cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24486052.v1
title: <b>Docking and MD simulation initial structures</b>

description: Our research centered on the NLRP3 protein, which plays a pivotal role in the context of neuroinflammation, a major contributing factor in Alzheimer's Disease (AD). When NLRP3 is activated, it releases inflammatory molecules that worsen brain damage. Our aim was to identify potential compounds that can inhibit NLRP3 and reduce inflammation in neurons, possibly providing a way to treat AD. A computational approach was utilized to screen a library of coumarin derivatives for compounds that meet drug-like criteria and could potentially penetrate the blood-brain barrier. We identified three promising coumarin-based compounds with better NLRP3-binding affinity than a known inhibitor. Our molecular dynamics simulations and binding energy calculations further supported these compounds as potential leads for inhibiting the NLRP3 inflammasome and potentially treating AD.
DOI: 10.6084/m9.figshare.24249766
title: Supplementary Material for: Mesenchymal Stromal Cells Facilitate Neutrophil Trained Immunity by Reprogramming Hematopoietic Stem Cells

description: Novel therapeutics are urgently needed to prevent opportunistic infections in immunocompromised individuals undergoing cancer treatments or other immune suppressive therapies. Trained immunity is a promising strategy to reduce this burden of disease. We previously demonstrated that mesenchymal stromal cells (MSCs) preconditioned with a class A CpG oligodeoxynucleotide (CpG-ODN), a Toll-like receptor 9 (TLR9) agonist, can augment emergency granulopoiesis in a murine model of neutropenic sepsis. Here, we used a chimeric mouse model to demonstrate that MSCs secrete paracrine factors that act on lineage negative c-kit+ hematopoietic stem cells (HSCs), leaving them ‘poised’ to enhance emergency granulopoiesis months after transplantation. Chimeric mice developed from HSCs exposed to conditioned media from MSCs and CpG-ODN preconditioned MSCs showed significantly higher bacterial clearance and increased neutrophil granulopoiesis following lung infection than control mice. By CUT&RUN chromatin sequencing and cytometry by time of flight (CyTOF) approaches, we identified that MSC conditioned media leaves H3K4me3 histone marks in HSCs at genes involved in myelopoiesis and in signaling persistence by the mTOR pathway. Both soluble factors and extracellular vesicles (EV) from MSCs mediated these effects on HSCs and proteomic analysis by mass spectrometry revealed soluble calreticulin as a potential mediator. In summary, this study demonstrates that trained immunity can be mediated by paracrine factors from MSCs to induce neutrophil trained immunity by reprogramming HSCs for long-lasting functional changes in neutrophil mediated anti-microbial immunity.
DOI: 10.6084/m9.figshare.24249766.v1
title: Supplementary Material for: Mesenchymal Stromal Cells Facilitate Neutrophil Trained Immunity by Reprogramming Hematopoietic Stem Cells

description: Novel therapeutics are urgently needed to prevent opportunistic infections in immunocompromised individuals undergoing cancer treatments or other immune suppressive therapies. Trained immunity is a promising strategy to reduce this burden of disease. We previously demonstrated that mesenchymal stromal cells (MSCs) preconditioned with a class A CpG oligodeoxynucleotide (CpG-ODN), a Toll-like receptor 9 (TLR9) agonist, can augment emergency granulopoiesis in a murine model of neutropenic sepsis. Here, we used a chimeric mouse model to demonstrate that MSCs secrete paracrine factors that act on lineage negative c-kit+ hematopoietic stem cells (HSCs), leaving them ‘poised’ to enhance emergency granulopoiesis months after transplantation. Chimeric mice developed from HSCs exposed to conditioned media from MSCs and CpG-ODN preconditioned MSCs showed significantly higher bacterial clearance and increased neutrophil granulopoiesis following lung infection than control mice. By CUT&RUN chromatin sequencing and cytometry by time of flight (CyTOF) approaches, we identified that MSC conditioned media leaves H3K4me3 histone marks in HSCs at genes involved in myelopoiesis and in signaling persistence by the mTOR pathway. Both soluble factors and extracellular vesicles (EV) from MSCs mediated these effects on HSCs and proteomic analysis by mass spectrometry revealed soluble calreticulin as a potential mediator. In summary, this study demonstrates that trained immunity can be mediated by paracrine factors from MSCs to induce neutrophil trained immunity by reprogramming HSCs for long-lasting functional changes in neutrophil mediated anti-microbial immunity.
DOI: 10.5281/zenodo.10065672
title: Article data of The Impact of  MDR-1 Gene Polymorphism (rs1128503) on Response to Imatinib and nilotinib Treatment in A Sample of Iraqi Chronic Myeloid Leukemia-Chronic Phase Patients
DOI: 10.5281/zenodo.10065683
title: Restricted Access Test
DOI: 10.5281/zenodo.10065682
title: Restricted Access Test
DOI: 10.5519/qd.44ltx6ak
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (28 records)
DOI: 10.5281/zenodo.10065673
title: Article data of The Impact of  MDR-1 Gene Polymorphism (rs1128503) on Response to Imatinib and nilotinib Treatment in A Sample of Iraqi Chronic Myeloid Leukemia-Chronic Phase Patients
DOI: 10.5519/qd.4axd3uzi
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (297 records)
DOI: 10.6084/m9.figshare.24486208
title: Maxent results.rar

