cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23632506
title: Additional file 4 of A novel polypeptide CAPG-171aa encoded by circCAPG plays a critical role in triple-negative breast cancer

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.23632506.v1
title: Additional file 4 of A novel polypeptide CAPG-171aa encoded by circCAPG plays a critical role in triple-negative breast cancer

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.7227974.v1
title: Additional file 2: of Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China

description: Taxa composition of each module (ecological cluster). (XLSX 48Â kb)
DOI: 10.6084/m9.figshare.12470690
title: Additional file 1 of Less invasive surfactant administration versus endotracheal surfactant instillation followed by limited peak pressure ventilation in preterm infants with respiratory distress syndrome in China: study protocol for a randomized controlled trial

description: Additional file 1.
DOI: 10.6084/m9.figshare.12470690.v1
title: Additional file 1 of Less invasive surfactant administration versus endotracheal surfactant instillation followed by limited peak pressure ventilation in preterm infants with respiratory distress syndrome in China: study protocol for a randomized controlled trial

description: Additional file 1.
DOI: 10.6084/m9.figshare.7227974
title: Additional file 2: of Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China

description: Taxa composition of each module (ecological cluster). (XLSX 48Â kb)
DOI: 10.6084/m9.figshare.20335185
title: Data.rar

description: Data for the research article on nature communications.
DOI: 10.6084/m9.figshare.7228001.v1
title: Additional file 1: of Automated muscle histopathology analysis using CellProfiler

description: MuscleAnalyzer pipeline (ND2) for CellProfiler version 2.2.0. (CPPIPE 19Â kb)
DOI: 10.6084/m9.figshare.7228001
title: Additional file 1: of Automated muscle histopathology analysis using CellProfiler

description: MuscleAnalyzer pipeline (ND2) for CellProfiler version 2.2.0. (CPPIPE 19Â kb)
DOI: 10.6084/m9.figshare.1460843
title: Thyroid hormone induction of mitochondrial activity is coupled to mitophagy via ROS-AMPK-ULK1 signaling

description: Currently, there is limited understanding about hormonal regulation of mitochondrial turnover. Thyroid hormone (T<sub>3</sub>) increases oxidative phosphorylation (OXPHOS), which generates reactive oxygen species (ROS) that damage mitochondria. However, the mechanism for maintenance of mitochondrial activity and quality control by this hormone is not known. Here, we used both in vitro and in vivo hepatic cell models to demonstrate that induction of mitophagy by T<sub>3</sub> is coupled to oxidative phosphorylation and ROS production. We show that T<sub>3</sub> induction of ROS activates CAMKK2 (calcium/calmodulin-dependent protein kinase kinase 2, β) mediated phosphorylation of PRKAA1/AMPK (5′ AMP-activated protein kinase), which in turn phosphorylates ULK1 (unc-51 like autophagy activating kinase 1) leading to its mitochondrial recruitment and initiation of mitophagy. Furthermore, loss of ULK1 in T<sub>3</sub>-treated cells impairs both mitophagy as well as OXPHOS without affecting T<sub>3</sub> induced general autophagy/lipophagy. These findings demonstrate a novel ROS-AMPK-ULK1 mechanism that couples T<sub>3</sub>-induced mitochondrial turnover with activity, wherein mitophagy is necessary not only for removing damaged mitochondria but also for sustaining efficient OXPHOS.
DOI: 10.6084/m9.figshare.12470516.v1
title: Additional file 2 of Genetic Dissection and Functional Differentiation of ALKa and ALKb, Two Natural Alleles of the ALK/SSIIa Gene, Responding to Low Gelatinization Temperature in Rice

