title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=784 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Metabolomics of a cell line-derived xenograft model reveals circulating metabolic signatures for malignant mesothelioma link: https://peerj.com/articles/12568 last-modified: 2022-01-04 description: BackgroundMalignant mesothelioma (MM) is a rare and highly aggressive cancer. Despite advances in multidisciplinary treatments for cancer, the prognosis for MM remains poor with no effective diagnostic biomarkers currently available. The aim of this study was to identify plasma metabolic biomarkers for better MM diagnosis and prognosis by use of a MM cell line-derived xenograft (CDX) model.MethodsThe MM CDX model was confirmed by hematoxylin and eosin staining and immunohistochemistry. Twenty female nude mice were randomly divided into two groups, 10 for the MM CDX model and 10 controls. Plasma samples were collected two weeks after tumor cell implantation. Gas chromatography-mass spectrometry analysis was conducted. Both univariate and multivariate statistics were used to select potential metabolic biomarkers. Hierarchical clustering analysis, metabolic pathway analysis, and receiver operating characteristic (ROC) analysis were performed. Additionally, bioinformatics analysis was used to investigate differential genes between tumor and normal tissues, and survival-associated genes.ResultsThe MM CDX model was successfully established. With VIP > 1.0 and P-value < 0.05, a total of 23 differential metabolites were annotated, in which isoleucine, 5-dihydrocortisol, and indole-3-acetamide had the highest diagnostic values based on ROC analysis. These were mainly enriched in pathways for starch and sucrose metabolism, pentose and glucuronate interconversions, galactose metabolism, steroid hormone biosynthesis, as well as phenylalanine, tyrosine and tryptophan biosynthesis. Further, down-regulation was observed for amino acids, especially isoleucine, which is consistent with up-regulation of amino acid transporter genes SLC7A5 and SLC1A3 in MM. Overall survival was also negatively associated with SLC1A5, SLC7A5, and SLC1A3.ConclusionWe found several altered plasma metabolites in the MM CDX model. The importance of specific metabolic pathways, for example amino acid metabolism, is herein highlighted, although further investigation is warranted. creator: Yun Gao creator: Ziyi Dai creator: Chenxi Yang creator: Ding Wang creator: Zhenying Guo creator: Weimin Mao creator: Zhongjian Chen uri: https://doi.org/10.7717/peerj.12568 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Gao et al. title: Development and validation of a novel risk score to predict 5-year mortality in patients with acute myocardial infarction in China: a retrospective study link: https://peerj.com/articles/12652 last-modified: 2022-01-04 description: BackgroundThe disease burden from ischaemic heart disease remains heavy in the Chinese population. Traditional risk scores for estimating long-term mortality in patients with acute myocardial infarction (AMI) have been developed without sufficiently considering advances in interventional procedures and medication. The goal of this study was to develop a risk score comprising clinical parameters and intervention advances at hospital admission to assess 5-year mortality in AMI patients in a Chinese population.MethodsWe performed a retrospective observational study on 2,722 AMI patients between January 2013 and December 2017. Of these patients, 1,471 patients from Changsha city, Hunan Province, China were assigned to the development cohort, and 1,251 patients from Xiangtan city, Hunan Province, China, were assigned to the validation cohort. Forty-five candidate variables assessed at admission were screened using least absolute shrinkage and selection operator, stepwise backward regression, and Cox regression methods to construct the C2ABS2-GLPK score, which was graded and stratified using a nomogram and X-tile. The score was internally and externally validated. The C-statistic and Hosmer-Lemeshow test were used to assess discrimination and calibration, respectively.ResultsFrom the 45 candidate variables obtained at admission, 10 potential predictors, namely, including Creatinine, experience of Cardiac arrest, Age, N-terminal Pro-Brain Natriuretic Peptide, a history of Stroke, Statins therapy, fasting blood Glucose, Left ventricular end-diastolic diameter, Percutaneous coronary intervention and Killip classification were identified as having a close association with 5-year mortality in patients with AMI and collectively termed the C2ABS2-GLPK score. The score had