cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19329304
title: Exhaled metabolic markers and relevant dysregulated pathways of lung cancer: a pilot study

description: The clinical application of lung cancer detection based on breath test is still challenging due to lack of predictive molecular markers in exhaled breath. This study explored potential lung cancer biomarkers and their related pathways using a typical process for metabolomics investigation. Breath samples from 60 lung cancer patients and 176 healthy people were analyzed by GC-MS. The original data were GC-MS peak intensity removing background signal. Differential metabolites were selected after univariate statistical analysis and multivariate statistical analysis based on OPLS-DA and Spearman rank correlation analysis. A multivariate PLS-DA model was established based on differential metabolites for pattern recognition. Subsequently, pathway enrichment analysis was performed on differential metabolites. The discriminant capability was assessed by ROC curve of whom the average AUC and average accuracy in 100-fold cross validations were 0.871 and 0.787, respectively. Eight potential biomarkers were involved in a total of 18 metabolic pathways. Among them, 11 metabolic pathways have <i>p</i>-value smaller than .1. Some pathways among them are related to risk factors or therapies of lung cancer. However, more of them are dysregulated pathways of lung cancer reported in studies based on genome or transcriptome data. We believe that it opens the possibility of using metabolomics methods to analyze data of exhaled breath and promotes involvement of knowledge dataset to cover more volatile metabolites. Although a series of related research reported diagnostic models with highly sensitive and specific prediction, the clinical application of lung cancer detection based on breath test is still challenging due to disease heterogeneity and lack of predictive molecular markers in exhaled breath. This study may promote the clinical application of this technique which is suitable for large-scale screening thanks to its low-cost and non-invasiveness. As a result, the mortality of lung cancer may be decreased in future.Key messagesIn the present study, 11 pathways involving 8 potential biomarkers were discovered to be dysregulated pathways of lung cancer.We found that it is possible to apply metabolomics methods in analysis of data from breath test, which is meaningful to discover convinced volatile markers with definite pathological and histological significance. In the present study, 11 pathways involving 8 potential biomarkers were discovered to be dysregulated pathways of lung cancer. We found that it is possible to apply metabolomics methods in analysis of data from breath test, which is meaningful to discover convinced volatile markers with definite pathological and histological significance.
DOI: 10.6084/m9.figshare.19329304.v1
title: Exhaled metabolic markers and relevant dysregulated pathways of lung cancer: a pilot study

description: The clinical application of lung cancer detection based on breath test is still challenging due to lack of predictive molecular markers in exhaled breath. This study explored potential lung cancer biomarkers and their related pathways using a typical process for metabolomics investigation. Breath samples from 60 lung cancer patients and 176 healthy people were analyzed by GC-MS. The original data were GC-MS peak intensity removing background signal. Differential metabolites were selected after univariate statistical analysis and multivariate statistical analysis based on OPLS-DA and Spearman rank correlation analysis. A multivariate PLS-DA model was established based on differential metabolites for pattern recognition. Subsequently, pathway enrichment analysis was performed on differential metabolites. The discriminant capability was assessed by ROC curve of whom the average AUC and average accuracy in 100-fold cross validations were 0.871 and 0.787, respectively. Eight potential biomarkers were involved in a total of 18 metabolic pathways. Among them, 11 metabolic pathways have <i>p</i>-value smaller than .1. Some pathways among them are related to risk factors or therapies of lung cancer. However, more of them are dysregulated pathways of lung cancer reported in studies based on genome or transcriptome data. We believe that it opens the possibility of using metabolomics methods to analyze data of exhaled breath and promotes involvement of knowledge dataset to cover more volatile metabolites. Although a series of related research reported diagnostic models with highly sensitive and specific prediction, the clinical application of lung cancer detection based on breath test is still challenging due to disease heterogeneity and lack of predictive molecular markers in exhaled breath. This study may promote the clinical application of this technique which is suitable for large-scale screening thanks to its low-cost and non-invasiveness. As a result, the mortality of lung cancer may be decreased in future.Key messagesIn the present study, 11 pathways involving 8 potential biomarkers were discovered to be dysregulated pathways of lung cancer.We found that it is possible to apply metabolomics methods in analysis of data from breath test, which is meaningful to discover convinced volatile markers with definite pathological and histological significance. In the present study, 11 pathways involving 8 potential biomarkers were discovered to be dysregulated pathways of lung cancer. We found that it is possible to apply metabolomics methods in analysis of data from breath test, which is meaningful to discover convinced volatile markers with definite pathological and histological significance.
DOI: 10.5061/dryad.nf568
title: Data from: Investigating the causes and consequences of symbiont shuffling in a multi-partner reef coral symbiosis under environmental change

