cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5124568.v1
title: Supplementary Material for: Single-Variant and Multi-Variant Trend Tests for Genetic Association with Next-Generation Sequencing That Are Robust to Sequencing Error

description: As with any new technology, next-generation sequencing (NGS) has potential advantages and potential challenges. One advantage is the identification of multiple causal variants for disease that might otherwise be missed by SNP-chip technology. One potential challenge is misclassification error (as with any emerging technology) and the issue of power loss due to multiple testing. Here, we develop an extension of the linear trend test for association that incorporates differential misclassification error and may be applied to any number of SNPs. We call the statistic the linear trend test allowing for error, applied to NGS, or <i>LTT</i><sub>ae,NGS</sub>. This statistic allows for differential misclassification. The observed data are phenotypes for unrelated cases and controls, coverage, and the number of putative causal variants for every individual at all SNPs. We simulate data considering multiple factors (disease mode of inheritance, genotype relative risk, causal variant frequency, sequence error rate in cases, sequence error rate in controls, number of loci, and others) and evaluate type I error rate and power for each vector of factor settings. We compare our results with two recently published NGS statistics. Also, we create a fictitious disease model based on downloaded 1000 Genomes data for 5 SNPs and 388 individuals, and apply our statistic to those data. We find that the <i>LTT</i><sub>ae,NGS</sub> maintains the correct type I error rate in all simulations (differential and non-differential error), while the other statistics show large inflation in type I error for lower coverage. Power for all three methods is approximately the same for all three statistics in the presence of non-differential error. Application of our statistic to the 1000 Genomes data suggests that, for the data downloaded, there is a 1.5% sequence misclassification rate over all SNPs. Finally, application of the multi-variant form of <i>LTT</i><sub>ae,NGS</sub> shows high power for a number of simulation settings, although it can have lower power than the corresponding single-variant simulation results, most probably due to our specification of multi-variant SNP correlation values. In conclusion, our <i>LTT</i><sub>ae,NGS</sub> addresses two key challenges with NGS disease studies; first, it allows for differential misclassification when computing the statistic; and second, it addresses the multiple-testing issue in that there is a multi-variant form of the statistic that has only one degree of freedom, and provides a single p value, no matter how many loci.
DOI: 10.6084/m9.figshare.5297758.v1
title: Bird Use of Organic Apple Orchards in Colorado

description: We examined bird use of organic apple orchards as well as how birds influence fruit production positively through control of an economically important insect pest (codling moth (<i>Cydia pomonella</i>)) and negatively through fruit damage. We conducted transect surveys, observed bird frugivory and assessed bird and insect damage with an exclosure experiment. We found that organic apple orchards in our study region provide habitat for a large number of both human-adapted and human-sensitive species and that the species in orchards were relatively similar to adjacent hedgerow habitats. Habitat use did not vary as a function of orchard characteristics, and apple damage by both birds and <i>C. pomonella</i> was consistent within and across apple blocks that varied in size. A small subset of bird species was observed foraging on apples yet the effect of birds as agents of fruit damage appeared rather minor and birds did not reduce <i>C. pomonella</i> damage.
DOI: 10.17632/bmsz34n3dk
title: Illicit Pills

description: The elements of this dataset correspond to segmentation masks of a subset of images from a large dataset available in https://www.ecstasydata.org/. The Illicit Pills dataset comprises 117 elements distributed in 5 classes which represent illicit amphetamine type stimulants (ATS) pills with distinct shapes.
DOI: 10.6084/m9.figshare.24116592.v1
title: All cycling and rate performance datasets

description: Data in CSV format contains the following properties: Doi,Year,Name,Abbreviation,Sintering temperature,Sintering time,Category,Cycle,Capacity,Retention,Current: mAg-1,Current: C,Voltage lower limit,Voltage upper limit,Elements.
DOI: 10.6084/m9.figshare.25102919.v1
title: Supplementary Material for: BANP Participates in the Chronic Intermittent Hypoxia-Induced Senescence of Vascular Endothelial Cells by Promoting P53 Phosphorylation and Nuclear Retention

