cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1263908
title: Binding of a chromen-4-one Schiff’s base with bovine serum albumin: capping with β-cyclodextrin influences the binding

description: This work deals with the synthesis of 6-methyl-3-[(4′-methylphenyl)imino]methyl-4H-chromen-4-one (MMPIMC), its binding to β-cyclodextrin, and the influence of the cyclodextrin complexation on the compound’s binding to bovine serum albumin (BSA). The 1:2 stoichiometry for the complexation of MMPIMC with β-cyclodextrin is determined with the binding constant of 1.90 × 10<sup>4</sup> M<sup>−2</sup>. The structure of host–guest complex plays a role in protein binding of MMPIMC. One- and two-dimensional NMR spectra are used to determine the mode of binding of the guest to β-cyclodextrin cavity and the structure of the inclusion complex is proposed. The binding of MMPIMC with BSA in the absence and the presence of β-cyclodextrin is studied. The binding strengths of MMPIMC–BSA (1.73 × 10<sup>5</sup> M<sup>−1</sup>) and β-cyclodextrin-complexed MMPIMC–BSA (9.0 × 10<sup>4</sup> M<sup>−1</sup>) show difference in magnitude. The Förster Resonance Energy Transfer efficiency and the proximity of the donor and acceptor molecules, are modulated by β-cyclodextrin. Molecular modeling is used to optimize the sites and mode of binding of MMPIMC with bovine serum albumin.
DOI: 10.6084/m9.figshare.1263924.v2
title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : details_V4ciliates_Biomarks.tab)

description: file : details_V4ciliates_Biomarks.tab Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.6084/m9.figshare.1264013 Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1263925.v1
title: network_output.tab.zip

description: Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1263924.v1
title: details_V4ciliates_Biomarks.tab

description: Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1263908.v2
title: Binding of a chromen-4-one Schiff’s base with bovine serum albumin: capping with β-cyclodextrin influences the binding

description: This work deals with the synthesis of 6-methyl-3-[(4′-methylphenyl)imino]methyl-4H-chromen-4-one (MMPIMC), its binding to β-cyclodextrin, and the influence of the cyclodextrin complexation on the compound’s binding to bovine serum albumin (BSA). The 1:2 stoichiometry for the complexation of MMPIMC with β-cyclodextrin is determined with the binding constant of 1.90 × 10<sup>4</sup> M<sup>−2</sup>. The structure of host–guest complex plays a role in protein binding of MMPIMC. One- and two-dimensional NMR spectra are used to determine the mode of binding of the guest to β-cyclodextrin cavity and the structure of the inclusion complex is proposed. The binding of MMPIMC with BSA in the absence and the presence of β-cyclodextrin is studied. The binding strengths of MMPIMC–BSA (1.73 × 10<sup>5</sup> M<sup>−1</sup>) and β-cyclodextrin-complexed MMPIMC–BSA (9.0 × 10<sup>4</sup> M<sup>−1</sup>) show difference in magnitude. The Förster Resonance Energy Transfer efficiency and the proximity of the donor and acceptor molecules, are modulated by β-cyclodextrin. Molecular modeling is used to optimize the sites and mode of binding of MMPIMC with bovine serum albumin.
DOI: 10.6084/m9.figshare.1263908.v1
title: Binding of a chromen-4-one Schiff’s base with bovine serum albumin: capping with β-cyclodextrin influences the binding

description: This work deals with the synthesis of 6-methyl-3-[(4′-methylphenyl)imino]methyl-4H-chromen-4-one (MMPIMC), its binding to β-cyclodextrin, and the influence of the cyclodextrin complexation on the compound’s binding to bovine serum albumin (BSA). The 1:2 stoichiometry for the complexation of MMPIMC with β-cyclodextrin is determined with the binding constant of 1.90 × 10<sup>4</sup> M<sup>−2</sup>. The structure of host–guest complex plays a role in protein binding of MMPIMC. One- and two-dimensional NMR spectra are used to determine the mode of binding of the guest to β-cyclodextrin cavity and the structure of the inclusion complex is proposed. The binding of MMPIMC with BSA in the absence and the presence of β-cyclodextrin is studied. The binding strengths of MMPIMC–BSA (1.73 × 10<sup>5</sup> M<sup>−1</sup>) and β-cyclodextrin-complexed MMPIMC–BSA (9.0 × 10<sup>4</sup> M<sup>−1</sup>) show difference in magnitude. The Förster Resonance Energy Transfer efficiency and the proximity of the donor and acceptor molecules, are modulated by β-cyclodextrin. Molecular modeling is used to optimize the sites and mode of binding of MMPIMC with bovine serum albumin.
DOI: 10.6084/m9.figshare.1263860
title: Subject Teachers

