cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8869586.v1
title: Temporal dynamics of mycorrhizal fungal communities and co-associations with grassland plant communities following experimental manipulation of rainfall

description: The data contains 4 files:<br>AM fungal community matrix, plant community matrix and treatment table (samples description), to correlate AM fungal community to plant community, and a fasta file containing DNA sequences for each fungal operational taxonomic unit.<br><br>OTUmatrix.csv<br>AM fungal community matrix. Matrix containing number of reads of Operational Taxonomic Units (OTU) of Glomeromycota Fungi for each molecular sample; ‘sample’ (sample ID) and OTU (other columns).<br><br>soilData.csv<br>Treatment table, description of each sample. Contains information on the treatments associated with each sample. Columns description: ‘sample’ (sample ID, which is the sample number used in the OTUmatrix), ‘Treatment’ (watering treatment applied in the plot from which the sample was collected), ‘Plot’ (plot number from which the sample was collected), ‘x.coord.m’ (X coordinates of the plots, for spatial analyses; values are distance in meters from plot 1), ‘y.coord.m’ (Y coordinates of the plots, for spatial analyses; values are distance in meters from plot 1), ‘Year’ (year of sample collection), ‘Season’ (season of sample collection), ‘Season.Year’ (sampling date), ‘month’ (number of month since the establishment of the experimental platform; for temporal analyses), ‘batch’ (<br><br>plantMATRIX.csv<br>Plant community matrix. Matrix containing sample description and biomass (grams) of each plant species for each sample. Columns description: ‘soilID’ (corresponding sample ID from the soilData and OTUmatrix), ‘plot’ (plot number from which the sample was collected), ‘year’ (year of sample collection), ‘month’ (month of the year) ,‘season’ (season of sample collection), ‘Season.Year’ (sampling date), ‘treatment’ (watering treatment applied in the plot from which the sample was collected), next columns contain plant species data.<br>
DOI: 10.17632/dhvrsdmvfz
title: chronic obstructive pulmonary disease hospitalization

description: Data regarding the relationship between walk,physical activity and the risk of chronic obstructive pulmonary disease hospitalization
DOI: 10.6084/m9.figshare.13009997.v3
title: VGEA: A snakemake pipeline for RNA virus genome assembly from next generation sequencing data

description: SARS-CoV-2, Lassa Virus (Human and Rodent) and HIV-1 Test Datasets for the VGEA Pipeline.
DOI: 10.6084/m9.figshare.27351165.v1
title: “Super-progenitor” species and the distribution of sampled descendants

description: Data from a manuscript exploring how descendant lineages are distributed across phylogenies of fossil clades.
DOI: 10.6084/m9.figshare.686126.v1
title: Analiza finansowa przedsiębiorstwa z punktu widzenia zarządzającego, na przykładzie przedsiębiorstwa z branży 42

description: Celem niniejszego raportu jest analiza wskaźnikowa przedsiębiorstwa z sektora robót związanych z budową obiektów inżynierii lądowej i wodnej na podstawie przedsiębiorstwa „E”. Przedmiotem analizy jest interpretacja podstawowych wskaźników płynności, rentowności, wypłacalności oraz sprawności w oparciu o wykonane obliczenia i dane sektorowe.
DOI: 10.6084/m9.figshare.8188316.v1
title: Supplementary Material for: Indirect Effects of Body Mass Index Growth on Glucose Dysregulation via Inflammation: Causal Moderated Mediation Analysis

description: <b><i>Objective:</i></b> No existing studies have examined the mediating role of chronic inflammation between obesity and dysregulated glucose homeostasis in adolescent samples. This study evaluated whether C-reactive protein (CRP), an inflammation biomarker, mediated the effects of growth (annual increase) in body mass index (BMI) on glycated hemoglobin (HbA<sub>1c</sub>). <b><i>Methods:</i></b> BMI and biomarker data were used from wave I to wave IV of the National Longitudinal Study of Adolescent to Adult Health (Add Health study; 4,545 adolescents; mean age = 14.9 years; 55.7% female) with valid CRP data. A causal moderated mediation analysis evaluated the direct and indirect effects of BMI slope on HbA<sub>1c</sub> via CRP across gender, with demographic and clinical characteristics as model covariates. <b><i>Results:</i></b> The participants displayed a linear BMI growth of 0.53–0.58 kg/m<sup>2</sup>/year throughout adolescence, with substantial interindividual variation. The BMI slope showed positive direct and indirect effects on HbA<sub>1c</sub> via CRP across gender, and there was a significant exposure-mediator interaction effect. A standardized increase in the BMI slope raised the probability of an abnormal HbA<sub>1c</sub> value by 6.0–8.5% in participants with various profiles. The total natural indirect effect accounted for 13.3–15.9% of the total effect in males and 21.2–22.7% in females. <b><i>Conclusions:</i></b> The findings provide support for the inflammation mechanism in the effects of adiposity on glucose homeostasis. In adolescents, excess BMI growth was linked with a higher risk of glucose dysregulation either directly or indirectly via chronic inflammation.
DOI: 10.17632/yrvtz3zryv
title: Nurses, Moral Distress, and COVID-19 in a Global Perspective – An Integrative Review

