cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10652984
title: Dataset for Habitat Puzzles: Linking Primate Invasions and Declines to Landscape Connectivity

description: Dataset for Habitat Puzzles: Linking Primate Invasions and Declines to Landscape Connectivity

Abstract 

The distribution of primate species in Brazil is currently heavily impacted by the exploitation and fragmentation of the Atlantic Forest. This forest is one of the world’s biodiversity hotspots, and its ecosystems are home to an extremely rich fauna. Fragmentation can lead to the decline of certain species, such as Sapajus nigritus (S. nigritus). Conversely, the proximity of roads and built-up areas can lead to the accidental introduction of species with invasive potential that compete with endemic species, including Callithrix jacchus, Callithrix penicillata, and their hybrids. Anticipating and estimating the invasive threat of marmosets and its amplification over time is an important issue for the conservation of declining primate populations. Similarly, knowing which environments are favorable for the spread of capuchins would make it easier to anticipate their dispersal and maintenance.

Using data on climate, human density, vegetation cover, and vegetation types, as well as coordinates indicating the presence and absence of these primates, a comparison of generalized linear models and random forest models enabled us to estimate the conditions for their presence. The study took place in the Atlantic forest fragments of the São João river basin in the state of Rio de Janeiro. By extrapolating the probability of the presence of individuals throughout this territory, these models predicted the most suitable habitats. Based on these predictions, and assuming that the resistance to movement of these animals is linked to the suitability of the environment for these species, we were able to model the connectivity between different habitats.

Our results show that the probability of marmoset presence increases with decreasing humidity, non-vegetation, and tree cover. The presence of S. nigritus is explained by an increase in the distance to the nearest road. While marmosets now occupy vegetation types under anthropogenic influence, S. nigritus prefers predominantly natural vegetation. Callithrix’s tolerance of anthropized habitats explains its dispersal potential. Comparisons between models showed that random forest models performed better than GLM models.

The territory occupied by the species corresponds to a 0.5-fold increase in the area already occupied by marmosets. This dispersal could primarily occur around territories close to their current presence. The possibilities for the dispersal of S. nigritus are quite significant and are not limited to forest fragments, contrary to our hypotheses. We can expect the existing distribution to multiply by 7.5. These results provide important information that will be used by local associations to manage the populations, habitats, and dispersal paths identified. This is all the more important as marmosets compete with the endangered golden lion tamarin.
DOI: 10.5281/zenodo.10652985
title: Dataset for Habitat Puzzles: Linking Primate Invasions and Declines to Landscape Connectivity

description: Dataset for Habitat Puzzles: Linking Primate Invasions and Declines to Landscape Connectivity

Abstract 

The distribution of primate species in Brazil is currently heavily impacted by the exploitation and fragmentation of the Atlantic Forest. This forest is one of the world’s biodiversity hotspots, and its ecosystems are home to an extremely rich fauna. Fragmentation can lead to the decline of certain species, such as Sapajus nigritus (S. nigritus). Conversely, the proximity of roads and built-up areas can lead to the accidental introduction of species with invasive potential that compete with endemic species, including Callithrix jacchus, Callithrix penicillata, and their hybrids. Anticipating and estimating the invasive threat of marmosets and its amplification over time is an important issue for the conservation of declining primate populations. Similarly, knowing which environments are favorable for the spread of capuchins would make it easier to anticipate their dispersal and maintenance.

Using data on climate, human density, vegetation cover, and vegetation types, as well as coordinates indicating the presence and absence of these primates, a comparison of generalized linear models and random forest models enabled us to estimate the conditions for their presence. The study took place in the Atlantic forest fragments of the São João river basin in the state of Rio de Janeiro. By extrapolating the probability of the presence of individuals throughout this territory, these models predicted the most suitable habitats. Based on these predictions, and assuming that the resistance to movement of these animals is linked to the suitability of the environment for these species, we were able to model the connectivity between different habitats.

Our results show that the probability of marmoset presence increases with decreasing humidity, non-vegetation, and tree cover. The presence of S. nigritus is explained by an increase in the distance to the nearest road. While marmosets now occupy vegetation types under anthropogenic influence, S. nigritus prefers predominantly natural vegetation. Callithrix’s tolerance of anthropized habitats explains its dispersal potential. Comparisons between models showed that random forest models performed better than GLM models.

