title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=271 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Trichoderma based formulations control the wilt disease of chickpea (Cicer arietinum L.) caused by Fusarium oxysporum f. sp. ciceris, better when inoculated as consortia: findings from pot experiments under field conditions link: https://peerj.com/articles/17835 last-modified: 2024-08-19 description: BackgroundCommercial/chemical pesticides are available to control Fusarium wilt of chickpea, but these antifungals have numerous environmental and human health hazards. Amongst various organic alternatives, use of antagonistic fungi like Trichoderma, is the most promising option. Although, Trichoderma spp. are known to control Fusarium wilt in chickpea but there are no reports that indicate the biocontrol efficacy of indigenous Trichoderma spp. against the local pathogen, in relation to environmental conditions.MethodsIn the present study, biological control activity of Trichoderma species formulations viz., Trichoderma asperellum, Trichoderma harzianum (strain 1), and Trichoderma harzianum (strain 2), either singly or in the form of consortia, was investigated against Fusarium oxysporum f. sp. ciceris, the cause of Fusarium wilt in chickpea, in multiyear pot trials under open field conditions. The antagonistic effect of Trichoderma spp. was first evaluated in in vitro dual culture experiments. Then the effects of Trichoderma as well as F. oxysporum, were investigated on the morphological parameters, disease incidence (DI), and disease severity (DS) of chickpea plants grown in pots.ResultsIn dual culture experiments, all the Trichoderma species effectively reduced the mycelial growth of F. oxysporum. T. asperellum, T. harzianum (strain 1), and T. harzianum(strain 2) declined the mycelial growth of F. oxysporumby 37.6%, 40%, and 42%. In open field pot trials, the infestation of F. oxysporum in chickpea plants significantly reduced the morphological growth of chickpea. However, the application of T. asperellum, T. harzianum (strain 1), and T. harzianum (strain 2), either singly or in the form of consortia, significantly overcome the deleterious effects of the pathogen, thereby resulted in lower DI (22.2% and 11.1%) and DS (86% and 92%), and ultimately improved the shoot length, shoot fresh weight and shoot dry weight by 69% and 72%, 67% and 73%, 68% and 75%, during the years 1 and 2, respectively, in comparison with infested control. The present study concludes the usefulness and efficacy of Trichoderma species in controlling wilt disease of chickpea plants under variable weather conditions. creator: Safeer A. Chohan creator: Muhammad Akbar creator: Umer Iqbal uri: https://doi.org/10.7717/peerj.17835 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chohan et al. title: Biological factors associated with long COVID and comparative analysis of SARS-CoV-2 spike protein variants: a retrospective study in Thailand link: https://peerj.com/articles/17898 last-modified: 2024-08-19 description: BackgroundPost-acute COVID-19 syndrome (long COVID) refers to the persistence of COVID-19 symptoms or exceptional symptoms following recovery. Even without conferring fatality, it represents a significant global public health burden. Despite many reports on long COVID, the prevalence and data on associated biological factors remain unclear and limited. This research aimed to determine the prevalence of long COVID during the two distinct epidemic periods in Thailand, due to the Delta and Omicron variants of SARS-CoV-2, and to investigate the biological factors associated with long COVID. In addition, the spike protein amino acid sequences of the Delta and Omicron variants were compared to determine the frequency of mutations and their potential biological implications.MethodsA retrospective cross-sectional study was established to recruit confirmed COVID-19 participants at Maharat Nakhon Ratchasima Hospital who had recovered for at least three months and were infected between June 2021 and August 2022. The demographic data and long COVID experience were collected via telephone interview. The biological factors were analyzed through binary logistic regression. The datasets of the SARS-CoV-2 spike protein amino acid sequence of the Delta and Omicron variants in Thailand were retrieved from GIDSAID to determine mutation frequencies and to identify possible roles of the mutations based on published data.ResultsData was collected from a total of 247 participants comprising 106 and 141 participants of the Delta and Omicron epidemic periods, respectively. Apart from the COVID-19 severity and health status, the baseline participant data of the two time periods were remarkably similar. The prevalence of long COVID observed in the Omicron period was higher than in the Delta period (74.5% vs. 66.0%). The biological factors associated with long COVID were epidemic variant, age, treatment with symptomatic medicines, and vaccination status. When the spike protein sequence data of the two variants were compared, it was observed that the Omicron variant exhibited a greater quantity of amino acid changes in its receptor-binding domain (RBD) and receptor-binding motif (RBM). The critical changes of the Omicron variant within these