cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24146709
title: Supplementary Material for: Two distinct characteristics of immune microenvironment in human hepatocellular carcinoma with Wnt/β-catenin mutations

description: Introduction Immunotherapy is becoming a promising approach for unresectable-hepatocellular carcinoma (HCC); the anti-tumor response is affected by the tumor microenvironment (TME). Although Wnt/β-catenin mutations are reported to cause non-inflamed phenotype, their role on TME remains controversial. We aimed to clarify the heterogeneity of immunophenotype in HCC with Wnt/β-catenin mutations. Methods This study includes 152 resected HCCs; mutations in the catenin beta-1, adenomatous polyposis coli, or AXIN1, or AXIN2 genes were defined as Wnt/β-catenin mutations. With hierarchical cluster analyses, TME were classified into inflamed or non-inflamed classes based on the gene expressions associated with T-cell activation. Expression profiles of molecules related to cell differentiation and biliary-stem cell markers were compared between the TME classes to investigate whether differences in tumor traits were associated with TME. Results Forty of 152 (26.3%) HCCs carried the Wnt/β-catenin mutations. Of these, 33 were classified as non-inflamed (33/40, 82.5%) and 7 as inflamed (7/40, 17.5%). Non-inflamed class was characterized by low number of CD3+, CD4+, and CD8+ cells on immunostaining, and high mRNA expressions of AXIN2 and GLUL, which are involved in the canonical Wnt/β-catenin signaling and hepatocyte differentiation, respectively. Non-inflamed tumors showed higher enhancement on the hepatobiliary-phase of gadolinium-ethoxybenzyl-diethylenetriamine (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) compared to inflamed tumors. HCCs classified as inflamed class are revealed to have high numbers of CD3+, CD4+, and CD8+ tumor infiltrating lymphocytes on immunostaining. This class is associated with increased expression of anti-epithelial cell adhesion molecule (EpCAM) and FOXM1 accompanied by upregulation of genes related to interferon-gamma signaling, dendritic cell migration, regulatory T cells and MDSC activation and recognized as low enhancement nodule on Gd-EOB-DTPA-enhanced MRI. Conclusion Heterogeneity of tumor traits and TME was observed in HCC with Wnt/β-catenin mutation. The potential was indicated that tumor traits and TME are determined not only by the activation of the HNF4A but also by FOXM1, both of which are downstream transcription factor of the Wnt/β-catenin signaling pathway.
DOI: 10.6084/m9.figshare.24146709.v1
title: Supplementary Material for: Two distinct characteristics of immune microenvironment in human hepatocellular carcinoma with Wnt/β-catenin mutations

description: Introduction Immunotherapy is becoming a promising approach for unresectable-hepatocellular carcinoma (HCC); the anti-tumor response is affected by the tumor microenvironment (TME). Although Wnt/β-catenin mutations are reported to cause non-inflamed phenotype, their role on TME remains controversial. We aimed to clarify the heterogeneity of immunophenotype in HCC with Wnt/β-catenin mutations. Methods This study includes 152 resected HCCs; mutations in the catenin beta-1, adenomatous polyposis coli, or AXIN1, or AXIN2 genes were defined as Wnt/β-catenin mutations. With hierarchical cluster analyses, TME were classified into inflamed or non-inflamed classes based on the gene expressions associated with T-cell activation. Expression profiles of molecules related to cell differentiation and biliary-stem cell markers were compared between the TME classes to investigate whether differences in tumor traits were associated with TME. Results Forty of 152 (26.3%) HCCs carried the Wnt/β-catenin mutations. Of these, 33 were classified as non-inflamed (33/40, 82.5%) and 7 as inflamed (7/40, 17.5%). Non-inflamed class was characterized by low number of CD3+, CD4+, and CD8+ cells on immunostaining, and high mRNA expressions of AXIN2 and GLUL, which are involved in the canonical Wnt/β-catenin signaling and hepatocyte differentiation, respectively. Non-inflamed tumors showed higher enhancement on the hepatobiliary-phase of gadolinium-ethoxybenzyl-diethylenetriamine (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) compared to inflamed tumors. HCCs classified as inflamed class are revealed to have high numbers of CD3+, CD4+, and CD8+ tumor infiltrating lymphocytes on immunostaining. This class is associated with increased expression of anti-epithelial cell adhesion molecule (EpCAM) and FOXM1 accompanied by upregulation of genes related to interferon-gamma signaling, dendritic cell migration, regulatory T cells and MDSC activation and recognized as low enhancement nodule on Gd-EOB-DTPA-enhanced MRI. Conclusion Heterogeneity of tumor traits and TME was observed in HCC with Wnt/β-catenin mutation. The potential was indicated that tumor traits and TME are determined not only by the activation of the HNF4A but also by FOXM1, both of which are downstream transcription factor of the Wnt/β-catenin signaling pathway.
DOI: 10.6084/m9.figshare.22100108.v1
title: All data for the paper

