cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10046615
title: Dataset related to article "Exploring the CXCR4/CXCR7/CXCL12 Axis in Primary Desmoid Tumors"

description: This record contains raw data related to article "Exploring the CXCR4/CXCR7/CXCL12 Axis in Primary Desmoid Tumors"
Background: Desmoid tumors have an extremely variable natural history. The uncertainty behind desmoid behavior reflects the complexity, which subtends its development and non-linear advancement. Apart from Wnt-βcatenin mutation, estrogen receptors, and COX-2 overexpression, little is known about the ability of desmoids to grow and recur while being unable to metastasize. Several tumors have been shown to express the CXCR4/CXCR7/CXCL12 axis, whose functions are essential for tumoral development.
Aims: This study aimed to investigate the expression of the CXCR4/CXCR7/CXCL12 axis in primary desmoid tumors and discuss the potential role of this key-signaling as an antiangiogenic therapeutic strategy.
Method: In this study, 3 μm-thick consecutive sections from each formalin-fixed and paraffin-embedded tissue block were treated with mouse monoclonal antibodies developed against CD34, CXCR4, CXCR7, and CXCL12.
Results: Two distinct vessel populations: CXCR4+ and CXCR4- vessels, have been found. Similarly, chemokine receptor CXCR7 expression in the entire desmoid tumor series positively stained a portion of tumor-associated vessels, identifying two distinct subpopulations of vessels: CXCR7+ and CXCR7- vessels. All 8 neoplastic tissue samples expressed CXCL12. Immunohistochemical positivity was identified in both stromal and endothelial vascular cells. Compared to CXCR4 and CXCR7, the vast majority of tumor-associated vessels were found to express this chemokine.
Conclusion: It is the first time, as per our knowledge, that CXCR4/CXCR7/CXCL12 axis expression has been identified in a desmoid type-fibromatosis series. CXCL12 expression by neoplastic cells, together with CXCR4 and CXCR7 expression by a subgroup of tumor-associated vessels, was detected in all desmoid tumor tissue samples examined. Since chemokines are known contributors to neovascularization, CXCR4/CXCR7/CXCL12 axis may play a role in angiogenesis in this soft-tissue tumor histotype, thereby supporting its growth.
DOI: 10.5281/zenodo.10046616
title: Dataset related to article "Exploring the CXCR4/CXCR7/CXCL12 Axis in Primary Desmoid Tumors"

description: This record contains raw data related to article "Exploring the CXCR4/CXCR7/CXCL12 Axis in Primary Desmoid Tumors"
Background: Desmoid tumors have an extremely variable natural history. The uncertainty behind desmoid behavior reflects the complexity, which subtends its development and non-linear advancement. Apart from Wnt-βcatenin mutation, estrogen receptors, and COX-2 overexpression, little is known about the ability of desmoids to grow and recur while being unable to metastasize. Several tumors have been shown to express the CXCR4/CXCR7/CXCL12 axis, whose functions are essential for tumoral development.
Aims: This study aimed to investigate the expression of the CXCR4/CXCR7/CXCL12 axis in primary desmoid tumors and discuss the potential role of this key-signaling as an antiangiogenic therapeutic strategy.
Method: In this study, 3 μm-thick consecutive sections from each formalin-fixed and paraffin-embedded tissue block were treated with mouse monoclonal antibodies developed against CD34, CXCR4, CXCR7, and CXCL12.
Results: Two distinct vessel populations: CXCR4+ and CXCR4- vessels, have been found. Similarly, chemokine receptor CXCR7 expression in the entire desmoid tumor series positively stained a portion of tumor-associated vessels, identifying two distinct subpopulations of vessels: CXCR7+ and CXCR7- vessels. All 8 neoplastic tissue samples expressed CXCL12. Immunohistochemical positivity was identified in both stromal and endothelial vascular cells. Compared to CXCR4 and CXCR7, the vast majority of tumor-associated vessels were found to express this chemokine.
Conclusion: It is the first time, as per our knowledge, that CXCR4/CXCR7/CXCL12 axis expression has been identified in a desmoid type-fibromatosis series. CXCL12 expression by neoplastic cells, together with CXCR4 and CXCR7 expression by a subgroup of tumor-associated vessels, was detected in all desmoid tumor tissue samples examined. Since chemokines are known contributors to neovascularization, CXCR4/CXCR7/CXCL12 axis may play a role in angiogenesis in this soft-tissue tumor histotype, thereby supporting its growth.
DOI: 10.6084/m9.figshare.24116619.v1
title: An inorganic mineral-based protocell with prebiotic radiation fitness

