cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1397459.v1
title: dsS2SNetStdTIs_NB

description: Standardized S2SNet TIs dataset of nucleotide binding proteins
DOI: 10.6084/m9.figshare.1397460.v3
title: dsS2SNetTIs_NB

description: S2SNet TIs dataset of nucleotide binding proteins
DOI: 10.6084/m9.figshare.1397471.v2
title: Selective inhibition of esophageal cancer cells by combination of HDAC inhibitors and Azacytidine

description: Esophageal cancers are highly aggressive tumors with poor prognosis despite some recent advances in surgical and radiochemotherapy treatment options. This study addressed the feasibility of drugs targeting epigenetic modifiers in esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) cells. We tested inhibition of histone deacetylases (HDACs) by SAHA, MS-275, and FK228, inhibition of DNA methyltransferases by Azacytidine (AZA) and Decitabine (DAC), and the effect of combination treatment using both types of drugs. The drug targets, HDAC1/2/3 and DNMT1, were expressed in normal esophageal epithelium and tumor cells of ESCC or EAC tissue specimens, as well as in non-neoplastic esophageal epithelial (Het-1A), ESCC (OE21, Kyse-270, Kyse-410), and EAC (OE33, SK-GT-4) cell lines. <i>In vitro</i>, HDAC activity, histone acetylation, and p21 expression were similarly affected in non-neoplastic, ESCC, and EAC cell lines post inhibitor treatment. Combined MS-275/AZA treatment, however, selectively targeted esophageal cancer cell lines by inducing DNA damage, cell viability loss, and apoptosis, and by decreasing cell migration. Non-neoplastic Het-1A cells were protected against HDACi (MS-275)/AZA treatment. RNA transcriptome analyses post MS-275 and/or AZA treatment identified novel regulated candidate genes (up: <i>BCL6, Hes2</i>; down: <i>FAIM, MLKL</i>), which were specifically associated with the treatment responses of esophageal cancer cells. In summary, combined HDACi/AZA treatment is efficient and selective for the targeting of esophageal cancer cells, despite similar target expression of normal and esophageal cancer epithelium, <i>in vitro</i> and in human esophageal carcinomas. The precise mechanisms of action of treatment responses involve novel candidate genes regulated by HDACi/AZA in esophageal cancer cells. Together, targeting of epigenetic modifiers in esophageal cancers may represent a potential future therapeutic approach.
DOI: 10.6084/m9.figshare.1397459.v3
title: dsS2SNetStdTIs_NB

description: Standardized S2SNet TIs dataset of nucleotide binding proteins
DOI: 10.6084/m9.figshare.1397460.v2
title: dsS2SNetTIs_NB

description: S2SNet TIs dataset of nucleotide binding proteins
DOI: 10.6084/m9.figshare.1397471.v4
title: Selective inhibition of esophageal cancer cells by combination of HDAC inhibitors and Azacytidine

description: Esophageal cancers are highly aggressive tumors with poor prognosis despite some recent advances in surgical and radiochemotherapy treatment options. This study addressed the feasibility of drugs targeting epigenetic modifiers in esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) cells. We tested inhibition of histone deacetylases (HDACs) by SAHA, MS-275, and FK228, inhibition of DNA methyltransferases by Azacytidine (AZA) and Decitabine (DAC), and the effect of combination treatment using both types of drugs. The drug targets, HDAC1/2/3 and DNMT1, were expressed in normal esophageal epithelium and tumor cells of ESCC or EAC tissue specimens, as well as in non-neoplastic esophageal epithelial (Het-1A), ESCC (OE21, Kyse-270, Kyse-410), and EAC (OE33, SK-GT-4) cell lines. <i>In vitro</i>, HDAC activity, histone acetylation, and p21 expression were similarly affected in non-neoplastic, ESCC, and EAC cell lines post inhibitor treatment. Combined MS-275/AZA treatment, however, selectively targeted esophageal cancer cell lines by inducing DNA damage, cell viability loss, and apoptosis, and by decreasing cell migration. Non-neoplastic Het-1A cells were protected against HDACi (MS-275)/AZA treatment. RNA transcriptome analyses post MS-275 and/or AZA treatment identified novel regulated candidate genes (up: <i>BCL6, Hes2</i>; down: <i>FAIM, MLKL</i>), which were specifically associated with the treatment responses of esophageal cancer cells. In summary, combined HDACi/AZA treatment is efficient and selective for the targeting of esophageal cancer cells, despite similar target expression of normal and esophageal cancer epithelium, <i>in vitro</i> and in human esophageal carcinomas. The precise mechanisms of action of treatment responses involve novel candidate genes regulated by HDACi/AZA in esophageal cancer cells. Together, targeting of epigenetic modifiers in esophageal cancers may represent a potential future therapeutic approach.
DOI: 10.6084/m9.figshare.1397459.v2
title: dsS2SNetStdTIs_NB

