A Computational Method of Defining Potential Biomarkers based on Differential Sub-Networks

Huang, Xin; Lin, Xiaohui; Zeng, Jun; Wang, Lichao; Yin, Peiyuan; Zhou, Lina; Hu, Chunxiu; Yao, Wei

doi:10.1038/s41598-017-14682-5

Cited by 16 publications

(7 citation statements)

References 55 publications

(38 reference statements)

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“…Pearson correlation coefficients (PCC) is used to measure vector similarity and the relationship of the vectors and to construct networks [ 51 ]. The closer the correlation coefficient is to 1 or −1, the stronger the correlation degree is; the closer the correlation coefficient is to 0, the weaker the correlation degree is.…”

Section: Resultsmentioning

confidence: 99%

Characteristic Volatile Fingerprints and Odor Activity Values in Different Citrus-Tea by HS-GC-IMS and HS-SPME-GC-MS

Ding

Zhao-Ping

et al. 2020

Molecules

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Citrus tea is an emerging tea drink produced from tea and the pericarp of citrus, which consumers have increasingly favored due to its potential health effects and unique flavor. This study aimed to simultaneously combine the characteristic volatile fingerprints with the odor activity values (OAVs) of different citrus teas for the first time by headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS) and headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). Results showed that the establishment of a citrus tea flavor fingerprint based on HS-GC-IMS data can provide an effective means for the rapid identification and traceability of different citrus varieties. Moreover, 68 volatile compounds (OAV > 1) were identified by HS-SPME-GC-MS, which reflected the contribution of aroma compounds to the characteristic flavor of samples. Amongst them, the contribution of linalool with sweet flower fragrance was the highest. Odorants such as decanal, β-lonone, β-ionone, β-myrcene and D-limonene also contributed significantly to all samples. According to principal component analysis, the samples from different citrus teas were significantly separated. Visualization analysis based on Pearson correlation coefficients suggested that the correlation between key compounds was clarified. A comprehensive evaluation of the aroma of citrus tea will guide citrus tea flavor quality control and mass production.

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Section: Resultsmentioning

confidence: 99%

Characteristic Volatile Fingerprints and Odor Activity Values in Different Citrus-Tea by HS-GC-IMS and HS-SPME-GC-MS

Ding

Zhao-Ping

et al. 2020

Molecules

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“…The process used to generate this analysis is limited because it ignores known gene functions and over-represents the distance among genes that may be related. To avoid these limitations, it is necessary to incorporate biological knowledge into the analyses; for example, that includes common functional responses between related genes . Thus, the similarities between both tissues need to be assessed using more than just cluster analysis, and to explore similarities between both tissues, GO categories and pathway analyses were used.…”

Section: Resultsmentioning

confidence: 99%

Blood Transcriptomics Analysis of Fish Exposed to Perfluoro Alkyls Substances: Assessment of a Non-Lethal Sampling Technique for Advancing Aquatic Toxicology Research

Rodríguez-Jorquera

Collí-Dulá

Kroll

et al. 2018

Environ. Sci. Technol.

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In contrast to mammals, the blood from other vertebrates such as fish contains nucleated red cells. Using a fathead minnow (Pimephales promelas) oligonucleotide microarray, we compared altered transcripts in the liver and whole blood after exposure to environmentally relevant concentrations of perfluorooctanesulfonic acid (PFOS) and a mixture of seven types of perfluoro alkyl substances (PFAS), including perfluorooctanoic acid (PFOA). We used quantitative polymerase chain reactions and cell-based assays to confirm the main effects and found that blood responded with a greater number of altered genes than the liver. The exposure to PFAS altered similar genes with central roles in a cellular pathway in both tissues, including estrogen receptor α and peroxisome proliferator activator β and γ, indicating that the genes previously associated with PFAS exposure are differentially expressed in blood and liver. The altered transcripts are involved with cholesterol metabolism and mitochondrial function. Our data confirmed that PFAS are weak xenoestrogens and exert effects on DNA integrity. Gene expression profiling from blood samples not related with the immune system, including very-low-density lipoprotein, vitellogenin, estrogen receptor, and thyroid hormone receptor, demonstrated that blood is a useful tissue for assessing endocrine disruption in non-mammalian vertebrates. We conclude that the use of blood for non-lethal sampling in genomics studies is informative and particularly useful for assessing the effects of pollution in endangered species. Further, using blood will reduce animal use and widen the experimental design options for studying the effects of contaminant exposure on wildlife.

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“…The decision to assess inflammatory changes through the ratio of biomarker levels at T 0 and T 4 was based in the large inter-individual variability reported in previous studies 13 – 24 , as well as, the expectation that only a subgroup of patients would have intense inspiratory efforts. In addition, we believe that the biomarker ratio, by representing a relationship is sensitive to changes, discriminates the most relevant interactions and allows a more personalized analysis 26 .…”

Section: Discussionmentioning

confidence: 99%

Inflammatory biomarkers and pendelluft magnitude in ards patients transitioning from controlled to partial support ventilation

Cornejo

Arellano

Ruiz-Rudolph

et al. 2022

Sci Rep

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The transition from controlled to partial support ventilation is a challenge in acute respiratory distress syndrome (ARDS) patients due to the risks of patient-self-inflicted lung injury. The magnitude of tidal volume (VT) and intrapulmonary dyssynchrony (pendelluft) are suggested mechanisms of lung injury. We conducted a prospective, observational, physiological study in a tertiary academic intensive care unit. ARDS patients transitioning from controlled to partial support ventilation were included. On these, we evaluated the association between changes in inflammatory biomarkers and esophageal pressure swing (ΔPes), transpulmonary driving pressure (ΔPL), VT, and pendelluft. Pendelluft was defined as the percentage of the tidal volume that moves from the non-dependent to the dependent lung region during inspiration, and its frequency at different thresholds (− 15, − 20 and − 25%) was also registered. Blood concentrations of inflammatory biomarkers (IL-6, IL-8, TNF-α, ANGPT2, RAGE, IL-18, Caspase-1) were measured before (T0) and after 4-h (T4) of partial support ventilation. Pendelluft, ΔPes, ΔPL and VT were recorded. Nine out of twenty-four patients (37.5%) showed a pendelluft mean ≥ 10%. The mean values of ΔPes, ΔPL, and VT were − 8.4 [− 6.7; − 10.2] cmH2O, 15.2 [12.3–16.5] cmH2O and 8.1 [7.3–8.9] m/kg PBW, respectively. Significant associations were observed between the frequency of high-magnitude pendelluft and IL-8, IL-18, and Caspase-1 changes (T0/T4 ratio). These results suggest that the frequency of high magnitude pendelluft may be a potential determinant of inflammatory response related to inspiratory efforts in ARDS patients transitioning to partial support ventilation. Future studies are needed to confirm these results.

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A Computational Method of Defining Potential Biomarkers based on Differential Sub-Networks

Cited by 16 publications

References 55 publications

Characteristic Volatile Fingerprints and Odor Activity Values in Different Citrus-Tea by HS-GC-IMS and HS-SPME-GC-MS

Characteristic Volatile Fingerprints and Odor Activity Values in Different Citrus-Tea by HS-GC-IMS and HS-SPME-GC-MS

Blood Transcriptomics Analysis of Fish Exposed to Perfluoro Alkyls Substances: Assessment of a Non-Lethal Sampling Technique for Advancing Aquatic Toxicology Research

Inflammatory biomarkers and pendelluft magnitude in ards patients transitioning from controlled to partial support ventilation

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