description: The dataset contains all the source data of the figures in this manuscript.
DOI: 10.6084/m9.figshare.24116619
title: An inorganic mineral-based protocell with prebiotic radiation fitness

description: The dataset contains all the source data of the figures in this manuscript.
DOI: 10.6084/m9.figshare.24354346.v1
title: Investigation of a Novel Monoclonal Antibody CSX-1004 for Fentanyl Overdose

description: Raw data from pharmacological testing of anti-fentanyl human IgG1 monoclonal antibody CSX-1004 including opioid binding kinetics, mAb pharmacokinetics in rats and monkeys, mouse antinociception and respiratory depression, squirrel monkey respiratory depression, operant responding and antinociception, anti-drug antibody testing in rats and human tissue cross-reactivity testing.
DOI: 10.6084/m9.figshare.24354346
title: Investigation of a Novel Monoclonal Antibody CSX-1004 for Fentanyl Overdose

description: Raw data from pharmacological testing of anti-fentanyl human IgG1 monoclonal antibody CSX-1004 including opioid binding kinetics, mAb pharmacokinetics in rats and monkeys, mouse antinociception and respiratory depression, squirrel monkey respiratory depression, operant responding and antinociception, anti-drug antibody testing in rats and human tissue cross-reactivity testing.
DOI: 10.25345/c5j38kv0s
title: MassIVE MSV000093581 - Comparison of glioblastoma cell culture platforms based on transcriptional similarity with paired tissue
title: In this study, we isolated GBM TSs and extracellular matrices (ECM) from tissues obtained from newly diagnosed IDH1 wild-type GBM patients, and cultured GBM TSs on five different culture platforms: (1) ordinary TS culture liquid media (LM), (2) collagen-based three-dimensional (3D) matrix, (3) patient normal ECM-based 3D matrix, (4) patient tumor ECM-based 3D matrix, and (5) mouse brain. To evaluate each culture platform, we obtained transcriptome data of all cultured GBM TSs using microarrays. The LM platform exhibited the most similar transcriptional program to paired tissues based on the four aspects, including GBM genes, stemness- and invasiveness-related genes, transcription factor activity, and canonical signaling pathways. GBM TSs can be cultured via an easy-to-handle, cost-efficient, and time-saving LM platform while preserving the transcriptional program of the originating tissues without supplementing artificially manipulated or patient-derived ECM or embedding into the mouse brain to imitate the tumor microenvironment of brain. In addition to applications in basic cancer research, GBM TSs cultured in LM may also serve as patient avatars in drug screening and pre-clinical evaluation of targeted therapy, and may function as a standardized and clinically relevant model for precision medicine owing to its scalability and reproducibility.
DOI: 10.6084/m9.figshare.24289690
title: Wood-based Superblack

description: This file contains all data regarding the Wood-based superblack manuscript.
DOI: 10.6084/m9.figshare.24289690.v1
title: Wood-based Superblack

description: This file contains all data regarding the Wood-based superblack manuscript.
DOI: 10.6084/m9.figshare.22756688.v1
title: Environmental modulation of global epistasis is governed by effective genetic interactions

description: Data correspond to the growth rates of a set of alleles in the presence of two different antifolate drugs: pyrimethamine and cycloguanil
DOI: 10.6084/m9.figshare.22756688
title: Environmental modulation of global epistasis is governed by effective genetic interactions

description: Data correspond to the growth rates of a set of alleles in the presence of two different antifolate drugs: pyrimethamine and cycloguanil
DOI: 10.6084/m9.figshare.23822754
title: National genomic surveillance integrating standardized quantitative susceptibility testing clarifies antimicrobial resistance in Enterobacterales

description: Source Data and Supplementary Dataset 1-6
DOI: 10.6084/m9.figshare.23822754.v1
title: National genomic surveillance integrating standardized quantitative susceptibility testing clarifies antimicrobial resistance in Enterobacterales

description: Source Data and Supplementary Dataset 1-6
DOI: 10.6084/m9.figshare.23250995
title: Prostate cancer genetic risk and associated aggressive disease in men of African ancestry

