cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/6909792b-fadf-4de6-ac2a-d32fa76a8339
title: Rectified airborne Lidar data over Thwaites Glacier catchment between 1st January and 30th December 2019

description: We present here the airborne Lidar data was collected over the Thwaites Glacier catchment and adjacent ice shelves during the 2018/19 and 2019/20 field seasons. The data was collected using a Riegl Q240i-80 scanning system mounted in the BAS aerogeophysically equipped twin otter aircraft. It provides a high resolution (0.2 to 0.4 points per m2), and high accuracy (~10 cm vertical) georeferenced and time stamped swath of surface elevation information. Each track is ~600 m wide. Such data provides critical information about how the surface of the Thwaites Glacier system is changing. The Thwaites 2019/20 aerogeophysical survey was carried out as part of the BAS National Capability contribution to the NERC/NSF International Thwaites Glacier Collaboration (ITGC) program, with additional funding for LIDAR data processing from the UK Foreign and Commonwealth Office.
description: Lidar data was collected using a Riegl Q240i-80 scanning system mounted in the camera bay of the BAS geophysically equipped twin otter. Coincident attitude data was collected using an iMAR inertial navigation system (INS) (from Lamont Doherty Earth Observatory for the Jan 2019 season, and from BAS for the December 2019 season). Data processing was carried out by a sub-contractor (Terratec - https://terratec.no/en/). For each season (January and December) a boresight calibration was carried out using the Terrasolid software modules Terramatch and Terrascan. This calibration utilised a specific calibration data-set collected over the BAS Rothera Research Station. After calculation of the boresight values the remaining data for each season were processed using Riprocess with the appropriate boresight values. During the main survey data was collected on as many flights as possible, but due to operational constraints Lidar data is not available on all flights. As Lidar was not a priority, swaths do not typically overlap, so further calibration in the main survey area was not possible. The generally feature poor ice surface would also hamper such calibration. In addition it must be noted that removal of spikes due to clouds or other atmospheric returns has not been carried out. However, most flights were flown in clear weather. The list of variables is as follows: * longitude x - in degrees from the WGS84 datum * latitude y - in degrees from the WGS84 datum * altitude z - in meters * intensity - arbitrary value between -128/128 * scan_angle - in degrees * GPS_time * datetime_utc - converted GPS time to UTC taking into account leap seconds in YYYY-MM-DD HH:MM:SS
description: Analysis of repeat passes over the Runway suggests the corrected data has an internal accuracy of ~10 cm. Note no de-spiking, or removal of cloud features has been undertaken.
DOI: 10.6084/m9.figshare.11967474.v2
title: Inshore hagfish gene model .gff3 - Kuraku Lab

description: Non-embargoed gene model oriented for gene-level analysis<br>
DOI: 10.6084/m9.figshare.21647660
title: Supplementary Material for: Treatment Patterns in Newly Diagnosed Patients with Crohn’s Disease Who Received Biologics Following Diagnosis: A Nationwide, Retrospective, Longitudinal, Observational Study Using a Medical Claims Database in Japan

description: <b><i>Introduction:</i></b> Crohn’s disease (CD) is a chronic inflammatory condition affecting any part of the gastrointestinal tract. Current therapies involve pharmacological efforts to dampen inflammation. Biologics are recommended for patients with steroid-dependent or steroid-refractory disease; however, little is known about current biologic use in real-world settings in Japan. <b><i>Methods:</i></b> This observational, longitudinal, cohort study utilized the Japan Medical Data Center (JMDC) database to analyze claims data of patients who were prescribed ≥1 biologic (adalimumab, infliximab, or ustekinumab) following a new CD diagnosis made between January 2009 and January 2019. We primarily assessed the type of first-line treatment prescribed within 6 months of a patient’s first CD diagnosis. <b><i>Results:</i></b> Of the 1,346 eligible patients, the most common prescriptions were 5-aminosalicylic acid (5-ASA) monotherapy (26.8%), 5-ASA plus biologic combination (26.3%), and biologic monotherapy (12.9%). First-line biologics were prescribed within 6 months of initial CD diagnosis in 61.1% of patients, either alone or in combination with other therapies. As an individual first-line treatment, the proportion of patients receiving prescriptions of infliximab was high (66.3%) and steroids, low (1.3%). Patients who had a procedure to inspect the small intestine, such as endoscopy (<i>n</i> = 508), were mostly treated with a nonbiologic therapy (74.8%), whereas those who had not (<i>n</i> = 838), mostly received biologics (alone or in combination, 82.8%) as a first-line treatment. <b><i>Conclusions:</i></b> In this study, we discovered the typical treatment pattern of patients with CD who received biologics and are registered in the JMDC database in Japan. Biologics were commonly used in the early phase of CD treatment. Treatment with traditional approaches such as steroids and nutritional therapy with evaluation for small intestine lesions, before turning to the use of biologics, may be prudent for achieving optimal outcomes.
DOI: 10.6084/m9.figshare.21647795
title: Supplementary Material for: Agreement between Noninvasive Hemoglobin and Laboratory Hemoglobin Measurements in Neonates: A Systematic Review and Meta-Analysis

