cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8100128.v2
title: Epigenome modulated xenobiotic detoxification pathways control DMBA-induced breast cancer in agouti A<sup>vy</sup>/a mice

description: Environmental xenobiotics with genotoxic activity are carcinogenic. However, individual differences in the susceptibility to xenobiotic-induced breast cancer remain unclear. Since epigenetic modifications could control the expression of metabolic enzymes, our goal was to determine whether epigenome modulated metabolic networks determine susceptibility to xenobiotic-induced breast cancer. The effect of epigenetic background on predisposition to carcinogen 7,12-dimethylbenz(a)anthracene (DMBA)-induced breast cancer development and progression was assessed using the A<sup>vy</sup>/a mouse model. In a randomized block design, 22 isogenic A<sup>vy</sup>/a (8 yellow, 7 slightly mottled, 7 pseudoagouti) and 8 wild type non-agouti (a/a black) age matched female mice were subjected to DMBA (30 mg/kg per mouse weight) once a week for 6 weeks to induce breast cancer. Compared to pseudoagouti littermates, a significant decrease in tumour latency with increased tumour burden was observed in slightly mottled and yellow littermates (<i>p</i> ≤ 0.05). However, tumour latency and tumour burden were similar in non-agouti a/a mice and A<sup>vy</sup>/a cohorts. Network analysis of differentially expressed liver genes identified altered metabolic gene networks among agouti phenotypes. Consequently, in HPLC analyses, DMBA metabolites were significantly increased in A<sup>vy</sup>/a pseudoagouti mice (<i>p</i> ≤ 0.05). Relative to A<sup>vy</sup>/a slightly mottled, A<sup>vy</sup>/a yellow and non-agouti a/a black mice, DMBA metabolites increased nine-, eight-, and four-fold, respectively, in A<sup>vy</sup>/a pseudoagouti mice. In agreement with this, seven phase 2 xenobiotic detoxification genes were significantly upregulated in A<sup>vy</sup>/a pseudoagouti mice (<i>p</i> ≤ 0.05). The Results from this study suggest that epigenome modulation of xenobiotic detoxification pathways may control xenobiotic-induced breast cancer susceptibility in A<sup>vy</sup>/a mice.
DOI: 10.6084/m9.figshare.8100050
title: Stereo-video, length estimate, and camera calibration data from Eyes on the size: accuracy of visual length estimates of white sharks, <i>Carcharodon carcharias</i>

description: Visual estimates have been used extensively to determine the length of large organisms that are logistically challenging to measure. However, there has been little effort to quantify the accuracy or validity of this technique despite inaccurate size estimates leading to incorrect population assessments and misinformed management strategies. Here, we compared visually estimated total length measurements of white sharks, <i>Carcharodon carcharias</i>, during cage-diving operations with measurements obtained from stereo-video cameras and assessed the accuracy of those estimates in relation to suspected biases (shark size, and observer experience and gender) using generalized linear mixed models and linear regressions. Observer experience on board cage-diving vessels had the greatest effect on the accuracy of visual length estimates, with <i>scientists</i> being more accurate (mean accuracy ± standard error: 23.0 ± 16.5 cm) than <i>crew</i> (39.9 ± 33.8 cm) and <i>passengers</i> (49.4 ± 38.5 cm). Observer gender and shark size had no impact on the overall accuracy of visual length estimates, but <i>passengers</i> overestimated sharks less than 3 m and underestimated sharks greater than 3 m. Our findings show that experience measuring animals is the most substantial driver of accurate visual length estimates regardless of the amount of exposure to the species being measured. <i>Scientists</i> were most accurate, even though <i>crew</i> observes white sharks more frequently. Our results show that visual length estimates are not impacted by shark size and are a valid measurement tool for many aspects of <i>C. carcharias</i> research, provided they come from people who have previously been involved in measuring animals, i.e. <i>scientists</i>.
DOI: 10.6084/m9.figshare.8100128.v1
title: Epigenome modulated xenobiotic detoxification pathways controls DMBA-induced breast cancer in agouti A<sup>vy</sup>/a mice