description: Supplementary Table 1. Summary of clinical information for 113 South African men with prostate cancer where deep sequence data was available (Jaratlerdsiri et al., 2022). Supplementary Table 2. Summary of clinical information for the exome study population. PSA, prostate-specific antigen; ISUP, International Society of Urological Pathology. Supplementary Table 3. Number of SNPs and proportion (out of 247,780 assayed variants) per minor allele frequency (MAF) interval for 780 samples genotyped on the Illumina HumanExome BeadChip v1.0 array, prior to and post-processing of rare variants (MAF£0.01) with zCall v3.4 (Goldstein et al., 2012). Supplementary Table 4. Risk allele frequency (RAF) in our South African population (sequence data and exome array data where available) compared to previously reported RAF in African ancestry controls (N=61,620) (Chen et al., 2023). Supplementary Table 5. Risk allele frequency (RAF) in our South African population (N=113) for the top 136 associated variants from the Uganda prostate cancer GWAS study (UGPCS) (Du et al., 2018) and for the African Ancestry prostate cancer study (AAPC) which were reported by Du et al., 2018. None of these variants were genotyped in the exome array. Supplementary Table 6. Risk allele frequencies (RAF) for the top 30 associated variants from the Ghana GWAS study (Cook et al., 2014) in South African PCa sequenced cases, and for the samples genotyped on the exomic array, where available. Supplementary Table 7. Risk allele frequencies, odds ratios (OR), and P-values for 397 known cancer variants out out of 2477 previously summarised (Harlemon et al., 2020) that were available on the exomic array. Supplementary Table 8. Genes significantly associated to PCa in the rare variant gene-based analysis, and the frequencies of each set of genotypes in cases compared to controls, as well as predicted consequences of each variant. Supplementary Table 9. Genes significantly associated to PCa in the gene-based analysis including common and rare variants, and the frequencies of each set of genotypes in cases compared to controls, as well as predicted consequences of each variant. Supplementary Table 10. Genes significantly associated to HRPCa in the gene-based analysis including common and rare variants, and the frequencies of each set of genotypes in cases compared to controls, as well as predicted consequences of each variant.
DOI: 10.5281/zenodo.10275882
title: REMIND SSP2-PkBudg1150 ei38 unfold datapackage
DOI: 10.5281/zenodo.10275883
title: REMIND SSP2-PkBudg1150 ei38 unfold datapackage
DOI: 10.6084/m9.figshare.24754047
title: Supplementary Material for: Clinical characteristics of pathogenic ACAN variants and 3-year response to growth hormone treatment: real-world data

description: Introduction Heterozygous variants in the ACAN gene may underlie disproportionate short stature with characteristically accelerated bone age (BA) maturation and/or early-onset osteoarthritis (OA). Methods To describe phenotype, analyze genotype-phenotype correlations and assess the response of growth hormone (GH) treatment in children with a heterozygous ACAN variant. Thirty-six subjects (23 boys, 13 girls) with ACAN-deficiency and treated for ≥1 year with GH were identified in the Dutch National Registry of GH treatment in children. Results We identified 25 different heterozygous ACAN variants in 36 subjects. Median (IQR) height SDS at start of GH was -2.6 SDS (-3.2 to -2.2). Characteristic features such as disproportion, advanced BA, early-onset OA and dysmorphic features like midface hypoplasia and brachydactyly were present in the majority of children, but in ~20% no specific features were reported. Subjects with a truncating ACAN variant had a shorter height SDS compared to subjects with a non-truncating variant (-2.8 SDS and -2.1 SDS respectively, P=0.002). After 3 years of GH, height gain SDS in prepubertal children was 1.0 SDS (0.9 to 1.4). In pubertal children, height SDS remained relatively stable. Conclusion The phenotype of subjects with pathogenic heterozygous ACAN variants is highly variable and genetic testing for ACAN-deficiency should be considered in any child with significant short stature, even in the absence of disproportion, specific dysmorphic features or bone-age advancement. Furthermore, children with ACAN-deficiency may benefit from GH with a modest but significant response, which is sustained during 3 years of treatment.
DOI: 10.34740/kaggle/dsv/7136411
title: OnlineFree
DOI: 10.34740/kaggle/dsv/7136410
title: AutoXGB
DOI: 10.5281/zenodo.10275875
title: Dataset for ESS microzonation study
title: Inegol seismic, resistivity, drilling data
DOI: 10.5281/zenodo.10275788
title: the supplementary of Novel plastid genome characteristics in Fugacium kawagutii and accelerated evolution of plastid proteins in dinoflagellates
DOI: 10.5281/zenodo.10275789
title: the supplementary of Novel plastid genome characteristics in Fugacium kawagutii and accelerated evolution of plastid proteins in dinoflagellates
DOI: 10.5281/zenodo.8347217
title: Integrated disturbance mapping over the Tibetan Plateau based on multiple detection algorithms

