cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1399208.v11
title: Destabilization of pluripotency in the absence of Mad2l2

description: The induction and maintenance of pluripotency requires the expression of several core factors at appropriate levels (Oct4, Sox2, Klf4, Prdm14). A subset of these proteins (Oct4, Sox2, Prdm14) also plays crucial roles for the establishment of primordial germ cells (PGCs). Here we demonstrate that the Mad2l2 (MAD2B, Rev7) gene product is not only required by PGCs, but also by pluripotent embryonic stem cells (ESCs), depending on the growth conditions. Mad2l2<sup>−/−</sup> ESCs were unstable in LIF/serum medium, and differentiated into primitive endoderm. However, they could be stably propagated using small molecule inhibitors of MAPK signaling. Several components of the MAPK cascade were up- or downregulated even in undifferentiated Mad2l2<sup>−/−</sup> ESCs. Global levels of repressive histone H3 variants were increased in mutant ESCs, and the epigenetic signatures on pluripotency-, primitive endoderm-, and MAPK-related loci differed. Thus, H3K9me2 repressed the Nanog promoter, while the promoter of Gata4 lost H3K27me3 and became de-repressed in LIF/serum condition. Promoters associated with genes involved in MAPK signaling also showed misregulation of these histone marks. Such epigenetic modifications could be indirect consequences of mutating Mad2l2. However, our previous observations suggested the histone methyltransferases as direct (G9a) or indirect (Ezh2) targets of Mad2l2. In effect, the intricate balance necessary for pluripotency becomes perturbed in the absence of Mad2l2.
DOI: 10.6084/m9.figshare.1399172
title: Conservation status and chemical defence data

description: Dataset used for analyses in the paper "chemical antipredator defence is linked to higher extinction risk".
DOI: 10.6084/m9.figshare.1409398.v229
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 of 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 leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the 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 that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1399160
title: Estimates of the influence of poverty on national cancer counts, by site and stage

description: These are the data used to generate Figure 2 in the manuscript, "The relationship between cancer incidence, stage, and poverty in the United States". The variable 'count' represents the actual single year case counts in the areas included in the study (16 states+Los Angeles) projected to the entire US. The variable 'countnopov' represents the expected case counts were all persons to be in the lowest poverty category, all other things being equal.
DOI: 10.6084/m9.figshare.1399208.v12
title: Destabilization of pluripotency in the absence of Mad2l2

description: The induction and maintenance of pluripotency requires the expression of several core factors at appropriate levels (Oct4, Sox2, Klf4, Prdm14). A subset of these proteins (Oct4, Sox2, Prdm14) also plays crucial roles for the establishment of primordial germ cells (PGCs). Here we demonstrate that the Mad2l2 (MAD2B, Rev7) gene product is not only required by PGCs, but also by pluripotent embryonic stem cells (ESCs), depending on the growth conditions. Mad2l2<sup>−/−</sup> ESCs were unstable in LIF/serum medium, and differentiated into primitive endoderm. However, they could be stably propagated using small molecule inhibitors of MAPK signaling. Several components of the MAPK cascade were up- or downregulated even in undifferentiated Mad2l2<sup>−/−</sup> ESCs. Global levels of repressive histone H3 variants were increased in mutant ESCs, and the epigenetic signatures on pluripotency-, primitive endoderm-, and MAPK-related loci differed. Thus, H3K9me2 repressed the Nanog promoter, while the promoter of Gata4 lost H3K27me3 and became de-repressed in LIF/serum condition. Promoters associated with genes involved in MAPK signaling also showed misregulation of these histone marks. Such epigenetic modifications could be indirect consequences of mutating Mad2l2. However, our previous observations suggested the histone methyltransferases as direct (G9a) or indirect (Ezh2) targets of Mad2l2. In effect, the intricate balance necessary for pluripotency becomes perturbed in the absence of Mad2l2.
DOI: 10.6084/m9.figshare.1399160.v2
title: Estimates of the influence of poverty on national cancer counts, by site and stage

description: These are the data used to generate Figure 2 in the manuscript, "The relationship between cancer incidence, stage, and poverty in the United States". The variable 'count' represents the actual single year case counts in the areas included in the study (16 states+Los Angeles) projected to the entire US. The variable 'countnopov' represents the expected case counts were all persons to be in the lowest poverty category, all other things being equal.
DOI: 10.6084/m9.figshare.1399172.v1
title: Conservation status and chemical defence data

description: Dataset used for analyses in the paper "chemical antipredator defence is linked to higher extinction risk".
DOI: 10.6084/m9.figshare.1409398.v230
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 of 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 leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the 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 that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1399159
title: Relative risk of cancer incidence by site, stage, and poverty level

