title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=490 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Combinative effects of β-elemene and propranolol on the proliferation, migration, and angiogenesis of hemangioma link: https://peerj.com/articles/15643 last-modified: 2023-07-12 description: Hemangioma (HA) is one of the most common benign vascular tumors among children. Propranolol is used as the first-line treatment for hemangioma and is a non-selective blocker of the β-adrenergic receptor. β-elemene is a compound extracted from Rhizoma zedoariae and has been approved for the treatment of tumors in clinical practice. However, the combinatorial effects of β-elemene and propranolol in the treatment of HA remains unclear. This study explored the combinative effects and mechanisms of β-elemene and propranolol using hemangioma-derived endothelial cells (HemECs). Cytotoxic assays showed that the combinatorial treatment of β-elemene and propranolol did not increase the cytotoxic effects of HemECs. Furthermore, functional analysis showed that the combinatorial treatment with β-elemene and propranolol significantly inhibited the proliferation, migration, and tube formation of the HemECs compared to the single treatment regimens. Mechanistic analysis showed that combinative treatment with β-elemene and propranolol synergistically down-regulated the hypoxia-inducible factor-1 alpha/vascular endothelial growth factor-A (HIF-1-α/VEGFA) signaling pathway. Additionally, in a xenograft tumor model, angiogenesis in the combinatorial treatment group was significantly lower than in the control, propranolol, and β-elemene treatment alone groups. Our results suggest that β-elemene combined with propranolol can significantly inhibit the proliferation, migration, and tube formation of HemECs via synergistically down-regulating the HIF-1-α/VEGFA signaling pathway without increasing any cytotoxic side effects. creator: Zhenyu Wang creator: Yinxian Chen creator: Lin Yang creator: Dunbiao Yao creator: Yang Shen uri: https://doi.org/10.7717/peerj.15643 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Effects of a compound Trichoderma agent on Coptis chinensis growth, nutrients, enzyme activity, and microbial community of rhizosphere soil link: https://peerj.com/articles/15652 last-modified: 2023-07-12 description: BackgroundRoot rot diseases are prevalent in many Coptis chinensis Franch. production areas, perhaps partially due to the overuse of synthetic fertilizers. Synthetic fertilizers can also lead to soil degradation. Trichoderma is widely used in biofertilizers and biopesticides. This study applied a combination of four Trichoderma species (compound Trichoderma agent, CTA) to C. chinensis and evaluated its effects on growth, as well as rhizosphere soil nutrients, enzyme activities, and microbial community structure. The purpose of this study was to estimate the potential of using CTA as a biofertilizer for C. chinensis, and determine if it could, at least partially, replace synthetic fertilizers to control root rot disease and maintain soil fertility.MethodCTA, compound fertilizer and sterile water were applied to C. chinensis plants. After 60 days, the soluble sugar, soluble protein, chlorophyll of leaves, and individual weight of each plant were measured. The rhizosphere soil nutrient content, enzymatic activity, and the microbial community were also determined. The results were analyzed to evaluate the effect of CTA on C. chinensis growth and soil fertility.ResultsCTA increased the soluble protein, chlorophyll, and individual weight of C. chinensis plants while compound fertilizer decreased chlorophyll. CTA increased the activities of urease and catalase in rhizosphere soil, whereas the compound fertilizer decreased urease, catalase, and alkaline phosphatase activities. CTA elevated soil pH, while compound fertilizer reduced it. CTA had no significant effects on soil nutrients and organic matter. CTA decreased the fungal number and alpha-diversity of fungi and bacteria, and both the fungal and bacterial communities were significantly different from the other two. CTA increased B/F value, which improved the rhizosphere microbial community. Both CTA and the compound fertilizer significantly altered the soil microbial community. The relative abundance of Ascomycota was higher and Basidiomycota was lower after CTA treatment than after the other two treatments, indicating that the soil treated with CTA was healthier than that of the other two treatments. CTA decreased harmful