cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22599479.v1
title: Additional file 2 of Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation

description: Additional file 2: Table S2. (1) Numbers of DEGs, DMRs and HV-dACRs identified across all samples. (2) Numbers of DEGs identified across all contrasts. (3) Numbers of unique genes identified in intersections between DEGs, DMRs and HV-dACRs. (4) Intersections between DMR and HV-dACRs with TEs and genes.
DOI: 10.6084/m9.figshare.22599475
title: Additional file 1 of The value of preoperative positron emission tomography/computed tomography in differentiating the invasive degree of hypometabolic lung adenocarcinoma

description: Additional file 1. Correlation of parameters with SUVmax.
DOI: 10.6084/m9.figshare.22601240
title: Additional file 25 of Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

description: Additional file 25: Table S16. Comparison of effect size estimates for sex-stratified analysis in the replication cohorts.
DOI: 10.6084/m9.figshare.25160225
title: MaridMap_IncludedPublications2016-2022.xlsx

description: A table containing information of all field investigations of bedforms studied by the MARID research group. Characteristics such as bedform height, length, shape and the processes influencing them can be taken from it, as well as the coordinates of the locations.
DOI: 10.6084/m9.figshare.25160225.v1
title: MaridMap_IncludedPublications2016-2022.xlsx

description: A table containing information of all field investigations of bedforms studied by the MARID research group. Characteristics such as bedform height, length, shape and the processes influencing them can be taken from it, as well as the coordinates of the locations.
DOI: 10.25375/uct.24866163.v1
title: A classified map illustrating alien and native vegetation in the Mpumalanga/Limpopo region (a). Multi-temporal imagery was used to illustrate examples of areas where there is a high concentration of the three woody alien species of main interest: wattles (b), pines (c), and eucalypts (d)

description: This data is from the master's thesis titled- Repeatable methods for classification of alien and native vegetation in the Montane grasslands. Figure 2.6 in the thesis is the result of this dataset. The dataset includes a shapefile of the South African boundary; a GeoTIFF generated from Google Earth Engine containing the classified map of the study area; as well as a QGIS file containing the final map produced for Figure 2.6.Date of data collection: February 2020.Location of data collection: Blyde River Conservancy and its surrounds, in Mpumalanga/Limpopo Provinces, South Africa. <br>
DOI: 10.25375/uct.24866163
title: A classified map illustrating alien and native vegetation in the Mpumalanga/Limpopo region (a). Multi-temporal imagery was used to illustrate examples of areas where there is a high concentration of the three woody alien species of main interest: wattles (b), pines (c), and eucalypts (d)

description: This data is from the master's thesis titled- Repeatable methods for classification of alien and native vegetation in the Montane grasslands. Figure 2.6 in the thesis is the result of this dataset. The dataset includes a shapefile of the South African boundary; a GeoTIFF generated from Google Earth Engine containing the classified map of the study area; as well as a QGIS file containing the final map produced for Figure 2.6.Date of data collection: February 2020.Location of data collection: Blyde River Conservancy and its surrounds, in Mpumalanga/Limpopo Provinces, South Africa. <br>
DOI: 10.25375/uct.24866322
title: Confusion matrix for land cover classification of a multi-temporal Sentinel-2 imagery.

description: This dataset is used to produce Figure 2.6 in the thesis titled- Repeatable methods for classification of alien and native vegetation in the Montane grasslands (2024).The dataset includes an Excel spreadsheet representing the number of sites for that class that were correctly classified as that class and off-diagonal elements represent misclassification between different classes. As well as an r script that compiles the data and runs the code to produce a confusion matrix for land cover classification of a multi-temporal Sentinel-2 imagery in 2019.Period of data collection: February 2020.Location of data collection: Blyde River Canyon Conservancy and its surrounds, in Mpumalanga/Limpopo Provinces, South Africa.<br>
DOI: 10.25375/uct.24866322.v1
title: Confusion matrix for land cover classification of a multi-temporal Sentinel-2 imagery.

