title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=581 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Feeding habits of four-finger threadfin fish, Eleutheronema tetradactylum, and its diet interaction with co-existing fish species in the coastal waters of Thailand link: https://peerj.com/articles/14688 last-modified: 2023-01-30 description: This study assessed the feeding habits of four-finger threadfin fish, Eleutheronema tetradactylum, and its diet relationship with other fish species in the tropics. Fish samples were collected from four locations along the coastal regions of Thailand. A whole year field sampling event was conducted to investigate the diet relationship of threadfin fish with other ten co-existing fish species in Pattani Bay during January 2021 and January 2022. E. tetradactylum was an active and specific predator with significant diet shift during ontogeny. Specifically, the juvenile fish fed largely on zooplankton especially Acetes/shrimp postlarvae, and small sized-fish fed on penaeid shrimps, while medium and large-sized fish shifted their diets to a combination of penaeid shrimp, fish and squid. Size and sex of fish as well as site of collection significantly affected gut fullness index and average number of food type (p < 0.05). Transitional sex fish predated almost entirely on other fishes (87.2%), whereas male and female fish fed mainly on penaeid shrimp (66.5%) and other fish (51.3%), respectively. Fish size and mouth opening controlled the size of prey, with the larger fish with larger mouth-opening fed primarily on the larger size of prey. Moreover, E. tetradactylum shared its diets inclusively with Epinephelus coioides, Johnius belangerii, Scomberomorus commerson, Scomberoides lysan, Otolithes ruber and Lutjanus russelli. Penaeid shrimp and teleost fish were the main food types shared by these fishes. This study provided important information on the feeding habits of E. tetradactylum and its diet relationship with other co-existing fish species living in the same habitat of a tropical coastal region. creator: Teuku Haris Iqbal creator: Sukree Hajisamae creator: Apiradee Lim creator: Sitthisak Jantarat creator: Wen-Xiong Wang creator: Karl W.K. Tsim uri: https://doi.org/10.7717/peerj.14688 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Iqbal et al. title: Genetic variants of IFIH1 and DHX58 affect the chronicity of hepatitis C in the Chinese Han population link: https://peerj.com/articles/14740 last-modified: 2023-01-30 description: Hepatitis C remains a major public health problem in the world. The host immune system plays a key role in viral clearance. This study aimed to investigate the connection between retinoic acid-inducible gene I-like (RIG-I-like) receptor gene polymorphism and hepatitis C chronicity in the Chinese Han population. The current study genotyped three SNPs (IFIH1 rs10930046 and DHX58 rs2074158, rs2074160) to assess their association with the chronicity of hepatitis C virus (HCV) infection among 1,590 participants (590 spontaneous HCV clearance cases and 1,000 persistent infection patients). Our research shows that DHX58 rs2074158-G allele (dominant model: adjusted OR = 1.53, 95% CI [1.20–1.95], P = 0.001; additive model: adjusted OR = 1.50, 95% CI [1.27–1.78], P < 0.001) and IFIH1 rs10930046-C allele (additive model: adjusted OR = 1.26, 95% CI [1.07–1.49], P = 0.005) were associated with chronic hepatitis C (CHC). And the risk of CHC increased in people carrying more unfavorable genotypes (rs2074158-AG/GG or rs10930046-CC), with the chronic rates for genotypes number from zero to two in 60.69%, 57.33%, and 85.93%, respectively (adjusted OR = 3.64, 95% CI [2.18–6.08]; P < 0.001). Genetic polymorphism of IFIH1 and DHX58 may be related to CHC in the Chinese Han population. Furthermore, the risk of CHC increases as the number of unfavorable genotypes carried by the HCV-infected person increases. IFIH1 rs10930046, DHX58 rs2074158, age, ALT, and AST levels were all independent predictors of CHC. creator: Peng Huang creator: Jing-Jing Wu creator: Jin-Wei Zhang creator: Yu-Qing Hou creator: Ping Zhu creator: Rong Yin creator: Rong-Bin Yu creator: Yun Zhang creator: Ming Yue creator: Wei Hou uri: https://doi.org/10.7717/peerj.14740 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Effects of summer savory (Satureja hortensis L.) and sweet corn (Zea mays L. saccharata) intercropping on crop production and essential oil profiles of summer savory link: https://peerj.com/articles/14753 last-modified: 2023-01-30 description: A 2-year field