cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27915888.v1
title: Data file for the manuscript-<b>Biomimetic Microhabitats for Augmented Coral Settlement and Reef Rehabilitation</b>

description: Anthropogenic stressors pose substantial threats to the future existence of coral reefs. Achieving successful coral recruitment stands as a bottleneck in reef restoration and hybrid reef engineering efforts. Here, we enhance coral settlement through the development of biomimetic microhabitats that replicate the chemical landscape of healthy reefs. We engineered a soft biomaterial, SNAP-X, composed of silica nanoparticles, biopolymers and algal exometabolites, to enrich reef microhabitats with bioactive molecules from crustose coralline algae. Coral settlement was enhanced over 20-fold using SNAP-X coated substrates compared to uncoated controls. SNAP-X is designed to gradually release chemical signals slowly (&gt; 1 month) under natural seawater conditions, and it can be rapidly applied to natural reef substrates via photopolymerization, further facilitating the light-assisted 3D printing of microengineered habitats. We anticipate that these biomimetic microhabitats will be widely used to augment coral settlement on degraded reefs and to support ecosystem processes on hybrid reefs.
DOI: 10.6084/m9.figshare.27979215.v1
title: The supplementary materials of "Water Cycling in the Deep Earth: Evidence from Emeishan Large Igneous Province"

description: The supplementary materials of "Water Cycling in the Deep Earth: Evidence from Emeishan Large Igneous Province", including a supplementary dataset (dataset for machine learning and the estimated water content of basalts in Emeishan LIP) and a supplementary code for clinopyroxene hygrometer.
DOI: 10.6084/m9.figshare.4789084.v2
title: Gender-related morphometric differences in mature and nestling Crowned Eagles, with comments on ringing of eagle nestlings in KwaZulu-Natal, South Africa

description: Although most raptor species are sexually dimorphic, many species are non-discrete in some metrics. A limited amount of existing data for southern Africa suggests that Crowned Eagles <i>Stephanoaetus coronatus</i> exhibit non-discrete sexual dimorphism. Consequently, we investigated gender-related morphometric data of Crowned Eagles with corresponding genetic avian sex tests. Immature (<i>n =</i> 13) and adult (<i>n</i> = 5) Crowned Eagles were trapped, measured and released in KwaZulu-Natal, South Africa from 2012 to 2015. Our results show that tarsus width, body mass, and DI claw (hallux) measurements are suitable for discriminating between sexes of mature Crowned Eagles. We comment on the use of South African Ringing Scheme (SAFRING) and colour read-rings as a marking technique in Crowned Eagles. Furthermore, we suggest suitable parameters for accessing nests and marking nestlings. To aid in the age estimates of nestling eagles, a reference of growth of known-age nestlings is provided.
DOI: 10.6084/m9.figshare.27020326.v1
title: <b>Application of Deep Neural Network in Atomistic Simulation for Boron Diffusion in Silicon After Ion Implantation</b>

description: Data for paper "<b>Application of Deep Neural Network in Atomistic Simulation for Boron Diffusion in Silicon After Ion Implantation</b>"
DOI: 10.17632/ys54hh6fhp
title: Marei et al. 2024 BOR

description: Temporal transcriptomic changes in murine granulosa cells at different timepoints after the start of a high-fat high-sugar diet in Swiss mice. This dataset contains the original lists of the GO term annotations and KEGG pathways that were find enriched after the Gene Set Enrichment Analyses. A REVIGO tool was used to create a reduced representation of the GO terms, and the results are also shown here in separate files.
DOI: 10.6084/m9.figshare.9777725.v1
title: Central nervous system proteins and monoclonal antibodies digested by human cysteine cathepsins S, L and B

