cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17705003.v1
title: Supplementary Material for: Effect of Hedan tablets on body weight and insulin resistance in patients with metabolic syndrome

description: Introduction: Apart from their recognized lipid-lowering effect, Hedan tablets, a mixture of Chinese herbal medicines, have demonstrated a certain weight-loss effect in clinical practice. The aim of this randomized, double-blind, placebo-controlled study is to verify the effect of Hedan tablets on body weight (BW) and insulin resistance (IR) in patients with metabolic syndrome (MetS). Methods: A total of 62 eligible patients with MetS were divided into two groups: the treatment group (Hedan tablets at 4.38 g/day tid) and the control group (placebo treatment). Both groups attended follow-ups at 8, 16, and 24 weeks during the process. The parameters of the assessment include lipid level, BW, triglyceride (TG) to high-density lipoprotein cholesterol (HDLc) ratio (TG/HDLc), homeostasis model assessment for IR (HOMA-IR) index, and adiponectin. Results: Patients in the treatment group showed a significant decrease in BW compared with the control group (−4.47 vs. 0.06 kg) after 8 weeks of treatment. A significant decrease in body mass index was also observed in the treatment group after 16 weeks of treatment (−1.79 vs. −0.03 kg/m2). In the treatment group, 20 out of 31 (64.5%) patients lost 5–10% BW and 4 out of 31 (12.9%) patients lost over 10% BW after 24 weeks of treatment. Although there were no significant changes in the patients’ HOMA-IR, the treatment group showed a significant reduction in TG/HDLc (−0.98 vs. −0.19) after 8 weeks of treatment and a significant increase in adiponectin (6.87 vs. −0.43) after 16 weeks of treatment. Discussion/Conclusion: The Hedan tablets significantly improve BW, BMI, TG/HDLc, and adiponectin in patients with MetS. Thus, Hedan tablets may be used as an adjunct to existing MetS management methods.
DOI: 10.6084/m9.figshare.5311027.v2
title: Locus-wise data on the number of alleles (Na), number of effective alleles (Ne), mean observed (Mean Ho) and expected (Mean He) heterozygosities, F statistics, and Hardy-Wienberg Equilibrium (HWE) obtained by analyzing seven populations of Spodoptera exigua.

description: Among four loci (Table 2), Spe09 had the highest number of alleles, whereas Spe06 had the lowest. Average observed and expected heterozygosities ranged from 0.007 to 0.172 and from 0.194 to 0.767, respectively. Locus Spe02 had the highest observed heterozygosity and locus Spe06 had the lowest observed heterozygosity. Loci Spe11 and Spe06 had the highest and lowest expected heterozygosity, respectively. The highest values of F<sub>is</sub> and F<sub>it</sub> were detected in Spe09 and the lowest on Spe02. F<sub>st </sub>values ranged from 0.123 to 0.346, detected in Spe06 and Spe02 loci, respectively. All four loci showed departures from the Hardy-Weinberg equilibrium.
DOI: 10.6084/m9.figshare.25487740.v1
title: Supplementary Material for: Internal Limiting Membrane Peeling and Inverted Flap Technique in Macular Hole: Postoperative Metamorphopsia and Optical Coherence Tomography

description: <b><i>Introduction:</i></b> We compared postoperative metamorphopsia and optical coherence tomography (OCT) findings between eyes that underwent internal limiting membrane (ILM) peeling and the inverted flap (IF) technique for macular hole (MH). <b><i>Methods:</i></b> This retrospective analysis included 64 eyes of 64 patients with idiopathic MH whose MH was closed after initial surgery. Thirty-nine patients were treated with pars plana vitrectomy (PPV) with ILM peeling, and 25 patients were treated with PPV with the IF technique. Best corrected visual acuity (BCVA), severity of metamorphopsia, and OCT images were collected before and 3, 6, and 12 months postoperatively. Based on the OCT images, the status of the external limiting membrane (ELM) and ellipsoid zone and the presence of hyperreflective plugs were assessed. <b><i>Results:</i></b> At baseline and 3, 6, and 12 months postoperatively, BCVA and severity of metamorphopsia were not significantly different between groups. The status of the ELM was significantly worse in the IF group than in the ILM peeling group at 3 and 6 months postoperatively. Significantly more hyperreflective plugs were observed in the IF group than in the ILM peeling group at 3 and 6 months postoperatively. Stepwise multiregression analysis revealed that hyperreflective plugs were significantly associated with the severity of metamorphopsia at 12 months postoperatively. <b><i>Discussion/Conclusion:</i></b> The alterations on the OCT were fewer in the ILM peeling group than in the IF group, while no significant differences were observed in postoperative severity of metamorphopsia between groups. Metamorphopsia was worse in eyes with hyperreflective plugs.
DOI: 10.6084/m9.figshare.12946990.v2
title: Boosting Random Forests to Reduce Bias; One-Step Boosted Forest and Its Variance Estimate

