Retrospective study on the correlation between serum MIF level and the condition and prognosis of patients with traumatic head injury
Objective This study aimed to investigate the correlation between serum levels of macrophage migration inhibitory factor (MIF) and the condition and prognosis of patients with traumatic brain injury (TBI). Methods A retrospective study design was used, and the clinical data of 131 TBI patients from February 2019 to January 2022 were analyzed. Patients were divided into mild (13–15 points), moderate (9–12 points), or severe (3–8 points) groups according to their Glasgow Coma Scale (GCS) score after admission. The serum levels of BDNF, MIF, and MBP in the three groups were compared, and their correlation with the severity of TBI was analyzed. Patients were then separated into a good prognosis group (4–5 points) and a poor prognosis group (≤3 points) based on their Glasgow Prognostic Score (GOS) after 6 months of follow-up. The predictive power of serum indexes and combined detection on prognosis was analyzed. Results Patients were classified into a mild group (n = 63), moderate group (n = 47), and severe group (n = 21) based on their GCS, with a significant difference noted in serum levels of MIF, MBP, and BDNF among patients with different degrees of severity (all P < 0.001). The MIF, MBP, and BDNF levels were lower in the mild group compared to the moderate (all P < 0.001) and severe group (all P < 0.001). Additionally, the MIF and BDNF levels in the moderate group were lower compared to the severe group (P = 0.011, P = 0.002). Patients with mild severity had lower serum MIF, MBP, and BDNF levels than those with other degrees, and these indexes were positively correlated with the severity of TBI (all P < 0.001, r = 0.62, r = 0.48, r = 0.58). Based on the GOS, patients were divided into a good prognosis group (n = 107) and a poor prognosis group (n = 24), with the levels of MIF, MBP, and BDNF in the good prognosis group being significantly lower than those in the poor prognosis group (P < 0.001, P = 0.007, P = 0.003). The area under the curve (AUC) of MIF was higher than that of MBP and BDNF in predicting the prognosis of TBI patients; however, the statistical differences were not significant (MIF vs. MBP, P = 0.239; MIF vs. BDNF, P = 0.211; BDNF vs. MBP, P = 0.899). The center line has a large displacement, CT annular cisterna compression, increased white blood cell count, MBP and BDNF were risk factors for prognosis in TBI patients (P = 0.005, P = 0.001, P = 0.005, P = 0.033, P = 0.044). Conclusion The serum levels of MIF, MBP, and BDNF in TBI patients were positively correlated with the severity of the disease, and MBP, BDNF levels had predictive value in determining patient prognosis.
Liu et al. (2023) Retrospective study on the correlation between serum MIF level and the condition and prognosis of patients with traumatic head injury. PeerJ 11:e15933 https://doi.org/10.7717/peerj.15933
Identification of novel key markers that are induced during traumatic brain injury in mice
Background Traumatic brain injury (TBI) has emerged as an increasing public health problem but has not been well studied, particularly the mechanisms of brain cellular behaviors during TBI. Methods In this study, we established an ischemia/reperfusion (I/R) brain injury mice model using transient middle cerebral artery occlusion (tMCAO) strategy. After then, RNA-sequencing of frontal lobes was performed to screen key inducers during TBI. To further verify the selected genes, we collected peripheral blood mononuclear cells (PBMCs) from TBI patients within 24 h who attended intensive care unit (ICU) in the Affiliated Hospital of Yangzhou University and analyzed the genes expression using RT-qPCR. Finally, the receiver operator characteristic (ROC) curves and co-expression with cellular senescence markers were applied to evaluate the predictive value of the genes. Results A total of six genes were screened out from the RNA-sequencing based on their novelty in TBI and implications in apoptosis and cellular senescence signaling. RT-qPCR analysis of PBMCs from patients showed the six genes were all up-regulated during TBI after comparing with healthy volunteers who attended the hospital for physical examination. The area under ROC (AUC) curves were all >0.7, and the co-expression scores of the six genes with senescence markers were all significantly positive. We thus identified TGM1, TGM2, ATF3, RCN3, ORAI1 and ITPR3 as novel key markers that are induced during TBI, and these markers may also serve as potential predictors for the progression of TBI.
