cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22249837.v1
title: Supplementary Material for: Chromosome 18 loss of heterozygosity in small intestinal neuroendocrine tumours: Multi-omic and tumour composition analyses

description: Background: Small intestinal neuroendocrine tumours (siNETs) are rare neoplasms which present with low mutational burden and can be subtyped based on copy number variation (CNV). Currently, siNETs can be molecularly classified as having chromosome 18 loss of heterozygosity (18LOH), multiple CNVs (MultiCNV), or no CNVs. 18LOH tumours have better progression free survival when compared to MultiCNV and NoCNV tumours, however the mechanism underlying this is unknown, and clinical practice does not currently consider CNV status. Methods: Here, we use genome-wide tumour DNA methylation (n=54) and gene expression (n=20 matched to DNA methylation) to better understand how gene regulation varies by 18LOH status. We then use multiple cell deconvolution methods to analyse how cell composition varies between 18LOH status, and determine potential associations with progression free survival. Results: We identified 27,464 differentially methylated CpG sites and 12 differentially expressed genes between 18LOH and non-18LOH (MultiCNV + NoCNV) siNETs. Although few differentially expressed genes were identified, these genes were highly enriched with the differentially methylated CpG sites compared to the rest of the genome. We identified differences in tumour micro-environment between 18LOH and non-18LOH tumours, including CD14+ infiltration in a subset of non-18LOH tumours which had the poorest clinical outcomes. Conclusions: We identify a small number of genes which appear to be linked to the 18LOH status of siNETs, and find evidence of potential epigenetic dysregulation of these genes. We also find a potential prognostic marker for worse progression free outcomes in the form of higher CD14 infiltration in non-18LOH siNETs.
DOI: 10.6084/m9.figshare.23617956
title: <strong>Supplementary Data S8</strong> - Genes of the Ehrlich Pathway

description: Variant effect counts by SnpEff extracted from Supplementary Data S3 per genes involved in the Ehrlich pathway (biosynthesis of fusel alcohols). Genes were selected according to Hazelwood et al. (2008).
DOI: 10.6084/m9.figshare.23617956.v1
title: <strong>Supplementary Data S8</strong> - Genes of the Ehrlich Pathway

description: Variant effect counts by SnpEff extracted from Supplementary Data S3 per genes involved in the Ehrlich pathway (biosynthesis of fusel alcohols). Genes were selected according to Hazelwood et al. (2008).
DOI: 10.5281/zenodo.8109406
title: crassadoma_gigantea_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.8109405
title: crassadoma_gigantea_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.8109398
title: Universal microbial reworking of dissolved organic matter along environmental gradients

description: Soils are losing increasing amounts of carbon annually to freshwaters as dissolved organic matter (DOM), which, if degraded, can increasingly offset their carbon sink capacity. DOM is more susceptible to degradation closer to its source and becomes increasingly dominated by the same (i.e., universal), difficult-to-degrade compounds as degradation proceeds. However, the processes underlying DOM degradation across environments are poorly understood. Here we found DOM changed similarly along soil-aquatic gradients irrespective of differences in environmental conditions. Using ultrahigh-resolution mass spectrometry, we tracked DOM along soil depths and hillslope positions in forest headwater catchments and related its composition to soil microbiomes and physico-chemical conditions. Along depths and hillslopes, carbohydrate-like and unsaturated hydrocarbon-like compounds increased in abundance-weighted mass, suggestive of microbial reworking of plant material. More than half of the variation in the abundance of these compounds was related to the expression of genes essential for degrading plant-derived carbohydrates. Our results implicate continuous microbial reworking in shifting DOM towards universal compounds in soils. By synthesising data from the land-to-ocean continuum, we suggest these processes can be generalised across ecosystems and spatiotemporal scales. Such general degradation patterns can be leveraged to predict DOM composition and its downstream reactivity along environmental gradients to inform management of soil-to-stream carbon losses.
DOI: 10.5281/zenodo.8109397
title: Universal microbial reworking of dissolved organic matter along environmental gradients

