cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1233457.v1
title: Gaussian Job Archive for C5H13NO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1233367
title: COMPARATIVE STUDY OF SELECTED PHYSICAL FITNESS VARIABLES OF U-19 BOYS OF URBAN AND RURALAREA OF MANDI DISTRICT OF HIMACHAL PRADESH

description: The aim of the study was to compare the physical fitness variables of U-19 boys of urban and rural area of Mandi District of Himachal Pradesh. The researcher undertook null hypothesis to compare the selected physical fitness variables. Random sampling device was used to select the subjects. 240 male subjects (120 from rural and 120 from urban area) were selected for the present<br>study, AAHPERD youth physical fitness test battery was administered on the subject. ‘t’test was applied to analyse the data.
DOI: 10.6084/m9.figshare.1233374
title: Flesh-footed Shearwater observations in British Columbia and Alaska

description: Observation and museum records of Flesh-footed Shearwaters (<em>Puffinus carneipes</em>) observed at-sea in British Columbia, Canada, and Alaska, USA. Data to accompany the article Bond, A.L., and J.L. Lavers. Flesh-footed Shearwaters (<em>Puffinus carneipes</em>) in the north-eastern Pacific Ocean: a summary and synthesis of records from Canada and Alaska. Canadian Field-Naturalist
DOI: 10.6084/m9.figshare.1233437
title: Nuclear tRNA gene predictions for 12 species in the genus Drosophila

description: Coordinates of nuclear tRNA gene predictions for 12 species in the genus Drosophila from Clark et al. (2007) "Evolution of genes and genomes on the Drosophila phylogeny" Nature 450: 203-218. tRNA gene annotations are in gff3 format on CAF1 assembly coordinates. These data have now been incorporated into official FlyBlase genome annotations. Details about the methods used to generate these tRNA gene predictions can be found here: http://dx.doi.org/10.6084/m9.figshare.1233438
DOI: 10.6084/m9.figshare.1233439.v1
title: Drosophila 12 Genomes Project Data

description: Data generated by Casey Bergman and colleagues as part of the Drosophila 12 Genomes Project.
DOI: 10.6084/m9.figshare.1233367.v1
title: COMPARATIVE STUDY OF SELECTED PHYSICAL FITNESS VARIABLES OF U-19 BOYS OF URBAN AND RURALAREA OF MANDI DISTRICT OF HIMACHAL PRADESH

description: The aim of the study was to compare the physical fitness variables of U-19 boys of urban and rural area of Mandi District of Himachal Pradesh. The researcher undertook null hypothesis to compare the selected physical fitness variables. Random sampling device was used to select the subjects. 240 male subjects (120 from rural and 120 from urban area) were selected for the present<br>study, AAHPERD youth physical fitness test battery was administered on the subject. ‘t’test was applied to analyse the data.
DOI: 10.6084/m9.figshare.1233359
title: CHCommon.log.tx

description: Log file for bat recordings on Colney Heath Common 24/5/20111. Contains details of equipment, location and analysis of each recorded file.
DOI: 10.6084/m9.figshare.1233374.v1
title: Flesh-footed Shearwater observations in British Columbia and Alaska

description: Observation and museum records of Flesh-footed Shearwaters (<em>Puffinus carneipes</em>) observed at-sea in British Columbia, Canada, and Alaska, USA. Data to accompany the article Bond, A.L., and J.L. Lavers. Flesh-footed Shearwaters (<em>Puffinus carneipes</em>) in the north-eastern Pacific Ocean: a summary and synthesis of records from Canada and Alaska. Canadian Field-Naturalist
DOI: 10.6084/m9.figshare.1233437.v1
title: Nuclear tRNA gene predictions for 12 species in the genus Drosophila

description: Coordinates of nuclear tRNA gene predictions for 12 species in the genus Drosophila from Clark et al. (2007) "Evolution of genes and genomes on the Drosophila phylogeny" Nature 450: 203-218. tRNA gene annotations are in gff3 format on CAF1 assembly coordinates. These data have now been incorporated into official FlyBlase genome annotations. Details about the methods used to generate these tRNA gene predictions can be found here: http://dx.doi.org/10.6084/m9.figshare.1233438
DOI: 10.6084/m9.figshare.1233359.v1
title: CHCommon.log.tx

