cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25413/sun.24972888.v1
title: Ship Motion Measurements and Human Responses Captured on the SA Agulhas II - SANAE 2021-2022

description: This dataset contains digitised human responses related to motion sickness recorded by participants on the SA Agulhas II during the South African National Antarctic Expedition (SANAE) Relief Voyage of 2021-2022 using paper-based questionnaire booklets, called daily diaries, and a mobile application, called Mariner 4.0.Additionally, this dataset contains ship motion measured by accelerometers in a specific array that enables the computation of z-oriented acceleration at points of interest on board beyond the array measurement locations. Acceleration measurements in the dataset are stored in 5-minute batches with a 10 Hz sample rate at the locations and orientations detailed in the associated readme file in the data collection. This dataset is a down-sampled subset of acceleration measurements sampled at 2048 Hz during the SANAE Relief Voyage of 2021-2022.Lastly, this dataset contains Motion Sickness Dose Values computed from ship motion measurements at each near-field communication tag installed shipboard, as detailed by position vectors in the supporting documentation.Note: A Readme file is included to guide dataset navigation and understanding.
DOI: 10.6084/m9.figshare.13323706
title: Additional file 2 of Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization

description: Additional file 2: Table S1. The comparison of [AT] values across ploymorphic sites among bread wheat and its wild progenitors. Table S2. Expression of candidate genes within qATD-3A and qATD-7D.
DOI: 10.6084/m9.figshare.21714653
title: Supplementary Materials for Genotypic and phenotypic spectrum and pathogenesis of WNT1 variants in a large cohort of patients with OI / osteoporosis

description:   
Mutations in <em>WNT1</em> can cause rare inherited disorders such as osteogenesis imperfecta (OI) and early-onset osteoporosis (EOOP). Due to its rarity, the clinical characteristics and pathogenic mechanism of <em>WNT1</em> mutations remain unclear. We aimed to explore the phenotypic and genotypic spectrum and treatment responses of a large cohort of patients with WNT1-related OI/OP and the molecular mechanisms of <em>WNT1 </em>variants. The phenotypes and genotypes of patients and their responses to bisphosphonates or denosumab were evaluated. Western blot analysis, qPCR, and immunofluorescence staining were used to evaluate the expression levels of WNT1, total β-catenin, and type I collagen in the tibial bone or skin from one patient. We included a total of 16 patients with 16 mutations identified in <em>WNT1</em>, including a novel mutation. The types of <em>WNT1</em> mutations were related to skeletal phenotypes, and biallelic nonsense mutations or frameshift mutations could lead to an earlier occurrence of fragility fractures and more severe skeletal phenotypes. Some rare comorbidities were identified in this cohort, including cerebral abnormalities, hematologic diseases, and pituitary adenoma. Bisphosphonates and denosumab significantly increased the spine and proximal hip BMD of patients with <em>WNT1</em> mutations and reshaped the compressed vertebrae. We reported for the first time a decreased β-catenin level in the bone of patient 10 with c.677C&gt;T and c.502G&gt;A compared to the healthy control, which revealed the potential mechanisms of WNT1-induced skeletal phenotypes. Biallelic nonsense mutations or frameshift mutations of <em>WNT1</em> could lead to an earlier occurrence of fragility fractures and a more severe skeletal phenotype in OI and EOOP induced by <em>WNT1</em> mutations. The reduced osteogenic activity caused by WNT pathway downregulation could be a potential pathogenic mechanism of WNT1 related OI and EOOP.
DOI: 10.6084/m9.figshare.7558895
title: Identification of novel microRNAs in rice (<i>Oryza sativa)</i> based on the cleavage signals in precursors

