cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14171069.v1
title: Summary Statistics for Gene-Fish Oil Interactions on Blood Lipids

description: These summary statistics are related to the manuscript, "Genome-wide association study of fish oil supplementation on lipid traits in 81,246 individuals reveals new gene-diet interaction loci" by Francis et al. in PLOS Genetics (2021)<br>Abstract: Fish oil supplementation is widely used for reducing serum triglycerides (TAGs) but has mixed effects on other circulating cardiovascular biomarkers. Many genetic polymorphisms have been associated with blood lipids, including high- and low-density-lipoprotein cholesterol (HDL-C, LDL-C), total cholesterol, and TAGs. Here, the gene-diet interaction effects of fish oil supplementation on these lipids were analyzed in a discovery cohort of up to 73,962 UK Biobank participants, using a 1-degree-of-freedom (1df) test for interaction effects and a 2-degrees-of-freedom (2df) test to jointly analyze interaction and main effects. Associations with <i>P</i> &lt; 1×10<sup>-6</sup> in either test (26,157; 18,300 unique variants) were advanced to replication in up to 7,284 participants from the Atherosclerosis Risk in Communities (ARIC) Study. Replicated associations reaching 1df <i>P</i> &lt; 0.05 (2,175; 1,763 unique variants) were used in meta-analyses. We found 13 replicated and 159 non-replicated (UK Biobank only) loci with significant 2df joint tests that were predominantly driven by main effects and have been previously reported. Four novel interaction loci were identified with 1df <i>P</i> &lt; 5×10<sup>-8 </sup>in meta-analysis. The lead variant in the <i>GJB6</i>-<i>GJB2</i>-<i>GJA3</i> gene cluster, rs112803755 (A&gt;G; minor allele frequency = 0.041), shows exclusively interaction effects. The minor allele is significantly associated with decreased TAGs in individuals with fish oil supplementation, but with increased TAGs in those without supplementation. This locus is significantly associated with higher <i>GJB2</i> expression of connexin 26 in adipose tissue; connexin activity is known to change upon exposure to omega-3 fatty acids. Significant interaction effects were also found in three other loci in the genes <i>SLC12A3 </i>(HDL-C), <i>ABCA6 </i>(LDL-C), and <i>MLXIPL</i> (LDL-C), but highly significant main effects are also present. Our study identifies novel gene-diet interaction effects for four genetic loci, whose effects on blood lipids are modified by fish oil supplementation. These findings highlight the need and possibility for personalized nutrition.
DOI: 10.6084/m9.figshare.16791118.v1
title: GNSS coordinate time series

description: The GNSS coordinate time series of the GPS stations used in the paper 'Potential Contributors to Common Mode Error in Array GPS Displacement Fields in Taiwan Island' in Remote Sensing.
DOI: 10.6084/m9.figshare.19448210.v1
title: Twitter responses to mass shooting on college campus

description: Gun violence is a growing problem facing college campuses. Little is understood to date in terms of campus community reactions and response to such instance of mass violence. Despite a rising focus in attention to threat assessment and other campus-based responses to violence since the 2007 Virginia Tech shooting, there exists a tremendous gap in empirical knowledge concerning needs, campus system functions, and other policy-relevant factors affecting responses to mass shooters. This study aims to generate basic science knowledge to inform campus-related policy concerning mass shootings and other violent incidents on college campuses. Using social media data following the 2019 UNCC campus shooting, we specifically seek to answer the following research questions (RQs):<br>1. What themes appear in student and community Twitter reactions in the immediate aftermath of a campus mass shooting?2. How do those themes vary over time?
DOI: 10.6084/m9.figshare.26096299.v1
title: SPSS citric acid production.sav

description: Spss data analysis
DOI: 10.6084/m9.figshare.4539874.v1
title: PowerPoint Slides for: Predicting Post-Transplant Recurrence of IgA Nephropathy: The Importance of Crescents

