cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8146215
title: Beyond 2D: a scalable and highly sensitive method for comprehensive 3D analysis of kidney biopsy tissue

description: The spatial organization of various cell populations is critical for the major physiological and pathological processes in the kidneys. Most evaluation of those processes typically comes from a conventional 2D tissue cross-section, visualizing a limited amount of cell organization. Therefore, the 2D analysis of kidney biopsy introduces selection bias. The 2D analysis potentially omits key pathological findings outside a 1-10μm thin sectioned area and lacks information on tissue organization, especially in a particular irregular structure such as crescentic glomeruli. Here, we introduce an easy-to-use and scalable method for obtaining high-quality images of molecules of interest in a large tissue volume, enabling a comprehensive evaluation of the 3D organization and cellular composition of kidney tissue, especially the glomerular structure. We showed that CUBIC and ScaleS clearing protocols could allow a 3D analysis of the kidney tissues in human and animal models of kidney disease. We also demonstrated that used paraffin-embedded human biopsy specimens previously examined via 2D evaluation could be applicable to 3D analysis, showing a potential utilization of this method in kidney biopsy tissue collected in the past. In summary, the 3D analysis of kidney biopsy provides a more comprehensive analysis and a minimized selection bias than 2D tissue analysis. Additionally, this method enables a quantitative evaluation of particular kidney structures and their surrounding tissues, with potential utilization from basic science investigation to applied diagnostic in nephrology.
DOI: 10.6084/m9.figshare.12160485
title: Additional file 8 of Genetic dissection of heat-responsive physiological traits to improve adaptation and increase yield potential in soft winter wheat

description: Additional file 8. Summary of all significant markers and their functional annotations associated with eight traits in SWAMP.
DOI: 10.25582/data.2023-01.2718793/2292291
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.12160491
title: Additional file 9 of Genetic dissection of heat-responsive physiological traits to improve adaptation and increase yield potential in soft winter wheat

description: Additional file 9. Summary of significant pleiotropic MTAs associated with PTs, GY and other yield related traits.
DOI: 10.25582/data.2023-01.2722567/2292292
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.12160491.v1
title: Additional file 9 of Genetic dissection of heat-responsive physiological traits to improve adaptation and increase yield potential in soft winter wheat

description: Additional file 9. Summary of significant pleiotropic MTAs associated with PTs, GY and other yield related traits.
DOI: 10.25582/data.2023-02.2731319/2292293
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.14256992
title: Additional file 6 of A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations

description: Additional file 6. Predictions of potential lncRNA-disease association on Dataset1
DOI: 10.25582/data.2023-02.2731790/2292294
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25549/usctheses-c3-624496
title: etd-DeeSylviaG-3790~002
DOI: 10.25582/data.2023-02.2731576/2292295
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.20024920
title: Additional file 1 of Comprehensive analysis of lncRNA-miRNA-mRNA networks during osteogenic differentiation of bone marrow mesenchymal stem cells

description: Additional file 1.
DOI: 10.6084/m9.figshare.20024920.v1
title: Additional file 1 of Comprehensive analysis of lncRNA-miRNA-mRNA networks during osteogenic differentiation of bone marrow mesenchymal stem cells

description: Additional file 1.
DOI: 10.25582/data.2023-01.2720097/2292296
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2726327/2292297
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.7442096.v2
title: Centromere protein F (CENPF), a microtubule binding protein, modulates cancer metabolism by regulating pyruvate kinase M2 phosphorylation signaling

description: Prostate cancer (PC) is the most commonly diagnosed cancer in men and is the second leading cause of male cancer-related death in North America. Metabolic adaptations in malignant PC cells play a key role in fueling the growth and progression of the disease. Unfortunately, little is known regarding these changes in cellular metabolism. Here, we demonstrate that centromere protein F (CENPF), a protein associated with the centromere-kinetochore complex and chromosomal segregation during mitosis, is mechanically linked to altered metabolism and progression in PC. Using the CRISPR-Cas9 system, we silenced the gene for CENPF in human PC3 cells. These cells were found to have reduced levels of epithelial-mesenchymal transition markers and inhibited cell proliferation, migration, and invasion. Silencing of CENPF also simultaneously improved sensitivity to anoikis-induced apoptosis. Mass spectrometry analysis of tyrosine phosphorylated proteins from CENPF knockout (CENPF<sup>KO</sup>) and control cells revealed that CENPF silencing increased inactive forms of pyruvate kinase M2, a rate limiting enzyme needed for an irreversible reaction in glycolysis. Furthermore, CENPF<sup>KO</sup> cells had reduced global bio-energetic capacity, acetyl-CoA production, histone acetylation, and lipid metabolism, suggesting that CENPF is a critical regulator of cancer metabolism, potentially through its effects on mitochondrial functioning. Additional quantitative immunohistochemistry and imaging analyzes on a series of PC tumor microarrays demonstrated that CENPF expression is significantly increased in higher-risk PC patients. Based on these findings, we suggest the CENPF may be an important regulator of PC metabolism through its role in the mitochondria.
DOI: 10.25582/data.2023-01.2712583/2292298
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2714754/2292299
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2713544/2292300
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2722627/2292301
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.20024923.v1
title: Additional file 2 of Comprehensive analysis of lncRNA-miRNA-mRNA networks during osteogenic differentiation of bone marrow mesenchymal stem cells

