title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=317 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Heavy metal levels and human health risk implications associated with fish consumption from the lower Omo river (Lotic) and Omo delta lake (Lentic), Ethiopia link: https://peerj.com/articles/17216 last-modified: 2024-04-29 description: This study is the first to determine the levels of heavy metals in commercially important fish species, namely Lates niloticus and Oreochromis niloticus and the potential human health risks associated with their consumption. A total of 120 fish samples were collected from the lower Omo river and Omo delta, with 60 samples from each water source. The fish tissue samples (liver and muscle) were analyzed using a flame atomic absorption spectrometer for nine heavy metals (Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn). The human health risk assessment tools used were the target hazard quotient (THQ), the hazard index (HI), and the target cancer risk (TCR). The mean levels of heavy metals detected in the liver and muscle of L. niloticus from the lower Omo river generally occurred in the order Fe > Zn > Pb> Cu > Mn> Cr > Co > Ni and Pb > Cu > Mn > Co > Ni, respectively. The mean levels of metals in the muscle and liver tissues of O. niloticus were in the order Fe > Pb > Zn > Mn > Cu > Cr > Co > Ni and Pb > Zn > Mn > Fe > Cu > Co > Ni, respectively. Similarly, the mean levels of heavy metals detected in the liver and muscle of L. niloticus from Omo delta occurred in the order Fe > Zn > Pb > Cu > Mn > Cr > Co > Ni and Fe > Pb > Zn > Mn > Cu > Co > Cr > Ni, respectively. The mean levels in the muscle and liver tissues of O. niloticus from the Omo delta were in the order Fe > Pb > Zn > Mn > Cu > Cr > Co > Ni and Pb > Fe > Zn > Mn > Co > Cu > Ni, respectively. The study revealed that the THQ values were below 1, indicating that consumption of L. niloticus and O. niloticus from the studied sites does not pose a potential non-carcinogenic health risk. Although the TCR values for Pb in this study were within the tolerable range, it’s mean concentration in the muscle and liver tissues of both fish species from the two water bodies exceeded the permissible limit established by FAO/WHO. This is a warning sign for early intervention, and it emphasizes the need for regular monitoring of freshwater fish. Therefore, it is imperative to investigate the pollution levels and human health risks of heavy metals in fish tissues from lower Omo river and Omo delta for environmental and public health concerns. creator: Abiy Andemo Kotacho creator: Girma Tilahun Yimer creator: Solomon Sorsa Sota creator: Yohannes Seifu Berego uri: https://doi.org/10.7717/peerj.17216 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kotacho et al. title: Assessment of sealing efficacy, radiopacity, and surface topography of a bioinspired polymer for perforation repair link: https://peerj.com/articles/17237 last-modified: 2024-04-29 description: BackgroundRoot perforation repair presents a significant challenge in dentistry due to inherent limitations of existing materials. This study explored the potential of a novel polydopamine-based composite as a root repair material by evaluating its sealing efficacy, radiopacity, and surface topography.MethodsConfocal microscopy assessed sealing ability, comparing the polydopamine-based composite to the gold standard, mineral trioxide aggregate (MTA). Radiopacity was evaluated using the aluminium step wedge technique conforming to ISO standards. Surface roughness analysis utilized atomic force microscopy (AFM), while field emission scanning electron microscopy (FESEM) visualized morphology.ResultsThe polydopamine-based composite exhibited significantly superior sealing efficacy compared to MTA (P < 0.001). Radiopacity reached 3 mm aluminium equivalent, exceeding minimum clinical requirements. AFM analysis revealed a smooth surface topography, and FESEM confirmed successful composite synthesis.ConclusionThis study demonstrates promising properties of the polydopamine-based composite for root perforation repair, including superior sealing efficacy, clinically relevant radiopacity, and smooth surface topography. Further investigation is warranted to assess its clinical viability and potential translation to endodontic practice. creator: Lakshmi Nidhi Rao creator: Aditya Shetty creator: Neevan Dsouza creator: Heeresh Shetty uri: https://doi.org/10.7717/peerj.17237 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rao et al. title: Systematics, distribution patterns and historical biogeography of the Central America wandering spider genus Kiekie Polotow & Brescovit, 2018 (Araneae: Ctenidae) link: https://peerj.com/articles/17242 last-modified: 2024-04-29 description: Kiekie Polotow & Brescovit, 2018 is a Neotropical genus of Ctenidae, with most of its species occuring in Central America. In this study, we review the systematics of Kiekie and describe five new species and the unknown females of K. barrocolorado Polotow & Brescovit, 2018 and K. garifuna Polotow & Brescovit, 2018, and the unknown male of K. verbena Polotow & Brescovit, 2018. In addition, we described the female of K. montanense which was wrongly assigned as K. griswoldi Polotow & Brescovit, 2018 (both species are sympatric). We provided a modified diagnosis for previously described species based on the morphology of the newly discovered species and in situ photographs of living specimens. We inferred a molecular phylogeny using four nuclear (histone H3, 28S rRNA, 18S rRNA and ITS-2) and three mitochondrial genes (cytochrome c oxidase subunit I or COI, 12S rRNA and 16S rRNA) to test the monophyly of the genus and the evolutionary relationships of its species. Lastly, we reconstruct the historical biogeography and map diversity and endemism distributional patterns of the different species. This study increased the number of known species of Kiekie from 13 to 18, and we describe a new genus, Eldivo which is sister lineage of Kiekie. Most of the diversity and endemism of the genus Kiekie is located in the montane ecosystems of Costa Rica followed by the lowland rainforest of the Pacific side (Limon Basin). Kiekie originated in the North America Tropical region, this genus started diversifying in the Late Miocene and spread to Lower Central America and South America. In that region, Kiekie colonized independently several times the montane ecosystems corresponding to periods of uplifting of Talamanca and Central Cordilleras. creator: Nicolas Hazzi creator: Gustavo Hormiga uri: https://doi.org/10.7717/peerj.17242 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hazzi and Hormiga title: A comprehensive dataset on biomechanics and motor control during human walking with discrete mechanical perturbations link: https://peerj.com/articles/17256 last-modified: 2024-04-29 description: BackgroundHumans have a remarkable capability to maintain balance while walking. There is, however, a lack of publicly available research data on reactive responses to destabilizing perturbations during gait.MethodsHere, we share a comprehensive dataset collected from 10 participants who experienced random perturbations while walking on an instrumented treadmill. Each participant performed six 5-min walking trials at a rate of 1.2 m/s, during which rapid belt speed perturbations could occur during the participant’s stance phase. Each gait cycle had a 17% probability of being perturbed. The perturbations consisted of an increase of belt speed by 0.75 m/s, delivered with equal probability at 10%, 20%, 30%, 40%, 50%, 60%, 70%, or 80% of the stance phase. Data were recorded using motion capture with 25 markers, eight inertial measurement units (IMUs), and electromyography (EMG) from the tibialis anterior (TA), soleus (SOL), lateral gastrocnemius (LG), rectus femoris (RF), vastus lateralis (VL), vastus medialis (VM), biceps femoris (BF), and gluteus maximus (GM). The full protocol is described in detail.ResultsWe provide marker trajectories, force plate data, EMG data, and belt speed information for all trials and participants. IMU data is provided for most participants. This data can be useful for identifying neural feedback control in human gait, biologically inspired control systems for robots, and the development of clinical applications. creator: Dana L. Lorenz creator: Antonie J. van den Bogert uri: https://doi.org/10.7717/peerj.17256 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lorenz and van den Bogert 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.