cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3179941.v2
title: Factors affecting the persistence of drug-induced reprogramming of the cancer methylome

description: Aberrant DNA methylation is a critical feature of cancer. Epigenetic therapy seeks to reverse these changes to restore normal gene expression. DNA demethylating agents, including 5-aza-2′-deoxycytidine (DAC), are currently used to treat certain leukemias, and can sensitize solid tumors to chemotherapy and immunotherapy. However, it has been difficult to pin the clinical efficacy of these agents to specific demethylation events, and the factors that contribute to the durability of response remain largely unknown. Here we examined the genome-wide kinetics of DAC-induced DNA demethylation and subsequent remethylation after drug withdrawal in breast cancer cells. We find that CpGs differ in both their susceptibility to demethylation and propensity for remethylation after drug removal. DAC-induced demethylation was most apparent at CpGs with higher initial methylation levels and further from CpG islands. Once demethylated, such sites exhibited varied remethylation potentials. The most rapidly remethylating CpGs regained &gt;75% of their starting methylation within a month of drug withdrawal. These sites had higher pretreatment methylation levels, were enriched in gene bodies, marked by H3K36me3, and tended to be methylated in normal breast cells. In contrast, a more resistant class of CpG sites failed to regain even 20% of their initial methylation after 3 months. These sites had lower pretreatment methylation levels, were within or near CpG islands, marked by H3K79me2 or H3K4me2/3, and were overrepresented in sites that become aberrantly hypermethylated in breast cancers. Thus, whereas DAC-induced demethylation affects both endogenous and aberrantly methylated sites, tumor-specific hypermethylation is more slowly regained, even as normal methylation promptly recovers. Taken together, these data suggest that the durability of DAC response is linked to its selective ability to stably reset at least a portion of the cancer methylome.
DOI: 10.6084/m9.figshare.3179935.v1
title: Stephan_DUV_Poster_Force2016.pdf

description: As part of the activities of the W3C Data on the Web Best Practices Working Group, the Dataset UsageVocabulary was developed to address aspects related to the consumption of published Web datasets.
DOI: 10.6084/m9.figshare.3179938.v2
title: The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin

description: Histone variants play a critical role in chromatin structure and epigenetic regulation. These “deviant” proteins have been historically considered as the evolutionary descendants of ancestral canonical histones, helping specialize the nucleosome structure during eukaryotic evolution. Such view is now challenged by 2 major observations: first, canonical histones present extremely unique features not shared with any other genes; second, histone variants are widespread across many eukaryotic groups. The present work further supports the ancestral nature of histone variants by providing the first <i>in vivo</i> characterization of a functional macroH2A histone (a variant long defined as a specific refinement of vertebrate chromatin) in a non-vertebrate organism (the mussel <i>Mytilus</i>) revealing its recruitment into heterochromatic fractions of actively proliferating tissues. Combined with <i>in silico</i> analyses of genomic data, these results provide evidence for the widespread presence of macroH2A in metazoan animals, as well as in the holozoan <i>Capsaspora</i>, supporting an evolutionary origin for this histone variant lineage before the radiation of Filozoans (including Filasterea, Choanoflagellata and Metazoa). Overall, the results presented in this work help configure a new evolutionary scenario in which histone variants, rather than modern “deviants” of canonical histones, would constitute ancient components of eukaryotic chromatin.
DOI: 10.6084/m9.figshare.3179941.v1
title: Factors affecting the Persistence of Drug-induced Reprogramming of the Cancer Methylome