description: MaxEnt results of Indonesian essential oil plant habitat
DOI: 10.6084/m9.figshare.24486208.v1
title: Maxent results.rar

description: MaxEnt results of Indonesian essential oil plant habitat
DOI: 10.17632/399rpcc49r.1
title: Immunocastration protocol testing - In vivo and post-mortem measurements

description: Scrotal dimensions (total width; length and width of the left and right sacs) of Bísaro pigs measured every 4 week in vivo, and after slaugther (aggregated weight, testis weight, epididymal weight, testis height, width and depth, and epididymal lenght and width). Animals were randomly assigned in three groups and vaccinated against GnRH with Improvac® (Zoetis) with the standard dosing regimen, using different protocols. Priming started at 9 (Grp1) and 13 weeks of age (Grp2 and Grp3). The booster was performed with two (Grp2 and 3) or three injections (Grp1), 4-weeks apart. Animals in Group 1 and 2 were kept in the farm until 57 week-old, and were revaccinated with two additional administrations (2nd cycle), starting at 49 weeks of age (8 weeks before slaughter). Animals in Group 3 where slaughtered at 37 weeks of age. Eleven animals were kept as intact males throughout the whole experiment (GrpC). Animals in the control group were also maintained until 57 week-old.
DOI: 10.17632/zdmn5w6zw7.4
title: Self-stabilization of barchan dune chasing

description: Barchan dunes are often found in a variety of environments. They exhibit group-like self-stabilizing characteristics when interacting with each other. Under the premise of local similarity, water tunnel experiments have been widely used to study the fascinating dune interactions, especially contact interactions, i.e., collisions; however, non-contact interactions (i.e., chasing) and the fluid mechanisms behind them have not been studied sufficiently. To bridge this gap, we performed water tunnel experiments combined with numerical simulations to demonstrate the flow structure around two chasing dunes. Our results suggest that the distance between two dunes may become stable due to a combination of three factors: repulsion effect between the two dunes, which widens the distance, and impediment to downstream dune movement, embracing effect which shrinks the distance, and the difference in dune size, whose specific effect depends on the relative position of the two dunes. The first two factors are achieved by two special vortex structures. Based on this model, we propose a scaling law to describe the equilibrium of the dune chasing and a governing equation to explain the breakdown of such equilibrium, and they are both experimentally verified. Our model provides a framework to explain the self-stabilizing mechanisms of barchan dune swarms. The supporting information contains eight movies and their accompanying images as examples of our experiments, as well as the raw data of the dune distance over time of all the tests.
DOI: 10.21227/2zz3-f173
title: Indian Regions Soil Image Database (IRSID): A dataset for classification of Indian soil types

description: Indian Regions Soil Image Database (IRSID) : A dataset for classification of Indian soil typesThe database “Indian Regions Soil Image Database (IRSID)”, represent the Indian soil types. The dataset provides information on the soil for each image. This helps in the development and evaluation of an image analysis algorithm for the classification of soil type. The dataset consists of original color images of the sand, clay, sandy loam, loam, and loam sandy soil types. The images of the soil samples are collected from two different regions in Andhra Pradesh state, India. As the samples collected region is situated near the Godavari basin, most of the soil samples collected are either sand or clay. The samples that are collected in Madanapalle, Andhra Pradesh, India are sandy loam and loam soils. The total number of soil samples collected is 16 numbers. The soil images are captured by using an android mobile camera with 48 megapixels ISOCELL GM2 sensor with an f/2.0 aperture lens. The ISOCELL imager providesa broader, clearer viewing experience to mobile device users. Smart Wide Dynamic Range (WDR) technology of ISOCELL can capture the details more accurately in both bright and dark areas, even in high contrast lighting conditions. The collected test samples were tested in the soil mechanics lab by using sieve analysis and hydrometer test to find out the percentage of sand, silt, and clay in each soil sample. By plotting these percentage values on the USDA soil texture triangle, soil texture type can be identified. The test data of each sample is provided in .csv file.
DOI: 10.5281/zenodo.4458453
title: A call to eradicate non-inclusive terms from science

