cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12623172.v1
title: Additional file 1 of The polyphenol-rich extract from chokeberry (Aronia melanocarpa L.) modulates gut microbiota and improves lipid metabolism in diet-induced obese rats

description: Additional file 1 Table S1. Chromatography condition. Table S2. Primer sequences. Figure S1. The weight (g) of heart, kidney, spleen, lung, pancreas and testicle in the Control, HF, AM and SV group rat. Values are means ± SEMs. Figure S2. Gut microbiota compositions at the genus level in HF, AM and SV group at day 10, day 20, day 30, day 40 after diet intervention. Values are presented as mean ± SEM. *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; ns P &gt; 0.05. Figure S3. The relative contents of bile acids in HF, AM and SV group rat at day 10, day 20, day 30, day 40 after diet intervention. Values are presented as mean ± SEM. *P&lt;0.05; **P&lt;0.01; ***P&lt;0.001; ns P&gt;0.05. Figure S4. Microbiota compositions at the genus level in HF, AM and SV group at day 40 after diet intervention. Values are presented as mean ± SEM. *P&lt;0.05; **P&lt;0.01; ***P&lt;0.001; ns P&gt;0.05. Figure S5. The weight (g) of liver, kidney, spleen, iWAT, eWAT, pWAT and iBAT in FMT-HF and FMT-AM group rat. Values are means ± SEMs. Figure S6. Microbiota compositions at the genus level in FMT-HF and FMT-AM group at day 10, day 20, day 30 after microbiota transplantation from CBPs treatment rat. Values are presented as mean ± SEM. *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; ns P &gt; 0.05.
DOI: 10.6084/m9.figshare.13671755
title: An epithelial-mesenchymal transition-related long non-coding RNA signature to predict overall survival and immune microenvironment in kidney renal clear cell carcinoma

description: Kidney renal clear cell carcinoma (ccRCC) is a malignant tumor originating from renal tubular epithelium, lncRNAs can regulate the occurrence and development of EMT by targeting EMT transcription factors. We constructed a new survival signature based on EMT-related differentially expressed lncRNAs obtained from the Cancer Genome Atlas (TCGA-KIRC). We first determined 1377 EMT-related lncRNAs, lncRNA AL035661.1 with the largest correlation coefficient and the target gene was <i>PFN2</i> (cor = 0.843; <i>P</i>= 1.37E-146). Meanwhile, we found an AUC of 0.758 in our signature and we predicted the AUC values of the patients’ 1, 2, 3-year survival rate as 0.768, 0.749, and 0.762 in TCGA cohort, respectively. Multivariate COX analysis was performed to determine if risk score was an independent prognostic predictor of OS. The results indicated that our risk score can be an independent predictor for OS (Univariate: HR = 1.350, 95% CI = 1.276–1.428, <i>P</i>&lt; 0.001; Multivariate: HR = 1.295, 95% CI = 1.201–1.396, <i>P</i>&lt; 0.001). We identified novel EMT-related lncRNAs markers for ccRCC prognosis. The underlying mechanism between EMT-related lncRNAs in ccRCC and tumor immunity is still unclear and requires further study.
DOI: 10.6084/m9.figshare.7380599.v2
title: Cognitive and behavioral impairments in German and Chinese ALS populations – a post-hoc comparison of national study data

description: This study aimed to clarify whether differences between German and Chinese studies using the standardized Edinburgh Cognitive and Behavioural ALS Screen (ECAS), might be explained by differences in translated versions of ECAS, by patient demographic or clinical characteristics or by population-specific factors. Comparisons were performed on data from two previous studies in Germany and China. We found except for spelling task (<i>p</i> = 0.05), no differences between control groups of two countries were detected after adjusting for demographics. In contrast, differences were observed in scores on total ECAS, ALS-specific function such as different executive functions (all <i>p</i> &lt; 0.01) and language (<i>p</i> = 0.02), even after correcting for demographic and clinical variables. Chinese ALS cohort performed worse in executive subfunction scores for sentence completion, alternation, social cognition, digit span and language comprehension; they performed better in spelling. Chinese ALS cohort more frequently exhibited disinhibition (<i>p</i> = 0.02), whereas German cohort more frequently exhibited loss of sympathy (<i>p</i> = 0.01) and stereotyped behavior (<i>p</i> = 0.03). Chinese and German ALS cohorts showed a distinctly different pattern in executive and language function. Most of the differences might be related to distinct differences between populations as only spelling might be affected by different language versions of ECAS. Socio-cultural factors might explain behavioral profile differences.
DOI: 10.6084/m9.figshare.7380797
title: An agp file indicating how contigs are scaffolded

