary_Material

description: The three-dimensional structure of AP-III-a4 and ENO1, and PROCHECK assessment results
DOI: 10.6084/m9.figshare.21581847.v1
title: Supplementary_Material

description: The three-dimensional structure of AP-III-a4 and ENO1, and PROCHECK assessment results
DOI: 10.6084/m9.figshare.21581823
title: Compiled DMS and VEP predictions

description: Compiled DMS measurements and variant effect prediction outputs for 26 proteins.
DOI: 10.6084/m9.figshare.21581902
title: Additional file 2 of Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome

description: Additional file 2: Table S3 A list of the Hungate genome files used to create the simulated data. Shown in the table are the Hungate genome files used to create the simulated data. They are separated into the complete (single-contig) and draft (multi-contig) genomes, as this meant they were treated differently. The tool InSilicoSeq was used to create the simulated data, and has the capability to handle draft genomes. The draft, multi-contig genomes were used with the --draft option, and the complete, single-contig genomes were used with the --genomes option. These are the same files added to the custom databases containing Hungate genome sequences (Hungate, RefHun, RefHunRUG and HunRUG).
DOI: 10.6084/m9.figshare.21581902.v1
title: Additional file 2 of Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome

description: Additional file 2: Table S3 A list of the Hungate genome files used to create the simulated data. Shown in the table are the Hungate genome files used to create the simulated data. They are separated into the complete (single-contig) and draft (multi-contig) genomes, as this meant they were treated differently. The tool InSilicoSeq was used to create the simulated data, and has the capability to handle draft genomes. The draft, multi-contig genomes were used with the --draft option, and the complete, single-contig genomes were used with the --genomes option. These are the same files added to the custom databases containing Hungate genome sequences (Hungate, RefHun, RefHunRUG and HunRUG).
DOI: 10.6084/m9.figshare.21581932
title: Additional file 2 of Deeper genomic insights into tomato CLE genes repertoire identify new active peptides

description: Additional file 2.
DOI: 10.6084/m9.figshare.21581932.v1
title: Additional file 2 of Deeper genomic insights into tomato CLE genes repertoire identify new active peptides

description: Additional file 2.
DOI: 10.6084/m9.figshare.21581984
title: Additional file 2 of A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition

description: Additional file 2: Table S1. List of the proteins identified by TChAP.
DOI: 10.6084/m9.figshare.21581984.v1
title: Additional file 2 of A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition

description: Additional file 2: Table S1. List of the proteins identified by TChAP.
DOI: 10.6084/m9.figshare.21581987
title: Additional file 3 of A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition

description: Additional file 3: Table S2. MS Data set of Ty1 proteins identified by TChAP.
DOI: 10.6084/m9.figshare.21581987.v1
title: Additional file 3 of A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition

description: Additional file 3: Table S2. MS Data set of Ty1 proteins identified by TChAP.
DOI: 10.6084/m9.figshare.21581990
title: Additional file 4 of A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition

description: Additional file 4: Table S3. Gene Ontology enrichment analysis of Biological Process and Cellular Component of Ty1 IN partners identified by TChAP.
DOI: 10.6084/m9.figshare.21581990.v1
title: Additional file 4 of A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition

description: Additional file 4: Table S3. Gene Ontology enrichment analysis of Biological Process and Cellular Component of Ty1 IN partners identified by TChAP.
DOI: 10.6084/m9.figshare.21581993
title: Additional file 5 of A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition

description: Additional file 5: Table S4. Identification of IN phosphorylated residues. (A) Netphos 3.1 server-prediction results of Ty1 IN. (B) Identification of IN phosphorylated peptides by LC MS-MS.
DOI: 10.6084/m9.figshare.21581993.v1
title: Additional file 5 of A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition

description: Additional file 5: Table S4. Identification of IN phosphorylated residues. (A) Netphos 3.1 server-prediction results of Ty1 IN. (B) Identification of IN phosphorylated peptides by LC MS-MS.
DOI: 10.6084/m9.figshare.21582011
title: Additional file 1 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 1. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for linear interaction effects with $$M=48$$ M = 48 .
DOI: 10.6084/m9.figshare.21582011.v1
title: Additional file 1 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 1. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for linear interaction effects with $$M=48$$ M = 48 .
DOI: 10.6084/m9.figshare.21582014
title: Additional file 2 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 2. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for linear interaction effects with $$M=192$$ M = 192 .
DOI: 10.6084/m9.figshare.21582014.v1
title: Additional file 2 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 2. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for linear interaction effects with $$M=192$$ M = 192 .
DOI: 10.6084/m9.figshare.21582017
title: Additional file 3 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 3. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for symmetric interaction effects with $$M=48$$ M = 48 .
DOI: 10.6084/m9.figshare.21582017.v1
title: Additional file 3 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 3. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for symmetric interaction effects with $$M=48$$ M = 48 .
DOI: 10.6084/m9.figshare.21582020
title: Additional file 4 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 4. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for symmetric interaction effects with $$M=192$$ M = 192 .
DOI: 10.6084/m9.figshare.21582020.v1
title: Additional file 4 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 4. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for symmetric interaction effects with $$M=192$$ M = 192 .
DOI: 10.6084/m9.figshare.21582023
title: Additional file 5 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 5. Simulation results (Power) for linear interaction effects with $$M=48$$ M = 48 of GLMM and GEE at aggregated level with AR1 correlation structure $$\sigma_{c}^{2}=0.8,\ r=0.8$$ σ c 2 = 0.8 , r = 0.8 under USDo2 with different hypothesis testing methods and with different estimators for the standard error of the parameter estimates.
DOI: 10.6084/m9.figshare.21582023.v1
title: Additional file 5 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

description: Additional file 5. Simulation results (Power) for linear interaction effects with $$M=48$$ M = 48 of GLMM and GEE at aggregated level with AR1 correlation structure $$\sigma_{c}^{2}=0.8,\ r=0.8$$ σ c 2 = 0.8 , r = 0.8 under USDo2 with different hypothesis testing methods and with different estimators for the standard error of the parameter estimates.
DOI: 10.6084/m9.figshare.21582025
title: Additional file 1 of A randomised controlled trial to compare clinical and cost-effectiveness of an online parent-led treatment for child anxiety problems with usual care in the context of COVID-19 delivered in Child and Adolescent Mental Health Services in the UK (Co-CAT): a study protocol for a randomised controlled trial

description: Additional file 1. Indicative topic guides.
DOI: 10.6084/m9.figshare.21582025.v1
title: Additional file 1 of A randomised controlled trial to compare clinical and cost-effectiveness of an online parent-led treatment for child anxiety problems with usual care in the context of COVID-19 delivered in Child and Adolescent Mental Health Services in the UK (Co-CAT): a study protocol for a randomised controlled trial

description: Additional file 1. Indicative topic guides.
DOI: 10.6084/m9.figshare.21582050
title: Additional file 1 of The effect of mindfulness and metacognition on anxiety symptoms: a case-control study

description: Additional file 1.
DOI: 10.6084/m9.figshare.21582050.v1
title: Additional file 1 of The effect of mindfulness and metacognition on anxiety symptoms: a case-control study

description: Additional file 1.
DOI: 10.6084/m9.figshare.21582056.v1
title: Additional file 1 of Generalized class polynomials

description: Supplementary file 1 (txt 0 KB)
DOI: 10.6084/m9.figshare.21582056
title: Additional file 1 of Generalized class polynomials

description: Supplementary file 1 (txt 0 KB)
DOI: 10.6084/m9.figshare.21582037
title: Additional file 1 of Eight-year experience of maternal death surveillance in Morocco: qualitative study of stakeholders’ views at a subnational level

description: Additional file 1. Assessment of health region level MDSS in Morocco. Figure S1. Score by health region for each level of implementation. Figure S2. Implementation progress on the schematic scoring scale.
DOI: 10.6084/m9.figshare.21582037.v1
title: Additional file 1 of Eight-year experience of maternal death surveillance in Morocco: qualitative study of stakeholders’ views at a subnational level