description: Analysis of this data can be found in MDPI IJMS article Human Cysteine Cathepsins Degrade Immunoglobulin G In Vitro in a Predictable Manner (https://www.mdpi.com/1422-0067/20/19/4843)<br>Three datasets, containing detected and sequence-aligned peptides after digestion of proteins with human cysteine cathepsins S, L and B, using nano liquid chromotography mass spectrometer. See manuscript for details regarding method (link/reference TBA).<br>1: Recombinant proteins from the human central nervous system (Tau, alpha-synuclein and myelin basic protein isoforms), digested at pH 6. <br><br>2: Therapeutic monoclonal antibodies (adalimumab, alemtuzumab, infliximab, natalizumab, rituximab and ocrelizumab), digested at pH 6. Enzyme to substrate ratio 1:100 for cathepsin S and B, 1:300 for cathepsin L. <br><br>3: Therapeutic monoclonal antibodies (adalimumab and infliximab), digested at pH 4, 5 and 6. Enzyme to substrate ratio 1:100 for all cathepsins. <br><sup>Notes: Contains partly overlapping data with dataset 2 (adalimumab, pH 6). This supplementary set does not include data from negative controls.</sup>
DOI: 10.17632/z3jj3jd62f
title: Key research in Insulin Resistance and Alzheimer’s Disease (2010 – 2020): A 10-year Bibliometric Analysis

description: Brain deficit particularly in Alzheimer’s Disease (AD) has recently gained interest specifically to explore the connection of insulin resistance in Type 2 Diabetes Mellitus (T2DM) and this neurodegeneration disease. In this bibliometric study, 2663 Scopus publications were evaluated from the key search of insulin resistance, T2DM, and AD. The publications were all selected based on the criteria that have been set, which is publications that were published from 2010 until 2020. Some network maps were visualized using VOSviewer software, which was employed in this study to clarify research focus, documents that produced total citation per year, citescores, source normalized impact per year (SNIP), and publication trend. The software can weigh the importance of cite publication based on the T2DM and AD key research in the bibliometric analysis.
DOI: 10.6084/m9.figshare.28219067.v2
title: Qualitative Data Quantitative Data

description: <b>Magnetic resonance imaging (MRI)</b> is a highly effective and non-invasive imaging modality for the detection and evaluation of prostate cancer (PCa). Among the various MRI sequences, <b>diffusion-weighted MRI (DW-MRI)</b> stands out as a sensitive technique that plays a critical role in identifying and characterizing prostate lesions. This technique leverages the sensitivity of tissue diffusion characteristics, which are quantified by the <b>b-value</b> and the <b>apparent diffusion coefficient (ADC)</b>. The b-value determines the sensitivity of the imaging to water diffusion, while the ADC provides quantitative measurements of tissue diffusivity, both of which are crucial for accurate diagnosis and differentiation of prostate cancer from benign conditions. Determining the optimal <b>b-value</b> and <b>ADC value</b> in DW-MRI enhances the diagnostic accuracy of prostate cancer and contributes to better patient outcomes, standardized imaging practices, and scientific advancements in oncologic imaging. This ensures more effective and non-invasive management of prostate cancer, addressing a critical need in men's health.
DOI: 10.6084/m9.figshare.21453852.v2
title: Genome annotation

description: Genome annotation for<em> Chrysomela aeneicollis</em>
DOI: 10.6084/m9.figshare.8202137.v1
title: rsEEG eyes closed SPSS file JoN

description: as above<br>
DOI: 10.17632/3ngwcbj5r7
title: Analysis of wood combustion products

description: The data presented in this dataset are related to the research paper “Granulation of fly ash and biochar with organic lake sediments – A way to sustainable utilization of waste from bioenergy production” [1] in the context of waste material investigation and possible valorization instead of disposal. This article provides a comprehensive chemical and physical characterization of wood combustion products – fly ashes, bottom ashes, mixed ashes and biochar. Multiple analytical techniques and methodology were exploited to investigate the composition of wood combustion products, among them a loss on ignition, potentiometry, colourimetry, X-ray diffractometry, X-ray fluorescence spectrometry, inductively coupled plasma optical emission spectrometry, gas chromatography. General parameters detected were the content of dry matter, gravimetric water, volatile matter, amount of ash and fixed carbon. The elemental analysis involved determining C, H, N and O. Physical properties were described by bulk density, solid density, total porosity, electric conductivity, specific weight and mass ratio assessment of particle size distribution. The mineralogical composition was described by major crystalline phases of samples and the content of oxides. Chemical properties and composition were characterized by pH, the content of ammonium, nitrates, nitrites, exchangeable elements and cation exchange capacity as well as after the 3-step speciation and analytical quantification of trace and major elements (Al, As, Ba, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Sb, Se, Sr, Ti, Tl, V and Zn) and detection of polycyclic aromatic hydrocarbons.
DOI: 10.6084/m9.figshare.17111399.v1
title: Supplementary Material for: The Dorsal Skinfold Chamber as a New Tympanic Membrane Wound Healing Model: Intravital Insights into the Pathophysiology of Epithelialized Wounds

