Effects of food hydrocolloids on quality attributes of extruded red Jasmine rice noodle
The aim of this study was to examine the quality characteristics of extruded red Jasmine rice flour (RJF) noodle that had been prepared with hydrocolloids, namely guar gum (GG), carboxymethyl cellulose (CMC), and xanthan gum (XG) at the concentrations of 0.0 (control sample), 0.2, and 0.4% (w/w), respectively. The use of hydrocolloids had no effect on total phenolic contents, antioxidant properties (DPPH, ABTS, and FRAP), color, and X-ray diffraction patterns (p > 0.05). In contrast, the hydrocolloids tended to increase the expansion ration of the noodle. GG and CMC improved cooking, textural, and sensory properties. Ultimately, 0.2%-GG showed the lowest cooking loss (5.07%) when compared with others. Moreover, it also provided the noodle with better textural properties such as tensile strength, extensibility, hardness, cohesiveness, and chewiness (p < 0.05). For these reasons, the highest acceptability (6.75) for the noodle was achieved with GG02. XG resulted in lower overall acceptability (5.05), particularly the 0.4%-XG recipe (p < 0.05). Thus, usage of 0.2%-GG was the best option for improving the qualities of extruded RJF noodle. XG was deemed ineffective for improving the noodle.
Kraithong et al. (2020) Effects of food hydrocolloids on quality attributes of extruded red Jasmine rice noodle. PeerJ 8:e10235 https://doi.org/10.7717/peerj.10235
Prognostic model of invasive ductal carcinoma of the breast based on differentially expressed glycolysis-related genes
Background Invasive ductal carcinoma (IDC) is a common pathological type of breast cancer that is characterized by high malignancy and rapid progression. Upregulation of glycolysis is a hallmark of tumor growth, and correlates with the progression of breast cancer. We aimed to establish a model to predict the prognosis of patients with breast IDC based on differentially expressed glycolysis-related genes (DEGRGs). Methods Transcriptome data and clinical data of patients with breast IDC were from The Cancer Genome Atlas (TCGA). Glycolysis-related gene sets and pathways were from the Molecular Signatures Database (MSigDB). DEGRGs were identified by comparison of tumor tissues and adjacent normal tissues. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression were used to screen for DEGRGs with prognostic value. A risk-scoring model based on DEGRGs related to prognosis was constructed. Receiver operating characteristic (ROC) analysis and calculation of the area under the curve (AUC) were used to evaluate the performance of the model. The model was verified in different clinical subgroups using an external dataset (GSE131769). A nomogram that included clinical indicators and risk scores was established. Gene function enrichment analysis was performed, and a protein-protein interaction network was developed. Results We analyzed data from 772 tumors and 88 adjacent normal tissues from the TCGA database and identified 286 glycolysis-related genes from the MSigDB. There were 185 DEGRGs. Univariate Cox regression and LASSO regression indicated that 13 of these genes were related to prognosis. A risk-scoring model based on these 13 DEGRGs allowed classification of patients as high-risk or low-risk according to median score. The duration of overall survival (OS) was longer in the low-risk group (P < 0.001), and the AUC was 0.755 for 3-year OS and 0.726 for 5-year OS. The results were similar when using the GEO data set for external validation (AUC for 3-year OS: 0.731, AUC for 5-year OS: 0.728). Subgroup analysis showed there were significant differences in OS among high-risk and low-risk patients in different subgroups (T1-2, T3-4, N0, N1-3, M0, TNBC, non-TNBC; all P < 0.01). The C-index was 0.824, and the AUC was 0.842 for 3-year OS and 0.808 for 5-year OS from the nomogram. Functional enrichment analysis demonstrated the DEGRGs were mainly involved in regulating biological functions. Conclusions Our prognostic model, based on 13 DEGRGs, had excellent performance in predicting the survival of patients with IDC of the breast. These DEGRGs appear to have important biological functions in the progression of this cancer.
