cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24171816
title: <b>Identification of key genes related to oxidative stress in Type 2 Diabetes Mellitus and prediction of potential traditional Chinese medicine based on comprehensive bioinformatics analysis</b>

description: <b>Background:</b><b> </b>The oxidative stress (OS) process can significantly impact diabetes, especially type 2 diabetes mellitus (T2DM). This study aimed to identify OS-related genes which may play important roles in T2DM and to screen for traditional Chinese medicine (TCM) that could be applied.<b>Methods:</b><b> </b>The GSE23343 data set was downloaded from the Gene Expression Omnibus (GEO) database and differentially expressed genes (DEGs) were identified between healthy and T2DM patients. Then, weighted gene co-expression network analysis (WGCNA) was applied. The modules which showed high correlation with clinical traits were selected and the core genes in the modules were identified. OS-related genes were obtained from searching the GeneCards database. The overlapping set of DEGs, WGCNA modular genes, and OS-related genes yielded hub genes in OS-related T2DM. These genes were examined in GSE15653 dataset. Potential TCMs were found by mapping the hub genes with the Coremine Medical database.<b>Results:</b><b> </b>A total of 394 DEGs (136 up-regulated and 258 down-regulated DEGs.) were identified in the GSE23343 cohort. WGCNA results showed that the turquoise module (cor=–0.56, P=0.02) and the brown module (cor=0.66, P=0.004) were the most negatively and positively correlated with T2DM, respectively, and 1016 key keys were identified from the two key modules. We identified three up-regulated hub genes (IL33, S100A8, GOLM1) and three down-regulated hub genes (SNRNP70, HGFAC, GOLM1), which performed well in distinguishing T2DM from healthy samples (AUC&gt;0.8). In addition, six plants used in TCM are predicted to affect expression of these genes.<b>Conclusion:</b><b> </b>IL33, S100A8, GOLM1, SNRNP70, HGFAC, and OSGIN1 are key biomarker genes in OS-related T2DM. TCMs could supplement current therapies by affecting expressions of these genes.
DOI: 10.6084/m9.figshare.16305444.v1
title: Additional file 7 of DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A2 in human vulnerable atherosclerotic plaque

description: Additional file 7. Genes list of hypomethylated in SYM vs. ASYM plaques and upregulated in rupture vs. stable (GSE41571) and early vs. advanced (GSE28829) plaques
DOI: 10.6084/m9.figshare.7392551.v1
title: A Best Evidence Medical Education (BEME) systematic review of: What works best for health professions students using mobile (hand-held) devices for educational support on clinical placements? BEME Guide No. 52

description: <b>Background:</b> Ingrained assumptions about clinical placements (clerkships) for health professions students pursuing primary basic qualifications might undermine best educational use of mobile devices. <b>Question:</b> What works best for health professions students using mobile (hand-held) devices for educational support on clinical placements? <b>Methods:</b> A Best Evidence Medical Education (BEME) effectiveness-review of “justification” complemented by “clarification” and “description” research searched: <i>MEDLINE, Educational Resource Information Center, Web of Science, Cumulative Index to Nursing and Allied Health Literature, PsycInfo, Cochrane Central, Scopus</i> (1988–2016). Reviewer-pairs screened titles/abstracts. One pair coded, extracted, and synthesized evidence, working within the pragmatism paradigm. <b>Summary of results:</b> From screening 2279 abstracts, 49 articles met inclusion-criteria, counting four systematic reviews for context. The 45 articles of at least Kirkpatrick K2 primary research mostly contributed K3 (39/45, 86.7%), mixed methods (21/45, 46.7%), and S3-strength (just over one-half) evidence. Mobile devices particularly supported student: assessment; communication; clinical decision-making; logbook/notetaking; and accessing information (in about two-thirds). Informal and hidden curricula included: <i>concerns about:</i> disapproval; confidentiality and privacy; security;—<i>distraction by</i> social connectivity and busy clinical settings; and <i>mixed messages about</i> policy. <b>Discussion and conclusion:</b> This idiosyncratic evidence-base of modest robustness suggested that mobile devices provide potentially powerful educational support on clinical placement, particularly with student transitions, metalearning, and care contribution. Explicit policy must tackle informal and hidden curricula though, addressing concerns about transgressions.
DOI: 10.6084/m9.figshare.16305438
title: Additional file 5 of DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A2 in human vulnerable atherosclerotic plaque

