cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1282530.v1
title: Genome-wide analysis of <i>in vivo</i> TRF1 binding to chromatin restricts its location exclusively to telomeric repeats

description: Telomeres are nucleoprotein structures at the ends of eukaryotic chromosomes that protect them from degradation, end-to-end fusions, and fragility. In mammals, telomeres are composed of TTAGGG tandem repeats bound by a protein complex called shelterin, which has fundamental roles in the regulation of telomere protection and length. The telomeric repeat binding factor 1 (TERF1 or TRF1) is one of the components of shelterin and has been shown to be essential for telomere protection. Telomeric repeats can also be found throughout the genome, as Internal or Interstitial Telomeric Sequences (ITSs). Some of the components of shelterin have been described to bind to ITSs as well as other extra-telomeric regions, which in the case of RAP1 exert a key role in transcriptional regulation. Here, we set to address whether TRF1 can be found at extra-telomeric sites both under normal conditions and upon induction of telomere shortening. In particular, we performed a ChIP-sequencing technique to map TRF1 binding sites in MEFs wild-type and deficient for the telomerase RNA component (<i>Terc<sup>−/−</sup></i>), with increasingly short telomeres. Our findings indicate that TRF1 is exclusively located at telomeres both under normal conditions, as well as under extreme telomere shortening. These results indicate that in mice not all members of shelterin have extra-telomeric roles as it was described for RAP1.
DOI: 10.6084/m9.figshare.1282528
title: Inactivation of the budding yeast cohesin loader Scc2 alters gene expression both globally and in response to a single DNA double strand break

description: Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding.
DOI: 10.6084/m9.figshare.1282525
title: Hydrogen emission & recombination coefficients with kappa electron distribution

description: This list provides an extensive data set for the emission and total recombination coefficients of hydrogen and total recombination coefficients to the 2s two-photon transitions with a kappa electron energy distribution rather than the more traditional Maxwell-Boltzmann distribution. The data are mainly relevant to thin and relatively cold plasma found in planetary nebulae and H II regions. The data set is complementary to previous data sets provided by Hummer and Storey and Storey and Hummer under a Maxwell-Boltzmann distribution assumption based on thermodynamic equilibrium. The data set is structured as a function of electron number density, temperature and kappa. An interactive fortran 77 and C++ data servers are also provided as an accessory to probe the data and obtain Lagrange-interpolated values in all three variables between the explicitly given values.
DOI: 10.6084/m9.figshare.1282525.v1
title: Hydrogen emission & recombination coefficients with kappa electron distribution

description: This list provides an extensive data set for the emission and total recombination coefficients of hydrogen and total recombination coefficients to the 2s two-photon transitions with a kappa electron energy distribution rather than the more traditional Maxwell-Boltzmann distribution. The data are mainly relevant to thin and relatively cold plasma found in planetary nebulae and H II regions. The data set is complementary to previous data sets provided by Hummer and Storey and Storey and Hummer under a Maxwell-Boltzmann distribution assumption based on thermodynamic equilibrium. The data set is structured as a function of electron number density, temperature and kappa. An interactive fortran 77 and C++ data servers are also provided as an accessory to probe the data and obtain Lagrange-interpolated values in all three variables between the explicitly given values.
DOI: 10.6084/m9.figshare.1282528.v2
title: Inactivation of the budding yeast cohesin loader Scc2 alters gene expression both globally and in response to a single DNA double strand break

description: Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding.
DOI: 10.6084/m9.figshare.1282524
title: Computed List of H2D+ Lines

description: A comprehensive, calculated line list of frequencies and transition probabilities for the singly deuterated isotopologue of H3+, H2D+, is presented. The line list, called ST1, contains over 22 million rotational-vibrational transitions occurring between more than 33 thousand energy levels; it covers frequencies up to 18500cm-1. All energy levels with rotational quantum number, J, up to 20 are considered, making the line list useful for temperatures up to at least 3000K. About 15% of these levels are fully identified with six rotational and vibrational quantum numbers. The list is calculated using a previously proposed, high accuracy, ab initio model and consistency checks are carried out to test and validate the results. These checks confirm the accuracy of the list. A temperature-dependent partition function, valid over a more extended temperature range than those previously published, and cooling function are presented.
DOI: 10.6084/m9.figshare.1282528.v1
title: Inactivation of the budding yeast cohesin loader Scc2 alters gene expression both globally and in response to a single DNA double strand break

