title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=538 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Investigation of the hydration process and biological activity of a novel nanosilver incorporated dicalcium silicate based retrograde filling material link: https://peerj.com/articles/14632 last-modified: 2023-02-01 description: BackgroundAlthough several materials have been used for retrograde filling following apical surgeries, there is no consensus on a single best material. Tricalcium silicate-based types of cement have been developed as root-end filling materials mainly due to tricalcium silicate’s hydraulic properties. However, its unfavorable setting characteristics and minimal antimicrobial properties have necessitated the introduction of new additives into the existing commercially available materials. To design an affordable product based on a dicalcium silicate with a shorter set time, minimal cytotoxic complications, and enhanced antibacterial activity, we developed a new endodontic cement from pure raw materials, intending to satisfy the prerequisites of ideal retrograde material.MethodsThe composition of the experimental calcium silicate-based cement included the addition of calcium chloride and silver nanoparticles in varying concentrations. Structural characterization was carried out using energy dispersive analysis by X-rays using scanning electron microscope (EDAX SEM) and hydration characteristics were performed using an X-ray diffractometer (XRD). The experimental material was further evaluated for biocompatibility using MTT ([3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide)assay and antibacterial activity was evaluated using an agar diffusion test against Enterococcus faecalis.ResultsThe structural characterization and hydration characteristics revealed that the experimental cement was dicalcium silicate based with favorable biocompatibility and enhanced antibacterial activity. Tricalcium silicate based mineral trioxide aggregate (MTA) also had favourable biocompatibility, however, its antibacterial activity was significantly decreased when compared to the novel cement.ConclusionAll hydraulic cements that are available in the dental market are predominantly tricalcium silicate-based materials. There has been no evidence in the literature to date wherein it has been explored whether a dicalcium silicate-based hydraulic cement can solely be used in root-end cavities. The findings of the study revealed a dicalcium silicate based retrograde filling material with favourable biocompatibility exhibited immediately as well as in the set samples. Incorporation of silver nanoparticles boosted the antibacterial activity when compared to that of ProRoot MTA. This material could potentially reinstate the usual hype created with tricalcium silicate types of cement since dicalcium silicate cements also exhibit similar properties. creator: Teena Dsouza creator: Aditya Shetty creator: Sudarshan Kini creator: Veena Shetty creator: Shama Rao creator: Rajesha Payaradka creator: Nijil Satheesan creator: Neevan Dsouza creator: Heeresh Shetty uri: https://doi.org/10.7717/peerj.14632 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dsouza et al. title: Correlations between horizontal jump and sprint acceleration and maximal speed performance: a systematic review and meta-analysis link: https://peerj.com/articles/14650 last-modified: 2023-02-01 description: ObjectivesThe purpose of this study is to determine the associations between horizontal jump and sprint acceleration, as well as maximal speed performance.MethodsA systematic literature search was performed using PubMed, MEDLINE (EBSCOhost), and Web of Science. The studies that were included in this review must meet the following criteria: (1) well-trained individuals over the age of 18 years old; (2) Pearson’s correlation coefficients between sprint time and horizontal jump distance were provided; (3) the sprint distance was limited to 0–100 m. The quality of the studies was assessed using a modified version of the Downs and Black Quality Index test. A random-effects model was used to determine the effect sizes, and heterogeneity between studies was examined using the Q statistic and I2.ResultsFrom the identified 2,815 studies, 27 studies were included in this study (two from reference lists). The sprint time of the sprint acceleration phase was moderately and negatively correlated with the standing long jump (r =  − 0.45, z = 