description: Additional file 2: Table S1. Primers used in this study. Table S2. Distributions of three main ALK haplotypes and thermo-properties determined by differential scanning calorimeter (DSC) among 440 rice accessions. Table S3. Distributions of three main ALK haplotypes from 440 rice accessions amongst the five rice subpopulations (indica, aus, aromatic, and temperate and tropical japonica) and subgroups (admixture and unclassified).
DOI: 10.6084/m9.figshare.12470516
title: Additional file 2 of Genetic Dissection and Functional Differentiation of ALKa and ALKb, Two Natural Alleles of the ALK/SSIIa Gene, Responding to Low Gelatinization Temperature in Rice

description: Additional file 2: Table S1. Primers used in this study. Table S2. Distributions of three main ALK haplotypes and thermo-properties determined by differential scanning calorimeter (DSC) among 440 rice accessions. Table S3. Distributions of three main ALK haplotypes from 440 rice accessions amongst the five rice subpopulations (indica, aus, aromatic, and temperate and tropical japonica) and subgroups (admixture and unclassified).
DOI: 10.6084/m9.figshare.1460845
title: Repetitive stimulation of autophagy-lysosome machinery by intermittent fasting preconditions the myocardium to ischemia-reperfusion injury

description: Autophagy, a lysosomal degradative pathway, is potently stimulated in the myocardium by fasting and is essential for maintaining cardiac function during prolonged starvation. We tested the hypothesis that intermittent fasting protects against myocardial ischemia-reperfusion injury via transcriptional stimulation of the autophagy-lysosome machinery. Adult C57BL/6 mice subjected to 24-h periods of fasting, every other day, for 6 wk were protected from in-vivo ischemia-reperfusion injury on a fed day, with marked reduction in infarct size in both sexes as compared with nonfasted controls. This protection was lost in mice heterozygous null for <i>Lamp2</i> (coding for lysosomal-associated membrane protein 2), which demonstrate impaired autophagy in response to fasting with accumulation of autophagosomes and SQSTM1, an autophagy substrate, in the heart. In <i>lamp2</i> null mice, intermittent fasting provoked progressive left ventricular dilation, systolic dysfunction and hypertrophy; worsening cardiomyocyte autophagosome accumulation and lack of protection to ischemia-reperfusion injury, suggesting that intact autophagy-lysosome machinery is essential for myocardial homeostasis during intermittent fasting and consequent ischemic cardioprotection. Fasting and refeeding cycles resulted in transcriptional induction followed by downregulation of autophagy-lysosome genes in the myocardium. This was coupled with fasting-induced nuclear translocation of TFEB (transcription factor EB), a master regulator of autophagy-lysosome machinery; followed by rapid decline in nuclear TFEB levels with refeeding. Endogenous TFEB was essential for attenuation of hypoxia-reoxygenation-induced cell death by repetitive starvation, in neonatal rat cardiomyocytes, in-vitro. Taken together, these data suggest that TFEB-mediated transcriptional priming of the autophagy-lysosome machinery mediates the beneficial effects of fasting-induced autophagy in myocardial ischemia-reperfusion injury.
DOI: 10.6084/m9.figshare.7228013
title: Additional file 2: of Automated muscle histopathology analysis using CellProfiler

description: MuscleAnalyzer pipeline (ND2) for CellProfiler version 3.0.0. (CPPIPE 17Â kb)
DOI: 10.6084/m9.figshare.7228013.v1
title: Additional file 2: of Automated muscle histopathology analysis using CellProfiler

description: MuscleAnalyzer pipeline (ND2) for CellProfiler version 3.0.0. (CPPIPE 17Â kb)
DOI: 10.6084/m9.figshare.7228022
title: Additional file 3: of Automated muscle histopathology analysis using CellProfiler

description: MuscleAnalyzer pipeline (TIFF) for CellProfiler version 3.0.0. (CPPIPE 17Â kb)
DOI: 10.6084/m9.figshare.7228022.v1
title: Additional file 3: of Automated muscle histopathology analysis using CellProfiler

description: MuscleAnalyzer pipeline (TIFF) for CellProfiler version 3.0.0. (CPPIPE 17Â kb)
DOI: 10.6084/m9.figshare.25273687
title: Supplementary Material for: Lucio Phenomenon: An Unusual Case of Skin Necrosis