description: Additional file 5. GO analysis of the genes differentially hypermethylated in SYM and ASYM plaques
DOI: 10.6084/m9.figshare.21546733.v1
title: Additional file 4 of Downregulation of zinc finger protein 71 in laryngeal squamous cell carcinoma tissues and its potential molecular mechanism and clinical significance: a study based on immunohistochemistry staining and data mining

description: Additional file 4: Table S4. Gene list of positively and differentially co-expressed genes of ZNF71.
DOI: 10.6084/m9.figshare.16305438.v1
title: Additional file 5 of DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A2 in human vulnerable atherosclerotic plaque

description: Additional file 5. GO analysis of the genes differentially hypermethylated in SYM and ASYM plaques
DOI: 10.6084/m9.figshare.16305447
title: Additional file 8 of DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A2 in human vulnerable atherosclerotic plaque

description: Additional file 8. GO analysis of the genes hypomethylated in SYM vs. ASYM plaques and upregulated in rupture vs. stable (GSE41571) and early vs. advanced (GSE28829) plaques
DOI: 10.6084/m9.figshare.16305420
title: Additional file 11 of DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A2 in human vulnerable atherosclerotic plaque

description: Additional file 11. Distribution of SYM plaques, ASYM plaques, and LIMAs between Human Infinium Methylation 450K and MethylationEPIC BeadChip
DOI: 10.6084/m9.figshare.16305444
title: Additional file 7 of DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A2 in human vulnerable atherosclerotic plaque

description: Additional file 7. Genes list of hypomethylated in SYM vs. ASYM plaques and upregulated in rupture vs. stable (GSE41571) and early vs. advanced (GSE28829) plaques
DOI: 10.6084/m9.figshare.16305447.v1
title: Additional file 8 of DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A2 in human vulnerable atherosclerotic plaque

description: Additional file 8. GO analysis of the genes hypomethylated in SYM vs. ASYM plaques and upregulated in rupture vs. stable (GSE41571) and early vs. advanced (GSE28829) plaques
DOI: 10.6084/m9.figshare.19451227
title: Additional file 1 of Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome

description: Additional file 1: Supplemental Table S2. list of enzymes that significantly associated with enterolactone concentration.
DOI: 10.6084/m9.figshare.25140821
title: Raw data for application examples in CyDotian software manuscript

description: This document mainly includes coding sequences of PME-domain and pro-region of Type-1 PME in representative plants, raw data from fusion gene analysis by LIR inference, raw data from repeat sequence studies within four Cruciferae representative species and graphical abstract.
DOI: 10.6084/m9.figshare.25140821.v1
title: Raw data for application examples in CyDotian software manuscript

description: This document mainly includes coding sequences of PME-domain and pro-region of Type-1 PME in representative plants, raw data from fusion gene analysis by LIR inference, raw data from repeat sequence studies within four Cruciferae representative species and graphical abstract.
DOI: 10.4121/d629b478-b9ce-49ff-b0b2-12e1cc56bfdd.v2
title: 20211106 20211108 Storm deployment - Nearshore - RealDune/REFLEX

description: Nearshore field measurements of the November storm deployment of the RealDune/REFLEX experiments at the Dutch coast in Autumn/Winter 2021/2022. This dataset is part of the data collection 'Nearshore coastal measurements of calm, moderate, and storm conditions at two artifical dunes along the Dutch Coast during the RealDune/REFLEX experiments'.
DOI: 10.6084/m9.figshare.16305505
title: Additional file 4 of Discovery of metabolic biomarkers for gestational diabetes mellitus in a Chinese population

description: Additional file 4. Table S1: List of DEMs in the second trimester group.
DOI: 10.6084/m9.figshare.16305508
title: Additional file 5 of Discovery of metabolic biomarkers for gestational diabetes mellitus in a Chinese population

description: Additional file 5. Table S2: List of DEMs in the third trimester group.
DOI: 10.6084/m9.figshare.23647623
title: Supplementary Materials for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification

description: Title: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification
<br>
Author list: Xudong Yang, Xu Zhang, Tiantian Xue, Xiaoxia Zhang, Fusheng Yang, Jianghong Yu, Steven B. Janssens, Shengxiang Yu (yushengxiang@ibcas.ac.cn)
<br>
Four_traits_states.csv: States summary of four traits.
<br>
Species_distribution_points_to_extract_climate_data.csv: The longitude and latitude data obtained for each species were used to extract corresponding climate variables.
<br>
R_Hydrangeeae_biogeography.zip: The main R language codes involved in this study.
<br>
MCC.tre: Timetree of Hydrangeeae
DOI: 10.6084/m9.figshare.16305487.v1
title: Additional file 10 of Discovery of metabolic biomarkers for gestational diabetes mellitus in a Chinese population

