cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12965648
title: Additional file 1 of Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks

description: Additional file 1. Interventions (stimuli or inhibitors) and their most-direct target proteins among the 35 proteins of interest in the RPPA dataset. N/A means there is either no target protein among the proteins of interest or the target proteins are not clear.
DOI: 10.6084/m9.figshare.12965648.v1
title: Additional file 1 of Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks

description: Additional file 1. Interventions (stimuli or inhibitors) and their most-direct target proteins among the 35 proteins of interest in the RPPA dataset. N/A means there is either no target protein among the proteins of interest or the target proteins are not clear.
DOI: 10.6084/m9.figshare.7037501.v1
title: A pivotal role of FOS-mediated BECN1/Beclin 1 upregulation in dopamine D2 and D3 receptor agonist-induced autophagy activation

description: Autophagy dysfunction is implicated in the pathogenesis of Parkinson disease (PD). BECN1/Beclin 1 acts as a critical regulator of autophagy and other cellular processes; yet, little is known about the function and regulation of BECN1 in PD. In this study, we report that dopamine D2 and D3 receptor (DRD2 and DRD3) activation by pramipexole and quinpirole could enhance <i>BECN1</i> transcription and promote autophagy activation in several cell lines, including PC12, MES23.5 and differentiated SH-SY5Y cells, and also in tyrosine hydroxylase positive primary midbrain neurons. Moreover, we identified a novel FOS (FBJ murine osteosarcoma viral oncogene homolog) binding sequence (5′-TGCCTCA-3′) in the rat and human <i>Becn1</i>/<i>BECN1</i> promoter and uncovered an essential role of FOS binding in the enhancement of <i>Becn1</i> transcription in PC12 cells in response to the dopamine agonist(s). In addition, we demonstrated a critical role of intracellular Ca<sup>2+</sup> elevation, followed by the enhanced phosphorylation of CAMK4 (calcium/calmodulin-dependent protein kinase IV) and CREB (cAMP responsive element binding protein) in the increases of FOS expression and autophagy activity. More importantly, pramipexole treatment ameliorated the SNCA/α-synuclein accumulation in rotenone-treated PC12 cells that overexpress wild-type or A53T mutant SNCA by promoting autophagy flux. This effect was also demonstrated in the substantia nigra and the striatum of <i>SNCA</i><sup>A53T</sup> transgenic mice. The inhibition of SNCA accumulation by pramipexole was attenuated by cotreatment with the DRD2 and DRD3 antagonists and <i>Becn1</i> siRNAs. Thus, our findings suggest that DRD2 and DRD3 agonist(s) may induce autophagy activation via a BECN1-dependent pathway and have the potential to reduce SNCA accumulation in PD.
DOI: 10.6084/m9.figshare.19620197
title: The biological behavior of tRNA-derived fragment tRF-Leu-AAG in pancreatic cancer cells

description: Pancreatic cancer (PC) is a life-threatening cancer with increasing incidence in developed countries. Reports indicate that tRNA-derived fragments (tRFs) are possible therapeutic targets and biomarkers for cancer treatment. Nonetheless, the effect of tRF-Leu-AAG on PC is unclear. This study aims to explore the role of tRF-Leu-AAG and upstream frameshift mutant 1 (UPF1) in the development of PC and its potential underlying mechanisms. High-throughput second-generation sequencing techniques were used to detect the expression of tRFs in cancerous and adjacent normal tissues from PC patients. The role of tRF-Leu-AAG proliferation in PC cells was investigated via the Cell Counting Kit-8 (CCK8) assay. The effect of tRF-Leu-AAG on the invasion and migration ability of PC cells was also determined by the transwell assay. Thereafter, the downstream target genes of tRF-Leu-AAG were comprehensively predicted using bioinformatics analysis databases. We also used the Dual-Luciferase Reporter assay to assess the nexus between tRF-Leu-AAG and UPF1. Eventually, Western Blot was used to validate the expression of UPF1 in PC cells. A total of 33 tRF expressions significantly varied from PC patients. RT-qPCR confirmed that the expression of tRF-Leu-AAG was observably up-regulated in PC cells as compared to the control cells. Importantly, knockdown of tRF-Leu-AAG observably inhibited cell proliferation, migration, and invasion. Furthermore, according to the predicted frameshift database results, the UPF1 acted as downstream target genes for tRF-Leu-AAG and significantly down-regulated UPF1 expression.
DOI: 10.6084/m9.figshare.12965630
title: Additional file 5 of Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