description: <b><i>Background and Objective:</i></b> The noninvasive hemoglobin (NHb) devices are recently evaluated as an alternative to laboratory hemoglobin (LHb) in neonates. This systematic review explores the diagnostic accuracy of NHb devices for neonatal hemoglobin measurement. <b><i>Methods:</i></b> Literature related to the comparison of NHb device with LHb in neonates was searched from Medline, PubMed Central, PubMed, Web of Science, Google Scholar, and Scopus databases after PROSPERO registration. The quality of included publications was assessed by QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies). The pooled correlation coefficient and bias (precision) in Bland-Altman difference plots were used for summary statistics using MetaXL 5.0 software. <b><i>Results:</i></b> A total of 1,477 paired NHb-LHb observations were analyzed from 1,047 neonates in 10 studies. Massimo radical-pulse co-oximetry (8 studies) and Mediscan-2000 (2 studies) were used for NHb estimation. The pooled correlation coefficient between NHb and LHb was <i>r</i> = 0.94 (95% CI: 0.83–0.98, <i>p</i> &lt; 0.001), and the pooled bias (precision) was −0.013 (1.4) gm/dL between NHb and LHb measurements in Bland-Altman analysis. NHb device had better precision in stable neonates (0.91gm/dL) over sick neonates (1.66 gm/dL). <b><i>Conclusions:</i></b> Hemoglobin measurement by NHb is excellently correlated with LHb measurement with a minimal average difference. It may be used as a screening tool for hemoglobin measurement in neonates to avoid frequent phlebotomy.
DOI: 10.5281/zenodo.6574366
title: Challenges of the New Accreditation in Digital Competences for Citizens (ACTIC): Update, Validation and Results

description: The aim of this study is to explain the process used to update and validate the Catalan Accreditation of Information and Communications Technology Skills (ACTIC), conducted by the Open University of Catalonia and the Blanquerna Foundation of Ramon Llull University, at the initiative of the Catalan Department for Digital Policy and Public Administration, Government of Catalonia. Using a mixed method, the study is divided into 3 phases and presents the definitions of the 5 competence areas, 19 competences, 3 achievement levels and a total of 233 indicators. The definitions were validated by a group of experts. As a result of the study, three key dimensions have emerged that improve digital awareness among citizens while empowering them and providing them with a way of having their skills accredited and acknowledged in the workplace: (i) identity, centred around participatory, social, ethical and civic issues; (ii) skills learning among citizens; and (iii) technological development and digital autonomy of citizens.
DOI: 10.5281/zenodo.7038756
title: Tables and data for "Downward Trend in Methane Detected in a Northern Colorado Oil and Gas Production Region Using AIRS Satellite Data"

description: These are tables and data files for the paper "Downward Trend in Methane Detected in a Northern Colorado Oil and Gas Production Region Using AIRS Satellite Data" submitted to the Journal of Atmospheric Research: Atmospheres
DOI: 10.6084/m9.figshare.11967789.v3
title: Inshore hagfish genome assembly - Kuraku Lab

description: Genome assembly from which a non-embargoed gene model oriented for gene-level analysis was derived.<br>
DOI: 10.6084/m9.figshare.20352996.v1
title: Enhancement of Antimicrobial Peptide Activity by Ribonuclease

