cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6254520
title: Dataset related to article "Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism"

description: This record contains raw data related to article “Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism" X-linked acrogigantism (X-LAG) is the most severe form of pituitary gigantism and is characterized by aggressive growth hormone (GH)- secreting pituitary tumors that occur in early childhood. X-LAG is associated with chromosome Xq26.3 duplications (the X-LAG locus typically includes VGLL1, CD40LG, ARHGEF6, RBMX, and GPR101) that lead to massive pituitary tumoral expression of GPR101, a novel regulator of GH secretion. The mechanism by which the duplications lead to marked pituitary misexpression of GPR101 alone was previously unclear. Using Hi-C and 4C-seq, we characterized the normal chromatin structure at the X-LAG locus.We showed that GPR101 is located within a topologically associating domain (TAD) delineated by a tissue-invariant border that separates it from centromeric genes and regulatory sequences. Next, using 4C-seq with GPR101, RBMX, and VGLL1 viewpoints, we showed that the duplications in multiple X-LAG-affected individuals led to ectopic interactions that crossed the invariant TAD border, indicating the existence of a similar and consistent mechanism of neo-TAD formation in X-LAG.We then identified several pituitary active cis-regulatory elements (CREs) within the neo-TAD and demonstrated in vitro that one of them significantly enhanced reporter gene expression. At the same time, we showed that the GPR101 promoter permits the incorporation of new regulatory information. Our results indicate that X-LAG is a TADopathy of the endocrine system in which Xq26.3 duplications disrupt the local chromatin architecture forming a neo-TAD. Rewiring GPR101- enhancer interaction within the new regulatory unit is likely to cause the high levels of aberrant expression of GPR101 in pituitary tumors caused by X-LAG.
DOI: 10.5281/zenodo.5970465
title: Dataset related to article "Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism"

description: This record contains raw data related to article “Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism" X-linked acrogigantism (X-LAG) is the most severe form of pituitary gigantism and is characterized by aggressive growth hormone (GH)- secreting pituitary tumors that occur in early childhood. X-LAG is associated with chromosome Xq26.3 duplications (the X-LAG locus typically includes VGLL1, CD40LG, ARHGEF6, RBMX, and GPR101) that lead to massive pituitary tumoral expression of GPR101, a novel regulator of GH secretion. The mechanism by which the duplications lead to marked pituitary misexpression of GPR101 alone was previously unclear. Using Hi-C and 4C-seq, we characterized the normal chromatin structure at the X-LAG locus.We showed that GPR101 is located within a topologically associating domain (TAD) delineated by a tissue-invariant border that separates it from centromeric genes and regulatory sequences. Next, using 4C-seq with GPR101, RBMX, and VGLL1 viewpoints, we showed that the duplications in multiple X-LAG-affected individuals led to ectopic interactions that crossed the invariant TAD border, indicating the existence of a similar and consistent mechanism of neo-TAD formation in X-LAG.We then identified several pituitary active cis-regulatory elements (CREs) within the neo-TAD and demonstrated in vitro that one of them significantly enhanced reporter gene expression. At the same time, we showed that the GPR101 promoter permits the incorporation of new regulatory information. Our results indicate that X-LAG is a TADopathy of the endocrine system in which Xq26.3 duplications disrupt the local chromatin architecture forming a neo-TAD. Rewiring GPR101- enhancer interaction within the new regulatory unit is likely to cause the high levels of aberrant expression of GPR101 in pituitary tumors caused by X-LAG.
DOI: 10.6084/m9.figshare.13392821
title: HTVC023P-type.mafft

description: concatenated alignment of 5 conserved core proteins from the HTVC023P-type Pelagiphages. Corresponding tree available ("HTVC023P-type.newick)
DOI: 10.6084/m9.figshare.13393145
title: Podoviridae_Autographiviridae.mafft

description: sequence alignment alignment of DNA polymerase sequences of representative Podoviridae and Autographiviridae sequences including Pelagiphage sequences and closely related environmental sequences.
DOI: 10.6084/m9.figshare.13393145.v1
title: Podoviridae_Autographiviridae.mafft

description: sequence alignment alignment of DNA polymerase sequences of representative Podoviridae and Autographiviridae sequences including Pelagiphage sequences and closely related environmental sequences.
DOI: 10.6084/m9.figshare.13393298
title: GOV2_curli_frequencies.csv

description: Frequencies (normalized by proteins per stations) of curli operon components CsgG, CsgF, CsgAB, FecR in GOV2.0 (Gregory et al. 2019).
DOI: 10.6084/m9.figshare.13393160
title: Podoviridae_Autographiviridae.newick