description: This dataset is used to produce Figure 2.6 in the thesis titled- Repeatable methods for classification of alien and native vegetation in the Montane grasslands (2024).The dataset includes an Excel spreadsheet representing the number of sites for that class that were correctly classified as that class and off-diagonal elements represent misclassification between different classes. As well as an r script that compiles the data and runs the code to produce a confusion matrix for land cover classification of a multi-temporal Sentinel-2 imagery in 2019.Period of data collection: February 2020.Location of data collection: Blyde River Canyon Conservancy and its surrounds, in Mpumalanga/Limpopo Provinces, South Africa.<br>
DOI: 10.25375/uct.24885267
title: Combined HMM post-processing analyses of river plots and bar plots of the gross (grey) and net (colour) change in each land cover class (i.e. NVF, Aliens, Indigenous Forest, Grassland, and Mixed Woody Grassland) under their respective management classes (i.e. Barloworld/Commercial, Communal, Forestry/Conservation, and Plantations) between 1990 and 2020

description: This dataset was used to produce land cover change analyses for Figures 3.8 (A-D) and Figures 3.9 (A -D) as part of a master's thesis titled- Repeatable methods for classification of alien and native vegetation in the Montane grasslands (2024).This dataset encompasses forty-five data entries. This includes 11 Hidden Markov Model (HMM) post-processed GeoTIFFS for 1990 until 2020 under each management class (i.e. Barloworld/Commercial, Communal, Forestry/Conservation, and Plantations). An r. script is also included to combine all GeoTIFFS then format and run code to produce river plots and bar graphs for the four management classes. The dataset aims to illustrate the changes among each land cover class (i.e. NVF, Aliens, Indigenous Forest, Grassland, and Mixed Woody Grassland) under the different management classes. This helps identify drivers of land cover change in the various management classes and the entire study area. It is also important to note that the land cover changes will portray realistic changes because they are HMM post-processed.Date of data collection: February 2020Location of data collection: Blyde River Canyon Conservancy and its surrounds, in Mpumalanga/Limpopo Provinces, South Africa.
DOI: 10.25375/uct.24885267.v1
title: Combined HMM post-processing analyses of river plots and bar plots of the gross (grey) and net (colour) change in each land cover class (i.e. NVF, Aliens, Indigenous Forest, Grassland, and Mixed Woody Grassland) under their respective management classes (i.e. Barloworld/Commercial, Communal, Forestry/Conservation, and Plantations) between 1990 and 2020

description: This dataset was used to produce land cover change analyses for Figures 3.8 (A-D) and Figures 3.9 (A -D) as part of a master's thesis titled- Repeatable methods for classification of alien and native vegetation in the Montane grasslands (2024).This dataset encompasses forty-five data entries. This includes 11 Hidden Markov Model (HMM) post-processed GeoTIFFS for 1990 until 2020 under each management class (i.e. Barloworld/Commercial, Communal, Forestry/Conservation, and Plantations). An r. script is also included to combine all GeoTIFFS then format and run code to produce river plots and bar graphs for the four management classes. The dataset aims to illustrate the changes among each land cover class (i.e. NVF, Aliens, Indigenous Forest, Grassland, and Mixed Woody Grassland) under the different management classes. This helps identify drivers of land cover change in the various management classes and the entire study area. It is also important to note that the land cover changes will portray realistic changes because they are HMM post-processed.Date of data collection: February 2020Location of data collection: Blyde River Canyon Conservancy and its surrounds, in Mpumalanga/Limpopo Provinces, South Africa.
DOI: 10.5281/zenodo.10409777
title: Wind measurement data from the publication: "Development of a load model validation framework applied to synthetic turbulent wind field evaluation"

description: Dataset description:

This datasat represents supplementary material used in the contribution "Development of a load model validation framework applied tosynthetic turbulent wind field evaluation" by Meyer, Huhn and Gottschall.

Wind measurements from the Testfeld BHV are made available. For installation details, see the mentioned reference.