description: Virtual colony count data evaluating the enhancement of antimicrobial peptide activity by ribonuclease and inhibition by tRNA
DOI: 10.6084/m9.figshare.21130154
title: Supplementary Material for: Risk factors for arteriovenous fistula thrombus development: a systematic review and meta-analysis

description: Background: Risk factors like femal sex, fistula location, hypertension, albumin, diabetes, age and other factors are related to arteriovenous fistula thrombus (AVFT), but the consistency and magnitude of their associations have not been confirmed by meta-analysis. Objectives：The purpose of this study was to provide a comprehensive and up-to-date synthesis of evidence on the association between potential risk factors and AVFT. Methods: In this systematic review and meta-analysis, PubMed, Embase, Cochrane Library, and Web of Science databases were searched for articles published up to April 20th, 2022, and cohort, cross-sectional, and case-control studies examining the association (odds ratio [OR]) between potential risk factors and AVFT were identified. The other inclusion criteria were sufficient data for analysis and non-overlapping datasets, excluding reviews, meta-analyse and articles with overlapping datasets. Extracted variables included first author, publication year, study type, sample size, percentage of women, vascular access type, risk or protective factors, and measure of association (adjusted estimates of effect of all risk factors). The study protocol is registered at PROSPERO (CRD42020201884) and followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Results: Among the 27 identified studies, data from 24 cohort, 2 case-control and 1 cross-sectional study were included in this review. When compared to non-AVFT, our data showed that the significant risk factors were arteriovenous graft (pooled OR = 6.28, 95% CI = 1.79-22.02, p=0.004, I2=87%), age (pooled OR = 1.06, 95% CI = 1.00-1.13, p=0.05, I2=98%), female sex (pooled OR = 2.62, 95% CI = 2.56-2.69, p&lt;0.00001, I2=0%), c-reactive protein (pooled OR = 1.18, 95% CI = 1.08-1.30, p=0.0005, I2=90%), fistula site (distal) (pooled OR = 3.64, 95% CI = 1.74-7.62, p=0.0006, I2=47%), hypertension (pooled OR = 1.21, 95% CI = 1.00-1.47, p=0.05, I2=46%), CD34+KDR+ cell (pooled OR = 1.85, 95% CI = 1.33-2.57, p=0.0002, I2=0%) and eprex use (pooled OR = 5.36, 95% CI = 1.82-15.77, p=0.002, I2=0%). Conclusions: The meta-analysis suggests that AVG, age, female sex, CRP level, fistula site (distal), hypertension, CD34+KDR+ cell and the use of eprex are independent risk factors for AVFT. Therefore, clinical medical staff should treat these risk factors carefully, identify them early and prevent them early to reduce the occurrence of AVFT.
DOI: 10.5281/zenodo.6659435
title: MargNet: Photometric identification of compact galaxies, stars and quasars

description: This page contains the accompanying deep learning models, dataset and code for the paper on MargNet, titled "Photometric identification of compact galaxies, stars and quasars using multiple neural networks". <strong>Deep Learning Models</strong>: MargNet is a deep learning-based classifier for identifying stars, quasars and compact galaxies using photometric parameters and images from the Sloan Digital Sky Survey. MargNet consists of a combination of Convolutional Neural Network (CNN) and Artificial Neural Network (ANN) architectures. The deep learning Keras model for each experiment was saved as an h5 file after training. All saved models (organised by different experiments, as described in the paper) are available in SavedModels.zip. <strong>Dataset</strong>: Our dataset consists of 240,000 compact objects and an additional 150,000 faint objects consisting of an equal number of stars, galaxies and quasars. This data is available as NumPy arrays and CSV files, as described below: SDSS ObjID of each object (objlist.npy) SDSS 5-band images of each object cropped to 32*32 pixels (X.npy) The set of 24 photometric features for each object (dnnx.npy) The classification label for each object (y.npy) SDSS spreadsheet containing all the features from dnnx, labels from y, ObjIDs from objlist and a couple of more SDSS specific parameters (photofeatures.csv) The complete dataset (organised by different experiments, as described in the paper) is available in Dataset.zip.<br> (Note: objlist, X, dnnx and y are in the same order. So, objlist[0], X[0], dnnx[0] and y[0] correspond to the same object.) <strong>Code</strong>: All our code was written in Python in the form of Jupyter Notebooks. A copy of our code has also been made available on GitHub, but not all files could be included on GitHub due to the storage limit. So a complete copy of the repository has also been mirrored here on Zenodo and is contained in MargNet_RepositoryMirror.tgz
DOI: 10.5281/zenodo.6799998
title: Model Output and Figure Scripts for: "Uncertainty in reconstructing paleo-elevation of the Antarctic Ice Sheet from temperature-sensitive ice core records"