description: An agp file indicating how contigs are scaffolded
DOI: 10.6084/m9.figshare.10002092.v1
title: reputationdynamics from The interdependence of corporate reputation and ownership: a network approach to quantify reputation

description: reputationdynamics.m is the script to calculate reputation of firms.
DOI: 10.6084/m9.figshare.10002095
title: Visualization from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: visualization.R is the script to perform statistical analysis.
DOI: 10.6084/m9.figshare.7380599.v1
title: Cognitive and behavioral impairments in German and Chinese ALS populations – a post-hoc comparison of national study data

description: This study aimed to clarify whether differences between German and Chinese studies using the standardized Edinburgh Cognitive and Behavioural ALS Screen (ECAS), might be explained by differences in translated versions of ECAS, by patient demographic or clinical characteristics or by population-specific factors. Comparisons were performed on data from two previous studies in Germany and China. We found except for spelling task (<i>p</i> = 0.05), no differences between control groups of two countries were detected after adjusting for demographics. In contrast, differences were observed in scores on total ECAS, ALS-specific function such as different executive functions (all <i>p</i> &lt; 0.01) and language (<i>p</i> = 0.02), even after correcting for demographic and clinical variables. Chinese ALS cohort performed worse in executive subfunction scores for sentence completion, alternation, social cognition, digit span and language comprehension; they performed better in spelling. Chinese ALS cohort more frequently exhibited disinhibition (<i>p</i> = 0.02), whereas German cohort more frequently exhibited loss of sympathy (<i>p</i> = 0.01) and stereotyped behavior (<i>p</i> = 0.03). Chinese and German ALS cohorts showed a distinctly different pattern in executive and language function. Most of the differences might be related to distinct differences between populations as only spelling might be affected by different language versions of ECAS. Socio-cultural factors might explain behavioral profile differences.
DOI: 10.5281/zenodo.10592110
title: camvis2 - Estimation of Visibility on Webcam Images using Multi-Magnification Convolutional Networks

description: This dataset contains the data files of the camera-based visibility estimation project proposed on the MeteoSwiss/camvis2 github repository.

The contents of this data repository are as follows:

1 (Necessary) Dataset creation files: These files are used to create the dataset on which the models are trained and evaluated. It is necessary to download the compressed archives containing the files, decompress them and merge them with the corresponding directory in the data/raw/ directory of the project repository. The dataset creation files are the following archives: depth_maps.tar.gz and images.tar.gz.

2 (Facultative) Preprocessed dataset files: If you want to avoid creating the dataset, you can also get the preprocessed version of the dataset files in the processed.tar.gz archive. Similary, If you want to use these files, you need to download the compressed archive, extract its content and put them in the data/processed directory of the project repository.

3 (Facultative) Model training outputs. These files might be helpful if you don't have access to a GPU or don't want to train the models yourself for another reason. In the checkpoints.tar.gz archive, you'll find the pretrained weights of our models for each of the three experiments we provide in the run_scripts/ directory of the project repository. The content of this archive belongs to outputs/checkpoints.

4 (Facultative) Model evalutation outputs. Mostly useful if you want to compare your results with ours. Again, you'll find the outputs that correspond to every experiment provided in run_scripts/, but this time at evaluation-time. The outputs are stored in the following archives: val_cf_matrices.tar.gz, val_histplots.tar.gz, val_images.tar.gz, val_scores.tar.gz. They are to be put into the corresponding subdirectories in the outputs/ directory, in the project repository.
DOI: 10.5281/zenodo.10592111
title: camvis2 - Estimation of Visibility on Webcam Images using Multi-Magnification Convolutional Networks

description: This dataset contains the data files of the camera-based visibility estimation project proposed on the MeteoSwiss/camvis2 github repository.