description: phylogenetic reconnstruction of DNA polymerase sequences of representative Podoviridae and Autographiviridae sequences including Pelagiphage sequences and closely related environmental sequences.
DOI: 10.6084/m9.figshare.13392710
title: HTVC023P-type.newick

description: viral phylogeny of HTVC023P-type isolates and circular environmental genomes based on 5 conserved proteins. Rooted using Pseudomonas phage PaMx11 and Alphaproteobacteria phage PhiJL001.2 models were used to calculate this tree, both resulting in the same topology with slightly different UFbootstrap support. The alignment corresponding to this tree is called HTVC023P-type.mafft and contains the concatenated trimmed alignment of all 5 proteins
DOI: 10.6084/m9.figshare.13392710.v1
title: HTVC023P-type.newick

description: viral phylogeny of HTVC023P-type isolates and circular environmental genomes based on 5 conserved proteins. Rooted using Pseudomonas phage PaMx11 and Alphaproteobacteria phage PhiJL001.2 models were used to calculate this tree, both resulting in the same topology with slightly different UFbootstrap support. The alignment corresponding to this tree is called HTVC023P-type.mafft and contains the concatenated trimmed alignment of all 5 proteins
DOI: 10.6084/m9.figshare.13393160.v1
title: Podoviridae_Autographiviridae.newick

description: phylogenetic reconnstruction of DNA polymerase sequences of representative Podoviridae and Autographiviridae sequences including Pelagiphage sequences and closely related environmental sequences.
DOI: 10.6084/m9.figshare.13392581
title: AC.mafft

description: viral and cellular adenylate cyclase sequence alignment used for the phylogenetic reconstruction of viral AC evolutionary history.
DOI: 10.6084/m9.figshare.13392590
title: AC.newick

description: phylogenetic reconstruction of viral and cellular adenylate cyclase sequences. corresponding alignment is available (AC.mafft)
DOI: 10.6084/m9.figshare.13392590.v1
title: AC.newick

description: phylogenetic reconstruction of viral and cellular adenylate cyclase sequences. corresponding alignment is available (AC.mafft)
DOI: 10.6084/m9.figshare.13392482
title: CsgF.mafft

description: alignment of viral and cellular CsgF sequences used for phylogenetic reconstruction of the origin of the viral AMG CsgF which is part of the curli operon in some marine phages
DOI: 10.6084/m9.figshare.13392482.v1
title: CsgF.mafft

description: alignment of viral and cellular CsgF sequences used for phylogenetic reconstruction of the origin of the viral AMG CsgF which is part of the curli operon in some marine phages
DOI: 10.6084/m9.figshare.13392581.v1
title: AC.mafft

description: viral and cellular adenylate cyclase sequence alignment used for the phylogenetic reconstruction of viral AC evolutionary history.
DOI: 10.6084/m9.figshare.13392422
title: CsgF.newick

description: newick formatted phylogenetic tree of viral and cellular CsgF sequences corresponding to the alignment file "CsgF.mafft"
DOI: 10.6084/m9.figshare.13392422.v1
title: CsgF.newick

description: newick formatted phylogenetic tree of viral and cellular CsgF sequences corresponding to the alignment file "CsgF.mafft"
DOI: 10.6084/m9.figshare.13393298.v1
title: GOV2_curli_frequencies.csv

description: Frequencies (normalized by proteins per stations) of curli operon components CsgG, CsgF, CsgAB, FecR in GOV2.0 (Gregory et al. 2019).
DOI: 10.6084/m9.figshare.13392362
title: FecR.mafft

description: alignment of viral FecR sequences and closely related cellular homologs.
DOI: 10.6084/m9.figshare.13392392
title: FecR.newick

description: newick formatted treefile corresponding to the alignment "FecR.mafft"
DOI: 10.6084/m9.figshare.13392392.v1
title: FecR.newick

description: newick formatted treefile corresponding to the alignment "FecR.mafft"
DOI: 10.6084/m9.figshare.13392821.v1
title: HTVC023P-type.mafft

description: concatenated alignment of 5 conserved core proteins from the HTVC023P-type Pelagiphages. Corresponding tree available ("HTVC023P-type.newick)
DOI: 10.6084/m9.figshare.13392362.v1
title: FecR.mafft

description: alignment of viral FecR sequences and closely related cellular homologs.
DOI: 10.6084/m9.figshare.13389176.v1
title: env_and_ssg_HTVC023P-type_genomes.fna

description: contains 12 genomic sequences encoding genomes from the HTVC023P-type Pelagiphages. 11 from environmental datasets (GOV2) and 1 from a single cell genome from Pachiadaki et al. 2019
DOI: 10.6084/m9.figshare.13389443
title: CsgG.mafft