description: ABSTRACT

Aim

This integrative review aims to synthesize the current literature on moral distress in nurses during the COVID-19 in healthcare. The objectives are: 
1. To review empirical data on the impacts of moral distress nurses experience during the COVID-19 in healthcare. 
2. To explore the current literature for strategies to EASE (Equip, Alleviate, Support, and Educate) nurses' moral distress during a pandemic.

Design/Method
An integrative review guided by the Whittemore and Knafl (2005) method.

Results
Of the 299 studies identified, six published met inclusion criteria. Greece, Iran, Romania, Switzerland, and United States were among the countries with nurses suffering from moral distress due to COVID-19. Three overarching concepts were identified: impact of moral distress on nurses, factors for moral distress, and improved quality of work conditions as an intervention for moral distress. Strategies to EASE (Equip, Alleviate, Support, and Educate) nurses' moral distress during a pandemic were explored.

Keywords
Moral Distress, COVID-19, Pandemic, Nurse, Mental health, Integrative Review, Healthcare, COVID-19 Pandemic
DOI: 10.6084/m9.figshare.23522799.v1
title: Supplementary Material for: Encephalitis as a clinical manifestation of COVID-19: A Case Series

description: COVID-19 is a novel virus which causes a variety of clinical manifestations in the body some of which are still yet to be discovered. The main aim of our study is to highlight the neurological manifestations of COVID-19 as it is still new to the medical world and to emphasize the fact that the physicians have to be vary of the possibility that patients affected with COVID-19 can present with encephalitis. Only a few studies are available so far regarding the neurological manifestations of this novel virus which highlights the need of this study. We present a case series of four patients who were found to have COVID-19 encephalitis. There is still no disease defining test for diagnosis so the mainstay of diagnosis is exclusion of all the common causes of encephalitis. Brain MRI and CSF analysis performs an ancillary in the diagnostic tools. Our study also supports the use of IV Tocilizumab (4-8 mg/kg) and IV methylprednisolone (0.5-2 mg/kg) as possible treatment options with good results as the patients described in our case series responded well to these medications.
DOI: 10.6084/m9.figshare.26894230.v1
title: SALT Study - Data for skeletal muscle mass analysis

description: This dataset is part of the SALT Study with general information to evaluate the association between sleep patterns and skeletal muscle mass. Skeletal muscle mass was estimated using two different methods: by formula using the second version of the Lee equation, and by bio-impedance analysis. Sleep patters were evaluated usign a simple questionnaire. This dataset includes baseline information as well as data from the following 5 evaluations after baseline.
DOI: 10.6084/m9.figshare.27683376.v1
title: <b>Effects of nitrogen application on soil respiration and its components in a </b><b><i>Pinus tabulaeformis</i></b><b> plantation</b>

description: The study site is located in the Ziwuling region (35°03′–36°07′N, 108°10′–109°18′E) on the Loess Plateau, China. In September 2015, a 40-year-old <i>P. tabulaeformis</i> plantation was chosen as the research site. The experiment included four N application levels: no N (CK), low N (LN), medium N (MN), and high N (HN), corresponding to 0, 5, 10, and 20 g N m<sup>−2</sup> a<sup>−1</sup>, with three replicates per level. N fertilization, applied as granular urea (46% N). In September 2019 and September 2020, all annual samples were collected prior to N application, and relevant physicochemical factors were subsequently determined. Rs and its components were measured at September 2019 and September 2020 using a portable infra-red gas analyzer (LI-COR 8100) with soil chamber (LI-COR Inc., USA).
DOI: 10.6084/m9.figshare.28193204.v1
title: Supplementary Material for: Identifying novel inflammatory protein biomarkers and drug targets of inflammatory bowel disease by integrating Mendelian randomization, bioinformatics, and druggability analysis