description: Soils are losing increasing amounts of carbon annually to freshwaters as dissolved organic matter (DOM), which, if degraded, can increasingly offset their carbon sink capacity. DOM is more susceptible to degradation closer to its source and becomes increasingly dominated by the same (i.e., universal), difficult-to-degrade compounds as degradation proceeds. However, the processes underlying DOM degradation across environments are poorly understood. Here we found DOM changed similarly along soil-aquatic gradients irrespective of differences in environmental conditions. Using ultrahigh-resolution mass spectrometry, we tracked DOM along soil depths and hillslope positions in forest headwater catchments and related its composition to soil microbiomes and physico-chemical conditions. Along depths and hillslopes, carbohydrate-like and unsaturated hydrocarbon-like compounds increased in abundance-weighted mass, suggestive of microbial reworking of plant material. More than half of the variation in the abundance of these compounds was related to the expression of genes essential for degrading plant-derived carbohydrates. Our results implicate continuous microbial reworking in shifting DOM towards universal compounds in soils. By synthesising data from the land-to-ocean continuum, we suggest these processes can be generalised across ecosystems and spatiotemporal scales. Such general degradation patterns can be leveraged to predict DOM composition and its downstream reactivity along environmental gradients to inform management of soil-to-stream carbon losses.
DOI: 10.34740/kaggle/dsv/6072516
title: Arabic sign language dataset
DOI: 10.6084/m9.figshare.23617911
title: <strong>Supplementary Data S7 -</strong> Pivot Table from S6

description: Pivot table based on Supplementary Data S6 summarizing counts of significantly (p_adj &lt; 0.05) associated SNPs per gene.
DOI: 10.6084/m9.figshare.23617911.v1
title: <strong>Supplementary Data S7 -</strong> Pivot Table from S6

description: Pivot table based on Supplementary Data S6 summarizing counts of significantly (p_adj &lt; 0.05) associated SNPs per gene.
DOI: 10.5281/zenodo.8109473
title: endocladia_muricata_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.8109472
title: endocladia_muricata_decontaminated_gx.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23617776
title: <strong>Supplementary Data S6</strong> - PLINK associattion testing

description: Output from association testing of individual missense variants in PLINK for the “kveik” vs “beer” phenotype. Sequence substitution and gene columns have been added from SnpEff annotation.
DOI: 10.6084/m9.figshare.21652007.v4
title: Construction of Chinese baijiu compound database using text mining and its application in assisting compound identification of liquid chromatography-high-resolution mass spectrometry data

description: Comprehensive understanding of the molecular composition in Chinese baijiu is of a great value for understanding the flavor and improving the quality. Liquid chromatography-mass spectrometry (LC-MS) is a good tool for the analysis of Chinese baijiu. However, lack of the related database makes corresponding LC-MS data difficult to be annotated. Therefore, a Chinese baijiu compound database (CBDB) containing 5709 compounds was constructed based on literatures and text mining, and further a Chinese baijiu LC-MS database (LCMS-CBDB) was built by endowing each compound with retention time, exact mass, and MS/MS spectrum. In total 468 compounds were identified in six Chinese baijiu samples by searching LCMS-CBDB. Further, database enhancement strategies were proposed based on biological transformations and theoretical homologue expansion, which allows the identification of new compounds. Four monoglycerides were successfully identified and validated using the extended CBDB, three of them were reported in baijiu for the first time.
DOI: 10.6084/m9.figshare.23617770
title: <strong>Supplementary Data S5</strong> - Gene Ontology enriched terms (MF)

description: Results from Gene Ontology enrichment analysis in SGD of the genes with at least three high-impact variants. Significant terms from the molecular function ontology.
DOI: 10.6084/m9.figshare.23617770.v1
title: <strong>Supplementary Data S5</strong> - Gene Ontology enriched terms (MF)

description: Results from Gene Ontology enrichment analysis in SGD of the genes with at least three high-impact variants. Significant terms from the molecular function ontology.
DOI: 10.6084/m9.figshare.21652007
title: Construction of Chinese baijiu compound database using text mining and its application in assisting compound identification of liquid chromatography-high-resolution mass spectrometry data