description: <b><i>Background:</i></b> Tympanic membrane perforations (TMPs) are a common complication of trauma and infection. Persisting perforations result from the unique location of the tympanic membrane. The wound is surrounded by air of the middle ear and the external auditory canal. The inadequate wound bed, growth factor, and blood supply lead to circular epithelialization of the perforation’s edge and premature interruption of defect closure. Orthotopic animal models use mechanical or chemical tympanic membrane laceration to identify bioactive wound dressings and overcome premature epithelialization. However, all orthotopic models essentially lack repetitive visualization of the biomaterial-wound interface. Therefore, recent progress in 3D printing of customized wound dressings has not yet been transferred to the unique wound setup of the TMP. Here, we present a novel application for the mice dorsal skinfold chamber (DSC) with an epithelialized full-thickness defect as TMP model. <b><i>Methods:</i></b> A circular 2-mm defect was cut into the extended dorsal skinfold using a biopsy punch. The skinfold was either perforated through both skin layers without prior preparation or perforated on 1 side, following resection of the opposing skin layer. In both groups, the wound was sealed with a coverslip or left unclosed (<i>n</i> = 4). All animals were examined for epithelialization of the edge (histology), size of the perforation (planimetry), neovascularization (repetitive intravital fluorescence microscopy), and inflammation (immunohistology). <b><i>Results:</i></b> The edge of the perforation was overgrown by the cornified squamous epithelium in all pre­parations. Reduction in the perforation’s size was enhanced by application of a coverslip. Microsurgical preparation before biopsy punch perforation and sealing with a coverslip enabled repetitive high-quality intravital fluorescence microscopy. However, spontaneous reduction of the perforation occurred frequently. Therefore, the direct biopsy punch perforation without microsurgical preparation was favorable: spontaneous reduction did not occur throughout 21 days. Moreover, the visualization of the neovascularization was sufficient in intravital microscopy. <b><i>Conclusions:</i></b> The DSC full-thickness defect is a valuable supplement to orthotopic TMP models. Repetitive intravital microscopy of the epithelialized edge enables investigation of the underlying pathophysiology during the transition from the inflammation to the proliferation phase of wound healing. Using established analysis procedures, the present model provides an effective platform for the screening of bioactive materials and transferring progress in tissue engineering to the special conditions of tympanic membrane wound healing.
DOI: 10.6084/m9.figshare.24912525.v1
title: Force Plate Normative Data for Isometric Knee Flexor and Plantar Flexor Peak Force Capabilities of English Football League Players

description: This spreadsheet contains anonymised peak force and relative peak force data obtained by a force plate system for the isometric knee flexor tests performed with 30 and 90 degrees of knee flexion and the kneeling isometric plantar flexor test. The sample is professional English football league players who completed in League 2 (4th tier) or National League (5th tier) at the time of testing. All together, four football clubs participated in the testing (1 League 2 and 3 National League) to provide a combined sample of 91 players. Following a dynamic warm-up, three trials of each of these tests were performed unilaterally and with maximum-effort at the beginning of the pre-season training period (2023-24 season). The tests were performed in a randomised order with around 30-60 seconds of rest between trials and at least 3-5 minutes of rest given between tests. Only the mean value across the three trials performed are presented in this spreadsheet. The data were collected on Hawkin Dynamics force plates and analysed by their software. Here is the link to the Hawkin Dynamics metric database that explains how each metric included in the spreadsheet was measured: https://www.hawkindynamics.com/hawkin-metric-databaseEthics approval was granted from the author's institution and informed consent was provided by each player for their anonymised data to be uploaded to this repository for research use.
DOI: 10.6084/m9.figshare.5128546.v1
title: Supplementary Material for: The Conundrum of Papillary Breast Lesions within the C3 Category