description: Additional file 10. Table S7: Candidate metabolite biomarkers in the second- and third-trimester groups.
DOI: 10.6084/m9.figshare.16305487
title: Additional file 10 of Discovery of metabolic biomarkers for gestational diabetes mellitus in a Chinese population

description: Additional file 10. Table S7: Candidate metabolite biomarkers in the second- and third-trimester groups.
DOI: 10.6084/m9.figshare.16305508.v1
title: Additional file 5 of Discovery of metabolic biomarkers for gestational diabetes mellitus in a Chinese population

description: Additional file 5. Table S2: List of DEMs in the third trimester group.
DOI: 10.6084/m9.figshare.3558675
title: Data Paper. Data Paper

description: File List Climate_data.txt (MD5: 2177e250ad42ca1c88c283d1f20c7265) Population_dynamics_data.txt (MD5: f392760fde47de38f641648dcd8ffe76) Georeference_location_data.kmz (MD5: 0e74aff74928cdc4558da7758e8bc7c3) Description Long-term data sets of population dynamics of plants are scarce, yet provide valuable information for addressing critical ecological and evolutionary questions. Such data can be used to determine how climate change affects demographic viability and evolutionary stable demographic strategies. Here we provide a long-term data set with longitudinal (1997–2012) individual records for 3835 plants of the chamaephyte <i>Cryptantha flava</i> L. (A. Nelson) Payson (Boraginaceae) near Redfleet State Park in Uintah County, Utah, USA (40° 35' 42.63" N, 109°25' 55.92" W, 1790 m a.s.l.). We used permanent plots to track the individual responses (survival, changes in size, reproduction, and recruitment) to artificial manipulations of precipitation via rainout shelters in 1998 and 1999 in subsets of those plots. These data provide unique opportunities to examine the effect of ambient climatic variation and interpret longer-term climate change effects on native plant species’ population dynamics in interaction with the surrounding plant communities. We provide the following data and data formats: (1) monthly background precipitation and temperature at the closest permanent weather station, (2) individual-level population dynamics from 1997 to 2012 with point location (<i>x, y</i> coordinates) of the individuals of <i>C. flava</i> within the permanent plots as well as microhabitat conditions, and (3) geo-referenced location of each permanent plot. <i>Key words</i><i>: </i><i> climate change; Colorado Plateau desert; </i>Cryptantha flava;<i> long-term demography; plant population dynamics; rainout shelter.</i>
DOI: 10.6084/m9.figshare.3558672
title: Appendix A. Detailed concentration information of added nutrients in batch and life table experiments.

description: Detailed concentration information of added nutrients in batch and life table experiments.
DOI: 10.6084/m9.figshare.3558672.v1
title: Appendix A. Detailed concentration information of added nutrients in batch and life table experiments.

description: Detailed concentration information of added nutrients in batch and life table experiments.
DOI: 10.6084/m9.figshare.3558669
title: Appendix B. Fatty acid and sterol profiles of terrestrial particulate organic carbon (t-POC), bacteria, and phytoplankton diets.

description: Fatty acid and sterol profiles of terrestrial particulate organic carbon (t-POC), bacteria, and phytoplankton diets.
DOI: 10.6084/m9.figshare.3558669.v1
title: Appendix B. Fatty acid and sterol profiles of terrestrial particulate organic carbon (t-POC), bacteria, and phytoplankton diets.

description: Fatty acid and sterol profiles of terrestrial particulate organic carbon (t-POC), bacteria, and phytoplankton diets.
DOI: 10.6084/m9.figshare.3558666
title: Appendix C. Results of Cox regression survival analysis of experiments.

description: Results of Cox regression survival analysis of experiments.
DOI: 10.6084/m9.figshare.3558666.v1
title: Appendix C. Results of Cox regression survival analysis of experiments.

description: Results of Cox regression survival analysis of experiments.
DOI: 10.6084/m9.figshare.3558663
title: Appendix D. Correlations between different nutrients of diets and offspring and body size of Daphnia.

