Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods
Background Many coral reefs worldwide are experiencing declines in hard corals, resulting in other benthic organisms, e.g., soft corals, becoming more dominant. As such, more studies on the ecophysiology of soft corals are needed. Despite many methods for asexual reproduction of hard corals, effective methods for soft corals, i.e., without a hard skeleton, are scarce. This study, thus, assessed four fragmentation methods, the glue, rubber band, tunnel mesh, and plug mesh method for the pulsating soft coral Xenia umbellata that is widely distributed in the tropical Indo-Pacific. Methods Methods were comparatively assessed by determining the required time and labor for the fragmentation plus the health status of the fragmented corals by measuring their oxygen fluxes and pulsation rates, i.e., a special feature of this soft coral that can be used as a proxy for its health. Results There were no significant health status differences between methods. This was indicated by similar gross photosynthesis (between 7.4 to 9.7 μg O2 polyp−1 h−1) and pulsating rates (between 35 and 44 pulses min−1) among methods. In terms of time/labor intensity and success rates, i.e., the percentage of fragments attached to the desired surface, the plug mesh method was the most efficient method with a significantly higher success rate (95 ± 5%), while the others had a success rate between 5 ± 5 and 45 ± 15%. The time needed for fragmentation, though not significant, was also the shortest (78 ± 11 s fragment−1), while other methods required between 84 ± 14 and 126 ± 8 s frag−1. The plug mesh method may thus be a valuable tool related to the reproduction of soft corals for use in subsequent experimental work.
Kim et al. (2022) Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods. PeerJ 10:e12589 https://doi.org/10.7717/peerj.12589
A novel nutritional index as a predictor of mortality in dilated cardiomyopathy: a retrospective study
Background Research has associated nutritional status with the prognosis of cardiovascular diseases. This study aimed to investigate the prognostic value of a novel nutritional index, triglycerides × total cholesterol × body weight index (TCBI), in patients with dilated cardiomyopathy (DCM). Methods This retrospective cohort study enrolled 445 patients with DCM. The median follow-up period was 2.8 years, and the primary endpoint was all-cause death. Results During follow-up, the all-cause mortality was observed in 135 out of 445 patients (30.3%). In Kaplan–Meier survival analysis, the third TCBI tertile had a lower mortality risk (T3 vs. T2 vs. T1: 16.9% vs. 35.1% vs. 38.9%; log-rank P < 0.001). In the multivariable Cox regression analysis, patients in the third tertile were associated with a decreased mortality, whereas there was no significant difference between the T2 and T1 groups. Moreover, TCBI could significantly improve risk stratification (continuous net reclassification improvement and integrated discrimination improvement) over the Geriatric Nutritional Risk Index (GNRI) and N-terminal pro-brain natriuretic peptide (NT-proBNP). Conclusions TCBI is independently associated with long-term survival in patients with DCM. Combination of TCBI and other biomarkers, such as GNRI and NT-proBNP, can significantly improve prognostic prediction. Further studies with larger sample size are required to validate our results.
Wang et al. (2022) A novel nutritional index as a predictor of mortality in dilated cardiomyopathy: a retrospective study. PeerJ 10:e12704 https://doi.org/10.7717/peerj.12704
Plasma FGF21 concentrations are regulated by glucose independently of insulin and GLP-1 in lean, healthy humans
Background Fibroblast growth factor 21 (FGF21) treatment improves metabolic homeostasis in diverse species, including humans. Physiologically, plasma FGF21 levels increase modestly after glucose ingestion, but it is unclear whether this is mediated by glucose itself or due to a secondary effect of postprandial endocrine responses. A refined understanding of the mechanisms that control FGF21 release in humans may accelerate the development of small-molecule FGF21 secretagogues to treat metabolic disease. This study aimed to determine whether FGF21 secretion is stimulated by elevations in plasma glucose, insulin, or glucagon-like peptide-1 (GLP-1) in humans. Methods Three groups of ten healthy participants were included in a parallel-group observational study. Group A underwent a hyperglycemic infusion; Group B underwent a 40 mU/m2/min hyperinsulinemic euglycemic clamp; Group C underwent two pancreatic clamps (to suppress endogenous insulin secretion) with euglycemic and hyperglycemic stages with an infusion of either saline or 0.5 pmol/kg/min GLP-1. Plasma FGF21 concentrations were measured at baseline and during each clamp stage by ELISA. Results Plasma FGF21 was unaltered during hyperglycemic infusion and hyperinsulinemic euglycemic clamps, compared to baseline. FGF21 was, however, increased by hyperglycemia under pancreatic clamp conditions (P < 0.05), while GLP-1 infusion under pancreatic clamp conditions did not change circulating FGF21 levels. Conclusion Increases in plasma FGF21 are likely driven directly by changes in plasma glucose independent of changes in insulin or GLP-1 secretion. Ecologically valid postprandial investigations are now needed to confirm our observations from basic science infusion models.