description: Additional file 2.
DOI: 10.25582/data.2023-02.2731991/2292302
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.19500911
title: Additional file 1 of Hydrogel supplemented with human platelet lysate enhances multi-lineage differentiation of mesenchymal stem cells

description: Additional file 1: Table S1. Protein profile of SHED cultured at HPL.
DOI: 10.25582/data.2023-01.2717358/2292303
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2731730/2292304
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2719811/2292305
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2717914/2292306
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2731680/2292307
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2718784/2292308
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2718343/2292309
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2718495/2292310
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.19500920
title: Additional file 4 of Hydrogel supplemented with human platelet lysate enhances multi-lineage differentiation of mesenchymal stem cells

description: Additional file 4: Table S4. The expression positive rate of surface markers in flow cytometry.
DOI: 10.6084/m9.figshare.7442096
title: Centromere protein F (CENPF), a microtubule binding protein, modulates cancer metabolism by regulating pyruvate kinase M2 phosphorylation signaling

description: Prostate cancer (PC) is the most commonly diagnosed cancer in men and is the second leading cause of male cancer-related death in North America. Metabolic adaptations in malignant PC cells play a key role in fueling the growth and progression of the disease. Unfortunately, little is known regarding these changes in cellular metabolism. Here, we demonstrate that centromere protein F (CENPF), a protein associated with the centromere-kinetochore complex and chromosomal segregation during mitosis, is mechanically linked to altered metabolism and progression in PC. Using the CRISPR-Cas9 system, we silenced the gene for CENPF in human PC3 cells. These cells were found to have reduced levels of epithelial-mesenchymal transition markers and inhibited cell proliferation, migration, and invasion. Silencing of CENPF also simultaneously improved sensitivity to anoikis-induced apoptosis. Mass spectrometry analysis of tyrosine phosphorylated proteins from CENPF knockout (CENPF<sup>KO</sup>) and control cells revealed that CENPF silencing increased inactive forms of pyruvate kinase M2, a rate limiting enzyme needed for an irreversible reaction in glycolysis. Furthermore, CENPF<sup>KO</sup> cells had reduced global bio-energetic capacity, acetyl-CoA production, histone acetylation, and lipid metabolism, suggesting that CENPF is a critical regulator of cancer metabolism, potentially through its effects on mitochondrial functioning. Additional quantitative immunohistochemistry and imaging analyzes on a series of PC tumor microarrays demonstrated that CENPF expression is significantly increased in higher-risk PC patients. Based on these findings, we suggest the CENPF may be an important regulator of PC metabolism through its role in the mitochondria.
DOI: 10.6084/m9.figshare.7442096.v3
title: Centromere protein F (CENPF), a microtubule binding protein, modulates cancer metabolism by regulating pyruvate kinase M2 phosphorylation signaling