description: Introduction: Inflammatory proteins have the potential to be used as therapeutic targets for inflammatory bowel disease (IBD).
Methods: We conducted Mendelian randomization (MR) analysis to probe causal associations between 91 circulating inflammatory proteins and IBD in the discovery and replication cohorts. Subsequently, we conducted meta-analysis of results from two cohorts. We further conducted protein-protein interaction (PPI), enrichment analysis, and druggability evaluation to elucidate our results and prioritize potential therapeutic targets.
Results: By integrating data from two cohorts, we demonstrated that genetically predicted CD40 (odds ratio [OR] = 0.878, 95% confidence interval [CI] = 0.838-0.919) and C-X-C motif chemokine ligand (CXCL)5 (OR = 0.884, 95%CI = 0.841-0.930) decreased IBD risk. However, genetically predicted CXCL9 (OR = 1.184, 95%CI = 1.084-1.294), Interleukin (IL)-18 (OR = 1.140, 95%CI = 1.076-1.208), CD6 (OR = 1.096, 95%CI = 1.045-1.150), and 4E-binding protein 1 (4E-BP1) (OR = 1.154, 95%CI = 1.070-1.244) increased IBD risk. Moreover, genetically predicted CD40 (OR = 0.855, 95%CI = 0.801-0.912) decreased Crohn’s disease (CD) risk. Genetically predicted fibroblast growth factor 21 (FGF21) (OR = 1.259, 95%CI = 1.135-1.397) and 4E-BP1 (OR = 1.202, 95%CI = 1.088-1.327) increased CD risk. We found no inflammatory protein associated with ulcerative colitis. Additionally, CD was significantly associated with elevated levels of three circulating inflammatory proteins, which are suggested to be the consequences of CD. PPI analysis demonstrated interactions between CXCL5, CXCL9, IL-18, CD40, and FGF21. Enrichment analysis indicated these identified proteins significantly enriched in inflammation-related signaling pathways, including interleukin signaling, cytokine signaling, and NF-κB pathway. Three proteins (CD40, IL-18, 4E-BP1) have been targeted for drug development on cancers and immune-related diseases, with potentials of therapeutic targets for IBD.
Conclusions: Our results provide new biomarkers and drug targets for CD. Moreover, we further demonstrate critical roles of inflammation and immunity in the occurrence and development of IBD.
DOI: 10.6084/m9.figshare.26012284.v1
title: Long_term_SB_Impacts

description: In this study, we use the Community Atmosphere Model version 6, coupled with chemistry (CAM6-Chem) and Community Emissions Data System (CEDS) inventory to investigate the solid biofuel emission impacts on air quality and human health for 2000-2019.All data are formatted as IDLSAV.Array size (lon x lat): (3600, 1800).<br>
DOI: 10.6084/m9.figshare.26301310.v1
title: CEG1.5

description: Food web analyses remain relatively novel in paleontology, hindered in part by cryptic ecological attributes of extinct fossil organisms, incomplete preservation, and the analytical challenges posed by complex networks. While ecological attribute data are becoming increasingly available through new resources such as BITE, EOL, TraitBase, and others, training and educational resources on analytical methods remain sparse. We hope to stimulate new avenues of research in paleoecology and train the next generation of ecological network modelers by providing instruction on the construction and modeling of paleocommunity food webs.
DOI: 10.6084/m9.figshare.27965037.v1
title: Light competition underpins eutrophication-induced plant diversity loss by modulating the gain and loss of resource-acquisitive species

description: A full-factorial field experiment independently manipulating understory light, nitrogen and phosphorus in a randomized block design on the Tibetan Plateau
DOI: 10.6084/m9.figshare.17204018.v1
title: DataforPlotingFigures.xlsx

description: This database is for the review paper "Nature-based framework for sustainable afforestation in global drylands under changing climate".
DOI: 10.6084/m9.figshare.26196209.v1
title: Travel time to nearest hospitals

