cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20317624.v1
title: Additional file 2 of An epigenome-wide association study of insulin resistance in African Americans

description: Additional file2. Table S1. List of CpG sites within the HOXA5 DMR; Table S2. Previously reported EWAS for insulin resistance; Table S3. DMPs reported in previous insulin resistance EWAS; Table S4. Association between candidate CpG sites reported in previous studies and HOMA-IR in African American men.Table S5. Summary statistics from the main HOMA-IR analysis in African American men for candidate CpG sites; Table S6. Candidate probes that successfully replicated in African American men; Table S7a. Chromatin states of top 100 DMPs associated with insulin resistance in African American men from clusterProfiler; Table S7b. Chromatin states of top 100 DMPs associated with insulin resistance in African American men from the EWAS Toolkit; Table S8. Gene function and associated phenotypes in GWAS catalog and GeneCards; Table S9A. Traits associated with the three identified DMPs (annotated genes) in the EWAS catalog; Table S9B. Traits associated with genes in the 500kb vicinity of HOXA5, OSR1, and ST18 in the EWAS catalog; Table S10. R packages used in the analyses.
DOI: 10.6084/m9.figshare.20317628.v1
title: Additional file 2 of Maternal serum concentrations of one-carbon metabolism factors modify the association between biomarkers of arsenic methylation efficiency and birth weight

description: Additional file 2: Table S1. Results from models fit using the leave-one-out approach.
DOI: 10.6084/m9.figshare.20317628
title: Additional file 2 of Maternal serum concentrations of one-carbon metabolism factors modify the association between biomarkers of arsenic methylation efficiency and birth weight

description: Additional file 2: Table S1. Results from models fit using the leave-one-out approach.
DOI: 10.6084/m9.figshare.20317643.v1
title: Additional file 4 of Allosteric activation of the metabolic enzyme GPD1 inhibits bladder cancer growth via the lysoPC-PAFR-TRPV2 axis

description: Additional file 4: Table S4. The pathways base on gene set enrichment analysis.
DOI: 10.6084/m9.figshare.20317651.v1
title: Additional file 1 of Nutritional management and maize variety combination effectively control Striga asiatica in southern Africa

description: Additional file 1: Table S1. Amounts of single super phosphate and phosphorus used. Table S2. Mean squares for maize heights from week 1 to week 11 after crop emergence. Table S3. Mean squares for S. asiatica attachments and counts. Figure S1. S. asiatica counts across the six maize genotypes in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines represent standard errors pooled from three replications. Figure S2. Leaf biomass (g) of the Striga infected and uninfected maize hybrids grown in pots in response to different phosphorus levels under glasshouse environment at the University of Zimbabwe in the 2014–2015 crop growing season. Vertical bars are the standard errors shared from three replications. Figure S3. Striga infected and uninfected cultivar effects on cob biomass (g) of the maize hybrids grown in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines denotes standard errors shared from three replications. Figure S4. Effects of variety on Striga haustorial attachments on roots of six maize hybrids grown in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines shows standard errors shared from three replications. Figure S5. Striga infected and uninfected cultivar effects on grain yield (g) of the maize hybrids grown in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines shows standard errors shared from the three replications. Figure S6. Maize grain yield (g) of the Striga infected and uninfected maize hybrids grown in pots at different phosphorus levels under glasshouse environment at the University of Zimbabwe in the 2014–2015 crop growing season. Vertical bars are the standard errors shared from three replications. Figure S7. Phosphorus effects on root:shoot of the Striga infected and uninfected maize hybrids grown in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines depicts standard errors shared from three replications.
DOI: 10.6084/m9.figshare.20317651
title: Additional file 1 of Nutritional management and maize variety combination effectively control Striga asiatica in southern Africa

