cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20023673.v1
title: Xu et al 2022 GRL-Table SI.xlsx

description: <strong>Supporting Information</strong> Table S1-S5 for Closing the global marine 226Ra budget reveals the biological pump as a dominant removal flux in the upper ocean <br> <strong>Table S1</strong>. River water and 226Ra fluxes, dissolved 226Ra concentration, and sediment desorption efficiency for rivers around the world. <strong>Table S2</strong>. Diffusive flux of 226Ra from coastal and shelf sediment. <strong>Table S3</strong>: Summary of 226Ra activity for all oceans. <strong>Table S4</strong>: Upwelling-downwelling velocity between the upper and lower ocean. <strong>Table S5</strong>. Estimates and values of the particle scavenging rate coefficient (<em>k</em>) in the ocean.
DOI: 10.6084/m9.figshare.12476393.v2
title: Community isolation drives lower fish biomass and species richness, but higher functional evenness, in a river metacommunity

description: <b>This project contains:</b><b>Datasets (2)</b><b>R codes (2)</b><b>An archive with notes</b>
DOI: 10.6084/m9.figshare.13643039.v1
title: Supplementary Material for: Probability of Prostate Cancer Diagnosis following Negative Systematic and Targeted MRI: Transrectal Ultrasound Fusion Biopsy: A Real-Life Observational Study

description: <b><i>Introduction:</i></b> The risk of occult prostate carcinoma (PCa) after negative multiparametric MRI (mpMRI)-transrectal fusion biopsy (F-Bx) is unknown. To determine the false-negative predictive value, we examined PCa detection after prior negative F-Bx. <b><i>Methods:</i></b> Between December 2012 and November 2016, 491 patients with suspected PCa and suspicious mpMRI findings underwent transrectal F-Bx. Patients with benign pathology (<i>n</i> = 191) were eligible for our follow-up (FU) survey. Patient characteristics and clinical parameters were correlated to subsequent findings of newly detected PCa. <b><i>Results:</i></b> Complete FU with a median of 31 (interquartile range: 17–39) months was available for 176/191 (92.2%) patients. Of those, 54 men had either surgical interventions on the prostate or re-Bxs. Newly detected PCa was evident in 14/176 (7.95%) patients stratified to ISUP ≤2 in 10 and ≥3 in 4 cases. The comparison of patients with newly detected PCa to those without cancerous findings in FU showed significant differences in prostate-specific antigen (PSA) density (0.16 vs. 0.13 ng/mL<sup>2</sup>) and prostate volume (45 vs. 67 mL, both <i>p</i> &lt; 0.05). Both factors are significant predictors for newly detected cancer after initial negative F-Bx. <b><i>Conclusion:</i></b> Only PSA density (&gt;0.13 ng/mL<sup>2</sup>) and small prostate volume are significant predictors for newly detected PCa after initial negative F-Bx. Despite negative mpMRI/TRUS F-Bx results, patients should be further monitored due to a risk of developing PCa over time. Notwithstanding the limitation of our study that not all patients underwent another Bx, we assume that the false-negative rate is low but existing. Our data represent a real-world scenario.
DOI: 10.6084/m9.figshare.11396223.v1
title: Supplementary Material for: High Metabolic Tumour Volume on 18-Fluorodeoxyglucose Positron Emission Tomography Predicts Poor Survival from Neuroendocrine Neoplasms

