cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12292910.v1
title: Identification of long non-coding RNAs in the early growth stage of Holstein mammary gland

description: In Holsteins, emerging evidence suggests that long non-coding RNAs (lncRNAs) are actively involved in the regulation of mammary gland development. However, the lncRNA expression pattern in the early growth stage of Holstein mammary gland remains little known. In this study, we comprehensively analyzed 11 mammary gland tissue RNA-Seq datasets derived from Holstein heifer calves (ca. 8 weeks old) retrieved from the Sequence Read Archive database. We identified a total of 588 lncRNAs in the intergenic region. By comparing the sequences with NONCODEv5 database, 241 novel lncRNAs were detected in the mammary gland. Prediction of <i>cis</i>-regulated target gene revealed that 364 out of 588 lncRNAs potentially targeted 417 protein-coding genes. Furthermore, Gene Ontology enrichment determined that potential target genes were mainly involved in the terms associated with energy metabolism and cell differentiation, such as cellular respiration, respiratory electron transport chain, electron transport chain, and regulation of cell differentiation, which were closely related to mammary gland development. This study provides potential candidate lncRNAs in regulating mammary gland development in the early growth stage of Holsteins, as well as a better general understanding of Holstein mammary gland development.
DOI: 10.6084/m9.figshare.13251563.v1
title: Comparative morphology of labial cartilages in sharks (Chondrichthyes, Elasmobranchii)

description: During the last years, feeding mechanisms of sharks have been documented mainly based on their stomach contents supplemented by video footages of feeding behaviours in some species. Rare kinematic analyses of shark jaws contributed additionally to our knowledge. However, not all structures important to prey capture in sharks have been investigated yet. Here, we summarize the current knowledge about labial cartilages in sharks and compare them on a morphological base. Labial cartilages are considered a plesiomorph character found in extinct and extant species and their number and size varies a lot between species. We identified labial cartilages in representatives of 27 from 36 shark families and detected different numbers, sizes and forms of labial cartilages, as well as differing positioning along the jaws. The morphology of labial cartilages can help to identify suction-feeding in sharks and to estimate the quality of the suction generated by a species. We were able to summon different shark taxa according to their morphology and positioning of labial cartilages into eight groups, which we consider morphological modules. To determine if these modules bare a phylogenetic signal further testing with rigorous methodologies and more shark species as well as batomorphs needs to be done. This study therefore only can represent a first starting point providing future research pathways.
DOI: 10.6084/m9.figshare.12292910
title: Identification of long non-coding RNAs in the early growth stage of Holstein mammary gland

description: In Holsteins, emerging evidence suggests that long non-coding RNAs (lncRNAs) are actively involved in the regulation of mammary gland development. However, the lncRNA expression pattern in the early growth stage of Holstein mammary gland remains little known. In this study, we comprehensively analyzed 11 mammary gland tissue RNA-Seq datasets derived from Holstein heifer calves (ca. 8 weeks old) retrieved from the Sequence Read Archive database. We identified a total of 588 lncRNAs in the intergenic region. By comparing the sequences with NONCODEv5 database, 241 novel lncRNAs were detected in the mammary gland. Prediction of <i>cis</i>-regulated target gene revealed that 364 out of 588 lncRNAs potentially targeted 417 protein-coding genes. Furthermore, Gene Ontology enrichment determined that potential target genes were mainly involved in the terms associated with energy metabolism and cell differentiation, such as cellular respiration, respiratory electron transport chain, electron transport chain, and regulation of cell differentiation, which were closely related to mammary gland development. This study provides potential candidate lncRNAs in regulating mammary gland development in the early growth stage of Holsteins, as well as a better general understanding of Holstein mammary gland development.
DOI: 10.6084/m9.figshare.12258224
title: Biogeography and ecology of geographically distant populations of sibling <i>Cryptocephalus</i> leaf beetles