description: Correlations between different nutrients of diets and offspring and body size of Daphnia.
DOI: 10.6084/m9.figshare.3558663.v1
title: Appendix D. Correlations between different nutrients of diets and offspring and body size of Daphnia.

description: Correlations between different nutrients of diets and offspring and body size of Daphnia.
DOI: 10.6084/m9.figshare.3558660
title: Appendix E. Principal component analysis of diets and Daphnia.

description: Principal component analysis of diets and Daphnia.
DOI: 10.6084/m9.figshare.3558660.v1
title: Appendix E. Principal component analysis of diets and Daphnia.

description: Principal component analysis of diets and Daphnia.
DOI: 10.6084/m9.figshare.3558657
title: Appendix F. The parameter estimates of t-POC diets for power functions.

description: The parameter estimates of t-POC diets for power functions.
DOI: 10.6084/m9.figshare.3558657.v1
title: Appendix F. The parameter estimates of t-POC diets for power functions.

description: The parameter estimates of t-POC diets for power functions.
DOI: 10.6084/m9.figshare.3558654
title: Appendix A. Additional information of the fish assemblages of the studied reservoirs.

description: Additional information of the fish assemblages of the studied reservoirs.
DOI: 10.6084/m9.figshare.3558651
title: Appendix A. Temporal and spatial variation in air temperature within the study region.

description: Temporal and spatial variation in air temperature within the study region.
DOI: 10.6084/m9.figshare.3558648
title: Appendix B. Netting effort and growth data for principal fish species.

description: Netting effort and growth data for principal fish species.
DOI: 10.6084/m9.figshare.3558645
title: Appendix C. Density and isotopic values of sampled invertebrate taxa.

description: Density and isotopic values of sampled invertebrate taxa.
DOI: 10.6084/m9.figshare.3558642
title: Appendix D. Stomach contents of LSR whitefish, perch, and DR whitefish.

description: Stomach contents of LSR whitefish, perch, and DR whitefish.
DOI: 10.6084/m9.figshare.3558639
title: Appendix E. Stable-isotope mixing model values of LSR whitefish, perch, and DR whitefish.

description: Stable-isotope mixing model values of LSR whitefish, perch, and DR whitefish.
DOI: 10.6084/m9.figshare.3558639.v1
title: Appendix E. Stable-isotope mixing model values of LSR whitefish, perch, and DR whitefish.

description: Stable-isotope mixing model values of LSR whitefish, perch, and DR whitefish.
DOI: 10.6084/m9.figshare.3558636
title: Appendix A. Mass–length regressions used to estimate body mass from the estimated body length of preserved soil organisms.

description: Mass–length regressions used to estimate body mass from the estimated body length of preserved soil organisms.
DOI: 10.6084/m9.figshare.3558633
title: Appendix A. Overview of the results for linear models to explain maximum dispersal distances using different combinations of plant traits, and histograms of maximum dispersal distance data for different dispersal syndromes and growth forms.

description: Overview of the results for linear models to explain maximum dispersal distances using different combinations of plant traits, and histograms of maximum dispersal distance data for different dispersal syndromes and growth forms.
DOI: 10.6084/m9.figshare.3558630
title: Appendix B. Overview of the predictive power of models with random and fixed effects included in the models.

description: Overview of the predictive power of models with random and fixed effects included in the models.
DOI: 10.6084/m9.figshare.3558624
title: Supplement 2. Function dispeRsal for predicting seed dispersal distances in R, and instructions for using dispeRsal.

description: File List dispeRsal.rda (MD5: 3589cb5b047c9a44e83fd624dabbacad) instructions.pdf (MD5: b5114a42cb9a0e1856e3fa87a3f8db89) Description dispeRsal.rda – includes the function dispeRsal to predict maximum seed dispersal distances from simple plant traits in software R (R Development Core Team 2012) as well as a dataframe used for the predictive models, an example dataframe, a dataframe for assigning taxonomic families to orders and modified versions of the TPLck and TPL functions from the Taxonstand (Cayuela et al. 2012) package for handling synonymies in the data provided by the user. Full details and instructions for using dispeRsal can be found in the instructions file. instructions.pdf – detailed instructions for using dispeRsal function to predict maximum seed dispersal distances with confidence intervals for user’s own data sets. Future updates of the tool and the underlying data can be found on a webpage at<br> http://www.botany.ut.ee/dispersal. To achieve ongoing improvements to the models, we ask the research community to contact us with further data on measured seed dispersal distances and associated plant traits.
DOI: 10.6084/m9.figshare.3558621
title: Appendix A. Population mean soil depth (cm), soil moisture (%), PC1 (N, P, K), PC2 (Ca, Mg), and vegetation height (cm) in 24 populations of Primula farinosa, measured in 2008–2010.