regions had a significant function in enhancing virus transmissibility and host immune response resistance.ConclusionThis study revealed informative data associated with long COVID in Thailand. More attention should be given to long COVID caused by unique virus variants and other biological factors to prepare a healthcare management strategy for COVID-19 patients after recovery. creator: Supanchita Kiatratdasakul creator: Pirom Noisumdaeng creator: Nattamon Niyomdecha uri: https://doi.org/10.7717/peerj.17898 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kiatratdasakul et al. title: Bioinformatics analysis of oxidative stress genes in the pathogenesis of ulcerative colitis based on a competing endogenous RNA regulatory network link: https://peerj.com/articles/17213 last-modified: 2024-08-16 description: BackgroundUlcerative colitis (UC) is a common chronic disease associated with inflammation and oxidative stress. This study aimed to construct a long noncoding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network based on bioinformatics analysis and to explore oxidative stress-related genes underlying the pathogenesis of UC.MethodsThe GSE75214, GSE48959, and GSE114603 datasets were downloaded from the Gene Expression Omnibus database. Following differentially expressed (DE) analysis, the regulatory relationships among these DERNAs were identified through miRDB, miRTarBase, and TargetScan; then, the lncRNA-miRNA-mRNA network was established. The Molecular Signatures Database (MSigDB) was used to search oxidative stress-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for functional annotation and enrichment analyses. Based on the drug gene interaction database DGIdb, drugs that interact with oxidative stress-associated genes were explored. A dextran sulfate sodium (DSS)-induced UC mouse model was used for experimental validation.ResultsA total of 30 DE-lncRNAs, 3 DE-miRNAs, and 19 DE-mRNAs were used to construct a lncRNA-miRNA-mRNA network. By comparing these 19 DE-mRNAs with oxidative stress-related genes in MSigDB, three oxidative stress-related genes (CAV1, SLC7A11, and SLC7A5) were found in the 19 DEM sets, which were all negatively associated with miR-194. GO and KEGG analyses showed that CAV1, SLC7A11, and SLC7A5 were associated with immune inflammation and steroid hormone synthesis. In animal experiments, the results showed that dexamethasone, a well-known glucocorticoid drug, could significantly decrease the expression of CAV1, SLC7A11, and SLC7A5 as well as improve UC histology, restore antioxidant activities, inhibit inflammation, and decrease myeloperoxidase activity.ConclusionSLC7A5 was identified as a representative gene associated with glucocorticoid therapy resistance and thus may be a new therapeutic target for the treatment of UC in the clinic. creator: Qifang Li creator: Yuan Liu creator: Bingbing Li creator: Canlei Zheng creator: Bin Yu creator: Kai Niu creator: Yi Qiao uri: https://doi.org/10.7717/peerj.17213 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: A retrospective evaluation of individual thigh muscle volume disparities based on hip fracture types in followed-up patients: an AI-based segmentation approach using UNETR link: https://peerj.com/articles/17509 last-modified: 2024-08-16 description: BackgroundHip fractures are a common and debilitating condition, particularly among older adults. Loss of muscle mass and strength is a common consequence of hip fractures, which further contribute to functional decline and increased disability. Assessing changes in individual thigh muscles volume in follow-up patients can provide valuable insights into the quantitative recovery process and guide rehabilitation interventions. However, accurately measuring anatomical individual thigh muscle volume can be challenging due to various, labor intensive and time-consuming.Materials and MethodsThis study aimed to evaluate differences in thigh muscle volume in followed-up hip fracture patients computed tomography (CT) scans using an AI based automatic muscle segmentation model. The study included a total of 18 patients at Gyeongsang National University, who had undergone surgical treatment for a hip fracture. We utilized the automatic segmentation algorithm which we have already developed using UNETR (U-net Transformer) architecture, performance dice score = 0.84, relative absolute volume difference 0.019 ± 0.017%.ResultsThe results revealed intertrochanteric fractures result in more significant muscle volume loss (females: −97.4 cm3, males: –178.2 cm3) compared to femoral neck fractures (females: −83 cm3, males: −147.2 cm3). Additionally, the study uncovered substantial disparities in the susceptibility to volume loss among specific thigh muscles, including the Vastus lateralis, Adductor longus and brevis, and Gluteus maximus, particularly in cases of intertrochanteric fractures.ConclusionsThe use of an automatic muscle segmentation model based on deep learning algorithms enables efficient and accurate analysis of thigh muscle volume differences in followed up hip fracture patients. Our findings emphasize the significant muscle loss tied to sarcopenia, a critical condition among the elderly. Intertrochanteric fractures resulted in greater muscle volume deformities, especially