cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3530915.v1
title: Supplement 1. Data set used in the meta-analysis and associated references.

description: File List RefTableS1.txt -- contains the full reference for studies cited in TableS1.csv<br> TableS1.csv -- contains the data used in the meta-analysis Description This data set has been compiled by the authors of this article as part of their participation in Adaptive Synthesis Workshop III, Bio.M.E.R.G.E. (Biotic Mechanisms of Ecosystem Regulation in the Global Environment) organized by Shahid Naeem, Columbia University. The authors would appreciate being first contacted by those individuals interested in conducting further analyses based on this data set. TableS1.csv consists of data and statistics from 28 studies that examined the effects of either consumer (detritivore) or detrital diversity on resource depletion (RD), standing stocks of consumers (SSc), and/or standing stocks of detritus (SSd). Reasons behind non-calculable (n/c) entries are outlined in the article text. In the file TableS1.csv, the columns are: Expt = Experiment<br> Study = study citation, see reference list in this Supplement<br> From = Data source (F = Figure, T = Table)<br> TL = Trophic level manipulated (TD = consumer, BU = detritus)<br> Response = Response metric (RD = resource depletion, SSd = standing stock detritus, SSc = standing stock consumers)<br> RD = RD measure (C = consumption, I = instantaneous, T = temporal change)<br> Consumer = Consumer type (B = bacteria, F = fungi, M = metazoa)<br> System = (A = aquatic, T = terrestrial)<br> Setting = Experiment setting (1 = lab or greenhouse, 2 = field)<br> Manip = Richness manipulation (1 = full assembly, 2 = random assembly, 3 = nonrandom)<br> MaxS = Maximum richness<br> Length = Experiment duration (days)<br> PopDyn = Population dynamics (Y = occurred, N = did not occur)<br> LRR = log response ratio<br> vLRR = variance in LRR<br> ciLRR = (+/-) 95% CI for LRR<br> Z = Power function exponent<br> r2Z = Power function r-squared<br> seZ = S.E. power function exponent Cell values that are either not calculable or not applicable are indicated as 'NA'.<br> Checksum values for the numerical columns are: Setting: 120<br> Manip: 145<br> MaxS: 690<br> Length: 10205.66<br> LRR: 7.8815<br> vLRR: 1251.237<br> ciLRR: 101.6575<br> Z: 7.4845<br> r2Z: 4819.6<br> seZ: 8.3824
DOI: 10.6084/m9.figshare.12589571.v1
title: SPSS DATA-WMI & TE .sav

description: The data set and questionnaire for workplace management initiatives and talent engagement
DOI: 10.6084/m9.figshare.28252139.v1
title: Supplementary Material for: Paediatric paraganglioma with variant of unknown significance on genetic testing.

description: Introduction: Sympathetic paragangliomas (PGLs), are rare neuroendocrine tumours originating from chromaffin cells, primarily in the thorax, abdomen, and pelvis. Paediatric paragangliomas are particularly uncommon, but they represent a notable cause of secondary hypertension in children. These tumours frequently have a genetic basis, with up to 40% of patients carrying germline mutations, including variants of unknown significance (VUS), which present diagnostic and management challenges. 

Case presentation: In this case report, we describe a 10-year-old male who presented with seizures and hypertensive crisis, later diagnosed with a functional PGL. Biochemical tests confirmed elevated catecholamines, and imaging revealed a 3 cm para-aortic tumour. Genetic testing identified a heterozygous mutation in the FH gene classified as VUS. Surgical resection of the tumour was curative, with no recurrence after two years of follow-up. 

Conclusion: This case underscores the complexities of interpreting VUS in paediatric PGL and highlights the need for long-term follow-up and further research into the clinical significance of these genetic findings.
DOI: 10.6084/m9.figshare.5121583.v1
title: Supplementary Material for: Cognitive Function and Dialysis Adequacy: No Clear Relationship