Li et al. (2023) Identification of novel key markers that are induced during traumatic brain injury in mice. PeerJ 11:e15981 https://doi.org/10.7717/peerj.15981
Development and validation of the Exteroceptive Body Awareness (EBA-q) questionnaire
The conscious processing of body signals influences higher-order psychological and cognitive functions, including self-awareness. Dysfunctions in the processing of these signals has been connected to neurological and psychiatric disorders characterized by altered states of self-consciousness. Studies indicate that perceiving the body through interoceptive signals (e.g., from internal organs such as heartbeat and breathing) is distinct from perceiving the body through exteroceptive signals (e.g., by relying on visual, tactile and olfactory cues). While questionnaires are available for assessing interoception, there are no validated self-report instruments for measuring bodily exterception. To fill this gap, we performed three studies to develop and validate a novel scale designed to assess bodily self-consciousness based on the processing of exteroceptive bodily signals. Exploratory factor analysis (Study 1, N = 302) led to an 18-item questionnaire comprised of four factors. We called this instrument Exteroceptive Body Awareness questionnaire (EBA-q). Confirmatory factor analysis (Study 2, N = 184) run on a second sample showed an acceptable fit for a bifactor model, suggesting researchers may use the questionnaire as a unidimensional scale reflecting exteroceptive bodily self-consciousness, or use each of its four sub-scales, reflecting “visuo-tactile body awareness”, “spatial coordination”, “awareness of body changes” and “awareness of clothing fit”. Overall EBA-q showed good internal consistency. Convergent and divergent validity were assessed via cross-validation with existing body awareness questionnaires (Study 3, N = 366) and behavioral measures (Study 3, N = 64) of exteroceptive and interoceptive bodily self-consciousness. Research applications are discussed within a multi-faceted model of exteroception and interoception as distinct, but at the same time interconnected, dimensions of bodily self-consciousness.
Vabba et al. (2023) Development and validation of the Exteroceptive Body Awareness (EBA-q) questionnaire. PeerJ 11:e15382 https://doi.org/10.7717/peerj.15382
Signatures of prescribed fire in the microbial communities of Cornus florida are largely undetectable five months post-fire
Prescribed burn is a management tool that influences the physical structure and composition of forest plant communities and their associated microorganisms. Plant-associated microorganisms aid in host plant disease tolerance and increase nutrient availability. The effects of prescribed burn on microorganisms associated with native ecologically and economically important tree species, such as Cornus florida L. (flowering dogwood), are not well understood, particularly in aboveground plant tissues (e.g., leaf, stem, and bark tissues). The objective of this study was to use 16S rRNA gene and ITS2 region sequencing to evaluate changes in bacterial and fungal communities of five different flowering dogwood-associated niches (soil, roots, bark, stem, and leaves) five months following a prescribed burn treatment. The alpha- and beta-diversity of root bacterial/archaeal communities differed significantly between prescribed burn and unburned control-treated trees. In these bacterial/archaeal root communities, we also detected a significantly higher relative abundance of sequences identified as Acidothermaceae, a family of thermophilic bacteria. No significant differences were detected between prescribed burn-treated and unburned control trees in bulk soils or bark, stem, or leaf tissues. The findings of our study suggest that prescribed burn does not significantly alter the aboveground plant-associated microbial communities of flowering dogwood trees five months following the prescribed burn application. Further studies are required to better understand the short- and long-term effects of prescribed burns on the microbial communities of forest trees.
Kapoor et al. (2023) Signatures of prescribed fire in the microbial communities of Cornus florida are largely undetectable five months post-fire. PeerJ 11:e15822 https://doi.org/10.7717/peerj.15822
Exogenous hydrogen sulfide improves salt stress tolerance of Reaumuria soongorica seedlings by regulating active oxygen metabolism
Hydrogen sulfide (H2S), as an endogenous gas signaling molecule, plays an important role in plant growth regulation and resistance to abiotic stress. This study aims to investigate the mechanism of exogenous H2S on the growth and development of Reaumuria soongorica seedlings under salt stress and to determine the optimal concentration for foliar application. To investigate the regulatory effects of exogenous H2S (donor sodium hydrosulfide, NaHS) at concentrations ranging from 0 to 1 mM on reactive oxygen species (ROS), antioxidant system, and osmoregulation in R. soongorica seedlings under 300 mM NaCl stress. The growth of R. soongorica seedlings was inhibited by salt stress, which resulted in a decrease in the leaf relative water content (LRWC), specific leaf area (SLA), and soluble sugar content in leaves, elevated activity levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT); and accumulated superoxide anion (O2–), proline, malondialdehyde (MDA), and soluble protein content in leaves; and increased L-cysteine desulfhydrase (LCD) activity and endogenous H2S content. This indicated that a high level of ROS was produced in the leaves of R. soongorica seedlings and seriously affected the growth and development of R. soongorica seedlings. The exogenous application of different concentrations of NaHS reduced the content of O 2–, proline and MDA, increased the activity of antioxidant enzymes and the content of osmoregulators (soluble sugars and soluble proteins), while the LCD enzyme activity and the content of endogenous H2S were further increased with the continuous application of exogenous H2S. The inhibitory effects of salt stress on the growth rate of plant height and ground diameter, the LRWC, biomass, and SLA were effectively alleviated. A comprehensive analysis showed that the LRWC, POD, and proline could be used as the main indicators to evaluate the alleviating effect of exogenous H2S on R. soongorica seedlings under salt stress. The optimal concentration of exogenous H2S for R. soongorica seedlings under salt stress was 0.025 mM. This study provides an important theoretical foundation for understanding the salt tolerance mechanism of R. soongorica and for cultivating high-quality germplasm resources.