description: sequence alignment of curli operon component CsgG including viral and cellular homologs
DOI: 10.6084/m9.figshare.13389176
title: env_and_ssg_HTVC023P-type_genomes.fna

description: contains 12 genomic sequences encoding genomes from the HTVC023P-type Pelagiphages. 11 from environmental datasets (GOV2) and 1 from a single cell genome from Pachiadaki et al. 2019
DOI: 10.6084/m9.figshare.13389443.v1
title: CsgG.mafft

description: sequence alignment of curli operon component CsgG including viral and cellular homologs
DOI: 10.6084/m9.figshare.13389509.v1
title: CsgG.newick

description: treefile corresponding to the alignment presented in CsgG.mafft
DOI: 10.6084/m9.figshare.13389509
title: CsgG.newick

description: treefile corresponding to the alignment presented in CsgG.mafft
DOI: 10.5281/zenodo.6908605
title: First-principles investigation of phase stability in substoichiometric zirconium carbide under high pressure

description: This is a data set that supports a first-principles investigation into the phase stability of zirconium carbide under high pressure. High throughput density function theory data is used to train a cluster expansion. The trained model is used to sample the phase space of the substoichiometric ZrC system into high pressures. This sampling sheds insight on how pressure affects the stability and partial vacancy ordering in the ZrC system.
description: {"references": ["Larsen, A. H.; Mortensen, J. J.; Blomqvist, J.; Castelli, I. E.; Christensen, R.; Du\u0142ak, M.; Friis, J.; Groves, M. N.; Hammer, B.; Hargus, C.; Hermes, E. D.; Jennings, P. C.; Jensen, P. B.; Kermode, J.; Kitchin, J. R.; Kolsbjerg, E. L.; Kubal, J.; Kaasb- jerg, K.; Lysgaard, S.; Maronsson, J. B.; Maxson, T.; Olsen, T.; Pastewka, L.; Peterson, A.; Rostgaard, C.; Schi\u00f8tz, J.; Sch \u0308utt, O.; Strange, M.; Thygesen, K. S.; Vegge, T.; Vilhelmsen, L.; Walter, M.; Zeng, Z.; Ja- cobsen, K. W. \"The atomic simulation environment \u2013 a Python library for working with atoms.\" J. Phys.: Condens. Matter 2017, 29, 273002.", "Angqvist, M.; Mu \u0303noz, W. A.; Rahm, J. M.; Fransson, E.; Durniak, C.; Rozyczko, P.; Rod, T. H.; Erhart, P. \"ICET \u2013 A Python Library for Constructing and Sam- pling Alloy Cluster Expansions.\" Adv. Theory Simul. 2019, 2, 1900015.", "Clark, S. J.; Segall, M. D.; Pickard, C. J.; Hasnip, P. J.; Probert, M. I. J.; Refson, K.; Payne, M. C. \"First principles methods using CASTEP.\" Z. Kristallogr. - Cryst. Mater. 2005, 220, 567\u2013570."]}
DOI: 10.5281/zenodo.6908604
title: First-principles investigation of phase stability in substoichiometric zirconium carbide under high pressure

description: This is a data set that supports a first-principles investigation into the phase stability of zirconium carbide under high pressure. High throughput density function theory data is used to train a cluster expansion. The trained model is used to sample the phase space of the substoichiometric ZrC system into high pressures. This sampling sheds insight on how pressure affects the stability and partial vacancy ordering in the ZrC system.
description: {"references": ["Larsen, A. H.; Mortensen, J. J.; Blomqvist, J.; Castelli, I. E.; Christensen, R.; Du\u0142ak, M.; Friis, J.; Groves, M. N.; Hammer, B.; Hargus, C.; Hermes, E. D.; Jennings, P. C.; Jensen, P. B.; Kermode, J.; Kitchin, J. R.; Kolsbjerg, E. L.; Kubal, J.; Kaasb- jerg, K.; Lysgaard, S.; Maronsson, J. B.; Maxson, T.; Olsen, T.; Pastewka, L.; Peterson, A.; Rostgaard, C.; Schi\u00f8tz, J.; Sch \u0308utt, O.; Strange, M.; Thygesen, K. S.; Vegge, T.; Vilhelmsen, L.; Walter, M.; Zeng, Z.; Ja- cobsen, K. W. \"The atomic simulation environment \u2013 a Python library for working with atoms.\" J. Phys.: Condens. Matter 2017, 29, 273002.", "Angqvist, M.; Mu \u0303noz, W. A.; Rahm, J. M.; Fransson, E.; Durniak, C.; Rozyczko, P.; Rod, T. H.; Erhart, P. \"ICET \u2013 A Python Library for Constructing and Sam- pling Alloy Cluster Expansions.\" Adv. Theory Simul. 2019, 2, 1900015.", "Clark, S. J.; Segall, M. D.; Pickard, C. J.; Hasnip, P. J.; Probert, M. I. J.; Refson, K.; Payne, M. C. \"First principles methods using CASTEP.\" Z. Kristallogr. - Cryst. Mater. 2005, 220, 567\u2013570."]}
DOI: 10.6084/m9.figshare.18785699
title: Datasets of productivity and vegetation composition of boreal stands from an experiment comparing silviculture scenarios of increasing intensity after 20 years

