cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7978759
title: SWECO25: Bioclimatic (bioclim)

description: The Bioclimatic category contains the "chclim25" dataset.

The chclim25 dataset (bioclimatic category) describes the past, current, and future climate of Switzerland. After resampling the “CHclim25: A high spatial and temporal resolution climate dataset for Switzerland” source data (Broennimann et al., 2021) to the SWECO25 grid, we generated individual precipitation and temperature (min, max, mean) layers at a yearly time step over the 1981-2017 period. In addition, we generated 30-y average climate normal (1981-2010) layers for 28 climate parameters. Layers for the same 28 parameters were also generated for three future periods (2020-2049, 2045-2070, 2070-2099) computed by using their average values projected from for four global climate models (HADGEM, ECEARTH, MPIESM, and IPSL) under three greenhouse gas concentration trajectories or representative concentration pathways (RCPs), RCP2.6, RCP4.5, and RCP8.5. This dataset includes a total of 428 layers. Final values were rounded and multiplied by 100.

The detailed list of layers available is provided in SWECO25_datalayers_details_bioclim.csv and includes information on the category, dataset, variable name (long), variable name (short), period, sub-period, start year, end year, attribute, radii, unit, and path.

References:

Broennimann, O. CHclim25: A high spatial and temporal resolution climate dataset for Switzerland. (Lausanne, Switzerland, 2021).

Külling, N., Adde, A., Fopp, F., Schweiger, A. K., Broennimann, O., Rey, P.-L., Giuliani, G., Goicolea, T., Petitpierre, B., Zimmermann, N. E., Pellissier, L., Altermatt, F., Lehmann, A., & Guisan, A. (2024). SWECO25: A cross-thematic raster database for ecological research in Switzerland. Scientific Data, 11(1), Article 1. https://doi.org/10.1038/s41597-023-02899-1

Versioning

V2: 1) data update: all layers "tave", "tmin", "tmax" for "present" period have been divided by 10 to fit description. 2) metadata update. 
description: We gratefully acknowledge financial support through the Action Plan of the Swiss Biodiversity Strategy by the Federal Office for the Environment (FOEN) for financing the ValPar.CH and SwissCatchment projects. All the institutions and contributors who made the input data freely available are gratefully acknowledged.
DOI: 10.5281/zenodo.10635645
title: Supplementary Material - The conservation status of the Cretan Endemic Arthropods under Natura 2000 network

description: Arthropod decline has been globally and locally documented, yet they are still not sufficiently protected. Crete (Greece), a Mediterranean biodiversity hotspot, is a continental island renowned for its diverse geology, ecosystems and endemicity of flora and fauna, with continuous research on its Arthropod fauna dating back to the 19th century. Here we investigate the conservation status of the Cretan Arthropods using Preliminary Automated Conservation Assessments (PACA) and the overlap of Cretan Arthropod distributions with the Natura 2000 protected areas. Moreover we investigate their endemicity hotspots and propose candidate Key Biodiversity Areas. In order to perform these analyses, we assembled occurrences of the endemic Arthropods in Crete located in the collections of the Natural History Museum of Crete together with literature data. These assessments resulted in 75% of endemic Arthropods as potentially threatened. The hotspots of endemic taxa and the candidate Key Biodiversity Areas are distributed mostly on the mountainous areas where the Natura 2000 protected areas have great coverage. Yet human activities have significant impact even in those areas, while some taxa are not sufficiently covered by Natura 2000. These findings call for countermeasures and conservation actions.

The code is available here https://github.com/savvas-paragkamian/arthropods_assessment_crete and a zipped version of the repository is included here (arthropods_assessment_crete-1.2.0.tar). 

Supplementary Material 1 is the  Supplementary-material-1.xlsx file which contains the Arthropod occurrences as compiled from the literature and the specimens of the NHMC. In addition all references of the literature are included in a separate sheet.