description: Prostate cancer (PC) is the most commonly diagnosed cancer in men and is the second leading cause of male cancer-related death in North America. Metabolic adaptations in malignant PC cells play a key role in fueling the growth and progression of the disease. Unfortunately, little is known regarding these changes in cellular metabolism. Here, we demonstrate that centromere protein F (CENPF), a protein associated with the centromere-kinetochore complex and chromosomal segregation during mitosis, is mechanically linked to altered metabolism and progression in PC. Using the CRISPR-Cas9 system, we silenced the gene for CENPF in human PC3 cells. These cells were found to have reduced levels of epithelial-mesenchymal transition markers and inhibited cell proliferation, migration, and invasion. Silencing of CENPF also simultaneously improved sensitivity to anoikis-induced apoptosis. Mass spectrometry analysis of tyrosine phosphorylated proteins from CENPF knockout (CENPF<sup>KO</sup>) and control cells revealed that CENPF silencing increased inactive forms of pyruvate kinase M2, a rate limiting enzyme needed for an irreversible reaction in glycolysis. Furthermore, CENPF<sup>KO</sup> cells had reduced global bio-energetic capacity, acetyl-CoA production, histone acetylation, and lipid metabolism, suggesting that CENPF is a critical regulator of cancer metabolism, potentially through its effects on mitochondrial functioning. Additional quantitative immunohistochemistry and imaging analyzes on a series of PC tumor microarrays demonstrated that CENPF expression is significantly increased in higher-risk PC patients. Based on these findings, we suggest the CENPF may be an important regulator of PC metabolism through its role in the mitochondria.
DOI: 10.25582/data.2023-01.2722736/2292311
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732045/2292312
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2722594/2292313
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732009/2292314
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.19500917
title: Additional file 3 of Hydrogel supplemented with human platelet lysate enhances multi-lineage differentiation of mesenchymal stem cells

description: Additional file 3: Table S3. Down-regulated differential abundance proteins in HPL treated SHED.
DOI: 10.6084/m9.figshare.19500920.v1
title: Additional file 4 of Hydrogel supplemented with human platelet lysate enhances multi-lineage differentiation of mesenchymal stem cells

description: Additional file 4: Table S4. The expression positive rate of surface markers in flow cytometry.
DOI: 10.25582/data.2023-01.2720902/2292315
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25549/usctheses-c3-625039
title: etd-LiNanzhou-3793~21
DOI: 10.25549/usctheses-c3-624583
title: etd-DeeSylviaG-3790~089
DOI: 10.25582/data.2023-01.2713565/2292316
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2720661/2292317
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25549/usctheses-c3-625065
title: etd-LiNanzhou-3793~47
DOI: 10.6084/m9.figshare.20025279
title: Range of factors in the reduction of hyperhydricity associated with in vitro shoots of Salvia santolinifolia Bioss

description: Abstract Hyperhydricity is a serious physiological disorder and affects In vitro propagation of many plants and as well of Salvia santolinifolia. The donor material to initiate the in vitro culture was the callus taken from the in vitro shoots produced on Murashig and Skoogs (MS) medium at 4.0 mg/l BA. This callus formed numerous hyperhydric shoots on culturing upon the medium of the same composition. The aim was to systematically evaluate the effect of cytokinins (Benzyladnine (BA) and N6-(-2-isopentenyl) adenine (2iP), culture vessels magnitude, medium solidification, source of nitrogen and calcium chloride for the alleviation of hyperhydricity. In the tissue cultures of S. santolinifolia BA and 2iP induced severe hyperhydricity, when other factors i.e. culture vessels magnitude and a suitable concentration of agar, ammonium nitrate (NH4NO3), potassium nitrate (KNO3) & calcium chloride (CaCl2.2H2O) were not optimized. After 30 days’ culture, we observed 83.82% hyperhydric shoots at increased level (1.5 mg/l 2iP) and 81.59% at decreased levels (1.0 mg/l 2iP). On the other hand, hyperhydricity percentage at decreased (0.4%) and at increased (0.8%) levels of agar were 72.37% and 39.08%, respectively. MS medium modification with NH4NO3 (412 mg/l), KNO3 (475 mg/l) and CaCl2.2H2O (880 mg/l) was found the best medium to reduced hyperhydricity (23.6%).
DOI: 10.25582/data.2023-01.2722690/2292318
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2713114/2292319
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2722676/2292320
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2730927/2292321
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-02.2731489/2292322
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2718348/2292323
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2720809/2292324
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732072/2292325
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25549/usctheses-c3-625099
title: etd-LiNanzhou-3793~81
DOI: 10.25582/data.2023-02.2732160/2292326
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25549/usctheses-c3-621883
title: etd-PrasadAdit-3772~78
DOI: 10.25582/data.2023-01.2718305/2292327
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2719532/2292328
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2718133/2292329
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2719349/2292330
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2719447/2292331
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2720955/2292332
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2720622/2292333
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2719798/2292334
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2731655/2292335
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2716754/2292336
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2719821/2292337
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2717915/2292338
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2731737/2292339
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-02.2726438/2292340
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2717908/2292341
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2723368/2292342
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2717410/2292343
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2717457/2292344
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25549/usctheses-c3-625050
title: etd-LiNanzhou-3793~32
DOI: 10.25582/data.2023-01.2718047/2292345
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2731632/2292346
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-02.2732170/2292347
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2719487/2292348
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25549/usctheses-c3-624559
title: etd-DeeSylviaG-3790~065
DOI: 10.25549/usctheses-c3-625055
title: etd-LiNanzhou-3793~37
DOI: 10.25582/data.2023-01.2720508/2292349
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2712485/2292350
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732019/2292351
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25549/usctheses-c3-624728
title: etd-DeeSylviaG-3790~234
DOI: 10.25582/data.2023-02.2731496/2292352
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25549/usctheses-c3-625096
title: etd-LiNanzhou-3793~78
DOI: 10.25582/data.2023-02.2731996/2292353
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2719519/2292354
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25549/usctheses-c3-625051
title: etd-LiNanzhou-3793~33
DOI: 10.25582/data.2023-01.2720455/2292355
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2731415/2292356
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2718456/2292357
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2718749/2292358
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2731515/2292359
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2717360/2292360
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25549/usctheses-c3-625060
title: etd-LiNanzhou-3793~42
DOI: 10.25582/data.2023-01.2718011/2292361
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.19500914.v1
title: Additional file 2 of Hydrogel supplemented with human platelet lysate enhances multi-lineage differentiation of mesenchymal stem cells