description: Ensuring equitable access to health services is crucial for public welfare and social equity, and is a key objective of the United Nations' Sustainable Development Goals (SDGs). However, existing datasets often define hospital accessibility using travel time to hospitals in geographic dimension only, without considering the supply (hospital capacity) and demand (population distribution) dynamics. To overcome this limitation, we developed and validated a national-scale 1 KM map of both hospital travel time and hospital accessibility in China. We used Gaussian two-step floating catchment area (Ga2SFCA) model to calculate hospital accessibility, incorporating hospital capacity and service population. Various file types and statistical indicators are provided, making the dataset highly accessible for non-specialists. The dataset fills the gap in publicly available nationwide hospital accessibility data for China and can serve as a critical tool in optimizing resource allocation and developing targeted strategies to improve healthcare equity.
DOI: 10.6084/m9.figshare.7886243.v1
title: S1 Data. Validation brainstem masks and Application datasets, SUIT and SUITer scripts.

description: <b>S1 Data. Validation brainstem masks and Application datasets, SUIT and SUITer scripts.</b><br>
DOI: 10.17632/sdvj4fypgr
title: 30_landmark_Tridacna_maxima_ right _valve_Red_sea_saudiarabia_coast_GM

description: 30_landmark_tridana_maxima_Red_sea_saudiarabia_coast analysed by geometric morphometric (Right valves)
DOI: 10.6084/m9.figshare.5124136.v1
title: Supplementary Material for: Childhood Obesity Is Associated with Changes in the Serum Metabolite Profile

description: <b><i>Objective: </i></b>The human serum metabolite profile is reflective of metabolic processes, including pathophysiological changes characteristic of diseases. Therefore, investigation of serum metabolite concentrations in obese children might give new insights into biological mechanisms associated with childhood obesity. <b><i>Methods: </i></b>Serum samples of 80 obese and 40 normal-weight children between 6 and 15 years of age were analyzed using a mass spectrometry-based metabolomics approach targeting 163 metabolites. Metabolite concentrations and metabolite ratios were compared between obese and normal-weight children as well as between children of different pubertal stages. <b><i>Results: </i></b>Metabolite concentration profiles of obese children could be distinguished from those of normal-weight children. After correction for multiple testing, we observed 14 metabolites (glutamine, methionine, proline, nine phospholipids, and two acylcarnitines, <i>p </i>&lt; 3.8 × 10<sup>–4</sup>) and 69 metabolite ratios (<i>p</i> &lt; 6.0 × 10<sup>–6</sup>) to be significantly altered in obese children. The identified metabolite markers are indicative of oxidative stress and of changes in sphingomyelin metabolism, in β-oxidation, and in pathways associated with energy expenditure. In contrast, pubertal stage was not associated with metabolite concentration differences. <b><i>Conclusion: </i></b>Our study shows that childhood obesity influences the composition of the serum metabolome. If replicated in larger studies, the altered metabolites might be considered as potential biomarkers in the generation of new hypotheses on the biological mechanisms behind obesity.
DOI: 10.6084/m9.figshare.25408165.v1
title: genome annotation

description: The first reference genome of <i>E. polyphekadion</i><i>in</i> this study will provide pivotal genetic resources.
DOI: 10.6084/m9.figshare.17098955.v1
title: Supplementary Material for: Clinical Utility of Surgical Lung Biopsy for Patients with Acute Respiratory Distress Syndrome: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Surgical lung biopsy (SLB) is performed in patients with acute respiratory distress syndrome (ARDS); however, its clinical utility remains unclear. <b><i>Objectives:</i></b> We categorized the pathological diagnoses and investigated the predictive value for short-term mortality. <b><i>Method:</i></b> Three electronic databases (MEDLINE, the Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov) were searched for the included studies. The QUADAS-2 was used to evaluate the risk of bias and its applicability. The types and populations of pathological diagnoses were investigated. The pooled sensitivity, positive likelihood ratio (LR+), negative likelihood ratio (LR−), and diagnostic odds ratio (DOR) were estimated at a fixed specificity. Hierarchical summary receiver operating characteristic curves were drawn. <b><i>Results:</i></b> A total of 16 studies that enrolled 758 patients were included. The pathological diagnoses were as follows: diffuse alveolar damage (DAD) 29.9%; infection 24.7%; interstitial lung disease 17.2%; malignancy 3.6%; cardiovascular disease 3.6%; drug toxicity 2.3%; connective tissue disease 2.2%; allergic disease 1.1%; and nonspecific diagnosis 15.4%. To predict short-term mortality, 13 studies that enrolled 613 patients used DAD as an index test and recorded a mortality rate of 56.9% (349 of 613 patients). A total of 3 studies that used index tests other than DAD were excluded. The pooled sensitivity, fixed specificity, LR+, LR−, and DOR were 0.46 (95% confidence interval [CI]: 0.29–0.56), 0.69, 1.48 (95% CI: 0.92–1.81), 0.78 (95% CI: 0.63–1.03), and 1.90 (95% CI: 0.89–2.86), respectively. <b><i>Conclusions:</i></b> SLB is unlikely to provide a specific diagnosis and should not be recommended for confirming DAD or predicting ARDS prognosis.
DOI: 10.6084/m9.figshare.799703.v1
title: Binding energy of trypsin-BPTI complex with PyGBe and APBS