description: Additional file 5: Table S4. GFOLD values of the salt-responsive genes identified in the time points studied in the four genotypes.
DOI: 10.6084/m9.figshare.12965630.v1
title: Additional file 5 of Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

description: Additional file 5: Table S4. GFOLD values of the salt-responsive genes identified in the time points studied in the four genotypes.
DOI: 10.6084/m9.figshare.12965633.v1
title: Additional file 6 of Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

description: Additional file 6: Table S5. Details of over-represented gene categories during the osmotic phase.
DOI: 10.6084/m9.figshare.12276785
title: Additional file 6 of The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica

description: Additional file 6: Table S2. Genomic locations of the lost and transferred plastid genes in Aeginetia indica. The annotation, sequence alignment, alignment position and sequence identity are all based on the chloroplast genes of Lindenbergia philippensis. * indicates gene also present in the plastome of Aeginetia indica.
DOI: 10.5517/ccdc.csd.cc2gkr82
title: CCDC 2281174: Experimental Crystal Structure Determination

description: Related Article: Mishika Virmani|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2h0jnq
title: CCDC 2294423: Experimental Crystal Structure Determination

description: Related Article: Xianran Wang, Yuying Wu, Feng Gao, Youfu Wang|2024|New J.Chem.|48|3192|doi:10.1039/D3NJ05858A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.16998954.v1
title: XRD raw data of (Al63Cu25Fe12)100-xCex (x = 0.1 at%) sample from Influence of cerium content on the microstructure and thermal expansion properties of suction cast Al-Cu-Fe alloys

description: 2CExrd
DOI: 10.6084/m9.figshare.16998957.v1
title: XRD raw data of (Al63Cu25Fe12)100-xCex (x = 2 at%) sample from Influence of cerium content on the microstructure and thermal expansion properties of suction cast Al-Cu-Fe alloys

description: 5CExrd
DOI: 10.6084/m9.figshare.12276779.v1
title: Additional file 5 of The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica

description: Additional file 5: Table S1. Gene contents of the plastomes of five holoparasitic plants and one autotrophic relative Lindenbergia philippensisin. Black boxes indicate the absence of genes, white boxes indicate the presence of genes, and gray boxes indicate pseudogenes.
DOI: 10.6084/m9.figshare.7037498
title: Tomato HsfA1a plays a critical role in plant drought tolerance by activating <i>ATG</i> genes and inducing autophagy

description: Autophagy plays critical roles in plant responses to stress. In contrast to the wealth of information concerning the core process of plant autophagosome assembly, our understanding of the regulation of autophagy is limited. In this study, we demonstrated that transcription factor HsfA1a played a critical role in tomato tolerance to drought stress, in part through its positive role in induction of autophagy under drought stress. <i>HsfA1a</i> expression was induced by drought stress. Virus-induced <i>HsfA1a</i> gene silencing reduced while its overexpression increased plant drought tolerance based on both symptoms and membrane integrity. <i>HsfA1a</i>-silenced plants were more sensitive to endogenous ABA-mediated stomatal closure, while its overexpression lines were resistant under drought stress, indicating that phytohormone ABA did not play a major role in <i>HsfA1a</i>-induced drought tolerance. On the other hand, <i>HsfA1a</i>-silenced plants increased while its overexpression decreased the levels of insoluble proteins which were highly ubiquitinated under drought stress. Furthermore, drought stress induced numerous <i>ATGs</i> expression and autophagosome formation in wild-type plants. The expression of <i>ATG10</i> and <i>ATG18f</i>, and the formation of autophagosomes were compromised in <i>HsfA1a</i>-silenced plants but were enhanced in <i>HsfA1a</i>-overexpressing plants. Both electrophoretic mobility shift assay and chromatin immunoprecipitation coupled with qPCR analysis revealed that HsfA1a bound to <i>ATG10</i> and <i>ATG18f</i> gene promoters. Silencing of <i>ATG10</i> and <i>ATG18f</i> reduced HsfA1a-induced drought tolerance and autophagosome formation in plants overexpressing <i>HsfA1a</i>. These results demonstrate that HsfA1a induces drought tolerance by activating <i>ATG</i> genes and inducing autophagy, which may promote plant survival by degrading ubiquitinated protein aggregates under drought stress.
DOI: 10.6084/m9.figshare.8091578
title: IRON OXIDE AND Fe2O3/Al2O3 USED TO CATALYZE REMOVING HYDROGEN FROM TAIL CHLORINE AT LOW TEMPERATURE