Supplementary Material 2 1 is the  Supplementary-material-2.docx which contains two (2) supplementary figures and two (2) supplementary tables.
DOI: 10.5281/zenodo.7709460
title: Supplementary Material - The conservation status of the Cretan Endemic Arthropods under Natura 2000 network

description: Arthropod decline has been globally and locally documented, yet they are still not sufficiently protected. Crete (Greece), a Mediterranean biodiversity hotspot, is a continental island renowned for its diverse geology, ecosystems and endemicity of flora and fauna, with continuous research on its Arthropod fauna dating back to the 19th century. Here we investigate the conservation status of the Cretan Arthropods using Preliminary Automated Conservation Assessments (PACA) and the overlap of Cretan Arthropod distributions with the Natura 2000 protected areas. Moreover we investigate their endemicity hotspots and propose candidate Key Biodiversity Areas. In order to perform these analyses, we assembled occurrences of the endemic Arthropods in Crete located in the collections of the Natural History Museum of Crete together with literature data. These assessments resulted in 75% of endemic Arthropods as potentially threatened. The hotspots of endemic taxa and the candidate Key Biodiversity Areas are distributed mostly on the mountainous areas where the Natura 2000 protected areas have great coverage. Yet human activities have significant impact even in those areas, while some taxa are not sufficiently covered by Natura 2000. These findings call for countermeasures and conservation actions.

The code is available here https://github.com/savvas-paragkamian/arthropods_assessment_crete and a zipped version of the repository is included here (arthropods_assessment_crete-1.2.0.tar). 

Supplementary Material 1 is the  Supplementary-material-1.xlsx file which contains the Arthropod occurrences as compiled from the literature and the specimens of the NHMC. In addition all references of the literature are included in a separate sheet.

Supplementary Material 2 1 is the  Supplementary-material-2.docx which contains two (2) supplementary figures and two (2) supplementary tables.
DOI: 10.6084/m9.figshare.12144465.v1
title: Additional file 6 of Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: a multi-omics study

description: Additional file 6: Data S4. KEGG pathway functional enrichment of DEGs.
DOI: 10.6084/m9.figshare.14248541.v2
title: Gaussian Process-Aided Function Comparison Using Noisy Scattered Data

description: This work proposes a nonparametric method to compare the underlying mean functions given two noisy datasets. The motivation for the work stems from an application of comparing wind turbine power curves. Comparing wind turbine data presents new problems, namely the need to identify the regions of difference in the input space and to quantify the extent of difference that is statistically significant. Our proposed method, referred to as funGP, estimates the underlying functions for different data samples using Gaussian process models. We build a confidence band using the probability law of the estimated function differences under the null hypothesis. Then, the confidence band is used for the hypothesis test as well as for identifying the regions of difference. This identification of difference regions is a distinct feature, as existing methods tend to conduct an overall hypothesis test stating whether two functions are different. Understanding the difference regions can lead to further practical insights and help devise better control and maintenance strategies for wind turbines. The merit of funGP is demonstrated by using three simulation studies and four real wind turbine datasets.
DOI: 10.6084/m9.figshare.16869720.v1
title: Additional file 3 of De novo transcriptome analysis provides insights into the salt tolerance of Podocarpus macrophyllus under salinity stress

description: Additional file 3: Supplementary Dataset 2. Gene co-expression clusters of the downregulated DEGs in P. macrophyllus under LS salt stress.
DOI: 10.5281/zenodo.10635720
title: Age and sex influence antibody profiles associated with tuberculosis progression

description: Systems serology datasets for the Adolescent Cohort Study and Grand Challenges 6-74 used to generate all analyses for the paper.
DOI: 10.5281/zenodo.10635721
title: Age and sex influence antibody profiles associated with tuberculosis progression

description: Systems serology datasets for the Adolescent Cohort Study and Grand Challenges 6-74 used to generate all analyses for the paper.
DOI: 10.6084/m9.figshare.12144471
title: Additional file 8 of Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: a multi-omics study

description: Additional file 8: Data S6. RNA-seq data for genes involved in lipid metabolism.
DOI: 10.6084/m9.figshare.12144477
title: Additional file 9 of Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: a multi-omics study

description: Additional file 9: Data S7. RNA-seq data for genes involved in carotenogenesis.
DOI: 10.6084/m9.figshare.14248536.v2
title: High-Dimensional Cost-constrained Regression Via Nonconvex Optimization