description: Comprehensive understanding of the molecular composition in Chinese baijiu is of a great value for understanding the flavor and improving the quality. Liquid chromatography-mass spectrometry (LC-MS) is a good tool for the analysis of Chinese baijiu. However, lack of the related database makes corresponding LC-MS data difficult to be annotated. Therefore, a Chinese baijiu compound database (CBDB) containing 5709 compounds was constructed based on literatures and text mining, and further a Chinese baijiu LC-MS database (LCMS-CBDB) was built by endowing each compound with retention time, exact mass, and MS/MS spectrum. In total 468 compounds were identified in six Chinese baijiu samples by searching LCMS-CBDB. Further, database enhancement strategies were proposed based on biological transformations and theoretical homologue expansion, which allows the identification of new compounds. Four monoglycerides were successfully identified and validated using the extended CBDB, three of them were reported in baijiu for the first time.
DOI: 10.6084/m9.figshare.21652007.v5
title: Construction of Chinese baijiu compound database using text mining and its application in assisting compound identification of liquid chromatography-high-resolution mass spectrometry data

description: Comprehensive understanding of the molecular composition in Chinese baijiu is of a great value for understanding the flavor and improving the quality. Liquid chromatography-mass spectrometry (LC-MS) is a good tool for the analysis of Chinese baijiu. However, lack of the related database makes corresponding LC-MS data difficult to be annotated. Therefore, a Chinese baijiu compound database (CBDB) containing 5709 compounds was constructed based on literatures and text mining, and further a Chinese baijiu LC-MS database (LCMS-CBDB) was built by endowing each compound with retention time, exact mass, and MS/MS spectrum. In total 468 compounds were identified in six Chinese baijiu samples by searching LCMS-CBDB. Further, database enhancement strategies were proposed based on biological transformations and theoretical homologue expansion, which allows the identification of new compounds. Four monoglycerides were successfully identified and validated using the extended CBDB, three of them were reported in baijiu for the first time.
DOI: 10.6084/m9.figshare.23617764
title: <strong>Supplementary Data S4: </strong>Gene Ontology enriched terms (BP)

description: Results from Gene Ontology enrichment analysis in SGD of the genes with at least three high-impact variants. Significant terms from the biological process ontology.
DOI: 10.6084/m9.figshare.23617764.v1
title: <strong>Supplementary Data S4: </strong>Gene Ontology enriched terms (BP)

description: Results from Gene Ontology enrichment analysis in SGD of the genes with at least three high-impact variants. Significant terms from the biological process ontology.
DOI: 10.6084/m9.figshare.23617749
title: <strong>Supplementary Data S3</strong> - Variant Effect Predictions Per Gene

description: Count matrix of variant effect classes per gene as predicted by SnpEff (see Materials and Methods). Gene description added from BioMart export.
DOI: 10.6084/m9.figshare.23617749.v1
title: <strong>Supplementary Data S3</strong> - Variant Effect Predictions Per Gene

description: Count matrix of variant effect classes per gene as predicted by SnpEff (see Materials and Methods). Gene description added from BioMart export.
DOI: 10.5281/zenodo.8109494
title: eupentacta_quinquesemita_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.8109493
title: eupentacta_quinquesemita_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.8109547
title: eutonina_indicans_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.8109546
title: eutonina_indicans_decontaminated_gx.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23617728
title: <strong>Supplementary Data S2</strong> - Filtered Variant Calls

description: Filtered and annotated variants with ploidy = 4 as given by GATK and annotated by SnpEff (see Materials and Methods) in VCF format.
DOI: 10.6084/m9.figshare.23617728.v1
title: <strong>Supplementary Data S2</strong> - Filtered Variant Calls

description: Filtered and annotated variants with ploidy = 4 as given by GATK and annotated by SnpEff (see Materials and Methods) in VCF format.
DOI: 10.6084/m9.figshare.23617701
title: <strong>Supplementary Data S1 </strong>- Unfiltered Variant Calls

description: Unfiltered variant calls with ploidy = 4 as given by GATK in VCF format.
DOI: 10.6084/m9.figshare.23617701.v1
title: <strong>Supplementary Data S1 </strong>- Unfiltered Variant Calls

description: Unfiltered variant calls with ploidy = 4 as given by GATK in VCF format.
DOI: 10.5281/zenodo.8109568
title: heterotrichella_gracilis_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.8109567
title: heterotrichella_gracilis_decontaminated_gx.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23606709.v1
title: Supplementary Material for: Enrichment of Immune-Related Genes in Aggressive Primary Breast Angiosarcoma: A Case Report

