cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20216669
title: DYNC1LI2 regulates localization of the chaperone-mediated autophagy receptor LAMP2A and improves cellular homeostasis in cystinosis

description: The dynein motor protein complex is required for retrograde transport but the functions of the intermediate-light chains that form the cargo-binding complex are not elucidated and the importance of individual subunits in maintaining cellular homeostasis is unknown. Here, using mRNA arrays and protein analysis, we show that the dynein subunit, DYNC1LI2 (dynein, cytoplasmic 1 light intermediate chain 2) is downregulated in cystinosis, a lysosomal storage disorder caused by genetic defects in CTNS (cystinosin, lysosomal cystine transporter). Reconstitution of DYNC1LI2 expression in <i>ctns</i><sup>-/-</sup> cells reestablished endolysosomal dynamics. Defective vesicular trafficking in cystinotic cells was rescued by DYNC1LI2 expression which correlated with decreased endoplasmic reticulum stress manifested as decreased expression levels of the chaperone HSPA5/GRP78, and the transcription factors ATF4 and DDIT3/CHOP. Mitochondrial fragmentation, membrane potential and endolysosomal-mitochondrial association in cystinotic cells were rescued by DYNC1LI2. Survival of cystinotic cells to oxidative stress was increased by DYNC1LI2 reconstitution but not by its paralog DYNC1LI1, which also failed to decrease ER stress and mitochondrial fragmentation. DYNC1LI2 expression rescued the localization of the chaperone-mediated autophagy (CMA) receptor LAMP2A, CMA activity, cellular homeostasis and LRP2/megalin expression in cystinotic proximal tubule cells, the primary cell type affected in cystinosis. DYNC1LI2 failed to rescue phenotypes in cystinotic cells when LAMP2A was downregulated or when co-expressed with dominant negative (DN) RAB7 or DN-RAB11, which impaired LAMP2A trafficking. DYNC1LI2 emerges as a regulator of cellular homeostasis and potential target to repair underlying trafficking and CMA in cystinosis, a mechanism that is not restored by lysosomal cystine depletion therapies. <b>Abbreviations</b>: ACTB: actin, beta; ATF4: activating transcription factor 4; CMA: chaperone-mediated autophagy; DYNC1LI1: dynein cytoplasmic 1 light intermediate chain 1; DYNC1LI2: dynein cytoplasmic 1 light intermediate chain 2; ER: endoplasmic reticulum; LAMP1: lysosomal associated membrane protein 1; LAMP2A: lysosomal associated membrane protein 2A; LIC: light-intermediate chains; LRP2/Megalin: LDL receptor related protein 2; PTCs: proximal tubule cells; RAB: RAB, member RAS oncogene family; RAB11FIP3: RAB11 family interacting protein 3; RILP: Rab interacting lysosomal protein
DOI: 10.5281/zenodo.10667165
title: Dataset related to article "A virtual biopsy of liver parenchyma to predict the outcome of liver resection"

description: This record contains raw data related to article “A virtual biopsy of liver parenchyma to predict the outcome of liver resection"

Abstract



The preoperative risk assessment of liver resections (LR) is still an open issue. Liver parenchyma characteristics influence the outcome but cannot be adequately evaluated in the preoperative setting. The present study aims to elucidate the contribution of the radiomic analysis of non-tumoral parenchyma to the prediction of complications after elective LR. All consecutive patients undergoing LR between 2017 and 2021 having a preoperative computed tomography (CT) were included. Patients with associated biliary/colorectal resection were excluded. Radiomic features were extracted from a virtual biopsy of non-tumoral liver parenchyma (a 2 mL cylinder) outlined in the portal phase of preoperative CT. Data were internally validated. Overall, 378 patients were analyzed (245 males/133 females-median age 67 years-39 cirrhotics). Radiomics increased the performances of the preoperative clinical models for both liver dysfunction (at internal validaton, AUC = 0.727 vs. 0.678) and bile leak (AUC = 0.744 vs. 0.614). The final predictive model combined clinical and radiomic variables: for bile leak, segment 1 resection, exposure of Glissonean pedicles, HU-related indices, NGLDM_Contrast, GLRLM indices, and GLZLM_ZLNU; for liver dysfunction, cirrhosis, liver function tests, major hepatectomy, segment 1 resection, and NGLDM_Contrast. The combined clinical-radiomic model for bile leak based on preoperative data performed even better than the model including the intraoperative data (AUC = 0.629). The textural features extracted from a virtual biopsy of non-tumoral liver parenchyma improved the prediction of postoperative liver dysfunction and bile leak, implementing information given by standard clinical data. Radiomics should become part of the preoperative assessment of candidates to LR.
DOI: 10.5281/zenodo.10667166
title: Dataset related to article "A virtual biopsy of liver parenchyma to predict the outcome of liver resection"