description: Different populations of two closely related species, <i>Cryptocephalusflavipes</i> and <i>C. bameuli</i>, from western (Alps, Apennines and Pyrenees) and central Europe (Poland, Ukraine and Pannonia) were analysed. On the basis of DNA sequences from two genes, <i>cox1</i> and <i>ef1-α</i>, distinctiveness of both species was confirmed. Nevertheless, possible hybrids were identified in Carpathian mountains. We found a significant genetic differentiation among populations of <i>C. flavipes</i> and <i>C. bameuli</i> from distant regions but a high genetic similarity between populations of <i>C. bameuli</i> from north and south of the Carpathians. Demographic estimates suggest a past population expansion in the case of <i>C. bameuli</i> and a recent one for <i>C. flavipes</i>, possibly occurred during Pleistocene and Holocene, respectively. Distribution modelling showed that <i>C. flavipes</i> is typically present in the mountain systems, whereas <i>C. bameuli</i> is associated with hilly areas of central and eastern Europe. Based on the present data, Last Glacial Maximum refugia of both species were located in the Alpine region and Black Sea coasts, but on different elevations. The characterization of the insect diet, through a DNA metabarcoding approach targeting the <i>trnL</i> plant intron, demonstrated a significant differentiation of food preferences between the two species, as well as between geographic populations within the species.
DOI: 10.6084/m9.figshare.12258224.v1
title: Biogeography and ecology of geographically distant populations of sibling <i>Cryptocephalus</i> leaf beetles

description: Different populations of two closely related species, <i>Cryptocephalusflavipes</i> and <i>C. bameuli</i>, from western (Alps, Apennines and Pyrenees) and central Europe (Poland, Ukraine and Pannonia) were analysed. On the basis of DNA sequences from two genes, <i>cox1</i> and <i>ef1-α</i>, distinctiveness of both species was confirmed. Nevertheless, possible hybrids were identified in Carpathian mountains. We found a significant genetic differentiation among populations of <i>C. flavipes</i> and <i>C. bameuli</i> from distant regions but a high genetic similarity between populations of <i>C. bameuli</i> from north and south of the Carpathians. Demographic estimates suggest a past population expansion in the case of <i>C. bameuli</i> and a recent one for <i>C. flavipes</i>, possibly occurred during Pleistocene and Holocene, respectively. Distribution modelling showed that <i>C. flavipes</i> is typically present in the mountain systems, whereas <i>C. bameuli</i> is associated with hilly areas of central and eastern Europe. Based on the present data, Last Glacial Maximum refugia of both species were located in the Alpine region and Black Sea coasts, but on different elevations. The characterization of the insect diet, through a DNA metabarcoding approach targeting the <i>trnL</i> plant intron, demonstrated a significant differentiation of food preferences between the two species, as well as between geographic populations within the species.
DOI: 10.6084/m9.figshare.14130623.v2
title: Dataset Genomic Association between SNP Markers and Diseases in the “Curraleiro Pé-Duro” Cattle

description: This dataset describes the genetic and statistics used to analyse SNPs linked to MHC genes in Curraleiro Pé-Duro cattle and his linkage with reproductive diseases in cattle.
DOI: 10.6084/m9.figshare.14130623
title: Dataset Genomic Association between SNP Markers and Diseases in the “Curraleiro Pé-Duro” Cattle

description: This dataset describes the genetic and statistics used to analyse SNPs linked to MHC genes in Curraleiro Pé-Duro cattle and his linkage with reproductive diseases in cattle.
DOI: 10.6084/m9.figshare.14130623.v1
title: Dataset Genomic Association between SNP Markers and Diseases in the “Curraleiro Pé-Duro” Cattle

description: This dataset describes the genetic and statistics used to analyse SNPs linked to MHC genes in Curraleiro Pé-Duro cattle and his linkage with reproductive diseases in cattle.
DOI: 10.25345/c5wj84
title: MassIVE MSV000087496 - Decoding location bias information of cAMP signaling in a class B GPCR
title: The parathyroid hormone (PTH) type 1 receptor (PTHR) is a class B G proteincoupled receptor (GPCR) that regulates mineral ion, vitamin D, and bone homeostasis. Activation of the PTHR by PTH induces both transient cell surface and sustained endosomal cAMP production, but determination as to whether the spatial (location) or temporal (duration) dimension of cAMP signaling encodes for biological outcomes has remained elusive. Here we show that epimerization of a single amino acid in PTH (PTH7d) results in a biased ligand permitting the demonstration that similar elevations and durations of cAMP generated by the same receptor in separate cell locations plasma membrane vs endosomes mediate distinct physiological responses. PTH7d stabilizes a unique active PTHR conformation that triggers spatial bias of sustained cAMP signaling from the plasma membrane due to impaired barrestin (barr) coupling to the receptor. We further demonstrate the physiological importance of subcellular signaling location by the PTHR, as studies in cells and mice reveal that sustained cAMP produced by cell surface PTHR fails to mimic effects by sustained endosomal cAMP on the cellular production of the rate limiting hydroxylase catalyzing the formation of active Vitamin D, as well as serum elevation of active Vitamin D and Ca2+ in mice. These results unveil subcellular signaling location as a means to achieve specificity in PTHR mediated biological outcomes and raise the prospect of rational drug design based upon spatiotemporal manipulation of GPCR signaling.
DOI: 10.5281/zenodo.4784614
title: Dissolution Kinetics and Diffusion Coefficients of Nitrogen Gas in Liquid Hydrocarbons under Titan Surface Conditions

