cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48597/hgwd-nyv3
title: Inorganics in precipitation at Schmücke

description: Measurement of Inorganics in precipitation at Schmücke
DOI: 10.48597/jbuv-mhkb
title: Inorganics in precipitation at Westerland

description: Measurement of Inorganics in precipitation at Westerland
DOI: 10.48597/jgjt-5sfg
title: Inorganics in precipitation at Zingst

description: Measurement of Inorganics in precipitation at Zingst
DOI: 10.48597/jhd2-p335
title: Inorganics in precipitation at Zingst

description: Measurement of Inorganics in precipitation at Zingst
DOI: 10.48597/k7hp-uwpj
title: Inorganics in air and particle phase at Schauinsland

description: Measurement of Inorganics in air and particle phase at Schauinsland
DOI: 10.15468/vffvz9
title: Inventaire et atlas des Hyménoptères Pompilidae du Massif armoricain et des départements voisins - Atlas des Hyménoptères Pompilidae du Massif armoricain et des départements voisins : valorisation culots 2018

description: Identification des pompiles dans les culots de piégeage obtenus dans les départements du nord-ouest de la France
DOI: 10.48597/kesf-un4f
title: pH at Schmücke

description: Measurement of pH at Schmücke
DOI: 10.48597/kmr8-wh85
title: Nitrogen_dioxide at Diabla Gora

description: Measurement of Nitrogen_dioxide at Diabla Gora
DOI: 10.48597/ktxc-ksvd
title: Inorganics in air and particle phase at Deuselbach

description: Measurement of Inorganics in air and particle phase at Deuselbach
DOI: 10.48597/mjz6-aadw
title: Nitrogen_dioxide at Waldhof

description: Measurement of Nitrogen_dioxide at Waldhof
DOI: 10.48597/mwe4-whdg
title: Sulphate_total at Svratouch

description: Measurement of Sulphate_total at Svratouch
DOI: 10.48597/n5m6-q7gh
title: Inorganics in precipitation at Waldhof

description: Measurement of Inorganics in precipitation at Waldhof
DOI: 10.48597/njzk-hcsz
title: Precipitation_amount at Westerland

description: Measurement of Precipitation_amount at Westerland
DOI: 10.48597/ntev-t7hm
title: Nitrogen_dioxide at Deuselbach

description: Measurement of Nitrogen_dioxide at Deuselbach
DOI: 10.48597/p8pv-gqgc
title: Pm25_mass at Chaumont

description: Measurement of Pm25_mass at Chaumont
DOI: 10.48597/par8-jaqq
title: OC/EC, iron and inorganics in air and particle phase at Illmitz

description: Measurement of OC/EC, iron and inorganics in air and particle phase at Illmitz
DOI: 10.48597/pey9-3at2
title: Heavy metals at Vorhegg

description: Measurement of Heavy metals at Vorhegg
DOI: 10.15468/alk3ew
title: Système d'Information sur la Nature et les Paysages d'Ile de France - Données du naturaliste Lalevée Frédéric provenant de la base de donnée du SINP Île-de-France CETTIA

description: Jeux de données provenant de la base de données CETTIA du Système d'Information sur la Nature et les Paysages d'Ile de France. Il concerne la faune à l'exception des insectes.
DOI: 10.15468/s9z3kt
title: Projet de parc éolien sur la commune d'Envronville - Données Chiroptères

description: Données Chiroptérologiques sur la zone d'implantation potentielle du projet de parc éolien d'Envronville
DOI: 10.6084/m9.figshare.13055459.v3
title: PRCC-TFE3 fusion-mediated PRKN/parkin-dependent mitophagy promotes cell survival and proliferation in PRCC-TFE3 translocation renal cell carcinoma