description: Primary breast angiosarcoma is an extremely rare disease with a poor prognosis. Primary angiosarcoma is distinct from secondary angiosarcoma, which usually occurs in patients who have been previously treated for breast cancer. The low incidence of primary breast angiosarcoma has hindered the elucidation of its etiology and potential therapies. Here, we report a case of a patient with primary breast angiosarcoma who experienced recurrence after surgery. The tumor was refractory to systemic treatments, and the patient died 18 months after the surgery. We used RNA sequencing for gene expression profiling of the tumor. A high tumor inflammation signature score indicated enrichment in immune-related signaling. CIBERSORTx, a tool used to characterize the cellular composition of complex tissues based on gene expression, indicated that the immune cells in the tumor were predominantly macrophages, and this was confirmed using immunohistochemical analysis. These findings indicate the possible use of checkpoint immunotherapy for the treatment of primary breast angiosarcoma.
DOI: 10.6084/m9.figshare.23617269
title: Beaubec_charred_plant_remains

description: CSV of data from Beaubec
DOI: 10.6084/m9.figshare.23617269.v2
title: Beaubec_charred_plant_remains

description: CSV of data from Beaubec
DOI: 10.6084/m9.figshare.23617269.v1
title: Beaubec_charred_plant_remains

description: CSV of data from Beaubec
DOI: 10.6084/m9.figshare.23606772.v1
title: Supplementary Material for: Head and Neck Solitary Fibrous Tumor Presenting as Salivary Gland Tumor: Two Case Reports and Review of the Literature

description: Solitary fibrous tumors (SFTs) are soft tumors (mesenchymal origin) that most likely develop from adult mesenchymal stem cells. SFTs are not common in the head and neck region, and the characteristics of tumors in this location are unclear. The present study describes the clinicopathological findings of 2 cases of SFTs arising in the parotid gland and buccal space, presenting as salivary gland tumors. The first case is a 76-year-old man presenting with a painless tumor on the right parotid gland who subsequently underwent partial superficial parotidectomy. According to the results of histopathological analysis, the tumor consisted of stellate and spindle-shaped cells proliferating on a mucous-like substrate. Immunohistochemical staining revealed that neoplastic cells were positive for CD34, vimentin, Bcl2, and STAT6. The second case is of a 64-year-old man presenting with a painless lump on his right cheek. Based on the findings of fine needle aspiration cytology, a tumor derived from myoepithelial cells of the minor salivary gland or a nonepithelial tumor was suspected. The patient underwent surgical resection via an intraoral approach. Histopathologically, the tumor consisted of spindle-shaped cells with rod-shaped or irregular nuclei. Immunohistochemical staining revealed that the neoplastic cells were positive for CD34, CD99, Bcl2, and STAT6. Briefly, SFT should be considered in the differential diagnosis of a well-marginalized lesion in the salivary gland and oral cavity. STAT6 immunohistochemistry is the most specific and sensitive method of diagnosing SFT. A thorough understanding of the morphological changes associated with SFT and their correlation with clinical, immunohistochemical, and molecular characteristics is important to avoid misdiagnosis.
DOI: 10.5281/zenodo.8106080
title: cgtg

description: c
DOI: 10.5281/zenodo.8106079
title: cgtg

description: c
DOI: 10.23636/fy17-kb09
title: Incunabula Printed Catalogue Dataset: Volumes 1-10

description: This dataset includes the catalogue entries derived from volumes 1-10 of the "Catalogue of books printed in the 15th century now at the British Museum" (know as BMC). The BMC was published between 1908-2007 and comprises detailed descriptions of the incunabula collection at the British Library. The dataset was created as part of an AHRC-RLUK Professional Practice Fellowship project to enable computational analysis with the catalogue descriptions and to encourage further reuse of the descriptions in online resources and in digital scholarship.
description: The dataset was created using automated layout analysis, text recognition and catalogue entry detection. Transkribus was used to train a structure model for the pages with catalogue entries and the code used for the entry detection was developed by Isaac Dunford and improved by Harry Lloyd. More information is available at https://github.com/britishlibrary/Incunabula-Catalogue-Entry-Detection . The dataset includes the raw and processed data outputs as described in the readme file. The text is released under CC0 1.0 Universal Public Domain and the images are released under CC-BY 4.0 license. Contact us at digitalresearch@bl.uk if you have questions, or to let us know how you used our data.
description: UK
DOI: 10.5281/zenodo.7333241
title: Data

