cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2973
title: Large scale phenotype imputation and in vivo functional validation implicate ADAMTS14 as a novel adiposity gene - Supplementary data

description: Obesity remains an unmet global health burden. Detrimental anatomical distribution of body fat is a major driver of obesity-mediated mortality risk and is demonstrably heritable. However, our understanding of the full genetic contribution to human adiposity is incomplete, as few studies measure adiposity directly. To address this, we imputed DXA adiposity phenotypes in UK Biobank from the 5,000 directly measured participants onto the rest of the cohort, greatly increasing our discovery power. GWAS on these imputed phenotypes in over 390,000 participants yielded hundreds of novel associations, six of which were replicated in independent DXA cohorts. The leading causal gene candidate, ADAMTS14, was further investigated in a mouse knockout model. Concordant with the GWAS data, the Adamts14–/– mice exhibited reduced adiposity and weight-gain under obesogenic conditions, alongside an improved metabolic rate and health. Phenotypic imputation at scale has offered deeper biological insights into the genetics of human adiposity that could lead to novel therapeutic targets.
DOI: 10.7488/ds/3095
title: Structural diversity and tree density drives variation in the biodiversity-ecosystem function relationship of woodlands and savannas
title: Biodiversity-Ecosystem Function Relationship in southern African woodlands
title: SEOSAW anonymised data for Biodiversity-Ecosystem Function Relationship manuscript

description: Positive biodiversity-ecosystem function relationships (BEFRs) have been widely documented, but it is unclear if BEFRs should be expected in disturbance-driven systems. Disturbance may limit competition and niche differentiation, which are frequently posited to underlie BEFRs. We provide the first exploration of the relationship between tree species diversity and biomass, one measure of ecosystem function, across southern African woodlands and savannas, an ecological system rife with disturbance from fire, herbivores and humans. We used &gt;1000 vegetation plots distributed across 10 southern African countries, and structural equation modelling, to determine the relationship between tree species diversity and aboveground woody biomass, accounting for interacting effects of resource availability, disturbance by fire, tree stem density and vegetation type. We found positive effects of tree species diversity on aboveground biomass, operating via increased structural diversity. The observed BEFR was highly dependent on organismal density, with a minimum threshold of c. 180 mature stems ha-1. We found that water availability mainly affects biomass indirectly, via increasing species diversity. The study underlines the close association between tree diversity, ecosystem structure, environment and function in highly disturbed savannas and woodlands. We suggest that tree diversity is an under-appreciated determinant of wooded ecosystem structure and function.
DOI: 10.7488/ds/2975
title: SUPERSEDED - Average male, female and mixed gender mouse TSPO brain maps, generated using TSPO PET radiotracer [18F]LW223 (unnormalized to injected dose)

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2988 ## [18F]LW223 is a novel Positron Emission Tomography (PET) radiotracer which can be used to detetect 18kDa translocator protein (TSPO) distribution in vivo. Murine brain TSPO maps were generated using average SUV at 90-120 minutes post-[18F]LW223 injection in healthy male (n=9, age 14.7 ± 6.2 weeks, mean ± SD) and female (n=5, age 11.6 ± 2.5 weeks, mean ± SD) C57Bl6/J mice. Three average maps are available to download as NIfTI (.nii) files: 1) averge male TSPO map; 2) average female TSPO map; 3) average TSPO map of both sexes. The maps were smoothed using 0.2 mm Gaussian filter.
DOI: 10.7488/ds/3098
title: Inhibitory synapse loss and accumulation of amyloid beta in inhibitory presynaptic terminals in Alzheimer’s disease - Kurucu et al

