cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3564178
title: Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

description: Data used to test the robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data, described in Holland et al. 2020. The folder <em>data </em>contains<em> </em>raw data and the folder <em>output</em> contains intermediate and final results of all analyses. The associated analyses code and more information are available on GitHub. <strong>Abstract</strong> <strong>Background</strong> Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. <strong>Results</strong> To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community. <strong>Conclusions</strong> Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used. For questions related to the data please write an email to christian.holland@bioquant.uni-heidelberg.de or use the GitHub issue system.
DOI: 10.5281/zenodo.3564179
title: Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

description: Data used to test the robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data, described in Holland et al. 2020. The folder <em>data </em>contains<em> </em>raw data and the folder <em>output</em> contains intermediate and final results of all analyses. The associated analyses code and more information are available on GitHub. <strong>Abstract</strong> <strong>Background</strong> Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. <strong>Results</strong> To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community. <strong>Conclusions</strong> Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used. For questions related to the data please write an email to christian.holland@bioquant.uni-heidelberg.de or use the GitHub issue system.
DOI: 10.5286/isis.e.rb1910024-2
title: Origin of the structural relaxation in ice V and the H/D volume isotope effect

description: Ice V is disordered monoclinic polymorph of water ice, with a complex structural topology. In our work on ice V (recovered to atmospheric pressure at liquid-nitrogen temperatures) we have observed a structural relaxation we believe is due to a change in the orientational order of the water molecules. To test this hypothesis, we propose to measure high-quality structural datasets from both the un-relaxed and the relaxed forms of D2O ice V using high-resolution neutron powder diffraction. Our earlier work also showed that ice V exhibits negative linear expansion along its c-axis, a property we believe to be correlated with anomalous lattice expansion due to isotopic substitution. Since these isotope effects have proven so challenging to predict computationally, experimental verification of these correlations are essential, and we propose also to measure high-resolution data from H2O ice V.
DOI: 10.5286/isis.e.rb1920479
title: Low-temperature magnetic correlations in SrTb2O4

description: We propose to probe the development of the magnetic correlations in SrTb2O4 using WISH neutron diffractometer. In a magnetic sense, SrTb2O4 consists of triangular zig-zag ladders and is therefore affected by geometrical frustration. Our initial measurements for T&gt;1.5 K (using CYCLOPS and D7 instruments at the ILL) revealed a disordered magnetic ground state, which we now want to examine at sub 1 K temperatures. We are particularly interested in the details of the low-temperature diffuse scattering signal, which we have studied in similar compounds (SrEr2O4, SrHo2O4, SrDy2O4, BaDy2O4) allowing us to claim an unusual coexistence of magnetic orders with different correlation lengths as well as a peculiar field dependence with metamagnetic transitions and magnetisation plateaux.
DOI: 10.5286/isis.e.rb1920479-1
title: Low-temperature magnetic correlations in SrTb2O4

description: We propose to probe the development of the magnetic correlations in SrTb2O4 using WISH neutron diffractometer. In a magnetic sense, SrTb2O4 consists of triangular zig-zag ladders and is therefore affected by geometrical frustration. Our initial measurements for T&gt;1.5 K (using CYCLOPS and D7 instruments at the ILL) revealed a disordered magnetic ground state, which we now want to examine at sub 1 K temperatures. We are particularly interested in the details of the low-temperature diffuse scattering signal, which we have studied in similar compounds (SrEr2O4, SrHo2O4, SrDy2O4, BaDy2O4) allowing us to claim an unusual coexistence of magnetic orders with different correlation lengths as well as a peculiar field dependence with metamagnetic transitions and magnetisation plateaux.
DOI: 10.5286/isis.e.rb1920505
title: Measurement of Residual Stress in MELD deposited Al6061 by Neutron Diffraction

description: MELD, which is also referred to as additive friction stir deposition, is an emerging solid-state process that is uniquely suited for large-scale additive manufacturing and repair of metals and alloys .The work outlined forms part of a collaborative project between the University of Nottingham and Virginia Tech on the development of process modelling capabilities to predict the deposition geometry, thermal profiles, deformation and residual stress and resultant microstructures generated by the process to create a tool to improve understanding of the interaction of and optimisation of process parameters. The objective of this proposal is to validate an initial sequentially coupled thermo-mechanical model of the process.
DOI: 10.5286/isis.e.rb1920505-1
title: Measurement of Residual Stress in MELD deposited Al6061 by Neutron Diffraction