description: This folder contains the raw laboratory data used in the publication, <em>Dissolution kinetics and diffusion coefficients of nitrogen gas in liquid hydrocarbons under Titan surface conditions </em>by K. K. Farnsworth et al.
DOI: 10.5281/zenodo.4784613
title: Dissolution Kinetics and Diffusion Coefficients of Nitrogen Gas in Liquid Hydrocarbons under Titan Surface Conditions

description: This folder contains the raw laboratory data used in the publication, <em>Dissolution kinetics and diffusion coefficients of nitrogen gas in liquid hydrocarbons under Titan surface conditions </em>by K. K. Farnsworth et al.
DOI: 10.6084/m9.figshare.14669634.v1
title: RNA-seq_bigwig

description: RNA-seq_bigwig
DOI: 10.6084/m9.figshare.14669634
title: RNA-seq_bigwig

description: RNA-seq_bigwig
DOI: 10.25345/c5rv5v
title: MassIVE MSV000087497 - Epigenetic regulation of nuclear lamina-associated heterochromatin domains by HAT1 and the acetylation of newly synthesized histones
title: When DNA is replicated in eukaryotic cells, critical regulatory information conveyed by chemical modifications to DNA bases, histone proteins, and by the 3D architecture of the genome must be faithfully transmitted from parental to daughter cells. During DNA replication, parental nucleosomes are disrupted and re-deposited on the nascent DNA near their original location to preserve the spatial memory of the epigenetic modifications. Newly synthesized histones must be also incorporated into the nascent chromatin to maintain nucleosome density. Transfer of modification patterns from parental histones to new histones is a fundamental step in epigenetic inheritance. New histones have been thought to play a passive role in this process. Here we report that HAT1, which acetylates lysines 5 and 12 of newly synthesized histone H4 during replication-coupled chromatin assembly, regulates the epigenetic inheritance of chromatin states. HAT1 regulates the accessibility of large domains of heterochromatin termed HAT1-dependent Accessibility Domains (HADs). HADs are mega base-scale domains that comprise ~10% of the mouse genome. HADs display a high degree of overlap with a subset of Lamin-Associated Domains (LADs). HAT1 is required to maintain nuclear structure and integrity and physically associates with the nuclear lamina. HAT1 functions as a global negative regulator of H3 K9me2/3 and HADs correspond to the regions of the genome that have the highest density of H3 K9me3 peaks. These results indicate that HAT1 and the acetylation of newly synthesized histones are critical regulators of the epigenetic inheritance of heterochromatin and suggest a new mechanism for the epigenetic regulation of nuclear lamina-heterochromatin interactions.
DOI: 10.5517/ccdc.csd.cc10kv5l
title: CCDC 940669: Experimental Crystal Structure Determination

description: Related Article: Anna Wadas, Adam Gorczynski, Iwona A. Rutkowska, Ewelina Seta, Ewelina Szaniawska, Maciej Kubicki, Adam Lewera, Maciej Gorzkowski, Aneta Januszewska, Rafal Jurczakowski, Barbara Palys, Violetta Patroniak, Pawel J. Kulesza|2021|Electrochimica Acta|388|138550|doi:10.1016/j.electacta.2021.138550
DOI: 10.17632/9dksyngjm6.1
title: Data for: Metamorphic evolution of Daqingshan supracrustal rocks and garnet-bearing granite from the North China Craton: constraints from phase equilibria modelling, geochemistry, and SHRIMP U-Pb geochronology