description: Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding.
DOI: 10.6084/m9.figshare.1282522
title: Computed List of Dielectronic Recombination Lines of C+

description: A computed list of transition lines for the atomic ion C+ is generated using R-matrix, Autostructure and Emissivity codes. These lines are produced by dielectronic recombination and subsequent cascade decays of the low-lying autoionizing states above the threshold of C2 1Se with a principal quantum number n&lt;5 for the captured electron. The line list contains 6187 optically-allowed transitions which include many C II lines observed in the astronomical spectra. Beside the transition lines, the data also include level energies for the bound and resonance states, radiative transition probabilities, recombination rate coefficients, and oscillator strengths. A 26-term C2+ atomic target was used within an intermediate coupling scheme in the production of these data. The theoretical results for energy and fine structure splitting agree very well with the available experimental data for both resonances and bound states. The data were also validated by comparison to theoretical data previously reported in the literature which include radiative transition probabilities, effective dielectronic recombination rate coefficients and autoionization probabilities.
DOI: 10.6084/m9.figshare.1282523
title: Computed List of Collision Strengths for Nebular [O III] Optical and Infrared Lines

description: The list presents electron collision strengths as a function of the electron excitation energy for the forbidden lines of the astronomically abundant doubly-ionized oxygen ion, O2+, in an intermediate coupling scheme using the Breit-Pauli relativistic terms as implemented in an R-matrix atomic scattering code. An atomic target for the R-matrix scattering defined by 72 atomic terms is used in these calculations with Gailitis averaging in the region beneath thresholds where the effective quantum number is greater than 10.
DOI: 10.6084/m9.figshare.1282524.v1
title: Computed List of H2D+ Lines

description: A comprehensive, calculated line list of frequencies and transition probabilities for the singly deuterated isotopologue of H3+, H2D+, is presented. The line list, called ST1, contains over 22 million rotational-vibrational transitions occurring between more than 33 thousand energy levels; it covers frequencies up to 18500cm-1. All energy levels with rotational quantum number, J, up to 20 are considered, making the line list useful for temperatures up to at least 3000K. About 15% of these levels are fully identified with six rotational and vibrational quantum numbers. The list is calculated using a previously proposed, high accuracy, ab initio model and consistency checks are carried out to test and validate the results. These checks confirm the accuracy of the list. A temperature-dependent partition function, valid over a more extended temperature range than those previously published, and cooling function are presented.
DOI: 10.6084/m9.figshare.1282522.v2
title: Computed List of Dielectronic Recombination Lines of C+

description: A computed list of transition lines for the atomic ion C+ is generated using R-matrix, Autostructure and Emissivity codes. These lines are produced by dielectronic recombination and subsequent cascade decays of the low-lying autoionizing states above the threshold of C2 1Se with a principal quantum number n&lt;5 for the captured electron. The line list contains 6187 optically-allowed transitions which include many C II lines observed in the astronomical spectra. Beside the transition lines, the data also include level energies for the bound and resonance states, radiative transition probabilities, recombination rate coefficients, and oscillator strengths. A 26-term C2+ atomic target was used within an intermediate coupling scheme in the production of these data. The theoretical results for energy and fine structure splitting agree very well with the available experimental data for both resonances and bound states. The data were also validated by comparison to theoretical data previously reported in the literature which include radiative transition probabilities, effective dielectronic recombination rate coefficients and autoionization probabilities.
DOI: 10.6084/m9.figshare.1282523.v1
title: Computed List of Collision Strengths for Nebular [O III] Optical and Infrared Lines

description: The list presents electron collision strengths as a function of the electron excitation energy for the forbidden lines of the astronomically abundant doubly-ionized oxygen ion, O2+, in an intermediate coupling scheme using the Breit-Pauli relativistic terms as implemented in an R-matrix atomic scattering code. An atomic target for the R-matrix scattering defined by 72 atomic terms is used in these calculations with Gailitis averaging in the region beneath thresholds where the effective quantum number is greater than 10.
DOI: 10.6084/m9.figshare.1282522.v1
title: List of Dielectronic Recombination Lines of C+