description: This contains all the data for the aforementioned paper, including both raw and intermediate data (i.e. data produced during the analysis which are subsequently used). Geolocator location estimates for all individuals are contained in the 'Positions_Allindivs.csv' file.
DOI: 10.6084/m9.figshare.24146691
title: Netcdf of figures

description: The data used to create figures of study on Tropical instability waves (TIWs) and the equatorial intraseasonal Kelvin waves (IEKWs) in the Pacific Ocean. Here we investigate the energetics of this interaction based on a tropical Pacific configuration of a regional ocean model over the period 1993-2019. We compare two oceanic simulations: the control run (CR) that simulates realistically the mean circulation and intraseasonal variability with the linear (LIN) simulation that reduces the TIWs activity. We analyze the tendency terms of the TIW kinetic energy of selected upwelling and downwelling Kelvin wave events.
DOI: 10.5281/zenodo.8338470
title: Dataset to paper "ECN with QUIC: Challenges in the Wild"

description: In the following you can find the according measurements of our IMC'23 paper "ECN with QUIC: Challenges in the Wild" for the publicly available toplists. Please note that we cannot publicly share our CZDS-based measurements due to their proprietary license. All data is available as line-delimited json files which have been zstandard compressed. If you use any portion of our work, please consider citing our publication. <pre><code>@Inproceedings { 2023-sander-quic-ecn, title = {ECN with QUIC: Challenges in the Wild}, year = {2023}, month = {10}, publisher = {ACM}, booktitle = {Proceedings of the Internet Measurement Conference (IMC '23)}, DOI = {10.1145/3618257.3624821}, author = {Sander, Constantin and Kunze, Ike and Bl{\"o}cher, Leo and Kosek, Mike and Wehrle, Klaus} }</code></pre>
DOI: 10.5281/zenodo.8338469
title: Dataset to paper "ECN with QUIC: Challenges in the Wild"

description: In the following you can find the according measurements of our IMC'23 paper "ECN with QUIC: Challenges in the Wild" for the publicly available toplists. Please note that we cannot publicly share our CZDS-based measurements due to their proprietary license. All data is available as line-delimited json files which have been zstandard compressed. If you use any portion of our work, please consider citing our publication. <pre><code>@Inproceedings { 2023-sander-quic-ecn, title = {ECN with QUIC: Challenges in the Wild}, year = {2023}, month = {10}, publisher = {ACM}, booktitle = {Proceedings of the Internet Measurement Conference (IMC '23)}, DOI = {10.1145/3618257.3624821}, author = {Sander, Constantin and Kunze, Ike and Bl{\"o}cher, Leo and Kosek, Mike and Wehrle, Klaus} }</code></pre>
DOI: 10.5281/zenodo.8348518
title: Biomimetic Dispersive Solid-Phase Microextraction as a Novel Concept for High-Throughput Estimation of Human Oral Absorption of Organic Compounds

description: Statistical data of the fourteen <em>in-vitro </em>MLR models evaluated for the prediction of the effective permeability of organic compounds across the human intestine, presented in Table S1 and Table 2 of the article Analytical Chemistry, 95, 2023, 13123−13131. <br> (DOI: 10.1021/acs.analchem.3c01749)
DOI: 10.5281/zenodo.8348519
title: Biomimetic Dispersive Solid-Phase Microextraction as a Novel Concept for High-Throughput Estimation of Human Oral Absorption of Organic Compounds

description: Statistical data of the fourteen <em>in-vitro </em>MLR models evaluated for the prediction of the effective permeability of organic compounds across the human intestine, presented in Table S1 and Table 2 of the article Analytical Chemistry, 95, 2023, 13123−13131. <br> (DOI: 10.1021/acs.analchem.3c01749)
DOI: 10.4121/5f99d080-f049-483a-a9ad-07212045a80e
title: Dataset on knowledge states and stages and their impact on innovation performance