description: <b><i>Introduction:</i></b> Lucio leprosy is a non-nodular diffuse type of lepromatous leprosy first described by Lucio and Alvarado. Lucio phenomenon is a rare vasculonecrotic reaction characterized by cutaneous necrosis with minimal constitutional features. <b><i>Case Presentation:</i></b> We describe an unusual case of a 53-year-old man from Central India who had blisters, ulcers, and widespread erosions on his foot, forearms, and arms. The diagnosis of lepromatous leprosy with the Lucio phenomenon was established after thorough evaluation by clinical findings, histopathological findings, and slit-skin smear examination. <b><i>Conclusion:</i></b> Lucio phenomenon is an uncommon cause of cutaneous infarction and necrosis. Primary care physicians should keep a high index of suspicion in patients with cutaneous necrosis and minimal constitution features. Since leprosy is a relatively curable disease, primary care physicians should think of a rare form of lepromatous leprosy presenting with cutaneous necrosis, especially in non-endemic zones.
DOI: 10.6084/m9.figshare.25273696
title: Supplementary Material for: Netherton Syndrome with a Novel Likely Pathogenic Variant c.420del (p.Ser141ProfsTer5) in SPINK5 Gene: A Case Report

description: <b><i>Introduction:</i></b> Netherton syndrome (NS) is a rare autosomal recessive genodermatosis in the group of congenital ichthyosis. The clinical manifestations of the syndrome vary from a very mild clinical manifestation occurring with the picture of ichthyosis linearis circumflexa to exfoliative erythroderma. It can be fatal in the first days of a newborn’s life due to dehydration, hypothermia, weight loss, respiratory infections, and sepsis. A specific anomaly of the hair trichorrexis invaginata is considered pathognomonic for the syndrome. Genetic testing of <i>SPINK5</i> gene is key to confirming the diagnosis and starting early treatment. <b><i>Case Presentation:</i></b> We present a case report of NS in a 6-year-old boy who suffered from generalized erythroderma and desquamation of the skin from birth. The patient has atopic diathesis, recurrent skin infections, increased levels of IgE, and delayed physical development. Two genetic variants in <i>SPINK5</i> gene with clinical significance were identified. The first detected variant is a nonsense mutation, predicted to cause loss of normal protein function either by protein truncation or by nonsense-mediated mRNA decay. The second variant is a likely pathogenic frameshift mutation that truncates the protein in 5 amino acids. The child was treated with acitretin, without satisfactory effect. <b><i>Conclusion:</i></b> The genetic variant we have described correlates with a severe clinical phenotype of NS. The second genetic variant of the <i>SPINK5</i> gene, inherited from the father in our case, is novel and has never been published in the literature.
DOI: 10.6084/m9.figshare.7228067
title: Additional file 6: of Automated muscle histopathology analysis using CellProfiler

description: Sample image dataset. (RAR 358466Â kb)
DOI: 10.6084/m9.figshare.7228067.v1
title: Additional file 6: of Automated muscle histopathology analysis using CellProfiler

description: Sample image dataset. (RAR 358466Â kb)
DOI: 10.5281/zenodo.10697072
title: Original data of the Survey research (Serra e Classe, 2024)
DOI: 10.5281/zenodo.10697073
title: Original data of the Survey research (Serra e Classe, 2024)
DOI: 10.6084/m9.figshare.21384024
title: traffic_crash_modeling_data&code

description: This project is linked to a manuscript submited to International Journal of Geographical Information Science: Uncovering the association between traffic crashes and street-level built-environment features using street view images.
DOI: 10.6084/m9.figshare.8276870
title: Long non-coding RNA slincRAD functions in methylation regulation during the early stage of mouse adipogenesis