description: <b><i>Objectives:</i></b> To identify features that could define papillary ductal cell proliferation within the C3 category and to subcategorise papillary lesions into benign papillomas which can be managed conservatively and atypical/malignant papillary neoplasms which require surgical intervention. <b><i>Study Design:</i></b> A blind microscopic rescreen of all C3 cases was conducted. The corresponding histological outcome was compared with the cytology. Statistical analysis was performed using papillary versus non-papillary outcomes and benign versus atypical/malignant papillary lesions. In addition, macropapillary lesions (papilloma and encysted papillary carcinoma) were plotted against micropapillary ductal carcinoma in situ. <b><i>Results:</i></b> Two hundred thirty FNA cases reported as C3 included 72 papillary neoplasms (52 benign papillomas and 20 atypical/malignant papillary lesions). Features specific to papillary lesions within C3 include macropapillary fragments, complex sheets, palisading strips, cystic background, cohesion and a decreased nuclear-to-cytoplasmic ratio. Features favouring atypical/malignant papillary lesions include decreased numbers of bare bipolar nuclei, discohesion and a non-cystic background. These features are common to most breast malignancies; however, identification of papillary features often results in a downgraded diagnosis from C5. <b><i>Conclusions:</i></b> This study supports the ability to reliably identify papillary ductal cell proliferation within C3. Certain features can distinguish papillary lesions from other C3 pathologies. This separation is likely to be clinically useful as papillary lesions may require a different management approach.
DOI: 10.6084/m9.figshare.7262195.v4
title: matrix.xlsx

description: Metabolomics was firstly used to explore prognosticbiomarkers of cervical cancer.
DOI: 10.6084/m9.figshare.12728480.v1
title: Electromagnetic Propagation Model

description: It is a dataset of the propagation model of pathloss and shadowing with different parameters that include correlation distances (10m, 15m, 20m, 25m, 30m) and standard deviations ( 2dB, 4dB, 6dB, 8dB,10dB, 12dB).
DOI: 10.6084/m9.figshare.14386880.v1
title: Dataset 11. ¿Cómo aportaría la enseñanza-aprendizaje de la IA dentro del plan de estudio en K-12?

description: Resultados de 11 artículos.
DOI: 10.6084/m9.figshare.27905100.v1
title: Pre and Post surveys for Virtual reality vs In Person Frog Dissections

description: Pre and post surveys for VR vs In person frog dissections
DOI: 10.17632/bz9hrkspnw
title: Publications on the Fintech research

description: All 1989 publications on the topic of the Fintech on Scopus for bibliometric analysis!
DOI: 10.6084/m9.figshare.4091325.v1
title: PowerPoint Slides for: Dietary Magnesium and Kidney Function Decline: The Healthy Aging in Neighborhoods of Diversity across the Life Span Study

description: <b><i>Background:</i></b> Prior studies suggest that certain aspects of the diet related to magnesium intake, such as dietary acid load, protein intake and dietary patterns rich in fruits and vegetables, may impact kidney disease risk. We hypothesized that lower dietary magnesium intake would be prospectively associated with more rapid kidney function decline. <b><i>Methods:</i></b> Among participants in the Healthy Aging in Neighborhoods of Diversity across the Life Span study with estimated glomerular filtration rate (eGFR) ≥60 ml/min/1.73 m<sup>2</sup> at baseline (2004-2009), dietary magnesium intake was calculated from two 24-hour dietary recalls. Rapid decline was defined as ≥3% eGFR decline per year. <b><i>Results:</i></b> Median (25th-75th percentile) dietary magnesium intake was 116 (96-356) mg/1,000 kcal. Among 1,252 participants, those with lower dietary magnesium intake were younger, and were more likely to be African-American men. A total of 177 participants (14.1%) experienced rapid eGFR decline over a median follow-up of 5 years. Lower dietary magnesium intake was significantly associated with a greater odds of rapid eGFR decline (OR for tertile 1 vs. 3: 2.02, 95% CI 1.05-3.86, p value for trend across tertiles = 0.02) in analyses adjusted for sociodemographics (age, sex, race, education level, health insurance status, poverty status), kidney disease risk factors (smoking status, diabetes, hemoglobin A1c, hypertension, body mass index), baseline eGFR and dietary factors (total energy intake; diet quality; dietary intake of fiber, sodium, calcium, potassium and phosphorus). <b><i>Conclusions:</i></b> In this urban population, lower dietary magnesium intake was independently associated with greater odds of rapid kidney function decline.
DOI: 10.6084/m9.figshare.c.3662366_d763.v1
title: Full body CT scan of an Eucrossorhinus dasypogon (RMNH.PISC.7411)