experiment evaluated the effects of sweet corn-summer savory intercropping on crop productivity and essential oil (EO) composition of summer savory. Five cropping patterns of Corn 100%:Savory 0%, C75:S25, C50:S50, C25:S75, and C0:S100 were tested. The highest corn yield (2,440 kg ha−1) was obtained in a corn monoculture, but was not significantly different from C75:S25 or C50:S50. However, in both years the highest savory yield was obtained in S100 (793.3 g m−2 and 816.6 g m−2, respectively). Savory yields decreased as the proportion of corn increased. The land equivalent ratios in C25:S75, C50:S50, and C75:S25 were 1.54 ± 0.07, 1.56 ± 0.03, and 1.35 ± 0.1, respectively. Monocropped savory had the highest EO value followed by C25:S75 and C50:C50. However, no significant differences were found among these three treatments. Gas chromatography-mass spectrometry (GC–MS) analysis showed that the major components were carvacrol (35.88%–42.96%), γ-terpinene (18.45%–20.03%), ρ-cymene (11.77%–12.24%), and α-terpinene (2.75%–3.96%). The highest amount of carvacrol was recorded in C25:S75 (42.96%). This study suggests that intercropping of corn and savory represents an effective sustainable strategy, especially for smallholders, as a way to increase their overall land productivity and to improve the quality of savory’s EO. creator: Ruhollah Naderi creator: Farzad Bijani creator: Akbar Karami creator: Bhagirath S. Chauhan creator: Todd P. Egan uri: https://doi.org/10.7717/peerj.14753 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Naderi et al. title: Prediction model for missed abortion of patients treated with IVF-ET based on XGBoost: a retrospective study link: https://peerj.com/articles/14762 last-modified: 2023-01-30 description: AimIn this study, we established a model based on XGBoost to predict the risk of missed abortion in patients treated with in vitro fertilization-embryo transfer (IVF-ET), evaluated its prediction ability, and compared the model with the traditional logical regression model.MethodsWe retrospectively collected the clinical data of 1,017 infertile women treated with IVF-ET. The independent risk factors were screened by performing a univariate analysis and binary logistic regression analysis, and then, all cases were randomly divided into the training set and the test set in a 7:3 ratio for constructing and validating the model. We then constructed the prediction models by the traditional logical regression method and the XGBoost method and tested the prediction performance of the two models by resampling.ResultsThe results of the binary logistic regression analysis showed that several factors, including the age of men and women, abnormal ovarian structure, prolactin (PRL), anti-Müllerian hormone (AMH), activated partial thromboplastin time (APTT), anticardiolipin antibody (ACA), and thyroid peroxidase antibody (TPO-Ab), independently influenced missed abortion significantly (P < 0.05). The area under the receiver operating characteristic curve (AUC) score and the F1 score with the training set of the XGBoost model (0.877 ± 0.014 and 0.730 ± 0.019, respectively) were significantly higher than those of the logistic model (0.713 ± 0.013 and 0.568 ± 0.026, respectively). In the test set, the AUC and F1 scores of the XGBoost model (0.759 ± 0.023 and 0.566 ± 0.042, respectively) were also higher than those of the logistic model (0.695 ± 0.030 and 0.550 ± 049, respectively).ConclusionsWe established a prediction model based on the XGBoost algorithm, which can accurately predict the risk of missed abortion in patients with IVF-ET. This model performed better than the traditional logical regression model. creator: Guanghui Yuan creator: Bohan Lv creator: Xin Du creator: Huimin Zhang creator: Mingzi Zhao creator: Yingxue Liu creator: Cuifang Hao uri: https://doi.org/10.7717/peerj.14762 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yuan et al. title: Association of job stress, FK506 binding protein 51 (FKBP5) gene polymorphisms and their interaction with sleep disturbance link: https://peerj.com/articles/14794 last-modified: 2023-01-30 description: BackgroundSleep disturbance is an outcome of multiple factors including environmental and genetic influences. Job stress, a complex environmental factor, likely affects sleep quality, significantly reducing the quality of life of workers. Additionally, FK506 binding protein 51 (FKBP5) may be a pathogenic factor for sleep disturbance as it regulates hypothalamic–pituitary–adrenal (HPA) axis activity, where HPA axis has been found to be