 

File description:



Lidar_HWS.nc - Horizontal wind speed measurements (10 min averages) from a WindCube V2 vertical profiler for one day with a low-level jet occurrence (



2021-04-20)



Cups_HWS.nc - Horizontal wind speed measurements (10 min averages) from cup anemometer installed on a met mast for the same day

Ensemble_averaged_Spectra.nc - Ensemble averaged spectra for neutral and near neutral situations from a Gill Windmaster at 110m above ground level, used to fit the Mann and KSEC model parameters


 

Referencing:

When used, please cite like the following:

Meyer, Paul J., Matthias L. Huhn, and Julia Gottschall. 2024. "Development of a Load Model Validation Framework Applied to Synthetic Turbulent Wind Field Evaluation" Energies 17, no. 4: 797. https://doi.org/10.3390/en17040797
DOI: 10.5281/zenodo.10409776
title: Wind measurement data from the publication: "Development of a load model validation framework applied to synthetic turbulent wind field evaluation"

description: Dataset description:

This datasat represents supplementary material used in the contribution "Development of a load model validation framework applied tosynthetic turbulent wind field evaluation" by Meyer, Huhn and Gottschall.

Wind measurements from the Testfeld BHV are made available. For installation details, see the mentioned reference.

 

File description:



Lidar_HWS.nc - Horizontal wind speed measurements (10 min averages) from a WindCube V2 vertical profiler for one day with a low-level jet occurrence (



2021-04-20)



Cups_HWS.nc - Horizontal wind speed measurements (10 min averages) from cup anemometer installed on a met mast for the same day

Ensemble_averaged_Spectra.nc - Ensemble averaged spectra for neutral and near neutral situations from a Gill Windmaster at 110m above ground level, used to fit the Mann and KSEC model parameters


 

Referencing:

When used, please cite like the following:

Meyer, Paul J., Matthias L. Huhn, and Julia Gottschall. 2024. "Development of a Load Model Validation Framework Applied to Synthetic Turbulent Wind Field Evaluation" Energies 17, no. 4: 797. https://doi.org/10.3390/en17040797
DOI: 10.6084/m9.figshare.1632160
title: Epithelial morphological reversion drives Profilin-1-induced elevation of p27<sup>kip1</sup> in mesenchymal triple-negative human breast cancer cells through AMP-activated protein kinase activation

description: Profilin-1 (Pfn1) is an important regulator of actin polymerization that is downregulated in human breast cancer. Previous studies have shown Pfn1 has a tumor-suppressive effect on mesenchymal-like triple-negative breast cancer cells, and Pfn1-induced growth suppression is partly mediated by upregulation of cell-cycle inhibitor p27<sup>kip1</sup> (p27). In this study, we demonstrate that Pfn1 overexpression leads to accumulation of p27 through promoting AMPK activation and AMPK-dependent phosphorylation of p27 on T198 residue, a post-translational modification that leads to increased protein stabilization of p27. This pathway is mediated by Pfn1-induced epithelial morphological reversion of mesenchymal breast cancer through cadherin-mediated restoration of adherens junctions. These findings not only elucidate a potential mechanism of how Pfn1 may inhibit proliferation of mesenchymal breast cancer cells, but also highlight a novel pathway of cadherin-mediated p27 induction and therefore cell-cycle control in cells.
DOI: 10.6084/m9.figshare.22599482.v1
title: Additional file 3 of Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation

description: Additional file 3: Dataset S1. List of DEGs identified within 18 accessions among WT samples.
DOI: 10.6084/m9.figshare.22599500.v1
title: Additional file 8 of Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation

description: Additional file 8: Dataset S5. Names and coordinates of DEGs universal across 19  mutant vs WT contrasts.
DOI: 10.48612/msupe/v669-u87g-tpdf
title: Методика "Проблемные ситуации": результаты бикластеризации

description: В рамках  апробации методики «Проблемные ситуации»  обследовано 67 человек с тяжелыми хроническими психическими расстройствами, проходивших стационарную судебно-психиатрическую экспертизу в связи с решением вопроса об изменении гражданско-правового статуса в 2021 - 2022 гг. В отношении 12  человек судебно-психиатрическое заключение соответствовало дееспособности; 24 - ограниченной дееспособности; 31 - недееспособности. Проблемные ситуации, относящиеся к четырем тематическим блокам (понимание гражданско-правовых вопросов;  межличностных и социальных аспектов; медицинских вопросов; чрезвычайных ситуаций),  на основании наличия в ответах испытуемых выделенных ранее  вторичных параметров, оценивались как решенные верно (1) или неверно (0) . Полученная в результате бинарная матрица преобразовывалась с применением процедуры бикластеризации с целью выделения кластеров испытуемых, характеризующихся сочетаниями параметров, которые отражали  верность/неверность решения проблемных ситуаций четырех  тематических блоков. Установлено, что  представленность  испытуемых с  экспертным выводом, соответствующим  недееспособности, дееспособности или ограниченной дееспособности, в полученных  кластерах достоверно различается, что доказывает прогностическую валидность методики "Проблемные ситуации".
DOI: 10.6084/m9.figshare.14391424.v1
title: Additional file 1 of Identification of prognostic alternative splicing events related to the immune microenvironment of hepatocellular carcinoma