good discrimination (C-statistic = 0.811, 95% confidence intervals (CI) [0.786–0.836]) and calibration (calibration slope = 0.988) in the development cohort. In the external validation cohort, the score performed well in both discrimination (C-statistic = 0.787, 95% CI [0.756–0.818]) and calibration (calibration slope = 0.976). The patients were stratified into low- (≤148), medium- (149 to 218) and high-risk (≥219) categories according to the C2ABS2-GLPK score. The predictive performance of the score was also validated in all subpopulations of both cohorts.ConclusionThe C2ABS2-GLPK score is a Chinese population-based risk assessment tool to predict 5-year mortality in AMI patients based on 10 variables that are routinely assessed at admission. This score can assist physicians in stratifying high-risk patients and optimizing emergency medical interventions to improve long-term survival in patients with AMI. creator: Yan Tang creator: Yuanyuan Bai creator: Yuanyuan Chen creator: Xuejing Sun creator: Yunmin Shi creator: Tian He creator: Mengqing Jiang creator: Yujie Wang creator: Mingxing Wu creator: Zhiliu Peng creator: Suzhen Liu creator: Weihong Jiang creator: Yao Lu creator: Hong Yuan creator: Jingjing Cai uri: https://doi.org/10.7717/peerj.12652 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tang et al. title: Pecan agroforestry systems improve soil quality by stimulating enzyme activity link: https://peerj.com/articles/12663 last-modified: 2022-01-04 description: BackgroundForest and plantation intercropping are efficient agroforestry systems that optimize land use and promote agroforestry around the world. However, diverse agroforestry systems on the same upper-plantation differently affect the physical and chemical properties of the soil.MethodsThe treatments for this study included a single cultivation (CK) pecan control and three agroforestry systems (pecan + Paeonia suffruticosa + Hemerocallis citrina, pecan + Paeonia suffruticosa, and pecan + Paeonia lactiflora). Soil samples were categorized according to the sampling depth (0–20 cm, 20–40 cm, 40–60 cm).ResultsThe results demonstrated that the bulk density (BD) of soil under the pecan agroforestry system (PPH and PPL) was reduced by 16.13% and 7.10%, respectively, and the soil moisture content (MC) and total soil porosity (TPO) increased. Improvements in the physical properties of the soil under the PPS agroforestry system were not obvious when compared with the pecan monoculture. The soil total phosphorus (TP), total nitrogen (TN), available potassium (AK), and total carbon (TC) increased significantly, while the soil urease (S-UE), alkaline phosphatase (S-AKP), and 1,4-β-N-acetylglucosamines (S-NAG) enzyme activity also increased significantly, following agroforestry. Overall, the pecan agroforestry system significantly improved the physical properties of the pecan plantation soil, enriched the soil nutrients, and increased the activity of soil enzymes related to TC, TN, and TP cycles. creator: Zhaocheng Wang creator: Mengyu Zhou creator: Hua Liu creator: Cheng Huang creator: Yuhua Ma creator: Hao xin Ge creator: Xiang Ge creator: Songling Fu uri: https://doi.org/10.7717/peerj.12663 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Measuring evidence-based practice in physical therapy: a mix-methods study link: https://peerj.com/articles/12666 last-modified: 2022-01-04 description: BackgroundEvidence-based practice (EBP) is considered the “holy grail” to manage patients by health practitioners (such as physical therapists). However, sometimes, patients are not treated with the best interventions for their condition. Although studies already explored the facilitators and barriers for this issue, they increase in the level of importance if the information gathered are context appropriated. As the profession is relatively new in Portugal, currently little is known about the implementation of EBP in Portuguese physical therapists context. So, the aim of this study is to know if the Portuguese physical therapists use an EBP, and collect and deeper understand the factors, barriers and facilitators associated with EBP.MethodsThis study incorporated a mixed-methods design (quantitative and qualitative). In an attempt to ensure the correct population sample, a national professional association e-mail database and the e-mails of past students from national schools were requested. For the quantitative data it was choose an e-survey, adapted from the EBP: Beliefs, Attitudes, Knowledge, and Behaviors of Physical Therapists Portuguese version questionnaire, consisted of 55 close-ended questions. It was analyzed response