Ilyonectria mors-panacis and Corynebacterium sp. And increased beneficial Ralstonia picketti. Trichoderma spp. could exist in C. chinensis rhizosphere soil for a long time. The functional prediction results demonstrated that CTA reduced some rhizosphere phytopathogenic fungi. Correlation analysis showed that CTA elevated rhizosphere pH and enzyme activities. In summary, synthetic fertilizers damaged soil fertility, and the overuse of them might be responsible for root rot disease, while CTA could promote C. chinensis growth, improve soil and decrease the incidence and severity of C. chinensis root rot disease. Therefore, as a biofertilizer, CTA can, at least partially, replace synthetic fertilizers in C. chinensis production. Combining it with organic fertilizer will increase the potential of Trichoderma. creator: Li X. Wu creator: Yu Wang creator: Hui Lyu creator: Xia D. Chen uri: https://doi.org/10.7717/peerj.15652 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wu et al. title: HDAC inhibition delays photoreceptor loss in Pde6b mutant mice of retinitis pigmentosa: insights from scRNA-seq and CUT&Tag link: https://peerj.com/articles/15659 last-modified: 2023-07-12 description: PurposeThis research aimed to ascertain the neuroprotective effect of histone deacetylase (HDAC) inhibition on retinal photoreceptors in Pde6brd1 mice, a model of retinitis pigmentosa (RP).MethodsSingle-cell RNA-sequencing (scRNA-seq) explored HDAC and poly (ADP-ribose) polymerase (PARP)-related gene expression in both Pde6b-mutant rd1 and wild-type (WT) mice. The CUT&Tag method was employed to examine the functions of HDAC in rd1 mice. Organotypic retinal explant cultures from WT and rd1 mice were exposed to the HDAC inhibitor SAHA (suberoylanilide hydroxamic acid) postnatally, from day 5 to day 11. The terminal deoxynucleotidyl transferase-mediated nick-end labeling (TUNEL) assay was applied to quantify the percentage of photoreceptor loss in the outer nuclear layer (ONL). HDAC activity was confirmed to be inhibited by SAHA through an HDAC activity assay. Moreover, the study evaluated PARP activity, a key driver of the initial response to DNA damage during photoreceptor degeneration, following HDAC inhibition.ResultsThe scRNA-seq revealed that diverse roles of HDAC and PARP isoforms in photoreceptor cell death. HDAC-related genes appeared to regulate cell death and primary immunodeficiency. Alterations in HDAC activity were consistent with the TUNEL-positive cells in the ONL at different time points. Notably, SAHA significantly postponed photoreceptor loss and decreased HDAC and PARP activity, thereby implicating both in the same degenerative pathway.ConclusionsThis study highlights that the interaction between HDAC inhibition and PARP can delay photoreceptor cell death, proposing a promising therapeutic approach for RP. creator: Yujie Dong creator: Jie Yan creator: Wenrong Xu creator: François Paquet-Durand creator: Zhulin Hu creator: Kangwei Jiao uri: https://doi.org/10.7717/peerj.15659 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dong et al. title: Effect of sit-to-stand-based training on muscle quality in sedentary adults: a randomized controlled trial link: https://peerj.com/articles/15665 last-modified: 2023-07-12 description: The aim of this study was to compare the effects of sit-to-stand (STS) training programs with 5 vs. 10 repetitions on muscle architecture and muscle function in sedentary adults. Sixty participants were randomly assigned into three groups: five-repetition STS (5STS), 10-repetition STS (10STS), or a control group (CG). Participants performed three sets of five or 10 repetitions of the STS exercise three times per week for 8 weeks. Before and after 8 weeks, all groups performed ultrasound measures to evaluate muscle thickness (MT), pennation angle (PA), and fascicle length (FL), and the five-repetition STS test to estimate the relative STS power and muscle quality index (MQI). After 8 weeks, both experimental groups improved MQI (40–45%), relative STS power (29–38%), and MT (8–9%) (all p < 0.001; no differences between the 5STS vs. 10STS groups). These improvements in both groups resulted in differences regarding the CG, which did not present any change. In addition, only the 5STS group improved PA (15%; p = 0.008) without differences to the 10STS and CG.This suggests that STS training is time-effective and low-cost for improving muscle function and generating adaptations in muscle architecture. creator: Rodrigo Lizama-Pérez creator: Luis Javier Chirosa-Ríos