description: Additional file 1. Screening differentially expressed AS events related to prognosis by univariate analysis in the HCC cohort.
DOI: 10.6084/m9.figshare.22601267
title: Additional file 29 of Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

description: Additional file 29: Table S19. Comparison of sex-stratified effect sizes in the UK Biobank for BMI, waist hip ratio adjusted for BMI, alcohol use, and smoking status.
DOI: 10.6084/m9.figshare.13166579
title: Scalable Algorithms for Large Competing Risks Data

description: This paper develops two orthogonal contributions to scalable sparse regression for competing risks time-to-event data. First, we study and accelerate the broken adaptive ridge method (BAR), a surrogate <i>ℓ</i>
 <sub>0</sub>-based iteratively reweighted <i>ℓ</i>
 <sub>2</sub>-penalization algorithm that achieves sparsity in its limit, in the context of the Fine-Gray (1999) proportional subdistributional hazards (PSH) model. In particular, we derive a new algorithm for BAR regression, named cycBAR, that performs cyclic update of each coordinate using an explicit thresholding formula. The new cycBAR algorithm effectively avoids fitting multiple reweighted <i>ℓ</i>
 <sub>2</sub>-penalizations and thus yields impressive speedups over the original BAR algorithm. Second, we address a pivotal computational issue related to fitting the PSH model. Specifically, the computation costs of the log-pseudo likelihood and its derivatives for PSH model grow at the rate of <i>O</i>(<i>n</i>
 <sup>2</sup>) with the sample size <i>n</i> in current implementations. We propose a novel forward-backward scan algorithm that reduces the computation costs to <i>O</i>(<i>n</i>). The proposed method applies to both unpenalized and penalized estimation for the PSH model and has exhibited drastic speedups over current implementations. Finally, combining the two algorithms can yields &gt;1,000 fold speedups over the original BAR algorithm. Illustrations of the impressive scalability of our proposed algorithm for large competing risks data are given using both simulations and a United States Renal Data System data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.25160780
title: Coding sequences of PME-domain and pro-region of Type-1 PME in representative plants

description: Coding sequences of PME-domain and pro-region of Type-1 PME in representative plants
DOI: 10.6084/m9.figshare.25160780.v1
title: Coding sequences of PME-domain and pro-region of Type-1 PME in representative plants

description: Coding sequences of PME-domain and pro-region of Type-1 PME in representative plants
DOI: 10.35097/1918
title: Polymersome-Encapsulated Chemosensors
DOI: 10.6084/m9.figshare.25160993
title: Raw data from fusion gene analysis by LIR inference

description: Raw data from fusion gene analysis by LIR inference
DOI: 10.6084/m9.figshare.25160993.v1
title: Raw data from fusion gene analysis by LIR inference

description: Raw data from fusion gene analysis by LIR inference
DOI: 10.6084/m9.figshare.11593977
title: Diagonally Dominant Principal Component Analysis

description: We consider the problem of decomposing a large covariance matrix into the sum of a low-rank matrix and a diagonally dominant matrix, and we call this problem the “diagonally dominant principal component analysis (DD-PCA).” DD-PCA is an effective tool for designing statistical methods for strongly correlated data. We showcase the use of DD-PCA in two statistical problems: covariance matrix estimation and global detection in multiple testing. Using the output of DD-PCA, we propose a new estimator for estimating a large covariance matrix with factor structure. Thanks to a nice property of diagonally dominant matrices, this estimator enjoys the advantage of simultaneous good estimation of the covariance matrix and the precision matrix (by a plain inversion). A plug-in of this estimator to linear discriminant analysis and portfolio optimization yields appealing performance in real data. We also propose two new tests for testing the global null hypothesis in multiple testing when the <i>z</i>-scores have a factor covariance structure. Both tests first use DD-PCA to adjust the individual <i>p</i>-values and then plug in the adjusted <i>p</i>-values to the higher criticism (HC) test. These new tests significantly improve over the HC test and compare favorably with other existing tests. For computation of DD-PCA, we propose an iterative projection algorithm and an ADMM algorithm. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.11593977.v1
title: Diagonally-Dominant Principal Component Analysis