description: soil data
DOI: 10.5281/zenodo.7333240
title: Data

description: soil data
DOI: 10.6084/m9.figshare.22726298
title: Anomaly Detection in Microservices-based Systems

description: This repository contains two datasets used for anomaly detection in microservices-based systems. The datasets are summarized versions of several CSV files containing data from normal and anomalous instances. The two datasets provided here are representative of service and application anomalies. For more detailed information, please refer to the README file included in the repository.
DOI: 10.5281/zenodo.8109538
title: Amino sugars and neutral sugars in the biomass of different taxa

description: Amino sugar and neutra sugar necromass biomarkers in the biomass of archaea, bacteria, fungi and plant species.
DOI: 10.5281/zenodo.8109539
title: Amino sugars and neutral sugars in the biomass of different taxa

description: Amino sugar and neutra sugar necromass biomarkers in the biomass of archaea, bacteria, fungi and plant species.
DOI: 10.6084/m9.figshare.22820843
title: Supplementary Material for: Intracranial stenosis treated with stenting in patient with suspected cerebral vasculitis: two case reports.

description: Central nervous system vasculitis (CNSV) is an uncommon and poorly understood form of vasculitis. Early recognition is important because medical treatment might improve the outcome. However, randomized clinical trials on CNSV treatment do not exist. Endovascular treatment has been reported in few cases, but no data exist for intracranial stenting. We report two cases of patients with suspected CNSV and recurrent clinical episodes, treated with intracranial stenting. A 48-year-old man had relapsing episodes of right hemiparesis. Neuroradiological exams showed severe left carotid terminus stenosis. Despite immunosuppressive therapy, neuroradiological follow-up exams showed a worsening of the aforementioned stenosis with many transient episodes of weakness in the right limbs and aphasia. A 64-year-old woman had a sudden onset of dysarthria and transient aphasia. Neuroradiological exams showed a severe arterial stenosis involving the origin of left ACA and MCA. Despite dual antiplatel therapy she presented an acute onset of severe aphasia, due to an occlusion of the left carotid terminus and proximal MCA. In both cases endovascular procedure and intracranial stenting was performed, with marked improvement of cerebral blood flow. No more clinical episodes were reported. Intracranial stenting may be a valid therapeutic option in selected patients with CNSV and involvement of medium or large size vessels with clinical worsening despite best medical treatment.
DOI: 10.6084/m9.figshare.22820843.v1
title: Supplementary Material for: Intracranial stenosis treated with stenting in patient with suspected cerebral vasculitis: two case reports.

description: Central nervous system vasculitis (CNSV) is an uncommon and poorly understood form of vasculitis. Early recognition is important because medical treatment might improve the outcome. However, randomized clinical trials on CNSV treatment do not exist. Endovascular treatment has been reported in few cases, but no data exist for intracranial stenting. We report two cases of patients with suspected CNSV and recurrent clinical episodes, treated with intracranial stenting. A 48-year-old man had relapsing episodes of right hemiparesis. Neuroradiological exams showed severe left carotid terminus stenosis. Despite immunosuppressive therapy, neuroradiological follow-up exams showed a worsening of the aforementioned stenosis with many transient episodes of weakness in the right limbs and aphasia. A 64-year-old woman had a sudden onset of dysarthria and transient aphasia. Neuroradiological exams showed a severe arterial stenosis involving the origin of left ACA and MCA. Despite dual antiplatel therapy she presented an acute onset of severe aphasia, due to an occlusion of the left carotid terminus and proximal MCA. In both cases endovascular procedure and intracranial stenting was performed, with marked improvement of cerebral blood flow. No more clinical episodes were reported. Intracranial stenting may be a valid therapeutic option in selected patients with CNSV and involvement of medium or large size vessels with clinical worsening despite best medical treatment.