Solomon et al. (2022) Plasma FGF21 concentrations are regulated by glucose independently of insulin and GLP-1 in lean, healthy humans. PeerJ 10:e12755 https://doi.org/10.7717/peerj.12755
DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.
Antich et al. (2022) DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets. PeerJ 10:e12758 https://doi.org/10.7717/peerj.12758
Optimized nitrogen rate, plant density, and irrigation level reduced ammonia emission and nitrate leaching on maize farmland in the oasis area of China
Nitrogen fertilizers play a key role in crop production to meet global food demand. Inappropriate application of nitrogen fertilizer coupled with poor irrigation and other crop management practices threaten agriculture and environmental sustainability. Over application of nitrogen fertilizer increases nitrogen gas emission and nitrate leaching. A field experiment was conducted in China’s oasis irrigation area in 2018 and 2019 to determine which nitrogen rate, plant density, and irrigation level in sole maize (Zea mays L.) cropping system reduce ammonia emission and nitrate leaching. Three nitrogen rates of urea (46-0-0 of N-P2O5-K2O), at (N0 = 0 kg N ha−1, N1 = 270 kg N ha−1, and N2 = 360 kg N ha−1) were combined with three plant densities (D1 = 75,000 plants/ha−1, D2 = 97,500 plants/ha−1, and D3 = 120,000 plants/ha−1) with two irrigation levels (W1 = 5,250 m3/hm2 and W2 = 4,740 m3/hm2) using a randomized complete block design. The results showed that, both the main and interaction effects of nitrogen rate, plant density, and irrigation level reduced nitrate leaching (p < 0.05). In addition, irrigation level × nitrogen rate significantly (p < 0.05) reduced ammonia emission. Nitrate leaching and ammonia emission decreased with higher irrigation level and higher plant density. However, high nitrogen rates increased both nitrate leaching and ammonia emission. The study found lowest leaching (0.35 mg kg−1) occurring at the interaction of 270 kg N ha−1 × 120,000 plants/ha−1 × 4,740 m3/hm2, and higher plant density of 120,000 plants/ha−1 combined with 0 kg N ha−1 and irrigation level of 5,250 m3/hm2 recorded the lowest ammonia emission (0.001 kg N)−1. Overall, ammonia emission increased as days after planting increased while nitrate leaching decreased in deeper soil depths. These findings show that, though the contributory roles of days after planting, soil depth, amount of nitrogen fertilizer applied and year of cultivation cannot be undermined, it is possible to reduce nitrate leaching and ammonia emission through optimized nitrogen rate, plant density and regulated irrigation for agricultural and environmental sustainability.
Asibi et al. (2022) Optimized nitrogen rate, plant density, and irrigation level reduced ammonia emission and nitrate leaching on maize farmland in the oasis area of China. PeerJ 10:e12762 https://doi.org/10.7717/peerj.12762
Reconstructing the transmission dynamics of varicella in Japan: an elevation of age at infection
Background In Japan, routine two-dose immunization against varicella has been conducted among children at ages of 12 and 36 months since 2014, and the vaccination coverage has reached around 90%. To understand the impact of routine varicella vaccination, we reconstructed the epidemiological dynamics of varicella in Japan. Methods Epidemiological and demographic datasets over the past three decades were analyzed to reconstruct the number of susceptible individuals by age and year. To estimate the annual risk of varicella infection, we fitted a balance equation model to the annual number of cases from 1990 to 2019. Using parameter estimates, we reconstructed varicella dynamics starting from 1990 and modeled future dynamics until 2033. Results Overall varicella incidence declined over time and the annual risk of infection among children younger than 10 years old decreased monotonically starting in 2014. Conversely, varicella incidence among teenagers (age 10 to 14 years) has increased each year since 2014. A substantial number of unvaccinated individuals born before the routine immunization era remained susceptible and aged without contracting varicella, while the annual risk of infection among teenagers aged 10 to 14 years increased starting in 2011 despite gradual expansion of varicella vaccine coverage. The number of susceptible individuals decreased over time in all age groups. Modeling indicated that susceptibility rates among pre-school children aged 1 to 4 years will remain low. Conclusion Routine varicella vaccination has successfully reduced infections in pre-school and early primary school age children, but has also resulted in increased infection rates among adolescents. This temporary increase was caused both by the increased age of susceptible individuals and increased transmission risk among adolescents resulting from the dynamic nature of varicella transmission. Monitoring susceptibility among adolescents will be important to prevent outbreaks over the next decade.