description: New climate model output and figure scripts for the paper "Uncertainty in reconstructing paleo-elevation of the Antarctic Ice Sheet from temperature-sensitive ice core records".
DOI: 10.5281/zenodo.7100536
title: Biases in LWP adjustments, code and dataset

description: Code and source data to reproduce the figures in article: Antti Arola, Antti Lipponen, Pekka Kolmonen, Timo H. Virtanen, Nicolas Bellouin, Daniel P. Grosvenor, Edward Gryspeerdt, Johannes Quaas, and Harri Kokkola: Aerosol Effects on Clouds Are Concealed by Natural Cloud Heterogeneity and Satellite Retrieval Errors, submitted to Nature Communications, 2022.
description: The code consists of short Matlab scripts which are comprehensively commented and straightforward to use. A separate user guide or installation guide is not needed. Matlab is required for running the codes, but no toolboxes or other installation is required. The codes have been tested with Matlab version 2017b. Running the codes takes a few minutes at the most on a regular laptop. Input data and comprehensive output examples are provided.
DOI: 10.5291/ill-data.7-05-496
title: Elucidating the role of energy dissipation and electronic friction in nanoscale diffusion
DOI: 10.6084/m9.figshare.21641282
title: Supplementary Material for: Association between Anatomical Variations of the Circle of Willis and Covert Vascular Brain Injury in the General Population

description: <b><i>Background and Purpose:</i></b> The circle of Willis (COW) is a circulatory anastomosis located at the base of the brain. Little is known about the association between covert vascular brain injury and COW configurations in the general population. We explored this relationship in a community-based Chinese sample. <b><i>Methods:</i></b> A total of 1,055 patients (mean age, 54.8 ± 8.9 years; 36.0% men) without intracranial arterial stenosis were included in the analysis. Magnetic resonance imaging was performed to evaluate the presence of imaging markers of covert vascular brain injury, including white matter hyperintensities (WMHs), lacunes, cerebral microbleeds (CMBs), enlarged perivascular spaces, and brain atrophy. Magnetic resonance angiography was used to classify the COW configurations according to the completeness, symmetry, and presence of the fetal posterior cerebral artery (FTP). The association between vascular lesions and variations in COW was analyzed. <b><i>Results:</i></b> Among the 1,055 patients, 104 (9.9%) had a complete COW. Completeness correlated with age (<i>p</i> = 0.001). Incomplete COW was positively associated with WMH severity (OR = 2.071; 95% CI, 1.004–4.270) and CMB presence (OR = 1.542; 95% CI, 1.012–2.348), independent of age and sex. The presence of FTP was associated with lacunes (OR = 1.878; 95% CI, 1.069–3.298), more severe WMHs (OR = 1.739; 95% CI, 1.064–2.842), and less severe enlarged perivascular spaces (OR = 0.562; 95% CI, 0.346–0.915). <b><i>Conclusions:</i></b> COW configuration was significantly related to various covert vascular brain injuries.
DOI: 10.6084/m9.figshare.21646685
title: Supplementary Material for: The Olfactomedin-4-Defined Human Neutrophil Subsets Differ in Proteomic Profile in Healthy Individuals and Patients with Septic Shock