description: This record contains raw data related to article “A virtual biopsy of liver parenchyma to predict the outcome of liver resection"

Abstract



The preoperative risk assessment of liver resections (LR) is still an open issue. Liver parenchyma characteristics influence the outcome but cannot be adequately evaluated in the preoperative setting. The present study aims to elucidate the contribution of the radiomic analysis of non-tumoral parenchyma to the prediction of complications after elective LR. All consecutive patients undergoing LR between 2017 and 2021 having a preoperative computed tomography (CT) were included. Patients with associated biliary/colorectal resection were excluded. Radiomic features were extracted from a virtual biopsy of non-tumoral liver parenchyma (a 2 mL cylinder) outlined in the portal phase of preoperative CT. Data were internally validated. Overall, 378 patients were analyzed (245 males/133 females-median age 67 years-39 cirrhotics). Radiomics increased the performances of the preoperative clinical models for both liver dysfunction (at internal validaton, AUC = 0.727 vs. 0.678) and bile leak (AUC = 0.744 vs. 0.614). The final predictive model combined clinical and radiomic variables: for bile leak, segment 1 resection, exposure of Glissonean pedicles, HU-related indices, NGLDM_Contrast, GLRLM indices, and GLZLM_ZLNU; for liver dysfunction, cirrhosis, liver function tests, major hepatectomy, segment 1 resection, and NGLDM_Contrast. The combined clinical-radiomic model for bile leak based on preoperative data performed even better than the model including the intraoperative data (AUC = 0.629). The textural features extracted from a virtual biopsy of non-tumoral liver parenchyma improved the prediction of postoperative liver dysfunction and bile leak, implementing information given by standard clinical data. Radiomics should become part of the preoperative assessment of candidates to LR.
DOI: 10.6084/m9.figshare.7109516.v1
title: Additional file 6: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: 92 genes in JWB phytoplasma genome assigned to Pathogen Host Interactions Database. (XLS 46 kb)
DOI: 10.25549/one-ouc17551644
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.6084/m9.figshare.7109609
title: MOESM1 of Decreased RIG-I expression is associated with poor prognosis and promotes cell invasion in human gastric cancer

description: Additional file 1. Â Gene profile after knockdown of RIG-I in AGS.
DOI: 10.6084/m9.figshare.7109624
title: MOESM2 of Decreased RIG-I expression is associated with poor prognosis and promotes cell invasion in human gastric cancer

description: Additional file 2. Gene profile after knockdown of RIG-I in SGC-7901.
DOI: 10.6084/m9.figshare.12872159.v1
title: Additional file 6 of Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses

description: Additional file 6 : Table S6 KEGG enrichment analysis of the DEGs in C7–2 and C7–2t.
DOI: 10.25549/one-ouc17555598
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17555590
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17555589
title: Mattachine Society, Tavern Guild (1964-1967)
DOI: 10.25549/one-ouc17551646
title: Mattachine Society, correspondence, Dale Olson (1954-1956)
DOI: 10.6084/m9.figshare.7109744.v1
title: Additional file 10: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Genes acquired by the event of HGT in the Cardinium cSfur genome. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7109810.v1
title: Additional file 7: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: COG category cluster numbers in 17 bacteroides species. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7109837.v1
title: Additional file 9: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Transport proteins in the Cardinium cSfur genome. (XLSX 15 kb)
DOI: 10.25549/one-ouc17551649
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.6084/m9.figshare.7109744
title: Additional file 10: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Genes acquired by the event of HGT in the Cardinium cSfur genome. (XLSX 14 kb)
DOI: 10.25549/one-ouc17551650
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17552752
title: Mattachine Society, International Committee for Sexual Equality (1955-1960)
DOI: 10.6084/m9.figshare.7109783.v1
title: Additional file 4: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Gene clusters among three Cardinium genomes. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.7109810
title: Additional file 7: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: COG category cluster numbers in 17 bacteroides species. (XLSX 10 kb)
DOI: 10.25549/one-ouc17551652
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.6084/m9.figshare.7109801
title: Additional file 6: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: General features of genomes of 17 cytophagales (A) and P- and S- endosymbiont genome size and GC content (B). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7109756
title: Additional file 1: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Microbial Genome Database organism codes and locus tags for the genes used in the phylogenomic tree. (XLSX 105 kb)
DOI: 10.25549/one-ouc17552754
title: Mattachine Society, National Planning Conference of Homosexual Organizations (1966-1967)
DOI: 10.6084/m9.figshare.19688347.v1
title: Additional file 1 of Albumin to Globulin ratio, Neutrophil to Lymphocyte ratio, and Globulin levels do not outperform ESR or CRP when diagnosing periprosthetic joint infection