in key muscle groups, across both genders. Notably, while most muscles exhibited volume reduction following hip fractures, the sartorius, vastus and gluteus groups demonstrated more significant disparities in individuals who sustained intertrochanteric fractures. This non-invasive approach provides valuable insights into the extent of muscle atrophy following hip fracture and can inform targeted rehabilitation interventions. creator: Hyeon Su Kim creator: Shinjune Kim creator: Hyunbin Kim creator: Sang-Youn Song creator: Yonghan Cha creator: Jung-Taek Kim creator: Jin-Woo Kim creator: Yong-Chan Ha creator: Jun-Il Yoo uri: https://doi.org/10.7717/peerj.17509 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Kim et al. title: A systematic review on the morphology structure, propagation characteristics, resistance physiology and exploitation and utilization of Nitraria tangutorum Bobrov. link: https://peerj.com/articles/17830 last-modified: 2024-08-16 description: Nitraria tangutorum Bobrov., belonging to the family Nitrariaceae, is a drought-tolerant and salt-loving plant and has drawn attention for its good economic and ecological value. As one of the main group species and dominant species in China’s desert and semi-desert regions, N. tangutorum possesses superior tolerance to drought, high temperature, cold, barren, high salinity and alkalinity and wind and sand. Its root system is well developed, with many branches and a strong germination capacity. Once buried in sandy soil, N. tangutorum can quickly produce a large number of adventitious roots, forming new plants and continuously expanding the shrubs, forming fixed and semi-fixed shrub sand dunes. Sand dune shrubs can trap and fix a large amounts of quicksand, prevent desert expansion and erosion, and play an important role in maintaining regional ecosystem balance and improving ecological environmental quality. In addition, the phytochemical screening studies report that N. tangutorum contains an abundance of various compounds including flavonoids, alkaloids, phenolic acids and polysaccharides. These compounds confer a range of beneficial bioactivities such as antioxidant, anti-inflammatory, anti-tumor, anti-fatigue, liver protection, neuroprotection, cardiovascular protection, lowering blood lipid, regulating blood sugar level and immunoregulation. The fruits of N. tangutorum also contain vitamin C, amino acids, minerals and microelements. It has been traditionally used as a nutritional food source and in folk medicine to treat diseases of the spleen and stomach, abnormal menstruation, indigestion, and hyperlipidemia. N. tangutorum, as a wild plant with medicinal and edible homology, possesses remarkable economic and medicinal values. This detailed, comprehensive review gathers and presents all the information related to the morphological structure, propagation characteristics, resistance physiology and exploitation and utilization of N. tangutorum, providing a theoretical basis for the researchers to conduct future in-depth research on N. tangutorum. creator: Xiaolan Li creator: Hanghang Liu creator: Chaoqun Li creator: Yi Li uri: https://doi.org/10.7717/peerj.17830 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Comparative study of the antibacterial effects of wound secretions of different cultivars of Chinese fir link: https://peerj.com/articles/17850 last-modified: 2024-08-16 description: BackgroundThe bark of Chinese fir (Cunninghamia lanceolata), the largest afforestation tree species in the forest areas of southern China, is susceptible to injuries and bites from small animals. The population of small animals has recently increased owing to improvements in the ecological environment across various forested areas, thus increasing the incidence of injuries in the bark of Chinese fir. Following such injuries, the bark secretes light yellow or milky white secretions, the function of which remains unclear. The present study aimed to reveal the antibacterial effect of exudates of different Chinese fir cultivars on five bacterial species.MethodsThe research involved three-year-old plantations of Taxus chinensis var. koraiensis and Yangkou3 and three-year-old container plantations of Taxus chinensis var. pendula, Yang 061, and Yang 020. The antibacterial effects of exudates were analyzed using the filter paper diffusion method. The minimum inhibitory concentration for each secretion and the bacterial inhibition zone were determined.ResultsThe exudates of the different Chinese fir bark exhibited notable antibacterial effects on Bacillus subtilis, Salmonella paratyphi B, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. However, the extent of these antibacterial effects varied among the different Chinese fir cultivars, as the minimum inhibitory concentrations (MICs) of the exudates against the five bacterial species varied. The mean MIC of Pseudomonas aeruginosa was lower potency, whereas that of Escherichia coli was the lowest. Notably, the antibacterial efficacy of the exudates was mainly influenced by the composition of the secretions rather than the number of secretions, with organic acid compounds and terpenoids potentially contributing to the antibacterial effects against E. coli and Bacillus subtilis, respectively.ConclusionThis