frequencies and associations between variables with logistic regression analyses. For the qualitative data, it was choose to perform semi-structured interviews in purposefully selected physical therapists to include different sociodemographic factors (especially those found to be statistically significant in the logistic regression) and survey responses regarding the physical therapists’ beliefs, attitudes, knowledge, and behaviors. The interviews were performed in an online software, where only audio contact was performed. The audios were anonymized and verbatim transcribed, and the texts explored by the thematic approach.ResultsFrom the 277 physical therapists that shown interest in participating in the study, 193 fully completed the questionnaire and, from those, 10 participated in the interviews. The Portuguese physical therapists reported positive beliefs, attitudes, knowledge, and behaviors regarding EBP. Among the physical therapists characteristics it seems that age (younger therapists), education (participating in continuing education courses; belonging to practice-orientated organizations; having a doctorate degree; pursuing a higher academic degree; and being a clinical instructor), and workplace (working for someone else account; and academic sector) are the main factors in the Portuguese EBP implementation. The Portuguese physical therapists, beyond the physical therapists individual characteristics and workplace, also stated that evidence, patients, clinical experience, schools, country and physical therapy characteristics, may behave as facilitators or barriers when performing an EBP. creator: Ricardo M. Ferreira creator: Pedro N. Martins creator: Nuno Pimenta creator: Rui S. Gonçalves uri: https://doi.org/10.7717/peerj.12666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ferreira et al. title: RNA sequencing-based exploration of the effects of blue laser irradiation on mRNAs involved in functional metabolites of D. officinales link: https://peerj.com/articles/12684 last-modified: 2022-01-04 description: Dendrobium officinale Kimura et Migo (D. officinale) has promising lung moisturizing, detoxifying, and immune boosting properties. Light is an important factor influencing functional metabolite synthesis in D. officinale. The mechanisms by which lasers affect plants are different from those of ordinary light sources; lasers can effectively address the shortcomings of ordinary light sources and have significant interactions with plants. Different light treatments (white, blue, blue laser) were applied, and the number of red leaves under blue laser was greater than that under blue and white light. RNA-seq technology was used to analyze differences in D. officinale under different light treatments. The results showed 465, 2,107 and 1,453 differentially expressed genes (DEGs) in LB-B, LB-W and W-B, respectively. GO, KEGG and other analyses of DEGs indicated that D. officinale has multiple blue laser response modes. Among them, the plasma membrane, cutin, suberine and wax biosynthesis, flavone and flavonol biosynthesis, heat shock proteins, etc. play central roles. Physiological and biochemical results verified that blue laser irradiation significantly increases POD, SOD, and PAL activities in D. officinale. The functional metabolite results showed that blue laser had the greatest promoting effect on total flavonoids, polysaccharides, and alkaloids. qPCR verification combined with other results suggested that CRY DASH, SPA1, HY5, and PIF4 in the blue laser signal transduction pathway affect functional metabolite accumulation in D. officinale through positively regulated expression patterns, while CO16 and MYC2 exhibit negatively regulated expression patterns. These findings provide new ideas for the efficient production of metabolites in D. officinale. creator: Hansheng Li creator: Yuqiang Qiu creator: Gang Sun creator: Wei Ye uri: https://doi.org/10.7717/peerj.12684 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Human-wildlife conflicts with crocodilians, cetaceans and otters in the tropics and subtropics link: https://peerj.com/articles/12688 last-modified: 2022-01-04 description: Conservation of freshwater biodiversity and management of human-wildlife conflicts are major conservation challenges globally. Human-wildlife conflict occurs due to attacks on people, depredation of fisheries, damage to fishing equipment and entanglement in nets. Here we review the current literature on conflicts with tropical and subtropical crocodilians, cetaceans and otters in freshwater and brackish habitats. We also present a new multispecies case study of conflicts with four