description: In this article, we propose using the principle of boosting to reduce the bias of a random forest prediction in the regression setting. From the original random forest fit, we extract the residuals and then fit another random forest to these residuals. We call the sum of these two random forests a <i>one-step boosted forest</i>. We show with simulated and real data that the one-step boosted forest has a reduced bias compared to the original random forest. The article also provides a variance estimate of the one-step boosted forest by an extension of the infinitesimal Jackknife estimator. Using this variance estimate, we can construct prediction intervals for the boosted forest and we show that they have good coverage probabilities. Combining the bias reduction and the variance estimate, we show that the one-step boosted forest has a significant reduction in predictive mean squared error and thus an improvement in predictive performance. When applied on datasets from the UCI database, one-step boosted forest performs better than random forest and gradient boosting machine algorithms. Theoretically, we can also extend such a boosting process to more than one step and the same principles outlined in this article can be used to find variance estimates for such predictors. Such boosting will reduce bias even further but it risks over-fitting and also increases the computational burden. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21940127.v1
title: Supplementary Material for: Improved Basic Cytogenetics Challenges Holocentricity of Butterfly Chromosomes

description: Mitotic chromosomes of butterflies, which look like dots or short filaments in most published data, are generally considered to lack localised centromeres and thus to be holokinetic. This particularity, observed in a number of other invertebrates, is associated with meiotic particularities known as “inverted meiosis,” in which the first division is equational, i.e., centromere splitting-up and segregation of sister chromatids instead of homologous chromosomes. However, the accurate analysis of butterfly chromosomes is difficult because (1) their size is very small, equivalent to 2 bands of a mammalian metaphase chromosome, and (2) they lack satellite DNA/heterochromatin in putative centromere regions and therefore marked primary constrictions. Our improved conditions for basic chromosome preparations, here applied to 6 butterfly species belonging to families Nymphalidae and Pieridae challenges the holocentricity of their chromosomes: in spite of the absence of primary constrictions, sister chromatids are recurrently held together at definite positions during mitotic metaphase, which makes possible to establish karyotypes composed of acrocentric and submetacentric chromosomes. The total number of chromosomes per karyotype is roughly inversely proportional to that of non-acrocentric chromosomes, which suggests the occurrence of frequent robertsonian-like fusions or fissions during evolution. Furthermore, the behaviour and morphological changes of chromosomes along the various phases of meiosis do not seem to differ much from those of canonical meiosis. In particular, at metaphase II chromosomes clearly have 2 sister chromatids, which refutes that anaphase I was equational. Thus, we propose an alternative mechanism to holocentricity for explaining the large variations in chromosome numbers in butterflies: (1) in the ancestral karyotype, composed of about 62 mostly acrocentric chromosomes, the centromeres, devoid of centromeric heterochromatin/satellite DNA, were located at contact with telomeric heterochromatin; (2) the instability of telomeric heterochromatin largely contributed to drive the multiple rearrangements, principally chromosome fusions, which occurred during butterfly evolution.
DOI: 10.17632/9p8zyvmdy2
title: The relativistic Schrödinger equation through FFTW 3: An extension of quantumfdtd

description: In order to solve the time-independent three-dimensional Schrödinger equation, one can transform the time-dependent Schrödinger equation to imaginary time and use a parallelized iterative method to obtain the full three-dimensional eigen-states and eigen-values on very large lattices. In the case of the non-relativistic Schrödinger equation, there exists a publicly available code called quantumfdtd which implements this algorithm. In this paper, we (a) extend the quantumfdtd code to include the case of the relativistic Schrödinger equation and (b) add two optimized Fast Fourier Transform (FFT) based kinetic energy terms for non-relativistic cases. The new kinetic energy terms (two non-relativistic and one relativistic) are computed using the parallelized FFT-algorithm provided by the FFTW 3 library. The resulting quantumfdtd v3 code, which is publicly released with this paper, is backwards compatible with version 2, supporting explicit finite-differences schemes in addition to the new FFT-based schemes. Finally, we (c) extend the original code so that it supports arbitrary external file-based potentials and the option to project out distinct parity eigen-states from the solutions. Herein, we provide details of the quantumfdtd v3 implementation, comparisons and tests of the three new kinetic energy terms, and code documentation.
DOI: 10.17632/f2vkfd5s8t
title: Slow Tourism