7.48, p < 0.001), single leg standing long jump (r =  − 0.48, z = 3.49, p < 0.001) and horizontal drop jump distance (r =  − 0.48, z = 3.49, p < 0.001), and was largely and negatively correlated with multiple jump distance (r =  − 0.69, z = 6.02, p < 0.001). Out of five studies assessed the standing triple jump, three studies reported significant positive association with the sprint acceleration performance. The sprint time of maximal speed phase was very largely and negatively associated with standing long jump distance (r =  − 0.73, z = 4.44, p < 0.001) and multiple jump distance (r =  − 0.76, z = 6.86, p < 0.001).ConclusionsThis review indicates the moderate to very large associations between horizontal jump and sprint acceleration and maximal speed performance, and the highest magnitude of associations between them is found in the multiple jump. Moreover, compared to the sprint acceleration performance, there are greater associations between maximal speed performance and standing long jump and multiple jump distance. creator: Junlei Lin creator: Jie Shen creator: Junjie Zhang creator: Aiguo Zhou creator: Wenxia Guo uri: https://doi.org/10.7717/peerj.14650 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lin et al. title: Determination and risk assessment of pharmaceutical residues in the urban water cycle in Selangor Darul Ehsan, Malaysia link: https://peerj.com/articles/14719 last-modified: 2023-02-01 description: The environmental fate of non-steroidal anti-inflammatory drugs (NSAIDs) in the urban water cycle is still uncertain and their status is mainly assessed based on specific water components and information on human risk assessments. This study (a) explores the environmental fate of NSAIDs (ibuprofen, IBU; naproxen, NAP; ketoprofen, KET; diazepam, DIA; and diclofenac, DIC) in the urban water cycle, including wastewater, river, and treated water via gas chromatography-mass spectrophotometry (GCMS), (b) assesses the efficiency of reducing the targeted NSAIDs in sewage treatment plant (STP) using analysis of variance (ANOVA), and (c) evaluates the ecological risk assessment of these drugs in the urban water cycle via teratogenic index (TI) and risk quotient (RQ). The primary receptor of contaminants comes from urban areas, as a high concentration of NSAIDs is detected (ranging from 5.87 × 103 to 7.18 × 104 ng/L). The percentage of NSAIDs removal in STP ranged from 25.6% to 92.3%. The NAP and KET were still detected at trace levels in treated water, indicating the persistent presence in the water cycle. The TI values for NAP and DIA (influent and effluent) were more than 1, showing a risk of a teratogenic effect. The IBU, KET, and DIC had values of less than 1, indicating the risk of lethal embryo effects. The NAP and DIA can be classified as Human Pregnancy Category C (2.1 > TI ≥ 0.76). This work proved that these drugs exist in the current urban water cycle, which could induce adverse effects on humans and the environment (RQ in high and low-risk categories). Therefore, they should be minimized, if not eliminated, from the primary sources of the pollutant (i.e., STPs). These pollutants should be considered a priority to be monitored, given focus to, and listed in the guideline due to their persistent presence in the urban water cycle. creator: Zarimah Mohd Hanafiah creator: Wan Hanna Melini Wan Mohtar creator: Teh Sabariah Abd Manan creator: Nur Aina Bachi creator: Nurfaizah Abu Tahrim creator: Haris Hafizal Abd Hamid creator: Abdulnoor Ghanim creator: Amirrudin Ahmad creator: Nadiah Wan Rasdi creator: Hamidi Abdul Aziz uri: https://doi.org/10.7717/peerj.14719 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mohd Hanafiah et al. title: Multifaceted roles of aerobic glycolysis and oxidative phosphorylation in hepatocellular carcinoma link: https://peerj.com/articles/14797 last-modified: 2023-02-01 description: Liver cancer is a common malignancy with high morbidity and mortality rates. Changes in liver metabolism are key factors in the development of primary hepatic carcinoma, and mitochondrial dysfunction is closely related to the occurrence and development of tumours. Accordingly, the study of the metabolic mechanism of mitochondria in primary hepatic carcinomas has gained increasing attention. A growing body of research suggests that defects in mitochondrial respiration are not generally responsible for aerobic glycolysis, nor are they typically selected during tumour evolution. Conversely, the