description: <i>Background/Aims:</i> Cognitive impairment is common in hemodialysis patients and may be impacted by multiple patient and treatment characteristics. The impact of dialysis dose on cognitive function remains uncertain, particularly in the current era of increased dialysis dose and flux. <i>Methods:</i> We explored the cross-sectional relationship between dialysis adequacy and cognitive function in a cohort of maintenance hemodialysis patients. Adequacy was defined as the average of the 3 most proximate single pool Kt/V assessments. A detailed neurocognitive battery was administered during the 1st hour of dialysis. Multivariable linear regression models were adjusted for age, sex, education, race and other clinical and demographic characteristics. <i>Results:</i> Among 273 patients who underwent cognitive testing, the mean (SD) age was 63 (17) years and the median dialysis duration was 13 months, 47% were woman, 22% were African American, and 48% had diabetes. The mean (SD) Kt/V was 1.51 (0.24). In univariate, parsimonious and multivariable models, there were no significant relationships between decreased cognitive function and lower Kt/V. <i>Conclusion:</i> In contrast to several older studies, there is no association between lower Kt/V and worse cognitive performance in the current era of increased dialysis dose. Future studies should address the longitudinal relationship between adequacy of dialysis and cognitive function to confirm these findings.
DOI: 10.6084/m9.figshare.7150664.v1
title: Poor emotion regulation ability mediates the link between depressive symptoms and affective bipolarity

description: People's relationship between positive and negative affect varies on a continuum from relatively independent to bipolar opposites, with stronger bipolar opposition being termed <i>affective bipolarity</i>. Experiencing more depressive symptoms is associated with increased bipolarity, but the processes underlying this relation are not yet understood. Here, we sought to replicate this link, and to examine the role of two potential mediating mechanisms: emotion regulation ability, and trait brooding. Drawing from the <i>Dynamic Model of Affect</i>, we hypothesised that (a) a poor ability to regulate negative emotion, and (b) the tendency to brood over one's depressed feelings would predict stronger affective bipolarity, and mediate the relationship between depressive symptoms and affective bipolarity. To measure affective bipolarity, we calculated within-person affect correlations using two weeks of experience sampling data from a community sample (<i>n </i>= 100). Mediation analyses indicated that baseline assessments of an inability to regulate negative emotions in general, but not brooding specifically, mediated the relation between depressive symptoms and affective bipolarity. These findings highlight an initial mechanism through which depressive symptoms are associated with lower emotional complexity and flexibility.
DOI: 10.6084/m9.figshare.17932061.v1
title: iris_Train.csv

description: iris
DOI: 10.6084/m9.figshare.21836169.v2
title: Apple leaf disease data

description: Alternaria blotch. Brown spot. Grey spot. Mosaic. Rust.
DOI: 10.6084/m9.figshare.15138231.v1
title: The impact of long-term physical inactivity on adipose tissue immunometabolism

description: These files constitute the Supplementary Materials for the manuscript titled: The impact of long-term physical inactivity on adipose tissue immunometabolism, submitted to JCEM.<br>File List Summary:<br>Supplementary Data File 1 <br>Supplementary Figures 1–9Supplementary Tables 1–5<br>
DOI: 10.6084/m9.figshare.14170838.v1
title: Data and code

description: Data and code
DOI: 10.6084/m9.figshare.16992388.v2
title: Sonmez_Extended_Data3

description: Homozygous SNP/indel variants identified between Sonmez and CS
DOI: 10.6084/m9.figshare.22577347.v1
title: The viable system model and the viability theory: Collaborations paths

description: The cybernetic viable system model (VSM) and viability theory (VT) are based on common assumptions. Both are tools for understanding and designing organizations. What, then, are the specific notions or concepts they share? What are their points of contact? To answer these questions, we identify the various mathematical concepts of control theory used in VSM and study the advances made in VT. We also summarize the various concepts in each approach. It is shown that VSM emphasizes general structures whereas VT puts the accent on the behaviour of particular dynamic systems. Our general conclusions are that: (1) VSM contributes important cybernetic concepts while VT provides precise notions of tychastic viability, viability and invariant sets as well as capture and absorption basins; and (2) control theory strongly enriched by system dynamics techniques is the most important <i>theoretical and practical</i> bridge between VSM and VT. These various characteristics of the two methods lend themselves to fruitful collaboration between them and form the basis of an attractive agenda for further research.
DOI: 10.6084/m9.figshare.3568149.v1
title: Appendix D. Leaf stomatal conductance and transpiration in response to vapor pressure deficit (VPD).