study demonstrates the antibacterial effect of wound secretion of different Chinese fir cultivars, highlighting their varying efficacy on different bacterial species. Moreover, the antibacterial ability of the exudates of the strains was mainly determined by the composition of the wound secretions, and there was no noticeable relationship with the number of wound secretions. The results of this study offers a theoretical basis for screen Chinese fir cultivars with high-disease-resistant. creator: Yu Jiang creator: Yalin Zeng creator: Jianing Zhu creator: Linjun Sun creator: Pengfei Wu creator: Ming Li creator: Xiangqing Ma uri: https://doi.org/10.7717/peerj.17850 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Jiang et al. title: Efficacy of tanshinone IIA in rat models with myocardial ischemia–reperfusion injury: a systematic mini-review and meta-analysis link: https://peerj.com/articles/17885 last-modified: 2024-08-16 description: BackgroundMyocardial ischemia–reperfusion injury (MIRI) refers to severe damage to the ischemic myocardium following the restoration of blood flow, and it is a major complication of reperfusion therapy for myocardial infarction. Notably, drugs such as metoprolol have been utilized to reduce ischemia–reperfusion injury. Tanshinone IIA is a major constituent extracted from Salvia miltiorrhiza Bunge. Recently, tanshinone IIA has been studied extensively in animal models for controlling MIRI. Therefore, we conducted a meta-analysis on the application of tanshinone IIA in rat models with MIRI to evaluate the therapeutic effects of tanshinone IIA.MethodsA comprehensive search was conducted across PubMed, Web of Science, Embase, the Cochrane Library, the China National Knowledge Infrastructure database, the Wanfang database, and the Chinese Scientific Journal Database to gather studies on tanshinone IIA intervention in rat models with MIRI.We employed SYRCLE’s risk of bias tool to assess study quality. The primary outcome indicators were superoxide dismutase (SOD) and malondialdehyde (MDA). Myocardial infarction area was a secondary outcome indicator. This study was registered at PROSPERO (registration number CRD 42022344447).ResultsAccording to the inclusion and exclusion criteria, 15 eligible studies were selected from 295 initially identified studies. In rat models with MIRI, tanshinone IIA significantly increased SOD levels while reducing MDA levels and myocardial infarction area. Moreover, the duration of myocardial ischemia influenced the effectiveness of tanshinone IIA. However, additional high-quality research studies are needed to establish the efficacy and definitive guidelines for the use of tanshinone IIA. Animal studies demonstrated that tanshinone IIA exerted a significant therapeutic effect when the ischemia duration was less than 40 minutes. Tanshinone IIA was found to be more effective when administered via intravenous, intraperitoneal, and intragastric routes at doses above 5 mg/kg. Additionally, treatment with tanshinone IIA at all stages—prior to myocardial ischemia, after ischemia but before reperfusion, prior to ischemia and after reperfusion, and after reperfusion—showed satisfactory results.ConclusionsTanshinone IIA enhanced SOD activity and reduced MDA levels, thereby ameliorating oxidative stress damage during MIRI. Additionally, it reduced the myocardial infarction area, indicating its effectiveness in mitigating MIRI-induced damage in rats and demonstrating a myocardial protective effect. These findings contribute valuable insights for developing MIRI treatment strategies. creator: Xiaobin Zhang creator: Hehe Jiang creator: Linlin Zhang creator: Chen Chen creator: Mengzhen Xing creator: Dongqing Du creator: Yujie Li creator: Yuning Ma creator: Yuxia Ma creator: Chunjing Li uri: https://doi.org/10.7717/peerj.17885 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Zhang et al. title: Seasonality and alternative floral resources affect reproductive success of the alfalfa leafcutting bee, Megachile rotundata link: https://peerj.com/articles/17902 last-modified: 2024-08-16 description: BackgroundManaged populations of the alfalfa leafcutting bee (ALCB), Megachile rotundata (F.), are often not sustainable. In addition to numerous mortality factors that contribute to this, the dense bee populations used to maximize alfalfa pollination quickly deplete floral resources available to bees later in the summer. Providing alternative floral resources as alfalfa declines may help to improve ALCB reproduction.MethodsWe examined the relationship between floral resource availability and ALCB reproduction and offspring condition via (1) a field study using alfalfa plots with and without late-blooming wildflower strips to supply food beyond alfalfa bloom, and (2) a field-cage study in which we provided bees with alfalfa, wildflowers, or both as food resources.ResultsIn the field study, bee cell production closely followed alfalfa floral density with an initial peak followed by large declines prior to wildflower bloom. Few bees visited wildflower strips, whose presence or absence was not associated with any measure of bee reproduction. However, we found that female offspring from cells provisioned earlier in the season, when alfalfa predominated as a source of