description: 3.1 Electron probe microanalysis of minerals The mineral compositions for the supracrustal rocks and the garnetbearing granite were analysed by using an electron microprobe at the Key Laboratory of Orogen and Crustal Evolution of the Ministry of Education, Peking University, Beijing, China, using operating conditions of 5 kv accelerating voltage, 1 × 10–8 A beam current, and 1 μm spot diameter. For calibration, 53 standard samples of well-defined natural minerals (SPI Supplies, West Chester, Pennsylvania, USA) were used. The results are presented in SupplementaryTables 1 to 5. 3.2 Whole-rock geochemistry The major-element compositions of the minerals were measured using an Axios X-ray fluorescence (XRF) spectrometer at the China National Research Center for Geoanalysis, Beijing, China. Trace-element analysis was conducted using an Elan 9000 inductively coupled plasma mass spectrometer (ICP–MS; PerkinElmer, Waltham, Massachusetts, USA) with better than 10% accuracy of analysis. The major and trace element compositions and analytical precisions for each element are given in Supplementary Table 6. 3.3 Zircon U–Pb dating Zircon crystals were obtained using standard crushing and separation techniques, and U–Pb dating was conductedusing the SIMS II ion microprobe at the Beijing SIMS Center, Chinese Academy of Geological Sciences (CAGS). The hand-picked crystals together with the TEMORA standard, having a conventionally determined 206Pb/238U age of 417 Ma (Black et al., 2003), were cast in epoxy resin discs and were polished. All grains were photographed in both transmitted and reflected light and were then imaged using cathodoluminescence (CL) to reveal the internal structure and to identify the preferred locations for SIMS analysis. The U–Pb dating information is given in Supplementary Table 7.
DOI: 10.6084/m9.figshare.14669655
title: SRR3414629.uniq.sorted.bam

description: рNA seq
DOI: 10.6084/m9.figshare.14669655.v1
title: SRR3414629.uniq.sorted.bam

description: рNA seq
DOI: 10.6084/m9.figshare.14669667
title: SRR3414629.uniq.sorted.bam.bai

description: рNASEQ
DOI: 10.6084/m9.figshare.14669667.v1
title: SRR3414629.uniq.sorted.bam.bai

description: рNASEQ
DOI: 10.5281/zenodo.4784610
title: Supporting data for Xu et al. 2021 - Weather and Forecasting

description: This is the dataset underpinning the paper "Deep Learning Experiments for Tropical Cyclone Intensity Forecasts" submitted to the journal Weather and Forecasting in 2021. 24-hour model data used in LOYO testing (before scaling):<br> `NOAA_reanalysis_vars_global_w_dvs24.csv`<br> `NOAA_operational_vars_global_w_dvs24.csv` 24-hour model data used in LOYO testing (after scaling):<br> `train_global_fill_REA_na_wo_img_scaled.csv` 2019 operational data reserved for 24-hour model independent test:<br> `NOAA_operational_vars_global_wLabels_fill_na_Y2019.csv` 2020 operational data reserved for 24-hour model independent test:<br> `NOAA_operational_vars_global_wLabels_fill_na_Y2020.csv` 6-hour model data used in LOYO testing (before scaling):<br> `NOAA_reanalysis_vars_global_w_dvs6.csv`
description: The operational forecast portion of this research was supported by the Deep Science Agile Initiative at Pacific Northwest National Laboratory (PNNL). It was conducted under the Laboratory Directed Research and Development Program at PNNL. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy under contract DE‐AC05‐76RL01830. The synthetic tropical cyclone portion of this research was supported by the Multisector Dynamics program areas of the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research as part of the multi-program, collaborative Integrated Coastal Modeling (ICoM) project.
DOI: 10.5281/zenodo.4784609
title: Supporting data for Xu et al. 2021 - Weather and Forecasting

description: This is the dataset underpinning the paper "Deep Learning Experiments for Tropical Cyclone Intensity Forecasts" submitted to the journal Weather and Forecasting in 2021. 24-hour model data used in LOYO testing (before scaling):<br> `NOAA_reanalysis_vars_global_w_dvs24.csv`<br> `NOAA_operational_vars_global_w_dvs24.csv` 24-hour model data used in LOYO testing (after scaling):<br> `train_global_fill_REA_na_wo_img_scaled.csv` 2019 operational data reserved for 24-hour model independent test:<br> `NOAA_operational_vars_global_wLabels_fill_na_Y2019.csv` 2020 operational data reserved for 24-hour model independent test:<br> `NOAA_operational_vars_global_wLabels_fill_na_Y2020.csv` 6-hour model data used in LOYO testing (before scaling):<br> `NOAA_reanalysis_vars_global_w_dvs6.csv`
description: The operational forecast portion of this research was supported by the Deep Science Agile Initiative at Pacific Northwest National Laboratory (PNNL). It was conducted under the Laboratory Directed Research and Development Program at PNNL. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy under contract DE‐AC05‐76RL01830. The synthetic tropical cyclone portion of this research was supported by the Multisector Dynamics program areas of the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research as part of the multi-program, collaborative Integrated Coastal Modeling (ICoM) project.
DOI: 10.6084/m9.figshare.14669412
title: SI_Tables (2).xlsx