description: Vegetation surveys were conducted in July 2009 in humid boreal stands from an experimental design comparing silviculture scenarios of increasing intensity: (i) careful logging around advance growth (CLAAG); (ii) CLAAG followed by pre-commercial thinning; (iii) plantation followed by mechanical release of crop trees using motor-manual brushsaws; and (iv) plantation followed by chemical release of crop trees using herbicide and within five naturally disturbed sites. The surveys comprise data about the density of snags and of living trees (defined as having a diameter at breast height (1.3 m), DBH ≥ 1.1 cm), dendrometric measurements (DBH, height and basal area) of conifer and deciduous species, percent cover of trees and high regeneration (defined as having a height ≥ 60 cm and a DBH &lt; 1cm), shrub (defined as having a height &lt; 60 cm), herbaceous species and various taxonomic groups (ferns, mosses, sphagnum, lichens, grasses and <em>Lycopodium L.</em>). Data of the ratio of intercepted light to full sunlight conditions averaged by plot, derived from Photosynthetic photon flux density (PPFD) readings, are also provided. <br> This dataset covers clean and analysed data. The metadata are provided in the Metadata.txt file. <br> More details in: Urli M., Thiffault N. and Chalifour D. (2022) Datasets of tree and stand productivity and vegetation composition of boreal stands from an experiment comparing silviculture scenarios of increasing intensity after 20 years. Data In Brief. 108387<br>
DOI: 10.6084/m9.figshare.18785699.v3
title: Datasets of productivity and vegetation composition of boreal stands from an experiment comparing silviculture scenarios of increasing intensity after 20 years

description: Vegetation surveys were conducted in July 2009 in humid boreal stands from an experimental design comparing silviculture scenarios of increasing intensity: (i) careful logging around advance growth (CLAAG); (ii) CLAAG followed by pre-commercial thinning; (iii) plantation followed by mechanical release of crop trees using motor-manual brushsaws; and (iv) plantation followed by chemical release of crop trees using herbicide and within five naturally disturbed sites. The surveys comprise data about the density of snags and of living trees (defined as having a diameter at breast height (1.3 m), DBH ≥ 1.1 cm), dendrometric measurements (DBH, height and basal area) of conifer and deciduous species, percent cover of trees and high regeneration (defined as having a height ≥ 60 cm and a DBH &lt; 1cm), shrub (defined as having a height &lt; 60 cm), herbaceous species and various taxonomic groups (ferns, mosses, sphagnum, lichens, grasses and <i>Lycopodium L.</i>). Data of the ratio of intercepted light to full sunlight conditions averaged by plot, derived from Photosynthetic photon flux density (PPFD) readings, are also provided.<br>This dataset covers clean and analysed data. The metadata are provided in the Metadata.txt file.<br>More details in:Urli M., Thiffault N. and Chalifour D. (submitted) Datasets of tree and stand productivity and vegetation composition of boreal stands from an experiment comparing silviculture scenarios of increasing intensity after 20 years. Data In Brief<br>
DOI: 10.5281/zenodo.6568306
title: Community Established Best Practice Recommendations for Tephra Studies-from Collection through Analysis