description: Source code and data associated with a commentary (Khan, 2021; eLife) that shows an increase of non-inclusive terms with racial connotations used in life-science literature and calls for action to make science inclusive for all.
DOI: 10.5281/zenodo.6950788
title: Na Wind-Temperature Lidar Data at Andes Lidar Observatory on 10/30/2016

description: Measurement made by the Na Wind-Temperature Lidar at the Andes Lidar Observatory in Cerro Pachón, Chile. It includes Na density, temperature, zonal, meridional, and vertical wind, from 80 to 115 km altitude at 0.5-km intervals and from 23.7 UT 10/29/2016 to 8.9 UT 10/30/2016 at 0.1-hour intervals. Errors of these values are also included. -999 represents missing values.
DOI: 10.5281/zenodo.8136987
title: Data files for A "Boreing" Night of Observations of the Upper Mesosphere and Lower Thermosphere Over the Andes Lidar Observatory

description: The files in this set are data obtained from the ANI2 airglow imager located at the Andes Lidar Observatory.in Chile (30.23S, 70.73W, 2530 m). The files are named for a JGR paper by J. Hecht et al. entitled A "Boreing" Night of Observations of the Uppe rMesosphere and Lower Thermosphere Over the Andes Lidar Observatory. The files are published here so as to be available for review. This paper should appear in JGR Atmospheres sometime in late 2023 or early 2024. The files that are text files are meant to be read with IDL as discussed in the readme file.
DOI: 10.6084/m9.figshare.22360708
title: Supplementary Material for: Associations and Prognostic Significance of Fluctuations in Diabetic Retinopathy Severity in Eyes Treated for Diabetic Macular Edema

description: Introduction: The aim of our study was to investigate factors associated with diabetic retinopathy (DR) severity fluctuations in patients undergoing intravitreal injections for diabetic macular edema and to explore risk factors for proliferative DR (PDR). Methods: We graded ultra-widefield fundus photography imaging at each visit using the Early Treatment Diabetic Retinopathy Study severity scale (DRSS). We calculated the deviation from the mode (DM) of DRSS values as a proxy of DR severity fluctuations, and we analyzed its clinical associations with linear models. We computed risk factors for PDR with Cox hazard models. We included the DRSS area-under-the-curve (AUC) of DRSS scores as a covariate in all analyses. Results: We included 111 eyes with median follow-up of 44 months. Higher DRSS-AUC values (=+0.03 DRSS DM for unitary DRSS/month increase, p=0.01) and a higher number of anti-VEGF injections (=+0.07 DRSS DM for injection, p=0.045) were associated with wider DR severity fluctuations. Higher DRSS-AUC values (HR=1.45 for unitary DRSS/month increase, p=0.001) and wider DR severity fluctuations (HR=22.35 4th quartile vs. 1st-3rd quartile of DRSS DM, p=0.01) were risk factors for PDR. Discussion/Conclusion: Patients with larger DR variability in response to intravitreal injections may be at higher risk of DR progression. We advocate attentive follow-up in these patients to recognize PDR early.
DOI: 10.6084/m9.figshare.22361131
title: Supplementary Material for: Effects of Exercise on Physical Function and Quality of Life In Prostate Cancer Patients Receiving Androgen Deprivation Therapy: High intensity interval training vs. Moderate-intensity continuous training

description: Introduction: We assessed the effects of exercise on the physical function and health quality of life (hQoL) in prostate cancer patients underwent androgen deprivation therapy (ADT). Additionally, the effects of high-intensity interval training (HIIT) on the physical function and hQoL in these patients were compared with those of moderate-intensity continuous training (MICT). Methods: Seventeen prostate cancer patients underwent ADT were prospectively allocated to either HIIT (n=9) or MICT (n=8). In these patients, physical function and hQoL were measured before and after 12 weeks of exercise and 3–6 months after the exercise program, respectively. Results: Although the whole-body total mass significantly increased after the exercise program, it was equivalent regardless of the exercise methods. After the exercise program, muscle strength and endurance improved and tended to be maintained until 3–6 months later. Improvement in muscle endurance was more prominent after HIIT, and that in muscle strength was more prominent after MICT. Performance in the senior fitness test improved after the exercise program, and HIIT was more effective for lower and upper muscle endurance and flexibility although MICT was more effective for the others. The hQoL significantly improved at 3–6 months after the exercise program. Conclusion: The 12-week exercise program has a positive effect on the physical function and hQoL in prostate cancer patients who underwent ADT. In these patients, compared with MICT, HIIT may be a better option for improving muscle endurance, which is thought to be significant for preventing falls and fracture in elderly patients.
DOI: 10.3334/cdiac/cli.ndp020
title: An Updated Global Grid Point Surface Air Temperature Anomaly Data Set: 1851-1990 (revised 1991) (NDP-020)