description: This file bundle includes data, figures and plotting scripts of solvation energy and binding energy calculations for trypsin-BPTI complex using PyGBe and APBS. Errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation). This result is part of the paper: —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: <em>—Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods</em>. Christopher Cooper, Lorena A. Barba. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.154331 <strong>Acknowledgement:</strong><br>This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.19928981.v1
title: 'Sensory analysis of specialty coffee from different environmental conditions in the region of Matas de Minas, Minas Gerais, Brazil

description: ABSTRACT Specialty coffees can be differentiated in various ways, including the environmental conditions in which they are produced and the sensory composition of the drink. This study aimed to evaluate the effect of altitude, slope exposure and fruit color on the sensory attributes of cafes of the region of Matas de Minas. Sampling points were georeferenced in four altitude ranges (&lt; 700 m; 700 ≤ x ≤ 825 m, 825 &lt; x &lt; 950 m and ≥ 950 m) of the coffee crop; two fruit colors of var. Catuaí (yellow and red); and two slope exposures (North-facing and South-facing). Coffee fruit at the cherry stage were processed and submitted to sensory analysis. The sensory attributes evaluated were overall perception, clean cup, balance, aftertaste, sweetness, acidity, body and flavor, which made up the final score. The scores were examined by ANOVA and means were compared by the Tukey test (p ≤ 0.05). From the sensory standpoint, coffee fruits of both colors are similar, as well as the coffees from both slope exposures when these factors were analyzed separately. However, at higher altitudes, Yellow Catuaí produces coffees with better sensory quality. Similarly, coffees from North-facing slopes, at higher altitudes produce better quality cup. The altitude is the main factor that interferes with coffee quality in the area. All factors together contribute to the final quality of the beverage produced in the region of Matas de Minas.
DOI: 10.6084/m9.figshare.23790057.v1
title: A single-cell transcriptome atlas of the African lungfish lungs and gills highlights the respiratory evolution

description: The cell type annotation files of African lungfish lung and gill.
DOI: 10.6084/m9.figshare.25422607.v1
title: Supplementary Material for: Identification of Lung Adenocarcinoma Subtypes Based on MHC-II Gene Expression Profile and Immunological Analysis

description: Background: Major histocompatibility complex class II molecule (MHC-II) is pivotal in anti-tumor immunity, and targeting MHC-II in tumors may help improve patient survival. But function of MHC-II in the immunotherapy and prognosis of lung adenocarcinoma (LUAD) patients has not been thoroughly studied and reported.
Methods: We selected LUAD-related MHC-II genes from public databases based on previous literature reports. We identified different subtypes according to expression differences of these genes in different LUAD samples through cluster analysis. We used R package to conduct a series of analyses on different subtypes, exploring their survival differences, gene expression differences, pathway enrichment differences, and differences in immune characteristics and immune therapy. Finally, we screened potential drugs from the CMap database.
Results: We identified two MHC-II-related LUAD subtypes. Our analyses presented that patients with cluster2 subtype showed better prognosis, higher immune scores, higher levels of immune cell infiltration and immune function activation. In addition, patients with this subtype had higher immunophenoscore, lower TIDE scores, and DEPTH scores. We also identified 10 small molecule drugs, such as Lenalidomie, VX-745, and tyrphostin-AG-1295.
Conclusion: Overall, MHC-II is not only a potential biomarker for accurately distinguishing LUAD subtypes, but also a predictive factor for their survival. Our study offers novel insights into understanding of impact of MHC-II in LUAD and offers a new perspective for improving the accurate classification of LUAD patients and enhancing drug treatment.