The territory occupied by the species corresponds to a 0.5-fold increase in the area already occupied by marmosets. This dispersal could primarily occur around territories close to their current presence. The possibilities for the dispersal of S. nigritus are quite significant and are not limited to forest fragments, contrary to our hypotheses. We can expect the existing distribution to multiply by 7.5. These results provide important information that will be used by local associations to manage the populations, habitats, and dispersal paths identified. This is all the more important as marmosets compete with the endangered golden lion tamarin.
DOI: 10.25582/data.2023-01.2710754/2298121
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732602/2298122
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2706510/2298123
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706104/2298124
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710951/2298125
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14329448
title: Additional file 9 of High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12

description: Additional file 9: Table S5. Transcriptional level of genes involved in TOR signal pathways in T. reesei RUT-C30.
DOI: 10.6084/m9.figshare.12756692
title: Additional file 3 of Transgelin interacts with PARP1 in human colon cancer cells

description: Additional file 3. The metadata of peptide identified with high-performance liquid chromatography/tandem mass spectrometry. The dataset included two sheets; the NC sheet contained peptides identified in the RKO-CTRL-FLAG group, while the TAGLN sheet contained peptides identified in the RKO-TAGLN-FLAG group.
DOI: 10.25582/data.2023-01.2706959/2298126
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14329433.v1
title: Additional file 4 of High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12

description: Additional file 4: Table S1. Transcriptional level of total DEGs in T. reesei RUT-C30 with or without 100 μM rapamycin.
DOI: 10.6084/m9.figshare.14329448.v1
title: Additional file 9 of High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12

description: Additional file 9: Table S5. Transcriptional level of genes involved in TOR signal pathways in T. reesei RUT-C30.
DOI: 10.6084/m9.figshare.14329442
title: Additional file 7 of High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12

description: Additional file 7: Table S4. Transcriptional level of DEGs related to “Biosynthesis of secondary metabolites” in T. reesei RUT-C30.
DOI: 10.25582/data.2023-01.2709986/2298127
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710562/2298128
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14329433
title: Additional file 4 of High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12

description: Additional file 4: Table S1. Transcriptional level of total DEGs in T. reesei RUT-C30 with or without 100 μM rapamycin.
DOI: 10.25582/data.2023-02.2732732/2298129
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2709532/2298130
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.12756697.v1
title: Additional file 1 of TET2 suppresses nasopharyngeal carcinoma progression by inhibiting glycolysis metabolism

description: Additional file 1: Table S1. Proteins potentially interacted with TET2 identified by mass spectrometry.
DOI: 10.6084/m9.figshare.12756875
title: Additional file 11 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 11: Table S7. The differences of flowering time between early- and late- flowering B. napus lines.
DOI: 10.6084/m9.figshare.12756890
title: Additional file 16 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 16: Table S10. Significantly overrepresented GO terms (a) and KEGG pathways (b) in the common genes of EV vs. ER and LV vs. LR.
DOI: 10.25582/data.2023-01.2709890/2298131
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.12756899.v1
title: Additional file 19 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 19: Table S11. List of flowering time genes in B. napus from our RNA-sequencing data using Arabidopsis flowering genes as queries.
DOI: 10.6084/m9.figshare.12756875.v1
title: Additional file 11 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 11: Table S7. The differences of flowering time between early- and late- flowering B. napus lines.
DOI: 10.6084/m9.figshare.12756890.v1
title: Additional file 16 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 16: Table S10. Significantly overrepresented GO terms (a) and KEGG pathways (b) in the common genes of EV vs. ER and LV vs. LR.
DOI: 10.6084/m9.figshare.12756923.v1
title: Additional file 26 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 26: Table S15. Gene-specific primers used for qRT-PCR verification. Bnactin7 is the internal reference gene.
DOI: 10.25582/data.2023-01.2708758/2298132
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.12756697
title: Additional file 1 of TET2 suppresses nasopharyngeal carcinoma progression by inhibiting glycolysis metabolism

description: Additional file 1: Table S1. Proteins potentially interacted with TET2 identified by mass spectrometry.
DOI: 10.6084/m9.figshare.12756878.v1
title: Additional file 12 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 12: Table S8. Summary of read numbers and mapped reads from the RNA-Seq of four samples (EV, ER, LV and LR). EV: leaves of early-flowering at vegetative stage, LV: leaves of late-flowering at vegetative stage, ER: leaves of late-flowering at reproductive stage, LR: leaves of late-flowering at reproductive stage.
DOI: 10.6084/m9.figshare.12756905
title: Additional file 20 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 20: Table S12. The detailed information of different haplotypes detected in seven candidate genes.
DOI: 10.25582/data.2023-01.2706470/2298133
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.12756914
title: Additional file 23 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 23: Table S13. The common QTLs detected by both GWAS and linkage mapping.
DOI: 10.6084/m9.figshare.12756917
title: Additional file 24 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 24: Table S14. List of SNP markers with pleiotropic effect.
DOI: 10.6084/m9.figshare.19571978.v1
title: Additional file 1 of Mapping the distributions of blood-sucking mites and mite-borne agents in China: a modeling study