description: This file includes 1226 DICOM files of a female Eucrossorhinus dasypogon specimen housed in the spirit collection of Naturalis Biodiversity Center, Leiden, the Netherlands with registrationnumber RMNH.PISC.7411. The specimen is scanned in a medical CT scanner (Toshiba Aquilion 64) at the Leiden University Medical Center, the Netherlands at 100 kV and 150 mAs with a slice thickness of 0.5 mm.
DOI: 10.6084/m9.figshare.9956648.v1
title: Dataset for: Assessing method agreement for paired repeated binary measurements administered by multiple raters

description: Method comparison studies are essential for development in medical and clinical fields. These studies often compare a cheaper, faster, or less invasive measuring method with a widely used one to see if they have sufficient agreement for interchangeable use. Moreover, unlike simply reading measurements from devices, e.g., reading body temperature from a thermometer, the response measurement in many clinical and medical assessments is impacted not only by the measuring device but also by the rater. For example, widespread inconsistencies are commonly observed among raters in psychological or cognitive assessment studies due to different characteristics such as rater training and experience, especially in large-scale assessment studies when many raters are employed. This paper proposes a model-based approach to assess agreement of two measuring methods for paired repeated binary measurements under the scenario where the agreement between two measuring methods and the agreement among raters are required to be studied simultaneously. Based upon the generalized linear mixed models (GLMM), the decision on the adequacy of interchangeable use is made by testing the equality of fixed effects of methods. Approaches for assessing method agreement, such as the Bland-Altman diagram and Cohen's kappa, are also developed for repeated binary measurements based upon the latent variables in GLMMs. We assess our novel model-based approach by simulation studies and a real clinical application, in which patients are evaluated repeatedly for delirium with two validated screening methods. Both the simulation studies and the real data analyses demonstrate that our proposed approach can effectively assess method agreement.
DOI: 10.17632/tw34c7hv7z
title: polycystic ovary syndrome

description: Aim : explore pathophysiology of polycystic ovary syndrome. We have conducted a case control study.  Polycystic ovary syndrome were diagnosis according to Rotterdam criteria. For all participants blood analysis were made on the third day of meases.
DOI: 10.6084/m9.figshare.10298093.v2
title: Alignment files

description: Mutliple sequence alignments for all genes analysed and included in the paper "Phylogenetic evidence for the reductive evolution of stomata in bryophytes". Additional genes that were analysed, but not included in the paper are also included.
DOI: 10.6084/m9.figshare.25331947.v1
title: Raw research data: Effects of repeated sprint and plyometric training on jumping performance in under-15 volleyball players

description: Raw research data: Effects of repeated sprint and plyometric training on jumping performance in under-15 volleyball players.
DOI: 10.6084/m9.figshare.25421128.v2
title: Paper Artifacts

description: <i>Abstract</i>—<i>Context:</i> Modern open-source operating systems consist of numerous independent packages crafted by countless developers worldwide. To effectively manage this diverse array of software originating from various entities, Linux distributions have devised package management tools to streamline the pro- cess. Despite offering convenience in software installation, systems like Ubuntu’s apt may obscure the health of the upstream source. <i>Objective:</i> Employing the libyears software metric established by the CHOASS project, we aim to assess the holistic health of one of the leading Linux distributions at the package level and in its upstream source. Simplifying and making metrics easily applicable is a pivotal goal in the software engineering community. Here, we demonstrate the application of the libyears metric to a heterogeneous package management system. <i>Method:</i> We classified the package version data, then applied the libyears method in a two-pronged approach. First, we derived a novel approach to derive the libyears from the version number itself, and then we calculated the libyears using the upstream date of the source of the package date. <i>Results:</i> Our approach to calculating the libyears directly from the version number as well as our work to classify the different types of version numbering schemes shows that it can help indicate the freshness of a project. However, the extensive manual effort required to produce a libyears value, for even a minimal subset of core packages, limits its usefulness as a metric for evaluating overall distribution health. This result led directly to the development of Package Version Activity Classifier (PVAC), a novel method for systematically assessing the staleness of packages across multiple distribution releases. <i>Conclusions:</i> We present a novel way to systematically evaluate the health of projects with heterogeneous package management systems, such as Ubuntu, by examining staleness of its packages. The PVAC method we propose examines extends previous work by the software engineering research community by identifying packages with little to no development activity in the version of packages included within a distribution release.