description: Dynamic symbioses may critically mediate impacts of climate change on
 diverse organisms, with repercussions for ecosystem persistence in some
 cases. On coral reefs, increases in heat-tolerant symbionts after thermal
 bleaching can reduce coral susceptibility to future stress. However, the
 relevance of this adaptive response is equivocal owing to conflicting
 reports of symbiont stability and change. We help reconcile this conflict
 by showing that change in symbiont community composition (symbiont
 shuffling) in Orbicella faveolata depends on the disturbance severity and
 recovery environment. The proportion of heat-tolerant symbionts
 dramatically increased following severe experimental bleaching, especially
 in a warmer recovery environment, but tended to decrease if bleaching was
 less severe. These patterns can be explained by variation in symbiont
 performance in the changing microenvironments created by differentially
 bleached host tissues. Furthermore, higher proportions of heat-tolerant
 symbionts linearly increased bleaching resistance but reduced
 photochemical efficiency, suggesting that any change in community
 structure oppositely impacts performance and stress tolerance. Therefore,
 even minor symbiont shuffling can adaptively benefit corals, although
 fitness effects of resulting trade-offs are difficult to predict. This
 work helps elucidate causes and consequences of dynamism in symbiosis,
 which is critical to predicting responses of multi-partner symbioses such
 as O. faveolata to environmental change.
description: Symbiont community
 structure and functionCunning_data.csvCunning_Readme.txtR code for data analysisR code for data analysisCunning_R_code.RCunning_Readme.txt
DOI: 10.6084/m9.figshare.24502771
title: Datasets for stiffness evaluation

description: Classification with single cell images for soft and stiff MSCs and RAW264.7 cells, regression with single cell images and related stiffness.
DOI: 10.5061/dryad.tr20q
title: Data from: Self-fertilization and herbivory in a rare alpine plant in California, Claytonia megarhiza (Montiaceae)

description: Reproduction in alpine habitats is challenging because of the short
 growing season, low temperatures, and high winds. This predicts
 alternative strategies for sexual reproduction in plants: compensatory
 measures such as larger floral displays and greater floral longevity to
 attract scarce pollinators and maintain outcrossing, or high levels of
 autonomous self-fertilization to assure reproduction in the absence of
 reliable pollinators. Here, we assessed the roles of animals (crawling
 insects, flying insects, and vertebrates) on the reproductive success of
 Claytonia megarhiza (A. Gray) S. Watson (alpine spring beauty). We
 measured fruit set and leaf herbivory while excluding animals from
 individual plants at a single site in Yosemite National Park, California.
 We found that plants were capable of setting fruit in the absence of
 pollinators and that, in the presence of animals, there was a 42%
 reduction in fruit set and a 159% increase in leaf damage. This suggests
 that Claytonia megarhiza may reproduce primarily by self-fertilization,
 and that herbivory may limit the reproductive success of this species near
 its southern range edge in California.
description: dataRaw data file from
 manipulative field experiment.occurrencesSpecimen data downloaded from Global Biodiversity Information Facility in Aug, 2014.r.codeR code for statistical analyses and figures.
DOI: 10.6084/m9.figshare.19941582.v1
title: Low Psoas-Muscle index is associated with decreased survival in hepatocellular carcinoma treated with transarterial chemoembolization