dysfunction of mitochondrial oxidative phosphorylation (OXPHOS) may promote the proliferation, metastasis, and invasion of primary hepatic carcinoma. This review presents the current paradigm of the roles of aerobic glycolysis and OXPHOS in the occurrence and development of hepatocellular carcinoma (HCC). Mitochondrial OXPHOS and cytoplasmic glycolysis cooperate to maintain the energy balance in HCC cells. Our study provides evidence for the targeting of mitochondrial metabolism as a potential therapy for HCC. creator: Ying Zhang creator: Wenhuan Li creator: Yuan Bian creator: Yan Li creator: Lei Cong uri: https://doi.org/10.7717/peerj.14797 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Zhang et al. title: Development of a novel mathematical model that explains SARS-CoV-2 infection dynamics in Caco-2 cells link: https://peerj.com/articles/14828 last-modified: 2023-02-01 description: Mathematical modeling is widely used to study within-host viral dynamics. However, to the best of our knowledge, for the case of SARS-CoV-2 such analyses were mainly conducted with the use of viral load data and for the wild type (WT) variant of the virus. In addition, only few studies analyzed models for in vitro data, which are less noisy and more reproducible. In this work we collected multiple data types for SARS-CoV-2-infected Caco-2 cell lines, including infectious virus titers, measurements of intracellular viral RNA, cell viability data and percentage of infected cells for the WT and Delta variants. We showed that standard models cannot explain some key observations given the absence of cytopathic effect in human cell lines. We propose a novel mathematical model for in vitro SARS-CoV-2 dynamics, which included explicit modeling of intracellular events such as exhaustion of cellular resources required for virus production. The model also explicitly considers innate immune response. The proposed model accurately explained experimental data. Attenuated replication of the Delta variant in Caco-2 cells could be explained by our model on the basis of just two parameters: decreased cell entry rate and increased cytokine production rate. creator: Vladimir Staroverov creator: Stepan Nersisyan creator: Alexei Galatenko creator: Dmitriy Alekseev creator: Sofya Lukashevich creator: Fedor Polyakov creator: Nikita Anisimov creator: Alexander Tonevitsky uri: https://doi.org/10.7717/peerj.14828 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Staroverov et al. title: Iron (oxyhydr)oxides are responsible for the stabilization of Cu and Zn in AMD after treatment with limestone link: https://peerj.com/articles/14663 last-modified: 2023-01-30 description: The formation and transformation of secondary iron (oxyhydr)oxides and their role in the stabilization of copper (Cu) and zinc (Zn) in acid mine drainage (AMD) after limestone treatment are worth studying to better understand the impacts of limestone AMD treatment. In this study, the wastewater from a copper mine ditch was sampled. Two different doses of limestone (S: 5.33 g L−1 and SS: 8.00 g L−1) were applied to adjust the pH range of the sampled AMD. The concentrations of Fe, Cu and Zn in the supernatant and the levels of iron (oxyhydr)oxides and heavy metals in AMD sediments were dynamically monitored for 300 days to analyze the transformation of the secondary iron mineral phase and the role iron (oxyhydr)oxides play in the removal and stabilization of Cu and Zn. The results showed that the pH rose rapidly to 6.82, decreased to 5.82 on the 150th day, and finally decreased to approximately 4.63 by the 300th day, when the dosage of limestone (S) was 5.33 g L−1. Goethite was the main form of iron oxides in the sediments. As the incubation time increased, so did the content of crystalline Fe (oxyhydr)oxides. In addition, the Cu and Zn content in the fraction of crystalline Fe (oxyhydr)oxides increased as the corresponding iron (oxyhydr)oxide increased. When the high dosage of limestone (8.00 g L−1 or SS) was applied, the pH remained at approximately at 7.46 during the whole period and goethite and lepidocrocite were present in the sediment. Amorphous/ poorly crystalline Fe-oxyhydroxide was the main product after SS limestone dosage, indicating that the risk of Cu and Zn reactivation in the sediment was higher with a higher limestone treatment dosage. creator: Yuan Ding creator: Yan Long creator: Weiya Wang creator: Zhe Wei creator: Shuo Cai uri: https://doi.org/10.7717/peerj.14663 