description: <b><i>Introduction:</i></b> The objective of this study was to examine the potential induction of senescence in vascular endothelial cells (VECs) by chronic intermittent hypoxia (CIH), a defining characteristic of obstructive sleep apnea (OSA). This investigation seeks to elucidate the underlying mechanisms that contribute to the development of cardiovascular diseases in patients with OSA, with a particular focus on CIH-induced vascular aging. <b><i>Methods:</i></b> The BioSpherix-OxyCycler system was used to establish models of CIH in both rats and human umbilical vein endothelial cells (HUVECs). To assess VECs’ senescence, various methods were employed including EdU incorporation assay, cell cycle analysis, senescence-associated β-galactosidase (SA-β-gal) staining, and senescence protein testing. Vascular aging was evaluated through measurements of carotid-femoral pulse wave velocity, intima-media thickness, and Ki67 immunohistochemical staining. In order to identify the molecular mechanisms associated with CIH-induced senescence in VECs, a bioinformatics study was conducted utilizing the Gene Expression Omnibus database. <b><i>Results:</i></b> Under conditions of CIH, HUVECs exhibited inhibited proliferation, arrested cell cycle, increased activity of SA-β-gal, and elevated expression levels of p53 and p21 compared to HUVECs under normoxic conditions. Similarly, rats exposed to CIH displayed increased carotid-femoral pulse wave velocity, intima-media thickness, vascular permeability, and SA-β-gal activity in VECs, along with decreased expression of arterial Ki67. BTG3-associated protein (BANP) was found to be highly expressed in CIH-induced VECs. Furthermore, the overexpression of BANP resulted in the senescence of VECs, along with elevated levels of p53 phosphorylation and nuclear localization. <b><i>Conclusions:</i></b> These findings demonstrate that CIH can induce VECs senescence and contribute to vascular aging. Additionally, BANP can induce VECs senescence by promoting p53 phosphorylation and nuclear retention. These discoveries offer novel insights into the increased cardiovascular risk associated with OSA, thereby presenting new possibilities for therapeutic intervention.
DOI: 10.6084/m9.figshare.682404.v1
title: Perioperative Smoking Cessation RCT (2013)

description: This is the supplemental data for the article published in <em>Anesthesia & Analgesia</em> in 2013 (citation pending).
DOI: 10.6084/m9.figshare.8281460.v1
title: Sholl analysis 8209 CIC

description: Sholl analysis 2019 paper
DOI: 10.17632/fvhwgwvfxc
title: Supplementary data set regarding development of a hyperspectral imaging technique using LA-ICP-MS to determine the spatial distribution of nutrients in soil cores

description: This supplementary raw data set belongs to the article entitled "Data set showing the development of a hyperspectral imaging technique using LA-ICP-MS to determine the spatial distribution of nutrients in soil cores" in Data in Brief journal. This data set can be used to reproduce images cited in the manuscript.
DOI: 10.6084/m9.figshare.16895959.v3
title: Dataset; Pleistocene Archaeological Sites of West Africa. Cerasoni et al. 2021

description: S1 - Dataset of archaeological sites.S2 - Script for paleoclimate reconstruction.<br>Both supplementary files are intended as supporting material for the study titled "Archaeological sites and palaeoenvironments of Pleistocene West Africa” for the the special issue “PaleoMaps: representations of Quaternary paleoenvironments, human–environment interaction and human dispersal” [eds. F. Henselowsky, C. Willmes, and M. Smith] on Journal of Maps.<br>
DOI: 10.6084/m9.figshare.28333805.v1
title: <b>Structured Interview for CKC Program Evaluation: Educators' Feedback and Experience</b>

description: We are interested in understanding the junior educators experience with the Consuming Knowledge Consciously (CKC) program and its impact on their teaching.
DOI: 10.6084/m9.figshare.28728617.v3
title: Example Data

description: Single-cell technologies have transformed our understanding of cellular heterogeneity through multimodal data acquisition. However, robust cell alignment remains a major challenge for data integration and harmonization, including batch correction, label transfer, and multiomics integration. Many existing methods constrain alignment based on rigid feature-wise distance metrics, limiting their ability to capture accurate cell correspondence across diverse cell populations and conditions. We introduce scGALA, a graph-based learning framework that redefines cell alignment by combining graph attention networks with a score-driven, task-independent optimization strategy. scGALA constructs enriched graphs of cell–cell relationships by integrating gene expression profiles with auxiliary information such as spatial coordinates and iteratively refines alignment via self-supervised graph link prediction, where a deep neural network is trained to identify and reinforce high-confidence correspondences across datasets. In extensive benchmarks, scGALA identifies over 25 percent more high-confidence alignments without compromising accuracy. By improving the core step of cell alignment, scGALA serves as a versatile enhancer for a wide range of single-cell data integration tasks.
DOI: 10.6084/m9.figshare.24021627.v1
title: Costa et al_Supplementary Information

description: Supplementary Information: Lagenocarpus rigidus (Cyperaceae) may facilitate the establishment of Catasetum gardneri (Orchidaceae) in restinga areas of Northeastern Brazil, in <b>Brazilian Journal of Botany</b>
DOI: 10.6084/m9.figshare.10284110.v1
title: Can a unique appearance of e-bikes, coupled with information on their characteristics, influence drivers’ gap acceptance?