description: We consider the problem of decomposing a large covariance matrix into the sum of a low-rank matrix and a diagonally dominant matrix, and we call this problem the “Diagonally-Dominant Principal Component Analysis (DD-PCA)”. DD-PCA is an effective tool for designing statistical methods for strongly correlated data. We showcase the use of DD-PCA in two statistical problems: covariance matrix estimation, and global detection in multiple testing. Using the output of DD-PCA, we propose a new estimator for estimating a large covariance matrix with factor structure. Thanks to a nice property of diagonally dominant matrices, this estimator enjoys the advantage of simultaneous good estimation of the covariance matrix and the precision matrix (by a plain inversion). A plug-in of this estimator to linear discriminant analysis and portfolio optimization yields appealing performance in real data. We also propose two new tests for testing the global null hypothesis in multiple testing when the <i>z</i>-scores have a factor covariance structure. Both tests first use DD-PCA to adjust the individual <i>p</i>-values and then plug in the adjusted <i>p</i>-values to the Higher Criticism (HC) test. These new tests significantly improve over the HC test and compare favorably with other existing tests. For computation of DD-PCA, we propose an iterative projection algorithm and an ADMM algorithm.
DOI: 10.6084/m9.figshare.22601486
title: Additional file 3 of Functional noninvasive detection of glycolytic pancreatic ductal adenocarcinoma

description: Additional file 3.
DOI: 10.6084/m9.figshare.14737076.v1
title: Additional file 4 of Coronavirus disease (COVID-19) pandemic: an overview of systematic reviews

description: Additional file 4: Appendix 4. Table of overlapping studies, containing the list of primary studies included, their visual overlap in individual systematic reviews, and the number in how many reviews each primary study was included.
DOI: 10.6084/m9.figshare.22601492
title: Additional file 5 of Functional noninvasive detection of glycolytic pancreatic ductal adenocarcinoma

description: Additional file 5.
DOI: 10.6084/m9.figshare.1632735
title: Epigenetic regulation of autophagy by the methyltransferase EZH2 through an MTOR-dependent pathway

description: Macroautophagy is an evolutionarily conserved cellular process involved in the clearance of proteins and organelles. Although the autophagy regulation machinery has been widely studied, the key epigenetic control of autophagy process still remains unknown. Here we report that the methyltransferase EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) epigenetically represses several negative regulators of the MTOR (mechanistic target of rapamycin [serine/threonine kinase]) pathway, such as <i>TSC2</i>, <i>RHOA</i>, <i>DEPTOR</i>, <i>FKBP11</i>, <i>RGS16</i> and <i>GPI</i>. EZH2 was recruited to these genes promoters via MTA2 (metastasis associated 1 family, member 2), a component of the nucleosome remodeling and histone deacetylase (NuRD) complex. MTA2 was identified as a new chromatin binding protein whose association with chromatin facilitated the subsequent recruitment of EZH2 to silenced targeted genes, especially <i>TSC2</i>. Downregulation of TSC2 (tuberous sclerosis 2) by EZH2 elicited MTOR activation, which in turn modulated subsequent MTOR pathway-related events, including inhibition of autophagy. In human colorectal carcinoma (CRC) tissues, the expression of MTA2 and EZH2 correlated negatively with expression of TSC2, which reveals a novel link among epigenetic regulation, the MTOR pathway, autophagy induction, and tumorigenesis.
DOI: 10.6084/m9.figshare.25161168
title: Testing the salinity of Cambrian to Silurian epicratonic seas

description: Tables S1–S6.
DOI: 10.6084/m9.figshare.25161168.v1
title: Testing the salinity of Cambrian to Silurian epicratonic seas

description: Tables S1–S6.