description: Additional file 1. The dataset for mites.
DOI: 10.25582/data.2023-01.2709721/2298134
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.5941084
title: Combined effect of boundary layer recirculation factor and stable energy on local air quality in the Pearl River Delta over southern China

description: Atmospheric boundary layer (ABL) has a significant impact on the spatial and temporal distribution of air pollutants. In order to gain a better understanding of how ABL affects the variation of air pollutants, atmospheric boundary layer observations were performed at Sanshui in the Pearl River Delta (PRD) region over southern China during the winter of 2013. Two types of typical ABL status that could lead to air pollution were analyzed comparatively: weak vertical diffusion ability type (WVDAT) and weak horizontal transportation ability type (WHTAT). Results show that (1) WVDAT was featured by moderate wind speed, consistent wind direction, and thick inversion layer at 600~1000 m above ground level (AGL), and air pollutants were restricted in the low altitudes due to the stable atmospheric structure; (2) WHTAT was characterized by calm wind, varied wind direction, and shallow intense ground inversion layer, and air pollutants accumulated in locally because of strong recirculation in the low ABL; (3) recirculation factor (RF) and stable energy (SE) were proved to be good indicators for horizontal transportation ability and vertical diffusion ability of the atmosphere, respectively. Combined utilization of RF and SE can be very helpful in the evaluation of air pollution potential of the ABL. <i>Implications</i>: Air quality data from ground and meteorological data collected from radio sounding in Sanshui in the Pearl River Delta showed that local air quality was poor when wind reversal was pronounced or temperature stratification state was stable. The combination of horizontal and vertical transportation ability of the local atmosphere should be taken into consideration when evaluating local environmental bearing capacity for air pollution.
DOI: 10.6084/m9.figshare.9614102
title: RETRACTED ARTICLE: Long noncoding RNA H19 regulates HIF-1α/AXL signaling through inhibiting miR-20b-5p in endometrial cancer

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: He Zhu, Yue-Mei Jin, Xue-Man Lyu, Li-Mei Fan & Fei Wu (2019) Long noncoding RNA H19 regulates HIF-1α/AXL signaling through inhibiting miR-20b-5p in endometrial cancer, Cell Cycle, 18:19, 2454-2464, DOI: 10.1080/15384101.2019.1648958 Since publication, the authors have found significant errors in the statistical analysis of the research reported in this article. As this error directly impacts the accuracy of the results and conclusions, the authors alerted the issue to the Editor and Publisher and all have agreed to retract the article to ensure the integrity of the scholarly record. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.25582/data.2023-01.2710967/2298135
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.9614102.v1
title: Long noncoding RNA H19 regulates HIF-1α/AXL signaling through inhibiting miR-20b-5p in endometrial cancer

description: In a variety of cancers, long non-coding RNAs (lncRNAs) were believed to play important roles. Nevertheless, <i>H19’s</i> possible molecular mechanism related to miR-20b-5p has not yet been explored in endometrial cancer. Differential lncRNAs in endometrial cancer were identified based on microarray analysis (GSE23339). In this research, in the first place, <i>H19</i> expression was detected to be increased but miR-20b-5p to be decreased in endometrial cancer tissues and cells. Besides, <i>H19</i> expression displayed a negative relationship to miR-20b-5p expression in endometrial cancer tissues. According to gain- and loss-of-function experiments of <i>H19</i>, like a ceRNA, <i>H19</i> elevated <i>AXL</i> level and <i>HIF-1α</i> expression so as to stimulate the migration, proliferation and EMT process of endometrial cancer. Additionally, the knockdown of <i>H19</i> slowed down tumor growth, promoted apoptosis and upregulated miR-20b-5p expression but lowered the expressions of <i>HIF-1α</i>, PCNA and <i>AXL in vivo</i>. Furthermore, <i>H19</i> was also verified to stimulate the activity of endometrial cancer with <i>AXL</i> inhibitor BGB324 <i>in vitro</i> and <i>in vivo</i>. To sum up, <i>H19</i> accelerates the tumor formation of endometrial cancer through the miR-20b-5p/<i>AXL</i>/<i>HIF-1α</i> signaling pathway, thereby providing a novel target for diagnosing and treating endometrial cancer.
DOI: 10.6084/m9.figshare.19571981.v1
title: Additional file 2 of Mapping the distributions of blood-sucking mites and mite-borne agents in China: a modeling study