description: This dataset contains the mapped representation of vegetation disturbance across the Tibetan Plateau, rendered at a 30-meter spatial resolution. The dataset comprehensively illustrates the extent of vegetation disturbance on the Tibetan Plateau during the period spanning 1986 to 2020. Notably, the map employs a categorization system, with values assigned to distinct classes: 0 denotes areas of disturbed vegetation, 1 denotes regions characterized by undisturbed vegetation, and 2 denotes zones devoid of vegetation.
DOI: 10.5281/zenodo.8347218
title: Integrated disturbance mapping over the Tibetan Plateau based on multiple detection algorithms

description: This dataset contains the mapped representation of vegetation disturbance across the Tibetan Plateau, rendered at a 30-meter spatial resolution. The dataset comprehensively illustrates the extent of vegetation disturbance on the Tibetan Plateau during the period spanning 1986 to 2020. Notably, the map employs a categorization system, with values assigned to distinct classes: 0 denotes areas of disturbed vegetation, 1 denotes regions characterized by undisturbed vegetation, and 2 denotes zones devoid of vegetation.
DOI: 10.6084/m9.figshare.24753681
title: <i>Bifidobacterium</i> inhibits fluoride-induced pyroptosis by down-regulating IL-17A in mouse testis.zip

description: Metadata for all samples used in this study have been deposited in Figshare.
DOI: 10.6084/m9.figshare.24753681.v1
title: <i>Bifidobacterium</i> inhibits fluoride-induced pyroptosis by down-regulating IL-17A in mouse testis.zip

description: Metadata for all samples used in this study have been deposited in Figshare.
DOI: 10.34740/kaggle/dsv/7136404
title: LUFlow Network Intrusion Detection Data Set
DOI: 10.24376/rd.sgul.22116965
title: ICODA

description: <strong>Description of the research</strong> The research was a secondary analysis of data collected among women who received antenatal and delivery services at Kawempe National Referral Hospital in Kampala, Uganda for the period before during and immediately post the COVID19 outbreak (i.e. Hospital antenatal, maternal and neonatal attendance for the period January 2020 to October 2021). The objective of the analysis was to assess for the adverse pregnancy and infant outcomes that can be attributed to the COVID19 pandemic. The period of analysis was stratified into pre-COVID, COVID and Immediate post-COVID. Pregnancy and infant outcomes were compared across the three time points to assess the adverse outcomes attributable to the pandemic. Results from the analysis was also intended to inform the development of a visualization dashboard that would be available and used by healthcare workers to inform their decisions during service delivery. <br> <strong>The data dictionary</strong> The data dictionary was compiled to provide reference for anyone accessing and using the data from the Electronic Health Record. The antenatal and labour & delivery registers used by healthcare workers to record patient information while offering services at the hospital were reviewed to identify variables included in the registers. The registers are part of the Health Management Information System tools developed by Ministry of Health and are used in all health facilities country-wide. The variables were reviewed during a stakeholder’s workshop that comprised of Ministry of Health officials, Kawempe Hospital management, heads of departments and selected health workers with the objective of identifying those that would be useful for monitoring pregnancies with potential adverse pregnancy and infant outcomes. During the stakeholder meetings, variable definitions were documented to provide clarity and consistency when using the data from the Electronic Health Record.
DOI: 10.5063/f1qz28fh
title: Data: Implementing a rapid geographic range expansion - the role of behavior changes