description: This NDP presents land-based monthly surface-air-temperature anomalies (departures from a 1951-1970 reference period mean) on a 5° latitude by 10° longitude global grid. Monthly surface-air-temperature anomalies (departures from a 1957-1975 reference period mean) for the Antarctic (grid points from 65°S to 85°S) are presented in a similar way as a separate data set. The data were derived primarily from the World Weather Records and from the archives of the United Kingdom Meteorological Office. This long-term record of temperature anomalies may be used in studies addressing possible greenhouse-gas-induced climate changes. To date, the data have been employed in producing regional, hemispheric, and global time series for determining whether recent (i.e., post-1900) warming trends have taken place. The present updated version of this data set is identical to the earlier version for all records from 1851-1978 except for the addition of the Antarctic surface-air-temperature anomalies beginning in 1957. Beginning with the 1979 data, this package differs from the earlier version in several ways. Erroneous data for some sites have been corrected after a review of the actual station temperature data, and inconsistencies in the representation of missing values have been removed. For some grid locations, data have been added from stations that had not contributed to the original set. Data from satellites have also been used to correct station records where large discrepancies were evident. The present package also extends the record by adding monthly surface-air-temperature anomalies for the Northern (grid points from 85°N to 0°) and Southern (grid points from 5°S to 60°S) Hemispheres for 1985-1990. In addition, this updated package presents the monthly-mean-temperature records for the individual stations that were used to produce the set of gridded anomalies. The periods of record vary by station. Northern Hemisphere data have been corrected for inhomogeneities, while Southern Hemisphere data are presented in uncorrected form.
DOI: 10.6084/m9.figshare.22087211
title: Supplementary Material for: Associations between Early Thyroid-Stimulating Hormone Levels and Morbidities in Extremely Preterm Neonates

description: <b><i>Introduction:</i></b> High-end cutoffs of thyroid-stimulating hormone (TSH) have been emphasized for hypothyroidism therapy in extremely preterm infants, but the significance of low TSH levels remains unknown. This study hypothesized that the spectrum of TSH levels by newborn screening after birth signifies specific morbidities in extremely preterm neonates. <b><i>Methods:</i></b> The multicenter population cohort analyzed 434 extremely preterm neonates receiving TSH screening at 24–96 h of age in 2008–2019. Neonates were categorized by blood TSH levels into group 1: TSH &lt;0.5 µU/mL, group 2: 0.5 ≤ TSH &lt;2 µU/mL, group 3: 2 ≤ TSH &lt;4 µU/mL, and group 4: TSH ≥4 µU/mL. Neonatal morbidities were categorized using the modified Neonatal Therapeutic Intervention Scoring System. <b><i>Results:</i></b> The four groups differed in gestational age, birth weight, and the postnatal age at blood sampling so did the proportions of mechanical ventilation usage (<i>p</i> = 0.01), hypoxic respiratory failure (<i>p</i> = 0.005), high-grade intraventricular hemorrhage (<i>p</i> = 0.007), and periventricular leukomalacia (<i>p</i> = 0.048). Group 1 had higher severity scores for respiratory distress syndrome (RDS; effect size 0.39 [95% confidence interval [CI]: 0.18–0.59]) and brain injury (0.36 [0.15–0.57]) than group 2, which remained significant after adjusting for gestational age, birth weight, dopamine usage, and the postnatal age at TSH screening (RDS: mean + 0.45 points [95% CI: 0.11–0.79]; brain injury: +0.32 [0.11–0.54]). <b><i>Conclusions:</i></b> Low TSH levels in extremely preterm neonates are associated with severe RDS and brain injuries. Studies recruiting more neonates with complete thyroid function data are necessary to understand central-peripheral interactions of the hypothalamic-pituitary-thyroid axis.
DOI: 10.14284/324
title: The intersect of the Exclusive Economic Zones and IHO sea areas, version 3. Available online at https://www.marineregions.org/