description: Additional file 1: Table S1. Amounts of single super phosphate and phosphorus used. Table S2. Mean squares for maize heights from week 1 to week 11 after crop emergence. Table S3. Mean squares for S. asiatica attachments and counts. Figure S1. S. asiatica counts across the six maize genotypes in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines represent standard errors pooled from three replications. Figure S2. Leaf biomass (g) of the Striga infected and uninfected maize hybrids grown in pots in response to different phosphorus levels under glasshouse environment at the University of Zimbabwe in the 2014–2015 crop growing season. Vertical bars are the standard errors shared from three replications. Figure S3. Striga infected and uninfected cultivar effects on cob biomass (g) of the maize hybrids grown in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines denotes standard errors shared from three replications. Figure S4. Effects of variety on Striga haustorial attachments on roots of six maize hybrids grown in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines shows standard errors shared from three replications. Figure S5. Striga infected and uninfected cultivar effects on grain yield (g) of the maize hybrids grown in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines shows standard errors shared from the three replications. Figure S6. Maize grain yield (g) of the Striga infected and uninfected maize hybrids grown in pots at different phosphorus levels under glasshouse environment at the University of Zimbabwe in the 2014–2015 crop growing season. Vertical bars are the standard errors shared from three replications. Figure S7. Phosphorus effects on root:shoot of the Striga infected and uninfected maize hybrids grown in pots under glasshouse conditions at the University of Zimbabwe in the 2014/15 rainfall season. Vertical lines depicts standard errors shared from three replications.
DOI: 10.6084/m9.figshare.14535403
title: Activating urban environments as social infrastructure through civic stewardship

description: Stewardship consists of acts of claims-making on space and caretaking of place that activate urban environments to function as social infrastructure. While stewardship practices are enacted by actors across the governance network, there is a need to better understand the role of civil society. Civic stewardship groups care and advocate for green, grey, and blue spaces, and can strengthen social trust and foster civic engagement. We conducted semi-structured interviews (n = 26) with a sample of New York City civic stewardship groups from a previous survey dataset (n = 754); the sample was stratified by network position and geographic scale. This paper analyzes how these groups operate in physical geographies and through relational networks. We describe the practices by which stewards activate and transform urban environments to create more sustainable cities, finding that activation of social infrastructure depends upon the degree of group connectivity and scale at which groups work.
DOI: 10.6084/m9.figshare.14535403.v1
title: Activating urban environments as social infrastructure through civic stewardship

description: Stewardship consists of acts of claims-making on space and caretaking of place that activate urban environments to function as social infrastructure. While stewardship practices are enacted by actors across the governance network, there is a need to better understand the role of civil society. Civic stewardship groups care and advocate for green, grey, and blue spaces, and can strengthen social trust and foster civic engagement. We conducted semi-structured interviews (n = 26) with a sample of New York City civic stewardship groups from a previous survey dataset (n = 754); the sample was stratified by network position and geographic scale. This paper analyzes how these groups operate in physical geographies and through relational networks. We describe the practices by which stewards activate and transform urban environments to create more sustainable cities, finding that activation of social infrastructure depends upon the degree of group connectivity and scale at which groups work.
DOI: 10.57770/s7edby
title: Regorafenib enhances antitumor immunity via inhibition of p38 kinase/Creb1/Klf4 axis in tumor-associated macrophages

description: Background: Regorafenib and other multikinase inhibitors may enhance antitumor efficacy of anti-program cell death-1 (anti-PD1) therapy in hepatocellular carcinoma (HCC). Its immunomodulatory effects, besides anti-angiogenesis, were not clearly defined. Methods: In vivo antitumor efficacy was tested in multiple syngeneic liver cancer models. Murine bone marrow-derived macrophages (BMDMs) were tested in vitro for modulation of polarization by regorafenib and activation of cocultured T cells. Markers of M1/M2 polarization were measured by quantitative reverse transcription PCR (RT-PCR), arginase activity, flow cytometry, and ELISA. Knockdown of p38 kinase and downstream Creb1/Klf4 signaling on macrophage polarization were confirmed by using knockdown of the upstream MAPK14 kinase, chemical p38 kinase inhibitor, and chromatin immunoprecipitation. Results: Regorafenib (5 mg/kg/day, corresponding to about half of human clinical dosage) inhibited tumor growth and angiogenesis in vivo similarly to DC-101 (anti-VEGFR2 antibody) but produced higher T cell activation and M1 macrophage polarization, increased the ratio of M1/M2 polarized BMDMs and proliferation/activation of cocultured T cells in vitro, indicating angiogenesis-independent immunomodulatory effects. Suppression of p38 kinase phosphorylation and downstream Creb1/Klf4 activity in BMDMs by regorafenib reversed M2 polarization. Regorafenib enhanced antitumor efficacy of adoptively transferred antigen-specific T cells. Synergistic antitumor efficacy between regorafenib and anti-PD1 was associated with multiple immune-related pathways in the tumor microenvironment. Conclusion: Regorafenib may enhance antitumor immunity through modulation of macrophage polarization, independent of its anti-angiogenic effects. Optimization of regorafenib dosage for rational design of combination therapy regimen may improve the therapeutic index in the clinic.
DOI: 10.57770/upjgk4
title: Harnessing stemness and PD-L1 expression by AT-rich interaction domain-containing protein 3B in colorectal cancer