description: <b><i>Background:</i></b> Most studies that have assessed the predictors of recurrent IgA nephropathy (IgAN) in the renal allograft have focused on post-transplant features. Identifying high-risk pre-transplant features of IgAN is useful for counseling patients and may help in tailoring post-transplant immunosuppression. <b><i>Methods:</i></b> We investigated the pre-transplant clinical and biopsy features of 62 patients with IgAN who received transplants at Columbia University Medical Center from 2001 to 2012 and compared the characteristics and outcomes of patients with IgAN recurrence to those without recurrence. The primary outcome was time to recurrent IgAN. Secondary outcomes were a composite of doubling of creatinine or allograft failure, and recurrent IgAN as a cause of allograft dysfunction. <b><i>Results:</i></b> Of the 62 patients, 14 had recurrent IgAN in the allograft. Mean time to recurrence was 2.75 years. Those with recurrent disease were younger at the time of native kidney biopsy (29 vs. 41 years, p &lt; 0.0009). Black race and Hispanic ethnicity composed a higher proportion of the recurrent disease group. On multivariable analysis, significant predictors of recurrent IgAN included age at diagnosis (hazards ratio (HR) 0.911, 95% CI 0.85-0.98), burden of crescents on native biopsy (HR 1.21 per 10% increase in crescents, 95% CI 1.00-1.47) and allograft rejection (HR 3.59, 95% CI 1.10-11.7). <b><i>Conclusions:</i></b> Features of native IgAN can help predict the risk of recurrent disease in the renal allograft. In particular, immunologically active disease represented by earlier age of onset and greater burden of crescents on native biopsy is more likely to recur after transplant.
DOI: 10.6084/m9.figshare.13614608.v1
title: Rodrigues et al 2021 Wolbachia driven mate choice evolution data

description: Two different datasets (both tab delimited text files) and two R scripts (both .r) are provided: 1. Rodrigues et al. Dataset_field-derived populations.txt2. Rodrigues et al. Dataset_evolved populations.txt3. Rodrigues et al. Script_Analyses_field-derivedpopulations.r 4. Rodrigues et al. Script_Analyses_evolvedpopulations.r<br>See description of file's content in word document "Rodrigues et al. Description Datasets".
DOI: 10.6084/m9.figshare.14742810.v2
title: SuppData_Navarro et al-2021-CommBiol

description: The file Supp_data_1.xlsx contains the origin and authentication information of the 1,031 selected strains.<br><br>The file Supp_data2.xlsx contains all phenotype scores obtained for the 1,031 fungal strains on the 5 tested industrial compounds, as well as phenotype correlation analysis and the list of " best score strains".<br>The file Supp_data3.xlsx contains statistical test results related to box plots shown in Fig.6 in the main article.<br><br><br>
DOI: 10.6084/m9.figshare.20012764.v1
title: Predator-prey relationship in the vertical distribution of mites on grapevines

description: ABSTRACT. Phytophagous mites can cause economic losses in many crops, including grapevines. The changes in their population levels may be associated with changes in the predator-prey relationship. Knowledge of the distribution of mites in plants is important for planning sampling strategies and facilitating control decisions. The aims of this study were to (i) evaluate the abundances of Tetranychus urticae (Tetranychidae) and Neoseiulus californicus (Phytoseiidae), and the correlations between them and environmental factors; (ii) determine their distribution on the top, middle, or base strata of the evaluated grapevines (Vitis vinifera, Chardonnay cultivar) and, additionally, report the first occurrence of damage caused by T. urticae in grapevine leaves in the state of Rio Grande do Sul, Southern Brazil. Sixteen samplings were conducted, divided between the 2018 and 2019 seasons. In each sampling, three leaves from the three strata of the plant (top, middle, and base) were collected from 20 plants, totaling 60 leaves per sampling. The predator-prey relationship and their association with environmental variables were evaluated with multivariate correlation, whereas the number of mites per plant leaf strata was compared using a generalized linear mixed model in R software. It was possible to observe the symptoms of damage caused by T. urticae attacks on grapevines in Southern Brazil, characterized by the presence of yellow spots and general yellowing of the vineyard. Our findings indicate that T. urticae and N. californicus individuals are strongly associated with each other regardless of the environmental variables, and such relationship occurs mainly on the lower strata (middle and base leaves) of grapevines. Thus, by taking into account the damage on the leaves of grapevines and the occurrence of T. urticae and N. californicus majorities on specific strata of these vineyards, we suggest that the lower strata of grapevines should be the priority targets for management strategies to control such mites.
DOI: 10.6084/m9.figshare.21548103.v1
title: Sex Ratio at Birth Estimates by Pakistan Province from 1980 to 2020