Li et al. (2020) Prognostic model of invasive ductal carcinoma of the breast based on differentially expressed glycolysis-related genes. PeerJ 8:e10249 https://doi.org/10.7717/peerj.10249
Identifying myocardial injuries in “normal-appearing” myocardium in pediatric patients with clinically suspected myocarditis using mapping techniques
Background Mapping techniques using cardiac magnetic resonance imaging have significantly improved the diagnostic accuracy for myocarditis with focal myocardial injuries. The aim of our study was to determine whether T1 and T2 mapping techniques could identify diffuse myocardial injuries in “normal-appearing” myocardium in pediatric patients with clinically suspected myocarditis and to evaluate the associations between diffuse myocardial injuries and cardiac function parameters. Methods Forty-six subjects were included in this study: 20 acute myocarditis patients, 11 subacute/chronic myocarditis patients and 15 control children. T2 values, native T1 values and the extracellular volume (ECV) of “normal-appearing” myocardium were compared among the three groups of patients. Associations between diffuse myocardial injuries and cardiac function parameters were also evaluated. Results The ECV of “normal-appearing” myocardium was significantly higher in the subacute/chronic myocarditis group than in the control group (30.1 ± 0.9 vs 27.0 ± 0.6, P =0.004). No significant differences in T1 and T2 values between the acute myocarditis and control groups were found. In the subacute/chronic myocarditis group, a significant association between ECV and left ventricle ejection fraction was found (P=0.03). Conclusions Diffuse myocardial injuries are likely to occur in subacute/chronic myocarditis patients with prolonged inflammatory responses. Mapping techniques have great value for the diagnosis and monitoring of myocarditis.
Wang et al. (2020) Identifying myocardial injuries in “normal-appearing” myocardium in pediatric patients with clinically suspected myocarditis using mapping techniques. PeerJ 8:e10252 https://doi.org/10.7717/peerj.10252
Tnni1b-ECR183-d2, an 87 bp cardiac enhancer of zebrafish
Background Several heart malformations are associated with mutations in the regulatory regions of cardiac genes. Troponin I type 1b (tnni1b) is important for the formation of the atrioventricular canal in zebrafish hearts; however, the regulation of tnni1b is poorly understand. We aimed to identify a small but functional enhancer that is distal to tnni1b. Methods Evolutionary Conserved Region (ECR) Browser was used to analyze the 219 kb zebrafish and human genomes covering the tnni1b gene as well as the 100 kb regions upstream and downstream of tnni1b. Putative transcription factor binding sites (TFBSs) were analyzed using JASPAR and PROMO, and the enhancer activity was identified using zebrafish embryos and the luciferase reporter assay. A correlation analysis between the enhancer and transcription factors (TFs) was performed via TF overexpression and TFBS mutation experiments and the electrophoretic mobility shift assay (EMSA). To analyze the conservation between zebrafish and human enhancers, human DNA fragments were functionally verified. Images were captured and analyzed by fluorescence microscopy or confocal microscopy. Results Combined with comparative analysis and functional validation, we identified a 183 bp ECR (termed tnni1b-ECR183) that was located approximately 84 kb upstream of tnni1b that had the heart-specific enhancer activity in zebrafish. TFBS analysis and the enhancer activity detection assay data showed that the 87 bp core region (termed tnni1b-ECR183-d2) was capable of driving specific GFP expression near the atrioventricular junction and increased luciferase expression in HEK293 and HL1 cell lines. The GFP pattern in zebrafish embryos was similar to the expression profiles of tnni1b. A correlation analysis showed that the enhancer activity of tnni1b-ECR183-d2 was increased when NKX2.5 (p = 0.0006) or JUN (p < 0.0001) was overexpressed and was decreased when the TFBSs of NKX2.5 (p < 0.0001) or JUN (p = 0.0018) were mutated. In addition, DNA-protein interactions were not observed between these TFs and tnni1b-ECR183-d2 in the EMSA experiment. The conservation analysis showed that tnni1b-ECR183-h179 (aligned from tnni1b-ECR183) drove GFP expression in the heart and skeletal muscles and increased the luciferase expression after NKX2.5 (p < 0.0001), JUN (p < 0.0001) or ETS1 (p < 0.0001) was overexpressed. Interestingly, the truncated fragment tnni1b-ECR183-h84 mainly drove GFP expression in the skeletal muscles of zebrafish and the enhancer activity decreased when NKX2.5 (p = 0.0028), ETS1 (p = 0.0001) or GATA4 (p < 0.0001) was overexpressed. Conclusions An 87 bp cardiac-specific enhancer located 84 kb upstream of tnni1b in zebrafish was positively correlated with NKX2.5 or JUN. The zebrafish and human enhancers in this study target different tissues. The GFP expression mediated by tnni1b-ECR183-d2 is a valuable tool for marking the domain around the atrioventricular junction.