description: Laboratory generated data and data used for plots<br>Table S1. Emission factor (g kg<sup>-1</sup>) for all fuels.Attached as a xlsx fileTable S2. Literature value used in Figure 3 (main text).Attached as a xlsx file
DOI: 10.5281/zenodo.4784629
title: El verso y el conflicto dramático en La vida es sueño, El alcalde de Zalamea y El mágico prodigioso de Pedro Calderón de la Barca

description: Corpus asociado al Trabajo Final de Maestría titulado "El verso y el conflicto dramático en La vida es sueño, El alcalde de Zalamea y El mágico prodigioso de Pedro Calderón de la Barca" para optar por el título de Magíster en Estudios Literarios de la Universidad Nacional de Colombia. 2021.
DOI: 10.5281/zenodo.4482923
title: El verso y el conflicto dramático en La vida es sueño, El alcalde de Zalamea y El mágico prodigioso de Pedro Calderón de la Barca

description: Corpus asociado al Trabajo Final de Maestría titulado "El verso y el conflicto dramático en La vida es sueño, El alcalde de Zalamea y El mágico prodigioso de Pedro Calderón de la Barca" para optar por el título de Magíster en Estudios Literarios de la Universidad Nacional de Colombia. 2021.
DOI: 10.13011/m3-ywxf-yw20
title: Dataset: Simulation of the electrochemical impedance in a three-dimensional, complex microstructure of solid oxide fuel cell cathode and its application in the microstructure characterization
DOI: 10.5281/zenodo.4784628
title: CoVaxxy Tweet IDs data set

description: A collection of Tweet IDs related to Covid-19 Vaccines, gathered from Twitter since Jan 4, 2021. Please see https://arxiv.org/abs/2101.07694 for more information.
DOI: 10.5281/zenodo.4735774
title: El verso y el conflicto dramático en La vida es sueño, El alcalde de Zalamea y El mágico prodigioso de Pedro Calderón de la Barca

description: Corpus asociado al Trabajo Final de Maestría titulado "El verso y el conflicto dramático en La vida es sueño, El alcalde de Zalamea y El mágico prodigioso de Pedro Calderón de la Barca" para optar por el título de Magíster en Estudios Literarios de la Universidad Nacional de Colombia. 2021.
DOI: 10.6073/pasta/10653d633cfe5b0bf4d1a325cd8c2d36
title: Topographic position amplifies consequences of short-interval stand- replacing fires on postfire tree establishment in subalpine conifer forests

description: Stand-replacing fires burned at 100 to 300-year intervals for millennia in subalpine conifer forests of western North America, but forests are burning more frequently as climate warms. Postfire tree regeneration is reduced when young forests reburn before recovering from previous fires or when drought occurs during postfire years. However, whether seedling vulnerabilities to harsh microclimate conditions may be amplified in short-interval (&lt; 30 years) fires is unclear. We conducted a field experiment to answer three questions: (1) How do germi- nation, survival, and establishment of lodgepole pine (Pinus contorta var. latifolia) and Douglas-fir (Pseudotsuga menziesii var. glauca) vary by aspect following high-severity, short-interval fires? (2) What environmental factors control germination, survival, and establishment of both species? (3) Based on our experimental evidence, what proportion of available seed would be expected to establish across landscapes that burned in these short-interval fires? One year postfire, we planted seeds of both species in north-facing, south-facing and flat plots at four sites across the Greater Yellowstone Ecosystem (Wyoming, USA). Soil microclimate was monitored continuously. Seed germination and seedling survival were measured every two weeks during the following growing season and at the beginning and end of the second growing season. Germination did not vary with aspect but increased with early-season soil moisture and temperature. Survival and establishment were low on south-facing aspects (&lt; 1% of seeds established for both species) and declined with warmer soil temperatures and drier soils. For lodgepole pine, we predicted establishment rates of &lt; 1% of available seed over 25% of the reburned landscape. Soil temperatures in short-interval fires were 2 ̊C warmer than similar areas of long-interval fire, with maximum temperatures frequently exceeding 40 °C. Topographic variation will mediate the consequences of short-interval fire for seedling establishment, leading to patchier tree regeneration as climate warming raises the likelihood of short-interval fires.
DOI: 10.6084/m9.figshare.14669769.v1
title: T0 25 Most Abundant OTUs - Counts and Taxonomy

description: File showing the normalized abundance and taxonomy classifications of the 25 most abundant OTUs in T0 microcosm samples.
DOI: 10.6084/m9.figshare.14669769
title: T0 25 Most Abundant OTUs - Counts and Taxonomy

description: File showing the normalized abundance and taxonomy classifications of the 25 most abundant OTUs in T0 microcosm samples.