cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/mc6w93m6n3.1
title: Male preference for conspecific females depends on male size in the splendid darter, Etheostoma barrenense

description: We sought to expand existing knowledge of mate preference in the darter fish species Etheostoma barrenense by investigating whether variation in preference for conspecifics among individual males correlates with body size and coloring. We observed that only large males preferred conspecific females and no effect due to coloration. This result may indicate that preferences are expressed only by older males, or males with a competitive advantage, as both may be correlated with larger body size. If larger males are indeed older, our finding suggests a possibility of learned mate choice in darters. Standard body lengths of all individuals were measured with a digital caliper, and males were designated as ‘small’ (&lt; 45 mm) or ‘large’ (&gt; 45 mm). Dichotomous mate choice trials were conducted presenting two female stimuli, one E. barrenense and one Etheostoma zonale, to a male E. barrenense. Time spent in the conspecific and heterospecific association zone was recorded and used to calculate proportion of time spent associating with the conspecific and heterospecific female and strength of preference (SOP). SOP was calculated as SOP = (TC¬ – TH) / (TC¬ + TH), where TC is the time spent in the conspecific association zone and TH is time spent in the heterospecific association zone. SOP ranges from +1 to -1, representing complete preference for the conspecific or heterospecific female, respectively. Following trials, fish were euthanized and photographed. Males’ standard lengths were measured digitally, and coloration was quantified using the software ImageJ. We quantified proportion of red body coloration and a ‘red score,’ calculated by measuring the average red(R), green(G) and blue (B) pixel values for red body area and dividing R by the sum of the averaged RGB pixel values. Larger red scores indicate more saturated red coloration, with a score of 1 indicating pure red. Data is recorded in the file “raw_data.csv.” We used R to perform appropriate hypothesis tests, treating male size as a categorical variable, and to generate a linear model testing the effect of male size and colour, as continuous variables, on SOP. Lastly, we performed post hoc analyses to determine any effect of female size on our findings, including a comparison of female size within trials and a linear model comparing the standard length of the male and his preferred female. All analyses are available in the file “all code.R.” Trials were videorecorded from ‘top’ and ‘side’ viewpoints. No significant difference was found for trials with recordings from both. One view was randomly chosen for analysis for these trials. These data are recorded in the file “view.csv.” Three photographed males could not be matched to their behavioural trial and one photographed male was not used in behavioural trials. Therefore, behavioural trials were performed on N=17 males, colour analysis was performed on N=18 males, and linear modelling was performed on N=14 males.
DOI: 10.6084/m9.figshare.13247060.v1
title: Supplemental tables

description: Instrumental variables (IVs) used in MR analyses
DOI: 10.5286/isis.e.rb2000158
title: Order-Disorder in A New Generation of Ceria-Zirconia Catalyst Supports: Continuation

description: Solid-state materials that have the property of oxygen storage are of significance for various applications of relevance to the environment, importantly as catalyst supports in three-way catalytic converters, used to remove toxic pollutants from automotive exhausts. The catalytic converter typically uses a ceria-zirconia (Ce1-xZrxO2) solid-solution as the redox-active catalyst support that can buffer the oxygen concentration to optimise the conversion of CO, NOx and unburnt hydrocarbons into N2, CO2 and water. While this is well-established technology, there is a pressing need to tune the properties of the redox-active support further to give faster, more efficient oxygen release/uptake that survives over many cycles at elevated temperatures. We will study the structures of some new compositions to complete the PDF thesis work of Aron Summer.
DOI: 10.5286/isis.e.rb2000158-1
title: Order-Disorder in A New Generation of Ceria-Zirconia Catalyst Supports: Continuation

description: Solid-state materials that have the property of oxygen storage are of significance for various applications of relevance to the environment, importantly as catalyst supports in three-way catalytic converters, used to remove toxic pollutants from automotive exhausts. The catalytic converter typically uses a ceria-zirconia (Ce1-xZrxO2) solid-solution as the redox-active catalyst support that can buffer the oxygen concentration to optimise the conversion of CO, NOx and unburnt hydrocarbons into N2, CO2 and water. While this is well-established technology, there is a pressing need to tune the properties of the redox-active support further to give faster, more efficient oxygen release/uptake that survives over many cycles at elevated temperatures. We will study the structures of some new compositions to complete the PDF thesis work of Aron Summer.
DOI: 10.5286/isis.e.rb2010576
title: The relationship between spin fluctuations and electronic heat capacity in La2-xSrxCuO4