description: Additional file 2: Table S2. Up-regulated differential abundance proteins in HPL treated SHED.
DOI: 10.25582/data.2023-02.2732130/2292362
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.19500911.v1
title: Additional file 1 of Hydrogel supplemented with human platelet lysate enhances multi-lineage differentiation of mesenchymal stem cells

description: Additional file 1: Table S1. Protein profile of SHED cultured at HPL.
DOI: 10.6084/m9.figshare.19500917.v1
title: Additional file 3 of Hydrogel supplemented with human platelet lysate enhances multi-lineage differentiation of mesenchymal stem cells

description: Additional file 3: Table S3. Down-regulated differential abundance proteins in HPL treated SHED.
DOI: 10.6084/m9.figshare.19500923
title: Additional file 5 of Hydrogel supplemented with human platelet lysate enhances multi-lineage differentiation of mesenchymal stem cells

description: Additional file 5: Table S5. Proteins related to cell migration and angiogenesis in term of protein profile.
DOI: 10.6084/m9.figshare.7442096.v1
title: Centromere protein F (CENPF), a microtubule binding protein, modulates cancer metabolism by regulating pyruvate kinase M2 phosphorylation signaling

description: Prostate cancer (PC) is the most commonly diagnosed cancer in men and is the second leading cause of male cancer-related death in North America. Metabolic adaptations in malignant PC cells play a key role in fueling the growth and progression of the disease. Unfortunately, little is known regarding these changes in cellular metabolism. Here, we demonstrate that centromere protein F (CENPF), a protein associated with the centromere-kinetochore complex and chromosomal segregation during mitosis, is mechanically linked to altered metabolism and progression in PC. Using the CRISPR-Cas9 system, we silenced the gene for CENPF in human PC3 cells. These cells were found to have reduced levels of epithelial-mesenchymal transition markers and inhibited cell proliferation, migration, and invasion. Silencing of CENPF also simultaneously improved sensitivity to anoikis-induced apoptosis. Mass spectrometry analysis of tyrosine phosphorylated proteins from CENPF knockout (CENPF<sup>KO</sup>) and control cells revealed that CENPF silencing increased inactive forms of pyruvate kinase M2, a rate limiting enzyme needed for an irreversible reaction in glycolysis. Furthermore, CENPF<sup>KO</sup> cells had reduced global bio-energetic capacity, acetyl-CoA production, histone acetylation, and lipid metabolism, suggesting that CENPF is a critical regulator of cancer metabolism, potentially through its effects on mitochondrial functioning. Additional quantitative immunohistochemistry and imaging analyses on a series of PC tumor microarrays demonstrated that CENPF expression is significantly increased in higher-risk PC patients. Based on these findings, we suggest the CENPF may be an important regulator of PC metabolism through its role in the mitochondria.
DOI: 10.6084/m9.figshare.19500923.v1
title: Additional file 5 of Hydrogel supplemented with human platelet lysate enhances multi-lineage differentiation of mesenchymal stem cells

description: Additional file 5: Table S5. Proteins related to cell migration and angiogenesis in term of protein profile.
DOI: 10.25582/data.2023-01.2723563/2292363
title: Data for EMSL Project 51287 from January 2023