description: <b><i>Introduction:</i></b> 18-Fluorodeoxyglucose (<sup>18</sup>F-FDG) positron emission tomography (PET) avidity in neuroendocrine neoplasms (NENs) has been associated with higher-grade disease. <sup>18</sup>F-FDG avidity and high SUV<sub>max</sub> have been demonstrated to predict poor outcome. Quantitative metrics of <sup>18</sup>F-FDG PET, specifically metabolic tumour volume (MTV) and total lesion glycolysis (TLG), have been shown to be prognostic factors in other malignancies, but these have not been investigated to date in NENs. <b><i>Methods:</i></b> Patients with NEN undergoing <sup>18</sup>F-FDG at Royal North Shore Hospital from 2012 to 2018 were included. Images were analysed with automated segmentation (SUV cut-off of 4) followed by contour verification by a nuclear medicine physician and manual segmentation where required. Variables collected included patient age, histological grade, MTV, TLG, and SUV<sub>max</sub>/SUV<sub>mean</sub>. The primary outcome was overall survival (OS), and the secondary outcome was progression-free survival (PFS). Univariate (UV) and multivariate (MV) analyses were performed for OS and PFS for MTV and TLG separately. For UV analysis, the median MTV and TLG were used to dichotomise the cohort. MTV/TLG for NENs of different histological grade were compared using ANOVA. <b><i>Results:</i></b> One hundred and ninety patients were included (median age 63.5, 49% female). Primary site: 42% small bowel, 32% pancreas, 15% other gastrointestinal, 6% lung, 6% other. Grade for gastroenteropancreatic NENs and bronchial NEN: G1/typical carcinoid 37%, G2/atypical carcinoid 40%, G3/large-cell/small-cell neuroendocrine carcinoma 16%, unknown 8%. Median MTV was 4.83 mL (range 0–3,161 mL) and median TLG was 29.22. Patients with high MTV had worse median OS compared to those with low MTV (29.7 months vs. not reached, HR 4.1, 95% CI 2.25–7.49, <i>p</i> &lt; 0.00001). Considered as a continuous variable, MTV predicted for poorer OS on UV (<i>p</i> &lt; 0.00001) and MV (<i>p</i> = 0.003) analyses. Whilst histological grade was significant on both UV and MV, SUV<sub>max</sub> was significant on UV (<i>p</i> &lt; 0.00001) but not MV (<i>p</i> = 0.76). Tumours of higher grade had higher MTV (mean MTV – G1: 39.6 mL, G2: 107 mL, G3: 337 mL; <i>p</i> = 0.0001 by ANOVA). <b><i>Conclusions:</i></b> Quantitative analysis of <sup>18</sup>F-FDG PET in NEN is feasible. High MTV/TLG are predictors of poor prognosis in NEN. Further analyses are underway to investigate a larger cohort of NEN patients.
DOI: 10.6084/m9.figshare.27162048.v1
title: Shelter visits vs availability for Sonoran Desert Tortoises in 2 Arizona populations

description: At Sugarloaf we monitored female tortoises (range 184–289 mm midline carapace length [CL]) weekly using radio telemetry in 1991–1993 and 1997–2005 as part of a reproductive ecology study (Averill-Murray 2002; Averill-Murray et al. 2018). During the 11 years of radio-tracking, all burrows used by both telemetered and opportunistically encountered tortoises were marked with numbered aluminum tags (n = 522). We use the term “burrow” specifically to refer to a subsurface cavity &gt;1/2 the tortoise’s length either formed by erosion or excavated by a tortoise or another animal (Burge 1978). We categorized burrow types as “rock” (cover provided by rocks or boulders, including large boulder piles in which the tortoise could not be visualized), “soil” (cover provided by soil or vegetation with no substantial rock component), and “packrat” (freestanding white-throated woodrat Neotomoa albigula nest independent of other shelter types; packrat nests inside rock shelters were categorized as “rock”). We did not individually mark “pallets” (shallow, scraped out areas &lt;1/2 tortoise length) or other temporary shelters unmodified by the tortoise (e.g., under trees, shrubs, or rock overhangs).At FMR, as part of a habitat-use study we attached radio transmitters (ATS, AVM, Telonics, or Wildlife Materials) to the anterior carapace of adult tortoises as above (Riedle et al. 2008). During the winter months (November through February) when tortoises were inactive, we located tortoises once a week. During the activity season (March through October) we located tortoises 2–3 times weekly, obtaining both morning and evening locations. From 2000 to 2003, we searched areas in which tortoises might occur within FMR, concentrating on sites suitable for burrow excavation, especially including incised washes with caliche caves and the volcanic hill. We also searched all washes within the study area, whether incised or not, and spent considerable time on the alluvial fans. We marked burrows in which we observed tortoises with individually numbered aluminum tags (n = 124), and we mapped locations of all caliche caves large enough to shelter a tortoise ≥180 mm CL (n = 463). Burrow types included caliche, rock, soil, and packrat.We tested hypotheses that shelter use did not differ by different shelter types. We used linear mixed-effects models in R package <i>nlme</i> to assess whether the number of shelters used (including pallets) varied by shelter type or sex, with individual tortoise ID specified as a random effect. We used GLMMs with a binomial distribution in R package <i>lme4</i> to determine whether tortoises used different types of burrows in proportion to their availability within their home ranges, again with tortoise ID as a random effect. We used permutation-based sign tests with R package <i>phuassess</i> to assess whether tortoises visited different shelter types relative to their availability. We conducted these analyses separately for FMR and Sugarloaf due to the lack of caliche burrows at Sugarloaf.
DOI: 10.4121/14573526.v1
title: Soil organic carbon stock and uncertainties, 1m depth, at 250m spatial resolution in Canada