description: The transition metal oxide, such as iron oxide and Fe2O3/Al2O3 is cheap and industrialized that are widely used to catalyze the reaction of chlorine and oxygen with hydrogen in mixture gas to remove hydrogen from tail chlorine at low temperature. The reaction gas was prepared by the same composition with industrial tail chlorine, namely Cl2 (65% ~ 80%), O2 (8% ~ 10%), N2 (6% ~16%) and H2 (1.5% ~ 4%). In this experiment, the fixed bed reactor and iron oxide or Fe2O3/Al2O3 were used as the reaction device and catalysts, respectively. The optimum conversion rate of hydrogen was 84.11% when the reaction temperature was at 70 °C with 3%wt. Fe2O3/Al2O3 and the calcination temperature was 500 °C. The results showed that the catalytic performance of Fe2O3/Al2O3 is superior to Fe2O3. The selectivity of the reaction of hydrogen and chloride was higher than that of hydrogen and oxygen. We also characterized the catalysts with XRD, XPS, SEM and N2 adsorption-desorption and the results showed that the iron oxide was dispersive uniformly on the support surface.
DOI: 10.5281/zenodo.10018374
title: Local adaptation in the Patagonian foundation tree species Nothofagus pumilio

description: Npumilio_specific_candidate_genes.xlsx 

Study-specific candidate genes. For annotation information on the 1,789 candidate genes from orthogroups, see Milesi at al 2023 (https://doi.org/10.1101/2023.01.05.522822 and Supplemental Tables S12-S14).
Contains contig, Uniprot-TAIR code and original species, and reason for inclusion in the candidate list (e.g. upregulated or downregulated in the heat stress-transcriptome study (https://doi.org/10.1371/journal.pone.0246615), or of interest for wood growth)
The list includes some duplicate contigs that are contained in the candidate gene set; they were left in for the "Reason" information
N_pumilio_06Nov2019_probe_coverage.txt

Probe design file as provided by IGA Technology Services
All called SNP variants. Data for 502 individual tree samples are included: 496 adult trees + 6 replicates.

variants-gatk_haplotypecaller_SNP_raw.vcf.gz are raw called variants.
variants-gatk_haplotypecaller_SNP.vcf.gz are coarsely quality-filtered and are the starting datasets for our downstream analyses.
Npumilio_IDs_vcforder_all_info.xlsx

Metadata for all samples in the .vcf files (in the same order), including site name, geographic coordinates and elevation
Npumilio_orthogroups.csv

Orthogroups, TAIR codes, and best-hit Nothofagus contigs for cross-referencing with orthogroup candidate gene set (Milesi at al 2023 (https://doi.org/10.1101/2023.01.05.522822 and Supplemental Tables S12-S14)).
DOI: 10.5281/zenodo.7930351
title: Local adaptation in the Patagonian foundation tree species Nothofagus pumilio

description: Npumilio_specific_candidate_genes.xlsx 

Study-specific candidate genes. For annotation information on the 1,789 candidate genes from orthogroups, see Milesi at al 2023 (https://doi.org/10.1101/2023.01.05.522822 and Supplemental Tables S12-S14).
Contains contig, Uniprot-TAIR code and original species, and reason for inclusion in the candidate list (e.g. upregulated or downregulated in the heat stress-transcriptome study (https://doi.org/10.1371/journal.pone.0246615), or of interest for wood growth)
The list includes some duplicate contigs that are contained in the candidate gene set; they were left in for the "Reason" information
N_pumilio_06Nov2019_probe_coverage.txt

Probe design file as provided by IGA Technology Services
All called SNP variants. Data for 502 individual tree samples are included: 496 adult trees + 6 replicates.

variants-gatk_haplotypecaller_SNP_raw.vcf.gz are raw called variants.
variants-gatk_haplotypecaller_SNP.vcf.gz are coarsely quality-filtered and are the starting datasets for our downstream analyses.
Npumilio_IDs_vcforder_all_info.xlsx

Metadata for all samples in the .vcf files (in the same order), including site name, geographic coordinates and elevation
Npumilio_orthogroups.csv