description: Skeletal muscle index (SMI) is a promising predictor of clinical outcomes in patients with malignant diseases. As a simpler surrogate of sarcopenia-psoas muscle index (PMI), its predict value for overall survival (OS) after transarterial chemoembolization (TACE) for hepatocellular carcinoma (HCC) has not been reported. To determine if changes in the PMI predicted OS in individuals with HCC treated with TACE. A retrospective analysis was performed in HCC patients treated with TACE between January 2018 and March 2019. The survival curve according to PMI was estimated by the Kaplan–Meier method and then compared by the log-rank test. Cox proportional hazards models were conducted to identify the prognostic factors for OS. Furthermore, the predictive abilities of PMI and SMI were compared by using Harrell’s concordance index (C-index). Two hundred and twenty-eight patients (175 men, mean age 59 ± 11 years) were analysed. The OS was less in patients with low PMI than those with high PMI (median OS: 16.9 vs. 38.5 months, <i>p</i> &lt; .001). Multivariate analysis found that either PMI (hazard ratio [HR] = 0.64; 95% confidence interval [CI], 0.45–0.91; <i>p</i> &lt; .001) or SMI (HR = 0.51; 95% CI, 0.36–0.72; <i>p</i> &lt; .001) was significantly associated with OS. In the multivariate analysis, the C-index for PMI was 0.78 and 0.79 for SMI (<i>p</i> = .985). PMI is a simple tool to predict OS in HCC patients treated with TACE. The predictive ability of PMI is comparable to that of SMI.
Key messagesLow psoas-muscle index is associated with decreased overall survival in hepatocellular carcinoma treated with transarterial chemoembolization (TACE).Psoas-muscle index has advantages of being faster and easier to acquire, which thus makes it more likely to achieve widespread clinical application. Low psoas-muscle index is associated with decreased overall survival in hepatocellular carcinoma treated with transarterial chemoembolization (TACE). Psoas-muscle index has advantages of being faster and easier to acquire, which thus makes it more likely to achieve widespread clinical application.
DOI: 10.6084/m9.figshare.24502771.v1
title: Datasets for stiffness evaluation

description: Classification with single cell images for soft and stiff MSCs and RAW264.7 cells.
DOI: 10.6084/m9.figshare.24502771.v2
title: Datasets for stiffness evaluation

description: Classification with single cell images for soft and stiff MSCs and RAW264.7 cells, regression with single cell images and related stiffness.
DOI: 10.6084/m9.figshare.19941582
title: Low Psoas-Muscle index is associated with decreased survival in hepatocellular carcinoma treated with transarterial chemoembolization

description: Skeletal muscle index (SMI) is a promising predictor of clinical outcomes in patients with malignant diseases. As a simpler surrogate of sarcopenia-psoas muscle index (PMI), its predict value for overall survival (OS) after transarterial chemoembolization (TACE) for hepatocellular carcinoma (HCC) has not been reported. To determine if changes in the PMI predicted OS in individuals with HCC treated with TACE. A retrospective analysis was performed in HCC patients treated with TACE between January 2018 and March 2019. The survival curve according to PMI was estimated by the Kaplan–Meier method and then compared by the log-rank test. Cox proportional hazards models were conducted to identify the prognostic factors for OS. Furthermore, the predictive abilities of PMI and SMI were compared by using Harrell’s concordance index (C-index). Two hundred and twenty-eight patients (175 men, mean age 59 ± 11 years) were analysed. The OS was less in patients with low PMI than those with high PMI (median OS: 16.9 vs. 38.5 months, <i>p</i> &lt; .001). Multivariate analysis found that either PMI (hazard ratio [HR] = 0.64; 95% confidence interval [CI], 0.45–0.91; <i>p</i> &lt; .001) or SMI (HR = 0.51; 95% CI, 0.36–0.72; <i>p</i> &lt; .001) was significantly associated with OS. In the multivariate analysis, the C-index for PMI was 0.78 and 0.79 for SMI (<i>p</i> = .985). PMI is a simple tool to predict OS in HCC patients treated with TACE. The predictive ability of PMI is comparable to that of SMI.
Key messagesLow psoas-muscle index is associated with decreased overall survival in hepatocellular carcinoma treated with transarterial chemoembolization (TACE).Psoas-muscle index has advantages of being faster and easier to acquire, which thus makes it more likely to achieve widespread clinical application. Low psoas-muscle index is associated with decreased overall survival in hepatocellular carcinoma treated with transarterial chemoembolization (TACE). Psoas-muscle index has advantages of being faster and easier to acquire, which thus makes it more likely to achieve widespread clinical application.
DOI: 10.5061/dryad.7gc05
title: Data from: Aerobic scope predicts dominance during early life in a tropical damselfish