description: Slow tourism experience data
DOI: 10.6084/m9.figshare.28715621.v1
title: ORF_TransDecoder.zip

description: <b>Open reading frame (ORF) predicted by </b><b>TransDecoder (v5.7.1) for 25 grassland plant species. </b><b>Species list:</b>Species_code Species_nameGerPra Geranium pratenseLeuVul Leucanthemum vulgare agg.TriFla Trisetum flavescensLotCor Lotus corniculatusCreBie Crepis biennisBelPer Bellis perennisDauCar Daucus carotaPruVul Prunella vulgarisTriPra Trifolium pratensePriVer Primula verisHolLan Holcus lanatusAloPra Alopecurus pratensisGalMol Galium mollugo agg.KnaArv Knautia arvensisMedVar Medicago x variaPlaLan Plantago lanceolataLuzCam Luzula campestrisVerCha Veronica chamaedrysArrEla Arrhenatherum elatiusTriDub Trifolium dubiumLatPra Lathyrus pratensisVicCra Vicia craccaRanAcr Ranunculus acrisPlaMed Plantago mediaAjuRep Ajuga reptans<br><br><b>Analyse pseudo code:</b>#! /usr/binLongOrf='path/to/TransDecoder-TransDecoder-v5.7.1/TransDecoder.LongOrfs'Predict='path/to/TransDecoder-TransDecoder-v5.7.1/TransDecoder.Predict'<br>for i in {01..25}; do# the number corresponding to a particular speciescd path/to/isoSeqData/BMK230426-BJ202-01P000$i;$LongOrf -t BMK230426-BJ202-01P000$i.flnc.clustered.isoforms.fa;$Predict -t BMK230426-BJ202-01P000$i.flnc.clustered.isoforms.fa;done<br>
DOI: 10.6084/m9.figshare.19579258.v1
title: Data for Bottom-up and top-down pressures mediate competition between two generalist insects

description: The effects of competition can have far reaching consequences for individuals, populations, and communities and therefore we should strive towards a deeper understanding of competitive interactions. In some cases, dietary generalists may be predicted to experience weak competition effects because of their ability to use a wide range of host plants. However, competition between insects frequently occurs indirectly which can hinder insects’ ability to avoid competitive interactions. Therefore, competition may be as strong in dietary generalists as in dietary specialists. Yet competition between insects that are dietary generalists is infrequently studied. We tested for evidence of competitive interactions between two common, temporally separated, generalist insects: the western tent caterpillar (<em>Malacosoma californicum</em>), which feeds early in the season, and the fall webworm (<em>Hyphantria cunea</em>), which feeds later in the season. Both species frequently use a common host plant species (chokecherry) as a preferred host at our field sites. We tested the relative strength of bottom-up effects resulting from competitive interactions between these two generalists with lab rearing trials at the relevant time of year for each insect. We recorded three common fitness measures (development time, pupal mass, and survival) for caterpillars reared on chokecherry with no damage from either of our focal species, with tent caterpillar damage, and with fall webworm damage. To test the strength of top-down pressures on fall webworm larval fitness and any potential interactions with bottom-up effects, we reared larvae in the field either exposed to or protected from predators on host plants that either did or did not have tent caterpillars feeding on them earlier in the season. We found evidence of bottom-up fitness effects on tent caterpillars and top-down and bottom-up fitness effects on fall webworms confirming that tent caterpillars and fall webworms compete indirectly. Tent caterpillars had lower pupal mass when reared on leaves from shrubs damaged by fall webworms. Fall webworms had lower pupal mass and longer development time when reared on leaves from shrubs damaged by tent caterpillars. In field trials, fall webworms reared on shrubs damaged by tent caterpillars had lower survival and pupal mass. We show evidence of indirect competition in temporally separated generalists through leaf quality (bottom-up effects) and natural enemies (top-down effects).
DOI: 10.6084/m9.figshare.24100209.v1
title: LD matrix file

description: ld_1kg_EUR_hm3_shrink.h5 is the LD matrix file for European 1000 Genome data.
DOI: 10.17632/9g6nv2cjgp
title: Supplemental materials for publication: Society of Dermatology Hospitalists supportive care guidelines for the management of Stevens-Johnson syndrome/toxic epidermal necrolysis in adults.