description: Adipocyte differentiation is a coordinated cellular process, which involves a series of dynamic molecular events. Up-regulation of long noncoding RNA <i>slincRAD</i> expression was found to occur in the early differentiation stages of 3T3-L1 cell, prior to the regulation of major transcription factors. By interacting with DNMT1 in S phase, <i>slincRAD</i> guides this essentially epigenetic factor to mediate promoter methylation of a batch of cell cycle-related genes, including cyclin-dependent kinase inhibitor <i>p21</i>. The regulation promotes the growth-arrested cells to re-enter into cell cycle under hormone induction and thereby advances the process of differentiation to clonal expansion stage. The abolishment of the interaction between <i>slincRAD</i> and DNMT1 by <i>slincRAD</i> knockdown results in a defective epigenetic regulation and finally compromised adipogenesis. Collectively, our study characterizes the epigenetic regulation of lncRNA involved in the early stage of adipogenesis.
DOI: 10.6084/m9.figshare.8276870.v2
title: Long non-coding RNA slincRAD functions in methylation regulation during the early stage of mouse adipogenesis

description: Adipocyte differentiation is a coordinated cellular process, which involves a series of dynamic molecular events. Up-regulation of long noncoding RNA <i>slincRAD</i> expression was found to occur in the early differentiation stages of 3T3-L1 cell, prior to the regulation of major transcription factors. By interacting with DNMT1 in S phase, <i>slincRAD</i> guides this essentially epigenetic factor to mediate promoter methylation of a batch of cell cycle-related genes, including cyclin-dependent kinase inhibitor <i>p21</i>. The regulation promotes the growth-arrested cells to re-enter into cell cycle under hormone induction and thereby advances the process of differentiation to clonal expansion stage. The abolishment of the interaction between <i>slincRAD</i> and DNMT1 by <i>slincRAD</i> knockdown results in a defective epigenetic regulation and finally compromised adipogenesis. Collectively, our study characterizes the epigenetic regulation of lncRNA involved in the early stage of adipogenesis.
DOI: 10.6084/m9.figshare.8276870.v1
title: ¬¬¬Long non-coding RNA slincRAD functions in methylation regulation during the early stage of mouse adipogenesis

description: Adipocyte differentiation is a coordinated cellular process, which involves a series of dynamic molecular events. Up-regulation of long noncoding RNA <i>slincRAD</i> expression was found to occur in the early differentiation stages of 3T3-L1 cell, prior to the regulation of major transcription factors. By interacting with DNMT1 in S phase, <i>slincRAD</i> guides this essentially epigenetic factor to mediate promoter methylation of a batch of cell cycle-related genes, including cyclin-dependent kinase inhibitor <i>p21</i>. The regulation promotes the growth-arrested cells to re-enter into cell cycle under hormone induction and thereby advances the process of differentiation to clonal expansion stage. The abolishment of the interaction between <i>slincRAD</i> and DNMT1 by <i>slincRAD</i> knockdown results in a defective epigenetic regulation and finally compromised adipogenesis. Collectively, our study characterizes the epigenetic regulation of lncRNA involved in the early stage of adipogenesis.
DOI: 10.6084/m9.figshare.21384008
title: 1_Main Dataset_Ren 2020+Shuangchenglong;2_Subsidiary Data matrix_CEA_2019+Shuangchenglong;3_Subsidiary Data matrix_M_2019+Shuangchenglong;4_Subsidiary Data matrix_GEA_2020+Shuangchenglong from New macronarian from the Middle Jurassic of Chongqing, China: phylogenetic and biogeographic implications for neosauropod dinosaur evolution

description: Main Dataset;Subsidiary Data matrix 2;Subsidiary Data matrix 3;Subsidiary Data matrix 4
DOI: 10.6084/m9.figshare.21384008.v1
title: 1_Main Dataset_Ren 2020+Shuangchenglong;2_Subsidiary Data matrix_CEA_2019+Shuangchenglong;3_Subsidiary Data matrix_M_2019+Shuangchenglong;4_Subsidiary Data matrix_GEA_2020+Shuangchenglong from New macronarian from the Middle Jurassic of Chongqing, China: phylogenetic and biogeographic implications for neosauropod dinosaur evolution