description: Environmental xenobiotics with genotoxic activity are carcinogenic. However, individual differences in the susceptibility to xenobiotic-induced breast cancer remain unclear. Since epigenetic modifications could control the expression of metabolic enzymes, our goal was to determine whether epigenome modulated metabolic networks determine susceptibility to xenobiotic-induced breast cancer. The effect of epigenetic background on predisposition to carcinogen 7,12-dimethylbenz(a)anthracene (DMBA)-induced breast cancer development and progression was assessed using the A<sup>vy</sup>/a mouse model. In a randomized block design, 22 isogenic A<sup>vy</sup>/a (8 yellow, 7 slightly mottled, 7 pseudoagouti) and 8 wild type non-agouti (a/a black) age matched female mice were subjected to DMBA (30 mg/kg per mouse weight) once a week for 6 weeks to induce breast cancer. Compared to pseudoagouti littermates, a significant decrease in tumour latency with increased tumour burden was observed in slightly mottled and yellow littermates (<i>p</i> ≤ 0.05). However, tumour latency and tumour burden were similar in non-agouti a/a mice and A<sup>vy</sup>/a cohorts. Network analysis of differentially expressed liver genes identified altered metabolic gene networks among agouti phenotypes. Consequently, in HPLC analyses, DMBA metabolites were significantly increased in A<sup>vy</sup>/a pseudoagouti mice (<i>p</i> ≤ 0.05). Relative to A<sup>vy</sup>/a slightly mottled, A<sup>vy</sup>/a yellow and non-agouti a/a black mice, DMBA metabolites increased nine-, eight-, and four-fold, respectively, in A<sup>vy</sup>/a pseudoagouti mice. In agreement with this, seven phase 2 xenobiotic detoxification genes were significantly upregulated in A<sup>vy</sup>/a pseudoagouti mice (<i>p</i> ≤ 0.05). The Results from this study suggest that epigenome modulation of xenobiotic detoxification pathways may control xenobiotic-induced breast cancer susceptibility in A<sup>vy</sup>/a mice.
DOI: 10.6084/m9.figshare.8100050.v1
title: Stereo-video, length estimate, and camera calibration data from Eyes on the size: accuracy of visual length estimates of white sharks, <i>Carcharodon carcharias</i>

description: Visual estimates have been used extensively to determine the length of large organisms that are logistically challenging to measure. However, there has been little effort to quantify the accuracy or validity of this technique despite inaccurate size estimates leading to incorrect population assessments and misinformed management strategies. Here, we compared visually estimated total length measurements of white sharks, <i>Carcharodon carcharias</i>, during cage-diving operations with measurements obtained from stereo-video cameras and assessed the accuracy of those estimates in relation to suspected biases (shark size, and observer experience and gender) using generalized linear mixed models and linear regressions. Observer experience on board cage-diving vessels had the greatest effect on the accuracy of visual length estimates, with <i>scientists</i> being more accurate (mean accuracy ± standard error: 23.0 ± 16.5 cm) than <i>crew</i> (39.9 ± 33.8 cm) and <i>passengers</i> (49.4 ± 38.5 cm). Observer gender and shark size had no impact on the overall accuracy of visual length estimates, but <i>passengers</i> overestimated sharks less than 3 m and underestimated sharks greater than 3 m. Our findings show that experience measuring animals is the most substantial driver of accurate visual length estimates regardless of the amount of exposure to the species being measured. <i>Scientists</i> were most accurate, even though <i>crew</i> observes white sharks more frequently. Our results show that visual length estimates are not impacted by shark size and are a valid measurement tool for many aspects of <i>C. carcharias</i> research, provided they come from people who have previously been involved in measuring animals, i.e. <i>scientists</i>.
DOI: 10.6084/m9.figshare.8099927
title: Danish DSL and Reddit word2vec word embeddings

description: The zip contains word2vec word embeddings trained on danish reddit sentences and danish DSL (https://dsl.dk/) sentences.
DOI: 10.6084/m9.figshare.8099924
title: Supplementary Material for: Whole-Genome Sequencing and Genomic Analysis of a Virulent Bacteriophage Infecting <b><i>Bacillus cereus</i></b>