Liu et al. (2023) Exogenous hydrogen sulfide improves salt stress tolerance of Reaumuria soongorica seedlings by regulating active oxygen metabolism. PeerJ 11:e15881 https://doi.org/10.7717/peerj.15881
Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction
Background A growing number of experiments have shown that microRNAs (miRNAs) can be used as target of small molecules (SMs) to regulate gene expression for treating diseases. Therefore, identifying SM-related miRNAs is helpful for the treatment of diseases in the domain of medical investigation. Methods This article presents a new computational model, called NIRBMSMMA (neighborhood-based inference (NI) and restricted Boltzmann machine (RBM)), which we developed to identify potential small molecule-miRNA associations (NIRBMSMMA). First, grounded on known SM-miRNAs associations, SM similarity and miRNA similarity, NI was used to predict score of an unknown SM-miRNA pair by reckoning the sum of known associations between neighbors of the SM (miRNA) and the miRNA (SM). Second, utilizing a two-layered generative stochastic artificial neural network, RBM was used to predict SM-miRNA association by learning potential probability distribution from known SM-miRNA associations. At last, an ensemble learning model was conducted to combine NI and RBM for identifying potential SM-miRNA associations. Results Furthermore, we conducted global leave one out cross validation (LOOCV), miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation to assess performance of NIRBMSMMA based on three datasets. Results showed that NIRBMSMMA obtained areas under the curve (AUC) of 0.9912, 0.9875, 0.8376 and 0.9898 ± 0.0009 under global LOOCV, miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation based on dataset 1, respectively. For dataset 2, the AUCs are 0.8645, 0.8720, 0.7066 and 0.8547 ± 0.0046 in turn. For dataset 3, the AUCs are 0.9884, 0.9802, 0.8239 and 0.9870 ± 0.0015 in turn. Also, we conducted case studies to further assess the predictive performance of NIRBMSMMA. These results illustrated the proposed model is a useful tool in predicting potential SM-miRNA associations.
Qu et al. (2023) Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction. PeerJ 11:e15889 https://doi.org/10.7717/peerj.15889
Genetic diversity analysis and molecular characteristics of wild centipedegrass using sequence-related amplified polymorphism (SRAP) markers
Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is commonly used as a low-maintenance warm-season turfgrass owing to its excellent adaptation to various soil types. A better understanding of the genetic diversity pattern of centipedegrass is essential for the efficient development and utilization of accessions. This study used fifty-five pairs of primers to detect the genetic variation and genetic structure of twenty-three wild centipedegrass accessions by Sequence-related amplified polymorphism (SRAP) markers. A total of 919 reliable bands were amplified, among which 606 (65.80%) were polymorphic and 160 (2.91%) were the monomorphic loci. The average polymorphic information content (PIC) value was 0.228. The unweighted pair group method with arithmetic mean (UPGMA) clustering analysis grouped the twenty-three accessions into two clusters. Meanwhile, the structure analysis showed that the tested accessions possessed two main genetic memberships (K = 2). The Mantel test significantly correlated the genetic and geographic distance matrices (r = 0.3854, p = 0.000140). Furthermore, geographical groups showed moderate genetic differentiation, and the highest intragroup genetic diversity was found in the Sichuan group (He = 0.201). Overall, the present research findings could promote the protection and collection of centipedegrass and provide comprehensive information to develop novel breeding strategies.