description: Leaf stomatal conductance and transpiration in response to vapor pressure deficit (VPD).
DOI: 10.6084/m9.figshare.22297369.v1
title: EM micrographs of NCAP+ZnCl2 in low ionic strength conditions. Used in Supplemental Figure 2d

description: EM micrographs of NCAP+ZnCl2 in low ionic strength conditions. Used in Supplemental Figure 2d
DOI: 10.6084/m9.figshare.24988260.v1
title: Supplementary Material for: Maternal diabetes and risk of hypospadias: a systemic review and meta-analysis

description: Abstract
Introduction: This study aims to investigate the association between maternal diabetes and the risk of hypospadias in male infants, as the relationship between them remains uncertain. Methods: To comprehensively evaluate the association between pregestational diabetes mellitus and gestational diabetes mellitus with hypospadias, we conducted a systematic review and meta-analysis. A thorough literature search was conducted, encompassing relevant publications published prior to January 2023. Crude odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) were calculated using a random-effects model. Results: Our meta-analysis comprised a total of 13 studies, 11 of which investigated the relationship between pregestational diabetes mellitus and hypospadias, while 9 studies explored the association between gestational diabetes mellitus and hypospadias. Notably, these investigations yielded compelling evidence of significant positive associations between pregestational diabetes mellitus and hypospadias (OR = 1.51, 95% CI = 1.13-2.03), as well as between gestational diabetes mellitus and hypospadias (OR = 1.18, 95% CI = 1.04-1.35). Conclusion: Our findings suggest that both pregestational diabetes mellitus and gestational diabetes mellitus are associated with an increased risk of hypospadias in offspring. Further investigations are needed to explore the optimal range of blood glucose during pregnancy that minimizes the risk of congenital malformation in the fetus, as well as to develop more effective measures for glycemic control in pregnant women.
DOI: 10.6084/m9.figshare.1122528.v1
title: Archaeology & Twitter Survey 2011

description: Results of my 2011 Archaeology & Twitter survey
DOI: 10.6084/m9.figshare.3550122.v1
title: Appendix F. Abundance of species that made the greatest contribution to dissimilarity among nitrogen treatments.

description: Abundance of species that made the greatest contribution to dissimilarity among nitrogen treatments.
DOI: 10.6084/m9.figshare.7763330.v3
title: AutoMated tool for Antimicrobial resistance Surveillance System (AMASS)

description: AutoMated tool for Antimicrobial resistance Surveillance System (AMASS) was developed as an offline, open−access and easy−to−use application that allows a hospital to perform data analysis independently and generate isolate−based and sample−based surveillance reports stratified by infection origin from routinely collected electronic databases. The application was built in R, which is a free software environment. The application has been placed within a user−friendly interface that only requires the user to double−click on the application icon. <br>AMASS performs data analysis and generates reports automatically. The raw data files required are hospital admission and microbiology databases. Firstly, the application cleans the microbiology data file and produces isolate−based and sample−based surveillance reports without stratification by infection origin. Secondly, the application then merges the microbiology and hospital admission data files, analyzes the merged data, and produces an isolated−based and sample−based surveillance reports with stratification by infection origin. Finally, the application then perform a statistical analysis to estimate all−cause mortality of patients with AMR infection and mortality attributable to AMR, which are automatically added into the AMR surveillance report.<br>AMASS aims to support the hospitals even those hospitals having only microbiology results. recorded electronica formats. For example, only isolate−based surveillance report without stratification by infection origin will be generated, if only microbiology data file is available and hospital admission data file is not available in the computer.<br> This is the AMASS.zip containing the AMASS application. Further, details on how to use the application can be found in http://mice.tropmedres.ac/home.aspx.
DOI: 10.6084/m9.figshare.91436.v1
title: Green Solvents (ACS GCI)

description: List of green solvents selected by the American Chemical Society Green Chemistry Institute. Format: XML DataSheet, used by SketchEl, Mobile Molecular DataSheet.
DOI: 10.6084/m9.figshare.9340712.v1
title: Hoehne_fish.csv

description: "Hoehne_fish.csv" = Raw data files of operculum-radii and age measurements of Eurasian perch from 13 gravel pit lakes in Lower Saxony, Germany, sampled by gillnetting and electrofishing."Hoehne_lakes.csv" = A range of biotic and abiotic environmental variables of the same 13 gravel pit lakes
DOI: 10.6084/m9.figshare.12909815.v1
title: DATASET - Physics-based earthquake simulations in slow-moving faults: a case study from the Eastern Betic Shear Zone (SE Spain)

