title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=595 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Impacts of river fragmentation on limiting individual dietary specialization of Amazonian predatory fish link: https://peerj.com/articles/14266 last-modified: 2022-12-15 description: Individual dietary specialization is one of the factors that promotes variation in resource use at the individual level. Here we used stable isotope analysis of multiple tissues with different turnover rates to examine the degree of individual specialization in two sub-populations of the predator Cichla temensis inhabiting both fragmented and undammed rivers within the Uatumã River basin of the Amazon. Our results showed that the undammed river provides better conditions to promote individual dietary specialization than the fragmented river. This study contributes to the understanding of how specific life history characteristics of populations of generalist predators are impacted by fragmentation within megadiverse environments such as the Amazon basin. creator: Jamerson Aguiar-Santos creator: Pieter deHart creator: Bruce Forsberg creator: Carlos Freitas uri: https://doi.org/10.7717/peerj.14266 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Aguiar-Santos et al. title: Neospongodes atlantica, a potential case of an early biological introduction in the Southwestern Atlantic link: https://peerj.com/articles/14347 last-modified: 2022-12-15 description: Soft corals (Anthozoa: Octocorallia) are discreet components in the Southwestern Atlantic reef communities. In Brazil, the native octocoral shallow-reef fauna is mostly represented by gorgonians. Consequently, except for the nephtheid Neospongodes atlantica, most of the known soft corals from this region are considered non-indigenous. Hitherto, the monotypic genus Neospongodes, which was proposed in the early 1900s, has been considered to be endemic to the Northeastern Brazilian coast. Herein, based on in situ records, we show that N. atlantica is a substrate generalist that has been probably expanding its distribution by dominating extensive shallow and mesophotic sandy and reef bottoms, generally outcompeting other reef benthic organisms, including Brazilian endemic species. Based on previously unidentified museum specimens, new records, and a broad literature review, we provide the most comprehensive modelling of the potential distribution of this species in the Southwestern Atlantic. Based on molecular inference supported by in-depth morphological analysis, the probable non-indigenous and, therefore, ancient introduction of N. atlantica in Brazilian waters is discussed. Finally, these results support that Neospongodes and the Indo-Pacific Stereonephthya are synonyms, which led us to propose the latter as taxonomically invalid. creator: Ralf T.S. Cordeiro creator: Ágatha Nascimento Carpinelli creator: Ronaldo B. Francini-Filho creator: Barbara de Moura Neves creator: Carlos D. Pérez creator: Umberto de Oliveira creator: Paulo Sumida creator: Henrique Maranhão creator: Leonardo H.U. Monteiro creator: Pedro Carneiro creator: Marcelo V. Kitahara uri: https://doi.org/10.7717/peerj.14347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cordeiro et al. title: Using a real-world network to model the trade-off between stay-at-home restriction, vaccination, social distancing and working hours on COVID-19 dynamics link: https://peerj.com/articles/14353 last-modified: 2022-12-15 description: BackgroundHuman behaviour, economic activity, vaccination, and social distancing are inseparably entangled in epidemic management. This study aims to investigate the effects of various parameters such as stay-at-home restrictions, work hours, vaccination, and social distance on the containment of pandemics such as COVID-19.MethodsTo achieve this, we have developed an agent based model based on a time-dynamic graph with stochastic transmission events. The graph is constructed from a real-world social network. The edges of graph have been categorized into three categories: home, workplaces, and social environment. The conditions needed to mitigate the spread of wild-type COVID-19 and the delta variant have been analyzed. Our purposeful agent based model has carefully executed tens of thousands of individual-based simulations. We propose simple relationships for the trade-offs between effective reproduction number (Re), transmission rate, working hours, vaccination, and stay-at-home restrictions.ResultsWe have found that the effect of a 13.6% increase in vaccination for wild-type (WT) COVID-19 is equivalent to reducing four hours of work or a one-day stay-at-home restriction. For the delta, 20.2% vaccination has the same effect. Also, since we can keep track of household and non-household infections, we observed that the change in household transmission rate does not significantly alter the Re. Household infections are not limited by transmission rate due to the high frequency of connections. For the specifications of COVID-19, the Re depends on the non-household transmissions rate.ConclusionsOur findings highlight that decreasing working hours is the least effective among the non-pharmaceutical interventions. Our results suggest that policymakers decrease work-related activities as a last resort and should probably not do so when the effects are minimal, as shown. Furthermore, the enforcement of stay-at-home restrictions is moderately effective and can be used in conjunction with