description: Standardized S2SNet TIs dataset of nucleotide binding proteins
DOI: 10.6084/m9.figshare.1409398.v254
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.1397471.v3
title: Selective inhibition of esophageal cancer cells by combination of HDAC inhibitors and Azacytidine

description: Esophageal cancers are highly aggressive tumors with poor prognosis despite some recent advances in surgical and radiochemotherapy treatment options. This study addressed the feasibility of drugs targeting epigenetic modifiers in esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) cells. We tested inhibition of histone deacetylases (HDACs) by SAHA, MS-275, and FK228, inhibition of DNA methyltransferases by Azacytidine (AZA) and Decitabine (DAC), and the effect of combination treatment using both types of drugs. The drug targets, HDAC1/2/3 and DNMT1, were expressed in normal esophageal epithelium and tumor cells of ESCC or EAC tissue specimens, as well as in non-neoplastic esophageal epithelial (Het-1A), ESCC (OE21, Kyse-270, Kyse-410), and EAC (OE33, SK-GT-4) cell lines. <i>In vitro</i>, HDAC activity, histone acetylation, and p21 expression were similarly affected in non-neoplastic, ESCC, and EAC cell lines post inhibitor treatment. Combined MS-275/AZA treatment, however, selectively targeted esophageal cancer cell lines by inducing DNA damage, cell viability loss, and apoptosis, and by decreasing cell migration. Non-neoplastic Het-1A cells were protected against HDACi (MS-275)/AZA treatment. RNA transcriptome analyses post MS-275 and/or AZA treatment identified novel regulated candidate genes (up: <i>BCL6, Hes2</i>; down: <i>FAIM, MLKL</i>), which were specifically associated with the treatment responses of esophageal cancer cells. In summary, combined HDACi/AZA treatment is efficient and selective for the targeting of esophageal cancer cells, despite similar target expression of normal and esophageal cancer epithelium, <i>in vitro</i> and in human esophageal carcinomas. The precise mechanisms of action of treatment responses involve novel candidate genes regulated by HDACi/AZA in esophageal cancer cells. Together, targeting of epigenetic modifiers in esophageal cancers may represent a potential future therapeutic approach.
DOI: 10.6084/m9.figshare.1397443
title: Proteomic analysis of reproduction proteins involved in litter size from porcine placenta

description: A gel-free and label-free quantitative proteomic approach based on a spectral counting strategy was performed to discover prolificacy-related proteins. Soluble proteins of porcine placenta from small litter size group (SLSG) and large litter size group (LLSG) were extracted and subsequently applied to in-solution tryptic digestion followed by liquid chromatography–tandem mass spectrometry analysis. Six and thirteen proteins were highly expressed in SLSG and LLSG, respectively. Of the dominantly expressed proteins, we chose prolificacy-related proteins such as puromycin-sensitive aminopeptidase (PSA) and retinol-binding protein 4 (RBP4). Western blot analysis confirmed that the processed form (70 kDa) of PSA was more expressed and RBP4 (23 kDa) was dominantly expressed in LLSG. These results indicate that PSA and RBP4 are representative proteins involved in porcine fertility traits, and this finding may help to increase litter size of pigs.
DOI: 10.6084/m9.figshare.1409398.v255
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.1409398.v256
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.12921368.v1
title: Model-based edge clustering