description: This dataset contains input and output files used to run the RSQSim earthquake simulations performed in our study: Herrero‐Barbero, P., Álvarez‐Gómez, J. A., Williams, C., Villamor, P., Insua‐Arévalo, J. M., Alonso‐Henar, J., & Martínez‐Díaz, J. J. <b>Physics‐based earthquake simulations in slow‐moving faults: a case study from the Eastern Betic Shear Zone (SE Iberian Peninsula).</b> <i>Journal of Geophysical Research: Solid Earth</i>, e2020JB021133. https://doi.org/10.1029/2020JB021133
DOI: 10.6084/m9.figshare.19623819.v1
title: Reliability of Drug History for Verification of Androgen Abuse in Men

description: Analytical methodology of steroid profiling and results of urine steroid profilesfor current, past and non-0users of non-prescribed androgens and related drugs
DOI: 10.6084/m9.figshare.5120698.v1
title: Supplementary Material for: Factors Influencing Uptake of Pharmacogenetic Testing in a Diverse Patient Population

description: <i>Background: </i>The successful integration of pharmacogenetic (PGx) testing into clinical care will require attention to patient attitudes. In this study, we aimed to identify the major reasons why patients would or would not consider PGx testing and whether these factors differed by race, socioeconomic and insurance status, and medical history. <i>Methods:</i> We developed and conducted a survey within the adult patient population of the Duke Family Medicine Center. <i>Results:</i> Of 75 completed surveys (65% African-American), 77% indicated they were ‘very likely’ or ‘somewhat likely’ to take a PGx test. Respondents who had experienced a side effect were significantly more likely to indicate they would take a PGx test and expressed greater interest in learning more about testing than those who had not. Drug safety and effectiveness were the major reasons to have PGx testing. Privacy concerns and lack of insurance coverage for testing were the major reasons to decline testing. <i>Conclusions:</i> We found no differences in interest in PGx tests by race or socioeconomic status, but found stronger interest from those with a history of side effects and private insurance. While the overall support of PGx testing is encouraging, greater reassurance of medical privacy and development of educational resources are needed.
DOI: 10.6084/m9.figshare.14447466.v1
title: Supplementary Material for: Evaluation of Potential Application of Wharton’s Jelly-Derived Human Mesenchymal Stromal Cells and its Conditioned Media for Dermal Regeneration using Rat Wound Healing Model

description: Mesenchymal stromal cells and the derived conditioned media represent an area of tremendous medical interest and, among other clinical applications, are currently being extensively explored for wound healing. The aim of this study was to comparatively evaluate the wound healing potential of xeno-free human umbilical cord-derived mesenchymal stromal cells (MSCs) and the conditioned media (CM) in a full-thickness excision wound model in rats. The evaluation parameters included rate of wound healing, serum cytokine analyses, collagen content, histopathology, and hyperspectral imaging as an independent qualitative and quantitative tool. Both the cell-based and cell-free approaches scored better in lower inflammation, as evidenced in lower IL-10 and stable IL-6 levels, and improved rate of wound healing (<i>p</i> &lt; 0.0001). More importantly, no adverse reaction or rejection was observed although human MSCs and CM were used in a xenogeneic model. The presence of hFGF, hHGF, hGCSF, hIL-1Ra, hVEGF, and hIL-6 in the secretome may elucidate the regenerative potential of the xeno-free cell-based and cell-free approaches which have translational value for advanced wound care. The results revealed the therapeutic potential of both the cell-based and cell-free approaches for wound healing.
DOI: 10.6084/m9.figshare.25054937.v6
title: Raw data and data for analysis in Rstudio.

description: This study investigated predictive processing during both silent and oral reading, revealing a more pronounced predictability effect in the context of oral reading.
DOI: 10.6084/m9.figshare.28853753.v1
title: Metagenome-assembled genomes