freshwater predators in the Western Amazon: black caiman (Melanosuchus niger), giant otter (Pteronura brasiliensis), boto (Inia geoffrensis) and tucuxi (Sotalia fluviatilis). Documented conflicts occur with 34 crocodilian, cetacean and otter species. Of the species reviewed in this study, 37.5% had conflicts frequently documented in the literature, with the saltwater crocodile (Crocodylus porosus) the most studied species. We found conflict severity had a positive relationship with species body mass, and a negative relationship with IUCN Red List status. In the Amazonian case study, we found that the black caiman was ranked as the greatest ‘problem’ followed by the boto, giant otter and tucuxi. There was a significant difference between the responses of local fishers when each of the four species were found entangled in nets. We make recommendations for future research, based on the findings of the review and Amazon case study, including the need to standardise data collection. creator: Patrick Cook creator: Joseph E. Hawes creator: João Vitor Campos-Silva creator: Carlos A. Peres uri: https://doi.org/10.7717/peerj.12688 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cook et al. title: Seasonal variations and co-occurrence networks of bacterial communities in the water and sediment of artificial habitat in Laoshan Bay, China link: https://peerj.com/articles/12705 last-modified: 2022-01-04 description: Marine bacteria in the seawater and seafloor are essential parts of Earth’s biodiversity, as they are critical participants of the global energy flow and the material cycles. However, their spatial-temporal variations and potential interactions among varied biotopes in artificial habitat are poorly understood. In this study, we profiled the variations of bacterial communities among seasons and areas in the water and sediment of artificial reefs using 16S rRNA gene sequencing, and analyzed the potential interaction patterns among microorganisms. Distinct bacterial community structures in the two biotopes were exhibited. The Shannon diversity and the richness of phyla in the sediment were higher, while the differences among the four seasons were more evident in the water samples. The seasonal variations of bacterial communities in the water were more distinct, while significant variations among four areas were only observed in the sediment. Correlation analysis revealed that nitrite and mud content were the most important factors influencing the abundant OTUs in the water and sediment, respectively. Potential interactions and keystone species were identified based on the three co-occurrence networks. Results showed that the correlations among bacterial communities in the sediment were lower than in the water. Besides, the abundance of the top five abundant species and five keystone species had different changing patterns among four seasons and four areas. These results enriched our understanding of the microbial structures, dynamics, and interactions of microbial communities in artificial habitats, which could provide new insights into planning, constructing and managing these special habitats in the future. creator: Guangjie Fang creator: Haolin Yu creator: Huaxiang Sheng creator: Chuanxi Chen creator: Yanli Tang creator: Zhenlin Liang uri: https://doi.org/10.7717/peerj.12705 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Fang et al. title: Developmental exposure to the DE-71 mixture of polybrominated diphenyl ether (PBDE) flame retardants induce a complex pattern of endocrine disrupting effects in rats link: https://peerj.com/articles/12738 last-modified: 2022-01-04 description: Polybrominated diphenyl ethers (PBDEs) are legacy compounds with continued widespread human exposure. Despite this, developmental toxicity studies of DE-71, a mixture of PBDEs, are scarce and its potential for endocrine disrupting effects in vivo is not well covered. To address this knowledge gap, we carried out a developmental exposure study with DE-71. Pregnant Wistar rat dams were exposed to 0, 40 or 60 mg/kg bodyweight/day from gestation day 7 to postnatal day 16, and both sexes were examined. Developmental exposure affected a range of reproductive toxicity endpoints. Effects were seen for both male and female anogenital distances (AGD), with exposed offspring of either sex displaying around 10% shorter AGD compared to controls. Both absolute and relative prostate weights were markedly reduced in exposed male offspring, with about 40% relative to controls. DE-71 reduced mammary gland outgrowth, especially in male offspring. These developmental in vivo effects suggest a complex effect pattern