description: Aberrant DNA methylation is a critical feature of cancer. Epigenetic therapy seeks to reverse these changes to restore normal gene expression. DNA demethylating agents, including 5-aza-2′-deoxycytidine (DAC), are currently used to treat certain leukemias, and can sensitize solid tumors to chemotherapy and immunotherapy. However, it has been difficult to pin the clinical efficacy of these agents to specific demethylation events and the factors that contribute to the durability of response remain largely unknown. Here we examined the genome-wide kinetics of DAC-induced DNA demethylation and subsequent remethylation after drug withdrawal in breast cancer cells. We find that CpGs differ in both their susceptibility to demethylation and propensity for remethylation after drug removal. DAC-induced demethylation was most apparent at CpGs with higher initial methylation levels and further from CpG islands. Once demethylated, such sites exhibited varied remethylation potentials. The most rapidly remethylating CpGs regained &gt;75% of their starting methylation within a month of drug withdrawal. These sites had higher pretreatment methylation levels, were enriched in gene bodies, marked by H3K36me3, and tended to be methylated in normal breast cells. In contrast, a more resistant class of CpG sites failed to regain even 20% of their initial methylation after 3 months. These sites had lower pretreatment methylation levels, were within or near CpG islands, marked by H3K79me2 or H3K4me2/3, and were overrepresented in sites that become aberrantly hypermethylated in breast cancers. Thus, whereas DAC-induced demethylation affects both endogenous and aberrantly methylated sites, tumor-specific hypermethylation is more slowly regained, even as normal methylation promptly recovers. Taken together, these data suggest that the durability of DAC response is linked to its selective ability to stably reset at least a portion of the cancer methylome.
DOI: 10.6084/m9.figshare.3179938
title: The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin

description: Histone variants play a critical role in chromatin structure and epigenetic regulation. These “deviant” proteins have been historically considered as the evolutionary descendants of ancestral canonical histones, helping specialize the nucleosome structure during eukaryotic evolution. Such view is now challenged by 2 major observations: first, canonical histones present extremely unique features not shared with any other genes; second, histone variants are widespread across many eukaryotic groups. The present work further supports the ancestral nature of histone variants by providing the first <i>in vivo</i> characterization of a functional macroH2A histone (a variant long defined as a specific refinement of vertebrate chromatin) in a non-vertebrate organism (the mussel <i>Mytilus</i>) revealing its recruitment into heterochromatic fractions of actively proliferating tissues. Combined with <i>in silico</i> analyses of genomic data, these results provide evidence for the widespread presence of macroH2A in metazoan animals, as well as in the holozoan <i>Capsaspora</i>, supporting an evolutionary origin for this histone variant lineage before the radiation of Filozoans (including Filasterea, Choanoflagellata and Metazoa). Overall, the results presented in this work help configure a new evolutionary scenario in which histone variants, rather than modern “deviants” of canonical histones, would constitute ancient components of eukaryotic chromatin.
DOI: 10.6084/m9.figshare.3179938.v1
title: The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin

description: Histone variants play a critical role in chromatin structure and epigenetic regulation. These “deviant” proteins have been historically considered as the evolutionary descendants of ancestral canonical histones, helping specialize the nucleosome structure during eukaryotic evolution. Such view is now challenged by 2 major observations: first, canonical histones present extremely unique features not shared with any other genes; second, histone variants are widespread across many eukaryotic groups. The present work further supports the ancestral nature of histone variants by providing the first <i>in vivo</i> characterization of a functional macroH2A histone (a variant long defined as a specific refinement of vertebrate chromatin) in a non-vertebrate organism (the mussel <i>Mytilus</i>) revealing its recruitment into heterochromatic fractions of actively proliferating tissues. Combined with <i>in silico</i> analyses of genomic data, these results provide evidence for the widespread presence of macroH2A in metazoan animals, as well as in the holozoan <i>Capsaspora</i>, supporting an evolutionary origin for this histone variant lineage before the radiation of Filozoans (including Filasterea, Choanoflagellata and Metazoa). Overall, the results presented in this work help configure a new evolutionary scenario in which histone variants, rather than modern “deviants” of canonical histones, would constitute ancient components of eukaryotic chromatin.
DOI: 10.6084/m9.figshare.3179833
title: The role of self-regulation in the context of driver distraction: A simulator study