description: <b>Project:</b> "In vitro modelling of the structure and metabolism of the porcine caecal microbiota in response to β-mannan exposure" (FigShare link).<b>Item description:</b> Metagenome-assembled genomes from a study using <i>in vitro</i> fermentation as a tool to investigate complex microbial communities extracted from the caecum of pigs, and their response to both <i>in vivo</i> and <i>in vitro</i> access to a microbiota-directed β-mannan fibre.<b>Abstract:</b> The intestinal microbiota plays a pivotal role in host health. Prebiotics and microbiota-directed fibres that target health-promoting microbes can potentially enhance the beneficial effects of the microbiota. β-mannans are fibres that may be utilised by a selection of beneficial bacteria, such as <i>Roseburia</i>, <i>Faecalibacterium</i>, and <i>Prevotella</i> species. Here, we conducted an <i>in vitro</i> fermentation experiment using porcine caecal material from an <i>in vivo</i> feeding trial with the inclusion of acetylated galactoglucomannan (AcGGM) from Norway spruce. We validated the effect of AcGGM on population abundance changes in the <i>in vitro</i> microbial community by comparison to an <i>in vivo</i> community. Functional data were obtained using metatranscriptomics to investigate gene expression of mannan-degrading enzymes during growth on AcGGM, and measurements of produced short-chain fatty acids. The <i>in vitro</i> fermentation identified several AcGGM-utilising taxa that significantly increased in abundance when grown on the substrate, while the same taxa were not observed to be more abundant in AcGGM-fed pigs. These taxa included several species with upregulated genes for mannan degradation that were previously unknown to utilise β-mannan.
DOI: 10.6084/m9.figshare.25843750.v1
title: MAG summary from DCME & SC05-UT metagenomes 2023

description: Excel file containing quality statistics and taxonomy of 106 draft metagenome assembled genomes (MAGs) from hybridSPADES assemblies from DCME and SC05-UT cultures.
DOI: 10.6084/m9.figshare.7719200.v1
title: Effects of Pesticides on Exposure and Susceptibility to Parasites can be Generalized to Pesticide Class and Type in Aquatic Communities

description: Data corresponding to Ecology Letters manuscript entitled "Effects of Pesticides on Exposure and Susceptibility to Parasites can be Generalized to Pesticide Class and Type in Aquatic Communities". All pertinent information regarding experimental design and analyses are contained within the manuscript. <br>Data is on first tab of excel file, metadata is on second tab of excel file.
DOI: 10.6084/m9.figshare.28831118.v1
title: experiment data (Time course of the twinkle-goes illusion and its relationship to neural theta oscillations)

description: Raw data and MATLAB codes for experiments and analyses.
DOI: 10.6084/m9.figshare.5532811.v1
title: Supplementary Material for: Cellular Immunotherapy in B-Cell Malignancy

description: In recent years, cellular immunotherapy in B-cell malignancies has been driven by adoptive transfer of genetically engineered T cells expressing chimeric antigen receptors (CARs). CARs consist of a single chain variable fragment (scFv) of a monoclonal antibody, a spacer domain, a transmembrane domain, an intracellular signaling domain, and additional costimulatory domains. The bulk of clinical data available is on CD19-targeting CAR T cells for the treatment of B-cell acute lymphocytic leukemia (B-ALL), chronic lymphocytic leukemia, and B-cell non-Hodgkin lymphoma. Results so far have been promising with impressive rates and depth of remission especially among B-ALL patients. However, CAR T-cell therapy is a complex multi-step process, and clinical trials so far differ profoundly in CAR construct used, gene transfer method, composition of the cellular product, lymphodepletion, and CAR T-cell dose used. Randomized trials will be needed to conclusively evaluate the implications of these differences. The treatment concept is associated with significant neurotoxicity and potentially lethal cytokine release syndrome, both of which require specific management. Improvements in CAR design may help to overcome toxicity, the effects of an immunosuppressive microenvironment, and tumor escape by development of antigen-negative clones. This review will explain the mechanism of action, summarize the clinical experience with this treatment modality so far, and explore future developments in the field.
DOI: 10.17632/jfx9x9zfmg.1
title: Learning Strategies Intervention 2024-25

description: Data from the article "Teaching Secondary School Students How to Learn: Effects of a Learning Strategies Intervention on Students’ Achievement" by Hector Ruiz-Martín, Miguel Ángel Vadillo and Marta Ferrero
DOI: 10.6084/m9.figshare.12942185.v1
title: GFR before and after alloHSCT_Dataset_20200831.xlsx

description: Assessment of kidney function using inulin-based and estimated glomerular filtration rates before and after allogeneic hematopoietic stem cell transplantation in pediatric patients
DOI: 10.6084/m9.figshare.1431150.v1
title: Maraviroc intensification of cART in patients with suboptimal immunological recovery: a 48-week, placebo-controlled randomized trial

description: File: Baseline immunological parameters. This SPSS file contains the baseline immunological parameters of the participants of the MIRS trial. Please see the 'variable view' of the SPSS file and the 'methods' section of the paper for more information. We have used SAS software for our analyses.