description: Additional file 1. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7109756.v1
title: Additional file 1: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Microbial Genome Database organism codes and locus tags for the genes used in the phylogenomic tree. (XLSX 105 kb)
DOI: 10.25549/one-ouc17551653
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.6084/m9.figshare.14974298
title: Metabolism-related long non-coding RNAs (lncRNAs) as potential biomarkers for predicting risk of recurrence in breast cancer patients

description: Metabolism affects the development, progression, and prognosis of various cancers, including breast cancer (BC). Our aim was to develop a metabolism-related long non-coding RNA (lncRNA) signature to assess the prognosis of BC patients in order to optimize treatment. Metabolism-related genes between breast tumors and normal tissues were screened out, and Pearson correlation analysis was used to investigate metabolism-related lncRNAs. In total, five metabolism-related lncRNAs were enrolled to establish prognostic signatures. Kaplan-Meier plots and the receiver operating characteristic (ROC) curves demonstrated good performance in both training and validation groups. Further analysis demonstrated that the signature was an independent prognostic factor for BC. A nomogram incorporating risk score and tumor stage was then constructed to evaluate the 3 – and 5-year recurrence-free survival (RFS) in patients with BC. In conclusion, this study identified a metabolism-related lncRNA signature that can predict RFS of BC patients and established a prognostic nomogram that helps guide the individualized treatment of patients at different risks.
DOI: 10.6084/m9.figshare.14974298.v1
title: Metabolism-related long non-coding RNAs (lncRNAs) as potential biomarkers for predicting risk of recurrence in breast cancer patients

description: Metabolism affects the development, progression, and prognosis of various cancers, including breast cancer (BC). Our aim was to develop a metabolism-related long non-coding RNA (lncRNA) signature to assess the prognosis of BC patients in order to optimize treatment. Metabolism-related genes between breast tumors and normal tissues were screened out, and Pearson correlation analysis was used to investigate metabolism-related lncRNAs. In total, five metabolism-related lncRNAs were enrolled to establish prognostic signatures. Kaplan-Meier plots and the receiver operating characteristic (ROC) curves demonstrated good performance in both training and validation groups. Further analysis demonstrated that the signature was an independent prognostic factor for BC. A nomogram incorporating risk score and tumor stage was then constructed to evaluate the 3 – and 5-year recurrence-free survival (RFS) in patients with BC. In conclusion, this study identified a metabolism-related lncRNA signature that can predict RFS of BC patients and established a prognostic nomogram that helps guide the individualized treatment of patients at different risks.
DOI: 10.25549/one-ouc17551654
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17551651
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551658
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551657
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17551812
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17551814
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17556171
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17556165
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17552966
title: Mattachine Society, Mattachine Society vs. San Francisco Police Department (1973)
DOI: 10.25549/one-ouc17556174
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17556173
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17556172
title: Mattachine Society, Tavern Guild (1964-1967)
DOI: 10.25549/one-ouc17555593
title: Mattachine Society, Long Beach (Harbor) Area Council director's notes (1958)
DOI: 10.24396/ordar-143
title: Bas-Rupt streamwater chemistry over twenty-one years Vosges mountains France