Suzuki et al. (2022) Reconstructing the transmission dynamics of varicella in Japan: an elevation of age at infection. PeerJ 10:e12767 https://doi.org/10.7717/peerj.12767
The value of diffusion weighted imaging-alberta stroke program early CT score in predicting stroke-associated pneumonia in patients with acute cerebral infarction: a retrospective study
Background In this study, we aimed to investigate the value of Diffusion-Weighted Imaging-Alberta Stroke Program Early CT Score (DWI-ASPECTS) in predicting stroke-associated pneumonia (SAP) in patients with acute ischemic stroke. Methods A total of 291 patients who suffered acute cerebral infarction for the first time were included in this retrospective study. DWI-ASPECTS was assessed and clinical data were collected in order to find the risk factors of SAP, and a logistic regression model was used to investigate the effect of predicting SAP. Furthermore, correlation analysis was used to explore the relationship between DWI-ASPECTS and the immume status of the body. Results Among the 291 patients, 74 (25.4%) subjects were diagnosed with SAP. Compared with non-SAP, the patients with SAP were older and had a higher rate of atrial fibrillation (AF), National Institutes of Health Stroke Scale (NIHSS) scores. The SAP group also had a significantly lower DWI-ASPECTS than did the non-SAP group (P < 0.01). In the multivariable logistic regression analysis, the DWI-ASPECTS (adjusted odds ratio [aOR] = 1.438; 95% CI [1.158–1.787]; P < 0.01) remained significant after adjusting for confounders. What’s more, the predictive ability of DWI-ASPECTS (AUC = 0.743 >0.7, 95% CI [0.678–0.800]) had acceptable discriminatory abilities. By the correlation analysis, DWI-ASPECTS was found to be negatively correlated with the count of white blood cell, neutrophils, monocytes, neutrophil-to-monocyte ratio and neutrophil-to-lymphocyte ratio, and positively correlated with the count of lymphocytes. Conclusions DWI-ASPECTS grades could predict stroke-associated pneumonia for patients with acute ischemic stroke, and combining grade with age, AF, or NIHSS could predict SAP events more accurately.
Zhao et al. (2022) The value of diffusion weighted imaging-alberta stroke program early CT score in predicting stroke-associated pneumonia in patients with acute cerebral infarction: a retrospective study. PeerJ 10:e12789 https://doi.org/10.7717/peerj.12789
Biological effects of gamma-ray radiation on tulip (Tulipa gesneriana L.)
Tulip, being an important ornamental plant, generally requires lengthy and laborious procedures to develop new varieties using traditional breeding methods requires. But ionizing radiation potentially accelerates the breeding process of ornamental plant species. The biological effects of γ-ray irradiation on tulip, therefore, were investigated through establishing an irradiation-mediated mutation breeding protocol to accelerate its breeding process. ISSR-PCR molecular marker technique was further used to identify the mutants of phenotypic variation plants. This study showed that low irradiation doses (5 Gy) stimulated bulb germination to improve the survival rate of tulip, while high irradiation doses (20 to 100 Gy) significantly (P < 0.05) inhibited its seed germination and growth, and decreased the flowering rate, petal number, flower stem length and flower diameter. More than 40 Gy significantly (P < 0.05) decreased the total chlorophyll content and increased the malondialdehyde (MDA) content in tulips. Interestingly, three types of both stigma variations and flower pattern variations, and four types of flower colour variations were observed. With increasing the irradiation dose from 5 to 100 Gy, the anthocyanin and flavonoid contents continuously decreased. Scanning electron microscopy (SEM) analysis evidenced that high irradiation doses altered the micromorphology of leaf stomata. Microscopic observations of tulip root apical mitosis further showed the abnormal chromosomal division behaviour occurring at different mitotic phases under irradiation treatment (80 Gy). Increasing the irradiation dose from 20 to 100 Gy enhanced the micronucleus rate. Moreover, the suspected genetic variation in tulips was evaluated by inter-simple sequence repeat (ISSR) analysis, and the percentage of polymorphic bands was 68%. Finally, this study concludes that that 80 Gy may be an appropriate radiation does to better enhance the efficiency of mutagenic breeds in tulip plants. Using γ-ray irradiation, therefore, is expected to offer a theoretical basis for mutation breeding in tulips.