The contents of this data repository are as follows:

1 (Necessary) Dataset creation files: These files are used to create the dataset on which the models are trained and evaluated. It is necessary to download the compressed archives containing the files, decompress them and merge them with the corresponding directory in the data/raw/ directory of the project repository. The dataset creation files are the following archives: depth_maps.tar.gz and images.tar.gz.

2 (Facultative) Preprocessed dataset files: If you want to avoid creating the dataset, you can also get the preprocessed version of the dataset files in the processed.tar.gz archive. Similary, If you want to use these files, you need to download the compressed archive, extract its content and put them in the data/processed directory of the project repository.

3 (Facultative) Model training outputs. These files might be helpful if you don't have access to a GPU or don't want to train the models yourself for another reason. In the checkpoints.tar.gz archive, you'll find the pretrained weights of our models for each of the three experiments we provide in the run_scripts/ directory of the project repository. The content of this archive belongs to outputs/checkpoints.

4 (Facultative) Model evalutation outputs. Mostly useful if you want to compare your results with ours. Again, you'll find the outputs that correspond to every experiment provided in run_scripts/, but this time at evaluation-time. The outputs are stored in the following archives: val_cf_matrices.tar.gz, val_histplots.tar.gz, val_images.tar.gz, val_scores.tar.gz. They are to be put into the corresponding subdirectories in the outputs/ directory, in the project repository.
DOI: 10.6084/m9.figshare.10002095.v1
title: Visualization from The interdependence of corporate reputation and ownership: a network approach to quantify reputation

description: visualization.R is the script to perform statistical analysis.
DOI: 10.6084/m9.figshare.10002104
title: firm_properties.csv from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: This file contains the id, integrated control value and operating value of firms.
DOI: 10.6084/m9.figshare.10002104.v1
title: firm_properties.csv from The interdependence of corporate reputation and ownership: a network approach to quantify reputation

description: This file contains the id, integrated control value and operating value of firms.
DOI: 10.6084/m9.figshare.7380857.v1
title: Additional file 1: of Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive

description: Table S1. Detail information of used pigs. Table S2. PCR primers used for amplification of pig mitogenomes. Table S3. Information of synonymous mutations in pig mitogenomes. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.10002113
title: Eigen from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: eigen.txt contains the eigen values of the ownership network.
DOI: 10.6084/m9.figshare.10002101.v1
title: Data from The interdependence of corporate reputation and ownership: a network approach to quantify reputation

description: data.csv contains the id, integrated control value and operating value of firms.
DOI: 10.6084/m9.figshare.10002110.v2
title: ownership network.txt from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: This file describes the ownership network used in the paper. Each line i,j,w denotes the ownership between firm i and firm j with weight w.
DOI: 10.6084/m9.figshare.10002113.v2
title: Eigen from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: eigen.txt contains the eigen values of the ownership network.
DOI: 10.6084/m9.figshare.12623235
title: Additional file 1 of Airway-invasion-associated pulmonary computed tomography presentations characteristic of invasive pulmonary Aspergillosis in non-immunocompromised adults: a National Multicenter Retrospective Survey in China

description: Additional file 1: Table S1. Underlying conditions of IPA patients. Figure S1. Radiological presentations of IPA patients.
DOI: 10.6084/m9.figshare.7380710
title: Additional file 1: of Proteome modifications on tomato under extreme high light induced-stress

description: Spreadsheet (excel file) containing the abundance (ratios) of all proteins identified in all samples. Please refer to Methods for details on the data acquisition, sample preparation and database match. The “Raw Data” tab is a list of all proteins matched to the Solanum lycopersicum database under 1% FDR. The “Filtered” tab contains the proteins presenting more than 2 unique peptides. The “DiffExp_Burned”, “DiffExp_Limit” and “DiffExp_Regular” tabs contain a list of proteins found differentially expressed in each of the treatments. Proteins in green font color are upregulated, and the ones in blue color are downregulated. (XLSX 2799 kb)
DOI: 10.6084/m9.figshare.24161671
title: Intracranial arterial stenosis and recurrence in stroke patients with different risk stratifications by Essen stroke risk score