involved in the regulation mechanism of sleep and stress response.ObjectivesThe main aim of this study was to investigate the association between job stress and FKBP5 gene polymorphism as well as their interaction with sleep disturbance in Chinese workers; to date, these relationships have not been explored.MethodsThis is a cross-sectional study. A total of 675 railway workers (53.8% male) completed a short Effort-Reward Imbalance questionnaire and the Pittsburgh Sleep Quality Index. The SNaPshot single nucleotide polymorphism (SNP) assay was carried out by screening for FKBP5 SNPs in every participant. Generalized multifactor dimensionality reduction (GMDR) was used to identify the strongest G×E interaction combination.ResultsThe findings showed that job stress was significantly associated with sleep disturbance; specifically, scores on the PSQI subscales (sleep disturbance, sleep medication, and daytime dysfunction) exhibited significant differences between the two job stress groups (X2 = 18.10, p = 0.01). Additionally, the FKBP5 SNP rs1360780-TT (adjusted odds ratio [AOR] = 4.98, 95% confidence interval [CI] = 2.80–8.84) and rs3800373-CC genotype (AOR = 2.06, CI = 1.10–3.86) were associated with an increased risk of sleep disturbance. Job stress and rs1360780 and rs3800373 variants showed a high-dimensional interaction with sleep disturbance as determined by the GMDR model.ConclusionThe FKBP5 gene may increase susceptibility to job stress and result in sleep disturbance, especially in the presence of negative work-related events. These findings contribute to the field of sleep disturbance prevention and treatment. creator: Peixin Li creator: Yuxi Wang creator: Baoying Liu creator: Chuancheng Wu creator: Chenzhou He creator: Xuejie Lv creator: Yu Jiang uri: https://doi.org/10.7717/peerj.14794 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Discrimination of foreign bodies in quinoa (Chenopodium quinoa Willd.) grains using convolutional neural networks with a transfer learning approach link: https://peerj.com/articles/14808 last-modified: 2023-01-30 description: The rising interest in quinoa (Chenopodium quinoa Willd.) is due to its high protein content and gluten-free condition; nonetheless, the presence of foreign bodies in quinoa processing facilities is an issue that must be addressed. As a result, convolutional neural networks have been adopted, mostly because of their data extraction capabilities, which had not been utilized before for this purpose. Consequently, the main objective of this work is to evaluate convolutional neural networks with a learning transfer for foreign bodies identification in quinoa samples. For experimentation, quinoa samples were collected and manually split into 17 classes: quinoa grains and 16 foreign bodies. Then, one thousand images were obtained from each class in RGB space and transformed into four different color spaces (L*a*b*, HSV, YCbCr, and Gray). Three convolutional neural networks (AlexNet, MobileNetv2, and DenseNet-201) were trained using the five color spaces, and the evaluation results were expressed in terms of accuracy and F-score. All the CNN approaches compared showed an F-score ranging from 98% to 99%; both color space and CNN structure were found to have significant effects on the F-score. Also, DenseNet-201 was the most robust architecture and, at the same time, the most time-consuming. These results evidence the capacity of CNN architectures to be used for the discrimination of foreign bodies in quinoa processing facilities. creator: Himer Avila-George creator: Miguel De-la-Torre creator: Jorge Sánchez-Garcés creator: Joel Jerson Coaquira Quispe creator: Jose Manuel Prieto creator: Wilson Castro uri: https://doi.org/10.7717/peerj.14808 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Avila-George et al. title: Exploring the mechanisms by which camel lactoferrin can kill Salmonella enterica serovar typhimurium and Shigella sonnei link: https://peerj.com/articles/14809 last-modified: 2023-01-30 description: There is a continuously increasing pressure associated with the appearance of Salmonella enterica Serovar typhimurium (S. typhimurium) and Shigella sonnei (S. sonnei) that have developed pathogenic multiple antibiotic resistance and the cost of cure and control of these enterobacteriaceae infections increases annually. The current report for first time demonstrated the distinguished antimicrobial action of camel lactoferrin (cLf) obtained from the milk of different clans of camel in Saudi Arabia against S. typhimurium and S. sonnei. These