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ding et al. title: Modeling knot features using branch scars from Mongolian oak (Quercus mongolica) link: https://peerj.com/articles/14755 last-modified: 2023-01-31 description: Wood quality is an important indicator for modern sawmills. Internal wood characteristics can be derived from their correlations with external appearances. In this study, we developed linear regression models to predict knot size from surface features of Mongolian oak (Quercus mongolica) using data collected from 53 trees. For this, manual measurements and X-ray computed tomography scanning technology was respectively used to obtain internal and external features of 1,297 knots. Our results showed that Mongolian oak knots were generally concentrated in the middle part of oak stems, with fewer knots observed at the top and base. The parameters of knot and scar showed significant correlations (P < 0.01), where length and diameter of the corresponding external scar increase with increasing the length and diameter of a knot. The corresponding external scar can be used as an effective indicator to predict the internal value of oak logs. The accuracy of our constructed model is more than 95% when assessed against independent test samples. These models thus can be applied to improve the practical production of oak timber and reduce commercial loss caused by knots. These additional data can improve the estimation of the influence of knots on wood quality and provide a theoretical foundation for investigating the characteristics of hardwood knots. creator: Xiu-jun Lu creator: Lei Wang creator: Hui-lin Gao creator: Hao Zhan creator: Xiao-lin Zhang uri: https://doi.org/10.7717/peerj.14755 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lu et al. title: The effect of short-term fallowing on the microbial communities in forest soil cultivated with ginseng: Preliminary research link: https://peerj.com/articles/14758 last-modified: 2023-01-31 description: BackgroundContinuous cultivation of ginseng crops in fixed plots can lead to disease outbreaks, yield losses and replanting failures. Fallow periods can help restore soil health and increase the sustainability of agricultural systems; however, taking land out of production for extended periods is often not feasible. Short-term fallow periods could restore soil health, but few studies have examined the effects of short-term fallow treatment on the health of soil in ginseng fields.MethodsIn this preliminary study, we used metagenomic analysis to assess changes in the abundance of major ginseng pathogens and soil health overall following a short-term fallow period in a region in the Changbai Mountains. A sample from a forest plot (Hx0ks), was compared to a sample from a field where ginseng was previously cultivated and then had been left fallow for two years (Hx2), and a sample from a field that had been fallow for two years and was subsequently replanted with ginseng (Clsd).ResultsSoil that was fallow for two years, and then replanted with ginseng, showed reduced nutrient content and lower diversity of soil bacterial and fungal communities than soil that remained fallow. Candidatus Solibacter (5%) and Rhizomicrobium (3%) were the most abudant bacterial genera in Hx2. Rhizomicrobium (4%) and Gemmatimonas (3%) were the most abundant bacterial genera in Clsd. Mortierella (22%) and Peziza (12%) dominated the fungal community in Hx2. Lecanicillium (38%) and Mortierella (13%) dominated the fungal community in Clsd. Fallow periods also increased the functional diversity of soil as predicted by PICRUSt and decreased the relative abundance of the pathogenic fungi.ConclusionsPreliminary findings were consistent with the hypothesis that fallow management in ginseng cultivation can improve soil microbial community structure and function and reduces the number of plant pathogens; however, testing this hypothesis will require replicated plots. creator: Yuqing Li creator: Feyisike Gbolayori Jones creator: Bing Zhang creator: Juntao Cui creator: Wei Zhang uri: https://doi.org/10.7717/peerj.14758 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Effects of lower and upper body fatigue in striking response time of amateur karate athletes link: https://peerj.com/articles/14764 last-modified: 2023-01-31 description: In combat sports, strikes or counter-strikes response time (RT) can be related to performance and sporting success. Moreover, training