description: MELD, which is also referred to as additive friction stir deposition, is an emerging solid-state process that is uniquely suited for large-scale additive manufacturing and repair of metals and alloys .The work outlined forms part of a collaborative project between the University of Nottingham and Virginia Tech on the development of process modelling capabilities to predict the deposition geometry, thermal profiles, deformation and residual stress and resultant microstructures generated by the process to create a tool to improve understanding of the interaction of and optimisation of process parameters. The objective of this proposal is to validate an initial sequentially coupled thermo-mechanical model of the process.
DOI: 10.5286/isis.e.rb1920741
title: Neutron scattering of sandstone subjected to uniaxial compression in cryogenic conditions

description: The exploitation of unconventional remote geological resources, such as those in Arctic formations, requires engineering designs that withstand the temperatures and pressures encountered. In a previous experiment (RB1810235, April 2018) comparing sandstone and limestone, we showed that limestone can mainly have tensile residual strains, while sandstone has compressive residual strains under otherwise similar thermal and loading conditions. Not enough experimental time was available in the previous beamtime to fully characterise sandstone however; therefore, this continuation proposal is to study frozen (cryogenic conditions) sandstone subjected to unconfined uniaxial compression loading conditions. In this proposal we aim to test core sandstone samples at high pressure (5-15 MPa) and low temperature conditions (as low as -5°C, -30°C).
DOI: 10.5286/isis.e.rb1920387
title: Influence of deposition strategy on microstructure heterogeneity and twinning in Wire + Arc Additive Manufactured Ti6Al4V

description: Wire and Arc Additive Manufacturing (WAAM) process is rapidly moving towards the production and qualification of large structural parts. Parts built by WAAM for structural applications require to perform under cyclic loading condition without compromising the safety. The presence of heterogeneous microstructure and considerable texture leads to anisotropic mechanical properties. More importantly, the microstructure heterogeneity leads to direction dependent deformation and damage under cyclic loading. Therefore, the proposed study aims to understand the influence of two deposition strategies and the microstructure heterogeneity in WAAM Ti6Al4V specimens subjected to low cycle fatigue. The outcomes will provide a mechanistic understanding of the relation between microstructure heterogeneity on the deformation and twinning in WAAM Ti6Al4V.
DOI: 10.5286/isis.e.rb1920387-1
title: Influence of deposition strategy on microstructure heterogeneity and twinning in Wire + Arc Additive Manufactured Ti6Al4V

description: Wire and Arc Additive Manufacturing (WAAM) process is rapidly moving towards the production and qualification of large structural parts. Parts built by WAAM for structural applications require to perform under cyclic loading condition without compromising the safety. The presence of heterogeneous microstructure and considerable texture leads to anisotropic mechanical properties. More importantly, the microstructure heterogeneity leads to direction dependent deformation and damage under cyclic loading. Therefore, the proposed study aims to understand the influence of two deposition strategies and the microstructure heterogeneity in WAAM Ti6Al4V specimens subjected to low cycle fatigue. The outcomes will provide a mechanistic understanding of the relation between microstructure heterogeneity on the deformation and twinning in WAAM Ti6Al4V.
DOI: 10.5286/isis.e.rb1920387-2
title: Influence of deposition strategy on microstructure heterogeneity and twinning in Wire + Arc Additive Manufactured Ti6Al4V

description: Wire and Arc Additive Manufacturing (WAAM) process is rapidly moving towards the production and qualification of large structural parts. Parts built by WAAM for structural applications require to perform under cyclic loading condition without compromising the safety. The presence of heterogeneous microstructure and considerable texture leads to anisotropic mechanical properties. More importantly, the microstructure heterogeneity leads to direction dependent deformation and damage under cyclic loading. Therefore, the proposed study aims to understand the influence of two deposition strategies and the microstructure heterogeneity in WAAM Ti6Al4V specimens subjected to low cycle fatigue. The outcomes will provide a mechanistic understanding of the relation between microstructure heterogeneity on the deformation and twinning in WAAM Ti6Al4V.
DOI: 10.5286/isis.e.rb1920388
title: Rh(I) in Topochemically Reduced Extended Oxides