creator: Guido Contreras-Díaz creator: Daniel Jerez-Mayorga creator: Daniel Jiménez-Lupión creator: Ignacio Jesús Chirosa-Ríos uri: https://doi.org/10.7717/peerj.15665 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lizama-Pérez et al. title: Establishment of a prognostic risk prediction modelfor non-small cell lung cancer patients with brainmetastases: a retrospective study link: https://peerj.com/articles/15678 last-modified: 2023-07-12 description: BackgroundPatients with non-small cell lung cancer (NSCLC) who develop brain metastases (BM) have a poor prognosis. This study aimed to construct a clinical prediction model to determine the overall survival (OS) of NSCLC patients with BM.MethodsA total of 300 NSCLC patients with BM at the Yunnan Cancer Centre were retrospectively analysed. The prediction model was constructed using the least absolute shrinkage and selection operator-Cox regression. The bootstrap sampling method was employed for internal validation. The performance of our prediction model was compared using recursive partitioning analysis (RPA), graded prognostic assessment (GPA), the update of the graded prognostic assessment for lung cancer using molecular markers (Lung-molGPA), the basic score for BM (BSBM), and tumour-lymph node-metastasis (TNM) staging.ResultsThe prediction models comprising 15 predictors were constructed. The area under the curve (AUC) values for the 1-year, 3-year, and 5-year time-dependent receiver operating characteristic (curves) were 0.746 (0.678–0.814), 0.819 (0.761–0.877), and 0.865 (0.774–0.957), respectively. The bootstrap-corrected AUC values and Brier scores for the prediction model were 0.811 (0.638–0.950) and 0.123 (0.066-0.188), respectively. The time-dependent C-index indicated that our model exhibited significantly greater discrimination compared with RPA, GPA, Lung-molGPA, BSBM, and TNM staging. Similarly, the decision curve analysis demonstrated that our model displayed the widest range of thresholds and yielded the highest net benefit. Furthermore, the net reclassification improvement and integrated discrimination improvement analyses confirmed the enhanced predictive power of our prediction model. Finally, the risk subgroups identified by our prognostic model exhibited superior differentiation of patients’ OS.ConclusionThe clinical prediction model constructed by us shows promise in predicting OS for NSCLC patients with BM. Its predictability is superior compared with RPA, GPA, Lung-molGPA, BSBM, and TNM staging. creator: Fei Hou creator: Yan Hou creator: Xiao-Dan Sun creator: Jia lv creator: Hong-Mei Jiang creator: Meng Zhang creator: Chao Liu creator: Zhi-Yong Deng uri: https://doi.org/10.7717/peerj.15678 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hou et al. title: Gazing left, gazing right: exploring a spatial bias in social attention link: https://peerj.com/articles/15694 last-modified: 2023-07-12 description: Faces oriented rightwards are sometimes perceived as more dominant than faces oriented leftwards. In this study, we explored whether faces oriented rightwards can also elicit increased attentional orienting. Participants completed a discrimination task in which they were asked to discriminate, by means of a keypress, a peripheral target. At the same time, a task-irrelevant face oriented leftwards or rightwards appeared at the centre of the screen. The results showed that, while for faces oriented rightwards targets appearing on the right were responded to faster as compared to targets appearing on the left, for faces oriented leftwards no differences emerged between left and right targets. Furthermore, we also found a negative correlation between the magnitude of the orienting response elicited by the faces oriented leftwards and the level of conservatism of the participants. Overall, these findings provide evidence for the existence of a spatial bias reflected in social orienting. creator: Mario Dalmaso creator: Giacomo Fedrigo creator: Michele Vicovaro uri: https://doi.org/10.7717/peerj.15694 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dalmaso et al. title: Oil and natural gas rents and CO2 emissions nexus in MENA: spatial analysis link: https://peerj.com/articles/15708 last-modified: 2023-07-12 description: BackgroundOil rents (OR) and natural gas rents (NGR) have significant contributions to the income of the Middle East and North Africa (MENA) economies and may increase emissions. Moreover, spatial autocorrelation is expected in carbon dioxide (CO2) emissions due to the geographically