description: Budget constraints become an important consideration in modern predictive modeling due to the high cost of collecting certain predictors. This motivates us to develop cost-constrained predictive modeling methods. In this article, we study a new high-dimensional cost-constrained linear regression problem, that is, we aim to find the cost-constrained regression model with the smallest expected prediction error among all models satisfying a budget constraint. The nonconvex budget constraint makes this problem NP-hard. In order to estimate the regression coefficient vector of the cost-constrained regression model, we propose a new discrete first-order continuous optimization method. In particular, our method delivers a series of estimates of the regression coefficient vector by solving a sequence of 0-1 knapsack problems. Theoretically, we prove that the series of the estimates generated by our iterative algorithm converge to a first-order stationary point, which can be a globally optimal solution under some conditions. Furthermore, we study some extensions of our method that can be used for general statistical learning problems and problems with groups of variables. Numerical studies using simulated datasets and a real dataset from a diabetes study indicate that our proposed method can solve problems of fairly high dimensions with promising performance.
DOI: 10.6084/m9.figshare.14248541.v1
title: Gaussian process aided function comparison using noisy scattered data

description: This work proposes a nonparametric method to compare the underlying mean functions given two noisy datasets. The motivation for the work stems from an application of comparing wind turbine power curves. Comparing wind turbine data presents new problems, namely the need to identify the regions of difference in the input space and to quantify the extent of difference that is statistically significant. Our proposed method, referred to as funGP, estimates the underlying functions for different data samples using Gaussian process models. We build a confidence band using the probability law of the estimated function differences under the null hypothesis. Then, the confidence band is used for the hypothesis test as well as for identifying the regions of difference. This identification of difference regions is a distinct feature, as existing methods tend to conduct an overall hypothesis test stating whether two functions are different. Understanding the difference regions can lead to further practical insights and help devise better control and maintenance strategies for wind turbines. The merit of funGP is demonstrated by using three simulation studies and four real wind turbine datasets. Supplementary material for this article is available online, including some detailed description and the computer code.
DOI: 10.6084/m9.figshare.13200278
title: Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19

description: This dataset comprises single-cell RNA-Seq data of nasopharyngeal samples of 32 COVID-19 
patients and 16 healthy controls, for a total of 48 samples. 25 COVID-19 patients and 10 controls were diagnosed with hypertension and treated with either ACE inhibitors (ACEi) or angiotensin receptor blockers(ARB) (SARS-CoV-2-positive: 10 ACEi and 15 ARB; SARS-CoV-2-negative: 6 ACEi and 4 ARB).<br>An
 in-depth description is presented in the manuscript "Delayed viral clearance and exacerbated airway hyperinflammation in hypertensive COVID-19 patients" 
(https://www.medrxiv.org/content/10.1101/2020.09.22.20199471v1).
DOI: 10.6084/m9.figshare.14772878.v1
title: Identification of Rad51 as a prognostic biomarker correlated with immune infiltration in hepatocellular carcinoma

description: Rad51, a DNA-repair-related gene, has been reported to be involved in multiple cancers. However, its link with immune infiltration in liver cancer still unknown. Therefore, more research into the roles and activities of Rad51 in hepatocellular carcinoma (HCC) is required. The International Cancer Genome Consortium (ICGC) was used to identify the DNA repair gene Rad51, and has been proved to be overexpressed in HCC patients. We plotted the Kapan-Meier curve, demonstrating that patients with high expression of Rad51 have a poor prognosis. By analyzing the patient data, we discovered that high expression of Rad51 in HCC is linked to clinical stage, pathological T stage, grade, and age. Rad51 was found to be an independent prognostic factor for HCC patients using the multivariate cox model. Moreover, Rad51 expression was found to be associated with the infiltration of immune cells (B cells, CD4 + T cells, CD8 + T cells, neutrophils, macrophages, and dendritic cells) and was intimately linked to the expression of immune cell markers in HCC. Through the analysis of differentially coexpressed genes (DCGs) of Rad51, GO and KEGG enrichment analyses suggested that the expression level of Rad51 might be relevant to neuroactive ligand-receptor interactions, the cell cycle, DNA replication, homologous recombination, oocyte meiosis, and the Fanconi anemia pathway. These findings indicated that Rad51 is a valuable biomarker for the prognosis of patients with liver cancer and that its expression has a significant correlation with immune infiltrations. <b>Abbreviations:</b> HCC: hepatocellular carcinoma; ICGC: International Cancer Genome Consortium TCGA: The Cancer Genome Atlas; TIMER: Tumor Immune Estimation Resource; CAF: Cancer-associated fibroblast; GEPIA: Gene Expression Profiling Interactive Analysis; GSEA: Gene set enrichment analysis; OS: overall survival; PFS: progression-free survival; RFS: relapse-free survival; DSS: disease-specific survival. Partial cor: partial correlation coefficient; HPA: Human Protein Atlas; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; CAF: Cancer-associated fibroblast; DCGs: differentially co-expressed genes
DOI: 10.6084/m9.figshare.14248535.v2
title: Super Resolution for Multi-Sources Image Stream Data Using Smooth and Sparse Tensor Completion and Its Applications in Data Acquisition of Additive Manufacturing

