cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7892435
title: Identification of transcription factors that regulate <i>ATG8</i> expression and autophagy in <i>Arabidopsis</i>

description: Autophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness. In <i>Arabidopsis thaliana</i>, the core machinery of autophagy is well defined, but its transcriptional regulation is largely unknown. The ATG8 (autophagy-related 8) protein plays central roles in decorating autophagosomes and binding to specific cargo receptors to recruit cargo to autophagosomes. We propose that the transcriptional control of <i>ATG8</i> genes is important during the formation of autophagosomes and therefore contributes to survival during stress. Here, we describe a yeast one-hybrid (Y1H) screen for transcription factors (TFs) that regulate <i>ATG8</i> gene expression in <i>Arabidopsis</i>, using the promoters of 4 <i>ATG8</i> genes. We identified a total of 225 TFs from 35 families that bind these promoters. The TF-<i>ATG8</i> promoter interactions revealed a wide array of diverse TF families for different promoters, as well as enrichment for families of TFs that bound to specific fragments. These TFs are not only involved in plant developmental processes but also in the response to environmental stresses. TGA9 (TGACG (TGA) motif-binding protein 9)/AT1G08320 was confirmed as a positive regulator of autophagy. TGA9 overexpression activated autophagy under both control and stress conditions and transcriptionally up-regulated expression of <i>ATG8B, ATG8E</i> and additional <i>ATG</i> genes via binding to their promoters. Our results provide a comprehensive resource of TFs that regulate <i>ATG8</i> gene expression and lay a foundation for understanding the transcriptional regulation of plant autophagy. <b>Abbreviations:</b> ABRC: <i>Arabidopsis</i> biological resource center; AP2-EREBP: APETALA2/Ethylene-responsive element binding protein; ARF: auxin response factor; ATF4: activating transcription factor 4; ATG: autophagy-related; ChIP: chromatin immunoprecipitation; DAP-seq: DNA affinity purification sequencing; FOXO: forkhead box O; GFP: green fluorescent protein; GO: gene ontologies; HB: homeobox; LD: long-day; LUC: firefly luciferase; MAP1LC3: microtubule associated protein 1 light chain 3; MDC: monodansylcadaverine; 3-MA: 3-methyladenine; OE: overexpressing; PCD: programmed cell death; qPCR: quantitative polymerase chain reaction; REN: renilla luciferase; RT: room temperature; SD: standard deviation; TF: transcription factor; TFEB: transcription factor EB; TGA: TGACG motif; TOR: target of rapamycin; TSS: transcription start site; WT: wild-type; Y1H: yeast one-hybrid.
DOI: 10.6084/m9.figshare.7892435.v2
title: Identification of transcription factors that regulate <i>ATG8</i> expression and autophagy in <i>Arabidopsis</i>

description: Autophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness. In <i>Arabidopsis thaliana</i>, the core machinery of autophagy is well defined, but its transcriptional regulation is largely unknown. The ATG8 (autophagy-related 8) protein plays central roles in decorating autophagosomes and binding to specific cargo receptors to recruit cargo to autophagosomes. We propose that the transcriptional control of <i>ATG8</i> genes is important during the formation of autophagosomes and therefore contributes to survival during stress. Here, we describe a yeast one-hybrid (Y1H) screen for transcription factors (TFs) that regulate <i>ATG8</i> gene expression in <i>Arabidopsis</i>, using the promoters of 4 <i>ATG8</i> genes. We identified a total of 225 TFs from 35 families that bind these promoters. The TF-<i>ATG8</i> promoter interactions revealed a wide array of diverse TF families for different promoters, as well as enrichment for families of TFs that bound to specific fragments. These TFs are not only involved in plant developmental processes but also in the response to environmental stresses. TGA9 (TGACG (TGA) motif-binding protein 9)/AT1G08320 was confirmed as a positive regulator of autophagy. TGA9 overexpression activated autophagy under both control and stress conditions and transcriptionally up-regulated expression of <i>ATG8B, ATG8E</i> and additional <i>ATG</i> genes via binding to their promoters. Our results provide a comprehensive resource of TFs that regulate <i>ATG8</i> gene expression and lay a foundation for understanding the transcriptional regulation of plant autophagy. <b>Abbreviations:</b> ABRC: <i>Arabidopsis</i> biological resource center; AP2-EREBP: APETALA2/Ethylene-responsive element binding protein; ARF: auxin response factor; ATF4: activating transcription factor 4; ATG: autophagy-related; ChIP: chromatin immunoprecipitation; DAP-seq: DNA affinity purification sequencing; FOXO: forkhead box O; GFP: green fluorescent protein; GO: gene ontologies; HB: homeobox; LD: long-day; LUC: firefly luciferase; MAP1LC3: microtubule associated protein 1 light chain 3; MDC: monodansylcadaverine; 3-MA: 3-methyladenine; OE: overexpressing; PCD: programmed cell death; qPCR: quantitative polymerase chain reaction; REN: renilla luciferase; RT: room temperature; SD: standard deviation; TF: transcription factor; TFEB: transcription factor EB; TGA: TGACG motif; TOR: target of rapamycin; TSS: transcription start site; WT: wild-type; Y1H: yeast one-hybrid.
DOI: 10.6084/m9.figshare.7892435.v1
title: Identification of transcription factors that regulate <i>ATG8</i> expression and autophagy in <i>Arabidopsis</i>