description: Population mean soil depth (cm), soil moisture (%), PC1 (N, P, K), PC2 (Ca, Mg), and vegetation height (cm) in 24 populations of Primula farinosa, measured in 2008–2010.
DOI: 10.6084/m9.figshare.3558621.v1
title: Appendix A. Population mean soil depth (cm), soil moisture (%), PC1 (N, P, K), PC2 (Ca, Mg), and vegetation height (cm) in 24 populations of Primula farinosa, measured in 2008–2010.

description: Population mean soil depth (cm), soil moisture (%), PC1 (N, P, K), PC2 (Ca, Mg), and vegetation height (cm) in 24 populations of Primula farinosa, measured in 2008–2010.
DOI: 10.6084/m9.figshare.3558618
title: Supplement 1. R code used to estimate potential and realized population growth rates of 24 populations of Primula farinosa.

description: File List R_code.txt (MD5: a2c1bc13d653916bbde67d5f0f4893d3) Description R code used to estimate potential and realized population growth rates of 24 populations of <i>Primula farinosa</i>. The code was based on the original code provided by Ellner and Rees (2006). Ellner, S. P., and M. Rees. 2006. Integral projection models for species with complex demography. American Naturalist 167:410–428.
DOI: 10.6084/m9.figshare.3558618.v1
title: Supplement 1. R code used to estimate potential and realized population growth rates of 24 populations of Primula farinosa.

description: File List R_code.txt (MD5: a2c1bc13d653916bbde67d5f0f4893d3) Description R code used to estimate potential and realized population growth rates of 24 populations of <i>Primula farinosa</i>. The code was based on the original code provided by Ellner and Rees (2006). Ellner, S. P., and M. Rees. 2006. Integral projection models for species with complex demography. American Naturalist 167:410–428.
DOI: 10.6084/m9.figshare.3558615
title: Appendix A. A table of results from the linear mixed model.

description: A table of results from the linear mixed model.
DOI: 10.6084/m9.figshare.3558612
title: Appendix A. Additional sampling procedures of ants and plants in a mature rainforest, São Nicolau Farm, municipality of Cotriguaçu, northern Mato Grosso, Brazil.

description: Additional sampling procedures of ants and plants in a mature rainforest, São Nicolau Farm, municipality of Cotriguaçu, northern Mato Grosso, Brazil.
DOI: 10.6084/m9.figshare.3558609
title: Appendix B. Detailed mathematical procedure used to determine the ants that interact more than expected by their natural abundances.

description: Detailed mathematical procedure used to determine the ants that interact more than expected by their natural abundances.
DOI: 10.6084/m9.figshare.3558609.v1
title: Appendix B. Detailed mathematical procedure used to determine the ants that interact more than expected by their natural abundances.

description: Detailed mathematical procedure used to determine the ants that interact more than expected by their natural abundances.
DOI: 10.6084/m9.figshare.3558606
title: Appendix C. Quantitative and qualitative ordinations of ant communities foraging on plants with and without extrafloral nectaries.

description: Quantitative and qualitative ordinations of ant communities foraging on plants with and without extrafloral nectaries.
DOI: 10.6084/m9.figshare.3558603
title: Appendix A. Specialization metrics, land use responses, and species lists.

description: Specialization metrics, land use responses, and species lists.
DOI: 10.6084/m9.figshare.3558600
title: Appendix A. Spectograms of Chipping Sparrow song types used to evaluate song diversity.

description: Spectograms of Chipping Sparrow song types used to evaluate song diversity.
DOI: 10.6084/m9.figshare.3558600.v1
title: Appendix A. Spectograms of Chipping Sparrow song types used to evaluate song diversity.

description: Spectograms of Chipping Sparrow song types used to evaluate song diversity.
DOI: 10.6084/m9.figshare.3558597
title: Appendix A. A list of papers testing the effects of age, together with environmental drivers and a table with all models tested for laying dates and egg volume.

description: A list of papers testing the effects of age, together with environmental drivers and a table with all models tested for laying dates and egg volume.