cLf subtypes showed comparable antimicrobial potential when tested against the two bacterial strains but were superior to either bovine (bLf) or human lactoferrin (hLf). The synergism between lactoferrins and antibiotics concerning their antibacterial efficacies against the two bacterial strains was evident. Exploring mechanisms by which camel lactoferrin can kill S. typhimurium and S. sonnei revealed that cLf affects bacterial protein profile. Besides, it interacts with bacterial lipopolysaccharides (LPS) and numerous membrane proteins of S. typhimurium and S. sonnei, with each bacterial strain possessing distinctive binding membrane proteins for lactoferrin. Furthermore, as evidenced by electron microscopy analysis, cLf induces extracellular and intracellular morphological changes in the test bacterial strains when used alone or in combination treatment with antibiotics. Lactoferrin and antibiotics combination strongly disrupts the integrity of the bacterial cells and their membranes. Therefore, cLf can kill S. typhimurium and S. sonnei by four different mechanisms, such as iron chelation, affecting some bacterial proteins, binding to bacterial LPS and membrane proteins, and impairing the integrity of the bacterial cells and their membranes. creator: Hussein A. Almehdar creator: Nawal Abd El-Baky creator: Ehab H. Mattar creator: Raed Albiheyri creator: Atif Bamagoos creator: Abdullah Aljaddawi creator: Vladimir N. Uversky creator: Elrashdy M. Redwan uri: https://doi.org/10.7717/peerj.14809 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Almehdar et al. title: A quantitative approach on environment-food nexus: integrated modeling and indices for cumulative impact assessment of farm management practices link: https://peerj.com/articles/14816 last-modified: 2023-01-30 description: BackgroundBest management practices (BMPs) are promising solutions that can partially control pollution discharged from farmlands. These strategies, like fertilizer reduction and using filter strips, mainly control nutrient (N and P) pollution loads in basins. However, they have secondary impacts on nutrition production and ecosystem. This study develops a method to evaluate the cumulative environmental impacts of BMPs. It also introduces and calculates food’s environmental footprint (FEF) for accounting the total environmental damages per nutrition production.MethodsThis study combines the soil and water assessment tool (SWAT) for basin simulation with the indices of ReCiPe, a life cycle impact assessment (LCIA) method. By these means, the effectiveness of BMPs on pollution loads, production yields, and water footprints (WFs) are evaluated and converted as equivalent environmental damages. This method was verified in Zrebar Lake, western Iran. Here, water consumption, as WFs, and eutrophication are the main indices that are converted into equivalent health and ecological impairments. Two methods, entropy and environmental performance index (EPI), are used for weighting normalized endpoints in last step.ResultsResults showed that using 25–50% less fertilizer and water for irrigation combined with vegetated filter strips reduce N and P pollution about 34–60% and 8–21%, respectively. These can decrease ecosystem damages by 5–9% and health risks by 7–14%. Here, freshwater eutrophication is a more critical damage in ecosystem. However, using less fertilizer adversely reduces total nutrition production by 1.7–3.7%. It means that BMPs can decline total ecological damages and health risks, which threatens nutrition production. FEF presents a tool to solve this dilemma about the sustainability of BMPs. In the study area, a 4–9% decrease in FEF means that BMPs are more environmental friendly than nutrition menacing. Finally, this study concludes that SWAT-ReCiPe with FEF provides a quantitative framework for environment-food nexus assessment. However, due to the uncertainties, this method is recommended as a tool for comparing management strategies instead of reporting certain values. creator: Shervin Jamshidi creator: Anahita Naderi uri: https://doi.org/10.7717/peerj.14816 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jamshidi and Naderi title: Microscopic polyangiitis plasma-derived exosomal miR-1287-5p induces endothelial inflammatory injury and neutrophil adhesion by targeting CBL link: https://peerj.com/articles/14579 last-modified: 2023-01-27 description: BackgroundAn inflammatory environment around the vessel wall caused by leukocyte infiltration is one of the characteristic histopathological features of