description: These are the data used to generate Figure 1 in the manuscript, "The relationship between cancer incidence, stage, and poverty in the United States". The relative risks are relative to the lowest poverty group (&lt;5% poverty). Confidence intervals are 95% CIs. The poisson regression model used to generate these results modeled expected counts based on age, sex, race, poverty, and log-population.
DOI: 10.6084/m9.figshare.1399185.v5
title: GlobWave multimission corrected Significant Wave Height for January, 2002

description: The complete GlobWave dataset is found at: ftp://ftp.ifremer.fr/ifremer/cersat/products/swath/altimeters/waves/data/ For access please consult: globwave.ifremer.fr/products/globwave-satellite-data
DOI: 10.6084/m9.figshare.1399160.v1
title: Estimates of the influence of poverty on national cancer counts, by site and stage

description: These are the data used to generate Figure 2 in the manuscript, "The relationship between cancer incidence, stage, and poverty in the United States". The variable 'count' represents the actual single year case counts in the areas included in the study (16 states+Los Angeles) projected to the entire US. The variable 'countnopov' represents the expected case counts were all persons to be in the lowest poverty category, all other things being equal.
DOI: 10.6084/m9.figshare.1399158
title: Cancer counts and populations by site, stage, sex, poverty, race, and age

description: This is a file containing cancer counts and populations stratified by site (21 most common stageable sites plus tobacco-related, HPV-related, and all stageable sites combined), stage (local, regional, distant, unknown), sex, census tract poverty category (&lt;5%, 5-9.9%, 10-19.9% and 20+% of households in the census tract of residence at diagnosis below poverty level as measured by the 2005-2009 American Community Survey), race (white, black, Asian and Pacific Islander, American Indian and Alaska Native, Hispanic), and age (0, 1-4, 5-9, then 5 year groups through 80-84, 85+) for 16 US states plus Los Angelese. These data are being used in the manuscript in preparation, "The relationship between cancer incidence, stage, and poverty in the United States". The populations were customized for this project, but are consistent with the populations published here: http://seer.cancer.gov/popdata/
DOI: 10.6084/m9.figshare.1399159.v1
title: Relative risk of cancer incidence by site, stage, and poverty level

description: These are the data used to generate Figure 1 in the manuscript, "The relationship between cancer incidence, stage, and poverty in the United States". The relative risks are relative to the lowest poverty group (&lt;5% poverty). Confidence intervals are 95% CIs. The poisson regression model used to generate these results modeled expected counts based on age, sex, race, poverty, and log-population.
DOI: 10.6084/m9.figshare.1409398.v231
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 of 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 leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the 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 that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1399154
title: Associations between prenatal physical activity, birth weight, and DNA methylation at genomically imprinted domains in a multiethnic newborn cohort

description: Birth weight is a commonly used indicator of the fetal environment and a predictor of future health outcomes. While the etiology of birth weight extremes is likely multifactorial, epidemiologic data suggest that prenatal physical activity (PA) may play an important role. The mechanisms underlying this association remain unresolved, although epigenetics has been proposed. This study aimed to estimate associations between prenatal PA, birth weight, and newborn DNA methylation levels at differentially methylated regions (DMRs) regulating 4 imprinted genes known to be important in fetal development. Study participants (N = 1281) were enrolled as part of the Newborn Epigenetics Study. Prenatal PA was ascertained using the Pregnancy Physical Activity Questionnaire, and birth weight data obtained from hospital records. Among 484 term mother-infant pairs, imprinted gene methylation levels were measured at DMRs using bisulfite pyrosequencing. Generalized linear and logistic regression models were used to estimate associations. After adjusting for preterm birth and race/ethnicity, we found that infants born to mothers in the highest quartile of total non-sedentary time had lower birth weight compared to infants of mothers in the lowest quartile (β = −81.16, SE = 42.02, <i>P</i> = 0.05). These associations appeared strongest among male infants (β = −125.40, SE = 58.10, <i>P</i> = 0.03). Methylation at the <i>PLAGL1</i> DMR was related to total non-sedentary time (<i>P</i> &lt; 0.05). Our findings confirm that prenatal PA is associated with reduced birth weight, and is the first study to support a role for imprinted gene plasticity in these associations. Larger studies are required.
DOI: 10.6084/m9.figshare.1399158.v1
title: Cancer counts and populations by site, stage, sex, poverty, race, and age