Wang et al. (2023) Genetic diversity analysis and molecular characteristics of wild centipedegrass using sequence-related amplified polymorphism (SRAP) markers. PeerJ 11:e15900 https://doi.org/10.7717/peerj.15900
Characteristics of water jump for better performance in collegiate male 3000 m steeplechase
Background The 3000 m steeplechase consists of 28 barriers and seven water-jumping obstacles. The water jump in the 3000 m steeplechase makes it different from the sprint hurdle events. It is important for coaches and athletes to understand how to clear the water jump successfully. I aimed to investigate whether the takeoff and landing distances for the water jump per lap differ between participants with good and worse records. Methods Data were collected from the men’s 3000 m steeplechase races (heats) at Kanto Intercollegiate race. A total of 48 men’s performances were analyzed (24 upper group, 24 lower group). Takeoff distance, landing distance and clearance time were analyzed. Takeoff distance, landing distance, total water jump distance and clearance time were subjected to mixed two-way ANOVAs with repeated factors of Lap (lap 1/lap 2/lap 3/lap 4/lap 5/lap 6/lap 7) with Group (upper group/lower group) as a between group factor. Results Takeoff distance was longer for upper group (1.43 m) than lower group (1.34 m) (p = .01). Landing distance was longer for upper group (2.95 m) than for lower group (2.74 m) (p = .01) and was longer for lap 1 (2.95 m) than last three laps (lap 5: 2.83 m, lap 6: 2.82 m, lap 7: 2.76 m) (p = .01). Discussion Individuals who were faster in 3000 m steeplechase exhibited longer water jump distance. The effect of fatigue might be greater for landing distance than for takeoff distance. Because the landing distance becomes shorter in the second half of the 3000 m steeplechase, it is important to note that athletes should aim to land as far away from the water pit as possible.
Maruo (2023) Characteristics of water jump for better performance in collegiate male 3000 m steeplechase. PeerJ 11:e15918 https://doi.org/10.7717/peerj.15918
Bacillus amyloliquefaciens 11B91 inoculation enhances the growth of quinoa (Chenopodium quinoa Willd.) under salt stress
Quinoa (Chenopodium quinoa Willd.) is a highly nutritious food product with a comprehensive development prospect. Here, we discussed the effect of Bacillus amyloliquefaciens 11B91 on the growth, development and salt tolerance (salt concentrations: 0, 150, 300 mmol·L−1) of quinoa and highlighted a positive role for the application of plant growth-promoting rhizobacteria bacteria in quinoa. In this artical, the growth-promoting effect of Bacillus amyloliquefaciens 11B91 on quinoa (Longli No.1) and the changes in biomass, chlorophyll content, root activity and total phosphorus content under salt stress were measured. The results revealed that plants inoculated with 11B91 exhibited increased maximum shoot fresh weight (73.95%), root fresh weight (75.36%), root dry weight (136%), chlorophyll a (65.32%) contents and chlorophyll b (58.5%) contents, root activity (54.44%) and total phosphorus content (16.66%). Additionally, plants inoculated with 11B91 under salt stress plants showed significantly improved, fresh weight (107%), dry weight (133%), chlorophyll a (162%) contents and chlorophyll b (76.37%) contents, root activity (33.07%), and total phosphorus content (42.73%).
Li et al. (2023) Bacillus amyloliquefaciens 11B91 inoculation enhances the growth of quinoa (Chenopodium quinoa Willd.) under salt stress. PeerJ 11:e15925 https://doi.org/10.7717/peerj.15925
A decision tree model to predict liver cirrhosis in hepatocellular carcinoma patients: a retrospective study
Background The severity of liver cirrhosis in hepatocellular carcinoma (HCC) patients is essential for determining the scope of surgical resection. It also affects the long-term efficacy of systemic anti-tumor therapy and transcatheter arterial chemoembolization (TACE). Non-invasive tools, including aspartate aminotransferase to platelet ratio index (APRI), fibrosis-4 (FIB-4), and γ-glutamyl transferase to platelet ratio (GPR), are less accurate in predicting cirrhosis in HCC patients. We aimed to build a novel decision tree model to improve diagnostic accuracy of liver cirrhosis. Patients and Methods The Mann-Whitney U test, χ2 test, and multivariate logistic regression analysis were used to identify independent cirrhosis predictors. A decision tree model was developed using machine learning algorithms in a training cohort of 141 HCC patients. Internal validation was conducted in 99 HCC patients. The diagnostic accuracy and calibration of the established model were evaluated using receiver operating characteristic (ROC) and calibration curves, respectively. Results Sex and platelet count were identified as independent cirrhosis predictors. A decision tree model integrating imaging-reported cirrhosis, APRI, FIB-4, and GPR was established. The novel model had an excellent diagnostic performance in the training and validation cohorts, with area under the curve (AUC) values of 0.853 and 0.817, respectively. Calibration curves and the Hosmer-Lemeshow test showed good calibration of the novel model. The decision curve analysis (DCA) indicated that the decision tree model could provide a larger net benefit to predict liver cirrhosis. Conclusion Our developed decision tree model could successfully predict liver cirrhosis in HCC patients, which may be helpful in clinical decision-making.
Zhou et al. (2023) A decision tree model to predict liver cirrhosis in hepatocellular carcinoma patients: a retrospective study. PeerJ 11:e15950 https://doi.org/10.7717/peerj.15950