description: This dataset contains subject teachers' diary entries assessing their enjoyment, anger, and anxiety directly after each math or physics class in four target classes. Diary phase lasted two weeks.
DOI: 10.6084/m9.figshare.1263859
title: Classroom Teachers

description: This dataset contains classroom teachers' diary entries assessing their enjoyment, anger, and anxiety directly after each math, German, and science class. Diary phase lasted two weeks.
DOI: 10.6084/m9.figshare.1263859.v1
title: Classroom Teachers

description: This dataset contains classroom teachers' diary entries assessing their enjoyment, anger, and anxiety directly after each math, German, and science class. Diary phase lasted two weeks.
DOI: 10.6084/m9.figshare.1263636
title: Leap Motion experiment raw data and analysis scripts - FEUP

description: Fileset for the Leap Motion experiment performed at FEUP.
DOI: 10.6084/m9.figshare.1263705
title: Assessing the impact of afforestation on soil organic C sequestration by means of sequential density fraction

description: The original data of article "Assessing the impact of afforestation on soil organic C sequestration by means of sequential density fraction" in PLOS ONE
DOI: 10.6084/m9.figshare.1263636.v1
title: Leap Motion experiment raw data and analysis scripts - FEUP

description: Fileset for the Leap Motion experiment performed at FEUP.
DOI: 10.6084/m9.figshare.1263628
title: What websites do London councils block on their library PCs?

description: All London councils were sent freedom of information requests to discover what categories of the internet they block on 28/10/14. Attached are their responses. A number of requests are still ongoing/being chased up, so this will be updated once these are resolved. If you believe there to be any errors, please get in touch.
DOI: 10.6084/m9.figshare.1263629
title: Bulk Domain Names (07-Dec-2014) -- varocarbas.com

description: (07-Dec-2014) 1996006 valid web domain names collected by the (bulk) crawling bots running on varocarbas.com.
DOI: 10.6084/m9.figshare.1263627
title: Gaussian Job Archive for C4H8I2OSe

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1263629.v1
title: Bulk Domain Names (07-Dec-2014) -- varocarbas.com

description: (07-Dec-2014) 1996006 valid web domain names collected by the (bulk) crawling bots running on varocarbas.com.
DOI: 10.6084/m9.figshare.1263628.v1
title: What websites do London councils block on their library PCs?

description: All London councils were sent freedom of information requests to discover what categories of the internet they block on 28/10/14. Attached are their responses. A number of requests are still ongoing/being chased up, so this will be updated once these are resolved. If you believe there to be any errors, please get in touch.
DOI: 10.6084/m9.figshare.1263626
title: 1000 Backlinks to vimeo.com (05-Dec-2014) -- varocarbas.com

description: High quality backlinks to vimeo.com. The retrieval process was completed on 05-Dec-2014.
DOI: 10.6084/m9.figshare.1263627.v1
title: Gaussian Job Archive for C4H8I2OSe

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1263625
title: 1000 Backlinks to wikipedia.org (04-Dec-2014) -- varocarbas.com

description: High quality backlinks to wikipedia.org. The retrieval process was completed on 04-Dec-2014.
DOI: 10.6084/m9.figshare.1263626.v1
title: 1000 Backlinks to vimeo.com (05-Dec-2014) -- varocarbas.com

description: High quality backlinks to vimeo.com. The retrieval process was completed on 05-Dec-2014.
DOI: 10.6084/m9.figshare.1263622
title: 1000 Backlinks to bit.ly (03-Dec-2014) -- varocarbas.com

description: High quality backlinks to bit.ly. The retrieval process was completed on 03-Dec-2014.
DOI: 10.6084/m9.figshare.1263624
title: 1000 Backlinks to qq.com (04-Dec-2014) -- varocarbas.com

description: High quality backlinks to qq.com. The retrieval process was completed on 04-Dec-2014.
DOI: 10.6084/m9.figshare.1263625.v1
title: 1000 Backlinks to wikipedia.org (04-Dec-2014) -- varocarbas.com

description: High quality backlinks to wikipedia.org. The retrieval process was completed on 04-Dec-2014.
DOI: 10.6084/m9.figshare.1263604
title: Gaussian Job Archive for C4H8I2OSe

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1263604.v1
title: Gaussian Job Archive for C4H8I2OSe