description: This project aimed to produce the first wall-to-wall estimate of C stocks in plants and soils of Canada at 250 m spatial resolution. This dataset contains the map with the soil organic carbon (SOC) in kg/m² for entire Canada in 1m depth, and the uncertainty in SOC predictions. The SOC stock map was produced using 6,533 ground soil samples, long-term climate data, remote sensing observations and a machine learning model. The soil samples containing the x and y coordinates, depth and SOC (in g/kg) information were overlaid with the stacked covariates (soil forming factors) to compose the regression matrix. Random forest models were trained using a recursive feature elimination scheme and a cross-validation assessment. The best model was used for spatial prediction of SOC over Canada in intermediate depths between 0 and 1 m. Afterwards, the SOC content maps were corrected with bulk density and coarse fragment information to compute the total carbon stock for each horizon. The horizons have been added to compose the 0-1m depth interval multiplied by root depths fraction to discount shallow soils. Water and ice/snow areas were removed using a mask based on the Land Cover of Canada map. The SOC stock uncertainty map was built using the first and third quantiles of RF quantile regression approach.<br>
DOI: 10.6084/m9.figshare.13585586.v1
title: G2PMineR_Vignette_Input

description: In this submission we have included VignetteIDs.csv and VignetteAbstractsStrings.csv<br>
DOI: 10.6084/m9.figshare.11345024.v5
title: Classic Psychedelics as a Psychotherapeutic Aid in the Treatment of Stimulant Use Disorder

description: Excel spreadsheet<br><b><br></b>
DOI: 10.60893/figshare.apl.26084584.v1
title: Supplement Number 1

description: Revised Supplementary materials
DOI: 10.15468/dl.u9a2tf
title: Occurrence Download

description: A dataset containing 713 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Blera fallax (Linnaeus, 1758)"
 ]
}

 The dataset includes 713 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009476-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.17815151.v1
title: Supplementary Material for: De-novo and depot-specific androgen production in human adipose tissue - a source of hyperandrogenism in women with obesity

description: Introduction: Obesity in women is often associated with hyperandrogenism but the role of adipose tissue (AT) in androgen synthesis remains unclear. Therefore, we studied whether AT could be a source of androgens promoting hyperandrogenism. Methods: Subcutaneous and visceral AT was collected from lean and obese women. Androgen levels were evaluated in serum, AT and cell culture supernatant. Gene and protein expression of steroidogenic enzymes were determined. Results: Obese subjects had elevated serum androgen levels, which reduced after weight loss. Androgens were measurable in AT and in cell culture supernatants of adipocytes. Steroids were higher in AT from obese women, with the highest difference for testosterone in visceral AT (+7.9 fold, p=0.032). Steroidogenic enzymes were expressed in human AT with depot-specific differences. Obese women showed a significantly higher expression of genes of the backdoor pathway and of CYP19 in visceral AT. Conclusion: The whole steroidogenic machinery of the classical and backdoor pathways of steroidogenesis, and the capacity for androgen biosynthesis, were found in both AT depots and cultured adipocytes. Therefore, we hypothesize that AT is a de novo site of androgen production and the backdoor pathway of steroidogenesis might be a new pathomechanism for hyperandrogenism in women with obesity.
DOI: 10.6084/m9.figshare.19477484.v1
title: Supplementary Material for: Sigmoid Volvulus in Myotonic Dystrophy Type I (Steinert Disease)

description: Myotonic dystrophy (MD) is a progressive multisystem genetic disorder that is characterized by progressive muscle weakness and wasting. MD1 (also known as Steinert disease) is associated with various clinical entities such as skeletal muscle weakness, myotonia, cardiac abnormalities, respiratory dysfunction, gastrointestinal involvement, and cognitive impairment. In this case report, we present a 32-year-old woman with MD1 who presented with a sigmoid volvulus, which was treated with endoscopic decompression.
DOI: 10.6084/m9.figshare.25388524.v1
title: Supplementary Material for Partitioning of tin between mafic minerals, Fe-Ti oxides and silicate melts: Implications for tin enrichment in magmatic processes