description: <b><i>Objective:</i></b> Infants with a weak immune system are prone to infection with <i>Bacillus cereus</i>, which is commonly found in natural environments. With the aim of achieving better control of this pathogenic bacterium, in the present study we characterized a new bacteriophage, ΦBC01. <b><i>Methods:</i></b> Bacteriophage particles were analyzed by transmission electron microscopy. Factors influencing adsorption were identified in a double-layer plaque assay. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was conducted to determine the size of major structural proteins. The complete genome of the phage was analyzed. <b><i>Results:</i></b> Bacteriophage particles (105.3 ± 3.1 nm icosahedral head and 208.8 ± 3.6 nm contractile tail) were identified as Myoviridae. ΦBC01 was found to have host specificity to <i>B. cereus</i>. Major structural proteins of ΦBC01 showed 2 well-pronounced bands of 99 and 56 kDa. The 158,385-bp genome sequence of ΦBC01 was determined: 56 of the 239 open reading frames were annotated, indicating involvement in bacteriophage DNA manipulation, cell lysis, packaging, virion structure, and other functions. <b><i>Conclusion:</i></b> Because of characterization and genotyping of a new bacteriophage from soil samples containing earthworms, this study provides a baseline for the development of alternatives to antibiotics.
DOI: 10.6084/m9.figshare.8099909
title: Supplementary Material for: Tropomyosin-Related Kinase Receptor and Neurotrophin Expression in Cutaneous Melanoma Is Associated with a Poor Prognosis and Decreased Survival

description: <b><i>Objective:</i></b> Normally, activation of tropomyosin-related kinase (TRK) receptors by neurotrophins (NTs) stimulates intracellular pathways involved in cell survival and proliferation. Dysregulation of NT/TRK signaling may affect neoplasm prognosis. Data on NT and TRK expression in melanomas are limited, and it is unclear whether NT/TRK signaling pathways are involved in the origin and progression of this neoplasm. <b><i>Methods:</i></b> We examined whether NT/TRK expression differs across different cutaneous melanoma grades and subtypes, and whether it is associated with melanoma prognosis and survival. A cross-sectional study was performed in which the expression of TrkA, TrkB, nerve growth factor (NGF), and brain-derived neurotrophic factor (BDNF) was analyzed by immunohistochemistry of 154 melanoma samples. We investigated NT/TRK expression associations with prognostic factors for melanoma, relapse-free survival (RFS), and overall survival (OS). <b><i>Results:</i></b> Of the 154 melanoma samples, 77 (55.4%) were TrkA immunopositive, 81 (58.3%) were TrkB immunopositive, 113 (81.3%) were BDNF immunopositive, and 104 (75.4%) were NGF immunopositive. We found NT/TRK expression associated strongly with several clinical prognostic factors, including the tumor-node-metastasis stage (<i>p</i> &lt; 0.001), histological subtype (<i>p</i> &lt; 0.001), and Clark level (<i>p</i> &lt; 0.05), as well as with a worse OS (<i>p</i> &lt; 0.05 for all, except TrkB) and RFS (<i>p</i> &lt; 0.05 for all). <b><i>Conclusions:</i></b> Our results show strong associations of NT/TRK expression with melanoma stage progression and a poor prognosis.
DOI: 10.6084/m9.figshare.8099927.v1
title: Danish DSL and Reddit word2vec word embeddings

description: The zip contains word2vec word embeddings trained on danish reddit sentences and danish DSL (https://dsl.dk/) sentences.
DOI: 10.6084/m9.figshare.8099891
title: The uigenes resulting from asparagus bean RNA-seq

description: The uigenes resulting from asparagus bean RNA-seq
DOI: 10.6084/m9.figshare.8099891.v1
title: The uigenes resulting from asparagus bean RNA-seq

description: The uigenes resulting from asparagus bean RNA-seq
DOI: 10.6084/m9.figshare.8099753
title: Raman scattering excited with 532 nm laser in bisphenol “AF” and its connection with bisphenol “A” and “S”