description: Log file for bat recordings on Colney Heath Common 24/5/20111. Contains details of equipment, location and analysis of each recorded file.
DOI: 10.6084/m9.figshare.1232234
title: GenomeSizeProject Data

description: Low coverage sequence data from maize landraces. See other figshare repository for teosinte data.
DOI: 10.6084/m9.figshare.1232209
title: γH2AX foci on apparently intact mitotic chromosomes: Not signatures of misrejoining events but signals of unresolved DNA damage

description: The presence of γH2AX foci on apparently intact mitotic chromosomes is controversial because they challenge the assumed relationship between γH2AX foci and DNA double-strand breaks (DSBs). In this work, we show that after irradiation during interphase, a variety of γH2AX foci are scored in mitotic cells. Surprisingly, approximately 80% of the γH2AX foci spread over apparently undamaged chromatin at Terminal or Interstitial positions and they can display variable sizes, thus being classified as Small, Medium and Big foci. Chromosome and chromatid breaks that reach mitosis are spotted with Big (60%) and Medium (30%) Terminal γH2AX foci, but very rarely are they signaled with Small γH2AX foci. To evaluate if Interstitial γH2AX foci might be signatures of misrejoining, an mFISH analysis was performed on the same slides. The results show that Interstitial γH2AX foci lying on apparently intact chromatin do not mark sites of misrejoining, and that misrejoined events were never signaled by a γH2AX foci during mitosis. Finally, when analyzing the presence of other DNA-damage response (DDR) factors we found that all γH2AX foci—regardless their coincidence with a visible break—always colocalized with MRE11, but not with 53BP1. This pattern suggests that these γH2AX foci may be hallmarks of both microscopically visible and invisible DNA damage, in which an active, although incomplete or halted DDR is taking place.
DOI: 10.6084/m9.figshare.1232210
title: The transcription factor p53: Not a repressor, solely an activator

description: The predominant function of the tumor suppressor p53 is transcriptional regulation. It is generally accepted that p53-dependent transcriptional activation occurs by binding to a specific recognition site in promoters of target genes. Additionally, several models for p53-dependent transcriptional repression have been postulated. Here, we evaluate these models based on a computational meta-analysis of genome-wide data. Surprisingly, several major models of p53-dependent gene regulation are implausible. Meta-analysis of large-scale data is unable to confirm reports on directly repressed p53 target genes and falsifies models of direct repression. This notion is supported by experimental re-analysis of representative genes reported as directly repressed by p53. Therefore, p53 is not a direct repressor of transcription, but solely activates its target genes. Moreover, models based on interference of p53 with activating transcription factors as well as models based on the function of ncRNAs are also not supported by the meta-analysis. As an alternative to models of direct repression, the meta-analysis leads to the conclusion that p53 represses transcription indirectly by activation of the p53-p21-DREAM/RB pathway.
DOI: 10.6084/m9.figshare.1232211
title: Genetic characterization of p27<sup>kip1</sup> and stathmin in controlling cell proliferation in vivo

description: The CDK inhibitor p27<sup>kip1</sup> is a critical regulator of cell cycle progression, but the mechanisms by which p27<sup>kip1</sup> controls cell proliferation in vivo are still not fully elucidated. We recently demonstrated that the microtubule destabilizing protein stathmin is a relevant p27<sup>kip1</sup> binding partner. To get more insights into the in vivo significance of this interaction, we generated p27<sup>kip1</sup> and stathmin double knock-out (DKO) mice. Interestingly, thorough characterization of DKO mice demonstrated that most of the phenotypes of p27<sup>kip1</sup> null mice linked to the hyper-proliferative behavior, such as the increased body and organ weight, the outgrowth of the retina basal layer and the development of pituitary adenomas, were reverted by co-ablation of stathmin. In vivo analyses showed a reduced proliferation rate in DKO compared to p27<sup>kip1</sup> null mice, linked, at molecular level, to decreased kinase activity of CDK4/6, rather than of CDK1 and CDK2. Gene expression profiling of mouse thymuses confirmed the phenotypes observed in vivo, showing that DKO clustered with WT more than with p27 knock-out tissue. Taken together, our results demonstrate that stathmin cooperates with p27<sup>kip1</sup> to control the early phase of G1 to S phase transition and that this function may be of particular relevance in the context of tumor progression.
DOI: 10.6084/m9.figshare.1232234.v2
title: GenomeSizeProject Data