Zhang et al. (2020) Tnni1b-ECR183-d2, an 87 bp cardiac enhancer of zebrafish. PeerJ 8:e10289 https://doi.org/10.7717/peerj.10289
Identification of the miRNA-mRNA regulatory pathways and a miR-21-5p based nomogram model in clear cell renal cell carcinoma
Background The purpose of this study was to determine the key microRNAs (miRNAs) and their regulatory networks in clear cell renal cell carcinoma (ccRCC). Methods Five mRNA and three microRNA microarray datasets were downloaded from the Gene Expression Omnibus database and used to screen the differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs). Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed with Metascape. A miRNA-mRNA network was mapped with the Cytoscape tool. The results were validated with data from The Cancer Genome Atlas (TCGA) and qRT-PCR. A nomogram model based on independent prognostic key DEMs, stage and grade was constructed for further investigation. Results A total of 26 key DEMs and 307 DEGs were identified. Dysregulation of four key DEMs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) was identified to correlate with overall survival. The results were validated with TCGA data and qRT-PCR. The nomogram model showed high accuracy in predicting the prognosis of patients with ccRCC. Conclusion We identified 26 DEMs that may play vital roles in the regulatory networks of ccRCC. Four miRNAs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) were considered as potential biomarkers in the prognosis of ccRCC, among which only miR-21-5p was found to be an independent prognostic factor. A nomogram model was then created on the basis of independent factors for better prediction of prognosis for patients with ccRCC. Our results suggest a need for further experimental validation studies.
Zhao et al. (2020) Identification of the miRNA-mRNA regulatory pathways and a miR-21-5p based nomogram model in clear cell renal cell carcinoma. PeerJ 8:e10292 https://doi.org/10.7717/peerj.10292
Biomechanics of lower limb in badminton lunge: a systematic scoping review
Background Badminton is a popular sport activity in both recreational and elite levels. A lot of biomechanical studies have investigated badminton lunge, since good lunge performance may increase the chances to win the game. This review summarized the current trends, research methods, and parameters-of-interest concerning lower-extremity biomechanics in badminton lunges. Methodology Databases including Web of Science, Cochrane Library, Scopus, and PubMed were searched from the oldest available date to September 2020. Two independent authors screened all the articles and 20 articles were eligible for further review. The reviewed articles compared the differences among playing levels, footwear designs, and lunge directions/variations, using parameters including ground reaction forces, plantar pressure distribution, kinematics, and kinetics. Results Elite badminton players demonstrated higher impact attenuation capability, more aggressive knee and ankle strategy (higher mechanical moment), and higher medial plantar load than amateur players. Footwear modifications can influence comfort perception and movement mechanics, but it remains inconclusive regarding how these may link with lunging performance. Contradicting findings in kinematics is possibly due to the variations in lunge and instructions. Conclusions Playing levels and shoe designs have significant effects on biomechanics in badminton lunges. Future studies can consider to use an unanticipated testing protocol and realistic movement intensity. They can study the inter-limb coordination as well as the contributions and interactions of intrinsic and extrinsic factors to injury risk. Furthermore, current findings can stimulate further research studying whether some specific footwear materials with structural design could potentially compromise impact attenuation, proprioception, and performance.
Lam et al. (2020) Biomechanics of lower limb in badminton lunge: a systematic scoping review. PeerJ 8:e10300 https://doi.org/10.7717/peerj.10300
Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields
Cadmium pollution is becoming a serious problem due to its nondegradability and substantial negative influence on the normal growth of crops, thereby harming human health through the food chain. Rhizospheric bacteria play important roles in crop tolerance. However, there is little experimental evidence which demonstrates how various cadmium concentrations affect the bacterial community in wheat fields including rhizosphere microorganisms and nonrhizosphere (bulk) microorganisms. In this study, 16S rRNA amplicon sequencing technology was used to investigate bacterial communities in rhizosphere and bulk soils under different levels of pollution in terms of cadmium concentration. Both the richness and diversity of the rhizosphere microorganism community were higher under nonpolluted soil and very mild and mild cadmium-contaminated soils than compared with bulk soil, with a shift in community profile observed under severe cadmium pollution. Moreover, cadmium at various concentrations had greater influence on bacterial composition than for the nonpolluted site. In addition, redundancy analysis (RDA) and Spearman’s analysis elucidated the impact of exchangeable Cd and total Cd on bacterial community abundance and composition. This study suggests that cadmium imposes a distinct effect on bacterial community, both in bulk and rhizosphere soils of wheat fields. This study increases our understanding of how bacterial communities in wheat fields shaped under different concentrations of cadmium.