description: Supplementary Material for Partitioning of tin between mafic minerals, Fe-Ti oxides and silicate melts: Implications for tin enrichment in magmatic processes
DOI: 10.6084/m9.figshare.23634396.v1
title: Nucleosome array deformation in chromatin is sustained by bending, twisting and kinking of linker DNA

description: PDBs of the main atomic configurations listed in Table I of the paper "Nucleosome array deformation in chromatin is sustained by bending, twisting and kinking of linker DNA", by F. Cleri, S. Giordano and R. Blossey
DOI: 10.6084/m9.figshare.24708135.v1
title: Table 1

description: Data for Mo isotopes of seep sediments from the South China Sea.
DOI: 10.6084/m9.figshare.735907.v1
title: Dataset S5 - RDP Classification of rRNAs

description: RDP classification of Metaxa-extracted rRNAs. Raw data.
DOI: 10.6084/m9.figshare.7900673.v1
title: gVCF_HG03391

description: 1000 Genomes gVCF mapped to hs37d5 for HG03391. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.22652611.v3
title: How to investigate the mechanical properties of a 3D printed parts using mechanics of composite material rules

description: A study for investigation of mechanical response of 3D printed PLA parts by FDM method has been performed and published in journal of IJRPR. The 3D printing process is an efficient and cost-effective production method for the rapid manufacture of parts that are complex in terms of geometry,<br> structure and mechanical behavior. Studying the mechanical behavior of these structures is very important to understand and optimize the performance of 3D<br> printed materials. In this article, the mechanical properties of 3D printed parts for PLA material are studied based on the constitutive stress-strain relationship<br> in a plane stress state, and the effect of fabrication angle on the anisotropy properties of the material is analyzed using simple tensile tests in different material<br> directions. Assuming an orthotropic behavior, the changes in strength due to anisotropy are investigated. It has been observed that the assumption of<br> orthotropic behavior is a suitable assumption to express the mechanical behavior of fabricated materials using 3D printing methods. The results obtained can<br> be used in software for numerical analysis of 3D printed parts similar to composite modeling.
DOI: 10.6084/m9.figshare.26501608.v1
title: eData-LTO-CP

description: None
DOI: 10.6084/m9.figshare.28731470.v1
title: Supplementary Material for: Bladder stone composition in JiangSu region of China: results from 421 stone analyses

description: Introduction: Accurate analysis of bladder stone composition is essential for appropriate treatment planning and recurrence prevention. The aim of this study was to evaluate the characteristics of bladder stone components in our center.
Materials and methods: A retrospective analysis on the composition of bladder stones collected in our center from January 2014 to March 2023 was conducted in the present work. Age, sex and laboratory examination of all patients were collected. Infrared spectroscopy was conducted for stone analysis.
Results: The most common stone component was calcium oxalate (43.0%), followed by uric acid (UA) stone (35.4%), calcium phosphate (12.10%), infection stone (9.0%) and cystine (0.5%). The highest stone prevalence appeared in patients aged over 60 years, and increased progressively with age. Furthermore, patients with UA stones were more likely to have a lower urinary pH. Additionally, patients with infection stones showed higher incidence of urinary tract infections than those with other types of stones. Patients with UA stones had higher average serum UA and creatinine levels. Uric acid stones are more likely to form multiple stones compared to stones of other composition. The volume of infectious stones is larger compared to stones of other compositions.
Conclusions: This study highlights the importance of gaining a deeper understanding of bladder stone composition, as it can lead to more effective evaluation, treatment, and prevention of stone disease.
DOI: 10.6084/m9.figshare.24069354.v1
title: Proteomic_Profiling_of_Cognitive_Function_summary_stat.zip

description: Summary Statistics of the manuscript entitled Identification of Circulating Proteins Associated with General Cognitive Function Among Middle-aged and Older Adults
DOI: 10.6084/m9.figshare.25156154.v2
title: The sex [Male (1) and female (2)] age (in years), weight (in lbs), #GPS Points (total after filtering), and the 100% MCP, 95% KDE, and 50% KDE home ranges (ha) for all cats sampled in the study. All cats were desexed. The personality scores (shown as a percent), were obtained from a survey, based on the “Feline Five” (Litchfield et al., 2017), that evaluated how much owners agreed or disagreed that their cats showed certain traits. Traits were then summed and converted into percentages. Bold cats are considered to have a low neuroticism score. Road density was estimated by summing the road lengths, measured in meters, within a fixed boundary centred on each cat’s mean latitude and longitude coordinates. The variable “major road” indicated the presence (1) or absence (0) of a major road near the cat’s home range. Roads were labeled as “major” based on Google Maps’ classification, related to traffic rates, and through “ground-truthing”.