description: Source genetic data for highland lowland maize and teosinte populations. Also, large files from genome size analyses are stored here.
DOI: 10.6084/m9.figshare.1232211.v2
title: Genetic characterization of p27<sup>kip1</sup> and stathmin in controlling cell proliferation in vivo

description: The CDK inhibitor p27<sup>kip1</sup> is a critical regulator of cell cycle progression, but the mechanisms by which p27<sup>kip1</sup> controls cell proliferation in vivo are still not fully elucidated. We recently demonstrated that the microtubule destabilizing protein stathmin is a relevant p27<sup>kip1</sup> binding partner. To get more insights into the in vivo significance of this interaction, we generated p27<sup>kip1</sup> and stathmin double knock-out (DKO) mice. Interestingly, thorough characterization of DKO mice demonstrated that most of the phenotypes of p27<sup>kip1</sup> null mice linked to the hyper-proliferative behavior, such as the increased body and organ weight, the outgrowth of the retina basal layer and the development of pituitary adenomas, were reverted by co-ablation of stathmin. In vivo analyses showed a reduced proliferation rate in DKO compared to p27<sup>kip1</sup> null mice, linked, at molecular level, to decreased kinase activity of CDK4/6, rather than of CDK1 and CDK2. Gene expression profiling of mouse thymuses confirmed the phenotypes observed in vivo, showing that DKO clustered with WT more than with p27 knock-out tissue. Taken together, our results demonstrate that stathmin cooperates with p27<sup>kip1</sup> to control the early phase of G1 to S phase transition and that this function may be of particular relevance in the context of tumor progression.
DOI: 10.6084/m9.figshare.1232234.v1
title: GenomeSizeProject Data

description: Source genetic data for highland lowland maize and teosinte populations. Also, large files from genome size analyses are stored here.
DOI: 10.6084/m9.figshare.1232209.v2
title: γH2AX foci on apparently intact mitotic chromosomes: Not signatures of misrejoining events but signals of unresolved DNA damage

description: The presence of γH2AX foci on apparently intact mitotic chromosomes is controversial because they challenge the assumed relationship between γH2AX foci and DNA double-strand breaks (DSBs). In this work, we show that after irradiation during interphase, a variety of γH2AX foci are scored in mitotic cells. Surprisingly, approximately 80% of the γH2AX foci spread over apparently undamaged chromatin at Terminal or Interstitial positions and they can display variable sizes, thus being classified as Small, Medium and Big foci. Chromosome and chromatid breaks that reach mitosis are spotted with Big (60%) and Medium (30%) Terminal γH2AX foci, but very rarely are they signaled with Small γH2AX foci. To evaluate if Interstitial γH2AX foci might be signatures of misrejoining, an mFISH analysis was performed on the same slides. The results show that Interstitial γH2AX foci lying on apparently intact chromatin do not mark sites of misrejoining, and that misrejoined events were never signaled by a γH2AX foci during mitosis. Finally, when analyzing the presence of other DNA-damage response (DDR) factors we found that all γH2AX foci—regardless their coincidence with a visible break—always colocalized with MRE11, but not with 53BP1. This pattern suggests that these γH2AX foci may be hallmarks of both microscopically visible and invisible DNA damage, in which an active, although incomplete or halted DDR is taking place.
DOI: 10.6084/m9.figshare.1232209.v1
title: γH2AX foci on apparently intact mitotic chromosomes: Not signatures of misrejoining events but signals of unresolved DNA damage