sessions are usually highly fatiguing, which is expected to impair basic skills, such as RT. Thus, this study aimed to investigate the effect of fatigue on punch and kick RTs of karate practitioners. Twelve individuals of both sexes from different levels (three yellow belts, three red belts, two orange belts, two green belts, one brown belt, and one black belt) were selected. Participants were aged 22 ± 3 years old, with a stature of 169.1 ± 6.5 cm, and a body mass of 65.5 ± 10 kg. Six visits were held with each participant. On the first 2 days, the RT of punches and kicks was measured by a validated smartphone app (TReaction). For the subsequent visits, a randomized incremental test for the upper or lower body was adopted as motor fatigue protocol, immediately followed by punches and kicks RT tests, also in random order. For induction of lower and upper body-specific muscle fatigue, the ITStriker app was used, which operates by emitting sound signals transmitted by a smartphone. One-way repeated measures ANOVA was performed, and significance was set at p ≤ 0.05. Regarding the mean punches RT, significant effects between situations for the upper (F(2,22) = 11.5; ω2 = 0.23; p < 0.001) and lower body (F(2,22) = 14.2; ω2 = 0.18; p < 0.001) fatigue protocols were found. The negative effect of the lower body fatigue protocol in punches RT was evident regardless of the order of the tests (punch RT first: Δ = 10.5%; t = 4.4; p < 0.001; d = 1.0; kick RT first: Δ = 11.4%; t = 4.8; p < 0.001; d = 1.1). Regarding mean kicks RT, significant effects were found between situations for the lower (F(2,22) = 16.6; ω2 = 0.27; p < 0.001) but not for the upper (F(2,22) = 2.3; ω2 = 0.02; p = 0.12) body fatigue protocols. Kick RTs were negatively affected by the lower body fatigue protocol regardless of the RT order applied (punch RT first: Δ = 7.5%; t = 3.0; p = 0.01; d = 0.8; kick RT first: Δ = 14.3%; t = 5.7; p < 0.001; d = 1.5). Upper body fatigue does not impair punch or kick RTs. Thus, it is concluded that the specificity of fatigue protocols and striking order should be considered while performing RT demanding techniques in karate practice. Specifically, lower body motor fatigue may impair both kicks and punches RT, which highlights the role of lower limbs in punches performance. Otherwise, upper body motor fatigue seems to induce impairments that are limited to the specific motor actions of this body segment. creator: Júlio Cesar Carvalho Rodrigues creator: Eduardo Macedo Penna creator: Hugo Enrico Souza Machado creator: Jader Sant’Ana creator: Fernando Diefenthaeler creator: Victor S. Coswig uri: https://doi.org/10.7717/peerj.14764 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rodrigues et al. title: Simultaneous functioning of different light-harvesting complexes—a strategy of adaptation of purple bacterium Rhodopseudomonas palustris to low illumination conditions link: https://peerj.com/articles/14769 last-modified: 2023-01-31 description: Novel peripheral light-harvesting (LH) complex designated as LL LH2 was isolated along with LH4 complex from Rhodopseudomonas palustris cells grown under low light intensity (LL). FPLC-MS/MS allowed to reveal PucABd and PucBabc apoproteins in LL LH2 complex, which is different from previously described LH4 complex containing PucABd, PucABa and PucBb. The main carotenoids in LL LH2 complex were rhodopin and 3,4-didehydrorhodopin. Three-dimensional modeling demonstrated which amino acid residues of all the β-subunits could interact with carotenoids (Car) and bacteriochlorophyll a (BChl a). Analysis of amino acid sequences of α-subunits of both LL complexes showed presence of different C-terminal motifs, IESSVNVG in αa subunit and IESSIKAV in αd subunit, in the same positions of C-termini, which could reflect different retention force of LL LH2 and LH4 on hydroxyl apatite, facilitating successful isolation of these complexes. Differences of these LL complexes in protein and carotenoid composition, in efficiency of energy transfer from Car to BChl a, which is two times lower in LL LH2 than in LH4, allow to assign it to a novel type of light-harvesting complex in Rhodopseudomonas palustris. creator: Olga Petrovna Serdyuk creator: Azat Vadimovich Abdullatypov creator: Lidiya Dmitrievna Smolygina creator: Aleksandr Aleksandrovich Ashikhmin creator: Maxim Alexandrovich Bolshakov uri: https://doi.org/10.7717/peerj.14769 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Serdyuk et al.