closed economies in the MENA region. Thus, we examine the impact of OR and NGR on CO2 emissions caring spatial dimensions and analyze the environmental Kuznets curve (EKC).MethodsWe apply the spatial Durbin model technique on the effects of OR, NGR, and economic growth on CO2 emissions in 17 MENA nations from 2000–2019, i.e., Algeria, Bahrain, Egypt, Iran, Iraq, Israel, Jordan, Kuwait, Libya, Morocco, Oman, Qatar, Saudi Arabia, Syria, Tunisia, the United Arab Emirates (UAE), and Yemen. Moreover, diagnostic tests are applied to reach the most appropriate spatial specification and to have the most robust results.ResultsThe results disclose that CO2 emissions have spillovers and emissions of any country can damage the environment of neighboring countries. The EKC is corroborated with a turning point of 38,698 constant 2015 US dollars. Israel and Qatar are in 2nd phase of the EKC, and 15 MENA economies are in 1st stage. Thus, the economic expansion of most economies has ecological concerns. The effect of natural gas rents is found statistically insignificant. Oil rents have minute negative effects on emissions of local economies with an elasticity coefficient of −0.2117. Nevertheless, these have a positive indirect effect with an elasticity coefficient of 0.5328. Thus, the net effect of oil rents is positive. One percent increase in oil rents could accelerate 0.3211% of emissions. Thus, we suggest the MENA countries reduce reliance on oil rents in their income to avoid the negative environmental effects of the oil sector. creator: Haider Mahmood creator: Najia Saqib creator: Anass Hamadelneel Adow creator: Muzaffar Abbas uri: https://doi.org/10.7717/peerj.15708 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mahmood et al. title: Changes in Coleopteran assemblages over a successional chronosequence in a Mexican tropical dry forest link: https://peerj.com/articles/15712 last-modified: 2023-07-12 description: Coleopterans are the most diverse animal group on Earth and constitute good indicators of environmental change. However, little information is available about Coleopteran communities’ responses to disturbance and land-use change. Tropical dry forests have undergone especially extensive anthropogenic impacts in the past decades. This has led to mosaic landscapes consisting of areas of primary forest surrounded by pastures, agricultural fields and secondary forests, which negatively impacts many taxonomic groups. However, such impacts have not been assessed for most arthropod groups. In this work, we compared the abundance, richness and diversity of Coleopteran morphospecies in four different successional stages in a tropical dry forest in western Mexico, to answer the question: How do Coleopteran assemblages associate with vegetation change over the course of forest succession? In addition, we assessed the family composition and trophic guilds for the four successional stages. We found 971 Coleopterans belonging to 107 morphospecies distributed in 28 families. Coleopteran abundance and richness were greatest for pastures than for latter successional stages, and the most abundant family was Chrysomelidae, with 29% of the individuals. Herbivores were the most abundant guild, accounting for 57% of the individuals, followed by predators (22%) and saprophages (21%) beetles. Given the high diversity and richness found throughout the successional chronosequence of the studied tropical dry forest, in order to have the maximum number of species associated with tropical dry forests, large tracts of forest should be preserved so that successional dynamics are able to occur naturally. creator: Edison A. Díaz-Álvarez creator: Cesar Manrique creator: Karina Boege creator: Ek del-Val uri: https://doi.org/10.7717/peerj.15712 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Díaz-Álvarez et al. title: Environmental DNA and visual encounter surveys for amphibian biomonitoring in aquatic environments of the Ecuadorian Amazon link: https://peerj.com/articles/15455 last-modified: 2023-07-11 description: BackgroundThe development of anthropogenic activities has generated a decline in aquatic fauna populations, and amphibians have been the most affected. The decline of batrachofauna is concerning, as 41% of all species worldwide are endangered. For this reason, rapid, efficient, and non-invasive biodiversity monitoring techniques are needed, and environmental DNA (eDNA) is one such tool that has been sparsely applied in Ecuador. This technique has allowed scientists generates information on