description: Bisphenol “AF,” a chemically similar replacement substitute for Bisphenol “A” which is a widespread environmental hormone, is studied by Raman spectroscopy (250–3500 cm<sup>–1</sup>). Experimentally observed scattering peaks are illuminated by Density Functional Theory calculations. Principal component analysis is executed on the experimental Raman spectra of Bisphenol “AF” together with spectra of Bisphenol “A” and “S” reported earlier. Eight correlating molecular frequencies of Bisphenol “AF,” “A,” and “S” are found in contrast to 12 such frequencies of Bisphenol “A” and “S” only. The refined list of correlating frequencies manifests the existence of correlation in bisphenol family and clue toward their grouping, identification, detection, and screening together with mechanism responsible for toxicity.
DOI: 10.6084/m9.figshare.8099768
title: Histological fissure findings

description: Dataset of the histological findings.
DOI: 10.6084/m9.figshare.8099753.v1
title: Raman scattering excited with 532 nm laser in bisphenol “AF” and its connection with bisphenol “A” and “S”

description: Bisphenol “AF,” a chemically similar replacement substitute for Bisphenol “A” which is a widespread environmental hormone, is studied by Raman spectroscopy (250–3500 cm<sup>–1</sup>). Experimentally observed scattering peaks are illuminated by Density Functional Theory calculations. Principal component analysis is executed on the experimental Raman spectra of Bisphenol “AF” together with spectra of Bisphenol “A” and “S” reported earlier. Eight correlating molecular frequencies of Bisphenol “AF,” “A,” and “S” are found in contrast to 12 such frequencies of Bisphenol “A” and “S” only. The refined list of correlating frequencies manifests the existence of correlation in bisphenol family and clue toward their grouping, identification, detection, and screening together with mechanism responsible for toxicity.
DOI: 10.6084/m9.figshare.8099768.v1
title: Histological fissure findings

description: Dataset of the histological findings.
DOI: 10.6084/m9.figshare.8099741
title: Waitrose_Reductions

description: Shows the reductions by line by time by location for Waitrose
DOI: 10.6084/m9.figshare.8099732
title: Location_data

description: This is the branch data for Waitrose as of 09-05-2019
DOI: 10.6084/m9.figshare.8099732.v1
title: Location_data

description: This is the branch data for Waitrose as of 09-05-2019
DOI: 10.6084/m9.figshare.8099741.v2
title: Waitrose_Reductions

description: Shows the reductions by line by time by location for Waitrose
DOI: 10.6084/m9.figshare.8099741.v1
title: Waitrose_Reductions

description: Shows the reductions by line by time by location for Waitrose
DOI: 10.26180/5cd3bef20b8f8
title: LSB Database.xlsx

description: The Global Long-Span Bridge database
DOI: 10.6084/m9.figshare.8099660
title: MOESM1 of Immune response profile of caruncular and trophoblast cell lines infected by high- (Nc-Spain7) and low-virulence (Nc-Spain1H) isolates of Neospora caninum

description: Additional file 1:Table S1. Statistical test results for mRNA expression levels. Table S2. Statistical test results for protein secretion.
DOI: 10.6084/m9.figshare.8099660.v1
title: MOESM1 of Immune response profile of caruncular and trophoblast cell lines infected by high- (Nc-Spain7) and low-virulence (Nc-Spain1H) isolates of Neospora caninum

description: Additional file 1:Table S1. Statistical test results for mRNA expression levels. Table S2. Statistical test results for protein secretion.
DOI: 10.6084/m9.figshare.8099603
title: MOESM2 of Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls

description: Additional file 2: Table S2. Proteins from CD8+ T cells differentially expressed in MS patients and healthy controls. The table displays proteins (n = 195) that are differentially expressed in CD8+ T cells from MS patients compared to healthy controls (p
DOI: 10.6084/m9.figshare.8099603.v1
title: MOESM2 of Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls

description: Additional file 2: Table S2. Proteins from CD8+ T cells differentially expressed in MS patients and healthy controls. The table displays proteins (n = 195) that are differentially expressed in CD8+ T cells from MS patients compared to healthy controls (p
DOI: 10.6084/m9.figshare.8099597
title: MOESM1 of Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls

description: Additional file 1: Table S1. Proteins from CD4+ T cells differentially expressed in MS patients and healthy controls. The table displays proteins (n = 228) that are differentially expressed in CD4+ T cells from MS patients compared to healthy controls (p
DOI: 10.6084/m9.figshare.8099597.v1
title: MOESM1 of Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls

description: Additional file 1: Table S1. Proteins from CD4+ T cells differentially expressed in MS patients and healthy controls. The table displays proteins (n = 228) that are differentially expressed in CD4+ T cells from MS patients compared to healthy controls (p
DOI: 10.6084/m9.figshare.8099543
title: Additional file 6: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S6. Names and accession numbers for 21 Basidiomycota species downloaded from GenBank and used for phylogenetic analysis. (XLSX 9â kb)
DOI: 10.6084/m9.figshare.8099543.v1
title: Additional file 6: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S6. Names and accession numbers for 21 Basidiomycota species downloaded from GenBank and used for phylogenetic analysis. (XLSX 9â kb)
DOI: 10.25934/00003513.0
title: Available IPD datapackage for study 'A Randomised Double-blind, Active-controlled Parallel Group Efficacy and Safety Study of BI 1356 ( 5.0 mg, Administered Orally Once Daily) Compared to Glimepiride Over Two Years in Type 2 Diabetic Patients With Insufficient Glycaemic Control Despite Metformin Therapy'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00003513.1
title: IPD datapackage for study 'A Randomised Double-blind, Active-controlled Parallel Group Efficacy and Safety Study of BI 1356 ( 5.0 mg, Administered Orally Once Daily) Compared to Glimepiride Over Two Years in Type 2 Diabetic Patients With Insufficient Glycaemic Control Despite Metformin Therapy' and research request: 'Stratification of SGLT2 inhibitor glucose lowering therapy in Type 2 diabetes'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.6084/m9.figshare.8099522
title: Additional file 3: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S3. Comparison of codon usage of 14 oxidative phosphorylation genes and the codon-anticodon recognition pattern of tRNA genes identified in A. borealis, A. gallica, A. sinapina, and A. solidipes. The number of plus signs indicates the presence and numbers of the respective tRNA gene. (XLSX 17â kb)
DOI: 10.6084/m9.figshare.8099525
title: Additional file 4: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S4. Classification of introns in mitogenomes of four Armillaria species. (XLSX 9â kb)
DOI: 10.6084/m9.figshare.8099522.v1
title: Additional file 3: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S3. Comparison of codon usage of 14 oxidative phosphorylation genes and the codon-anticodon recognition pattern of tRNA genes identified in A. borealis, A. gallica, A. sinapina, and A. solidipes. The number of plus signs indicates the presence and numbers of the respective tRNA gene. (XLSX 17â kb)
DOI: 10.6084/m9.figshare.8099525.v1
title: Additional file 4: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S4. Classification of introns in mitogenomes of four Armillaria species. (XLSX 9â kb)
DOI: 10.6084/m9.figshare.8099507
title: Additional file 2: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S2. Microsatellite or simples equence repeat (SSR) loci in four Armillaria mitogenomes. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.8099519
title: Additional file 2: of In silico modeling of phosphorylation dependent and independent c-Myc degradation

description: This file contains software specific codes for all the analysis performed inÂ this study including the codes for the two combined models in a pfd format. (RAR 10429 kb)
DOI: 10.6084/m9.figshare.8099519.v1
title: Additional file 2: of In silico modeling of phosphorylation dependent and independent c-Myc degradation

description: This file contains software specific codes for all the analysis performed inÂ this study including the codes for the two combined models in a pfd format. (RAR 10429 kb)
DOI: 10.6084/m9.figshare.8099507.v1
title: Additional file 2: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S2. Microsatellite or simples equence repeat (SSR) loci in four Armillaria mitogenomes. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.8099501
title: Additional file 1: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S1. Tandem repeats detected in four Armillaria mitogenomes using Tandem Repeats Finder. (XLSX 14â kb)