description: Domestic cats (<i>Felis catus</i>) play a dual role in society as both companion animals and predators. When provided with unsupervised outdoor access, cats can negatively impact native wildlife and create public health and animal welfare challenges. The effective implementation of management strategies, such as buffer zones or curfews, requires an understanding of home range size, the factors that influence their movement, and the types of habitats they use. Here, we used a community/citizen scientist approach to collect movement and habitat use data using GPS collars on owned outdoor cats in the Kitchener-Waterloo-Cambridge-Guelph region, southwestern Ontario, Canada.
DOI: 10.6084/m9.figshare.12380564.v1
title: A large deletion on CFA28 omitting ACSL5 is associated with lipid malabsorption in Australian Kelpies

description: Inborn errors of metabolism are rare genetic conditions characterised by a disruption of intermediary metabolic pathways, causing defective absorption and metabolism of dietary nutrients. In a Kelpie breeding population, 14 puppies presented with lipid malabsorption. Juvenile dogs exhibited stunted postnatal growth, steatorrhea, abdominal bloating and a wiry coat. Pancreatic enzyme supplementation improved growth and reduced juvenile mortality rates, though adult dogs remain smaller in stature and continue to suffer intolerance to dietary fat. Using genome-wide association analysis, an associated locus on CFA28 (P<sub>raw</sub>= 2.87E<sup>-06</sup>) was discovered and validated in a closely related population (P<sub>raw </sub>= 1.75E<sup>-45</sup>). A 103.7 kb deletion containing genes Acyl-CoA Synthetase Long Chain Family Member 5 (ACSL5) and Zinc Finger DHHC-Type Containing 6 (ZDHHC6), was characterised using whole transcriptomic data. Comparative analysis revealed no expression of ACSL5 and disrupted splicing of ZDHHC6 in jejunal tissue of affected Kelpies. ACSL5 plays a key role in long chain fatty acid absorption while ZDHHC6 has not been previously implicated in metabolic disorders. A PCR-based diagnostic test was developed and confirmed fully penetrant Mendelian recessive mode of inheritance. We conclude the structural variant causing a deletion of the ACSL5 gene is the most likely cause for lipid malabsorption in the Australian Kelpie.
DOI: 10.25377/sussex.12597101.v1
title: Data for research article 'Mushroom bodies are required for learnt visual navigation but not for innate visual behaviour in ants'

description: <b>Data for paper published in Current Biology (July 2020).</b><br> Data contains paths from individually recorded ants during the experiments (saved as Matlab files). You will need access to the MATLAB environment to view these files.<br>For details please see the README.doc file and view the experiment methods in the published paper.<br> <b>Abstract:</b>Visual navigation in ants has long been a focus of experimental study, but only recently have explicit hypotheses about the underlying neural circuitry been proposed. Indirect evidence suggests the mushroom bodies (MB) may be the substrate for visual memory in navigation tasks, whilst computational modelling shows that MB neural architecture could support this function. There is, however, no direct evidence that ants require MBs for visual navigation. Here we show that lesions of MB calyces impair ants’ visual navigation to a remembered food location yet leaves their innate responses to visual cues unaffected. Wood ants are innately attracted to large visual cues but we trained them to locate a food source at a specific angle away from such a cue. Subsequent lesioning of the MB calyces using procaine hydrochloride injection, caused ants to revert towards their innate cue attraction. Handling and saline injection control ants still approached the feeder. Path straightness of lesioned and control ants did not differ from each other but was lower than during training. Reversion towards the cue direction occurred irrespective of whether the visual cue was ipsi- or contralateral to the lesion site, showing this is not due simply to an induced motor bias. Monocular occlusion did not diminish ants’ ability to locate the feeder, suggesting that MB lesions are not merely interrupting visual input to the calyx. The demonstrated dissociation between innate and learnt visual responses provides direct evidence for a specific role of the MB in navigational memory.
DOI: 10.6084/m9.figshare.10257704.v1
title: Megaplasmid Acquisition Influences Nalidixic Acid Sensitivity

description: Supplemental data sets for the manuscript entitled "Genomic Background Governs Opposing Responses to Nalidixic Acid Upon Megaplasmid Acquisition in Pseudomonas"<br>.csv files containing the raw data underlying all analyses in the manuscript as well as .txt files containing all R scripts used for statistical analysis within the manuscript.