description: <b>Objective:</b> Car drivers tend to underestimate the speed of e-bikes and accept smaller gaps for crossing in front of them compared to conventional bicycles. As an explanation, it has been suggested that car drivers rely on their previous experience with conventional bicycles, which tells them that those mostly travel at low speeds. E-bikes, which look just like regular bicycles, do not conform to this expectation, resulting in potentially dangerous interactions. Based on this assumption, researchers have suggested to increase other road users’ awareness of e-bikes’ higher speeds by giving them a distinct appearance. The goal of our experiment was to investigate the effects of such a unique appearance, aided by clear instructions about the higher speeds of e-bikes, on gap acceptance. <b>Method:</b> In order to investigate the effect of appearance independent of the effect of bicycle type, we used video sequences of conventional bicycles and e-bikes approaching at different levels of speed. The riders (regardless of what type of bike they were actually riding) either wore an orange helmet as an indicator for an e-bike, or a gray helmet indicating a conventional bicycle. Fifty participants were asked to indicate the smallest acceptable gap for a left turn in front of the cyclist or e-bike rider. <b>Results:</b> The results showed significantly smaller acceptable gaps when confronted with the gray helmet (signal for bicycle) compared to the orange helmet (signal for e-bike), whereas there was no difference between the actual bicycle types. <b>Conclusions:</b> Overall, the results indicate that informing about e-bikes characteristics in combination with a unique appearance can lead to a more cautious behavior among car drivers.
DOI: 10.6084/m9.figshare.13378946.v4
title: Warming causes differential seedling mortalities in tropical tree species

description: Amplicon sequencing data of soil fungi for the warming effect on plant-soil feedback in a tropical montane rain forest.
DOI: 10.6084/m9.figshare.9742463.v1
title: Supplementary Material for: Therapeutic Drug Monitoring to Guide Clinical Decision Making in Inflammatory Bowel Disease Patients with Loss of Response to Anti-TNF: A Delphi Technique-Based Consensus

description: <b><i>Background:</i></b> Loss of response is frequently encountered in patients with inflammatory bowel disease (IBD) treated with antitumor necrosis factor (TNF) agents. Therapeutic drug monitoring (TDM) and antidrug antibody measurement are increasingly used in this setting. <b><i>Methods:</i></b> To establish a consensus on the use of TDM in the context of loss of response to anti-TNFs, we performed a vote using a Delphi-style process followed by an expert panel discussion among 8 IBD specialists practicing in Switzerland, Europe. Statements were rated on an even Likert-scale ranging from 1 (strong disagreement) to 4 (strong agreement), based on expert opinion and the available literature. <b><i>Results:</i></b> The experts agreed on the following statements: (i) loss of response is associated with inadequate drug levels in both Crohn’s disease and ulcerative colitis; (ii) best timepoint for measuring drug levels is prior to the next application (= trough levels) with different thresholds for anti-TNF agents (infliximab 5 μg/mL, adalimumab 8 μg/mL, certolizumab pegol 10 μg/mL); (iii) antidrug antibodies are predictive for loss of response; and (iv) antidrug-antibody titers and drug trough levels are key determinants in the treatment algorithm. Data about non-anti-TNF biologics were considered too limited to propose recommendations. <b><i>Conclusion:</i></b> A Delphi-style consensus among 8 IBD experts shows that TDM and measurement of antidrug-antibody titers are useful in the context of loss of response to anti-TNF. Optimal cutoff levels depend on the type of anti-TNF. These values are critical in the decision making process. More studies are needed to address the value of such measurements for non-anti-TNF biologics.
DOI: 10.6084/m9.figshare.28789004.v1
title: <b>Frailty, Nutrition, and Quality of Life in Urban-Dwelling Older Adults Facing Vulnerability: Observational Study in Primary Heath Care</b>