description: Autophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness. In <i>Arabidopsis thaliana</i>, the core machinery of autophagy is well defined, but its transcriptional regulation is largely unknown. The ATG8 (autophagy-related 8) protein plays central roles in decorating autophagosomes and binding to specific cargo receptors to recruit cargo to autophagosomes. We propose that the transcriptional control of <i>ATG8</i> genes is important during the formation of autophagosomes and therefore contributes to survival during stress. Here, we describe a yeast one-hybrid (Y1H) screen for transcription factors (TFs) that regulate <i>ATG8</i> gene expression in <i>Arabidopsis</i>, using the promoters of 4 <i>ATG8</i> genes. We identified a total of 225 TFs from 35 families that bind these promoters. The TF-<i>ATG8</i> promoter interactions revealed a wide array of diverse TF families for different promoters, as well as enrichment for families of TFs that bound to specific fragments. These TFs are not only involved in plant developmental processes but also in the response to environmental stresses. TGA9 (TGACG (TGA) motif-binding protein 9)/AT1G08320 was confirmed as a positive regulator of autophagy. TGA9 overexpression activated autophagy under both control and stress conditions and transcriptionally up-regulated expression of <i>ATG8B, ATG8E</i> and additional <i>ATG</i> genes via binding to their promoters. Our results provide a comprehensive resource of TFs that regulate <i>ATG8</i> gene expression and lay a foundation for understanding the transcriptional regulation of plant autophagy. <b>Abbreviations:</b> ABRC: <i>Arabidopsis</i> biological resource center; AP2-EREBP: APETALA2/Ethylene-responsive element binding protein; ARF: auxin response factor; ATF4: activating transcription factor 4; ATG: autophagy-related; ChIP: chromatin immunoprecipitation; DAP-seq: DNA affinity purification sequencing; FOXO: forkhead box O; GFP: green fluorescent protein; GO: gene ontologies; HB: homeobox; LD: long-day; LUC: firefly luciferase; MAP1LC3: microtubule associated protein 1 light chain 3; MDC: monodansylcadaverine; 3-MA: 3-methyladenine; OE: overexpressing; PCD: programmed cell death; qPCR: quantitative polymerase chain reaction; REN: renilla luciferase; RT: room temperature; SD: standard deviation; TF: transcription factor; TFEB: transcription factor EB; TGA: TGACG motif; TOR: target of rapamycin; TSS: transcription start site; WT: wild-type; Y1H: yeast one-hybrid.
DOI: 10.6084/m9.figshare.14183885
title: Additional file 2 of Cold stress in the harvest period: effects on tobacco leaf quality and curing characteristics

description: Additional file 2. Contains original data of figures and tables in the manuscript.
DOI: 10.6084/m9.figshare.14183885.v1
title: Additional file 2 of Cold stress in the harvest period: effects on tobacco leaf quality and curing characteristics

description: Additional file 2. Contains original data of figures and tables in the manuscript.
DOI: 10.6084/m9.figshare.8941022
title: Additional file 6 of Integrated identification of key genes and pathways in Alzheimerâ s disease via comprehensive bioinformatical analyses

description: Table S6. Information for biological process analysis of DEGs from entorhinal cortex. Included detailed information of results of biological process analysis of DEGs from entorhinal cortex. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8941022.v1
title: Additional file 6 of Integrated identification of key genes and pathways in Alzheimerâ s disease via comprehensive bioinformatical analyses