description: # Background # Synapse degeneration in Alzheimer’s disease (AD) correlates strongly with cognitive decline. There is well-established excitatory synapse loss in Alzheimer’s disease with known contributions of pathological amyloid beta (Ab) to excitatory synapse dysfunction and loss. Despite clear changes in circuit excitability in AD and model systems, relatively little is known about pathology in inhibitory synapses. # Methods # Here we examined human post-mortem brain samples (n=5 control, 10 AD cases) from temporal and occipital cortices to examine whether inhibitory synapses and neurons are lost in AD and whether Ab may contribute to inhibitory synapse degeneration. Inhibitory neurons were counted in all 6 cortical layers using stereology software, and array tomography was used to examine synapse density and accumulation of Ab in synaptic terminals. # Results # We observe differing inhibitory neuron densities in the different cortical layers and brain regions with significantly lower inhibitory neuron density in AD than in control cases. High-resolution array tomography imaging reveals plaque-associated loss of inhibitory synapses and accumulation of Ab in a small subset of inhibitory pre-synaptic terminals with the most accumulation near amyloid plaques. # Conclusions # Inhibitory neuron and synapse loss in AD may contribute to disrupted excitatory/inhibitory balance and cognitive decline. Future work is warranted to determine whether targeting inhibitory synapse loss could be a useful therapeutic strategy. # Acknowledgments # This study was funded by a European Academy of Neurology Fellowship, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 681181), Wellcome Trust PhD studentships, and the UK Dementia Research Institute which receives its funding from DRI Ltd, funded by the UK Medical Research Council. Several of our control participants were recruited through the Lothian Birth Cohort 1936 study in the University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology which were supported by Age UK (Disconnected Mind Project), BBSRC, and MRC (MR/K026992/1).
description: Images, spreadsheets, and statistical analysis files for Kurucu et al 2021.
DOI: 10.7488/ds/3791
title: Numerical investigation of the dynamics of a single rigid spherical particle in vortical cross-slot flow at moderate inertia

description: This data folder contains the rigid particle data obtained from literature and mesoscopic simulations. Simulations were performed with an in-house lattice Boltzmann-immersed boundary method (LB-IBM).
DOI: 10.7488/ds/3123
title: Student feedback on 'Controls 3' remote lab

description: n=21 students provided feedback in the form of responses to the User Experience Questionnaire (UEQ) as well as a custom survey focused on ease of use, usefulness and 'feeling of control' of the user interface components. The survey also attempts to highlight student perceptions of the difference in skills acquisition between remote and proximal labs as well as general perceptions of the advantages and disadvantages of remote labs.
DOI: 10.7488/ds/3787
title: Fan cells in lateral entorhinal cortex directly influence medial entorhinal cortex through synaptic connections in layer 1

description: Data used to generate figures and statistical outputs for https://www.biorxiv.org/content/10.1101/2022.08.25.505296v1. Analysis code used for this dataset can be found at https://github.com/MattNolanLab/lec_to_mec. # Abstract of the study: # Standard models for spatial and episodic memory suggest that the lateral entorhinal cortex (LEC) and medial entorhinal cortex (MEC) send parallel independent inputs to the hippocampus, each carrying different types of information. Here, we evaluate the possibility that information is integrated between divisions of the entorhinal cortex prior to reaching the hippocampus. We demonstrate that fan cells in layer 2 (L2) of LEC that receive neocortical inputs, and that project to the hippocampal dentate gyrus, also send axon collaterals to layer 1 (L1) of the MEC. Activation of inputs from fan cells evokes monosynaptic glutamatergic excitation of stellate and pyramidal cells in L2 of the MEC, typically followed by inhibition that contains fast and slow components mediated by GABAA and GABAB receptors, respectively. Inputs from fan cells also directly activate interneurons in L1 and L2 of MEC, with synaptic connections from L1 interneurons accounting for slow feedforward inhibition of L2 principal cell populations. The relative strength of excitation and inhibition following fan cell activation differs substantially between neurons and is largely independent of anatomical location. Our results demonstrate that the LEC, in addition to directly influencing the hippocampus, can activate or inhibit major hippocampal inputs arising from the MEC. Thus, local circuits in the superficial MEC may combine spatial information with sensory and higher order signals from the LEC, providing a substrate for integration of ‘what’ and ‘where’ components of episodic memories.
DOI: 10.7488/ds/3812
title: Validity of clinical severity scores for respiratory syncytial virus: a systematic review - data extraction sheet