description: Decisive for firms’ innovation performance is the way they process differentiated and integrated knowledge. Differentiation has been argued to create specialization advantages and integration to enable common ground. Biased by the advantages of producing and maintaining common ground over specialization, scholars overlooked the merits of differentiation. We use a congruence-incongruence approach that investigates whether matching-unmatching stages of knowledge differentiation and integration leads to different innovation performance. Our conceptualization proposes that matching stages of differentiation and integration (congruence) is more conducive of higher innovation performance compared to directing attention to one over the other (incongruence). We find support for this claim. Results show that a mismatch of knowledge states is conducive of lower levels of innovation performance. Our study proposes that awareness of the congruence and incongruence between the stages (producing vs maintaining) of different knowledge states (differentiation vs integration) plays a critical role for innovation research.
DOI: 10.4121/5f99d080-f049-483a-a9ad-07212045a80e.v1
title: Dataset on knowledge states and stages and their impact on innovation performance

description: Decisive for firms’ innovation performance is the way they process differentiated and integrated knowledge. Differentiation has been argued to create specialization advantages and integration to enable common ground. Biased by the advantages of producing and maintaining common ground over specialization, scholars overlooked the merits of differentiation. We use a congruence-incongruence approach that investigates whether matching-unmatching stages of knowledge differentiation and integration leads to different innovation performance. Our conceptualization proposes that matching stages of differentiation and integration (congruence) is more conducive of higher innovation performance compared to directing attention to one over the other (incongruence). We find support for this claim. Results show that a mismatch of knowledge states is conducive of lower levels of innovation performance. Our study proposes that awareness of the congruence and incongruence between the stages (producing vs maintaining) of different knowledge states (differentiation vs integration) plays a critical role for innovation research.
DOI: 10.6084/m9.figshare.24146748
title: Supplementary Material for: Two distinct characteristics of immune microenvironment in human hepatocellular carcinoma with Wnt/β-catenin mutations

description: Introduction Immunotherapy is becoming a promising approach for unresectable-hepatocellular carcinoma (HCC); the anti-tumor response is affected by the tumor microenvironment (TME). Although Wnt/β-catenin mutations are reported to cause non-inflamed phenotype, their role on TME remains controversial. We aimed to clarify the heterogeneity of immunophenotype in HCC with Wnt/β-catenin mutations. Methods This study includes 152 resected HCCs; mutations in the catenin beta-1, adenomatous polyposis coli, or AXIN1, or AXIN2 genes were defined as Wnt/β-catenin mutations. With hierarchical cluster analyses, TME were classified into inflamed or non-inflamed classes based on the gene expressions associated with T-cell activation. Expression profiles of molecules related to cell differentiation and biliary-stem cell markers were compared between the TME classes to investigate whether differences in tumor traits were associated with TME. Results Forty of 152 (26.3%) HCCs carried the Wnt/β-catenin mutations. Of these, 33 were classified as non-inflamed (33/40, 82.5%) and 7 as inflamed (7/40, 17.5%). Non-inflamed class was characterized by low number of CD3+, CD4+, and CD8+ cells on immunostaining, and high mRNA expressions of AXIN2 and GLUL, which are involved in the canonical Wnt/β-catenin signaling and hepatocyte differentiation, respectively. Non-inflamed tumors showed higher enhancement on the hepatobiliary-phase of gadolinium-ethoxybenzyl-diethylenetriamine (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) compared to inflamed tumors. HCCs classified as inflamed class are revealed to have high numbers of CD3+, CD4+, and CD8+ tumor infiltrating lymphocytes on immunostaining. This class is associated with increased expression of anti-epithelial cell adhesion molecule (EpCAM) and FOXM1 accompanied by upregulation of genes related to interferon-gamma signaling, dendritic cell migration, regulatory T cells and MDSC activation and recognized as low enhancement nodule on Gd-EOB-DTPA-enhanced MRI. Conclusion Heterogeneity of tumor traits and TME was observed in HCC with Wnt/β-catenin mutation. The potential was indicated that tumor traits and TME are determined not only by the activation of the HNF4A but also by FOXM1, both of which are downstream transcription factor of the Wnt/β-catenin signaling pathway.
DOI: 10.6084/m9.figshare.24146748.v1
title: Supplementary Material for: Two distinct characteristics of immune microenvironment in human hepatocellular carcinoma with Wnt/β-catenin mutations