description: We sought to investigate whether the prognostic value of intracranial arterial stenosis (ICAS) is consistent across different risk stratifications using the Essen Stroke Risk score (ESRS). We derived data from the Clopidogrel in High-Risk Patients with Acute Nondisabling Cerebrovascular Events trial. Patients without complete baseline brain imaging data were excluded. Participants were categorized into different risk groups based on ESRS (low risk, 0–2, and high risk ≥ 3). The main outcome was stroke recurrence within 3 and 12 months. Hazard ratios (HRs) and 95% confidence intervals (95%CIs) of ICAS, and other factors associated with stroke recurrence within 3 and 12 months were estimated using the Cox regression method. During the 3-month follow-up, 54 patients (7.9%) had recurrent stroke in the low-risk group, and 39 patients (9.6%) had recurrent stroke in the high-risk group. ICAS was associated with a higher risk of stroke within 3 months (HR = 2.761; 95%CI = 1.538–4.957; <i>P</i> &lt; 0.001) in the low-risk group, but not in the high-risk group (HR = 1.501; 95%CI = 0.701–3.213; <i>P</i> = 0.296). ICAS was independently associated with higher recurrent risk in the low-risk group (HR = 2.540; 95%CI = 1.472–4.381; <i>P</i> &lt; 0.001), but not in the high-risk group (HR = 1.951; 95%CI = 0.977–3.893; <i>P</i> = 0.058) within 12 months. ICAS was an independent predictor of both 3- and 12-month stroke recurrence in low-risk but not high-risk patients with minor ischemic stroke or transient ischemic attack according to ESRS stratification.
DOI: 10.6084/m9.figshare.24161671.v1
title: Intracranial arterial stenosis and recurrence in stroke patients with different risk stratifications by Essen stroke risk score

description: We sought to investigate whether the prognostic value of intracranial arterial stenosis (ICAS) is consistent across different risk stratifications using the Essen Stroke Risk score (ESRS). We derived data from the Clopidogrel in High-Risk Patients with Acute Nondisabling Cerebrovascular Events trial. Patients without complete baseline brain imaging data were excluded. Participants were categorized into different risk groups based on ESRS (low risk, 0–2, and high risk ≥ 3). The main outcome was stroke recurrence within 3 and 12 months. Hazard ratios (HRs) and 95% confidence intervals (95%CIs) of ICAS, and other factors associated with stroke recurrence within 3 and 12 months were estimated using the Cox regression method. During the 3-month follow-up, 54 patients (7.9%) had recurrent stroke in the low-risk group, and 39 patients (9.6%) had recurrent stroke in the high-risk group. ICAS was associated with a higher risk of stroke within 3 months (HR = 2.761; 95%CI = 1.538–4.957; <i>P</i> &lt; 0.001) in the low-risk group, but not in the high-risk group (HR = 1.501; 95%CI = 0.701–3.213; <i>P</i> = 0.296). ICAS was independently associated with higher recurrent risk in the low-risk group (HR = 2.540; 95%CI = 1.472–4.381; <i>P</i> &lt; 0.001), but not in the high-risk group (HR = 1.951; 95%CI = 0.977–3.893; <i>P</i> = 0.058) within 12 months. ICAS was an independent predictor of both 3- and 12-month stroke recurrence in low-risk but not high-risk patients with minor ischemic stroke or transient ischemic attack according to ESRS stratification.
DOI: 10.6084/m9.figshare.7380599
title: Cognitive and behavioral impairments in German and Chinese ALS populations – a post-hoc comparison of national study data