description: The file presented is the standardised data extraction sheet that was used to extract data for the systematic review on the validity of severity scores for respiratory syncytial virus in children (≤24 months). This systematic review was conducted as a part of the Preparing for RSV Immunisation and Surveillance in Europe (PROMISE) project, funded by the Innovative Medicines Initiative 2 Joint Undertaking (grant number: 101034339). The file is related to the upcoming publication Sheikh Z., E. Potter, Y. Li, R. Cohen, G. Dos Santos, L. Bont and H. Nair (in submission). Validity of clinical severity scores for respiratory syncytial virus: a systematic review.
DOI: 10.7488/ds/3806
title: ATR-FTIR spectra Rhynie chert fossils

description: The affinities of extinct organisms are often difficult to resolve using morphological data alone. Chemical analysis of carbonaceous specimens can complement traditional approaches, but the search for taxon-specific signals in ancient, thermally altered organic matter is challenging and controversial, partly because suitable positive controls are lacking. Here, we show that non-destructive Fourier Transform Infrared Spectroscopy (FTIR) resolves in-situ molecular fingerprints in the famous 407-Ma Rhynie chert fossil assemblage of Aberdeenshire, Scotland, an important early terrestrial Lagerstätte. Remarkably, unsupervised clustering methods (principal components analysis and K-mean) separate the fossil spectra naturally into eukaryotes and prokaryotes (cyanobacteria). Additional multivariate statistics and machine-learning approaches also differentiate prokaryotes from eukaryotes, and discriminate eukaryotic tissue types, despite the overwhelming influence of silica. We find that these methods can clarify the affinities of morphologically ambiguous taxa; in the Rhynie chert for example, we show that the problematic "nematophytes" have a plant-like composition. Overall, we demonstrate that the famously exquisite preservation of cells, tissues and organisms in the Rhynie chert accompanies similarly impressive preservation of molecular information. These results provide a compelling positive control that validates the use of infrared spectroscopy to investigate the affinity of organic fossils in chert. The dataset is related to the publication: Loron, C.C., Rodriguez Dzul, E., Orr, P.J., Gromov, A.V., Fraser, N.C. and McMahon, S., 'Molecular fingerprints resolve affinities of Rhynie chert organic fossils'. Nature Communications 14, 1387 (2023). https://doi.org/10.1038/s41467-023-37047-1
DOI: 10.7488/ds/3413
title: Effects of administration route on uptake kinetics of 18F‑sodium fluoride positron emission tomography in mice

description: 18F-sodium fluoride (18F-NaF) is a positron emission tomography (PET) radiotracer widely used in skeletal imaging and has also been proposed as a biomarker of active calcification in atherosclerosis. Like most PET radiotracers, 18F-NaF is typically administered intravenously. However in small animal research intravenous administrations can be challenging, because partial paravenous injection is common due to the small calibre of the superficial tail veins and repeat administrations via tail veins can lead to tissue injury therefore limiting the total number of longitudinal scanning points. In this paper, the feasibility of using intra-peritoneal route of injection of 8F-NaF to study calcification in mice was studied by looking at the kinetic and uptake profiles of normal soft tissues and bones versus intra-vascular injections. Dynamic PET was performed for 60 min on nineteen isoflurane-anesthetized male Swiss mice after femoral artery (n = 7), femoral vein (n = 6) or intraperitoneal (n = 6) injection of 8F-NaF. PET data were reconstructed and the standardised uptake value (SUV) and standardised uptake value ratio (SUVr) were estimated from the last three frames between 45- and 60-min and 8F-NaF uptake constant (Ki) was derived by Patlak graphical analysis. In soft tissue, the 18F-NaF perfusion phase changes depending on the type on injection route, whereas the uptake phase is similar regardless of the administration route. In bone tissue SUV, SUVr and Ki measures were not significantly different between the three administration routes. Comparison between PET and CT measures showed that bones that had the highest CT density displayed the lowest PET activity and conversely, bones where CT units were low had high 8F-NaF uptake. Intraperitoneal injection is a valid and practical alternative to the intra-vascular injections in small-animal 18F-NaF PET imaging providing equivalent pharmacokinetic data. CT outcome measures report on sites of stablished calcification whereas PET measures sites of higher complexity and active calcification.
description: There are four .zip files: - Femoral artery studies: These are the animals injected through the femoral artery. There is a PET (time corrected) and a CT file generated by Mediso software and PMOD respectively. - Femoral vein studies: These are the animals injected through the femoral vein. There is a PET (time corrected) and a CT file generated by Mediso software and PMOD respectively. - IP studies: These are the animals with intraperitoneal injection. There is a PET (time corrected) and a CT file generated by Mediso software and PMOD respectively. - Excel sheet TACs: This is a collection of all the Time Activity Curves and can be open with Excel. The recommended software to open these files (once unzipped) is PMOD.
DOI: 10.7488/ds/3811
title: Determining the Location of the Alpha-Synuclein Dimer Interface using Native Top-Down Fragmentation and Isotope Depletion-Mass Spectrometry