description: Table S6. Information for biological process analysis of DEGs from entorhinal cortex. Included detailed information of results of biological process analysis of DEGs from entorhinal cortex. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8941028
title: Additional file 7 of Integrated identification of key genes and pathways in Alzheimerâ s disease via comprehensive bioinformatical analyses

description: Table S7. Pathway enrichment analyses of DEGs. Included detailed information of pathway enrichment analyses of DEGs from hippocampus and entorhinal cortex. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8941028.v1
title: Additional file 7 of Integrated identification of key genes and pathways in Alzheimerâ s disease via comprehensive bioinformatical analyses

description: Table S7. Pathway enrichment analyses of DEGs. Included detailed information of pathway enrichment analyses of DEGs from hippocampus and entorhinal cortex. (XLSX 12 kb)
DOI: 10.24403/jp.1342497
title: Baumann, H. & Müller, T. : Farbatlas Geschützte und gefährdete Pflanzen. - Stuttgart : Verlag Eugen Ulmer, 2001 / [rezensiert von] H.-J. Zündorf
DOI: 10.5281/zenodo.10623280
title: Agroforestry species_Ethnobotanical_survey_database in Guinean-Congolese and Sudano-Guinean transition zones of Benin (West Africa)

description: Ethnobotanical survey data on the diversity, density and uses of agroforestry species in Guinean-Congolese and Sudano-Guinean transition zones of Benin (West Africa). The study identifies native agroforestry species with a high soil fertilisation potential, according to farmers.
DOI: 10.5281/zenodo.10623281
title: Agroforestry species_Ethnobotanical_survey_database in Guinean-Congolese and Sudano-Guinean transition zones of Benin (West Africa)

description: Ethnobotanical survey data on the diversity, density and uses of agroforestry species in Guinean-Congolese and Sudano-Guinean transition zones of Benin (West Africa). The study identifies native agroforestry species with a high soil fertilisation potential, according to farmers.
DOI: 10.5281/zenodo.10620888
title: What about the "Soft Factors"? Longitudinal Effects of Leadership Behaviors on Psychological Resources of Firefighters: Online Supplement

description: This is the online supplement for a study on leadership in fire services and its impact on the psychological resources of subordinates.

Abstract: In addition to adequate training and material equipment, firefighters need robust psychological resources (e.g., resilience, self-efficacy, team spirit) to fulfill their duties and remain healthy. However, recurrent exposure to disruptive events poses a threat to these resources. This study examines how leaders in fire services can support their subordinates in maintaining high levels of psychological resources. We hypothesize that person-oriented leadership is particularly effective in this respect. Specifically, we predict that person-oriented leader behaviors increase subordinates’ psychological resources and magnify the benefits of their performance behaviors in terms of resource acquisition. In a preregistered longitudinal study (five monthly measurements) with firefighters in Germany (N = 189), we tested our hypotheses using random intercept cross-lagged panel modeling. In line with our expectations, perceived person-oriented leader behaviors predicted subordinates’ resources on a month-to-month basis, and also in an additional follow-up survey one year later. However, person-oriented leadership effects on subordinates' performance behavior did not result in higher resources among subordinates. Notably, perceived task-oriented leader behaviors also predicted subordinates’ resources, but only on a month-to-month basis. Together, our findings show that person-oriented leadership can counterweight resource-draining working conditions in the fire services. We discuss possible mechanisms and time frames of the observed effects. 

The study was approved by the ethics committee of the [institution anonymized for review] and pre-registered with aspredicted.org (see https://aspredicted.org/blind.php?x=bw6cz7).