Orthogroups, TAIR codes, and best-hit Nothofagus contigs for cross-referencing with orthogroup candidate gene set (Milesi at al 2023 (https://doi.org/10.1101/2023.01.05.522822 and Supplemental Tables S12-S14)).
DOI: 10.6084/m9.figshare.23290436
title: Additional file 5 of High HSPB1 expression predicts poor clinical outcomes and correlates with breast cancer metastasis

description: Additional file 5.
DOI: 10.6084/m9.figshare.23290436.v1
title: Additional file 5 of High HSPB1 expression predicts poor clinical outcomes and correlates with breast cancer metastasis

description: Additional file 5.
DOI: 10.6084/m9.figshare.19096324.v1
title: Mesozoic tectonic transition of the northeastern North China Craton: Evidence from adakitic rocks in southeastern Jilin Province, China

description: Chronological and geochemical studies of adakites and adakitic rocks are important in understanding the tectonic evolution and geodynamic processes. We present new zircon U–Pb ages, Hf isotope, and geochemical analyses of adakitic rocks exposed in the Baishan area, southeastern Jilin Province, China. These new ages, together with existing age data, indicate that adakitic magmatism in southeastern Jilin Province can be subdivided into four stages: Early–Middle Triassic (251–235 Ma), Late Triassic (221–219 Ma), late Early–early Late Jurassic (176–156 Ma), and Early Cretaceous (ca. 130 Ma). Early–Middle Triassic adakitic rocks occur in a nearly E–W-trending belt within the northern margin of the northeastern North China Craton, indicating a compressional tectonic setting caused by the scissor-like closure of the Paleo-Asian Ocean from west to east. Late Triassic adakitic rocks occur in the Tonghua area and formed in an extensional setting caused by delamination after subduction and collision between the Yangtze Craton and NCC. Late Early–early Late Jurassic adakitic rocks occur in the Baishan and Kaiyuan areas and originated from partial melting of thickened lower crust in a compressional setting related to subduction of the Paleo-Pacific Plate. Early Cretaceous adakitic rocks occur in the Baishan area and were derived from partial melting of thickened lower crust above the subduction zone and delaminated lower crust, indicating that the subducting Paleo-Pacific Plate retreated to the eastern part of southern Jilin Province during the Early Cretaceous (ca. 130 Ma) and that the tectonic setting of the northeastern part of the NCC changed from compression to extension, starting in the east and progressing westward. In summary, the northeastern part of the NCC has been affected by a series of tectonic events during the Mesozoic, such as the closure of the Paleo-Asian Ocean, the collision between the NCC and YC, and the subduction of the Paleo-Pacific Plate.
DOI: 10.6084/m9.figshare.23290594.v1
title: Raw data and analysis code from Avoidance-motivational intensity modulated the effect of negative emotion on working memory

description: Although many studies have explored the association between negative emotion and working memory, the findings remain controversial. The present study investigated the role of avoidance-motivational intensity in modulating the effect of negative emotion on different processes (maintenance versus manipulation) of verbal and spatial working memory. Two experiments employed the modified delayed match-to-sample paradigms to separate the two processes of verbal and spatial working memory under different emotional states, respectively. In Experiment 1, participants were asked to perform the delayed match-to-sample task with or without reordering the characters (manipulation process of verbal working memory). In Experiment 2, mental rotation was used as the manipulation process of spatial working memory. The results showed that negative emotion only affected the manipulation process, but not the maintenance process. Relative to neutral and low avoidance-motivated negative conditions, the manipulation processes of both types of working memory were impaired under the high avoidance-motivated negative condition. No significant difference was observed between low avoidance-motivated negative condition and neutral condition. Our results are discussed in relation to efficiency processing theory and motivational dimensional model of affect. We conclude that negative emotional states with high avoidance-motivational intensity impair the manipulation process of verbal and spatial working memory.
DOI: 10.6084/m9.figshare.23290676
title: LncRNA AK001796 promotes cell proliferation via acting as a ceRNA of miR-150 in hepatocellular carcinoma