description: Background and Aims: Cancer stem cells (CSCs) have been shown to be responsible for the tumor initiation, metastasis, and therapeutic resistance of colorectal cancer (CRC). Recent studies have also indicated the importance of CSCs in escaping immune surveillance. However, the coordinated epigenetic control of the stem cell signature and the key molecule(s) involved in immunosurveillance of colorectal CSCs (CRCSCs) are unclear. Here, we investigated the role of a histone modifier, AT-rich interaction domain-containing protein 3B (ARID3B), in CRC. Methods: CRC patient-derived xenografts (PDXs) with knockout of ARID3B induced by CRISPR/Cas9 in vivo were used. Molecular/cellular biology assays were performed. Clinical data obtained from The Cancer Genome Atlas, as well as from our cohort (Taipei Veterans General Hospital), were analyzed. Results: ARID3B was crucial for the growth of CRC, and ARID3B promoted the stem-like features of CRC. Mechanistically, ARID3B activated Notch target genes, intestinal stem cell (ISC) genes, and programmed death-ligand 1 (PD-L1) through the recruitment of lysine-specific demethylase 4C (KDM4C) to modulate the chromatin configuration for transcriptional activation. Clinical sample analyses showed that the coexpression of ARID3B and the Notch target HES1 correlated with a worse outcome and that ARID3B and PD-L1 were highly expressed in the consensus molecular subtype 4 of CRC. Pharmacological inhibition of KDM4 activity reversed the ARID3B-induced signature. Conclusion: We reveal a noncanonical Notch pathway for activating Notch target genes, ISC genes, and PD-L1 in CRC. This finding explains the immune escape of CRCSCs and indicates a potential group that may benefit from immune checkpoint inhibitors. Epigenetic drugs for reversing stem-like features of CRC should also be investigated.
DOI: 10.57770/0vwdx3
title: Snail-induced claudin-11 prompts collective migration for tumour progression

description: Epithelial-mesenchymal transition (EMT) is a pivotal mechanism for cancer dissemination. However, EMT-regulated individual cancer cell invasion is difficult to detect in clinical samples. Emerging evidence implies that EMT is correlated to collective cell migration and invasion with unknown mechanisms. We show that the EMT transcription factor Snail elicits collective migration in squamous cell carcinoma by inducing the expression of a tight junctional protein, claudin-11. Mechanistically, tyrosine-phosphorylated claudin-11 activates Src, which suppresses RhoA activity at intercellular junctions through p190RhoGAP, maintaining stable cell-cell contacts. In head and neck cancer patients, the Snail-claudin-11 axis prompts the formation of circulating tumour cell clusters, which correlate with tumour progression. Overexpression of snail correlates with increased claudin-11, and both are associated with a worse outcome. This finding extends the current understanding of EMT-mediated cellular migration via a non-individual type of movement to prompt cancer progression.
DOI: 10.6084/m9.figshare.20317695
title: Raw Data

description: Raw Data
DOI: 10.6084/m9.figshare.20317695.v1
title: Raw Data

description: Raw Data
DOI: 10.34740/kaggle/dsv/3945788
title: AutoXGB
DOI: 10.6084/m9.figshare.19771108
title: Fig1 & Fig5 Flow Cytometry.zip

description: Fig1 & Fig5 Flow Cytometry
DOI: 10.6084/m9.figshare.19771108.v2
title: Fig1 & Fig5 Flow Cytometry.zip