description: When the electronic heat capacity of the high temperature superconductor La2-xSrxCuO4 is measured as a function of doping at its transition temperature, it is found to be peaked a critical value p=0.24. This suggests that there is a quantum critical point (QCP) at this composition. Here we propose to make detailed measurements of the spin excitations at the same temperature for two compositions to determine whether the peak and the underlying QCP can be understood in terms of spin fluctuations. Our results could demonstrate the spin excitations dominate the electronic thermal thermodynamic properties, which would have important consequences for the theory of cuprate superconductivity.
DOI: 10.5286/isis.e.rb2010576-1
title: The relationship between spin fluctuations and electronic heat capacity in La2-xSrxCuO4

description: When the electronic heat capacity of the high temperature superconductor La2-xSrxCuO4 is measured as a function of doping at its transition temperature, it is found to be peaked a critical value p=0.24. This suggests that there is a quantum critical point (QCP) at this composition. Here we propose to make detailed measurements of the spin excitations at the same temperature for two compositions to determine whether the peak and the underlying QCP can be understood in terms of spin fluctuations. Our results could demonstrate the spin excitations dominate the electronic thermal thermodynamic properties, which would have important consequences for the theory of cuprate superconductivity.
DOI: 10.5286/isis.e.rb2010576-2
title: The relationship between spin fluctuations and electronic heat capacity in La2-xSrxCuO4

description: When the electronic heat capacity of the high temperature superconductor La2-xSrxCuO4 is measured as a function of doping at its transition temperature, it is found to be peaked a critical value p=0.24. This suggests that there is a quantum critical point (QCP) at this composition. Here we propose to make detailed measurements of the spin excitations at the same temperature for two compositions to determine whether the peak and the underlying QCP can be understood in terms of spin fluctuations. Our results could demonstrate the spin excitations dominate the electronic thermal thermodynamic properties, which would have important consequences for the theory of cuprate superconductivity.
DOI: 10.5281/zenodo.3938899
title: Scanning electron diffraction tilt series data of an aluminium-steel interface region

description: This dataset contains scanning electron diffraction (SED) data used in the publication entitled "<strong>Microstructural and mechanical characterisation of a second generation hybrid metal extrusion & bonding aluminium-steel butt joint</strong>". The data denoted “SED_HYB_...” were recorded from an aluminium-steel interface region that includes aluminium and steel grains, an interfacial Al-Fe-Si layer, and dispersoids and some oxide particles located within the aluminium region. The nanoscale interfacial intermetallic phase layer is polycrystalline, and to increase the probability of recording data from intermetallic phase crystals oriented close to zone axes, the data were recorded in a tilt series covering 30 degrees, in steps of 1 degree. The file names give the goniometer x-tilt values in degrees, e.g. " SED_HYB_TX-150.hdf5" denotes an x-tilt of -15.0 degrees. SED data recorded from an Au cross-grating specimen, named "SED_AuX.hdf5", and from a MoO3 specimen, named "SED_MoO3.hdf5", are also included for calibration purposes.
DOI: 10.5281/zenodo.3938898
title: Scanning electron diffraction tilt series data of an aluminium-steel interface region

description: This dataset contains scanning electron diffraction (SED) data used in the publication entitled "<strong>Microstructural and mechanical characterisation of a second generation hybrid metal extrusion & bonding aluminium-steel butt joint</strong>". The data denoted “SED_HYB_...” were recorded from an aluminium-steel interface region that includes aluminium and steel grains, an interfacial Al-Fe-Si layer, and dispersoids and some oxide particles located within the aluminium region. The nanoscale interfacial intermetallic phase layer is polycrystalline, and to increase the probability of recording data from intermetallic phase crystals oriented close to zone axes, the data were recorded in a tilt series covering 30 degrees, in steps of 1 degree. The file names give the goniometer x-tilt values in degrees, e.g. " SED_HYB_TX-150.hdf5" denotes an x-tilt of -15.0 degrees. SED data recorded from an Au cross-grating specimen, named "SED_AuX.hdf5", and from a MoO3 specimen, named "SED_MoO3.hdf5", are also included for calibration purposes.
DOI: 10.6084/m9.figshare.13247060
title: Supplemental tables from: Rheumatoid arthritis and osteoporosis: a bi-directional Mendelian randomization study

description: Instrumental variables (IVs) used in MR analyses
DOI: 10.6084/m9.figshare.13247060.v3
title: Supplemental tables from: Rheumatoid arthritis and osteoporosis: a bi-directional Mendelian randomization study

description: Instrumental variables (IVs) used in MR analyses
DOI: 10.6084/m9.figshare.13247060.v2
title: Supplemental tables