description: Supplementary file 2: Sex Ratio at Birth Estimates by Pakistan Province from 1980 to 2020. <br> Dataset for: Chao, F., Wazir, M.A., & Ombao, H. (2022). Levels and trends estimate of sex ratio at birth for seven provinces of Pakistan from 1980 to 2020 with scenario-based probabilistic projections of missing female birth to 2050: A Bayesian modeling approach. <em>International Journal of Population Studies</em>, 8(2):51-70. https://doi.org/10.36922/ijps.v8i2.332
DOI: 10.6084/m9.figshare.23051519.v1
title: Supplementary Material for: Relapsed Waldenstrom’s Macroglobulinemia and Therapy-Related Myelodysplastic Syndrome with Complex Cytogenetics: A Treatment Dilemma

description: Waldenstrom’s macroglobulinemia (WM) is a lymphoplasmacytic lymphoma characterized by the infiltration of the bone marrow by clonal lymphoplasmacytic cells that produce monoclonal immunoglobulin M as defined by the World Health Organization Classification of hematological malignancies. Historically, the treatment options for WM were limited to alkylating agents and purine analogs. The introduction of immune therapy, including CD20 targeted therapy, proteasome inhibitors, and immune modulators, has provided benefit to those patients and has now become the standard of care. As WM patients become long-term survivors, treatment’s late toxicities have become more apparent. Here, we report a case of a 74-year-old female who presented to the hospital with fatigue and was diagnosed with WM. She was treated with bortezomib, doxorubicin, and bendamustine, followed by rituximab. After a remission period of 15 years, the patient had a relapse of WM, and bone marrow biopsy findings were consistent with intermediate-risk t-MDS with complex cytogenetics, presenting us with a treatment dilemma. We decided to treat WM, and the patient went into VGPR with residual lymphoma cells. Despite having dysplasia and complex cytogenetics, she did not have any cytopenia. Currently, she is under observation anticipating the progression of her MDS, given her intermediate I risk status. This case features the occurrence of t-MDS after therapy with bendamustine, cladribine, and doxorubicin. This highlights the need for closer monitoring and consideration of long-term adverse effects when treating patients with indolent lymphomas, especially WM. Late complications need to be considered, and risk versus benefit analysis needs to be carefully evaluated, especially in younger patients with WM.
DOI: 10.6084/m9.figshare.24800232.v1
title: HPMI: A retinal fundus image dataset for identification of high and pathological myopia based on deep learning

description: Myopia is one of the leading causes of visual impairment worldwide and can progress to high or pathological myopia (HM or PM) if proper measures were not taken. Accurate identification of HM and PH plays an important role for their intervention and treatment, which can be implemented leveraging deep learning technology on sufficient annotation image data. However, few efforts have been made to construct public accessible annotation data for this task. In this paper, we constructed a retinal fundus image dataset (called HPMI) to identify the HM and PM. This dataset consists of 4011 fundus images with their corresponding annotations for HM and PM, which were confirmed by multiple ophthalmic examinations (e.g., visual acuity and axial length). To the best of our knowledge, this is the largest fundus image dataset for the classification of HM and PM. Based on the dataset, we further validated the classification potential of three representative deep learning networks (i.e., ResNet50, DenseNet121, and InceptionV3) and analyzed the consistency between prediction results and annotations
DOI: 10.6084/m9.figshare.25866787.v1
title: Crop Wild Relatives – Inventories in Nåtö Nature Reserve, Åland Islands, 2023

description: Introduction: The crop wild relative (CWR) inventory in Nåtö, Åland Islands was carried out as a part of the Nordic project ‘Conservation and sustainable use of genetic resources in the Nordic countries’. During the project, CWR inventories were conducted in each Nordic country.Aim: The aim of the inventories was to investigate the distribution and status of CWR populations in target protected areas, which could in the future form a CWR conservation network. The goal was to learn from these experiences for the implementation of such tasks in the future and at the same time improve the quality of CWR conservation. The main aim was to promote CWR conservation, test inventory and <i>in situ</i> site selection methods and to eventually identify populations which would be suitable for long-term conservation.Method: The presence and status of CWR populations in Nåtö were described based on FAO CWR descriptors (Alercia et al. 2022). The selection of taxa for inventory was based on a revised Nordic CWR priority list (Fitzgerald et al. 2021). Nåtö was selected as a target site based on an earlier conservation gap analysis, which identified the most CWR species rich complementary conservation areas within Finland (Fitzgerald et al. 2020; 2023). The current inventory was carried out on 100x100 m Finnish uniform grid system (YKJ-grid) squares.Results: Altogether 44 squares and 367 priority CWR populations were inventoried. Data on taxon names, population size, count of individuals, potential threat and management needs were recorded. The report summarizes the results and the full taxon observation and population data results can be accessed through Finnish Biodiversity Information Facility (FinBIF, 2024).
DOI: 10.6084/m9.figshare.28557743.v1
title: Meningioma Recurrence