species diversity and amphibian community composition from a water sample. This study applied eDNA-based biomonitoring analyses and visual encounter surveys (VES) as inventory techniques to identify the diversity of aquatic amphibians in the Tena River micro-basin (TRMB).MethodsThe experimental design was divided into three components: (1) fieldwork: all amphibians were recorded by the VES technique and water samples were collected; (2) laboratory work: DNA isolation from amphibian tissue samples and eDNA-containing filters, amplification, electrophoresis, and sequencing were performed; (3) Data analysis: a local DNA reference database was constructed, and eDNA sequence data were processed for classification, taxonomic assignment, and ecological interpretation.ResultsUsing both eDNA and VES, we detected 33 amphibian species (13 with eDNA only, five with VES only, and 15 with both methods). These species belonged to six amphibian families: Hylidae being the richest with 14 species (three eDNA, one VES, and 10 with both methods), followed by Strabomantidae with nine species (six eDNA, one VES, and two with both methods). All families were detected with both methods, except for the Aromobatidae, having one single record (Allobates aff. insperatus) by VES. Individually, eDNA detected 28 species and had a detection probability (DP) of 0.42 CI [0.40–0.45], while VES recorded 20 species with a DP of 0.17 CI [0.14–0.20]. Similarly, using VES, Cochranella resplendens was detected for the first time in TRMB, while with eDNA, four mountain frogs Pristimantis acerus, Pristimantis eriphus, Pristimantis mallii, and Pristimantis sp. (INABIO 15591) previously recorded at 1,518 m.a.s.l. at altitudes below 600 m.a.s.l. were detected.ConclusionsResults obtained in this study showed that eDNA-based detection had a greater capacity to detect amphibians in aquatic environments compared to VES. The combination of VES and eDNA improves the sensitivity of species detection and provides more reliable, robust, and detailed information. The latter is essential for developing conservation strategies in the Ecuadorian Amazon. creator: Walter Quilumbaquin creator: Andrea Carrera-Gonzalez creator: Christine Van der heyden creator: H. Mauricio Ortega-Andrade uri: https://doi.org/10.7717/peerj.15455 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Quilumbaquin et al. title: Nutritional values of wild edible freshwater macrophytes link: https://peerj.com/articles/15496 last-modified: 2023-07-11 description: BackgroundThe social acceptability of wild freshwater macrophytes as locally consumed vegetables is widespread. Freshwater macrophytes have several uses; for example, they can be used as food for humans. This study determined the proximate composition and mineral content of three freshwater macrophyte species, i.e., Eichhornia crassipes, Limnocharis flava, and Neptunia oleracea.MethodsYoung shoots of E. crassipes, L. flava, and N. oleracea were collected from shallow channels of Puchong (3°00′11.89″N, 101°42′43.12″E), Ladang 10, Universiti Putra Malaysia (2°58′44.41″N, 101°42′44.45″E), and Kampung Alur Selibong, Langgar (06°5′50.9″N, 100°26′49.8″E), Kedah, Peninsular Malaysia. The nutritional values of these macrophytes were analysed by using a standard protocol from the Association of Official Analytical Chemists. Eight replicates of E. crassipes and L. flava and four replicates of N. oleracea were used for the subsequent analyses.ResultsIn the proximate analysis, N. oleracea possessed the highest percentage of crude protein (29.61%) and energy content (4,269.65 cal g−1), whereas L. flava had the highest percentage of crude fat (5.75%) and ash (18.31%). The proximate composition trend for each species was different; specifically, all of the species possessed more carbohydrates and fewer crude lipids. All of the species demonstrated a similar mineral trend, with high nitrogen and potassium and lower copper contents. Nitrogen and potassium levels ranged from 12,380–40,380 mg kg−1 and from 11,212-33,276 mg kg−1, respectively, and copper levels ranged from 16–27 mg kg−1. The results showed that all three plant species, i.e., E. crassipes, N. oleracea, and L. flava are plant-based sources of macro- and micronutrient beneficial supplements for human consumption. creator: Muta Harah Zakaria creator: Shiamala Devi Ramaiya creator: Nordiah Bidin creator: Nurul Nur Farahin Syed creator: Japar Sidik Bujang uri: https://doi.org/10.7717/peerj.15496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zakaria et al.