other measures if absolutely necessary. creator: Ramin Nashebi creator: Murat Sari creator: Seyfullah Kotil uri: https://doi.org/10.7717/peerj.14353 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nashebi et al. title: Prevalence of text neck posture, smartphone addiction, and its association with neck disorders among university students in the Kingdom of Saudi Arabia during the COVID-19 pandemic link: https://peerj.com/articles/14443 last-modified: 2022-12-15 description: The smartphone emerges as an inevitable gadget in modern society and its increased usage results in neck disorders among its users. However, the factors associated with neck disorders among smartphone users are ambiguous and less explored in the literature. The purpose of this research was to determine the prevalence of text neck posture, smartphone addiction/overuse, and its association with neck disorders among university students in the Kingdom of Saudi Arabia during the COVID-19 pandemic. A total of 313 university students who were aged 18 years and older, owned a smartphone, and used it during the preceding 12 months participated in this cross-sectional study. A self-administered questionnaire was used to collect data regarding the prevalence of text neck posture, smartphone addiction/overuse, neck disorders, and the level of physical activity. Binary logistic regression was used to determine the association between the prevalence of neck disorders and text neck posture, smartphone addiction/overuse, and level of physical activity. The 12 months prevalence of neck disorders due to smartphone use among the participants was found to be 46%. The neck disorders were more prevalent among participants who reported text neck posture (P < 0.001) and categorized as smartphone-addicted/overuse (P < 0.001). Measures to promote the awareness of healthy use of smartphones including postural education and to decrease its screen time are warranted to reduce neck disorders. creator: Mohamed Sherif Sirajudeen creator: Msaad Alzhrani creator: Ahmad Alanazi creator: Mazen Alqahtani creator: Mohamed Waly creator: Radhakrishnan Unnikrishnan creator: Hariraja Muthusamy creator: Wafa Alrubaia creator: Nidaa Alanazi creator: Mohamed K. Seyam creator: Faizan Kashoo creator: Mohammad Miraj creator: Shashikumar Channmgere Govindappa creator: Khalid Ahmed Alghamdi creator: Nasser M. Al-Hussinan uri: https://doi.org/10.7717/peerj.14443 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sirajudeen et al. title: Association between the CASC16 rs4784227 polymorphism and breast cancer risk and prognosis in a northeast Chinese Han population link: https://peerj.com/articles/14462 last-modified: 2022-12-15 description: BackgroundBreast cancer (BC) poses a serious threat to women worldwide. This research was designed to explore the association between the rs4784227 polymorphism of cancer susceptibility candidate gene 16 (CASC16) and BC susceptibility and prognosis, aiming to provide further information for the early detection of BC and to accelerate comprehensive cancer management.MethodsA total of 1,733 subjects were recruited for this case-control study, of which 828 are BC patients and 905 are healthy individuals. The relevance between SNP rs4784227 and BC risk in diverse genetic models was analyzed by using the SNPStats analysis program and was assessed by odds ratios (ORs) and 95% confidence intervals (CIs) using the binary logistic regression model. Pearson’s χ2 test was used to determine the correlation between the polymorphism and clinical characteristics of BC patients. Additionally, univariate survival analysis was performed by the Kaplan-Meier method and log-rank test, and multivariate survival analysis was performed by Cox regression.ResultsSNP rs4784227 was significantly associated with susceptibility to BC in the dominant model (CT/TT versus CC, OR = 1.237, 95% CI = 1.012–1.513, P = 0.038). The minor allele of SNP rs4784227 was significantly linked to an increased risk of BC (OR = 1.197, 95% CI = 1.022–1.401, P = 0.026). In addition, the rs4784227 polymorphism of CASC16 was associated with perineural invasion (P = 0.030), menstrual status (P = 0.016) and histological grade (P = 0.001, P = 0.003, P = 0.025; respectively) of BC patients. There was no significant association between the genotypes of rs4784227 and disease-free survival (DFS) or overall survival (OS) of breast cancer patients (P > 0.05).ConclusionsThe rs4784227 polymorphism of CASC16 may affect susceptibility to breast cancer and is associated with perineural invasion, menstrual status and histological grade in BC patients. Additionally, our results could not confirm that this polymorphism was related to breast cancer prognosis. creator: Yue Zhang creator: Changgui Kou creator: Lin Jia creator: Yangyang Gao creator: Xin Li creator: Hao Wu creator: Naifei Chen creator: Zheng Lv uri: https://doi.org/10.7717/peerj.14462 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network link: https://peerj.com/articles/14516 last-modified: 2022-12-15 description: Dynamic modelling has considerably improved our understanding of complex molecular mechanisms. Ordinary differential equations (ODEs) are the most detailed and popular approach to modelling the dynamics of molecular systems. However, their application in signalling networks, characterised by multi-state molecular complexes, can be prohibitive. Contemporary modelling methods, such as rule- based (RB) modelling, have addressed these issues. The