description: AI in radiology imaging
DOI: 10.17632/mvwr8mjz3k
title: Effects of ultrasound stimuli on mechanical and biological properties of ligament fibroblasts

description: Research hypothesis: Ultrasound stimulation on ligament fibroblasts will increase their elastic modulus, harmonic vibration, cell proliferation, migration, synthesis of extracellular matrix (ECM) (Collagen type I, type III and Fibronectin), and β-actin expression.

Data shows the elastic modulus (Pa); Harmonic of the natural frequency of vibration (Hz); cell proliferation (Cell number/mL) on 2nd, 4th, and 6th day of culture; cell migration length (um); synthesis of proteins: collagen type I (ng/mL), type III (ng/mL) and Fibronectin (ng/mL); β-actin area (cm2) for treated cells and the control group.

Following ultrasound stimulation (at either 1.0 W/cm2 (Group A-low dose) or 2.0 W/cm2 (Group B-high dose) for five days every 24 hours, Control cells (Group C) were manipulated identically with ultrasound off) the elastic modulus of ligament fibroblasts decreased (Group A, 22%; Group B, 31%) (p&lt;0.05). The harmonic of the natural frequency of vibration of ligament fibroblasts decreased (Group A, 13%; Group B, 17%). Cell proliferation and migration increased by 10% and 4%, (Group A), and decreased by 13% and 11%, (Group B) (p&lt;0.05). Synthesis of type I collagen was increased 100% following the high dose, but no type III collagen synthesis was detected in cells stimulated for the low dose or in control cells. Fibronectin production was significantly increased following ultrasound stimulation (79%, Group A; 61%, Group B). Most cells were viable (85%, Group A; 77%, Group B; 86%, Group C). The low dose of ultrasound decreased the β-actin area by 74%, and the high dose decreased the β-actin area by 31%.
DOI: 10.17632/ryzvs2zw9v
title: Network characterization data assessed in the chicken aortic ring assay using human adipose-derived stem cell secretomes

description: We present data assessed with the chicken aortic ring assay in the following six Excel files. First, we provide a data set covering the vessel area, maximum outgrowth radius and number of endpoints per aortic ring for the following matrices: egg white, bovine collagen, jellagel and matrigel (DiB_Figure_1_manuscript vessel network complexity). Second, secretome harvested from human adipose-derived stem cells (3 donors) cultivated as single cells, 250 cells/spheroid or 8000 cells/spheroid were applied in the chicken aortic ring assay. We provide data on the spheroid size, the protein concentration of the three secretomes, the weight of the embryos used for these experiments, the circumference of the aortic rings, the migration extent at days 1,4 and 7, the percentage of initial vessels and the number of loops per aortic ring (DiB_Figure_2_manuscript vessel network complexity). Next, the network was characterized at days 1,4 and 7. Here, we provide data on maximum outgrowth radius, maximum initial vessel length, speed mean vessel length and speed maximum vessel length, respectively (DiB_Figure_3_manuscript vessel network complexity). After that, sprouting parameters are presented. Raw data on vessel density, number of branches, mean branch length, relative frequency of branch length, number of junctions and number of junctions per initial vessels are provided (DiB_Figure_4_manuscript vessel network complexity). Finally, the raw data for these parameters for each donor are presented (DiB_Figure_S2_manuscript vessel network complexity); and the calculated angiogenic activity index (AAI) for each parameter is provided (DiB_Table_S1_manuscript vessel network complexity).
DOI: 10.6084/m9.figshare.19426334.v1
title: Data-Leaf trait network.xlsx

description: plant functional trait along a transect<br>
DOI: 10.17632/3rn68yxnvt
title: Acoustic Index dataset

description: There are two datasets.One is acoustic indices from four recording devices, another is acoustic indices of noisy bird sound signals with different SNRs and noises.
DOI: 10.6084/m9.figshare.25687137.v1
title: data and mods