description: Main Dataset;Subsidiary Data matrix 2;Subsidiary Data matrix 3;Subsidiary Data matrix 4
DOI: 10.6084/m9.figshare.21384132
title: Data for "Key factors controlling biotite/silicate melt Nb and Ta partitioning: Implications for Nb−Ta enrichment and fractionation in granites"

description: This file includes the supplementary dataset for the manuscript titled " Key factors controlling biotite/silicate melt Nb and Ta partitioning: Implications for Nb−Ta enrichment and fractionation in granites"
DOI: 10.6084/m9.figshare.21384186
title: Corn 3D point clouds

description: This data are corn point clouds collected by Terrestrial laser scanning. They contain a total of 48 individual corn point clouds in three different growing seasons. The data format is pcd, and each point cloud data contains the (x,y,z) coordinates of the points.
DOI: 10.6084/m9.figshare.21679601
title: The <i>Rauvolfia tetraphylla</i> genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids

description: Rauvolfia_tetraphylla_v1.1.transcripts (Predicted transcripts)<br>
Rauvolfia_tetraphylla_v1.1.cds (Predicted CDS)<br>
Rauvolfia_tetraphylla_v1.1.gff (Genome annotation file (GFF))<br>
Rauvolfia_tetraphylla_v1.1.pep (Predicted proteins)<br>
Rauvolfia_tetraphylla_genome_v1.0_2019_Oct_27.fasta (Genome)<br>
Rauvolfia_tetraphylla_Trinotate.xls (Gene functional annotation)
 Rauvolfia_tetraphylla_TPM.csv  (transcript relative expression matrix (TPM)
DOI: 10.6084/m9.figshare.21679628
title: <i>Rauvolfia tetraphylla</i> chromosome-scale genome to complete the ajmaline biosynthetic pathway

description: Rauvolfia_tetraphylla_v2.0.transcripts (Predicted transcripts)<br>Rauvolfia_tetraphylla_v2.0.cds (Predicted CDS)<br>Rauvolfia_tetraphylla_v2.0.gff3 (Genome annotation file (GFF))<br>Rauvolfia_tetraphylla_v2.0.pep (Predicted proteins)<br>Rauvolfia_tetraphylla_genome_v2.0.fasta (Genome)<br>Rauvolfia_tetraphylla_v2.0_Trinotate.xls (Gene functional annotation)
DOI: 10.5285/b82b58d085d0433b821f4ae31cb608de
title: HadISD: Global sub-daily, surface meteorological station data, 1931-2023, v3.4.0.2023f

description: This is version v3.4.0.2023f of Met Office Hadley Centre's Integrated Surface Database, HadISD. These data are global sub-daily surface meteorological data.

This update (v3.4.0.2023f) to HadISD corrects a long-standing bug which was discovered in autumn 2023 whereby the neighbour checks (and associated [un]flagging for some other tests) were not being implemented. For more details see the posts on the HadISD blog: https://hadisd.blogspot.com/2023/10/bug-in-buddy-checks.html & https://hadisd.blogspot.com/2024/01/hadisd-v3402023f-future-look.html

The quality controlled variables in this dataset are: temperature, dewpoint temperature, sea-level pressure, wind speed and direction, cloud data (total, low, mid and high level). Past significant weather and precipitation data are also included, but have not been quality controlled, so their quality and completeness cannot be guaranteed. Quality control flags and data values which have been removed during the quality control process are provided in the qc_flags and flagged_values fields, and ancillary data files show the station listing with a station listing with IDs, names and location information. 