description: The presence of γH2AX foci on apparently intact mitotic chromosomes is controversial because they challenge the assumed relationship between γH2AX foci and DNA double-strand breaks (DSBs). In this work, we show that after irradiation during interphase, a variety of γH2AX foci are scored in mitotic cells. Surprisingly, approximately 80% of the γH2AX foci spread over apparently undamaged chromatin at Terminal or Interstitial positions and they can display variable sizes, thus being classified as Small, Medium and Big foci. Chromosome and chromatid breaks that reach mitosis are spotted with Big (60%) and Medium (30%) Terminal γH2AX foci, but very rarely are they signaled with Small γH2AX foci. To evaluate if Interstitial γH2AX foci might be signatures of misrejoining, an mFISH analysis was performed on the same slides. The results show that Interstitial γH2AX foci lying on apparently intact chromatin do not mark sites of misrejoining, and that misrejoined events were never signaled by a γH2AX foci during mitosis. Finally, when analyzing the presence of other DNA-damage response (DDR) factors we found that all γH2AX foci—regardless their coincidence with a visible break—always colocalized with MRE11, but not with 53BP1. This pattern suggests that these γH2AX foci may be hallmarks of both microscopically visible and invisible DNA damage, in which an active, although incomplete or halted DDR is taking place.
DOI: 10.6084/m9.figshare.1232210.v2
title: The transcription factor p53: Not a repressor, solely an activator

description: The predominant function of the tumor suppressor p53 is transcriptional regulation. It is generally accepted that p53-dependent transcriptional activation occurs by binding to a specific recognition site in promoters of target genes. Additionally, several models for p53-dependent transcriptional repression have been postulated. Here, we evaluate these models based on a computational meta-analysis of genome-wide data. Surprisingly, several major models of p53-dependent gene regulation are implausible. Meta-analysis of large-scale data is unable to confirm reports on directly repressed p53 target genes and falsifies models of direct repression. This notion is supported by experimental re-analysis of representative genes reported as directly repressed by p53. Therefore, p53 is not a direct repressor of transcription, but solely activates its target genes. Moreover, models based on interference of p53 with activating transcription factors as well as models based on the function of ncRNAs are also not supported by the meta-analysis. As an alternative to models of direct repression, the meta-analysis leads to the conclusion that p53 represses transcription indirectly by activation of the p53-p21-DREAM/RB pathway.
DOI: 10.6084/m9.figshare.1232211.v1
title: Genetic characterization of p27<sup>kip1</sup> and stathmin in controlling cell proliferation in vivo

description: The CDK inhibitor p27<sup>kip1</sup> is a critical regulator of cell cycle progression, but the mechanisms by which p27<sup>kip1</sup> controls cell proliferation in vivo are still not fully elucidated. We recently demonstrated that the microtubule destabilizing protein stathmin is a relevant p27<sup>kip1</sup> binding partner. To get more insights into the in vivo significance of this interaction, we generated p27<sup>kip1</sup> and stathmin double knock-out (DKO) mice. Interestingly, thorough characterization of DKO mice demonstrated that most of the phenotypes of p27<sup>kip1</sup> null mice linked to the hyper-proliferative behavior, such as the increased body and organ weight, the outgrowth of the retina basal layer and the development of pituitary adenomas, were reverted by co-ablation of stathmin. In vivo analyses showed a reduced proliferation rate in DKO compared to p27<sup>kip1</sup> null mice, linked, at molecular level, to decreased kinase activity of CDK4/6, rather than of CDK1 and CDK2. Gene expression profiling of mouse thymuses confirmed the phenotypes observed in vivo, showing that DKO clustered with WT more than with p27 knock-out tissue. Taken together, our results demonstrate that stathmin cooperates with p27<sup>kip1</sup> to control the early phase of G1 to S phase transition and that this function may be of particular relevance in the context of tumor progression.
DOI: 10.6084/m9.figshare.1232205
title: Genome-wide DNA methylation analysis identifies a metabolic memory profile in patient-derived diabetic foot ulcer fibroblasts