description: This data and mods folder supports the analysis documented in the repository SDM-Preds-Novel-Conditions, which can be accessed at https://github.com/aallyn/SDM-Preds-Novel-Conditions.
DOI: 10.6084/m9.figshare.25880407.v1
title: SAIL - Gamma radiation data (ocean-only)

description: Quality-controlled observations of gamma radiation counts measured on board the sail ship NRP Sagres during the 2020 SAIL campaign (ocean-only observations, excluding coastal measurements).<br>The structure of the datafile is the following:<br>col 1: date (yyyy-mm-dd)col 2: time (HH:MM:SS)col 3: gamma counts (counts per minute)col 4: longitude (degrees E)col 5: latitude (degrees N)<br>
DOI: 10.6084/m9.figshare.28782539.v2
title: The Dataset of Herbal Combination Model Project

description: Traditional Chinese Medicine (TCM) utilizes intricate herbal formulations that exemplify the principles of compatibility and synergy. However, the rapid proliferation of herbal data has resulted in redundant information, complicating the understanding of their potential mechanisms. To address this issue, we first established a comprehensive database that encompasses 992 herbs, 18,681 molecules, and 2,168 targets. Consequently, we implemented a multi-network strategy based on a core information screening method to elucidate the highly intertwined relationships among the targets of various herbs and to refine herbal target information. Within a non-redundant network framework, separation and overlap analysis demonstrated that the networking of herbs preserves essential clinical information, including their properties, meridians, and therapeutic classifications. Furthermore, two notable trends emerged from the statistical analyses of classical TCM formulas: the separation of herbs and the overlap between herbs and diseases. This phenomenon is termed the Herbal Combination Model (HCM), validated through statistical analyses of two representative case studies: the common cold and rheumatoid arthritis. Additionally, in vivo and in vitro experiments with the new formula YanChuanQin (YHS - Corydalis Rhizoma, CW - Aconiti Radix, and QJ - Gentianae Macrophyllae Radix) for acute gouty arthritis further support the HCM. Overall, this computational method provides a systematic network strategy for exploring herbal combinations in complex and poorly understood diseases from a non-redundant perspective.
DOI: 10.11583/dtu.25348213.v1
title: Danish Residential Electric Vehicle Charging Profiles for Distribution Grid Planning and Design

description: The datasets contain percentile profiles for residential EV charging. The profiles are created based on a large dataset of around 3500 residential EV chargers owned by one of the largest charging point operators in Denmark. For each charger, data for the entire year of 2023 were used. Various percentile profiles are provided for different aggregation sizes (1-200 EVCs), seasons (summer and winter), days of the week (workday and weekend) as well as charger types, namely 3.7 kW (1-phase, 16 A), 7.8 kW (2-phase, 16 A) and 11 kW (3-phase, 16 A). Moreover, different group percentiles are provided indicated by the file name q_group0_95 uses the 95th-percentile. More information about the method and data can be found in an article submitted to CIRED Workshop 2024 with the title "Danish Electric Vehicle Charging Profiles for Distribution Grid Planning and Design".<br>
DOI: 10.17632/h2zf8gbv42
title: Software runtime execution trace dataset for runtime anomaly detection 

description: Here is the datasets for software runtime anomaly detection methods.
The data in the trainingDatasets folder contains times series collected during software execution. Due to the storage limits, we only upload partiall time series here, other data are provided on request. (email at the author)
As for the evaluationDatasets, here are two folder, the norm folder contains the samples with fixed length 1000 collected from normal runs,
the anomalies folder contains the samples collected from abnormal runs.
DOI: 10.17632/pvh7jcryx2
title: E-commerce user activities (dataset 230401_230715)

description: The dataset contains information about the collected customer behavior of an e-shop that has implemented a multi-variant user interface serving platform.
Data was retrieved from the database with a query:
SELECT s.token, s.fingerprint, s.userToken, s.siteId, s.userId, v.url, v.type, v.group, v.category, v.action, v.name, v.time, v.visitKey, v.groupSource FROM `visit` v JOIN session s ON v.sessionId=s.id WHERE v.`time` &gt; '2023-04-01' AND v.`time`&lt;'2023-07-15'
The dataset was used to cluster clients and assess the effectiveness of serving different UI variants.