description: In recent years there has been a growing interest in modifying the anion lattice of complex transition metal oxides, via topochemical manipulation, to tune the magnetic and electronic properties of these materials. These processes not only alter the electron count of the phase but also the local symmetry and coordination geometry of the transition metal centres. We have utilized low temperature topochemical anion deintercalation reactions to reduce a series of rhodium-containing Ruddlesden-Popper oxides, to yield the first extended oxide phases to contain Rh(I) centres. We propose to collect neutron powder diffraction data to determine the crystal structures of the reduced compounds and the nature of the magnetic ordering present at low temperature.
DOI: 10.5286/isis.e.rb1920741-1
title: Neutron scattering of sandstone subjected to uniaxial compression in cryogenic conditions

description: The exploitation of unconventional remote geological resources, such as those in Arctic formations, requires engineering designs that withstand the temperatures and pressures encountered. In a previous experiment (RB1810235, April 2018) comparing sandstone and limestone, we showed that limestone can mainly have tensile residual strains, while sandstone has compressive residual strains under otherwise similar thermal and loading conditions. Not enough experimental time was available in the previous beamtime to fully characterise sandstone however; therefore, this continuation proposal is to study frozen (cryogenic conditions) sandstone subjected to unconfined uniaxial compression loading conditions. In this proposal we aim to test core sandstone samples at high pressure (5-15 MPa) and low temperature conditions (as low as -5°C, -30°C).
DOI: 10.5286/isis.e.rb1910220-2
title: Dynamics of PDMS-g-PDMS bottlebrush polymers

description: Bottlebrush polymers, backbone with long side chains, are very interesting regarding their architecture, which is different from well known linear polymers. Not only the structure changes by grafting side chains to a backbone, also the dynamics are expected to change. By using neutron scattering we are able to clarify this statement in detail. Using deuterium labeling we can select different parts for detecting the dynamical behavior and therefore we are able to observe details of every component of our system. Combining three neutron spectrometers a broad range of relaxation times, including fast relaxation beyond the local dynamics are detectable and can be combined with NMR relaxometry in our own laboratory to cover an unprecedented time window.
DOI: 10.5286/isis.e.rb1920388-1
title: Rh(I) in Topochemically Reduced Extended Oxides

description: In recent years there has been a growing interest in modifying the anion lattice of complex transition metal oxides, via topochemical manipulation, to tune the magnetic and electronic properties of these materials. These processes not only alter the electron count of the phase but also the local symmetry and coordination geometry of the transition metal centres. We have utilized low temperature topochemical anion deintercalation reactions to reduce a series of rhodium-containing Ruddlesden-Popper oxides, to yield the first extended oxide phases to contain Rh(I) centres. We propose to collect neutron powder diffraction data to determine the crystal structures of the reduced compounds and the nature of the magnetic ordering present at low temperature.
DOI: 10.5286/isis.e.rb2000025
title: Silicon carbide neutron detectors

description: Silicon carbide is a promising technology for semiconductor neutron detectors and radiation-hard electronics. Lancaster University is developing a thin silicon carbide neutron detector on a chip in conjunction with partners in Japan and the UK, for applications including decommissioning at Fukushima Daiichi. The detector on a chip will be extremely small (3 mm thick) and rad-hard for robotic deployment in harsh environments. This work requires the silicon carbide detector performance to be characterised by experiment and simulation; the present experiments at ISIS support that characterisation.
DOI: 10.5286/isis.e.rb2000025-1
title: Silicon carbide neutron detectors

description: Silicon carbide is a promising technology for semiconductor neutron detectors and radiation-hard electronics. Lancaster University is developing a thin silicon carbide neutron detector on a chip in conjunction with partners in Japan and the UK, for applications including decommissioning at Fukushima Daiichi. The detector on a chip will be extremely small (3 mm thick) and rad-hard for robotic deployment in harsh environments. This work requires the silicon carbide detector performance to be characterised by experiment and simulation; the present experiments at ISIS support that characterisation.
DOI: 10.5286/isis.e.rb2000025-2
title: Silicon carbide neutron detectors

description: Silicon carbide is a promising technology for semiconductor neutron detectors and radiation-hard electronics. Lancaster University is developing a thin silicon carbide neutron detector on a chip in conjunction with partners in Japan and the UK, for applications including decommissioning at Fukushima Daiichi. The detector on a chip will be extremely small (3 mm thick) and rad-hard for robotic deployment in harsh environments. This work requires the silicon carbide detector performance to be characterised by experiment and simulation; the present experiments at ISIS support that characterisation.
DOI: 10.5286/isis.e.rb2000037
title: Resolving the enigma of self-assembled meso-structures in an H-bonding rich medium