description: Alpha-synuclein (αSyn), a 140-residue intrinsically disordered protein, comprises the primary proteinaceous component of pathology-associated Lewy body inclusions in Parkinson’s disease (PD). Due to its association with PD αSyn is studied extensively; however the endogenous structure and physiological roles of this protein are yet to be fully understood. Here, ion mobility-mass spectrometry and native top-down electron capture dissociation fragmentation have been used to elucidate the structural properties associated with a stable, naturally-occurring dimeric species of αSyn. This stable dimer appears in both wild-type (WT) αSyn and the PD-associated variant A53E. Furthermore, we integrated a novel method for generating isotopically depleted protein into our native top-down workflow. Isotope depletion increases signal-to-noise ratio and reduces the spectral complexity of fragmentation data, enabling the monoisotopic peak of low abundant fragment ions to be observed. This enables the accurate and confident assignment of fragments unique to the αSyn dimer to be assigned, and structural information about this species to be inferred. Using this approach, we were able to identify fragments unique to the dimer, which demonstrates a C-terminal to C-terminal interaction between the monomer subunits. The approach in this study holds promise for further investigation into the structural properties of endogenous multimeric species of αSyn. The data relates to the following publication: Kiani Jeacock, Alexandre Chappard, Kelly J. Gallagher, C. Logan Mackay, David P. A. Kilgour, Mathew H. Horrocks, Tilo Kunath and David J. Clarke. 'Determining the Location of the Alpha-Synuclein Dimer Interface using Native Top-Down Fragmentation and Isotope Depletion-Mass Spectrometry.' J. Am. Soc Mass Spec. (in submission).
DOI: 10.7488/ds/3414
title: Human iPSC-derived renal organoids engineered to report oxidative stress can predict drug-induced nephrotoxicity

description: Advances in regenerative medicine have led to the construction of many types of organoids, which reproduce important aspects of endogenous organs but may be limited or disorganised in nature. While their usefulness for restoring function remains unclear, they have undoubted usefulness in research, diagnostics and toxicology. In toxicology, there is an urgent need for better models for human kidneys. We used human iPS-cell (hiPSC)-derived renal organoids to identify HMOX1 as a useful marker of toxic stress via the oxidative stress pathway, then constructed an HMOX1 reporter in hiPSCs. We used two forms of hiPSC-derived HMOX1-reporter renal organoids to probe their ability to detect nephrotoxicants in a panel of blind-coded compounds. Our results highlight the potential usefulness, and some limitations, of HMOX1-reporter renal organoids as screening tools. The results may guide development of similar stress-reporting organoid assays for other stem-cell derived organs and tissues.
DOI: 10.7488/ds/3120
title: Dataset - Bottom Pressure and Free Surface Elevation Including Waves and Current Interaction

description: Force plates are commonly used in tank testing to measure loads acting on the foundation of a structure. These targeted measurements are overlaid by the hydrostatic and dynamic pressure acting on the force plate induced by the waves and currents. This paper presents the dataset of bottom force measurement with a six degree-of-freedom force plate (AMTI OR6-7 1000, surface area 0.464 m×0.508 m) combined with synchronised measurements of surface elevation and current velocity. The data covers a wave frequencies between 0.2 to 0.7 Hz and wave direction between 0◦ and 180◦. These variations are provided for 0 and 0.2 m/s current speed and a variation of current in the absence of waves covering 0 to 0.45 m/s. The dataset can be utilised as a validation dataset for models predicting bottom pressure based on free surface elevation. Additionally, the dataset provides the wave and current induced load acting on the specific load cell and a fixed water depth of 2 m, which can subsequently be removed to obtain the often-desired measurement of structural loads. This research was carried out at the FloWave Ocean Energy Research Facility of the Institute for Energy Systems, University of Edinburgh.
DOI: 10.7488/ds/3807
title: Additional files for 'Negative result: Inefficiency of MapReduce for comparing trees during phylogeny reconstruction'