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1263622.v2
title: 1000 Backlinks to bit.ly (03-Dec-2014) -- varocarbas.com

description: High quality backlinks to bit.ly. The retrieval process was completed on 03-Dec-2014.
DOI: 10.6084/m9.figshare.1263624.v2
title: 1000 Backlinks to qq.com (04-Dec-2014) -- varocarbas.com

description: High quality backlinks to qq.com. The retrieval process was completed on 04-Dec-2014.
DOI: 10.6084/m9.figshare.1263622.v1
title: 1000 Backlinks to bit.ly (03-Dec-2014) -- varocarbas.com

description: High quality backlinks to bit.ly. The retrieval process was completed on 03-Dec-2014.
DOI: 10.6084/m9.figshare.1263624.v1
title: 1000 Backlinks to qq.com (04-Dec-2014) -- varocarbas.com

description: High quality backlinks to qq.com. The retrieval process was completed on 04-Dec-2014.
DOI: 10.6084/m9.figshare.1263588
title: An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

description: Regular endurance exercise training induces beneficial functional and health effects in human skeletal muscle. The putative contribution to the training response of the epigenome as a mediator between genes and environment has not been clarified. Here we investigated the contribution of DNA methylation and associated transcriptomic changes in a well-controlled human intervention study. Training effects were mirrored by significant alterations in DNA methylation and gene expression in regions with a homogeneous muscle energetics and remodeling ontology. Moreover, a signature of DNA methylation and gene expression separated the samples based on training and gender. Differential DNA methylation was predominantly observed in enhancers, gene bodies and intergenic regions and less in CpG islands or promoters. We identified transcriptional regulator binding motifs of MRF, MEF2 and ETS proteins in the proximity of the changing sites. A transcriptional network analysis revealed modules harboring distinct ontologies and, interestingly, the overall direction of the changes of methylation within each module was inversely correlated to expression changes. In conclusion, we show that highly consistent and associated modifications in methylation and expression, concordant with observed health-enhancing phenotypic adaptations, are induced by a physiological stimulus.
DOI: 10.6084/m9.figshare.1263587
title: Genome-wide DNA methylation analysis in precursor B-cells

description: DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182–200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.
DOI: 10.6084/m9.figshare.1263588.v1
title: An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

description: ABSTRACTRegular endurance exercise training induces beneficial functional and health effects in human skeletal muscle. The putative contribution to the training response of the epigenome as a mediator between genes and environment has not been clarified. Here we investigated the contribution of DNA methylation and associated transcriptomic changes in a well-controlled human intervention study. Training effects were mirrored by significant alterations in DNA methylation and gene expression in regions with a homogeneous muscle energetics and remodeling ontology. Moreover, a signature of DNA methylation and gene expression separated the samples based on training and gender. Differential DNA methylation was predominantly observed in enhancers, gene bodies and intergenic regions and less in CpG islands or promoters. We identified transcriptional regulator binding motifs of MRF, MEF2 and ETS proteins in the proximity of the changing sites. A transcriptional network analysis revealed modules harboring distinct ontologies and, interestingly, the overall direction of the changes of methylation within each module was inversely correlated to expression changes. In conclusion, we show that highly consistent and associated modifications in methylation and expression, concordant with observed health-enhancing phenotypic adaptations, are induced by a physiological stimulus.
DOI: 10.6084/m9.figshare.1263587.v1
title: Genome-wide DNA methylation analysis in precursor B-cells

description: DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182 – 200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.
DOI: 10.6084/m9.figshare.1263587.v3
title: Genome-wide DNA methylation analysis in precursor B-cells

description: DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182–200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.
DOI: 10.6084/m9.figshare.1263588.v3
title: An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

description: Regular endurance exercise training induces beneficial functional and health effects in human skeletal muscle. The putative contribution to the training response of the epigenome as a mediator between genes and environment has not been clarified. Here we investigated the contribution of DNA methylation and associated transcriptomic changes in a well-controlled human intervention study. Training effects were mirrored by significant alterations in DNA methylation and gene expression in regions with a homogeneous muscle energetics and remodeling ontology. Moreover, a signature of DNA methylation and gene expression separated the samples based on training and gender. Differential DNA methylation was predominantly observed in enhancers, gene bodies and intergenic regions and less in CpG islands or promoters. We identified transcriptional regulator binding motifs of MRF, MEF2 and ETS proteins in the proximity of the changing sites. A transcriptional network analysis revealed modules harboring distinct ontologies and, interestingly, the overall direction of the changes of methylation within each module was inversely correlated to expression changes. In conclusion, we show that highly consistent and associated modifications in methylation and expression, concordant with observed health-enhancing phenotypic adaptations, are induced by a physiological stimulus.