description: A computed list of transition lines for the atomic ion C+ is generated using R-matrix, Autostructure and Emissivity codes. These lines are produced by dielectronic recombination and subsequent cascade decays of the low-lying autoionizing states above the threshold of C2 1Se with a principal quantum number n&lt;5 for the captured electron. The line list contains 6187 optically-allowed transitions which include many C II lines observed in the astronomical spectra. Beside the transition lines, the data also include level energies for the bound and resonance states, radiative transition probabilities, recombination rate coefficients, and oscillator strengths. A 26-term C2+ atomic target was used within an intermediate coupling scheme in the production of these data. The theoretical results for energy and fine structure splitting agree very well with the available experimental data for both resonances and bound states. The data were also validated by comparison to theoretical data previously reported in the literature which include radiative transition probabilities, effective dielectronic recombination rate coefficients and autoionization probabilities.
DOI: 10.6084/m9.figshare.1282468
title: Tricky maths and physical truths of the natural sciences

description: Mathematical tools and physical reality.
DOI: 10.6084/m9.figshare.1282467.v1
title: Dynamical Modeling of the Cell Cycle and Cell Fate Emergence in Caulobacter crescentus

description: The division of Caulobacter crescentus, a model organism for studying cell cycle and differentiation in bacteria, generates two cell types: swarmer and stalked. To complete its cycle, C. crescentus must first differentiate from the swarmer to the stalked phenotype. An important regulator involved in this process is CtrA, which operates in a gene regulatory network and coordinates many of the interactions associated to the generation of cellular asymmetry. Gaining insight into how such a differentiation phenomenon arises and how network components interact to bring about cellular behavior and function demands mathematical models and simulations. In this work, we present a dynamical model based on a generalization of the Boolean abstraction of gene expression for a minimal network controlling the cell cycle and asymmetric cell division in C. crescentus.
DOI: 10.6084/m9.figshare.1282458
title: Regulatory Design Governing Progression of Population Growth Phases in Bacteria

description: A core circuit, formed by a subset of regulatory interactions involving five global transcription factors (FIS, HNS, IHF, RpoS and GadX), has been identified by correlating information from the well- established transcriptional regulatory network of Escherichia coli and genome-wide expression data from cultures in these different growth phases. We propose a functional role for this circuit in controlling progression through these phases. Two alternative hypotheses for controlling the transition between the growth phases are first, a continuous graded adjustment to changing environmental conditions, and second, a discontinuous hysteretic switch at critical thresholds between growth phases. We formulate a simple mathematical model of the core circuit, consisting of differential equations based on the power-law formalism, and show by mathematical and computerassisted analysis that there are critical conditions among the parameters of the model that can lead to hysteretic switch behavior, which – if validated experimentally – would suggest that the transitions between different growth phases might be analogous to cellular differentiation. Based on these provocative results, we propose experiments to test the alternative hypotheses.
DOI: 10.6084/m9.figshare.1282458.v1
title: Regulatory Design Governing Progression of Population Growth Phases in Bacteria

description: A core circuit, formed by a subset of regulatory interactions involving five global transcription factors (FIS, HNS, IHF, RpoS and GadX), has been identified by correlating information from the well- established transcriptional regulatory network of Escherichia coli and genome-wide expression data from cultures in these different growth phases. We propose a functional role for this circuit in controlling progression through these phases. Two alternative hypotheses for controlling the transition between the growth phases are first, a continuous graded adjustment to changing environmental conditions, and second, a discontinuous hysteretic switch at critical thresholds between growth phases. We formulate a simple mathematical model of the core circuit, consisting of differential equations based on the power-law formalism, and show by mathematical and computerassisted analysis that there are critical conditions among the parameters of the model that can lead to hysteretic switch behavior, which – if validated experimentally – would suggest that the transitions between different growth phases might be analogous to cellular differentiation. Based on these provocative results, we propose experiments to test the alternative hypotheses.
DOI: 10.6084/m9.figshare.1282467.v2
title: Dynamical Modeling of the Cell Cycle and Cell Fate Emergence in Caulobacter crescentus