description: Recent developments of advanced imaging systems spur their applications in many areas, ranging from satellite remote sensing for geographic information to thermal imaging analysis for manufacturing process monitoring and control. Due to different specifications of imaging systems, the resulting image stream data (videos) have different spatial and temporal resolutions. This proposed work is based on the image stream data captured by multiple imaging systems for the same object with different but complementary spatial and temporal resolutions. For example, one system has high spatial but low temporal resolutions while the other one has opposite resolutions. The goal of this article is to develop a new super resolution method that integrates these different types of image stream data to improve both spatial and temporal resolutions, which is critical to obtaining more insightful information for more effective quality control of targeted processes or systems. To fulfill this goal, a new tensor completion model is developed by considering both smooth and sparse features simultaneously and is thus termed smooth and sparse tensor completion (SSTC). The results of the extensive case studies illustrate the superiority of our method over the elaborately selected benchmark methods.
DOI: 10.6084/m9.figshare.14772878
title: Identification of Rad51 as a prognostic biomarker correlated with immune infiltration in hepatocellular carcinoma

description: Rad51, a DNA-repair-related gene, has been reported to be involved in multiple cancers. However, its link with immune infiltration in liver cancer still unknown. Therefore, more research into the roles and activities of Rad51 in hepatocellular carcinoma (HCC) is required. The International Cancer Genome Consortium (ICGC) was used to identify the DNA repair gene Rad51, and has been proved to be overexpressed in HCC patients. We plotted the Kapan-Meier curve, demonstrating that patients with high expression of Rad51 have a poor prognosis. By analyzing the patient data, we discovered that high expression of Rad51 in HCC is linked to clinical stage, pathological T stage, grade, and age. Rad51 was found to be an independent prognostic factor for HCC patients using the multivariate cox model. Moreover, Rad51 expression was found to be associated with the infiltration of immune cells (B cells, CD4 + T cells, CD8 + T cells, neutrophils, macrophages, and dendritic cells) and was intimately linked to the expression of immune cell markers in HCC. Through the analysis of differentially coexpressed genes (DCGs) of Rad51, GO and KEGG enrichment analyses suggested that the expression level of Rad51 might be relevant to neuroactive ligand-receptor interactions, the cell cycle, DNA replication, homologous recombination, oocyte meiosis, and the Fanconi anemia pathway. These findings indicated that Rad51 is a valuable biomarker for the prognosis of patients with liver cancer and that its expression has a significant correlation with immune infiltrations. <b>Abbreviations:</b> HCC: hepatocellular carcinoma; ICGC: International Cancer Genome Consortium TCGA: The Cancer Genome Atlas; TIMER: Tumor Immune Estimation Resource; CAF: Cancer-associated fibroblast; GEPIA: Gene Expression Profiling Interactive Analysis; GSEA: Gene set enrichment analysis; OS: overall survival; PFS: progression-free survival; RFS: relapse-free survival; DSS: disease-specific survival. Partial cor: partial correlation coefficient; HPA: Human Protein Atlas; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; CAF: Cancer-associated fibroblast; DCGs: differentially co-expressed genes
DOI: 10.6084/m9.figshare.12144402
title: Additional file 11 of Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: a multi-omics study