description: This is a file containing cancer counts and populations stratified by site (21 most common stageable sites plus tobacco-related, HPV-related, and all stageable sites combined), stage (local, regional, distant, unknown), sex, census tract poverty category (&lt;5%, 5-9.9%, 10-19.9% and 20+% of households in the census tract of residence at diagnosis below poverty level as measured by the 2005-2009 American Community Survey), race (white, black, Asian and Pacific Islander, American Indian and Alaska Native, Hispanic), and age (0, 1-4, 5-9, then 5 year groups through 80-84, 85+) for 16 US states plus Los Angelese. These data are being used in the manuscript in preparation, "The relationship between cancer incidence, stage, and poverty in the United States". The populations were customized for this project, but are consistent with the populations published here: http://seer.cancer.gov/popdata/
DOI: 10.6084/m9.figshare.1399157.v1
title: A dynein independent role of Tctex-1 at the kinetochore

description: Dynein light chains are accessory subunits of the cytoplasmic dynein complex, a minus-end directed microtubule motor. Here, we demonstrate that the dynein light chain Tctex-1 associates with unattached kinetochores and is essential for accurate chromosome segregation. Tctex-1 knockdown in cells does not affect the localization and function of dynein at the kinetochore, but produces a prolonged mitotic arrest with a few misaligned chromosomes, which are subsequently missegregated during anaphase. This function is independent of Tctex-1's association with dynein. The kinetochore localization of Tctex-1 is independent of the ZW10-dynein pathway, but requires the Ndc80 complex. Thus, our findings reveal a dynein independent role of Tctex-1 at the kinetochore to enhance the stability of kinetochore-microtubule attachment.
DOI: 10.6084/m9.figshare.1409398.v232
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 of 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 leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the 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 that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1399157
title: A dynein independent role of Tctex-1 at the kinetochore

description: Dynein light chains are accessory subunits of the cytoplasmic dynein complex, a minus-end directed microtubule motor. Here, we demonstrate that the dynein light chain Tctex-1 associates with unattached kinetochores and is essential for accurate chromosome segregation. Tctex-1 knockdown in cells does not affect the localization and function of dynein at the kinetochore, but produces a prolonged mitotic arrest with a few misaligned chromosomes, which are subsequently missegregated during anaphase. This function is independent of Tctex-1's association with dynein. The kinetochore localization of Tctex-1 is independent of the ZW10-dynein pathway, but requires the Ndc80 complex. Thus, our findings reveal a dynein independent role of Tctex-1 at the kinetochore to enhance the stability of kinetochore-microtubule attachment.
DOI: 10.6084/m9.figshare.1399154.v1
title: Associations between prenatal physical activity, birth weight, and DNA methylation at genomically imprinted domains in a multiethnic newborn cohort

description: Birth weight is a commonly used indicator of the fetal environment and a predictor of future health outcomes. While the etiology of birth weight extremes is likely multifactorial, epidemiologic data suggest that prenatal physical activity (PA) may play an important role. The mechanisms underlying this association remain unresolved, although epigenetics has been proposed. This study aimed to estimate associations between prenatal PA, birth weight, and newborn DNA methylation levels at differentially methylated regions (DMRs) regulating four imprinted genes known to be important in fetal development. Study participants (N = 1281) were enrolled as part of the Newborn Epigenetics Study. Prenatal PA was ascertained using the Pregnancy Physical Activity Questionnaire, and birth weight data obtained from hospital records. Among 484 term mother-infant pairs, imprinted gene methylation levels were measured at DMRs using bisulfite pyrosequencing. Generalized linear and logistic regression models were used to estimate associations. After adjusting for preterm birth and race/ethnicity, we found that infants born to mothers in the highest quartile of total non-sedentary time had lower birth weight compared to infants of mothers in the lowest quartile (β = −81.16, SE = 42.02, <i>P</i> = 0.05). These associations appeared strongest among male infants (β = −125.40, SE = 58.10, <i>P</i> = 0.03). Methylation at the <i>PLAGL1</i> DMR was related to total non-sedentary time (<i>P</i> &lt; 0.05). Our findings confirm that prenatal PA is associated with reduced birth weight, and is the first study to support a role for imprinted gene plasticity in these associations. Larger studies are required.
DOI: 10.6084/m9.figshare.1399157.v3
title: A dynein independent role of Tctex-1 at the kinetochore

description: Dynein light chains are accessory subunits of the cytoplasmic dynein complex, a minus-end directed microtubule motor. Here, we demonstrate that the dynein light chain Tctex-1 associates with unattached kinetochores and is essential for accurate chromosome segregation. Tctex-1 knockdown in cells does not affect the localization and function of dynein at the kinetochore, but produces a prolonged mitotic arrest with a few misaligned chromosomes, which are subsequently missegregated during anaphase. This function is independent of Tctex-1's association with dynein. The kinetochore localization of Tctex-1 is independent of the ZW10-dynein pathway, but requires the Ndc80 complex. Thus, our findings reveal a dynein independent role of Tctex-1 at the kinetochore to enhance the stability of kinetochore-microtubule attachment.