description: Tephra is a unique volcanic product with an unparalleled role in understanding past eruptions, long-term behavior of volcanoes, and the effects of volcanism on climate and the environment. Tephra deposits also provide spatially widespread, extremely high-resolution time-stratigraphic markers across a range of sedimentary settings and are used in a range of disciplines (e.g., volcanology, climate science, archaeology, ecology, and impact assessment). Nonetheless, the study of tephra deposits is challenged by a lack of standardization that often inhibits data integration across geographic regions and across disciplines. Here we present comprehensive recommendations for tephra data gathering and reporting that were developed by the tephra science community to serve as guidelines for future investigators and to ensure that sufficient data are gathered for transparency and interoperability. Recommendations include standardized field and laboratory data collection along with reporting and correlation guidance. These are organized as tabulated lists of key metadata with their definition and purpose. They are system independent and usable for template, tool, and database development. This new standardized framework promotes consistent tephra documentation and archiving, fosters interdisciplinary communication, and improves effectiveness of data sharing among diverse communities of researchers. Wider adoption will help to expand the applicability and usability of tephra data and facilitate scientific collaboration and data reuse. For additional details, see the accompanying manuscript: Wallace, K.*, Bursik, M. Kuehn, S., Kurbatov, A., Abbott, P., Bonadonna, C., Cashman, K., Davies, S., Jensen, B., Lane, C., Plunkett, G., Smith, V. Tomlinson, E., Thordarsson, T., and Walker, D. Community established best practice recommendations for tephra studies—from collection through analysis. <em>Sci Data</em> <strong>9, </strong>447 (2022). https://doi.org/10.1038/s41597-022-01515-y *corresponding author: Kristi Wallace, kwallace@usgs.gov Open access article is available online here https://doi.org/10.1038/s41597-022-01515-y or as a PDF here https://www.nature.com/articles/s41597-022-01515-y.pdf.
description: Tephra data templates developed from the tephra best-practice recommendations and intended for sample registration and data upload to SESAR and EarthChem can be download from the EarthChem tephra portal (https://earthchem.org/communities/tephra/) and submitted for upload or used independently as data entry templates for personal use. Tephra data templates include: (a) sample information, (b) analytical method descriptions, and (c) geochemical data.
DOI: 10.17632/2fhw7c28f4.1
title: Observed hydrologic anomalies associated with the tectonic blocks before three consecutive earthquakes in Qinghai, China

description: Here we share our research data including earthquake data and hydrologic data.
DOI: 10.17632/kxy4fz57mp.1
title: Repository data Cusiana River Subasin

description: Dataset about te research paper: The effects of climate and forest cover variability on the hydrological regulation of an eastern Andean River basin
DOI: 10.17632/ds243x9mbs.1
title: Sustainable roadway construction data from Greenroads certified projects

description: Data was collected as part of the roadway construction certification offered by Greenroads International according to Greenroads Rating System v1.5. This dataset is the result of data collection efforts for 33 construction projects across the US and abroad. Data was initially collected by Greenroads International as part of its certification process and was later obtained by this dataset's contributors. Projects in pursuit of certification submit supporting documents as evidence for performing a roadway construction practice. For example, tracking the amount of water used in construction to earn points and satisfy a credit in Greenroads. We hypothesize this dataset is unique in that it contains information and statistics on roadway construction projects that are declared sustainable with numeric outcomes to act as performance benchmarks for future projects to follow.

Construction documents were first used to collect data on 12 sustainable performance benchmarks explained in the dataset (see Performance Benchmarks and Project Properties and Landscape Plans files). Sustainable performance benchmarks are established using median values of quantitatively measurable project outcomes. These benchmarks are defined in such a way that any roadway construction project regardless of size or scope may use them as sustainability achievement goals. In that, these performance benchmarks are somehow normalized to an aspect of the project’s size such as its monetary value, length, or area. Except for the source documents used to produce sustainable performance benchmarks, the dataset contains numeric values obtained from digesting several digitally formatted documents or spreadsheets submitted by project teams.

The other major construction document included in this dataset is the pay item list from 30 projects (three projects did not provide this data). Pay item lists contain all the items used in the bidding process of a project and include a short description of each item, a unit of measure, the unit price, and the total price (see Pay Item Lists for LCA and Construction Materials LCA files). Several other construction documents were used to reinforce projects’ pay item lists with enough information for environmental impact assessment. As a result, many other data attributes were added to the pay item list data for each project. These include but are not limited to material’s unit weights, breakdown of material constituents (e.g., how much cement is in a concrete item), transportation distances, etc. Finally, life cycle inventory (LCI) data for the primary construction materials (see Materials LCI file) were collected from publicly available sources and were embedded into the pay item list data for life cycle assessment of materials used to build roadways. We analyzed the resultant dataset to estimate the greenhouse gas emissions and energy consumption of projects.

When necessary, each dataset contains a metadata worksheet that explains data attributes.
DOI: 10.17632/52p7kh5vzc.1
title: A study of A sphingolipid-mTORC1 nutrient-sensing pathway regulates animal development by an intestinal peroxisome relocation dependent gut-brain crosstalk. Li et al.

description: Here is the raw data for all the statistical graphs and microscope pictures for "A study of A sphingolipid-mTORC1 nutrient-sensing pathway regulates animal development by an intestinal peroxisome relocation dependent gut-brain crosstalk".