description: Instrumental variables (IVs) used in MR analyses
DOI: 10.25934/00005771.0
title: Available IPD datapackage for study 'A Randomized, Double-blind Study of the Effect of Avastin Plus Gemcitabine and Erlotinib Compared With Placebo Plus Gemcitabine and Erlotinib on Overall Survival in Patients With Metastatic Pancreatic Cancer'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00005771.1
title: IPD datapackage for study 'A Randomized, Double-blind Study of the Effect of Avastin Plus Gemcitabine and Erlotinib Compared With Placebo Plus Gemcitabine and Erlotinib on Overall Survival in Patients With Metastatic Pancreatic Cancer' and research request: 'Predictors of therapeutic and adverse effects of medicines used in the treatment of GI cancers.'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5281/zenodo.3778152
title: Amorphous carbon films generated through simulated deposition with GAP from 1eV to 100eV

description: These amorphous carbon films were generated following the deposition protocol and methodology outlined by Caro et al., Phys. Rev. Lett. <strong>120</strong>, 166101 (2018) and, in more detail, in Caro et al. Phys. Rev. B <strong>102</strong>, 174201 (2020). Briefly, the structures were generated by depositing monoenergetic C atoms on a preexisting diamond (111) substrate. The interatomic potential used was the a-C GAP of Deringer and Csányi [Phys. Rev. B <strong>95</strong>, 094203 (2017)] and the molecular dynamics simulations (MD) were carried out with QUIP's GAP implementation [http://libatoms.github.io/] using LAMMPS [https://lammps.sandia.gov/] as MD engine. The final structures of the deposition simulations at 1, 2, 3, 4, 5, 6.5, 8, 10, 20, 60 and 100eV are provided in extended XYZ format, with obvious naming convention.
DOI: 10.6084/m9.figshare.13084805
title: Data from Jacobs et al., Current Biology "Cortical state fluctuations during sensory decision making"

description: Please follow the links below to get to the actual data.<br>The data is organised into three categories (one link for each):- Behaviour- Pupil- WidefieldEach link contains zipped folders with the datasets organised by experimental subject. Most subjects were recorded from on multiple days, which form subfolders within the subject folder. Within a day, there may have been several experiments, which are again contained in subfolders within the day folder. The companion code (https://github.com/eakjacobs/Jacobs_et_al_CurrentBiology) is structured according to this data organisation.<br>If downloading all data (behaviour, widefield and pupil) to analyse them jointly, please keep the datasets organised into their own folders (ie, behaviour, widefield and pupil) as this is the organisation the companion code expects.<br>Both behaviour and widefield data come in different formats; the companion code can handle all of them and transforms them into a standard format as part of the preprocessing (which can be saved if desired). If there are any problems with this, please raise an issue on GitHub and I will look into it.Please also note that because the data provided is in raw format, the timestamps of the behaviour, pupil and widefield data are not aligned yet; the companion code takes care of this.<br>The behavioural data can be found at: https://doi.org/10.5522/04/13176959<br>The widefield data can be found at: https://doi/org/10.5522/04/13194452<br>The pupil data can be found at: https://doi.org/10.5522/04/13194155<br>The data from the simultaneous widefield and neuropixels recordings can be found at: https://figshare.com/articles/dataset/ctx_wf_traces_mat/13118435 & https://figshare.com/articles/dataset/muscimol_traces_mat/13122521<br>The neuropixels data can be found at: https://figshare.com/articles/steinmetz/9598406
DOI: 10.6073/pasta/1270a5dd61dd77ee06ba204ac1bcf1fa
title: Meteorological data from El Verde Field Station: NADP Tower

description: Meteorological sensors are located at the top of a 20 m tower, the NADP Tower, behind the main buildings of El Verde Field Station, 350 masl. No large trees are present near the tower. Sensors are connected to a Campbell 1000X data logger, with a storage module, and downloaded every two weeks using a wireless radio connection from the laboratory to the tower. Data are compiled at the station before it is made available. The station was initiated in 2000. Complementary manual measurements of rainfall and maximum and minimum air temperatures are taken on a daily basis at a separate physical location.
DOI: 10.6073/pasta/dbe929e8317e1b3c36cbaf52da942dd3
title: El Verde Field Station Air temperature from automatic sensor

description: This is a long-term monitoring of air temperature in the same box where we measure manual min-max temperature at El Verde Field Station. The data set is meant as a back up to the long-term manual data set. Data is measured hourly using a HOBO Pendant data logger placed inside a wooden box: under the shade of trees. The min-max thermometer that is measured manually during work days is located next to the HOBO in the same box.
DOI: 10.21223/p3/3di3gc/tt3pht
title: Data_dictionary.xls