involving anti-androgenic, anti-estrogenic and maybe estrogenic mechanisms depending on tissues and developmental stages. Irrespective of the specific underlying mechanisms, these in vivo results corroborate that DE-71 causes endocrine disrupting effects and raises concern for the effects of PBDE-exposure on human reproductive health, including any potential long-term consequences of disrupted mammary gland development. creator: Louise Ramhøj creator: Karen Mandrup creator: Ulla Hass creator: Terje Svingen creator: Marta Axelstad uri: https://doi.org/10.7717/peerj.12738 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ramhøj et al. title: Predicting continuous ground reaction forces from accelerometers during uphill and downhill running: a recurrent neural network solution link: https://peerj.com/articles/12752 last-modified: 2022-01-04 description: BackgroundGround reaction forces (GRFs) are important for understanding human movement, but their measurement is generally limited to a laboratory environment. Previous studies have used neural networks to predict GRF waveforms during running from wearable device data, but these predictions are limited to the stance phase of level-ground running. A method of predicting the normal (perpendicular to running surface) GRF waveform using wearable devices across a range of running speeds and slopes could allow researchers and clinicians to predict kinetic and kinematic variables outside the laboratory environment.PurposeWe sought to develop a recurrent neural network capable of predicting continuous normal (perpendicular to surface) GRFs across a range of running speeds and slopes from accelerometer data.MethodsNineteen subjects ran on a force-measuring treadmill at five slopes (0°, ±5°, ±10°) and three speeds (2.5, 3.33, 4.17 m/s) per slope with sacral- and shoe-mounted accelerometers. We then trained a recurrent neural network to predict normal GRF waveforms frame-by-frame. The predicted versus measured GRF waveforms had an average ± SD RMSE of 0.16 ± 0.04 BW and relative RMSE of 6.4 ± 1.5% across all conditions and subjects.ResultsThe recurrent neural network predicted continuous normal GRF waveforms across a range of running speeds and slopes with greater accuracy than neural networks implemented in previous studies. This approach may facilitate predictions of biomechanical variables outside the laboratory in near real-time and improves the accuracy of quantifying and monitoring external forces experienced by the body when running. creator: Ryan S. Alcantara creator: W. Brent Edwards creator: Guillaume Y. Millet creator: Alena M. Grabowski uri: https://doi.org/10.7717/peerj.12752 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Alcantara et al. title: Efficacy of bakuchiol-garlic combination against virulent genes of Candida albicans link: https://peerj.com/articles/12251 last-modified: 2022-01-03 description: BackgroundPolymicrobial biofilms are notorious for causing intraoral tissue destruction. Streptococcus sanguinis and Streptococcus mitis, commensals of oral cavities, have been found co-existing with C. albicans in resistant oral infections. There is an urgent need to find alternative treatment options. This study aims to assess the efficacy of garlic (G) and bakuchiol (Bk) combination against candida virulent genes and their subsequently secreted proteins.MethodsIn vitro single species biofilms of C. albicans, and mixed species biofilms formed in combination with streptococci were exposed to bakuchiol and garlic extract (Bk+G). Gene expression of agglutinin-like sequence (ALS1), (ALS3), adhesin-like wall proteins (HWP1) and aspartyl proteinases (SAP5) were determined using qPCR and their subsequent proteins were assessed through Western blotting.ResultsVirulent genes were significantly downregulated in single species biofilms when they were treated with Bk+G combination. However, Bk+G did not have significant effect on ALS1 and HWP1 gene in polymicrobial biofilms. ALS3 and SAP5 were significantly downregulated in Bk+G treated polymicrobial biofilm. Similar results were portrayed in Western blotting.ConclusionBk+G combination exhibited antimicrobial effects against single and mixed species biofilms. The findings might provide insights for treating resistant candida infections. This combination could potentially serve as an herbal alternative to traditional antifungals following further research. creator: Ayesha Fahim creator: Wan Harun Himratul-Aznita creator: Puteri Shafinaz Abdul-Rahman creator: Mohammad K. Alam uri: https://doi.org/10.7717/peerj.12251 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Fahim et al.