provisions, eclosed with greater body sizes and proportion body lipids relative to total body mass. For bees restricted to cages, the proportion of offspring that survived to adults was highest on pure alfalfa diets. Adding wildflowers to cages with alfalfa did not affect adult offspring production or female offspring body size and lipid content. Furthermore, although similar numbers of adults were produced on wildflowers alone as with alfalfa alone, females eclosed with smaller body sizes and lower proportion body lipids on wildflowers despite the higher protein content we estimated for wildflower pollen. We found no evidence that adding the late-season wildflower species that we chose to plant enhanced ALCB offspring numbers. Our results highlight the importance of considering multiple measures of reproductive success, including offspring body size and lipid stores, when designing and evaluating floral resource management strategies for agroecosystems. creator: Casey M. Delphia creator: Laura A. Burkle creator: Joshua M. Botti-Anderson creator: Kevin M. O’Neill uri: https://doi.org/10.7717/peerj.17902 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Delphia et al. title: Does how individuals handle social situations exacerbate the relationship between physique anxiety and food addiction? The role of emotional expressive suppression and social avoidance and distress link: https://peerj.com/articles/17910 last-modified: 2024-08-16 description: BackgroundResearch on food addiction has increased significantly in recent years. It has been demonstrated that food addiction can lead to impairments in physiological, psychological, and social functioning in individuals. However, there is a lack of studies investigating the influence of how individuals handle social situations on food addiction and the specific mechanisms involved.MethodA cross-sectional survey was conducted with 1,151 university students, with a mean age of 21.44 (SD = 4.77) years. The sample comprised 74.46% female and 25.54% male students. Participants completed the Chinese version of the modified Yale Food Addiction Scale 2.0, the Social Physique Anxiety Scale, the Expressive Suppression Scale, and the Social Avoidance and Distress Scale. Statistical analyses were performed using SPSS 26.0 and the Process (Version 3.4) plug-in.ResultThe results of the study supported our hypothesis that the association between social physique anxiety and food addiction symptoms could be partially explained by expressive suppression and social avoidance and distress. This association remained significant even after adjusting for covariates such as gender, number of cigarettes smoked per day, bedtime, education, and BMI. Specifically, more severe social physique anxiety was found to be associated with frequent use of expressive suppression and social avoidance and distress, which in turn was associated with more severe food addiction symptoms.ConclusionThis study explored the role of expression suppression and social avoidance and distress in the relationship between social physique anxiety and food addiction symptoms. The findings provide a theoretical basis for developing interventions for food addiction in college students. These interventions could include helping students develop a healthy perception of body image, encouraging emotional expression, and promoting active social participation to reduce food addiction symptoms. creator: Yan Li creator: Yuxia Fan creator: Jing Lin creator: Shaobo Shi uri: https://doi.org/10.7717/peerj.17910 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Preoperative bedside test indicators as predictors of difficult video laryngoscopy in obese patients: a prospective observational study link: https://peerj.com/articles/17838 last-modified: 2024-08-15 description: PurposeThe aim of this study was to identify factors associated with difficult video laryngoscopy in obese patients.MethodsA total of 579 obese patients undergoing elective laparoscopic weight loss surgery were intubated with a single-lumen endotracheal tube using a video laryngoscopy under general anesthesia, and the patients were divided into two groups based on the Cormack-Lehane classification (difficult video laryngoscopy defined as ≥ 3): the easy video laryngoscopy group and the difficult video laryngoscopy group. Record the general condition of the patient, bedside testing indicators related to the airway, Cormack-Lehane classification during intubation, and intubation failure rate.ResultsThe findings of this study show that the incidence of difficult video laryngoscopy in obese patients is 4.8%. Multivariate logistic regression analysis indicated that body mass index was significantly associated with difficult video laryngoscopy (OR = 1.082, 95% CI [1.033–1.132], P < 0.001).ConclusionFor Chinese obese patients without known difficult airways, the incidence of difficult video laryngoscopy is 4.8%. Body mass index is associated factors for the occurrence of difficult video laryngoscopy, with an increased risk observed as body mass index rise. creator: Liumei Li creator: Guanyu Yang creator: ShiYing Li creator: Xue Liu creator: Ya Fei Zhu creator: Qinjun Chu uri: https://doi.org/10.7717/peerj.17838 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al.