description: Introduction Immunotherapy is becoming a promising approach for unresectable-hepatocellular carcinoma (HCC); the anti-tumor response is affected by the tumor microenvironment (TME). Although Wnt/β-catenin mutations are reported to cause non-inflamed phenotype, their role on TME remains controversial. We aimed to clarify the heterogeneity of immunophenotype in HCC with Wnt/β-catenin mutations. Methods This study includes 152 resected HCCs; mutations in the catenin beta-1, adenomatous polyposis coli, or AXIN1, or AXIN2 genes were defined as Wnt/β-catenin mutations. With hierarchical cluster analyses, TME were classified into inflamed or non-inflamed classes based on the gene expressions associated with T-cell activation. Expression profiles of molecules related to cell differentiation and biliary-stem cell markers were compared between the TME classes to investigate whether differences in tumor traits were associated with TME. Results Forty of 152 (26.3%) HCCs carried the Wnt/β-catenin mutations. Of these, 33 were classified as non-inflamed (33/40, 82.5%) and 7 as inflamed (7/40, 17.5%). Non-inflamed class was characterized by low number of CD3+, CD4+, and CD8+ cells on immunostaining, and high mRNA expressions of AXIN2 and GLUL, which are involved in the canonical Wnt/β-catenin signaling and hepatocyte differentiation, respectively. Non-inflamed tumors showed higher enhancement on the hepatobiliary-phase of gadolinium-ethoxybenzyl-diethylenetriamine (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) compared to inflamed tumors. HCCs classified as inflamed class are revealed to have high numbers of CD3+, CD4+, and CD8+ tumor infiltrating lymphocytes on immunostaining. This class is associated with increased expression of anti-epithelial cell adhesion molecule (EpCAM) and FOXM1 accompanied by upregulation of genes related to interferon-gamma signaling, dendritic cell migration, regulatory T cells and MDSC activation and recognized as low enhancement nodule on Gd-EOB-DTPA-enhanced MRI. Conclusion Heterogeneity of tumor traits and TME was observed in HCC with Wnt/β-catenin mutation. The potential was indicated that tumor traits and TME are determined not only by the activation of the HNF4A but also by FOXM1, both of which are downstream transcription factor of the Wnt/β-catenin signaling pathway.
DOI: 10.5281/zenodo.8204515
title: Data for thesis titled: The impact of processing conditions on enzymatic protein hydrolysis performance from sardine (Sardina pilchardus) by-products using Alcalase 2.4L, and the influence on final spray dried hydrolysate powder properties

description: The data answer the objectives that focused on: determining the substrate-specific optimum hydrolysis temperature and pH for the particular enzyme-substrate (Alcalase-sardine by-product) combination, investigating the effect of mixing speed, solids concentration and enzyme dosage on dry solids yield and protein recovery during enzymatic hydrolysis of sardine processing by-products, evaluating the influence of solids concentration on emulsion formation during enzymatic hydrolysis, determining the effect of solids concentration and emulsion formation on molecular weight distribution of protein hydrolysates, investigating the effect of mixing speed and solids concentration on the viscosity and mixing regime of material during enzymatic hydrolysis, establishing the role played by processing conditions (degree of hydrolysis (DH), maltodextrin addition and inlet air temperature) on powder recovery during spray drying, and investigating the role of DH, maltodextrin concentration and spray drying temperature on handling and storage properties of spray dried protein hydrolysates. This data also appears in journal papers with the following titles: Chiodza, K. & Goosen, N.J. 2023a. Evaluation of handling and storage stability of spray dried protein hydrolysates from sardine (Sardina pilchardus) processing by-products: Effect of enzymatic hydrolysis time, spray drying temperature and maltodextrin concentration. <em>Food and Bioproducts Processing</em>. (June, 30). DOI: https://doi.org/10.1016/j.fbp.2023.06.009. Chiodza, K. & Goosen, N.J. 2023b. Influence of mixing speed, solids concentration and enzyme dosage on dry solids yield and protein recovery during enzymatic hydrolysis of sardine (Sardina pilchardus) processing by-products using Alcalase 2.4L: a multivariable optimisation approach. <em>Biomass Conversion and Biorefinery</em>. 1:1–23. DOI: https://doi.org/10.1007/s13399-023-03829-2. Chiodza, K. & Goosen, N.J. 2023c. Emulsion formation during enzymatic protein hydrolysis and its effect on protein recovery and molecular weight distribution of protein hydrolysates from sardine (Sardina pilchardus) by-products. <em>Biomass Conversion and Biorefinery</em>. 1:1–12. DOI: https://doi.org/10.1007/s13399-023-04438-9.
DOI: 10.5281/zenodo.8204514
title: Data for thesis titled: The impact of processing conditions on enzymatic protein hydrolysis performance from sardine (Sardina pilchardus) by-products using Alcalase 2.4L, and the influence on final spray dried hydrolysate powder properties