description: The division of Caulobacter crescentus, a model organism for studying cell cycle and differentiation in bacteria, generates two cell types: swarmer and stalked. To complete its cycle, C. crescentus must first differentiate from the swarmer to the stalked phenotype. An important regulator involved in this process is CtrA, which operates in a gene regulatory network and coordinates many of the interactions associated to the generation of cellular asymmetry. Gaining insight into how such a differentiation phenomenon arises and how network components interact to bring about cellular behavior and function demands mathematical models and simulations. In this work, we present a dynamical model based on a generalization of the Boolean abstraction of gene expression for a minimal network controlling the cell cycle and asymmetric cell division in C. crescentus.
DOI: 10.6084/m9.figshare.1282452
title: Leaflet from Sheffield CCG re religious circumcision

description: An example of information made available to circumcising parents as Sheffield NHS stopped funding free non therapeutic circumcision (NTC) under general anaesthetic at the Children's Hospital - and developed an advice only service encouraging parents to access private services (normally early infant plastibell circumcsion). The leaflet advises that complications from 'medical circumcisions are rare in England' which is both untrue (presentations can run to 20% or more and readmission rates to 10% or more) and not relevant to a leaflet specifically about religious surgeries. Sheffield CCG needed only to look across to Leeds NHS figures to understand that religious infant cutting does not have rare complications either. The advice on local anaesthesia is also misleading too: DPNB has a high failure rate and pain remains a significant issue for circumcised infants (particularly with the apparent heightened response to pain in newborns and evidence of long term negative neurological effects. On circ pain see http://www.ncbi.nlm.nih.gov/pubmed/23759130 and at http://www.ncbi.nlm.nih.gov/pubmed/25365389
DOI: 10.6084/m9.figshare.1282440
title: 2011 data on NTC in Sheffield with readmission rates

description: Data collected from NHS Sheffield (PCT as was) and also children's hospital - an overlapping series of non therapeutic child circumcisions with readmission rates of c10-12% (depending on series/calculation as episodes/patients). Note 'admission' can mean being held for treatment in a specialist area of A&E - these cases are grouped with visits to ward I believe because the resource implications are similar: for purposes of assessing NTC complications they are assumed to be more serious on an individual and financial level.
DOI: 10.6084/m9.figshare.1282467.v3
title: Dynamical Modeling of the Cell Cycle and Cell Fate Emergence in Caulobacter crescentus

description: The division of Caulobacter crescentus, a model organism for studying cell cycle and differentiation in bacteria, generates two cell types: swarmer and stalked. To complete its cycle, C. crescentus must first differentiate from the swarmer to the stalked phenotype. An important regulator involved in this process is CtrA, which operates in a gene regulatory network and coordinates many of the interactions associated to the generation of cellular asymmetry. Gaining insight into how such a differentiation phenomenon arises and how network components interact to bring about cellular behavior and function demands mathematical models and simulations. In this work, we present a dynamical model based on a generalization of the Boolean abstraction of gene expression for a minimal network controlling the cell cycle and asymmetric cell division in C. crescentus.
DOI: 10.6084/m9.figshare.1282452.v1
title: Leaflet from Sheffield CCG re religious circumcision

description: An example of information made available to circumcising parents as Sheffield NHS stopped funding free non therapeutic circumcision (NTC) under general anaesthetic at the Children's Hospital - and developed an advice only service encouraging parents to access private services (normally early infant plastibell circumcsion). The leaflet advises that complications from 'medical circumcisions are rare in England' which is both untrue (presentations can run to 20% or more and readmission rates to 10% or more) and not relevant to a leaflet specifically about religious surgeries. Sheffield CCG needed only to look across to Leeds NHS figures to understand that religious infant cutting does not have rare complications either. The advice on local anaesthesia is also misleading too: DPNB has a high failure rate and pain remains a significant issue for circumcised infants (particularly with the apparent heightened response to pain in newborns and evidence of long term negative neurological effects. On circ pain see http://www.ncbi.nlm.nih.gov/pubmed/23759130 and at http://www.ncbi.nlm.nih.gov/pubmed/25365389