description: <b>Objective</b>: There is considerable evidence for the negative effects of driver distraction on road safety. In many experimental studies, drivers have been primarily viewed as passive receivers of distraction. Thus, there is a lack of research on the mediating role of their self-regulatory behavior. The aim of the current study was to compare drivers' performance when engaged in a system-paced secondary task with a self-paced version of this task and how both differed from baseline driving performance without distraction. <b>Methods</b>: Thirty-nine participants drove in a simulator while performing a secondary visual–manual task. One group of drivers had to work on this task in predefined situations under time pressure, whereas the other group was free to decide when to work on the secondary task (self-regulation group). Drivers' performance (e.g., lateral and longitudinal control, brake reaction times) was also compared with a baseline condition without any secondary task. <b>Results</b>: For the system-paced secondary task, distraction was associated with high decrements in driving performance (especially in keeping the lateral position). No effects were found for the number of collisions, probably because of the lower driving speeds while distracted (compensatory behavior). For the self-regulation group, only small impairments in driving performance were found. Drivers engaged less in the secondary task during foreseeable demanding or critical driving situations. <b>Conclusions</b>: Overall, drivers in the self-regulation group were able to anticipate the demands of different traffic situations and to adapt their engagement in the secondary task, so that only small impairments in driving performance occurred. Because in real traffic drivers are mostly free to decide when to engage in secondary tasks, it can be concluded that self-regulation should be considered in driver distraction research to ensure ecological validity.
DOI: 10.6084/m9.figshare.3179833.v1
title: The role of self-regulation in the context of driver distraction: A simulator study

description: <b>Objective</b>: There is considerable evidence for the negative effects of driver distraction on road safety. In many experimental studies, drivers have been primarily viewed as passive receivers of distraction. Thus, there is a lack of research on the mediating role of their self-regulatory behavior. The aim of the current study was to compare drivers' performance when engaged in a system-paced secondary task with a self-paced version of this task and how both differed from baseline driving performance without distraction. <b>Methods</b>: Thirty-nine participants drove in a simulator while performing a secondary visual–manual task. One group of drivers had to work on this task in predefined situations under time pressure, whereas the other group was free to decide when to work on the secondary task (self-regulation group). Drivers' performance (e.g., lateral and longitudinal control, brake reaction times) was also compared with a baseline condition without any secondary task. <b>Results</b>: For the system-paced secondary task, distraction was associated with high decrements in driving performance (especially in keeping the lateral position). No effects were found for the number of collisions, probably because of the lower driving speeds while distracted (compensatory behavior). For the self-regulation group, only small impairments in driving performance were found. Drivers engaged less in the secondary task during foreseeable demanding or critical driving situations. <b>Conclusions</b>: Overall, drivers in the self-regulation group were able to anticipate the demands of different traffic situations and to adapt their engagement in the secondary task, so that only small impairments in driving performance occurred. Because in real traffic drivers are mostly free to decide when to engage in secondary tasks, it can be concluded that self-regulation should be considered in driver distraction research to ensure ecological validity.
DOI: 10.18462/iir.rankine.2020.1171
title: Accurate modeling of heat pump cycles with steam injection in off-design regimes utilizing an integrated approach.
DOI: 10.6084/m9.figshare.3179476
title: example RDFORM

description: This is an example rdform for use with figmeta. This form allows organizational affiliations to be associated with authors on a dataset. Organizations are represented with GRID uri's
DOI: 10.6084/m9.figshare.3179428
title: U–Pb SIMS dating of some granitoids from eastern Blekinge, southern Sweden

description: Zircons from seven granitoids in eastern Blekinge have been dated using secondary ion mass spectrometry. The analyzed rocks include one Småland granitoid from north of the Småland-Blekinge Deformation Zone (SBDZ), two samples of megacrystic “Filipstad-type” granite from south of that zone and one sample each of the “Småland-type” Rödeby, Almö, Tjurkö and Jämjö granites. The results yield a crystallization age of 1778 ± 5 Ma for the Småland granitoid, and crystallization ages between 1770 ± 4 and 1758 ± 5 Ma for the other granitoids, in most cases substantially older than previous TIMS ages. These data show that the “Småland-type” granitoids in eastern Blekinge are similar in age to the surrounding Tving granitoids, and the more felsic of them may represent late-stage differentiates belonging to the same magmatic suite. As the Tving granitoids show differences both in degree of deformation, in geochemistry and in age, compared to the Småland granitoids north of the SBDZ, it is suggested that these represent two separate but closely related igneous suites, which could both be included within a TIB-1 supersuite. The investigated zircons showed very limited signs of metamorphic overprinting, and no metamorphic ages could be determined. However, the combined evidence from field observations and earlier U–Pb geochronology would suggest the presence of two separate metamorphic episodes in Blekinge, one in close connection with the formation of these rocks at 1.76–1.75 Ga and one connected to the intrusion of the Karlshamn granitoid suite at around 1.45 Ga.
DOI: 10.6084/m9.figshare.3179410
title: finance_artificial_mark_2159.txt