description: Additional file 1. Assessment of health region level MDSS in Morocco. Figure S1. Score by health region for each level of implementation. Figure S2. Implementation progress on the schematic scoring scale.
DOI: 10.6084/m9.figshare.21582071
title: Additional file 2 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

description: Additional file 2: Matching matrix of Levine32 dataset.
DOI: 10.6084/m9.figshare.21582071.v1
title: Additional file 2 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

description: Additional file 2: Matching matrix of Levine32 dataset.
DOI: 10.6084/m9.figshare.21582074.v1
title: Additional file 3 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

description: Additional file 3: Matching matrix of Bagwell dataset.
DOI: 10.6084/m9.figshare.21582074
title: Additional file 3 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

description: Additional file 3: Matching matrix of Bagwell dataset.
DOI: 10.6084/m9.figshare.21582077
title: Additional file 4 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

description: Additional file 4: Matching matrix of Kimmey-BM dataset.
DOI: 10.6084/m9.figshare.21582077.v1
title: Additional file 4 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

description: Additional file 4: Matching matrix of Kimmey-BM dataset.
DOI: 10.6084/m9.figshare.21582080
title: Additional file 5 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

description: Additional file 5: Matching matrix of Kimmey-PBMC dataset.
DOI: 10.6084/m9.figshare.21582080.v1
title: Additional file 5 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

description: Additional file 5: Matching matrix of Kimmey-PBMC dataset.
DOI: 10.6084/m9.figshare.21582122
title: Additional file 2 of Italian law n. 219/2017 on consent and advance directives: survey among Ethics Committees on their involvement and possible role

description: Additional file 2. Dataset with responses to the questionnaire (Italian).
DOI: 10.6084/m9.figshare.21582125
title: Additional file 3 of Italian law n. 219/2017 on consent and advance directives: survey among Ethics Committees on their involvement and possible role

description: Additional file 3. Dateset with responses to the questionnaire (English transaltion).
DOI: 10.6084/m9.figshare.21582125.v1
title: Additional file 3 of Italian law n. 219/2017 on consent and advance directives: survey among Ethics Committees on their involvement and possible role

description: Additional file 3. Dateset with responses to the questionnaire (English transaltion).
DOI: 10.6084/m9.figshare.21582127
title: Additional file 1 of A simple parasitological technique to increase detection of Strongyloides stercoralis in Bolivian primary health care system

description: Additional file 1. DATASET CBBA_SS: file containing the digitised database of the questionnaires and laboratory records coded.
DOI: 10.6084/m9.figshare.21582127.v1
title: Additional file 1 of A simple parasitological technique to increase detection of Strongyloides stercoralis in Bolivian primary health care system

description: Additional file 1. DATASET CBBA_SS: file containing the digitised database of the questionnaires and laboratory records coded.
DOI: 10.3886/e183081
title: Quantifying the Cost of Web Accessibility Barriers for Blind Users

description: This study quantifies the time disparity experienced by Blind users when they encounter web accessibility barriers. The resulting data illustrates a significant reason why web accessibility is imperative, by highlighting and measuring the cost of inaccessibility through the lens of the inequity that accessibility barriers place on the time of users with disabilities in both personal and business settings.
DOI: 10.3886/e183081v1
title: Quantifying the Cost of Web Accessibility Barriers for Blind Users

description: This study quantifies the time disparity experienced by Blind users when they encounter web accessibility barriers. The resulting data illustrates a significant reason why web accessibility is imperative, by highlighting and measuring the cost of inaccessibility through the lens of the inequity that accessibility barriers place on the time of users with disabilities in both personal and business settings.
DOI: 10.6084/m9.figshare.21582220
title: Additional file 1 of Bacterial colonization of the upper airways of children positive and negative for SARS-CoV-2 during the COVID-19 pandemic

description: Additional file 1. PCR Results.