description: A range of physiological traits are linked with aggression and dominance
 within social hierarchies, but the role of individual aerobic capacity in
 facilitating aggression has seldom been studied. Further, links previously
 observed between an individual's metabolic rate and aggression level
 may be context dependent and modulated by factors such as social stress
 and competitor familiarity. We examined these issues in juvenile Ambon
 damselfish, Pomacentrus amboinensis, which display intraspecific
 competition for territories during settlement on coral reefs. Individuals
 were measured for routine metabolic rate, aerobic scope, and anaerobic
 capacity using intermittent-flow respirometry before dyadic dominance
 contests. Post-contest, fish were measured for metabolic rate in isolation
 and while interacting with their previous competitor or a stranger in
 adjacent transparent respirometers. In arena contests, aerobic scope was
 correlated with aggression and dominance, while routine metabolic rate and
 anaerobic capacity were not related to dominance. Post-contest,
 subordinates showed a rise in metabolic rate and decrease in available
 aerobic scope, presumably due to social stress. Dominants increased
 metabolic rate in the presence of a previous competitor, possibly due to
 the stresses of hierarchy maintenance. Metabolic rate during aggressive
 interactions did not approach that measured during exhaustive exercise,
 suggesting individuals do not fully utilise their aerobic scope during
 aggression. A greater aerobic scope may, however, allow faster
 post-contest recovery. These results demonstrate a link between aerobic
 scope and dominance during intraspecific competition for territory.
 Selection on aerobic scope could therefore follow, either indirectly
 through correlations with other traits influencing resource-holding
 potential, or directly if aerobic scope carries benefits important for
 territory acquisition or holding, such as an enhanced capacity to cope
 with socially-induced stress.
description: Metabolic rate and
 behavioural data for juvenile Ambon damselfishMeasures of metabolic
 rates, before, after and during competitive interactions between juvenile
 Ambon damselfish. also includes behavioural data from dyadic
 trials.dryad data
 file.xlsx
DOI: 10.6084/m9.figshare.21435997
title: Hierarchical stratification of the factors related to exertional dyspnoea and exercise intolerance in male COPD patients

description: The order and extent of interactions across the factors affecting exertional dyspnoea (ED) and exercise intolerance (EI) in patients with chronic obstructive pulmonary disease (COPD) are not clear. We hypothesized that lung and non-lung variables were the primary variables, ED was the secondary variable and EI was the tertiary variable. Data on demographics, blood tests, cardiac imaging, lung function tests and invasive dead space fractions (V<sub>D</sub>/V<sub>T</sub>) during incremental exercise test of 46 male COPD subjects were obtained. These variables were categorized by factor analysis and pair-wise correlation analysis was conducted. The best factor of each category was selected and then multivariate regression was conducted. Peak tidal inspiratory flow (V<sub>T</sub>/T<sub>Ipeak</sub>), V<sub>D</sub>/V<sub>Tpeak</sub> and tidal lung expansion capability, and resting diffusing capacity of the lungs (D<sub>L</sub>CO)% predicted were the primary pulmonary factors most related to ED, whereas body mass index (BMI), haemoglobin and cholesterol levels were the primary non-pulmonary factors. In multivariate regression analysis, V<sub>T</sub>/T<sub>Ipeak</sub>, V<sub>D</sub>/V<sub>Tpeak</sub> and D<sub>L</sub>CO% were the primary factors most related to ED (<i>r</i><sup>2</sup> = 0.69); ED was most related to EI (<i>r</i> = −0.74 to −0.83). Using hierarchical stratification and statistical methods may improve understanding of the pathophysiology of ED and EI in patients with COPD.
KEY MESSAGESThe pathophysiology of exertional dyspnoea (ED) and exercise intolerance (EI) in chronic obstructive pulmonary disease (COPD) is complex. The order and extent of interactions across factors are not clear. In multivariate regression analysis, we found that tidal inspiratory flow, dead space fraction and resting diffusing capacity of the lungs % but not the non-pulmonary factors affected ED.Using correlation coefficients, we further found that ED was the secondary variable and EI was the tertiary variable.Hierarchical stratification of the important factors associated with ED and EI in patients with COPD clarifies their relationships and could be incorporated into management programmes and outcome studies for these patients. The pathophysiology of exertional dyspnoea (ED) and exercise intolerance (EI) in chronic obstructive pulmonary disease (COPD) is complex. The order and extent of interactions across factors are not clear. In multivariate regression analysis, we found that tidal inspiratory flow, dead space fraction and resting diffusing capacity of the lungs % but not the non-pulmonary factors affected ED. Using correlation coefficients, we further found that ED was the secondary variable and EI was the tertiary variable. Hierarchical stratification of the important factors associated with ED and EI in patients with COPD clarifies their relationships and could be incorporated into management programmes and outcome studies for these patients.
DOI: 10.6084/m9.figshare.21435997.v1
title: Hierarchical stratification of the factors related to exertional dyspnoea and exercise intolerance in male COPD patients