description: :unav
DOI: 10.21223/p3/3di3gc/qjkyhk
title: PTPVS112018_CJMRC_CUTERVO.tab

description: :unav
DOI: 10.21223/p3/3di3gc/ickrjk
title: PTPVS112018_CJMRC_CHOTA.tab

description: :unav
DOI: 10.21223/p3/3di3gc/9tdhbc
title: 01_PTPVS112018_CJMRC_CHOTA.tab

description: :unav
DOI: 10.21223/p3/3di3gc/7zxsqn
title: 01_PTPVS112018_CJMRC_CUTERVO.tab

description: :unav
DOI: 10.21223/p3/3di3gc
title: Dataset for: Potential new bio-fortified potato varieties high in iron and zinc to contribute to food and nutrition security in Cajamarca, Peru (Participatory Varietal Selection)

description: A select group of 30 tetraploid biofortified clones from cycle I will be evaluated using a farmer participatory variety selection (PVS) in the highland of Cajamarca during the campaign 2018-2019; yield components, micronutrients content (Fe Zn) and post-harvest traits will be determinated, with the main purpose to improve the food security and nutrition of families in situation of vulnerability through the identification of 3-5 potential new biofortified potatoes varieties with 25% of micronutrient concentration (Fe) above the local varieties
DOI: 10.5281/zenodo.4277593
title: Dataset for the paper "Slavic morphosyntax is primarily determined by its geographic location and contact configuration", Scando-Slavica Journal

description: This is the raw dataset for the paper "Slavic morphosyntax is primarily determined by its geographic location and contact configuration", Scando-Slavica
DOI: 10.5281/zenodo.4277592
title: Dataset for the paper "Slavic morphosyntax is primarily determined by its geographic location and contact configuration", Scando-Slavica Journal

description: This is the raw dataset for the paper "Slavic morphosyntax is primarily determined by its geographic location and contact configuration", Scando-Slavica
DOI: 10.5281/zenodo.4277001
title: ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs

description: Genomic DNA is packed by histone proteins that carry a multitude of post-translational modifications that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test.
description: The dataset contains several directories in gziped tar files. SetupFiles.tgz - directory with the files needed to define the regions of the genome used in the analysis. Analysis.tgz - analysis directory with the BED files in the paper. See https://github.com/nirfriedman/cfChIP-seq for code and for detailed instructions on setting up the directories.
DOI: 10.5281/zenodo.3967253
title: ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs

description: Genomic DNA is packed by histone proteins that carry a multitude of post-translational modifications that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test.
description: The dataset contains several directories in gziped tar files. SetupFiles.tgz - directory with the files needed to define the regions of the genome used in the analysis. Analysis.tgz - analysis directory with the BED files in the paper. See https://github.com/nirfriedman/cfChIP-seq for code and for detailed instructions on setting up the directories.
DOI: 10.5286/isis.e.rb1920425
title: Lipid Interactions with Styrene-Maleic Acid Copolymers on Surfaces

description: Polymer stabilized lipid nanodiscs offer enormous potential as tools for enabling membrane protein structural studies & biophysics. Previously we studied discs formed using a poly(styrene-alt-maleic acid) (PSMA) copolymers synthesised using RAFT controlled radical polymerisations. The RAFT method is a living polymerisation allowing us to grow either an alternating styrene (S) and maleic acid (MA) segment first or a pure styrene section. We have tethered the RAFT agent to oxide surfaces allowing us to grow the polymer from the interface, and have demonstrated that the surface tethered polymer interacts strongly with lipid vesicles, pulling them out of suspension. Here we wish to use neutron reflectivity with contrast variation to determine the surface structures which develop in this system, and how these vary with the position of the S-MA vs S blocks relative to the surface.
DOI: 10.5286/isis.e.rb1920425-1
title: Lipid Interactions with Styrene-Maleic Acid Copolymers on Surfaces

description: Polymer stabilized lipid nanodiscs offer enormous potential as tools for enabling membrane protein structural studies & biophysics. Previously we studied discs formed using a poly(styrene-alt-maleic acid) (PSMA) copolymers synthesised using RAFT controlled radical polymerisations. The RAFT method is a living polymerisation allowing us to grow either an alternating styrene (S) and maleic acid (MA) segment first or a pure styrene section. We have tethered the RAFT agent to oxide surfaces allowing us to grow the polymer from the interface, and have demonstrated that the surface tethered polymer interacts strongly with lipid vesicles, pulling them out of suspension. Here we wish to use neutron reflectivity with contrast variation to determine the surface structures which develop in this system, and how these vary with the position of the S-MA vs S blocks relative to the surface.