description: pH, conductivity, alcalinity measurements, dissolved cations, anions and carbon quantification, in the Bas-Rupt stream water between 2002 and 2023
DOI: 10.25549/one-ouc17555591
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17555594
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17555592
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17551810
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17551817
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17551820
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551819
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17551821
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551825
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551827
title: Mattachine Society, correspondence, Dale Olson (1954-1956)
DOI: 10.25549/one-ouc17551824
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551823
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17555595
title: Mattachine Society, Long Beach (Harbor) area council meeting minutes (1954-1955)
DOI: 10.25549/one-ouc17555597
title: Mattachine Society, Long Beach (Harbor) area council constitution and bylaws (1953-1954)
DOI: 10.25549/one-ouc17551830
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17551828
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551832
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17551837
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551833
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17551835
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17551841
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17551838
title: Mattachine Society, correspondence, Dale Olson (1954-1956)
DOI: 10.25549/one-ouc17552993
title: Mattachine Society, International Committee for Sexual Equality (1955-1960)
DOI: 10.25549/one-ouc17551842
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551839
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17551843
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17552995
title: Mattachine Society, National League for Social Understanding (1961-1965)
DOI: 10.25549/one-ouc17551846
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17552999
title: Mattachine Society, National Planning Conference of Homosexual Organizations (1966-1967)
DOI: 10.6084/m9.figshare.7109789
title: Additional file 5: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Genes in the two Cardinium plasmids (pcBtQ1 and pcher) and their homologous genes in the genomes of Cardinium cSfur and Amoebophilus asiaticus 5a2. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7109837
title: Additional file 9: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Transport proteins in the Cardinium cSfur genome. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7109783
title: Additional file 4: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Gene clusters among three Cardinium genomes. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.7109789.v1
title: Additional file 5: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: Genes in the two Cardinium plasmids (pcBtQ1 and pcher) and their homologous genes in the genomes of Cardinium cSfur and Amoebophilus asiaticus 5a2. (XLSX 11 kb)
DOI: 10.25549/one-ouc17555599
title: Mattachine Society, United States Customs Department correspondence (1966)
DOI: 10.25549/one-ouc17555600
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.6084/m9.figshare.12876502.v1
title: Additional file 1 of Reliability analysis of the Ahringer Caenorhabditis elegans RNAi feeding library: a guide for genome-wide screens

description: Additional file 1:Summary of the evaluation results of all the bacterial strains (16,256) in the Ahringer C. elegans RNAi feeding library. An Excel file which contains brief accounts of all the bacterial strains (16,256) in the Ahringer C. elegans RNAi feeding library. Information of the three groups (reliable, marginal and unreliable) are also shown in this file. (ZIP 3 MB)
DOI: 10.25549/one-ouc17551844
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.6084/m9.figshare.7109801.v1
title: Additional file 6: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

description: General features of genomes of 17 cytophagales (A) and P- and S- endosymbiont genome size and GC content (B). (XLSX 12 kb)
DOI: 10.25549/one-ouc17551860
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17551845
title: Mattachine Society, correspondence, Dale Olson (1954-1956)
DOI: 10.25549/one-ouc17553161
title: Mattachine Society, National League for Social Understanding (1961-1965)
DOI: 10.25549/one-ouc17551847
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17551849
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551850
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.6084/m9.figshare.20217524
title: Numerical simulation and experimental study of the damage law of EFP warhead charging of cylindrical shells under different angles

description: Abstract In this paper, LS-dyna software was used to simulate the charging process of cylindrical shell when EFP has different angles, and some interesting phenomena and laws were found. Cylindrical elastic wave σr was generated when the cylindrical shell was impacted by EFP. The cylindrical elastic wave σr was correlated with the time required for the cylindrical shell charge to be successfully detonated. When the EFP warhead penetration Angle θ ranges from 0° to 10°, the σr increases linearly with (cosθ)-1/2. With the increase of θ, the tangential velocity vy had an obvious effect on the impact of EFP on the cylindrical shell, and the linear relationship between the elastic wave σr and (cosθ)-1/2 does not change. When the θ was greater than 45°, EFP could not successfully impact and detonate the cylindrical shell charge. The EFP velocity was measured by velocity measurement method with an error of 1.3%. The experimental results have strong similarity with the simulation results, indicating that the parameters of the numerical simulation model have good reliability.