description: chinese finance dataset
DOI: 10.6084/m9.figshare.3179413
title: finance_news_43561.txt

description: Chinese finance dataset
DOI: 10.6084/m9.figshare.3179419.v1
title: Age and nature of 560–520 Ma calc-alkaline granitoids of Biarjmand, northeast Iran: insights into Cadomian arc magmatism in northern Gondwana

description: The Biarjmand granitoids and granitic gneisses in northeast Iran are part of the Torud–Biarjmand metamorphic complex, where previous zircon U–Pb geochronology show ages of ca. 554–530 Ma for orthogneissic rocks. Our new U–Pb zircon ages confirm a Cadomian age and show that the granitic gneiss is ~30 million years older (561.3 ± 4.7 Ma) than intruding granitoids (522.3 ± 4.2 Ma; 537.7 ± 4.7 Ma). Cadomian magmatism in Iran was part of an approximately 100-million-year-long episode of subduction-related arc and back-arc magmatism, which dominated the whole northern Gondwana margin, from Iberia to Turkey and Iran. Major REE and trace element data show that these granitoids have calc-alkaline signatures. Their zircon O (δ<sup>18</sup>O = 6.2–8.9‰) and Hf (–7.9 to +5.5; one point with εHf ~ –17.4) as well as bulk rock Nd isotopes (εNd(<i>t</i>) = –3 to –6.2) show that these magmas were generated via mixing of juvenile magmas with an older crust and/or melting of middle continental crust. Whole-rock Nd and zircon Hf model ages (1.3–1.6 Ga) suggest that this older continental crust was likely to have been Mesoproterozoic or even older. Our results, including variable zircon εHf(<i>t</i>) values, inheritance of old zircons and lack of evidence for juvenile Cadomian igneous rocks anywhere in Iran, suggest that the geotectonic setting during late Ediacaran and early Cambrian time was a continental magmatic arc rather than back-arc for the evolution of northeast Iran Cadomian igneous rocks.
DOI: 10.6084/m9.figshare.3179410.v1
title: finance_artificial_mark_2159.txt

description: chinese finance dataset
DOI: 10.6084/m9.figshare.3179413.v1
title: finance_news_43561.txt

description: Chinese finance dataset
DOI: 10.6084/m9.figshare.3179428.v1
title: U–Pb SIMS dating of some granitoids from eastern Blekinge, southern Sweden

description: Zircons from seven granitoids in eastern Blekinge have been dated using secondary ion mass spectrometry. The analyzed rocks include one Småland granitoid from north of the Småland-Blekinge Deformation Zone (SBDZ), two samples of megacrystic “Filipstad-type” granite from south of that zone and one sample each of the “Småland-type” Rödeby, Almö, Tjurkö and Jämjö granites. The results yield a crystallization age of 1778 ± 5 Ma for the Småland granitoid, and crystallization ages between 1770 ± 4 and 1758 ± 5 Ma for the other granitoids, in most cases substantially older than previous TIMS ages. These data show that the “Småland-type” granitoids in eastern Blekinge are similar in age to the surrounding Tving granitoids, and the more felsic of them may represent late-stage differentiates belonging to the same magmatic suite. As the Tving granitoids show differences both in degree of deformation, in geochemistry and in age, compared to the Småland granitoids north of the SBDZ, it is suggested that these represent two separate but closely related igneous suites, which could both be included within a TIB-1 supersuite. The investigated zircons showed very limited signs of metamorphic overprinting, and no metamorphic ages could be determined. However, the combined evidence from field observations and earlier U–Pb geochronology would suggest the presence of two separate metamorphic episodes in Blekinge, one in close connection with the formation of these rocks at 1.76–1.75 Ga and one connected to the intrusion of the Karlshamn granitoid suite at around 1.45 Ga.
DOI: 10.6084/m9.figshare.3179371
title: Supporting Data--Loudon et al., 2016 AJP