This online supplement includes



a codebook describing all instructions and items

raw data (anonymised) and analysis scripts (Note: The raw data contains only the information of persons who have agreed to the use of their data.)

a file with supplemental analyses

the theoretical rational and analyses of two pre-registered hypotheses not included in the manuscript
DOI: 10.5281/zenodo.10203421
title: Replisome dynamics in Caulobacter crescentus

description: Imaging data, MicrobeJ template & results, post-processing code and results, and spreadsheets containing manual records and annotations
DOI: 10.5281/zenodo.8160749
title: Replisome dynamics in Caulobacter crescentus

description: Imaging data, MicrobeJ template & results, post-processing code and results, and spreadsheets containing manual records and annotations
DOI: 10.5281/zenodo.8160750
title: Replisome dynamics in Caulobacter crescentus

description: Imaging data, MicrobeJ template & results, post-processing code and results, and spreadsheets containing manual records and annotations
DOI: 10.17882/98744
title: Scoring sheets for fisheries species sensitivity to climate change in Mozambique - ReMoTurb project

description: These files are the scoring sheets used for assessing the sensitivity of 40 important Mozambican fisheries species to climate change, including a list of references used in support. The scores were assigned during workshop sessions with the contributors at Ponta d'Oro in May 2022.
DOI: 10.5281/zenodo.10622926
title: CMAQ_dataset_2018_Dec
DOI: 10.5281/zenodo.10622927
title: CMAQ_dataset_2018_Dec
DOI: 10.5281/zenodo.10622976
title: CMAQ_dataset_2018_Dec
DOI: 10.5281/zenodo.4305576
title: Research data of ISR and GNSS observation

description: This is data used for a submitted article to an AGU journal  ( ISR and GNSS data).
DOI: 10.5281/zenodo.4305577
title: Research data of ISR and GNSS observation

description: This is data used for a submitted article to an AGU journal  ( ISR and GNSS data).
DOI: 10.6084/m9.figshare.14183946
title: Additional file 10 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 10: Table S9. List of differential RNA editing sites upon miRNA perturbation.
DOI: 10.5281/zenodo.10378447
title: Stable isotope data of a community of mid‑trophic level epipelagic species in the North Atlantic

description: A total of 495 individuals from a guild of 14 species (fishes, squids and crustaceans) were sampled along the west and south Iberia (Portuguese coast) aboard a research vessel during 2014, 2016 and 2017. Two seasonal oceanographic surveys were conducted each year to sample pelagic mid-trophic level species during spring and autumn. Specimens were captured with trawl hauls, and information on date, time, position of capture (latitude and longitude) and depth (m) were recorded. The body mass (g) and total length (in fishes; mm), mantle length (in squids; mm) or carapace width (in crustaceans; mm) were recorded for each individual. Stable isotopes of carbon (δ13C) and nitrogen (δ15N) were analysed in the muscle of each individual. Lipids were removed from samples by successive rinses in a 2:1 chloroform–methanol solution. More details of the methodology can be found in:

Ceia FR, Cherel Y, Silva AV, Garrido S, Angélico MM, da Silva JM, Laranjeiro MI, Ramos JA (2023) Drivers of niche partitioning in a community of mid-trophic level epipelagic species in the North Atlantic. Hydrobiologia, 850: 1583–1599. (DOI:10.1007/s10750-023-05160-3).
DOI: 10.21427/yqh2-1362
title: Survey on Outdoor Navigation Applications for People with Visual Impairment
DOI: 10.25318/3310073701-fra
title: Taux d’augmentation prévu des salaires et les raisons de l’anticipation d’un taux supérieur d’augmentation des salaires au cours des 12 prochains mois, quatrième trimestre de 2023

description: Taux d’augmentation prévu des salaires et les raisons de l’anticipation d’un taux supérieur d’augmentation des salaires au cours des 12 prochains mois, selon le Système de classification des industries de l’Amérique du Nord (SCIAN), l’effectif de l’entreprise, le type d’entreprise, l’activité de l'entreprise et le propriétaire majoritaire, quatrième trimestre de 2023.
DOI: 10.6084/m9.figshare.24807885
title: Data for Transcranial temporal interference stimulation over superior colliculus can regulate eye movements

description: ​We apply tTIS to the superior colliculus (SC), a deep brain region associated with eye saccades, to examine the evoked neural responses and the causal effects on saccadic behavior in mice.<br>We first constructed a tissue model to search for the tTIS electrode setup capable of stimulating deep brain regions. We then perform animal experiments with simultaneous recording of calcium-ion neural signals in the SC and saccadic eye behavior during tTIS administration.<br>
DOI: 10.6084/m9.figshare.24807885.v1
title: Data for Transcranial temporal interference stimulation over superior colliculus can regulate eye movements

description: ​We apply tTIS to the superior colliculus (SC), a deep brain region associated with eye saccades, to examine the evoked neural responses and the causal effects on saccadic behavior in mice.<br>We first constructed a tissue model to search for the tTIS electrode setup capable of stimulating deep brain regions. We then perform animal experiments with simultaneous recording of calcium-ion neural signals in the SC and saccadic eye behavior during tTIS administration.<br>
DOI: 10.5281/zenodo.5158955
title: NSCR_Dataset_2020

description: The University of Turin (UniTO) released the open-access dataset NSCR_Dataset collected for the  NEUROSTEMCELLREPAIR (602278) and NSC-Reconstruct (874758) European stem cell consortia for neural cell replacement, reprogramming and functional brain repair (602278)  (https://www.nsc-reconstruct.com/en/index.do).