description: This study aimed to clarify whether differences between German and Chinese studies using the standardized Edinburgh Cognitive and Behavioural ALS Screen (ECAS), might be explained by differences in translated versions of ECAS, by patient demographic or clinical characteristics or by population-specific factors. Comparisons were performed on data from two previous studies in Germany and China. We found except for spelling task (<i>p</i> = 0.05), no differences between control groups of two countries were detected after adjusting for demographics. In contrast, differences were observed in scores on total ECAS, ALS-specific function such as different executive functions (all <i>p</i> &lt; 0.01) and language (<i>p</i> = 0.02), even after correcting for demographic and clinical variables. Chinese ALS cohort performed worse in executive subfunction scores for sentence completion, alternation, social cognition, digit span and language comprehension; they performed better in spelling. Chinese ALS cohort more frequently exhibited disinhibition (<i>p</i> = 0.02), whereas German cohort more frequently exhibited loss of sympathy (<i>p</i> = 0.01) and stereotyped behavior (<i>p</i> = 0.03). Chinese and German ALS cohorts showed a distinctly different pattern in executive and language function. Most of the differences might be related to distinct differences between populations as only spelling might be affected by different language versions of ECAS. Socio-cultural factors might explain behavioral profile differences.
DOI: 10.6084/m9.figshare.10002092
title: reputationdynamics from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: reputationdynamics.m is the script to calculate reputation of firms.
DOI: 10.6084/m9.figshare.10002092.v2
title: reputationdynamics from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: reputationdynamics.m is the script to calculate reputation of firms.
DOI: 10.6084/m9.figshare.10002095.v2
title: Visualization from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: visualization.R is the script to perform statistical analysis.
DOI: 10.6084/m9.figshare.10002098
title: Perron from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: perron.m is the function file to calculate eigen value.
DOI: 10.6084/m9.figshare.10002098.v1
title: Perron from The interdependence of corporate reputation and ownership: a network approach to quantify reputation

description: perron.m is the function file to calculate eigen value.
DOI: 10.6084/m9.figshare.10002104.v2
title: firm_properties.csv from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: This file contains the id, integrated control value and operating value of firms.
DOI: 10.6084/m9.figshare.10002107.v2
title: Network from The interdependence of corporate reputation and ownership: a network approach to quantify reputation.

description: network.txt contains a list of weighted edges. Each line i,j,w describes ownership between firm i and firm j.
DOI: 10.6084/m9.figshare.7380716
title: Additional file 2: of Proteome modifications on tomato under extreme high light induced-stress

description: Spreadsheet (excel file) containing the identity and information of proteins from each Pattern (1–4) determined through the hierarchical clustering analysis. The “Interaction_Regular” tab shows the protein interaction network of the proteins with roles on immune and stress response found differentially expressed in the Regular sample. (XLSX 1181 kb)
DOI: 10.6084/m9.figshare.12096888
title: Additional file 2 of The preceding root system drives the composition and function of the rhizosphere microbiome

description: Additional file 2: Table S8 and Table S9. The relative abundance of microbial gene groups and taxonomic genus between different niches. This file includes the mean values and standard error for the heatmap in Fig. 4a and Fig. 4b.
DOI: 10.6084/m9.figshare.16815545.v1
title: Additional file 2 of Quantitative prediction model for affinity of drug–target interactions based on molecular vibrations and overall system of ligand-receptor

description: Additional file 2. Protein descriptor information.
DOI: 10.6084/m9.figshare.24496603.v1
title: A fast solution to the lasso problem with equality constraints

description: The equality-constrained lasso problem augments the standard lasso by imposing additional structure on regression coefficients. Despite the broad utilities of the equality-constrained lasso, existing algorithms are typically computationally inefficient and only applicable to linear and logistic models. In this paper, we devise a fast solution to the equality-constrained lasso problem with a two-stage algorithm: first obtaining candidate covariate subsets of increasing size from unconstrained lasso problems and then leveraging an efficient combined alternating direction method of multipliers/Newton-Raphson algorithm. Our proposed algorithm leads to substantial speedups in getting the solution path of the constrained lasso and can be easily adapted to generalized linear models and Cox proportional hazards models. We conduct extensive simulation studies to demonstrate the computational advantage of the proposed method over existing solvers. To further show the unique utility of our method, we consider two real-world data examples: a microbiome regression analysis and a myeloma survival analysis; neither example could be solved by naively fitting the constrained lasso problem on the full predictor set.
DOI: 10.6084/m9.figshare.7380617
title: The sequence and de novo assembly of Larimichthys crocea genome using PacBio and Hi-C technologies

description: A chromosome-level reference genome of L. crocea generated employing the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies.