title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=322 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Contrasting effects of increasing dissolved iron on photosynthesis and O2 availability in the gastric cavity of two Mediterranean corals link: https://peerj.com/articles/17259 last-modified: 2024-04-29 description: Iron (Fe) plays a fundamental role in coral symbiosis, supporting photosynthesis, respiration, and many important enzymatic reactions. However, the extent to which corals are limited by Fe and their metabolic responses to inorganic Fe enrichment remains to be understood. We used respirometry, variable chlorophyll fluorescence, and O2 microsensors to investigate the impact of increasing Fe(III) concentrations (20, 50, and 100 nM) on the photosynthetic capacity of two Mediterranean coral species, Cladocora caespitosa and Oculina patagonica. While the bioavailability of inorganic Fe can rapidly decrease, we nevertheless observed significant physiological effects at all Fe concentrations. In C. caespitosa, exposure to 50 nM Fe(III) increased rates of respiration and photosynthesis, while the relative electron transport rate (rETR(II)) decreased at higher Fe(III) exposure (100 nM). In contrast, O. patagonica reduced respiration, photosynthesis rates, and maximum PSII quantum yield (Fv/Fm) across all iron enrichments. Both corals exhibited increased hypoxia (<50 µmol O2 L−1) within their gastric cavity at night when exposed to 50 and 100 nM Fe(III), leading to increased polyp contraction time and reduced O2 exchange with the surrounding water. Our results indicate that C. caespitosa, but not O. patagonica, might be limited in Fe for achieving maximal photosynthetic efficiency. Understanding the multifaceted role of iron in corals’ health and their response to environmental change is crucial for effective coral conservation. creator: Walter Dellisanti creator: Qingfeng Zhang creator: Christine Ferrier-Pagès creator: Michael Kühl uri: https://doi.org/10.7717/peerj.17259 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dellisanti et al. title: Exploring exercise-driven exerkines: unraveling the regulation of metabolism and inflammation link: https://peerj.com/articles/17267 last-modified: 2024-04-29 description: Exercise has many beneficial effects that provide health and metabolic benefits. Signaling molecules are released from organs and tissues in response to exercise stimuli and are widely termed exerkines, which exert influence on a multitude of intricate multi-tissue processes, such as muscle, adipose tissue, pancreas, liver, cardiovascular tissue, kidney, and bone. For the metabolic effect, exerkines regulate the metabolic homeostasis of organisms by increasing glucose uptake and improving fat synthesis. For the anti-inflammatory effect, exerkines positively influence various chronic inflammation-related diseases, such as type 2 diabetes and atherosclerosis. This review highlights the prospective contribution of exerkines in regulating metabolism, augmenting the anti-inflammatory effects, and providing additional advantages associated with exercise. Moreover, a comprehensive overview and analysis of recent advancements are provided in this review, in addition to predicting future applications used as a potential biomarker or therapeutic target to benefit patients with chronic diseases. creator: Nihong Zhou creator: Lijing Gong creator: Enming Zhang creator: Xintang Wang uri: https://doi.org/10.7717/peerj.17267 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Microbial community structure and carbon transformation characteristics of different aggregates in black soil link: https://peerj.com/articles/17269 last-modified: 2024-04-29 description: BackgroundPrevious research on whole-soil measurements has failed to explain the spatial distribution of soil carbon transformations, which is essential for a precise understanding of the microorganisms responsible for carbon transformations. The microorganisms involved in the transformation of soil carbon were investigated at the microscopic scale by combining 16S rDNA sequencing technology with particle-level soil classification.MethodsIn this experiment,16S rDNA sequencing analysis was used to evaluate the variations in the microbial community structure of different aggregates in no-tillage black soil. The prokaryotic microorganisms involved in carbon transformation were measured before and after the freezing and thawing of various aggregates in no-tillage black soil. Each sample was divided into six categories based on aggregate grain size: >5, 2–5, 1–2, 0.5–1, 0.25–0.5, <0.25 mm, and bulk soil.ResultsThe relative abundance of Actinobacteria phylum in <0.25 mm aggregates was significantly higher compared to that in other aggregates. The Chao1 index, Shannon index, and phylogenetic diversity (PD) whole tree index of <0.25 mm aggregates were significantly smaller than those of in bulk soil and >5 mm aggregates. Orthogonal partial least-squares discrimination analysis showed that the microbial community composition of black soil aggregates was significantly different between <1 and >1 mm. The redundancy analysis (RDA) showed that the organic carbon conversion rate of 0.25–0.5 mm agglomerates had a significantly greater effect on their bacterial community structure. Moreover, humic acid conversion rates on aggregates <0.5 mm had a greater impact on community structure. The linear discriminant analysis effect size (LEfSe) analysis and RDA analysis were combined. Bradyrhizobium, Actinoplane, Streptomyces, Dactylosporangium, Yonghaparkia, Fleivirga, and Xiangella in <0.25 mm aggregates were positively correlated with soil organic carbon conversion rates. Blastococcus and Pseudarthrobacter were positively correlated with soil organic carbon conversion rates in 0.25–0.5 mm aggregates. In aggregates smaller than 1 mm, the higher the abundance of functional bacteria that contributed to the soil’s ability to fix carbon and nitrogen.DiscussionThere were large differences in prokaryotic microbial community composition between <1 and >1 mm aggregates. The <1 mm aggregates play an important role in soil carbon transformation and carbon fixation. The 0.25–0.5 mm aggregates had the fastest organic carbon conversion rate and increased significantly more than the other aggregates. Some genus or species of Actinobacteria and Proteobacteria play a positive role in the carbon transformation of <1 mm aggregates. Such analyses may help to identify microbial partners that play an important role in carbon transformation at the micro scale of no-till black soils. creator: Danqi Zhao creator: Wei Zhang creator: Juntao Cui uri: https://doi.org/10.7717/peerj.17269 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhao et al. title: Plasma-based lipidomics reveals potential diagnostic biomarkers for esophageal squamous cell carcinoma: a retrospective study link: https://peerj.com/articles/17272 last-modified: 2024-04-29 description: BackgroundEsophageal squamous cell carcinoma (ESCC) is highly prevalent and has a high mortality rate. Traditional diagnostic methods, such as imaging examinations and blood tumor marker tests, are not effective in accurately diagnosing ESCC due to their low sensitivity and specificity. Esophageal endoscopic biopsy, which is considered as the gold standard, is not suitable for screening due to its invasiveness and high cost. Therefore, this study aimed to develop a convenient and low-cost diagnostic method for ESCC using plasma-based lipidomics analysis combined with machine learning (ML) algorithms.MethodsPlasma samples from a total of 40 ESCC patients and 31 healthy controls were used for lipidomics study. Untargeted lipidomics analysis was conducted through liquid chromatography-mass spectrometry (LC-MS) analysis. Differentially expressed lipid features were filtered based on multivariate and univariate analysis, and lipid annotation was performed using MS-DIAL software.ResultsA total of 99 differential lipids were identified, with 15 up-regulated lipids and 84 down-regulated lipids, suggesting their potential as diagnostic targets for ESCC. In the single-lipid plasma-based diagnostic model, nine specific lipids (FA 15:4, FA 27:1, FA 28:7, FA 28:0, FA 36:0, FA 39:0, FA 42:0, FA 44:0, and DG 37:7) exhibited excellent diagnostic performance, with an area under the curve (AUC) exceeding 0.99. Furthermore, multiple lipid-based ML models also demonstrated comparable diagnostic ability for ESCC. These findings indicate plasma lipids as a promising diagnostic approach for ESCC. creator: Yang Chen creator: Yixuan Gu creator: Jinhua Rong creator: Luyin Xu creator: Xiancong Huang creator: Jing Zhu creator: Zhongjian Chen creator: Weimin Mao uri: https://doi.org/10.7717/peerj.17272 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Variational Bayesian phylogenies through matrix representation of tree space link: https://peerj.com/articles/17276 last-modified: 2024-04-29 description: In this article, we study the distance matrix as a representation of a phylogeny by way of hierarchical clustering. By defining a multivariate normal distribution on (a subset of) the entries in a matrix, this allows us to represent a distribution over rooted time trees. Here, we demonstrate tree distributions can be represented accurately this way for a number of published tree distributions. Though such a representation does not map to unique trees, restriction to a subspace, in particular one we call a “cube”, makes the representation bijective at the cost of not being able to represent all possible trees. We introduce an algorithm “cubeVB” specifically for cubes and show through well calibrated simulation study that it is possible to recover parameters of interest like tree height and length. Although a cube cannot represent all of tree space, it is a great improvement over a single summary tree, and it opens up exciting new opportunities for scaling up Bayesian phylogenetic inference. We also demonstrate how to use a matrix representation of a tree distribution to get better summary trees than commonly used maximum clade credibility trees. An open source implementation of the cubeVB algorithm is available from https://github.com/rbouckaert/cubevb as the cubevb package for BEAST 2. creator: Remco R. Bouckaert uri: https://doi.org/10.7717/peerj.17276 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bouckaert title: Association between passing return-to-sport testing and re-injury risk in patients after anterior cruciate ligament reconstruction surgery: a systematic review and meta-analysis link: https://peerj.com/articles/17279 last-modified: 2024-04-29 description: BackgroundInconsistent results have been obtained regarding the association between return-to-sport (RTS) testing and the risk of subsequent re-injury following anterior cruciate ligament reconstruction (ACLR). We therefore conducted a systematic review and meta-analysis to assess the potential association between passing of RTS and the risk of re-injury for patients after ACLR.MethodsThis meta-analysis was registered in INPLASY with the registration number INPLASY202360027. The electronic databases MedLine, EmBase, and the Cochrane library were systematically searched to identify eligible studies from their inception up to September 2023. The investigated outcomes included knee injury, secondary ACL, contralateral ACL injury, and graft rupture. The pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using the random-effects model.ResultsA total number of nine studies involving 1410 individuals were selected for the final quantitative analysis. We noted that passing RTS test was not associated with the risk of subsequent knee injury (OR: 0.95; 95% CI: 0.28–3.21; P = 0.929), secondary ACL injury (OR: 0.98; 95% CI: 0.55–1.75; P = 0.945), and contralateral ACL injury (OR: 1.53; 95% CI: 0.63–3.71; P = 0.347). However, the risk of graft rupture was significantly reduced (OR: 0.49; 95% CI: 0.33–0.75; P = 0.001).ConclusionsThis study found that passing RTS test was not associated with the risk of subsequent knee injury, secondary ACL injury, and contralateral ACL injury, while it was associated with a lower risk of graft rupture. Thus, it is recommended that patients after ACLR pass an RTS test in clinical settings. creator: Wenqi Zhou creator: Xihui Liu creator: Qiaomei Hong creator: Jingping Wang creator: Xiaobing Luo uri: https://doi.org/10.7717/peerj.17279 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhou et al. title: Anodal transcranial direct current stimulation enhances response inhibition and attention allocation in fencers link: https://peerj.com/articles/17288 last-modified: 2024-04-29 description: BackgroundThe aim of this study is to investigate the acute effects of anodal transcranial direct current stimulation (tDCS) on reaction time, response inhibition and attention in fencers.MethodsSixteen professional female fencers were recruited, and subjected to anodal tDCS and sham stimulation in the primary motor area (M1) one week apart in a randomized, crossover, single-blind design. A two-factor analysis of variance with repeated measures was used to analyze the effects of stimulation conditions (anodal stimulation, sham stimulation) and time (pre-stimulation, post-stimulation) on reaction time, response inhibition, and attention in fencers.ResultsThe study found a significant improvement in response inhibition and attention allocation from pre-stimulation to post-stimulation following anodal tDCS but not after sham stimulation. There was no statistically significant improvement in reaction time and selective attention.ConclusionsA single session of anodal tDCS could improve response inhibition, attention allocation in female fencers. This shows that tDCS has potential to improve aspects of an athlete’s cognitive performance, although we do not know if such improvements would transfer to improved performance in competition. However, more studies involving all genders, large samples, and different sports groups are needed in the future to further validate the effect of tDCS in improving the cognitive performance of athletes. creator: Jiansong Dai creator: Yang Xiao creator: Gangrui Chen creator: Zhongke Gu creator: Kai Xu uri: https://doi.org/10.7717/peerj.17288 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dai et al. title: Variation and interrelationships in the growth, yield, and lodging of oat under different planting densities link: https://peerj.com/articles/17310 last-modified: 2024-04-29 description: BackgroundOat is a dual-purpose cereal used for grain and forage. The demand of oat has been increasing as the understanding of the nutritional, ecological, and economic values of oat increased. However, the frequent lodging during the growing period severely affect the high yielding potential and the quality of the grain and forage of oat.MethodsTherefore, we used the lodging-resistant variety LENA and the lodging-sensitive variety QY2 as materials, implementing four different planting densities: 2.25×106 plants/ha (D1), 4.5×106 plants/ha (D2), 6.75×106 plants/ha (D3), and 9×106 plants/ha (D4). At the appropriate growth and development stages, we assessed agronomic traits, mechanical characteristics, biochemical compositions, yield and its components. The study investigated the impact of planting density on the growth, lodging, and yield of oat, as well as their interrelationships. Additionally, we identified the optimal planting density to establish a robust crop structure. The research aims to contribute to the high-yield and high-quality cultivation of oat.ResultsWe observed that with increasing planting density, plant height, grass and grain yields of both varieties first increased and then decreased; root fresh weight, stem diameter, stem wall thickness, stem puncture strength, breaking strength, compressive strength, lignin and crude fiber contents, and yield components decreased; whereas the lodging rate and lodging coefficient increased. Planting density affects lodging by regulating plant height, height of center of gravity, stem wall thickness, internode length, and root fresh weight of oat. Additionally, it can impact stem mechanical strength by modulating the synthesis of lignin and crude fiber, which in turn affecting lodging resistance. Plant height, height of center of gravity, stem wall thickness, internode length, root fresh weight, breaking strength, compressive strength, lignin and crude fiber content, single-plant weight, grain yield and 1,000-grain weight can serve as important indicators for evaluating oat stem lodging resistance. We also noted that planting density affected grain yield both directly and indirectly (by affecting lodging); high density increased lodging rate and decreased grain yield, mainly by reducing 1,000-grain weight. Nonetheless, there was no significant relationship between lodging and grass yield. As appropriate planting density can increase the yield while maintaining good lodging resistance, in this study, 4.5×106 plants/ha (D2) was found to be the best planting density for oat in terms of lodging resistance and grass and grain yield. These findings can be used as a reference for oat planting. creator: Lingling Liu creator: Guoling Liang creator: Wenhui Liu creator: Zeliang Ju uri: https://doi.org/10.7717/peerj.17310 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: Mechanisms and physiological relevance of acid-base exchange in functional units of the kidney link: https://peerj.com/articles/17316 last-modified: 2024-04-29 description: This review discusses the importance of homeostasis with a particular emphasis on the acid-base (AB) balance, a crucial aspect of pH regulation in living systems. Two primary organ systems correct deviations from the standard pH balance: the respiratory system via gas exchange and the kidneys via proton/bicarbonate secretion and reabsorption. Focusing on kidney functions, we describe the complexity of renal architecture and its challenges for experimental research. We address specific roles of different nephron segments (the proximal convoluted tubule, the loop of Henle and the distal convoluted tubule) in pH homeostasis, while explaining the physiological significance of ion exchange processes maintained by the kidneys, particularly the role of bicarbonate ions (HCO3−) as an essential buffer system of the body. The review will be of interest to researchers in the fields of physiology, biochemistry and molecular biology, which builds a strong foundation and critically evaluates existing studies. Our review helps identify the gaps of knowledge by thoroughly understanding the existing literature related to kidney acid-base homeostasis. creator: Elena Gantsova creator: Oxana Serova creator: Polina Vishnyakova creator: Igor Deyev creator: Andrey Elchaninov creator: Timur Fatkhudinov uri: https://doi.org/10.7717/peerj.17316 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gantsova et al. title: Density of cannabis outlets vs. cannabis use behaviors and prevalent cannabis use disorder: findings from a nationally-representative survey link: https://peerj.com/articles/17317 last-modified: 2024-04-29 description: BackgroundThailand recently decriminalized (de facto legalized) cannabis use and sales. However, nationally representative data are scarce with regard to cannabis use behaviors and its association with cannabis outlet density. The objectives of this study are: (1) to describe the prevalence of cannabis use behaviors and cannabis use disorder among the general adult population of Thailand; (2) to describe the extent that the density of cannabis outlets is associated with cannabis use behaviors, cannabis use disorder, and the amount of cannabis smoked per day.MethodsWe conducted a community-based cross-sectional study in 11 provinces and the Bangkok Metropolitan Area. Participants were residents of sampled communities aged 20 years or older. We requested literate participants to self-administer the questionnaire and interviewed participants who could not read. We analyzed data using descriptive statistics with sampling weight adjustments and multivariate logistic regression analyses.ResultsThe prevalence of current cannabis use was 15 percent. At a 400-m radius, participants who reported three cannabis outlets had 4.2 times higher odds of being current users than participants who reported no outlet (Adjusted OR = 4.82; 95% CI [3.04–7.63]). We found no association between outlet density and hazardous cannabis use or cannabis use disorder, nor association with the amount of cannabis use among cannabis smokers.Discussion and ConclusionThe patterns of association between outlet density and cannabis use behaviors were inconsistent. Furthermore, limitations regarding outlet density measurement and lack of temporality should be considered as caveats in the interpretation of the study findings. creator: Wit Wichaidit creator: Ilham Chapakiya creator: Aneesah Waeuseng creator: Kemmapon Chumchuen creator: Sawitri Assanangkornchai uri: https://doi.org/10.7717/peerj.17317 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wichaidit et al.