description: Fig1 & Fig5 Flow Cytometry
DOI: 10.6084/m9.figshare.19771108.v1
title: Fig1 & Fig5 Flow Cytometry.zip

description: Fig1 & Fig5 Flow Cytometry
DOI: 10.6084/m9.figshare.19771114
title: Fig6 Western Blot.zip

description: Fig6 Western Blot
DOI: 10.6084/m9.figshare.19771114.v2
title: Fig6 Western Blot.zip

description: Fig6 Western Blot
DOI: 10.6084/m9.figshare.19771114.v1
title: Fig6 Western Blot.zip

description: Fig6 Western Blot
DOI: 10.6084/m9.figshare.20317722.v1
title: Additional file 1 of Comparative analysis of a presbyopia-correcting intraocular lens that combines extended depth-of-focus and bifocal profiles with a standard monofocal intraocular lens

description: Additional file 1.
DOI: 10.6084/m9.figshare.20317722
title: Additional file 1 of Comparative analysis of a presbyopia-correcting intraocular lens that combines extended depth-of-focus and bifocal profiles with a standard monofocal intraocular lens

description: Additional file 1.
DOI: 10.6084/m9.figshare.20317908
title: Additional file 1 of KiESEL – The Children’s Nutrition Survey to Record Food Consumption for the youngest in Germany

description: Additional file 1. Supplementary File
DOI: 10.6084/m9.figshare.20317908.v1
title: Additional file 1 of KiESEL – The Children’s Nutrition Survey to Record Food Consumption for the youngest in Germany

description: Additional file 1. Supplementary File
DOI: 10.6084/m9.figshare.19149773
title: International assessment of interobserver reproducibility of flap delineation in head and neck carcinoma

description: <b>Background:</b> Several reports have suggested that radiotherapy after reconstructive surgery for head and neck cancer (HNC), could have deleterious effects on the flaps with respect to functional outcomes. To predict and prevent toxicities, flap delineation should be accurate and reproducible. The objective of the present study was to evaluate the interobserver variability of frequent types of flaps used in HNC, based on the recent GORTEC atlas. <b>Materials and methods:</b> Each member of an international working group (WG) consisting of 14 experts delineated the flaps on a CT set from six patients. Each patient had one of the five most commonly used flaps in HNC: a regional pedicled pectoralis major myocutaneous flap, a local pedicled rotational soft tissue facial artery musculo-mucosal (FAMM) (2 patients), a fasciocutaneous radial forearm free flap, a soft tissue anterolateral thigh (ALT) free flap, or a fibular free flap. The WG’s contours were compared to a reference contour, validated by a surgeon and a radiologist specializing in HNC. Contours were considered as reproducible if the median Dice Similarity Coefficient (DSC) was &gt; 0.7. <b>Results:</b> The median volumes of the six flaps delineated by the WG were close to the reference contour value, with approximately 50 cc for the pectoral, fibula, and ALT flaps, 20 cc for the radial forearm, and up to 10 cc for the FAMM. The volumetric ratio was thus close to the optimal value of 100% for all flaps. The median DSC obtained by the WG compared to the reference for the pectoralis flap, the FAMM, the radial forearm flap, ALT flap, and the fibular flap were 0.82, 0.40, 0.76, 0.81, and 0.76, respectively. <b>Conclusions:</b> This study showed that the delineation of four main flaps used for HNC was reproducible. The delineation of the FAMM, however, requires close cooperation between radiologist, surgeon and radiation oncologist because of the poor visibility of this flap on CT and its small size.
DOI: 10.6084/m9.figshare.19149773.v1
title: International assessment of interobserver reproducibility of flap delineation in head and neck carcinoma