The data are provided as one NetCDF file per station. Files in the station_data folder station data files have the format "station_code"_HadISD_HadOBS_19310101-20230101_v3.4.1.2023f.nc. The station codes can be found under the docs tab. The station codes file has five columns as follows: 1) station code, 2) station name 3) station latitude 4) station longitude 5) station height.

To keep informed about updates, news and announcements follow the HadOBS team on twitter @metofficeHadOBS.

For more detailed information e.g bug fixes, routine updates and other exploratory analysis, see the HadISD blog: http://hadisd.blogspot.co.uk/

References:
When using the dataset in a paper you must cite the following papers (see Docs for link to the publications) and this dataset (using the "citable as" reference) :

Dunn, R. J. H., (2019), HadISD version 3: monthly updates, Hadley Centre Technical Note.

Dunn, R. J. H., Willett, K. M., Parker, D. E., and Mitchell, L.: Expanding HadISD: quality-controlled, sub-daily station data from 1931, Geosci. Instrum. Method. Data Syst., 5, 473-491, doi:10.5194/gi-5-473-2016, 2016.

Dunn, R. J. H., et al. (2012), HadISD: A Quality Controlled global synoptic report database for selected variables at long-term stations from 1973-2011, Clim. Past, 8, 1649-1679, 2012, doi:10.5194/cp-8-1649-2012

Smith, A., N. Lott, and R. Vose, 2011: The Integrated Surface Database: Recent Developments and Partnerships. Bulletin of the American Meteorological Society, 92, 704–708, doi:10.1175/2011BAMS3015.1

For a homogeneity assessment of HadISD please see this following reference

Dunn, R. J. H., K. M. Willett, C. P. Morice, and D. E. Parker. "Pairwise homogeneity assessment of HadISD." Climate of the Past 10, no. 4 (2014): 1501-1522. doi:10.5194/cp-10-1501-2014, 2014.
DOI: 10.6084/m9.figshare.8277182
title: Optimal Sparse Linear Prediction for Block-missing Multi-modality Data Without Imputation

description: In modern scientific research, data are often collected from multiple modalities. Since different modalities could provide complementary information, statistical prediction methods using multimodality data could deliver better prediction performance than using single modality data. However, one special challenge for using multimodality data is related to block-missing data. In practice, due to dropouts or the high cost of measures, the observations of a certain modality can be missing completely for some subjects. In this paper, we propose a new direct sparse regression procedure using covariance from multimodality data (DISCOM). Our proposed DISCOM method includes two steps to find the optimal linear prediction of a continuous response variable using block-missing multimodality predictors. In the first step, rather than deleting or imputing missing data, we make use of all available information to estimate the covariance matrix of the predictors and the cross-covariance vector between the predictors and the response variable. The proposed new estimate of the covariance matrix is a linear combination of the identity matrix, the estimates of the intra-modality covariance matrix and the cross-modality covariance matrix. Flexible estimates for both the sub-Gaussian and heavy-tailed cases are considered. In the second step, based on the estimated covariance matrix and the estimated cross-covariance vector, an extended Lasso-type estimator is used to deliver a sparse estimate of the coefficients in the optimal linear prediction. The number of samples that are effectively used by DISCOM is the minimum number of samples with available observations from two modalities, which can be much larger than the number of samples with complete observations from all modalities. The effectiveness of the proposed method is demonstrated by theoretical studies, simulated examples, and a real application from the Alzheimer’s Disease Neuroimaging Initiative. The comparison between DISCOM and some existing methods also indicates the advantages of our proposed method.
DOI: 10.6084/m9.figshare.13520072
title: Visualizing Tumor in Real-time: A Highly Sensitive PSMA Probe for NIR-II Imaging and Intraoperative Tumor Resection

description: A novel NIR-II probe was developed, which demonstrated excellent optical properties and ultra-high affinity towards prostate-specific membrane antigen. The probe displayed remarkable performance in <i>in vivo </i>NIR-II imaging and intraoperative image-guided tumor resection, during which a missed residual tumor by the operator was successfully detected by the novel probe.