description: MicroRNAs (miRNAs) are crucial regulators of gene expression in plants and a growing number of novel miRNA genes have been cloned in rice in recent years. However, there is no evidence that all miRNAs have been discovered, especially for those low expression ones which are difficult to be found by conventional methods. By taking advantage of the finding that DCL1-mediated cleavage signals for the processing of the miRNA precursors could be used as the clues for novel miRNAs’ discovery, a genome-wide search for rice miRNA candidates was carried out. As a result, 51 previously validated miRNAs and 24 novel miRNA candidates were discovered. After target prediction and degradome sequencing data-based validation, coupled with reverse approach retest, 10 miRNA candidate–mRNA target pairs were further identified, providing a basis for in-depth functional analysis of these miRNA candidates. Besides, some isomiRs found in this study showed more likely to be the real miRNAs. We also found an exceptional example which did not obey the rule that 22-nt miRNAs have the ability to trigger the phased siRNAs production from the cleaved targets.
DOI: 10.6084/m9.figshare.25217978
title: Supplementary Material for: Gastrointestinal Variant of Lemierre Syndrome due to Fusobacterium Nucleatum: A Case Report

description: Introduction: Pyogenic liver abscess is a noteworthy health concern in North America, characterized by a mortality rate ranging from 2-12%. This condition is often polymicrobial, with Streptococcus species and Escherichia coli as the predominant causal pathogens in Western countries. Fusobacterium species, typically commensals of gastrointestinal, genital, and oral flora, have been implicated in the rare formation of tonsillar abscesses and Lemierre’s syndrome, including its gastrointestinal variant known as pylephlebitis.
Case Presentation: We present the case of an immunocompetent male with a 2-week history of abdominal distention and pain. Abdominal magnetic resonance imaging revealed multiseptated cystic hepatic masses and portal vein thrombosis. A subsequent liver biopsy confirmed Fusobacterium nucleatum etiology. The patient was initiated on intravenous cefepime and oral metronidazole antibiotics. Unfortunately, the patient succumbed to cardiac arrest before a final diagnosis could be established.
Conclusion: Fusobacterium species-associated liver abscess, coupled with the rare gastrointestinal variant of Lemierre syndrome (pylephlebitis), poses a significant mortality risk. This case underscores the rarity and clinical challenges associated with these conditions. Increased awareness among clinicians is crucial for early diagnosis and prompt intervention, potentially improving outcomes in such cases.
DOI: 10.6084/m9.figshare.19091018
title: Additional file 1 of Peripheral venous lactate levels substitute arterial lactate levels in the emergency department

description: Additional file 1. Title of data: Blood gas analysis data from patients. Description of data: Blood gas analysis data from patients.
DOI: 10.6084/m9.figshare.19091022.v1
title: Additional file 3 of miR-199b-3p contributes to acquired resistance to cetuximab in colorectal cancer by targeting CRIM1 via Wnt/β-catenin signaling

description: Additional file 3: Table S1. The DEGs between CTx resistance and non-CTx resistance groups in the GSE140971 dataset.
DOI: 10.6084/m9.figshare.19091018.v1
title: Additional file 1 of Peripheral venous lactate levels substitute arterial lactate levels in the emergency department

description: Additional file 1. Title of data: Blood gas analysis data from patients. Description of data: Blood gas analysis data from patients.
DOI: 10.6084/m9.figshare.19091088.v1
title: Additional file 1 of FTO suppresses glycolysis and growth of papillary thyroid cancer via decreasing stability of APOE mRNA in an N6-methyladenosine-dependent manner

description: Additional file 1: Table S1. The sequence of si-RNAs. Table S2. The sequence of primers. Table S3. The Antibodies for western blot, IHC and RIP. Table S4. Correlation between FTO expression and clinicopathological features of PTC patients in TCGA database (n = 428). Table S5. Correlation between APOE expression and clinicopathological features of PTC patients in TCGA database (n = 428).
DOI: 10.6084/m9.figshare.19091025.v1
title: Additional file 4 of miR-199b-3p contributes to acquired resistance to cetuximab in colorectal cancer by targeting CRIM1 via Wnt/β-catenin signaling