description: In a recent successful LOQ experiment (RB 1810629), we have unexpectedly observed possible multilayer stacking of sodium dodecyl sulfate (SDS; ~2wt%) bilayers in glycerol evident from the lamellar peaks in the SANS scans, contrasting with previous microscopy imaging, showing fibrous aggregates. We will address the questions: What intermolecular packing could lead to the lamellar peaks in our SANS data, comparing two possible geometries (lamellar sheets vs. multilayer cylinders)? How could SDS assemble into microfibres of ~ mm in length? We aim to use neutron diffraction to probe the effect of hydrogen-bonding in mediating such unexpected self-assembly behaviour in glycerol, the medium in which the phase was first observed. However, this initial study would prove to be a feasibility test on this type of technique for this system.
DOI: 10.5286/isis.e.rb2000037-1
title: Resolving the enigma of self-assembled meso-structures in an H-bonding rich medium

description: In a recent successful LOQ experiment (RB 1810629), we have unexpectedly observed possible multilayer stacking of sodium dodecyl sulfate (SDS; ~2wt%) bilayers in glycerol evident from the lamellar peaks in the SANS scans, contrasting with previous microscopy imaging, showing fibrous aggregates. We will address the questions: What intermolecular packing could lead to the lamellar peaks in our SANS data, comparing two possible geometries (lamellar sheets vs. multilayer cylinders)? How could SDS assemble into microfibres of ~ mm in length? We aim to use neutron diffraction to probe the effect of hydrogen-bonding in mediating such unexpected self-assembly behaviour in glycerol, the medium in which the phase was first observed. However, this initial study would prove to be a feasibility test on this type of technique for this system.
DOI: 10.5286/isis.e.rb2000038-2
title: ChipIR Commercial Access Infineon OX10 - week37/2019

description: High-voltage power semiconductor devices, such as IGBTs, diodes and MOSFETs are susceptible to destructive failure due to terrestrial cosmic radiation (CR), notably the nucleon part. As a consequence, device development has to ensure adequate radiation hardness for every device technology. This aim can only partly be met by device and technology simulations and, therefore, also calls for extensive device tests. In order to reduce testing times accelerated irradiation tests at facilities with a nucleon energy spectrum close to the natural terrestrial CR are essential. The thus obtained failures rates will be compared to simulation predictions and storage tests.
DOI: 10.5286/isis.e.rb1910396
title: Understanding the damage tolerance of fibre-reinforced ceramic matrix composites (FRCMCs) at ambient and elevated temperatures

description: Fiber reinforced ceramic matrix composites (FRCMCs) have numerous applications, such as engine components, rocket re-entry nozzles and military vehicles due to their light weight, combined strength and toughness at high temperature. With the commercialization of GE LEAP engine using a ceramic shrouds, FRCMC is regarded as a game changer in key engineering areas for high energy efficiency and safety. FRCMCs have a complex microstructure and as damage accumulates it shows non-linear stress-strain behaviour. This is exactly what we are going to study. Neutrons will tell us how much the lattice has deformed in the material under load; we then take digital images of the surface of the sample to calculate the total deformation. By comparing the two, the tolerance of damage in FRCMCs can be determined and correlated to its microstructure for optimizing the material design.
DOI: 10.5286/isis.e.rb1910396-1
title: Understanding the damage tolerance of fibre-reinforced ceramic matrix composites (FRCMCs) at ambient and elevated temperatures

description: Fiber reinforced ceramic matrix composites (FRCMCs) have numerous applications, such as engine components, rocket re-entry nozzles and military vehicles due to their light weight, combined strength and toughness at high temperature. With the commercialization of GE LEAP engine using a ceramic shrouds, FRCMC is regarded as a game changer in key engineering areas for high energy efficiency and safety. FRCMCs have a complex microstructure and as damage accumulates it shows non-linear stress-strain behaviour. This is exactly what we are going to study. Neutrons will tell us how much the lattice has deformed in the material under load; we then take digital images of the surface of the sample to calculate the total deformation. By comparing the two, the tolerance of damage in FRCMCs can be determined and correlated to its microstructure for optimizing the material design.