description: TFE3 (transcription factor binding to IGHM enhancer 3) nuclear translocation and transcriptional activity has been implicated in PINK1-PRKN/parkin-dependent mitophagy. However, the transcriptional control governing the mitophagy in TFE3/Xp11.2 translocation renal cell carcinoma (<i>TFE3</i> tRCC) is largely unknown. Here, we investigated the role and mechanisms of PRCC-TFE3 fusion protein, one of TFE3 fusion types in TFE3 tRCC, in governing mitophagy to promote development of <i>PRCC-TFE3</i> tRCC. We observed and analyzed mitophagy, transcriptional control of PRCC-TFE3 on PINK1-PRKN-dependent mitophagy, PRCC-TFE3 fusions nuclear translocation, cancer cell survival and proliferation under mitochondrial oxidative damage in <i>PRCC-TFE3</i> tRCC cell line. We found that nuclear-aggregated PRCC-TFE3 fusions constitutively activated expression of the target gene E3 ubiquitin ligase <i>PRKN</i>, leading to rapid PINK1-PRKN-dependent mitophagy that promoted cell survival under mitochondrial oxidative damage as well as cell proliferation through decreasing mitochondrial ROS formation. However, nuclear translocation of TFE3 fusions escaped from PINK1-PRKN-dependent mitophagy. Furthermore, we confirmed that PRCC-TFE3 fusion accelerated mitochondrial turnover by activating PPARGC1A/PGC1α-NRF1. In conclusion, our findings indicated a major role of PRCC-TFE3 fusion-mediated mitophagy and mitochondrial biogenesis in promoting proliferation of <i>PRCC-TFE3</i> tRCC.
DOI: 10.6084/m9.figshare.7813022
title: Additional file 7: of Transcriptomic analysis reveals the regulatory module of apple (Malus × domestica) floral transition in response to 6-BA

description: Table S5. The cytoscapeinput of SOC1 and SPL9 gene with other genes in modules ‘turquoise’ and ‘blue’. (XLSX 371 kb)
DOI: 10.6084/m9.figshare.17079538
title: Additional file 1 of Diagnostic accuracy of pooling urine, anorectal, and oropharyngeal specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae: a systematic review and meta-analysis

description: Additional file 1: Appendix 1. Search strategy. Appendix 2. Further details of multisite pooled sampling for chlamydia and gonorrhoea. Supplementary Figure 1. Receiver operating characteristic (ROC) curve for multisite pooled testing for chlamydia. Supplementary Figure 2. Assessment for small study effects for multisite pooled testing for chlamydia. Supplementary Figure 3. Risk of bias summary as percentage. Supplementary Figure 4. Receiver operating characteristic (ROC) curve for multisite pooled testing for gonorrhoea. Supplementary Figure 5. Assessment for small study effects for multisite pooled testing for gonorrhoea. Supplementary Table 1. Meta-regression of the accuracy of multisite pooled testing for chlamydia according to study characteristics. Supplementary Table 2. The positive predictive value (PPV) and negative predictive value (NPV) for multisite pooled testing for chlamydia, over a range of background prevalence of chlamydia. Supplementary Table 3. Risk of Bias summary. Supplementary Table 4. GRADE table for multisite pooled testing for chlamydia. Supplementary Table 5. Meta-regression of the accuracy of multisite pooled testing for gonorrhoea according to study characteristics. Supplementary Table 6. The positive predictive value (PPV) and negative predictive value (NPV) for multisite pooled testing for gonorrhoea, over a range of background prevalence of gonorrhoea. Supplementary Table 7. GRADE table for multisite pooled testing for gonorrhoea. Supplementary Table 8. Study characteristics, methods of pooling, reported sensitivity and specificity of multisite pooled testing. References.
DOI: 10.6084/m9.figshare.21443615
title: Additional file 1 of Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies

description: Additional file 1: Table S1. Clinical and mutational information of patients with GCVsig identified in this study and from our previous patients. Table S2. Patient and panel characteristics of GENIE and FM cohorts. Table S3. Concentrations used for the treatment of respective cell lines for WGS mutation experiments. Table S4. Cosine similarity of COSMICv3 signatures with GCVsig. Table S5. GENIE and FM samples analysed in the study with their trinucleotide mutational signature and similarity to GCVsig shown. Table S6. Mutational spectrum and sigfit contribution score to COSMIC signatures for H414, HCT116 and normal colon organoid H023. Table S7. Mutational spectrum of mouse myeloid cell line.
DOI: 10.6084/m9.figshare.7812944.v1
title: MOESM5 of A balanced game: chicken macrophage response to ALV-J infection

description: Additional file 5. KEGG pathways and the information of DEG involved in these KEGG pathways at 3 hpi and 36 hpi after ALV-J infection in MDM.
DOI: 10.6084/m9.figshare.7812959
title: Additional file 10: of Transcriptomic analysis reveals the regulatory module of apple (Malus Ă domestica) floral transition in response to 6-BA

description: Table S8. Transcription factors respond to 6-BA treatment. (XLSX 165 kb)
DOI: 10.6084/m9.figshare.21443615.v1
title: Additional file 1 of Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies

description: Additional file 1: Table S1. Clinical and mutational information of patients with GCVsig identified in this study and from our previous patients. Table S2. Patient and panel characteristics of GENIE and FM cohorts. Table S3. Concentrations used for the treatment of respective cell lines for WGS mutation experiments. Table S4. Cosine similarity of COSMICv3 signatures with GCVsig. Table S5. GENIE and FM samples analysed in the study with their trinucleotide mutational signature and similarity to GCVsig shown. Table S6. Mutational spectrum and sigfit contribution score to COSMIC signatures for H414, HCT116 and normal colon organoid H023. Table S7. Mutational spectrum of mouse myeloid cell line.
DOI: 10.6084/m9.figshare.13055820
title: DIA (Data Independent Acquisition) proteomic based study on maize filling-kernel stage drought stress-responsive proteins and metabolic pathways

description: Drought is one of the most severe environmental stressors hampering maize (<i>Zea mays</i> L.) production worldwide. Therefore, revealing the molecular mechanisms underpinning maize drought tolerance is critical for guiding drought resistance breeding and ensuring global food security. Herein, we performed a data-independent acquisition (DIA) proteomics-based comparative analysis of the proteome responses of two contrasting maize hybrids (drought-tolerant NongDan 476 and drought-sensitive ZhongXin 978) exposed to 12 days of water-deficit (drought) treatment at the kernel filling stage. Resultantly, our DIA-based analysis approach identified a total of 826 differentially abundant proteins (DAPs), among which 7 DAPs were specifically accumulated in tolerant genotype ND 476 under drought treatment conditions. Moreover, our results showed that there were significant differences in drought stress responses between the two hybrids at the proteomic level. Predominantly, our analysis revealed that maize drought tolerance is attributed to some key proteins such as chaperones, DNA replication related enzymes, vicilin and ABA-responsive RAB17 protein, participating in several metabolic networks including starch and sucrose metabolism, terpenoid backbone biosynthesis, cyanoamino acid metabolism and carbon metabolism pathways. Our findings provide further insights into the drought stress tolerance mechanisms in maize at the grain filling period, in addition to useful reference data for maize drought resistance breeding.
DOI: 10.6084/m9.figshare.7812986
title: Additional file 3: of Transcriptomic analysis reveals the regulatory module of apple (Malus Ă domestica) floral transition in response to 6-BA

description: Table S2 DEGs obtained by comparasion with B30 and C30, B50 and C50, and B70 and C70. (XLSX 1270 kb)
DOI: 10.6084/m9.figshare.7813004.v1
title: Additional file 5: of Transcriptomic analysis reveals the regulatory module of apple (Malus Ă domestica) floral transition in response to 6-BA

description: Table S3. KEGG pathways enriched for differentially expressed genes between 6-BA treatment and control at 30, 50, and 70 DAFB. (XLSX 110 kb)
DOI: 10.6084/m9.figshare.7813022.v1
title: Additional file 7: of Transcriptomic analysis reveals the regulatory module of apple (Malus × domestica) floral transition in response to 6-BA

description: Table S5. The cytoscapeinput of SOC1 and SPL9 gene with other genes in modules ‘turquoise’ and ‘blue’. (XLSX 371 kb)
DOI: 10.5281/zenodo.10727173
title: Red Social. Genealogía de D. José López Yepes

description: Archivo creado con Pajek de la Red genealógica (Red Modo 1 direccionada). Se incluyen los codirectores de las tesis.
DOI: 10.5281/zenodo.10727174
title: Red Social. Genealogía de D. José López Yepes

description: Archivo creado con Pajek de la Red genealógica (Red Modo 1 direccionada). Se incluyen los codirectores de las tesis.
DOI: 10.6084/m9.figshare.7812947
title: MOESM6 of A balanced game: chicken macrophage response to ALV-J infection

description: Additional file 6. ISG induced by ALV-J infection in chicken MDM at 3 hpi and 36 hpi.
DOI: 10.6084/m9.figshare.7813025.v1
title: Additional file 8: of Transcriptomic analysis reveals the regulatory module of apple (Malus Ă domestica) floral transition in response to 6-BA

description: Table S6. Hormone and sugar related differentially expressed genes in response to 6-BA treatment of â Nagafu No.2â apple buds. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.13055820.v1
title: DIA (Data Independent Acquisition) proteomic based study on maize filling-kernel stage drought stress-responsive proteins and metabolic pathways