description: Relational data can be studied using network analytic techniques which define the network as a set of actors and a set of edges connecting these actors. One important facet of network analysis that receives significant attention is community detection. However, while most community detection algorithms focus on clustering the actors of the network, it is very intuitive to cluster the edges. Connections exist because they were formed within some latent environment such as, in the case of a social network, a workplace or religious group, and hence by clustering the edges of a network we may gain some insight into these latent environments. We propose a model-based approach to clustering the edges of a network using a latent space model describing the features of both actors and latent environments. We derive a generalized EM algorithm for estimation and gradient-based Monte Carlo algorithms, and we demonstrate that the computational cost grows linearly in the number of actors for sparse networks rather than quadratically. We demonstrate the potential impact of our proposed approach on a patient transfer network, verifying these results by running simple epidemic simulations, and on a real friendship network amongst faculty members at a university in the United Kingdom.
DOI: 10.6084/m9.figshare.1397443.v2
title: Proteomic analysis of reproduction proteins involved in litter size from porcine placenta

description: A gel-free and label-free quantitative proteomic approach based on a spectral counting strategy was performed to discover prolificacy-related proteins. Soluble proteins of porcine placenta from small litter size group (SLSG) and large litter size group (LLSG) were extracted and subsequently applied to in-solution tryptic digestion followed by liquid chromatography–tandem mass spectrometry analysis. Six and thirteen proteins were highly expressed in SLSG and LLSG, respectively. Of the dominantly expressed proteins, we chose prolificacy-related proteins such as puromycin-sensitive aminopeptidase (PSA) and retinol-binding protein 4 (RBP4). Western blot analysis confirmed that the processed form (70 kDa) of PSA was more expressed and RBP4 (23 kDa) was dominantly expressed in LLSG. These results indicate that PSA and RBP4 are representative proteins involved in porcine fertility traits, and this finding may help to increase litter size of pigs.
DOI: 10.6084/m9.figshare.1409398.v257
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.12921368
title: Model-based edge clustering

description: Relational data can be studied using network analytic techniques which define the network as a set of actors and a set of edges connecting these actors. One important facet of network analysis that receives significant attention is community detection. However, while most community detection algorithms focus on clustering the actors of the network, it is very intuitive to cluster the edges. Connections exist because they were formed within some latent environment such as, in the case of a social network, a workplace or religious group, and hence by clustering the edges of a network we may gain some insight into these latent environments. We propose a model-based approach to clustering the edges of a network using a latent space model describing the features of both actors and latent environments. We derive a generalized EM algorithm for estimation and gradient-based Monte Carlo algorithms, and we demonstrate that the computational cost grows linearly in the number of actors for sparse networks rather than quadratically. We demonstrate the potential impact of our proposed approach on a patient transfer network, verifying these results by running simple epidemic simulations, and on a real friendship network amongst faculty members at a university in the United Kingdom.
DOI: 10.6084/m9.figshare.1397437
title: Cloud Computing

description: Recently researchers
DOI: 10.6084/m9.figshare.1397443.v1
title: Proteomic analysis of reproduction proteins involved in litter size from porcine placenta

description: A gel-free and label-free quantitative proteomic approach based on a spectral counting strategy was performed to discover prolificacy-related proteins. Soluble proteins of porcine placenta from small litter size group (SLSG) and large litter size group (LLSG) were extracted and subsequently applied to in-solution tryptic digestion followed by liquid chromatography–tandem mass spectrometry analysis. Six and thirteen proteins were highly expressed in SLSG and LLSG, respectively. Of the dominantly expressed proteins, we chose prolificacy-related proteins such as puromycin-sensitive aminopeptidase (PSA) and retinol-binding protein 4 (RBP4). Western blot analysis confirmed that the processed form (70 kDa) of PSA was more expressed and RBP4 (23 kDa) was dominantly expressed in LLSG. These results indicate that PSA and RBP4 are representative proteins involved in porcine fertility traits, and this finding may help to increase litter size of pigs.
DOI: 10.6084/m9.figshare.1409398.v258
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.1397437.v2
title: Cloud Computing

description: Recently researchers
DOI: 10.6084/m9.figshare.1397425
title: Diffusion data

description: Diffusion MRI data