Environmental Contamination and Remediation
Song et al. (2020) Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields. PeerJ 8:e10302 https://doi.org/10.7717/peerj.10302
Duration of hemodialysis associated with cardio-respiratory dysfunction and breathlessness: a multicenter study
Background Patients with hemodialysis suffer with protein-energy wasting and uremic myopathy lead to lack of physical activity and poor functional performance. However, ventilation abnormality in patients undergone hemodialysis remains controversial regarding the respiratory impairment. Therefore, the study aimed to determine the effect of duration of dialysis on respiratory function. Methods A multicenter study with cross-sectional study was designed in four hemodialysis outpatient clinics. Respiratory muscle strength (i.e., maximal inspiratory pressure (MIP) and maximal expiratory pressure (MEP)) pulmonary function test (i.e., forced vital capacity (FVC), forced expiratory volume in one second (FEV1) and FEV1/FVC ratio), functional capacity (6-minute walk test) and sensation of breathlessness were assessed prior to dialysis. Results A total of 100 hemodialysis patients were recruited with 38 females and 62 males. An average of duration of hemodialysis was 5.93± 4.96 years. Decreased MIP values, FEV1 values, FVC values, %FEV1 and %FVC were noted in patients with long duration of dialysis (defined as ≥ 5 years of dialysis) compared to those with short duration of dialysis (ps < .05). In addition, increased sensation of breathlessness was observed in patients with long duration of dialysis (p < .05). Furthermore, participants with long duration of dialysis had an increased risk of ventilatory restriction (OR 6.093, p = .007).
Yuenyongchaiwat et al. (2020) Duration of hemodialysis associated with cardio-respiratory dysfunction and breathlessness: a multicenter study. PeerJ 8:e10333 https://doi.org/10.7717/peerj.10333
Gut microbiota in hospitalized children with acute infective gastroenteritis caused by virus or bacteria in a regional Peruvian hospital
Background Acute infective gastroenteritis (AIG) is a leading cause of mortality in children worldwide. In Peru, more than 40% of cases of AIG occurring in children under 5 years old. The disruption of the gut microbiota can increase risk for several health complications especially in patients with gastric infections caused by viruses or bacteria. Objective The main objective of this study was to describe the prevalence of 13 representative bacteria from the gut microbiota (GM) in stools samples from children under 5 years of age with acute infective gastroenteritis. Results The most commonly isolated bacteria from the GM were Firmicutes (63.2% 74/117) Bacteriodetes (62.4%; 73/117), Lactobacillus (59.8%; 70/117), Prevotella (57.2%; 67/117), Proteobacterium (53.8%; 63/117), regardless of the etiological agent responsible for the AIG. Interestingly, despite the high prevalence of Firmicutes, Bacteroidetes, Lactobacillus and Prevotella across all samples, a visible reduction of these agents was observed especially among patients with a single bacterial infection or even bacteria–bacteria coinfections when compared to viral etiologies. Patients with exclusive or mixed breastfeeding registered the highest amount of gut microbiota bacteria, in contrast to infants who received formula or were not breastfed.
Taco-Masias et al. (2020) Gut microbiota in hospitalized children with acute infective gastroenteritis caused by virus or bacteria in a regional Peruvian hospital. PeerJ 8:e9964 https://doi.org/10.7717/peerj.9964
Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics
Background Although asthma is one of the most common chronic, noncommunicable diseases worldwide, the pathogenesis of childhood asthma is not yet clear. Genetic factors and environmental factors may lead to airway immune-inflammation responses and an imbalance of airway nerve regulation. The aim of the present study was to determine which serum proteins are differentially expressed between children with or without asthma and to ascertain the potential roles that these differentially expressed proteins (DEPs) may play in the pathogenesis of childhood asthma. Methods Serum samples derived from four children with asthma and four children without asthma were collected. The DEPs were identified by using isobaric tags for relative and absolute quantitation (iTRAQ) combined with liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses. Using biological information technology, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Cluster of Orthologous Groups of Proteins (COG) databases and analyses, we determined the biological processes associated with these DEPs. Key protein glucose-6-phosphate dehydrogenase (G6PD) was verified by enzyme linked immunosorbent assay (ELISA). Results We found 46 DEPs in serum samples of children with asthma vs. children without asthma. Among these DEPs, 12 proteins were significantly (>1.5 fold change) upregulated and 34 proteins were downregulated. The results of GO analyses showed that the DEPs were mainly involved in binding, the immune system, or responding to stimuli or were part of a cellular anatomical entity. In the KEGG signaling pathway analysis, most of the downregulated DEPs were associated with cardiomyopathy, phagosomes, viral infections, and regulation of the actin cytoskeleton. The results of a COG analysis showed that the DEPs were primarily involved in signal transduction mechanisms and posttranslational modifications. These DEPs were associated with and may play important roles in the immune response, the inflammatory response, extracellular matrix degradation, and the nervous system. The downregulated of G6PD in the asthma group was confirmed using ELISA experiment. Conclusion After bioinformatics analyses, we found numerous DEPs that may play important roles in the pathogenesis of childhood asthma. Those proteins may be novel biomarkers of childhood asthma and may provide new clues for the early clinical diagnosis and treatment of childhood asthma.
Li et al. (2020) Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics. PeerJ 8:e9971 https://doi.org/10.7717/peerj.9971