description: Drought is one of the most severe environmental stressors hampering maize (<i>Zea mays</i> L.) production worldwide. Therefore, revealing the molecular mechanisms underpinning maize drought tolerance is critical for guiding drought resistance breeding and ensuring global food security. Herein, we performed a data-independent acquisition (DIA) proteomics-based comparative analysis of the proteome responses of two contrasting maize hybrids (drought-tolerant NongDan 476 and drought-sensitive ZhongXin 978) exposed to 12 days of water-deficit (drought) treatment at the kernel filling stage. Resultantly, our DIA-based analysis approach identified a total of 826 differentially abundant proteins (DAPs), among which 7 DAPs were specifically accumulated in tolerant genotype ND 476 under drought treatment conditions. Moreover, our results showed that there were significant differences in drought stress responses between the two hybrids at the proteomic level. Predominantly, our analysis revealed that maize drought tolerance is attributed to some key proteins such as chaperones, DNA replication related enzymes, vicilin and ABA-responsive RAB17 protein, participating in several metabolic networks including starch and sucrose metabolism, terpenoid backbone biosynthesis, cyanoamino acid metabolism and carbon metabolism pathways. Our findings provide further insights into the drought stress tolerance mechanisms in maize at the grain filling period, in addition to useful reference data for maize drought resistance breeding.
DOI: 10.6084/m9.figshare.7812941
title: MOESM4 of A balanced game: chicken macrophage response to ALV-J infection

description: Additional file 4. GO terms and the information of DEG involved in these GO terms at 3 hpi and 36 hpi after ALV-J infection in MDM.
DOI: 10.6084/m9.figshare.7812941.v1
title: MOESM4 of A balanced game: chicken macrophage response to ALV-J infection

description: Additional file 4. GO terms and the information of DEG involved in these GO terms at 3 hpi and 36 hpi after ALV-J infection in MDM.
DOI: 10.6084/m9.figshare.21444642.v1
title: Random forest algorithm-based accurate prediction of rat acute oral toxicity

description: Predicting acute oral toxicity LD50 of chemicals in rats is a challenge since many factors affect toxicity data. In this paper, 40 descriptors were successfully used to develop a quantitative structure–activity relationship model for 8448 rat acute oral toxicity logLD50 by applying the random forest (RF) algorithm. To develop the optimal RF model, a training set (5914 chemicals) was used to establish models, a validation set (1267 chemicals) used to tune RF parameters and a test set (1267 chemicals) used to assess the performance of RF models. It yielded correlation coefficients <i>R</i> of 0.9695 and rms errors (log unit) of 0.3171 for the training set, <i>R </i>= 0.8322 and rms = 0.2889 for the validation set and <i>R</i> = 0.8335 and rms = 0.3060 for the test set. More than 99% of rat acute oral toxicity logLD50 in the dataset can be accurately predicted, although the dataset is large.
DOI: 10.6084/m9.figshare.13055993.v1
title: Functional Linear Regression: Dependence and Error Contamination

description: Functional linear regression is an important topic in functional data analysis. It is commonly assumed that samples of the functional predictor are independent realizations of an underlying stochastic process, and are observed over a grid of points contaminated by i.i.d. measurement errors. In practice, however, the dynamical dependence across different curves may exist and the parametric assumption on the error covariance structure could be unrealistic. In this paper, we consider functional linear regression with serially dependent observations of the functional predictor, when the contamination of the predictor by the white noise is genuinely functional with fully nonparametric covariance structure. Inspired by the fact that the autocovariance function of observed functional predictors automatically filters out the impact from the unobservable noise term, we propose a novel autocovariance-based generalized method-of-moments estimate of the slope function. We also develop a nonparametric smoothing approach to handle the scenario of partially observed functional predictors. The asymptotic properties of the resulting estimators under different scenarios are established. Finally, we demonstrate that our proposed method significantly outperforms possible competing methods through an extensive set of simulations and an analysis of a public financial dataset.
DOI: 10.6084/m9.figshare.21444642
title: Random forest algorithm-based accurate prediction of rat acute oral toxicity

description: Predicting acute oral toxicity LD50 of chemicals in rats is a challenge since many factors affect toxicity data. In this paper, 40 descriptors were successfully used to develop a quantitative structure–activity relationship model for 8448 rat acute oral toxicity logLD50 by applying the random forest (RF) algorithm. To develop the optimal RF model, a training set (5914 chemicals) was used to establish models, a validation set (1267 chemicals) used to tune RF parameters and a test set (1267 chemicals) used to assess the performance of RF models. It yielded correlation coefficients <i>R</i> of 0.9695 and rms errors (log unit) of 0.3171 for the training set, <i>R </i>= 0.8322 and rms = 0.2889 for the validation set and <i>R</i> = 0.8335 and rms = 0.3060 for the test set. More than 99% of rat acute oral toxicity logLD50 in the dataset can be accurately predicted, although the dataset is large.
DOI: 10.5281/zenodo.10726865
title: Unravelling the gut microbiome role in cardiovascular disease: A systematic review and a meta-analysis

description: This dataset contains supplementary data associated with the review paper titled "Unravelling the Gut Microbiome Role in Cardiovascular Disease: A Systematic Review and a Meta-analysis". The supplementary data provided here include database search strategy, characteristics of included studies in the systematic review and meta-analysis, information regarding metagenomic and metabolomic analysis, metabolic biomarkers of the studies included, quality assessment, and forest plots of bacteria genus relative abundance. 