description: eAppendix1: Search terms and strategies eAppendix2: Level of evidence and grade of recommendation calculation eAppendix3: Delphi Process eAppendix4: This is a supplemental document designed to provide visualizations and summary statistics for the responses to each statement that appeared in the survey. There are 135 statements split into 11 topic sections, with each topic section split into the “Recommendations” section as well as the “Uncertain and Inappropriate” classification section. Be mindful that tables correspond to the histogram immediately preceding the table (i.e. a histogram is followed by a table for the statement). eAppendix5: Suggested initial management of acute ocular SJS/TEN based on simple clinical grading system (adapted from Sotozono et al.)
DOI: 10.6084/m9.figshare.20760526.v1
title: Count of Questions Per Year

description: Count of Questions Per Year before and after filtering procedure for Stack Overflow (SO), Information Security (IS) and Software Engineering (SE) sites
DOI: 10.6084/m9.figshare.25592496.v1
title: Supplementary Material for: Association between hypertrophic cardiomyopathy and variations in sarcomere gene and calcium channel gene in adults

description: Introduction: Calcium channel gene variations have been reported to be associated with hypertrophic cardiomyopathy (HCM) in family, but the relationship between calcium channel gene variations and HCM remains undefined in population.
Methods: A total of 719 HCM unrelated patients were initially enrolled. Finally, 371 patients were identified based on inclusion and exclusion criteria, including 145 patients with gene negative, 28 patients with a single rare calcium channel gene variation (calcium gene variation), 162 patients with a single pathogenic/likely pathogenic sarcomere gene variation (sarcomere gene variation) and 36 patients with a single pathogenic/likely pathogenic sarcomere gene variation and a single rare calcium channel gene variation (double gene variations). Then the demographic, electrocardiographic, echocardiographic and follow-up data were collected.
Results: Patients with double gene variations were at an earlier age and had more percent of family history of HCM, and had thicker walls, higher left ventricular outflow tract pressure gradient, more pathological Q waves, and more bundle branch block as compared with those with single sarcomere gene variation. During the follow-up period, patients with double gene variations had more primary endpoints than other three groups (p=0.0013). Multivariate analysis showed that double gene variations was the independent predictor of for primary endpoint events in patients (HR 4.82, 95% CI 1.77 to 13.2; p=0.002).
Conclusion: We found that patients with double gene variations had more severe HCM phenotype and prognosis. The pathogenesis effects of sarcomere gene variation and calcium channel gene variation may be cumulative in HCM populations.
DOI: 10.6084/m9.figshare.7246262.v1
title: Supplementary Material for: The Differentially Expressed Circular RNAs in the Substantia Nigra and Corpus Striatum of Nrf2-Knockout Mice

description: <b><i>Background/Aims:</i></b> The nuclear factor erythroid 2-related factor 2 (Nrf2)-antioxidant response element (ARE) pathway plays a protective role in both acute neuronal damage and chronic neurodegeneration-related oxidative stress. Circular RNAs (circRNAs) are involved with various diseases in the central nervous system (CNS). This study aimed to identify the key circRNAs involved in Nrf2-neuroprotection against oxidative stress. <b><i>Methods:</i></b> The differentially expressed circRNAs (DEcircRNAs) in the substantia nigra and corpus striatum between Nrf2 (-/-) and Nrf2 (+/+) mice were identified by microarray analysis. Quantitative real-time polymerase chain reaction (qRT-PCR) was then used to validate the expression of selected DEcircRNAs in the substantia nigra and corpus striatum between Nrf2 (-/-) and Nrf2 (+/+) mice. Based on our previous microarray analysis of the differentially expressed mRNAs (DEmRNAs) in the substantia nigra and corpus striatum between Nrf2 (-/-) and Nrf2 (+/+) mice, the DEcircRNA-miRNA-DEmRNA interaction network was constructed. Functional annotation of DEmRNAs that shared the same binding miRNAs with DEcircRNAs was performed using gene ontology (GO) and pathway analyses. <b><i>Results:</i></b> A total of 65 and 150 significant DEcircRNAs were obtained in the substantia nigra and corpus striatum of Nrf2 (-/-) mice, respectively, and seventeen shared DEcircRNAs were found in both these two tissues. The qRT-PCR results were generally consistent with the microarray results. The DEcircRNA-miRNA-DEmRNA interaction network and pathway analysis indicated that mmu_circRNA_34132, mmu_circRNA_017077 and mmu-circRNA-015216 might be involved with Nrf2-mediated neuroprotection against oxidative stress. Mmu_circRNA_015216 and mmu_circRNA_017077 might play roles in the Nrf2-related transcriptional misregulation and Nrf2-mediated processes of rheumatoid arthritis, respectively. In addition to these two processes, mmu_circRNA_34132 may be a potential regulator of Nrf2-mediated protection for diabetes mellitus and Nrf2-mediated defence against ROS in hearts. <b><i>Conclusion:</i></b> In conclusion, our study identified the key DEcircRNAs in the substantia nigra and corpus striatum of Nrf2 (-/-) mice, which might provide new clues for further exploring the mechanism of Nrf2-mediated neuroprotection against oxidative stress and other Nrf2-mediated processes.
DOI: 10.6084/m9.figshare.21317979.v1
title: Data and code from "Evolutionary history of host trees amplifies the dilution effect of biodiversity on forest pests"