description: Abstract Long non-coding RNA AK001796 was initially identified altered in lung cancer. Recent research showed it could participate in the prognosis of hepatocellular carcinoma (HCC). However, the general biological role of AK001796 and its underlying mechanisms in HCC remain unclear. Here we demonstrated that the expression level of AK001796 in HCC tissues and cell lines was up-regulated. Silencing AK001796 suppressed the proliferation ability of HCC cells. Through dual luciferase reporter assays and loss/gain of functions studies, we identified that AK001796 could bind to miR-150, a star microRNA, promoting HCC proliferation. Furthermore, it was reported that growth factor receptor binding protein 2-associated binder 1 (GAB1) is a target gene of miR-150. Owing to AK001796 being a decoy for miR-150 and binding the same putative sites of miR-150 as GAB1, we presented that inhibition of miR-150 in AK001796 silencing cells reversed the reduction in GAB1. Subsequently, our findings demonstrated that silencing AK001796 can impair phospho-ERK1/2 and phospho-AKT. In conclusion, our investigation revealed that AK001796 promoted proliferation by enhancing phospho-ERK1/2 and phospho-AKT through AK001796/miR-150/GAB1 axis in HCC. These results provided further evidence for the critical roles of AK001796 accumulating HCC and suggested that AK001796 might act as an HCC biomarker in clinical treatment.
DOI: 10.6084/m9.figshare.23290691
title: RESEARCH ON IDENTIFICATION AND CLASSIFICATION METHOD OF IMBALANCED DATA SET OF PIG BEHAVIOR

description: ABSTRACT To address the problem of the low accuracy and poor robustness of modeling methods for imbalanced data sets of pig behavior identification and classification, the three commonly used re-sampling methods of under-sampling, SMOTE and Borderline-SMOTE are compared, and an adaptive boundary data augmentation algorithm AD-BL-SMOTE is proposed. The activity of the pigs was measured using triaxial accelerometers, which were fixed on the backs of the pigs. A multilayer feed-forward neural network was trained and validated with 21 input features to classify four pig activities: lying, standing, walking, and exploring. The results showed that re-sampling methods are an effective way to improve the performance of pig behavior identification and classification. Moreover, AD-BL-SMOTE could yield greater improvements in classification performance than the other three methods for balancing the training data set. The overall major mean accuracy of lying, standing, walking, and exploring by pigs A, B and C was significantly improved by using AD-BL-SMOTE, reaching 91.8%, 93.0% and 96.0%, respectively.
DOI: 10.6084/m9.figshare.19626076
title: Analysis of geochemical patterns in a soil profile over mineralized bedrock

description: Supplementary material 5
DOI: 10.6084/m9.figshare.19626076.v1
title: Analysis of geochemical patterns in a soil profile over mineralized bedrock

description: Supplementary material 5
DOI: 10.6084/m9.figshare.23290799
title: Prediction of health disorders in dairy cows monitored with collar based on Binary logistic analysis

description: ABSTRACT The objective of this study was to analyze data on physical activity and rumination time monitored via collars at the farm coupled with milk yield recorded by the rotary milking system to predict cows based on several disorders using the binary Logistic regression conducted with R software. Data for metritis (n=60), mastitis (n=98), lameness (n=35), and digestive disorders (n=52) were collected from 1,618 healthy cows used to construct the prediction model. To verify the feasibility and adaptability of the proposed method, we analyzed data of cows in the same herd (herd 1) not used to construct the model, and cows in another herd (herd 2) with data recorded by the same type of automated system, and led to detection of 75.0%, 64.2%, 74.2%, and 76.9% animals in herd 1 correctly predicted to suffer from metritis, mastitis, lameness, and digestive disorders, respectively. For cows in herd 2, 66.6%, 58.8%, 80.7%, and 71.4% were correctly predicted for metritis, mastitis, lameness, and digestive disorders, respectively. Compared with traditional clinical diagnoses by farm personnel, the algorithm developed allowed for earlier prediction of cows with a disorder.
DOI: 10.6084/m9.figshare.19626082
title: Analysis of geochemical patterns in a soil profile over mineralized bedrock

description: Supplementary material 10
DOI: 10.6084/m9.figshare.19626082.v1
title: Analysis of geochemical patterns in a soil profile over mineralized bedrock

description: Supplementary material 10
DOI: 10.6084/m9.figshare.19626085
title: Analysis of geochemical patterns in a soil profile over mineralized bedrock

description: Supplementary material 9
DOI: 10.6084/m9.figshare.19626085.v1
title: Analysis of geochemical patterns in a soil profile over mineralized bedrock

description: Supplementary material 9
DOI: 10.6084/m9.figshare.19626088
title: Analysis of geochemical patterns in a soil profile over mineralized bedrock

description: Supplementary material 7