description: Additional file 4: Table S2. The potential targets of miR-199b-3p predicted by Targetscan.
DOI: 10.6084/m9.figshare.7034792.v1
title: CASP4/caspase-11 promotes autophagosome formation in response to bacterial infection

description: CASP4/caspase-11-dependent inflammasome activation is important for the clearance of various Gram-negative bacteria entering the host cytosol. Additionally, CASP4 modulates the actin cytoskeleton to promote the maturation of phagosomes harboring intracellular pathogens such as <i>Legionella pneumophila</i> but not those enclosing nonpathogenic bacteria. Nevertheless, this non-inflammatory role of CASP4 regarding the trafficking of vacuolar bacteria remains poorly understood. Macroautophagy/autophagy, a catabolic process within eukaryotic cells, is also implicated in the elimination of intracellular pathogens such as <i>Burkholderia cenocepacia</i>. Here we show that CASP4-deficient macrophages exhibit a defect in autophagosome formation in response to <i>B. cenocepacia</i> infection. The absence of CASP4 causes an accumulation of the small GTPase RAB7, reduced colocalization of <i>B. cenocepacia</i> with LC3 and acidic compartments accompanied by increased bacterial replication <i>in vitro</i> and <i>in vivo</i>. Together, our data reveal a novel role of CASP4 in regulating autophagy in response to <i>B. cenocepacia</i> infection.
DOI: 10.6084/m9.figshare.19091088
title: Additional file 1 of FTO suppresses glycolysis and growth of papillary thyroid cancer via decreasing stability of APOE mRNA in an N6-methyladenosine-dependent manner

description: Additional file 1: Table S1. The sequence of si-RNAs. Table S2. The sequence of primers. Table S3. The Antibodies for western blot, IHC and RIP. Table S4. Correlation between FTO expression and clinicopathological features of PTC patients in TCGA database (n = 428). Table S5. Correlation between APOE expression and clinicopathological features of PTC patients in TCGA database (n = 428).
DOI: 10.6084/m9.figshare.19613629.v1
title: Additional file 4 of The burden of aortic aneurysm in China from 1990 to 2019: findings from the Global Burden of Disease Study 2019

description: Additional file 4.
DOI: 10.6084/m9.figshare.19613629
title: Additional file 4 of The burden of aortic aneurysm in China from 1990 to 2019: findings from the Global Burden of Disease Study 2019

description: Additional file 4.
DOI: 10.6084/m9.figshare.19613632
title: Additional file 5 of The burden of aortic aneurysm in China from 1990 to 2019: findings from the Global Burden of Disease Study 2019

description: Additional file 5.
DOI: 10.25345/c5b27q28d
title: MassIVE MSV000094078 - Quantitative proteomics profiling for the identification of targets in doxorubicin-resistant lung adenocarcinoma cells
title: LCMS/MS-based profiling for target identification in doxorubicin-resistant lung cancer cells.
DOI: 10.6084/m9.figshare.24336616
title: Epidemiological surveys revealed the risk of TAMV spill-over from ticks to hosts

description: Tick-borne viral diseases have become an increasingly important public health concern. Tamdy virus (TAMV) is a tick-borne virus of the genus <i>Orthonairovirus</i> in the family <i>Nairoviridae</i>. While some studies have suggested that TAMV is a pathogen associated with human febrile illness, its epidemiology and the risk of TAMV spill-over remain poorly understood. Ticks were collected in Xinjiang, China, and grouped into pools. RT-PCR assays were used to detect TAMV RNA in these pools. The seroprevalence of TAMV was investigated using Immunofluorescence assays, Western blotting, and Luciferase immunoprecipitation system (LIPS) assays. TAMV RNA was detected in 17 out of 363 tick pools, resulting in a minimum infection rate (MIR) of 4.7%. <i>Hyalomma asiaticum</i> and <i>Dermacentor nuttalli</i> were identified as major tick vectors of TAMV. Phylogenetic analysis demonstrated that TAMV strains from Xinjiang are closely related to strains from other countries. Seroprevalence studies showed that TAMV exposure has been occurring in Xinjiang since at least 2006. Antibody responses to TAMV were detected in 1.1% (26/2296) of animals, including domestic animals and wild rodents. The seropositivity rates were as follows: sheep (1.7%), dog (2.3%), <i>Marmota monax</i> (0.8%), <i>Meriones meridianus</i> (3.5%). The research findings reveal that TAMV can be transmitted by ticks to various animal species, posing a significant public health risk. The wide distribution of TAMV and its tick vectors emphasise the importance of early preparedness and control measures. This study highlights the necessity for maintaining vigilance in addressing emerging zoonotic diseases transmitted by ticks.
DOI: 10.6084/m9.figshare.24336616.v1
title: Epidemiological surveys revealed the risk of TAMV spill-over from ticks to hosts