Li et al. (2022) Biological effects of gamma-ray radiation on tulip (Tulipa gesneriana L.). PeerJ 10:e12792 https://doi.org/10.7717/peerj.12792
Prokaryotic expression, purification and evaluation of anti-cardiac fibrosis activity of recombinant TGF-β latency associated peptide
Background Cardiac fibrosis refers to the abnormal accumulation of extracellular matrix in the heart, which leads to the formation of cardiac scars. It causes systolic and diastolic dysfunction, and ultimately leads to cardiac dysfunction and arrhythmia. TGF-β1 is an important regulatory factor involved in cardiac fibrosis. Studies have shown that the N-terminal latency associated peptide (LAP) must be removed before TGF-β1 is activated. We hypothesize that recombinant LAP may inhibit cardiac fibrosis induced by TGF-β1. To evaluate anti-cardiac fibrosis activity of recombinant LAP, an experimental study was carried out and is reported here. Methods The pET28a-LAP plasmid was constructed and transformed into E. coli C43 (DE3) competent cells. The recombinant LAP protein was purified by Ni affinity chromatography. The cells were treated with TGF-β1 at different concentrations for 24 h. The expression of α-SMA was detected by Western blot. RTCA was used to detect the effect of recombinant LAP on the proliferation of H9C2 cells induced by 10 ng/mL TGF-β1. To detect the effect of LAP on the expression of fibrosis-related proteins, H9C2 cells were treated with 10 ng/mL TGF-β1 for 24 h, then added 60 μg/mL recombinant LAP for 48 h. The LAP group was treated with 60 μg/mL recombinant LAP alone. The LAP pre-protection group was treated with 10 ng/mL TGF-β1 and 60 μg/mL recombinant LAP at the same time. Western blot and immunofluorescence were used to detect the expression of α-SMA, collagen I and fibronectin and p-Smad2. Results The recombinant LAP was prokaryotic expressed and purified. 10 ng/mL was determined as the optimal working concentration of TGF-β1 to induce H9C2 cells fibrosis. RTCA results showed that 60 μg/mL LAP could effectively inhibit the proliferation of H9C2 cells induced by TGF-β1. Immunofluorescence results showed that compared with the control group, the fluorescence intensities of α-SMA, collagen I and FN increased significantly after TGF-β1 treatment. The fluorescence intensities in the TGF-β1+LAP group decreased significantly. Western blot results showed that 60 μg/mL LAP could inhibit the increase of α-SMA, collagen I and FN expression in H9C2 cells induced by TGF-β1. Compared with the control, the LAP alone group has no significant difference in α-SMA and p-Smad2 expression level. The expression of α-SMA and p-Smad2 in the TGF-β1 model group was significantly increased compared with the control group. Compared with the TGF-β1 group, both TGF-β1+LAP group and LAP pre-protection group significantly reduced the increase in α-SMA and p-Smad2 levels. Conclusions Recombinant LAP was prokaryotic expressed and purified. The results showed that recombinant LAP can inhibit the cell proliferation and expression increase of α-SMA, collagen I, fibronectin and p-Smad2 in H9C2 cells induced by TGF-β1. These results suggested that recombinant LAP might inhibit TGF-β1-induced fibrosis of H9C2 cells through the TGF-β/Smad pathway.
Song et al. (2022) Prokaryotic expression, purification and evaluation of anti-cardiac fibrosis activity of recombinant TGF-β latency associated peptide. PeerJ 10:e12797 https://doi.org/10.7717/peerj.12797
Segmentation of multi-temporal polarimetric SAR data based on mean-shift and spectral graph partitioning
Abstract Polarimetric SAR (PolSAR) image segmentation is a key step in its interpretation. For the targets with time series changes, the single-temporal PolSAR image segmentation algorithm is difficult to provide correct segmentation results for its target recognition, time series analysis and other applications. For this, a new algorithm for multi-temporal PolSAR image segmentation is proposed in this paper. Firstly, the over-segmentation of single-temporal PolSAR images is carried out by the mean-shift algorithm, and the over-segmentation results of single-temporal PolSAR are combined to get the over-segmentation results of multi-temporal PolSAR images. Secondly, the edge detectors are constructed to extract the edge information of single-temporal PolSAR images and fuse them to get the edge fusion results of multi-temporal PolSAR images. Then, the similarity measurement matrix is constructed based on the over-segmentation results and edge fusion results of multi-temporal PolSAR images. Finally, the normalized cut criterion is used to complete the segmentation of multi-temporal PolSAR images. The performance of the proposed algorithm is verified based on three temporal PolSAR images of Radarsat-2, and compared with the segmentation algorithm of single-temporal PolSAR image. Experimental results revealed the following findings: (1) The proposed algorithm effectively realizes the segmentation of multi-temporal PolSAR images, and achieves ideal segmentation results. Moreover, the segmentation details are excellent, and the region consistency is good. The objects which can’t be distinguished by the single-temporal PolSAR image segmentation algorithm can be segmented. (2) The segmentation accuracy of the proposed multi-temporal algorithm is up to 86.5%, which is significantly higher than that of the single-temporal PolSAR image segmentation algorithm. In general, the segmentation result of proposed algorithm is closer to the optimal segmentation. The optimal segmentation of farmland parcel objects to meet the needs of agricultural production is realized. This lays a good foundation for the further interpretation of multi-temporal PolSAR image.
Wang et al. (2022) Segmentation of multi-temporal polarimetric SAR data based on mean-shift and spectral graph partitioning. PeerJ 10:e12805 https://doi.org/10.7717/peerj.12805