description: Supplementary data for Guscott JC, Kim CS, Pinheiro M, Wood C, Winn MD, Guntoro F, Meagher TR and Barker D 'Negative result: Inefficiency of MapReduce for comparing trees during phylogeny reconstruction' (in submission). For further details, see 'README.txt' within the zipfile.
description: See 'README.txt' within the zipfile.
DOI: 10.7488/ds/3822
title: FODEX: X-band SAR Investigation

description: TanDEM-X high resolution spotlight bistatic single-polarisation synthetic aperture radar (SAR) images acquired from the German Aerospace Agency (DLR) for the Tropical Forest Degradation Experiment (FODEX) project. Processed into datacubes (netCDF format) for descending intensity, ascending intensity (created using SNAP software) and for descending phase height and coherence (created by Jose-Luis Bueso-Bello at DLR). In addition, a canopy height change map derived from UAV LiDAR campaigns in 2019 and 2021 over the FODEX field site in Peru, and field inventory data for the 8 FODEX core plots in Peru and Gabon. The dataset relates to the upcoming publication Harry Carstairs, Edward T.A. Mitchard, Iain McNicol, Jose-Luis Bueso-Bello, Chiara Aquino, Manuel J. Marca-Zevallos, Daniel Paucarmayta, and Mathias Disney (in submission). "X-band SAR intensity outperforms phase height and C-band intensity in predicting fine scale tropical forest dynamics”.
DOI: 10.7488/ds/3818
title: Self-contained, Beta-with-Spikes approximation to Wright-Fisher: Code and data

description: The dataset contains a refined version of data originally extracted from the 2019 Spanish Google Books corpus. It is related to the upcoming publication Guerrero Montero J. and Blythe R. A (in submission). "Self-contained Beta-with-Spikes Approximation for Inference Under a Wright-Fisher Model."
DOI: 10.7488/ds/3828
title: Tracking the Chemical Diversity of Enzymatically Oxidised Lignin - Supplementary Figures and Raw Data

description: Lignin is a complex heteroaromatic polymer which is one of the most abundant and diverse biopolymers on the planet. It comprises approximately one third of all woody plant matter, making it an attractive candidate as an alternative, renewable feedstock to petrochemicals to produce fine chemicals, such as vanillin. Hereinwe outline the comprehensive tracking of lignin degradation by an alkaliphilic laccase in a semi-quantitative manner using a combined chemical analysis approach utilising Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterise shifts in chemical diversity and relative abundance of ions, and NMR to highlight changes in the structure of lignin. Specifically,an alkaliphilic laccase was used to degrade an industrially relevant lignin,with compounds such as syringaresinol being almost wholly removed (95%) after 24 hours of treatment. Additionally, structural analyses reinforced these findings, indicating a &gt;50% loss of signal relating to β-β linkages, of which syringaresinol is representative. Ultimately, this work underlines a combined analytical approach that can be used to gain a broader, moresemi-quantitative understanding of the enzymatic activity of laccases within a complex and non-model mixture. The dataset is related to the upcoming publication Zak Towle, Faye Cruickshank, C. Logan Mackay, David J. Clarke and Louise E. Horsfall (in submission), 'Tracking the Chemical Diversity of Enzymatically Oxidised Lignin.'
DOI: 10.7488/ds/3193
title: BayesR+ GWAS - Genome and epigenome wide studies of plasma protein biomarkers for Alzheimer's disease implicate TBCA and TREM2 in disease risk

description: This dataset represents one of two datasets that correspond to the study: "Genome and epigenome wide studies of plasma protein biomarkers for Alzheimer's disease implicate TBCA and TREM2 in disease risk". The datasets represent genome-wide and epigenome-wide association studies (GWAS and EWAS) on the same set of 308 SOMAmers associated with Alzheimer's disease in the literature. This dataset represents the GWAS. GWAS was performed by Bayesian penalised regression through BayesR+ software. Analyses were performed using data from volunteers within the STRADL study and Generation Scotland.