description: It is generally thought that behavioral flexibility, the ability to change behavior when circumstances change, plays an important role in the ability of species to rapidly expand their geographic range. Great-tailed grackles (*Quiscalus mexicanus*) are a social, polygamous species that is rapidly expanding its geographic range by settling in new areas and habitats. They are behaviorally flexible and highly associated with human-modified environments, eating a variety of human foods in addition to foraging on insects and on the ground for other natural food items. They offer an opportunity to assess the role of behavior change over the course of their expansion. We compare behavior in wild-caught grackles from two populations across their range (an older population in the middle of the northern expansion front: Tempe, Arizona, and a more recent population on the northern edge of the expansion front: Woodland, California) to investigate whether certain behaviors (flexibility, innovativeness, exploration, and persistence) have higher averages and variances in the newer or older population. We find that grackles in the edge population were more innovative and less exploratory, and that there were no population differences in flexibility (measured by reversal learning) or persistence (the proportion of trials participated in). Results elucidate that the rapid geographic range expansion of great-tailed grackles is associated with individuals differentially expressing particular behaviors. Our findings highlight the value of population studies and of breaking down cognitive concepts into direct measures of individual abilities to better understand how species might adapt to novel circumstances.
DOI: 10.5281/zenodo.8425303
title: Supplementary Data to: "Organic Phases in Bivalve (Arctica islandica) Shells: Their Bulk and Amino Acid Nitrogen Stable Isotope Compositions" in Geochemistry, Geophysics, Geosystems

description: This dataset contains the data generated for publication "Organic Phases in Bivalve (<em>Arctica islandica</em>) Shells: Their Bulk and Amino Acid Nitrogen Stable Isotope Compositions", including the following files: Specimen_ID_shell_morphology_measurement: Description of locality of collection, shell ID, shell working ID and the shell morphology measurement which can be referred to Section 2.1 of the manuscript. EA_IRMS_raw_error_propagate: This file contains data showing the m/z 28 signal intensities of all measurements and the error propagation that mentioned in Section 2.3 of the manuscript. It also includes the calculation of analytical accuracy and precision. Statistics: The file contains the summary of statistical analyses performed in this manuscript. Refer to Section 2.7 and 3.3. Recovery: It contains the recovery of the total nitrogen contents or amino acid concentrations after different treatments and this was mentioned in Section 4.1 of the manucript. Mass_balance: The computation procedure that showed in Section 3.4 and discussed in Section 4.3 can be traced in this file. GC-C-IRMS_long_term_sd: The file shows the long-term precision of GC-C-IRMS computed from the mixed standard of amino acids BSIA_d15N: The file contains all the bulk d15N data that used in this manuscript. CSIA_d15N: The file contains all the amino acid d15N data that used in this manuscript. AA_Composition: The file shows AA percent data that used in this manuscript. <br> For details see main text of the manuscript. <br>
description: This research has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 856488).
DOI: 10.5522/04/20305401
title: GEOS-Chem model output for diagnosing sources of fine particles (PM2.5) in UK cities

description: Data are monthly and annual mean total and components of PM<sub>2.5</sub> over the UK in the lowest model layer for comparison to surface concentrations of PM2.5 and assessment of air quality in the UK and in target cities (Leicester, London, Birmingham). <br> Specifically, these are the PM<sub>2.5</sub> mass concentrations obtained with all natural and anthropogenic sources (appended as *_all-sources.nc). These include total PM<sub>2.5</sub> (*-total-pm25-*), black carbon (*-bc-*), ammonium (*-nh4-*), aerosol nitrate (*-no3-*), organic carbon (*-oc-*), and sulfate (*-so4-*). <br> Output also includes model values obtained after taking the difference between a simulation with all sources and multiple simulations with individual source contributors turned off. These sensitivity simulations include UK national emissions of agricultural ammonia (geos-chem-pm25-agr-only.nc), UK national emissions of anthropogenic dust (geos-chem-uk-anthrop-dust-only.nc), continental Europe anthropogenic emissions (geos-chem-uk-europe-only.nc), global natural dust emissions (geos-chem-uk-pm25-global-natural-dust-only.nc), global ship emissions (geos-chem-uk-pm25-global-ships-only.nc), all emission sources in Leicester (geos-chem-uk-pm25-Leicester-only.nc), all emission sources in Leicestershire county (geos-chem-uk-pm25-Leicestershire-only.nc), all emissions in London and Birmingham (geos-chem-London-Bham-only.nc), and UK national traffic tailpipe emissions (geos-chem-uk-pm25-traffic-only.nc). <br>
DOI: 10.6084/m9.figshare.14544207
title: Data and code from "Species richness is more important for ecosystem functioning than species turnover along an elevational gradient"

description: This package contains data of 22 ecosystem functions of microorganisms, plants and animals sampled along a 3.7 km elevational gradient across 13 major ecosystem types on Mt. Kilimanjaro, Tanzania.<br>Along with the raw data we provide R code to reproduce the analysis from the paper. For details about how to run the R code please have a look at the README file in the package. For details about the methods (e.g., field sampling or background of particular analyses) we refer to the original publication.