description: The specific granule glycoprotein olfactomedin-4 (Olfm4) marks a subset (1–70%) of human neutrophils and the Olfm4-high (Olfm4-H) proportion has been found to correlate with septic shock severity. The aim of this study was to decipher proteomic differences between the subsets in healthy individuals, hypothesizing that Olfm4-H neutrophils have a proteomic profile distinct from that of Olfm4 low (Olfm4-L) neutrophils. We then extended the investigation to septic shock. A novel protocol for the preparation of fixed, antibody-stained, and sorted neutrophils for LC-MS/MS was developed. In healthy individuals, 39 proteins showed increased abundance in Olfm4-H, including the small GTPases Rab3d and Rab11a. In Olfm4-L, 52 proteins including neutrophil defensin alpha 4, CXCR1, Rab3a, and S100-A7 were more abundant. The data suggest differences in important neutrophil proteins that might impact immunological processes. However, in vitro experiments revealed no apparent difference in the ability to control bacteria nor produce oxygen radicals. In subsets isolated from patients with septic shock, 24 proteins including cytochrome b-245 chaperone 1 had significantly higher abundance in Olfm4-H and 30 in Olfm4-L, including Fc receptor proteins. There was no correlation between Olfm4-H proportion and septic shock severity, but plasma Olfm4 concentration was elevated in septic shock. Thus, the Olfm4-H and Olfm4-L neutrophils have different proteomic profiles, but there was no evident functional significance of the differences in septic shock.
DOI: 10.25982/62384.253/1831503
title: Moab Desert Crust - Sample 4E

description: Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).
DOI: 10.5255/ukda-sn-856032
title: Data on Medication Adherence in Adults with Neurological Disorders: The NeuroGerAd Study, 2019-2020

description: In this study, 910 hospitalized older adults (mean age 70.1 years, SD 8.6 years) with neurological disorders (Parkinson's Disease and other movement disorders, N= 303; cerebrovascular disorders, N = 233; neuromuscular disorders, N= 168; epilepsy, N = 48; and miscellaneous neurological diagnoses, N= 158) received a comprehensive geriatric assessment and filled out self-report questionnaires. Data collection took place on the ward of neurology between February 2019 and March 2020. Procedures included a comprehensive baseline assessment during hospital stay and 2 follow-up interviews at 1 and 12 months after hospital discharge. Baseline assessments included demographical data, clinical data, self-report adherence, prescribed medication, mobility, depression, cognition, health care utilization, communication, personality, and health-related QoL. Follow-up interviews asked for changes of medication after discharge, reasons thereof, specific kind of change, and health-related QoL.
DOI: 10.5281/zenodo.6480140
title: Cheating interactions favor modularity in mutualistic networks

description: A fundamental fact about mutualisms is that these mutually beneficial interactions often harbor cheaters that benefit from the use of resources and services without providing any positive feedback to the other players. The role of cheaters on the evolutionary dynamics of mutualisms has long been recognized, yet their broader consequences to the community level, and beyond species they interact with, is still poorly understood. Because mutualisms form networks that often involve dozens to hundreds of species, indirect effects generated by cheaters may cascade through the whole community, reshaping trait evolution. Here, we study how harboring cheating interactions can influence coevolution in mutualistic networks. We combine a coevolutionary model, empirical data on animal-plant mutualistic networks, and numerical simulations and show that a higher frequency of cheating interactions in a network can lead to the formation of groups of species phenotypically similar to each other and distinct from other groups, generating higher trait disparity. The resulting clustered trait patterns, in turn, change the patterns of interaction in simulated networks, fostering the formation of modules of interacting species. Our results indicate that cheaters contribute to generate phenotypic clusters in mutualistic networks, counteracting selection for convergence imposed by mutualists, and favoring the emergence of modules of interacting species. Based on these results, we suggest that cheaters might be a fundamental element for our understanding of the evolution of mutualistic networks.
DOI: 10.5441/002/edbt.2017.07
title: Self-managed collections: Off-heap memory management for scalable query-dominated collections
DOI: 10.6084/m9.figshare.19744933.v15
title: Chatbot Ai-aun

description: Chatbot Ai-aun
DOI: 10.6084/m9.figshare.21065602
title: Population origin determines the adaptive potential for the advancement of flowering onset in Lupinus angustifolius (Fabaceae)

description: In this study we used artificial selection to asses the adaptive potential for advancing flowering onset in <em>Lupinus angustifolius</em> L. We establisehd different artificial selection lines in individuals from four populations from two contrasting latitudes in Spain that were sown in a common garden environment. Flowering onset, reproductive success and other plant traits (height, biomass, shoot growth, LDMC and SLA) were measured.
DOI: 10.6084/m9.figshare.21587505.v1
title: Dataset - polarization on zebrafish neurons

description: Data underlying the results presented in BOE # 474588, figure 3,4,5.