description: Diabetic foot ulcers (DFUs) are a serious complication of diabetes. Previous exposure to hyperglycemic conditions accelerates a decline in cellular function through metabolic memory despite normalization of glycemic control. Persistent, hyperglycemia-induced epigenetic patterns are considered a central mechanism that activates metabolic memory; however, this has not been investigated in patient-derived fibroblasts from DFUs. We generated a cohort of patient-derived lines from DFU fibroblasts (DFUF), and site- and age-matched diabetic foot fibroblasts (DFF) and non-diabetic foot fibroblasts (NFF) to investigate global and genome-wide DNA methylation patterns using liquid chromatography/mass spectrometry and the Illumina Infinium HumanMethylation450K array. DFFs and DFUFs demonstrated significantly lower global DNA methylation compared to NFFs (p = 0.03). Hierarchical clustering of differentially methylated probes (DMPs, p = 0.05) showed that DFFs and DFUFs cluster together and separately from NFFs. Twenty-five percent of the same probes were identified as DMPs when individually comparing DFF and DFUF to NFF. Functional annotation identified enrichment of DMPs associated with genes critical to wound repair, including angiogenesis (p = 0.07) and extracellular matrix assembly (p = 0.035). Identification of sustained DNA methylation patterns in patient-derived fibroblasts after prolonged passage in normoglycemic conditions demonstrates persistent metabolic memory. These findings suggest that epigenetic-related metabolic memory may also underlie differences in wound healing phenotypes and can potentially identify therapeutic targets.
DOI: 10.6084/m9.figshare.1232210.v1
title: The transcription factor p53: Not a repressor, solely an activator

description: The predominant function of the tumor suppressor p53 is transcriptional regulation. It is generally accepted that p53-dependent transcriptional activation occurs by binding to a specific recognition site in promoters of target genes. Additionally, several models for p53-dependent transcriptional repression have been postulated. Here, we evaluate these models based on a computational meta-analysis of genome-wide data. Surprisingly, several major models of p53-dependent gene regulation are implausible. Meta-analysis of large-scale data is unable to confirm reports on directly repressed p53 target genes and falsifies models of direct repression. This notion is supported by experimental re-analysis of representative genes reported as directly repressed by p53. Therefore, p53 is not a direct repressor of transcription, but solely activates its target genes. Moreover, models based on interference of p53 with activating transcription factors as well as models based on the function of ncRNAs are also not supported by the meta-analysis. As an alternative to models of direct repression, the meta-analysis leads to the conclusion that p53 represses transcription indirectly by activation of the p53-p21-DREAM/RB pathway.
DOI: 10.6084/m9.figshare.1232201
title: MI Wolf Survey 2013

description: Abstract: Whereas past wolf management in the United States was restricted to recovery, managers must now contend with publicly contentious post-recovery issues including regulated hunting seasons. Understanding stakeholder concerns associated with hunting can inform stakeholder engagement, communication, and policy development and evaluation. Social identity theory (SIT) has been used to understand how groups interact, why they conflict, and how collaboration may be achieved. Applying SIT to stakeholder conflicts about wolf hunting may help delineate groups according to their concern about, support for or opposition to the policy choice of hunting wolves. Our objective was to assess concerns about hunting as a tool to resolve conflict in Michigan, using SIT as a framework. We used a mixed-modal sampling approach (e.g., paper, Internet) with wolf hunting-related public meeting participants in March 2013. Survey questions focused on 12 concerns previously identified as associated with hunting as a management tool to resolve conflict. Respondents (n = 666) cared greatly about wolves but were divided over hunting wolves. Wolf conflicts, use of science in policy decisions, and maintaining a wolf population were the highest ranked concerns. Principle components analysis reduced concerns into three factors that explained 50.7% of total variance; concerns crystallized over justifications for hunting. General linear models revealed a lack of geographic influence on care, fear and support for hunting related to wolves. These findings challenge assumptions about regional differences and suggest a strong role for social identity in driving dichotomized public perceptions in wildlife management.