description: <b>The Stable Isotope Ecology of <i>Pan</i> in Uganda and Beyond</b><b> </b>James E. Loudon<sup>1*</sup>, Paul A. Sandberg<sup>2</sup>, Richard W. Wrangham<sup>3</sup>, Babette Fahey<sup>4</sup>, Matt Sponheimer<sup>5</sup><sup>1</sup>Department of Anthropology, East Carolina University, Greenville, NC 27858, USA<sup>2</sup>Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman OK 73072, USA<sup>3</sup>Department of Human Evolutionary Biology, Harvard University, Cambridge MA 02138, USA<sup>4</sup>Somerville, MA 02143, USA<sup>5</sup>Department of Anthropology, University of Colorado Boulder, Boulder, CO 80309, USA <sup>*</sup>E-mail: loudonj@ecu.eduThis is a research product, in whole or in part, of the Nutritional and Isotopic Ecology Lab (NIEL) at CU Boulder.<br>
DOI: 10.6084/m9.figshare.3179368
title: Descriptors and measurements of verbal violence in tweets

description: The purpose of this data collection was to test a scale for detecting verbal violence in Tweets. Workers at Mechanical Turk were first asked to complete a qualification test and then invited to code additional Tweets according to our scale. The qualification test involved a detailed explanation of each item of the scale, a walkthrough of a tweet that we had coded according to all 14 scale-items, a practice exercise, and a test. In the practice exercise, potential coders attempted to code a tweet on their own using our scale. After submitting their ratings, they were shown our own ratings for the same tweet and explanations for each of our ratings. The test component consisted of another coding task, in which coders were asked to code another tweet that we had already coded ourselves. The workers who, on test, with our ratings of that tweet on at least 11 out of the 14 items “passed” the test, earning the qualification that allowed them to participate in future coding tasks. Variables in the data include the ID of the Tweet (so that you may find it on Twitter; Twitter Terms of Service prohibit us from sharing the Tweets), the ID number we assigned to the coder, the rating that coder provided for each of the 14 items on our scale, the gender and age of the coder, and any comments the coder provided.
DOI: 10.6084/m9.figshare.3179371.v1
title: Supporting Data--Loudon et al., 2016 AJP

description: <b>The Stable Isotope Ecology of <i>Pan</i> in Uganda and Beyond</b><b> </b>James E. Loudon<sup>1*</sup>, Paul A. Sandberg<sup>2</sup>, Richard W. Wrangham<sup>3</sup>, Babette Fahey<sup>4</sup>, Matt Sponheimer<sup>5</sup><sup>1</sup>Department of Anthropology, East Carolina University, Greenville, NC 27858, USA<sup>2</sup>Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman OK 73072, USA<sup>3</sup>Department of Human Evolutionary Biology, Harvard University, Cambridge MA 02138, USA<sup>4</sup>Somerville, MA 02143, USA<sup>5</sup>Department of Anthropology, University of Colorado Boulder, Boulder, CO 80309, USA <sup>*</sup>E-mail: loudonj@ecu.eduThis is a research product, in whole or in part, of the Nutritional and Isotopic Ecology Lab (NIEL) at CU Boulder.<br>
DOI: 10.6084/m9.figshare.3179332
title: Kenya Long-term Exclosure Experiment (KLEE) dung count data

description: Starting in 2006, we have conducted biennial (roughly March and October) dung surveys along six-4 m x100 m permanent transects within each of the 18 KLEE plots and three control transects outside of the KLEE plots. This Excel worksheet features dung count data for each KLEE plot. Count data is broken down by herbivore species. To avoid recounting the same dung piles during subsequent surveys, we crush all recorded dung piles during each session. For animals that defecate in middens (such as steinbuck and Grant's gazelle), we used the number of dung pellets and differences in shape and color to estimate the number of separate defecation events. Dung piles for all major herbivore species could be positively identified to species in the field, with two exceptions. The dung of cattle and buffalo could not be distinguished, and we lumped them. The dung of plains and Grevy's zebras also could not be distinguished from each other; hence we grouped them as “zebra”. However, plains zebra far outnumber Grevy’s, so effectively we consider these to be plains zebra dung.