These supplementary materials provide additional details and analyses supporting the findings presented in the main paper. They are made available to facilitate further scrutiny, reproducibility, and transparency in research.

Contact:For any inquiries regarding the supplementary data, please contact the corresponding author: Isabel Miranda (PhD)Address: Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto Portugal.Tel: +351 225 513 600E-mail: imiranda@med.up.pt
DOI: 10.5281/zenodo.10726866
title: Unravelling the gut microbiome role in cardiovascular disease: A systematic review and a meta-analysis

description: This dataset contains supplementary data associated with the review paper titled "Unravelling the Gut Microbiome Role in Cardiovascular Disease: A Systematic Review and a Meta-analysis". The supplementary data provided here include database search strategy, characteristics of included studies in the systematic review and meta-analysis, information regarding metagenomic and metabolomic analysis, metabolic biomarkers of the studies included, quality assessment, and forest plots of bacteria genus relative abundance. 

These supplementary materials provide additional details and analyses supporting the findings presented in the main paper. They are made available to facilitate further scrutiny, reproducibility, and transparency in research.

Contact:For any inquiries regarding the supplementary data, please contact the corresponding author: Isabel Miranda (PhD)Address: Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto Portugal.Tel: +351 225 513 600E-mail: imiranda@med.up.pt
DOI: 10.6084/m9.figshare.7812944
title: MOESM5 of A balanced game: chicken macrophage response to ALV-J infection

description: Additional file 5. KEGG pathways and the information of DEG involved in these KEGG pathways at 3 hpi and 36 hpi after ALV-J infection in MDM.
DOI: 10.6084/m9.figshare.7812947.v1
title: MOESM6 of A balanced game: chicken macrophage response to ALV-J infection

description: Additional file 6. ISG induced by ALV-J infection in chicken MDM at 3 hpi and 36 hpi.
DOI: 10.6084/m9.figshare.7812959.v1
title: Additional file 10: of Transcriptomic analysis reveals the regulatory module of apple (Malus Ă domestica) floral transition in response to 6-BA

description: Table S8. Transcription factors respond to 6-BA treatment. (XLSX 165 kb)
DOI: 10.6084/m9.figshare.7813004
title: Additional file 5: of Transcriptomic analysis reveals the regulatory module of apple (Malus Ă domestica) floral transition in response to 6-BA

description: Table S3. KEGG pathways enriched for differentially expressed genes between 6-BA treatment and control at 30, 50, and 70 DAFB. (XLSX 110 kb)
DOI: 10.6084/m9.figshare.7813013
title: Additional file 6: of Transcriptomic analysis reveals the regulatory module of apple (Malus Ă domestica) floral transition in response to 6-BA

description: Table S4. H-clustering of differentially expressed genes in control and 6-BA treatment, corresponding to Fig. 4. (XLSX 1156 kb)
DOI: 10.6084/m9.figshare.7812821
title: Additional file 1: of Overexpressing p130/E2F4 in mesenchymal stem cells facilitates the repair of injured alveolar epithelial cells in LPS-induced ARDS mice

description: Relative intensity of each band on the representative image of western blot. The relative intensity of bands on the representative images of SP-A, SP-C and occludin in Western blot was shown in Additional file 1 (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7813025
title: Additional file 8: of Transcriptomic analysis reveals the regulatory module of apple (Malus Ă domestica) floral transition in response to 6-BA

description: Table S6. Hormone and sugar related differentially expressed genes in response to 6-BA treatment of â Nagafu No.2â apple buds. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7813028
title: Additional file 9: of Transcriptomic analysis reveals the regulatory module of apple (Malus Ă domestica) floral transition in response to 6-BA

description: Table S7. Flowering genes involved in thermosensory, autonomous and vernalization pathways. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7813178.v1
title: MOESM6 of Rapid validation of transcriptional enhancers using agrobacterium-mediated transient assay

description: Additional file 6. Supplemental Tables 1â 5.