description: Additional file 2. The dataset for mite-borne agents.
DOI: 10.25582/data.2023-02.2733189/2298136
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2705428/2298137
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709808/2298138
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14853485
title: Additional file 1 of Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction

description: Additional file 1: Table S1. Detailed information of DEGs from four pairwise comparisons.
DOI: 10.6084/m9.figshare.6468398
title: Supplemental Table 3. Estimated increments in each lipid levels (z-score) per 1 standard deviation of BMI, FMI, and FMP from simultaneous linear regression models in boys and girls

description: After
mutual adjustment, beta coefficients of BMI with TC, LDL-C, and TG, FMI with HDL were substantial reversed
or attenuated in both genders.
DOI: 10.25582/data.2023-02.2733121/2298139
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.6465476
title: Additional file 5: of Deep sequencing identification of miRNAs in pigeon ovaries illuminated with monochromatic light

description: KEGG pathway annotations for the target genes of differentially expressed miRNAs. (XLS 2500 kb)
DOI: 10.6084/m9.figshare.12756935
title: Additional file 5 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 5: Table S3. LD block analysis and SNP/candidate genes comparison in different studies.
DOI: 10.6084/m9.figshare.12756935.v1
title: Additional file 5 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 5: Table S3. LD block analysis and SNP/candidate genes comparison in different studies.
DOI: 10.25582/data.2023-01.2708296/2298140
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.12756923
title: Additional file 26 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 26: Table S15. Gene-specific primers used for qRT-PCR verification. Bnactin7 is the internal reference gene.
DOI: 10.6084/m9.figshare.19572534
title: Additional file 1 of Identification of microRNA–mRNA–TF regulatory networks in periodontitis by bioinformatics analysis

description: Additional file 1. R scripts for preprocessing and evaluating differential expression.
DOI: 10.6084/m9.figshare.19572555
title: Additional file 5 of Identification of microRNA–mRNA–TF regulatory networks in periodontitis by bioinformatics analysis

description: Additional file 5. GO analysis of the hug genes.
DOI: 10.6084/m9.figshare.19572561
title: Additional file 6 of Identification of microRNA–mRNA–TF regulatory networks in periodontitis by bioinformatics analysis

description: Additional file 6. The KEGG pathway enrichment analysis of hug genes.
DOI: 10.25582/data.2023-01.2710065/2298141
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.19572561.v1
title: Additional file 6 of Identification of microRNA–mRNA–TF regulatory networks in periodontitis by bioinformatics analysis

description: Additional file 6. The KEGG pathway enrichment analysis of hug genes.
DOI: 10.6084/m9.figshare.19572534.v1
title: Additional file 1 of Identification of microRNA–mRNA–TF regulatory networks in periodontitis by bioinformatics analysis

description: Additional file 1. R scripts for preprocessing and evaluating differential expression.
DOI: 10.25582/data.2023-01.2710909/2298142
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.12756938
title: Additional file 6 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 6: Table S4. Genes identified in LD block or 300 kb up- and down-stream of significant SNPs identified in GWAS.
DOI: 10.6084/m9.figshare.19572549
title: Additional file 4 of Identification of microRNA–mRNA–TF regulatory networks in periodontitis by bioinformatics analysis

description: Additional file 4. The KEGG pathway enrichment analysis of DEMs.
DOI: 10.6084/m9.figshare.19572564
title: Additional file 7 of Identification of microRNA–mRNA–TF regulatory networks in periodontitis by bioinformatics analysis

description: Additional file 7. GO analysis of the genes in Module 1.
DOI: 10.6084/m9.figshare.19572564.v1
title: Additional file 7 of Identification of microRNA–mRNA–TF regulatory networks in periodontitis by bioinformatics analysis

description: Additional file 7. GO analysis of the genes in Module 1.
DOI: 10.6084/m9.figshare.12756872
title: Additional file 10 of Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

description: Additional file 10: Table S6. Genes located in the confidence interval of significant QTLs identified by linkage mapping.