description: Tick-borne viral diseases have become an increasingly important public health concern. Tamdy virus (TAMV) is a tick-borne virus of the genus <i>Orthonairovirus</i> in the family <i>Nairoviridae</i>. While some studies have suggested that TAMV is a pathogen associated with human febrile illness, its epidemiology and the risk of TAMV spill-over remain poorly understood. Ticks were collected in Xinjiang, China, and grouped into pools. RT-PCR assays were used to detect TAMV RNA in these pools. The seroprevalence of TAMV was investigated using Immunofluorescence assays, Western blotting, and Luciferase immunoprecipitation system (LIPS) assays. TAMV RNA was detected in 17 out of 363 tick pools, resulting in a minimum infection rate (MIR) of 4.7%. <i>Hyalomma asiaticum</i> and <i>Dermacentor nuttalli</i> were identified as major tick vectors of TAMV. Phylogenetic analysis demonstrated that TAMV strains from Xinjiang are closely related to strains from other countries. Seroprevalence studies showed that TAMV exposure has been occurring in Xinjiang since at least 2006. Antibody responses to TAMV were detected in 1.1% (26/2296) of animals, including domestic animals and wild rodents. The seropositivity rates were as follows: sheep (1.7%), dog (2.3%), <i>Marmota monax</i> (0.8%), <i>Meriones meridianus</i> (3.5%). The research findings reveal that TAMV can be transmitted by ticks to various animal species, posing a significant public health risk. The wide distribution of TAMV and its tick vectors emphasise the importance of early preparedness and control measures. This study highlights the necessity for maintaining vigilance in addressing emerging zoonotic diseases transmitted by ticks.
DOI: 10.6084/m9.figshare.12278057
title: Economic use of plants is key to their naturalization success

description: The files include the R scripts and data files for the statistical analyses of van Kleunenen et al. 2020 (Economic use of plants is key to their naturalization success) Nature Communications.<br>The main R script file is 'vanKleunen_etal_2020_Rsyntax_MAIN.R'. It calls the datasets and phylogenetic tree. It also refers to two other R script files.
DOI: 10.25345/c56970854
title: MassIVE MSV000094079 - Quantifying the Human Proteome with Physical Access to DNA
title: In a human cell DNA is packed in histones and other chromatin-associated proteins that form a cohesive gel. At any given moment a specific subset of the nuclear proteome has physical access to the DNA and organizes chromatin structure, transcription, splicing, ribosome biogenesis, DNA replication, DNA repair and other molecular functions that are essential to the way the genome is read and maintained. What proteins are in physical contact with the DNA and how this direct DNA interactome changes during cellular perturbations is incompletely understood. Here, we apply zero-distance photo-crosslinking proteomics to identify and quantify proteins with direct, physical access to DNA in human breast cancer cells. Therefore, we apply metabolic labeling with the photo-activatable nucleotide 4-thiothymidine and develop a high-intensity UV source that allows for fast and efficient protein-DNA crosslinking in live cells. We devise a denaturing extraction procedure for photo-crosslinked protein-DNA complexes yielding remarkable purity, which we apply to derive a quantitative atlas of over one thousand proteins physically interacting with DNA and find hundreds of peptide-DNA crosslinks pinpointing their interface at single amino-acid resolution. Quantifying DNA interactomes differentially, we demonstrate the specific and dose-dependent recruitment of the estrogen receptor to DNA in breast cancer cells responding to increasing doses of estrogen. A quantitative comparison of DNA interactomes from cells treated with three genotoxic drugs reveals commonalities and differences in their transcriptional response, the structural reorganization of their chromatin, as well as their DNA repair in reaction to distinct types of DNA damage. Our refined approach provides a versatile resource of human protein-DNA interactions and methodology that is applicable to a variety of organisms and systems.
DOI: 10.17638/datacat.liverpool.ac.uk/2600
title: Understanding Control and Mechanisms of Shoulder Instability in FSHD. Ultrasound images and c3D mo