description: The data answer the objectives that focused on: determining the substrate-specific optimum hydrolysis temperature and pH for the particular enzyme-substrate (Alcalase-sardine by-product) combination, investigating the effect of mixing speed, solids concentration and enzyme dosage on dry solids yield and protein recovery during enzymatic hydrolysis of sardine processing by-products, evaluating the influence of solids concentration on emulsion formation during enzymatic hydrolysis, determining the effect of solids concentration and emulsion formation on molecular weight distribution of protein hydrolysates, investigating the effect of mixing speed and solids concentration on the viscosity and mixing regime of material during enzymatic hydrolysis, establishing the role played by processing conditions (degree of hydrolysis (DH), maltodextrin addition and inlet air temperature) on powder recovery during spray drying, and investigating the role of DH, maltodextrin concentration and spray drying temperature on handling and storage properties of spray dried protein hydrolysates. This data also appears in journal papers with the following titles: Chiodza, K. & Goosen, N.J. 2023a. Evaluation of handling and storage stability of spray dried protein hydrolysates from sardine (Sardina pilchardus) processing by-products: Effect of enzymatic hydrolysis time, spray drying temperature and maltodextrin concentration. <em>Food and Bioproducts Processing</em>. (June, 30). DOI: https://doi.org/10.1016/j.fbp.2023.06.009. Chiodza, K. & Goosen, N.J. 2023b. Influence of mixing speed, solids concentration and enzyme dosage on dry solids yield and protein recovery during enzymatic hydrolysis of sardine (Sardina pilchardus) processing by-products using Alcalase 2.4L: a multivariable optimisation approach. <em>Biomass Conversion and Biorefinery</em>. 1:1–23. DOI: https://doi.org/10.1007/s13399-023-03829-2. Chiodza, K. & Goosen, N.J. 2023c. Emulsion formation during enzymatic protein hydrolysis and its effect on protein recovery and molecular weight distribution of protein hydrolysates from sardine (Sardina pilchardus) by-products. <em>Biomass Conversion and Biorefinery</em>. 1:1–12. DOI: https://doi.org/10.1007/s13399-023-04438-9.
DOI: 10.6084/m9.figshare.24146760
title: Supplementary Tables from Comprehensive insights into the genetic background of Chinese populations using Y chromosome markers

description: China is located in East Asia. With a high genetic and cultural diversity, human migration in China has always been a hot topic of genetics research. To explore the origins and migration routes of Chinese males, 3333 Chinese individuals (Han, Hui, Mongolia, Yi and Kyrgyz) with 27 Y-STRs and 143 Y-SNPs from published literatures were analysed. Our data showed that there are five dominant haplogroups (O2-M122, O1- F265, C-M130, N-M231, R-M207) in China. Combining analysis of haplogroup frequencies, geographical positions and time to the most recent common ancestor (TMRCA), we found that haplogroup C-M130, N-M231 and R1-M173 and O1a-M175 probably migrated into China via the northern route. Interestingly, we found that haplogroup C*-M130 in China may originate in South Asia, whereas the major subbranches C2a-L1373 and C2b-F1067 migrated from northern China. The results of BATWING showed that the common ancestry of Y haplogroup in China can be traced back to 17 000 years ago, which was concurrent with global temperature increases after the Last Glacial Maximum.
DOI: 10.6084/m9.figshare.24146760.v1
title: Supplementary Tables from Comprehensive insights into the genetic background of Chinese populations using Y chromosome markers

description: China is located in East Asia. With a high genetic and cultural diversity, human migration in China has always been a hot topic of genetics research. To explore the origins and migration routes of Chinese males, 3333 Chinese individuals (Han, Hui, Mongolia, Yi and Kyrgyz) with 27 Y-STRs and 143 Y-SNPs from published literatures were analysed. Our data showed that there are five dominant haplogroups (O2-M122, O1- F265, C-M130, N-M231, R-M207) in China. Combining analysis of haplogroup frequencies, geographical positions and time to the most recent common ancestor (TMRCA), we found that haplogroup C-M130, N-M231 and R1-M173 and O1a-M175 probably migrated into China via the northern route. Interestingly, we found that haplogroup C*-M130 in China may originate in South Asia, whereas the major subbranches C2a-L1373 and C2b-F1067 migrated from northern China. The results of BATWING showed that the common ancestry of Y haplogroup in China can be traced back to 17 000 years ago, which was concurrent with global temperature increases after the Last Glacial Maximum.
DOI: 10.6084/m9.figshare.24146766.v1
title: Bioinformatic code used in study from Bathymetric evolution of black corals through deep time

description: Bioinformatic code used in study