description: The order and extent of interactions across the factors affecting exertional dyspnoea (ED) and exercise intolerance (EI) in patients with chronic obstructive pulmonary disease (COPD) are not clear. We hypothesized that lung and non-lung variables were the primary variables, ED was the secondary variable and EI was the tertiary variable. Data on demographics, blood tests, cardiac imaging, lung function tests and invasive dead space fractions (V<sub>D</sub>/V<sub>T</sub>) during incremental exercise test of 46 male COPD subjects were obtained. These variables were categorized by factor analysis and pair-wise correlation analysis was conducted. The best factor of each category was selected and then multivariate regression was conducted. Peak tidal inspiratory flow (V<sub>T</sub>/T<sub>Ipeak</sub>), V<sub>D</sub>/V<sub>Tpeak</sub> and tidal lung expansion capability, and resting diffusing capacity of the lungs (D<sub>L</sub>CO)% predicted were the primary pulmonary factors most related to ED, whereas body mass index (BMI), haemoglobin and cholesterol levels were the primary non-pulmonary factors. In multivariate regression analysis, V<sub>T</sub>/T<sub>Ipeak</sub>, V<sub>D</sub>/V<sub>Tpeak</sub> and D<sub>L</sub>CO% were the primary factors most related to ED (<i>r</i><sup>2</sup> = 0.69); ED was most related to EI (<i>r</i> = −0.74 to −0.83). Using hierarchical stratification and statistical methods may improve understanding of the pathophysiology of ED and EI in patients with COPD.
KEY MESSAGESThe pathophysiology of exertional dyspnoea (ED) and exercise intolerance (EI) in chronic obstructive pulmonary disease (COPD) is complex. The order and extent of interactions across factors are not clear. In multivariate regression analysis, we found that tidal inspiratory flow, dead space fraction and resting diffusing capacity of the lungs % but not the non-pulmonary factors affected ED.Using correlation coefficients, we further found that ED was the secondary variable and EI was the tertiary variable.Hierarchical stratification of the important factors associated with ED and EI in patients with COPD clarifies their relationships and could be incorporated into management programmes and outcome studies for these patients. The pathophysiology of exertional dyspnoea (ED) and exercise intolerance (EI) in chronic obstructive pulmonary disease (COPD) is complex. The order and extent of interactions across factors are not clear. In multivariate regression analysis, we found that tidal inspiratory flow, dead space fraction and resting diffusing capacity of the lungs % but not the non-pulmonary factors affected ED. Using correlation coefficients, we further found that ED was the secondary variable and EI was the tertiary variable. Hierarchical stratification of the important factors associated with ED and EI in patients with COPD clarifies their relationships and could be incorporated into management programmes and outcome studies for these patients.