NSCR-Dataset is a dataset of analysis of histological ex-vivo brain samples and behavioral parameters from Huntington's Disease (HD) rat models, after cell replacement approach of striatal progenitor cells at the site of grafting - the striatum, at different time point (see for details at short time-points: https://www.sciencedirect.com/science/article/pii/S2213671120301089?via%3Dihub). The UniTO team released this dataset publicly.


The dataset contains images of brain tissue stained for different cellular and molecular markers, acquired with transmission and confocal microscopes, from which analysis were performed, and the behavioral data obtained every month by testing the HD animals in different motor tasks.


High-resolution images have been acquired; the images will be made available.
DOI: 10.5281/zenodo.5158956
title: NSCR_Dataset_2020

description: The University of Turin (UniTO) released the open-access dataset NSCR_Dataset collected for the  NEUROSTEMCELLREPAIR (602278) and NSC-Reconstruct (874758) European stem cell consortia for neural cell replacement, reprogramming and functional brain repair (602278)  (https://www.nsc-reconstruct.com/en/index.do).


NSCR-Dataset is a dataset of analysis of histological ex-vivo brain samples and behavioral parameters from Huntington's Disease (HD) rat models, after cell replacement approach of striatal progenitor cells at the site of grafting - the striatum, at different time point (see for details at short time-points: https://www.sciencedirect.com/science/article/pii/S2213671120301089?via%3Dihub). The UniTO team released this dataset publicly.


The dataset contains images of brain tissue stained for different cellular and molecular markers, acquired with transmission and confocal microscopes, from which analysis were performed, and the behavioral data obtained every month by testing the HD animals in different motor tasks.


High-resolution images have been acquired; the images will be made available.
DOI: 10.5281/zenodo.8355003
title: Planetary perturbers: Flaring star-planet interactions in Kepler and TESS

description: This data set contains almost 13,000 de-trended Kepler and TESS light curves used in the publication with the same title (Ilin et al., in review). Each light curve is a fits file with the Kepler or TESS identifier, Quarter or Sector, and, if there are multiuple light curves per Quarter/Sector, the number of the light curve. The light curves can be read with any fits file handler (e.g., astropy), or with the lightkurve package. Each light curve contains arrays for the flux, detrended flux, time, and orbital phase of the innermost planet. Note that for transiting planets the orbital phase is set to zero around transit midtime, while for non-transiting planets, the phase zero is set arbitrarily. There is no particular reason for splitting the data in the zip files except for easier upload.
description: The data set will be updated with the link to the paper once it is accepted and published.
DOI: 10.34740/kaggle/dsv/7201924
title: EEG Pornography Addiction
DOI: 10.6084/m9.figshare.24709412
title: README.md from Pre-fertilization gamete thermal environment influences reproductive success, unmasking opposing sex-specific responses in Atlantic Salmon (<i>Salmo salar</i>)

description: File containing all the necessary info ton how to access the datasets and run the R scripts
DOI: 10.6084/m9.figshare.24709412.v1
title: README.md from Pre-fertilization gamete thermal environment influences reproductive success, unmasking opposing sex-specific responses in Atlantic Salmon (<i>Salmo salar</i>)

description: File containing all the necessary info ton how to access the datasets and run the R scripts
DOI: 10.5281/zenodo.7986277
title: Datasets for "Can the audience understand a business process model? Using Random Forest to classify level understandability based on personal and model factors"

description: This dataset contains evaluations of understandability incorporating audience characteristics and model characteristics.
The dataset has been collected in two conducted experiments. Audience' data was collected using students computing science and business and management students.


The main_dataset.csv file contains the dataset to build the predictive model.


The final_validation_dataset.csv file contains the dataset to evaluate the performance of the predictive model.