description: Upper limb images and c3D movement files for adults with and without Facioscapulohumeral dystrophy
DOI: 10.6084/m9.figshare.13324025
title: Additional file 8 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 8: Supplementary Data 8. Candidate regions and genes in these regions with KEGG and GO results for gradient zone.
DOI: 10.6084/m9.figshare.13324028
title: Additional file 9 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 9: Supplementary Data 9. Candidate regions and genes in these regions with KEGG and GO results for sexual maturity.
DOI: 10.6084/m9.figshare.13324022.v1
title: Additional file 7 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 7: Supplementary Data 7. Candidate regions and genes in these regions with KEGG and GO results for body weight.
DOI: 10.6084/m9.figshare.13324001
title: Additional file 1 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 1: Supplementary Data 1. Breed phenotypes.
DOI: 10.6084/m9.figshare.13324007.v1
title: Additional file 3 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 3: Supplementary Data 3. Candidate regions and genes in these regions with KEGG and GO results for coat color.
DOI: 10.6084/m9.figshare.13324028.v1
title: Additional file 9 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 9: Supplementary Data 9. Candidate regions and genes in these regions with KEGG and GO results for sexual maturity.
DOI: 10.6084/m9.figshare.13324016.v1
title: Additional file 5 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 5: Supplementary Data 5. Candidate regions and genes in these regions with KEGG and GO results for body height.
DOI: 10.6084/m9.figshare.13324016
title: Additional file 5 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 5: Supplementary Data 5. Candidate regions and genes in these regions with KEGG and GO results for body height.
DOI: 10.6084/m9.figshare.13323992
title: Additional file 10 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 10: Supplementary Data 10. Candidate regions and genes in these regions with KEGG and GO results for lean meat percentage.
DOI: 10.6084/m9.figshare.13323992.v1
title: Additional file 10 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 10: Supplementary Data 10. Candidate regions and genes in these regions with KEGG and GO results for lean meat percentage.
DOI: 10.6084/m9.figshare.13323998
title: Additional file 11 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 11: Supplementary Data 11. Candidate regions and genes in these regions with KEGG and GO results for dressing percentage.
DOI: 10.6084/m9.figshare.13324007
title: Additional file 3 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 3: Supplementary Data 3. Candidate regions and genes in these regions with KEGG and GO results for coat color.
DOI: 10.6084/m9.figshare.13324013.v1
title: Additional file 4 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 4: Supplementary Data 4. Candidate regions and genes in these regions with KEGG and GO results for ear shape.
DOI: 10.13145/bacdive128490.20170829.2
title: Geodermatophilus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive128491.20170829.2
title: Geodermatophilus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive128492.20170829.2
title: Geodermatophilus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive128493.20170829.2
title: Geodermatophilus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive128494.20170829.2
title: Geodermatophilus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive128495.20170829.2
title: Geodermatophilus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive128496.20170829.2
title: Geodermatophilus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130754.20170829.2
title: Vibrio sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130755.20170829.2
title: Vibrio sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.