description: This product is the result of overlaying the the Exclusive Economic Zones layer with the IHO Sea Areas (IHO, 1953). The combination of these two boundaries provides national regional sea areas for the global ocean.
DOI: 10.17632/479khyv5yb.1
title: LEST

description: Lead Exposure Survey Tool (LEST). LEST is an evidence-based research tool. The tool takes into consideration the regional sociocultural characteristics of the middle east and north Africa (MENA) member nations. It is designed to fit the various research questions in respect to lead exposure.
DOI: 10.5281/zenodo.7195608
title: Used data for doing tomography

description: Used data for doing tomography.
DOI: 10.6084/m9.figshare.24314017
title: Supplementary Material for: Efficacy and safety of acupuncture combined with herbal medicine for children and adolescents with Tourette syndrome: A Systematic Review and Meta-Analysis

description: Background: With the increasing prevalence of Tourette syndrome (TS), the search for alternative therapy for TS is a growing public concern. In recent years, a growing number of randomized controlled trials have revealed the value of acupuncture combined with herbal medicine for the treatment of TS; however, its holistic efficacy and safety remains unclear. This study aimed to evaluate the efficacy and safety of acupuncture combined with herbal medicine and to provide preliminary evidence for clinical practice. Methods: Eight databases were searched from their establishment to November 27, 2022 to collect randomized controlled trials (RCTs) of acupuncture combined with herbal medicine for TS treatment. Two researchers independently completed the study screening, data extraction and risk of bias assessment by using NoteExpress, Excel and Cochrane Risk of Bias Tool 2.0 (RoB 2.0). Stata 15.0 software was applied to conduct meta-analysis. Results: A total of 1400 participants in 18 RCTs were included. Compared with the Western medicine (WM) , acupuncture combined with herbal medicine had better curative effect in the field of effective rate (RR = 1.18, 95% CI [1.12, 1.23], P ＜ 0.05, I²= 0%), Yale Global Tic Severity Scale (YGTSS) total score (MD = -3.91, 95% CI [-5.49, -2.33], P ＜ 0.05, I² = 96.4%), TCM syndrome total score (MD = -2.42, 95% CI [-3.71,-1.13], P ＜ 0.05, I² = 87.1%) and serum IgE negative rate (RR = 3.41, 95% CI [1.69, 6.87], P ＜ 0.05, I² = 0%). Furthermore, acupuncture combined with herbal medicine reduced the adverse reaction rate (RR = 0.20, 95% CI [0.14,0.30], P ＜ 0.05, I² = 0%) and the recurrence rate (RR = 0.27, 95% CI [0.13,0.52], P ＜ 0.05, I² = 0%). Conclusion: This study demonstrated the efficacy and safety of acupuncture combined with herbal medicine, which is probably a better alternative therapy for TS. However, the small number, low quality and potential bias of the included studies caused the limitations of our results. More high-quality RCTs are required to provide supplementary evidence in the future.
DOI: 10.5281/zenodo.6585292
title: Opportunities and Security Risks of Technical Leverage: A Replication Study on the NPM Ecosystem

description: Metadata, technical leverage, and vulnerability reports for 14,042 stable releases and scripts used in "Opportunities and Security Risks of Technical Leverage: A Replication Study on the NPM Ecosystem" paper.
DOI: 10.5281/zenodo.7633943
title: Magnetic Properties of Lightning-Induced Glass Produced from Five Mineral Phases

description: The excel sheet contains raw and corrected vibrating sample magnetometry data of five igneous minerals (&lt; 32 µm powders of albite, labradorite, augite, hornblende, and magnetite) before and after high-current impulse experiments conducted at peak currents of 25 and 40 kA.
DOI: 10.5281/zenodo.8162177
title: Simulated spatially explicit dataset (300 m) on future forest cover changes in Southeast Asia projected under the baseline shared socioeconomic pathways

description: This is a simulated spatially explicit dataset on future forest cover changes in Southeast Asia projected under the baseline shared socioeconomic pathways. It includes six raster maps at a spatial resolution of 300 m: (1) 2015 baseline forest and non-forest map; (2) SSP1 2050 projected net forest gain map; (3) SSP2 2050 projected net forest gain map; (4) SSP3 2050 projected net forest loss map; (5) SSP4 2050 projected net forest gain map; and SSP5 2050 projected net forest loss map. This dataset is the result of a study published in Nature Communications (2019) (https://doi.org/10.1038/s41467-019-09646-4).