description: <b>Background:</b> Several reports have suggested that radiotherapy after reconstructive surgery for head and neck cancer (HNC), could have deleterious effects on the flaps with respect to functional outcomes. To predict and prevent toxicities, flap delineation should be accurate and reproducible. The objective of the present study was to evaluate the interobserver variability of frequent types of flaps used in HNC, based on the recent GORTEC atlas. <b>Materials and methods:</b> Each member of an international working group (WG) consisting of 14 experts delineated the flaps on a CT set from six patients. Each patient had one of the five most commonly used flaps in HNC: a regional pedicled pectoralis major myocutaneous flap, a local pedicled rotational soft tissue facial artery musculo-mucosal (FAMM) (2 patients), a fasciocutaneous radial forearm free flap, a soft tissue anterolateral thigh (ALT) free flap, or a fibular free flap. The WG’s contours were compared to a reference contour, validated by a surgeon and a radiologist specializing in HNC. Contours were considered as reproducible if the median Dice Similarity Coefficient (DSC) was &gt; 0.7. <b>Results:</b> The median volumes of the six flaps delineated by the WG were close to the reference contour value, with approximately 50 cc for the pectoral, fibula, and ALT flaps, 20 cc for the radial forearm, and up to 10 cc for the FAMM. The volumetric ratio was thus close to the optimal value of 100% for all flaps. The median DSC obtained by the WG compared to the reference for the pectoralis flap, the FAMM, the radial forearm flap, ALT flap, and the fibular flap were 0.82, 0.40, 0.76, 0.81, and 0.76, respectively. <b>Conclusions:</b> This study showed that the delineation of four main flaps used for HNC was reproducible. The delineation of the FAMM, however, requires close cooperation between radiologist, surgeon and radiation oncologist because of the poor visibility of this flap on CT and its small size.
DOI: 10.6084/m9.figshare.19346699
title: Diffusion tensor imaging in glioblastoma patients treated with volumetric modulated arc radiotherapy: a longitudinal study

description: Chemo- and radiotherapy (RT) is standard treatment for patients with high-grade glioma, but may cause side-effects on the patient’s cognitive function. Use of diffusion tensor imaging (DTI) to investigate the longitudinal changes in normal-appearing brain tissue in glioblastoma patients undergoing modern arc-based RT with volumetric modulated arc therapy (VMAT) or helical tomotherapy. The study included 27 patients newly diagnosed with glioblastoma and planned for VMAT or tomotherapy. All subjects underwent magnetic resonance imaging at the start of RT and at week 3, 6, 15, and 26. Fourteen subjects were additionally imaged at week 52. The DTI data were co-registered to the dose distribution maps. Longitudinal changes in fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), and axial diffusivity (AD) were assessed in the corpus callosum, the centrum semiovale, the hippocampus, and the amygdala. Significant longitudinal changes in FA, MD, and RD were mainly found in the corpus callosum. In the other examined brain structures, only sparse and transient changes were seen. No consistent correlations were found between biodose, age, or gender and changes in DTI parameters. Longitudinal changes in MD, FA, and RD were observed but only in a limited number of brain structures and the changes were smaller than expected from literature. The results suggest that modern, arc-based RT may have less negative effect on normal-appearing parts of the brain tissue up to 12 months after radiotherapy.
DOI: 10.6084/m9.figshare.19346699.v1
title: Diffusion tensor imaging in glioblastoma patients treated with volumetric modulated arc radiotherapy: a longitudinal study

description: Chemo- and radiotherapy (RT) is standard treatment for patients with high-grade glioma, but may cause side-effects on the patient’s cognitive function. Use of diffusion tensor imaging (DTI) to investigate the longitudinal changes in normal-appearing brain tissue in glioblastoma patients undergoing modern arc-based RT with volumetric modulated arc therapy (VMAT) or helical tomotherapy. The study included 27 patients newly diagnosed with glioblastoma and planned for VMAT or tomotherapy. All subjects underwent magnetic resonance imaging at the start of RT and at week 3, 6, 15, and 26. Fourteen subjects were additionally imaged at week 52. The DTI data were co-registered to the dose distribution maps. Longitudinal changes in fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), and axial diffusivity (AD) were assessed in the corpus callosum, the centrum semiovale, the hippocampus, and the amygdala. Significant longitudinal changes in FA, MD, and RD were mainly found in the corpus callosum. In the other examined brain structures, only sparse and transient changes were seen. No consistent correlations were found between biodose, age, or gender and changes in DTI parameters. Longitudinal changes in MD, FA, and RD were observed but only in a limited number of brain structures and the changes were smaller than expected from literature. The results suggest that modern, arc-based RT may have less negative effect on normal-appearing parts of the brain tissue up to 12 months after radiotherapy.