description: Updated 12/12/23See R script for code to fit model, and recreate figures in the manuscript. All files to create the figures are outputted from the modelling script.<br>Column in the data file include:inci: pest prevalenceevolDistScale: scaled evolutionary distance between pests' hosts and the trees within the plotbio1Scale: scaled temperaturebio12Scale: scaled precipitationnativity: nativity of pestpestKingdom: taxonomic kingdom of pestnoHostScale: scaled host breadthshannonScale: scaled Shannon diversity of plotpropHostScale: scaled proportion of hosts in plot<br>
DOI: 10.17632/c83z4df8ky
title: Deep peat map eastern Sumatra, Indonesia

description: Deep peat map for eastern Sumatra at 100 m spatial resolution as published in Vernimmen et al. 2020 (https://doi.org/10.1186/s13021-020-00139-2) Mapping deep peat carbon stock from a LiDAR based DTM and field measurements, with application to eastern Sumatra
DOI: 10.17632/nb8czb4c6s
title: Paleomagnetic data for the southern limb of the Tuzimaza anticline, northern Kuqa Depression, NW China

description: Paleomagnetic data for the southern limb of the Tuzimaza anticline, northern Kuqa Depression, NW China
DOI: 10.6084/m9.figshare.1314551.v1
title: Helioprop Tables

description: ROOT tables from the Helioprop code to be used for charge dependent modulation.
DOI: 10.6084/m9.figshare.13568234.v1
title: ANN training Data

description: Centerline based representation of CFD-based aortic hemodynamics for clinical and synthetic cases. This data includes centerline coordinates, local radii and local, average values of static pressure, wall shear stress, secondary flow degree and specific kinetic energy.<br>DISCLAIMER: The data/software provided here comes from a publicly funded project and cannot be used for commercial purposes. The terms and conditions of CC BY-NC apply.<br>
DOI: 10.6084/m9.figshare.23708766.v1
title: Dataset #2: Experimental study

description: Project Title: Add title here <br> Project Team: Add contact information for research project team members <br> Summary: Provide a descriptive summary of the nature of your research project and its aims/focal research questions. <br> Relevant publications/outputs: When available, add links to the related publications/outputs from this data. <br> Data availability statement: If your data is not linked on figshare directly, provide links to where it is being hosted here (i.e., Open Science Framework, Github, etc.). If your data is not going to be made publicly available, please provide details here as to the conditions under which interested individuals could gain access to the data and how to go about doing so. <br> Data collection details: 1. When was your data collected? 2. How were your participants sampled/recruited? <br> Sample information: How many and who are your participants? Demographic summaries are helpful additions to this section. <br> Research Project Materials: What materials are necessary to fully reproduce your the contents of your dataset? Include a list of all relevant materials (e.g., surveys, interview questions) with a brief description of what is included in each file that should be uploaded alongside your datasets. <br> List of relevant datafile(s): If your project produces data that cannot be contained in a single file, list the names of each of the files here with a brief description of what parts of your research project each file is related to. <br> Data codebook: What is in each column of your dataset? Provide variable names as they are encoded in your data files, verbatim question associated with each response, response options, details of any post-collection coding that has been done on the raw-response (and whether that's encoded in a separate column). <br> Examples available at: https://www.thearda.com/data-archive?fid=PEWMU17 https://www.thearda.com/data-archive?fid=RELLAND14