description: Additional file 11: Data S9. RNA-seq data for genes involved in CO2 fixation and central carbon metabolism.
DOI: 10.6084/m9.figshare.12144411
title: Additional file 12 of Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: a multi-omics study

description: Additional file 12: Data S10. RNA-seq data for genes involved in ROS scavenging and transport of certain metabolites.
DOI: 10.6084/m9.figshare.12144447.v1
title: Additional file 2 of Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: a multi-omics study

description: Additional file 2: Data S1. Change of metabolites in C. zofingiensis in response to salt stress.
DOI: 10.6084/m9.figshare.12144447
title: Additional file 2 of Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: a multi-omics study

description: Additional file 2: Data S1. Change of metabolites in C. zofingiensis in response to salt stress.
DOI: 10.6084/m9.figshare.21582059.v1
title: Additional file 1 of Identification of risk variants related to malignant tumors in children with birth defects by whole genome sequencing

description: Additional file 1.
DOI: 10.6084/m9.figshare.17919093.v1
title: Vitamin D<sub>3</sub> and carbamazepine protect against <i>Clostridioides difficile</i> infection in mice by restoring macrophage lysosome acidification

description: <i>Clostridioides difficile</i> infection (CDI) is a common cause of nosocomial diarrhea. TcdB is a major <i>C. difficile</i> exotoxin that activates macrophages to promote inflammation and epithelial damage. Lysosome impairment is a known trigger for inflammation. Herein, we hypothesize that TcdB could impair macrophage lysosomal function to mediate inflammation during CDI. Effects of TcdB on lysosomal function and the downstream pro-inflammatory SQSTM1/p62-NFKB (nuclear factor kappa B) signaling were assessed in cultured macrophages and in a murine CDI model. Protective effects of two lysosome activators (i.e., vitamin D<sub>3</sub> and carbamazepine) were assessed. Results showed that TcdB inhibited CTNNB1/β-catenin activity to downregulate MITF (melanocyte inducing transcription factor) and its direct target genes encoding components of lysosomal membrane vacuolar-type ATPase, thereby suppressing lysosome acidification in macrophages. The resulting lysosomal dysfunction then impaired autophagic flux and activated SQSTM1-NFKB signaling to drive the expression of IL1B/IL-1β (interleukin 1 beta), IL8 and CXCL2 (chemokine (C-X-C motif) ligand 2). Restoring MITF function by enforced MITF expression or restoring lysosome acidification with 1α,25-dihydroxyvitamin D<sub>3</sub> or carbamazepine suppressed pro-inflammatory cytokine expression <i>in vitro</i>. In mice, gavage with TcdB-hyperproducing <i>C. difficile</i> or injection of TcdB into ligated colon segments caused prominent MITF downregulation in macrophages. Vitamin D<sub>3</sub> and carbamazepine lessened TcdB-induced lysosomal dysfunction, inflammation and histological damage. In conclusion, TcdB inhibits the CTNNB1-MITF axis to suppress lysosome acidification and activates the downstream SQSTM1-NFKB signaling in macrophages during CDI. Vitamin D<sub>3</sub> and carbamazepine protect against CDI by restoring MITF expression and lysosomal function in mice. <b>Abbreviations:</b> ATP6V0B: ATPase H+ transporting V0 subunit b; ATP6V0C: ATPase H+ transporting V0 subunit c; ATP6V0E1: ATPase H+ transporting V0 subunit e1; ATP6V1H: ATPase H+ transporting V1 subunit H; CBZ: carbamazepine; CDI: <i>C. difficile</i> infection; CXCL: chemokine C-X-X motif ligand; IL: interleukin; LAMP1: lysosomal-associated membrane protein 1; LC3: microtubule-associated protein 1 light chain 3; LEF: lymphoid enhancer binding factor 1; MITF: melanocyte inducing transcription factor; NFKB: nuclear factor kappa B; PMA: phorbol 12-myristate 13-acetate; TcdA: Clostridial toxin A; TcdB: Clostridial toxin B; TFE3: transcription factor E3; TFEB: transcription factor EB.