description: Objective: To analyze the association between vulnerability, nutritional aspects, frailty, and quality of life (QoL) in older adults receiving care from Primary Health Care (PHC) services in an urban area. Methods: This was a cross-sectional study conducted with community-dwelling older adults. The following instruments were used to assess the variables of interest: the Vulnerable Elders Survey (VES-13), Mini Nutritional Assessment (MNA), Edmonton Frailty Scale (EFS), and the Medical Outcomes Study Short Form-36 (SF-36). Statistical procedures included association analyses, Spearman’s correlation, and binary logistic regression to identify predictors of the outcome. Results: A total of 323 individuals participated in the study, of whom 148 (45.8%) were classified as vulnerable according to the VES-13. Vulnerability showed a moderate negative correlation with nutritional status (r = -0.38; p &lt; 0.001). Frailty (EFS) and quality of life (SF-36) showed strong correlations, especially in domains related to physical and functional aspects (r &gt; 0.49; p &lt; 0.050). Binary logistic regression revealed frailty (EFS) as the main predictor of vulnerability (R² = 0.20; p &lt; 0.001; OR = 1.35 [95% CI: 1.24–1.48]), with functional independence (R² = 0.25; p &lt; 0.001; OR = 3.96 [95% CI: 2.74–5.73]) and functional performance (R² = 0.17; p &lt; 0.001; OR = 3.21 [95% CI: 2.21–4.67]) being the domains that most strongly increased the odds of vulnerability.Conclusion: There was a significant association between vulnerability, nutritional status, frailty, and quality of life. More refined analyses highlighted frailty, particularly in its functional domains, as a key predictor of vulnerability among older adults.
DOI: 10.6084/m9.figshare.24995351.v1
title: MKT DATASET COLLECTED FOR PHD PROGRAM

description: This data set has six files. five files for data and one file for supplementary materials. Data files are in Excel format and are accessible for free
DOI: 10.6084/m9.figshare.25013786.v1
title: ISX 220928 Run files

description: Peripheral human neutrophils were isolated as above and pretreated with 50 μg/mL of purified human THP, sialic acid (500 ng/mL, catalog no. A0812, Sigma Aldrich), or mock-treated, and incubated at 37°C in 5% CO2 for 30 min, and then incubated for an additional 2.5 h with PMA (25 nM). The following antibodies (0.5 μg/mL) and dyes (concentrations provided below) were added: Anti-MPO-FITC (clone M1/70, catalog no. 553310; BD Biosciences), Fc Block, Live/Dead Near IR (1:200 of stock, catalog no. L34975; Thermo Fisher Scientific), Sytox orange (100 nM, catalog no. S34861; Thermo Fisher Scientific), and Hoechst 33342 (200 nM, catalog no. 62249; Thermo Fisher Scientific). After a 30-minute incubation on ice, samples were washed 1X, resuspended in a 1:1 mixture of fresh FACS buffer and PBS. Cell morphology via imaging flow cytometry was assessed as described previously (PMID: 30985081). An Amnis ImageStream X Mark II imaging flow cytometer was used for data acquisition with a 60X objective, low flow rate and high sensitivity, and 405, 488, 561 and 635 nm lasers set to 120, 150, 100 and 150 mW respectively. Data were analyzed using the IDEAS version 6.3 software package. Clipped images were retained due to the large size of NETs, and single stained controls were used for compensation. Masking was performed using the default “object (tight)” and “morphology” algorithms as described (PMID: 30985081). Statistics reports were generated using IDEAS and processed IDEAS data analysis files (.daf) were then analyzed in FCS Express 7 to generate analysis plots.
DOI: 10.6084/m9.figshare.20468796.v2
title: ContractsSourceCode

description: The source coide of 26,799 contracts actually deployed on the Ethereum platform,
DOI: 10.6084/m9.figshare.c.3636602_d1.v1
title: Additional file 2: of An empirical study of race times in recreational endurance runners

description: Master Data Predicting Races Times Final. (XLSX 377Â kb)
DOI: 10.6084/m9.figshare.22153901.v1
title: colorimetric parameter and visual evaluation of red samples

description: colorimetric parameter and visual evaluation of red samples in acceptable tolerance
DOI: 10.6084/m9.figshare.28182365.v1
title: Supplementary files: Factors associated with mental health disorders undergraduate students: A meta-analysis

description: Supplementary files:Raw dataFunnel PlotQuality assessment
DOI: 10.6084/m9.figshare.1488540.v1
title: Indirect interactions in terrestrial plant communities: emerging patterns and research gaps Dataset

description: This is the dataset from: Sotomayor DA and Lortie CJ. 2015. Indirect interactions in terrestrial plant communities: emerging patterns and research gaps. Ecosphere 6(6): art103. http://dx.doi.org/10.1890/ES14-00117.1<br>Methods<br>This dataset corresponds to a systematic review on inidirect interactions in terrestrial plant communities which captured the literature published between 1990 and July 2014 using the ISI Web of Science (WoS), Scopus, and Google Scholar. The following keywords were used: "indirect", "plant", "interaction", "competition", "facilitation". The first three words were used together in combination with the last two words in separate queries (i.e. indirect* plant* interaction* competition OR indirect* plant* interaction* facilitation).<br>The initial serach yielded 490 research articles obtained from the WoS, which were screened in order to assess their relevance. Searches in both Scopus and Google Scholar were conducted to complement the WoS search. The following inclusion criteria were used: (1) studies explicitly dealing with indirect interactions in terrestrial ecosystems (i.e. 3 or more species reported in the interaction); (2) studies describing the results of experiments specifically designed to test effects of indirect interactions versus proposals of indirect interactions in discussion; and (3) primary empirical research reported (i.e., not reviews). Papers complying with these criteria were processed to extract data on (1) type of interaction tested; (2) number of species tested as targets, where target is defined as the species on which measurements of performance were taken; (3) role of the species involved in the interaction considering not only target species, but also species that were removed or mentioned by the authors as members of the interaction; (4) type of experiment and number of field sites; (5) type of ecosystem and geographical location of the study; and (6) type of measurements and statistical analysis performed.
DOI: 10.6084/m9.figshare.5122648.v1
title: Supplementary Material for: EX-HOM (EXome HOMozygosity): A Proof of Principle

description: <i>Objective:</i> We provide the proof of principle that exome sequencing of only two affected siblings born to first-cousin parents is capable of directly identifying a single candidate gene for an autosomal recessive disorder. This strategy, which we call EX-HOM (EXome HOMozygosity), combines in a single step the capacity of exome sequencing to identify all the coding variants present in a genome with the property of homozygosity mapping to limit the search for candidate genes to specific chromosomal regions. <i>Methods:</i> We sequenced the exomes of two siblings born to first-cousin parents affected with dysmyelinating leukodystrophy and spastic paraparesis caused by a mutation in <i>FA2H</i>. We used exome sequencing data to identify homozygous regions shared by the two affected siblings (EX-HOM regions), compared them with the regions of maximum LOD score obtained with SNP genotyping, and selected the candidate variants within. <i>Results:</i> We identified regions of shared homozygosity (&gt;1 Mb) accounting for about 290 Mb, containing only 3 candidate variants. Among these, the <i>FA2H</i> mutation remained the only plausible one. <i>Conclusion:</i> In single consanguineous pedigrees with a few affected sibs, EX-HOM can be a one-step approach to identify the candidate genetic defect, bypassing obstacles such as genetic heterogeneity and the need for large pedigrees.
DOI: 10.17632/ct47f5gbnc
title: Suppl.Table 1:

description: Mean GAS scores before and after intervention, data expressed as mean ± standard deviation and number (%). Significance is considered when p&lt;0.05 *ITT protocol with Last observation Carried Forward (LOCF)
DOI: 10.6084/m9.figshare.11877615.v2
title: Changing pollinator communities along a disturbance gradient in the Sundarbans mangrove forest: a case study on Acanthus ilicifolius and Avicennia officinalis

description: Data and supplementary materials accompanying the following paper:Akter, A., Biella, P., Batáry, P., & Klečka, J. (2020). Changing pollinator communities along a disturbance gradient in the Sundarbans mangrove forest: a case study on <i>Acanthus ilicifolius</i> and <i>Avicennia officinalis</i>. <i>Global Ecology and Conservation</i>, 24, e01282.DOI: https://doi.org/10.1016/j.gecco.2020.e01282<br>
DOI: 10.6084/m9.figshare.3113467.v4
title: Antioxidant enzyme responses induced by whiteflies in tobacco plants in defense against aphids: Catalase may play a dominant role

description: Antioxidant enzyme responses induced by whiteflies in tobacco plants in defense against aphids: Catalase may play a dominant role