microscopic polyangiitis (MPA); however, the pathogenic mechanisms are not fully understood. Studies have found that circulating microRNA (miRNA) can be used as potential biomarkers for the diagnosis and classification of anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitides (AAV), and the E3 ubiquitin ligase casitas B-lineage lymphoma (CBL) seems to be associated with inflammation. In addition, evidence indicates that miRNA can be tracked into exosomes and transferred into recipient cells to mediate the process of vascular endothelial injury. Herein, we aimed to identify the profiles of exosomal miRNA, and determine the effect of exosomal miR-1287-5p and its target gene CBL on vascular endothelial cells in MPA.MethodWe isolated plasma exosomes from patients with MPA (MPA-exo) and healthy controls (HC-exo) by ultracentrifugation and conducted exosome small-RNA sequencing to screen differential miRNA expression in MPA-exo (n = 3) compared to HC-exo (n = 3). We measured the expression levels of miR-1303, miR-1287-5p, and miR-129-1-3p using quantitative reverse transcription-polymerase chain reaction (qRT-PCR, n = 6) and performed dual luciferase reporter gene assays to confirm the downstream target gene of miR-1287-5p. In addition, we treated human umbilical vein endothelial cell (HUVEC) with MPA-exo, or transfected them with miR-1287-5p mimic/inhibitor or with CBL-siRNA/CBL-siRNA+ miR-1287-5p inhibitor. After cell culture, we evaluated the effects on vascular endothelial cells by examining the mRNA levels of IL-6, IL-8, MCP-1, ICAM-1 and E-selectin using qRT-PCR and performed neutrophil adhesion assay with haematoxylin staining.ResultTransmission electron microscopy, Western blot and nanoparticle tracking analysis showed that we successfully purified exosomes and MPA-exo could be absorbed into HUVEC. We screened a total of 1,077 miRNA by sequencing and observed a high abundance of miR-1287-5p in the exosomes obtained from MPA plasma. The dual luciferase reporter assay identified CBL as a downstream target gene of miR-1287-5p, and the results revealed that MPA-exo decreased CBL protein expression in HUVEC. In addition, treatment with MPA-exo, up-regulating miR-1287-5p or silencing of CBL in HUVEC significantly increased the mRNA expression of inflammatory factors (including IL-6, IL-8, and MCP-1) and adhesion molecules (including ICAM-1 and E-selection) and promoted the adhesion of neutrophils to HUVEC. However, down-regulating miR-1287-5p had the opposite effect.ConclusionOur study revealed that MPA-exo was involved in the intercellular transfer of miR-1287-5p and subsequently promote the development of acute endothelial injury in MPA. MiR-1287-5p and CBL agonists may be promising therapeutic approach for MPA-induced vascular inflammatory injury. creator: Yan Zhu creator: Liu Liu creator: Liepeng Chu creator: Jingjing Lan creator: Jingsi Wei creator: Wei Li creator: Chao Xue uri: https://doi.org/10.7717/peerj.14579 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhu et al. title: Plain set and stirred yogurt with different additives: implementation of food safety system as quality checkpoints link: https://peerj.com/articles/14648 last-modified: 2023-01-27 description: Hazard Analysis Critical Control Point (HACCP) is a risk management protocol developed to ensure food safety through a precautionary approach that is believed to offer assurances in producing safe food for customers. Yogurt is made in a number of phases, commencing with the collection of raw milk and ending with consumer consumption. While this is happening, major economic and health issues might arise from exposing the manufacturing line to biological, chemical, and/or physical contaminations. As a result, the decision tree approach was used to determine the CCPs during the production of yogurt. Additionally, biological dangers are incorporated as a by-product of the system’s implementation performance. In particular, the plain set and nut puree-honey-fortified stirred yogurt manufacturing techniques are highlighted for the first time in this study. The potential manufacturing risks are described for the first time, together with information on how HACCP plans may guard against major risks that could result in the production of yogurt that is not in compliance with established standards. creator: Aya Allam creator: Noha Shafik creator: Ahmed Zayed creator: Ibrahim Khalifa creator: Ibrahim A. Bakry creator: Mohamed A. Farag uri: https://doi.org/10.7717/peerj.14648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Allam et al.