advantages of RB modelling over ODEs have been presented and discussed in numerous reviews. In this study, we conduct a direct comparison of the time courses of a molecular system founded on the same reaction network but encoded in the two frameworks. To make such a comparison, a set of reactions that underlie an ODE model was manually encoded in the Kappa language, one of the RB implementations. A comparison of the models was performed at the level of model specification and dynamics, acquired through model simulations. In line with previous reports, we confirm that the Kappa model recapitulates the general dynamics of its ODE counterpart with minor differences. These occur when molecules have multiple sites binding the same interactor. Furthermore, activation of these molecules in the RB model is slower than in the ODE one. As reported for other molecular systems, we find that, also for the DARPP-32 reaction network, the RB representation offers a more expressive and flexible syntax that facilitates access to fine details of the model, easing model reuse. In parallel with these analyses, we report a refactored model of the DARPP-32 interaction network that can serve as a canvas for the development of more complex dynamic models to study this important molecular system. creator: Emilia M. Wysocka creator: Matthew Page creator: James Snowden creator: T. Ian Simpson uri: https://doi.org/10.7717/peerj.14516 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wysocka et al. title: Ethanolic extract of Ya-nang (Tiliacora triandra) leaf powder induces apoptosis in cholangiocarcinoma cell lines via induction of hyperacetylation and inhibition of growth signaling link: https://peerj.com/articles/14518 last-modified: 2022-12-15 description: ObjectiveTo develop alternative medicine for reducing undesired side effects of chemotherapy in CCA patients, the anticancer activity of Tiliacora triandra leaf powder ethanolic (TLPE) extract against cholangiocarcinoma cell lines was investigated.MethodsAntiproliferation was studied using the MTT assay while apoptosis induction and cell cycle arrest were analyzed by flow cytometry. The levels of key proteins and phenolic acid content were analyzed by western blotting and reversed-phase HPLC, respectively.ResultsTLPE extract inhibited CCA cell growth in a dose- and time-dependent manner, with IC50 values of 7.86 ± 0.05 µg/ml for KKU-M213B cells and 8.59 ± 0.36 µg/ml for KKU-100 cells at an exposure time of 72 h. TLPE extract inhibited the growth of CCA cell lines by inducing apoptosis of both cell lines and causing an increased population of KKU-100 cells at G0/G1 phase. TLPE extract up-regulated Ac-H3 but down-regulated p-ERK, p53, Bax, CDK4 and Bcl2 expressions in KKU-M213B cells. TLPE extract up-regulated Ac-H3, p21 and Bax but down-regulated p-ERK, p53, CDK4 and Bcl2 expressions in KKU-100 cells. Additionally, phenolic acids including p-hydroxybenzoic, vanillic, syringic, p-coumaric, ferulic and sinapinic acids were identified.ConclusionThese results suggest the possibility of developing T. triandra leaf powder ethanolic extract as a chemotherapeutic or chemoprevention agent for cholangiocarcinoma. creator: Arunta Samankul creator: Gulsiri Senawong creator: Prasan Swatsitang creator: Banchob Sripa creator: Chanokbhorn Phaosiri creator: Somdej Kanokmedhakul creator: Thanaset Senawong uri: https://doi.org/10.7717/peerj.14518 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Samankul et al. title: Embryonic exposure to fentanyl induces behavioral changes and neurotoxicity in zebrafish larvae link: https://peerj.com/articles/14524 last-modified: 2022-12-15 description: The use of fentanyl during pregnancy, whether by prescription or illicit use, may result in high blood levels that pose an early risk to fetal development. However, little is known regarding the neurotoxicity that might arise from excessive fentanyl exposure in growing organisms, particularly drug-related withdrawal symptoms. In this study, zebrafish embryos were exposed to fentanyl solutions (0.1, 1, and 5 mg/L) for 5 days post fertilization (dpf), followed by a 5-day recovery period, and then the larvae were evaluated for photomotor response, anxiety behavior, shoaling behavior, aggression, social preference, and sensitization behavior. Fentanyl solutions at 1 and 5 mg/L induced elevated anxiety, decreased social preference and aggressiveness, and behavioral sensitization in zebrafish larvae. The expression of genes revealed that embryonic exposure to fentanyl caused substantial alterations in neural activity (bdnf, c-fos) and neuronal development and plasticity (npas4a, egr1, btg2, ier2a, vgf). These results suggest that fentanyl exposure during embryonic development is neurotoxic, highlighting the importance of zebrafish as an aquatic species in research on the neurobehavioral effects of opioids in vertebrates. creator: Binjie Wang creator: Jiale Chen creator: Zhong Sheng creator: Wanting Lian creator: Yuanzhao Wu creator: Meng Liu uri: https://doi.org/10.7717/peerj.14524 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Non-random host tree infestation by the Neotropical liana Marcgravia longifolia link: https://peerj.com/articles/14535 last-modified: 2022-12-15 description: The question whether or not tropical lianas infest host trees randomly or they exert host selection has implications for the structure and dynamics of tropical rainforests, particularly if colonization by lianas impacts host fitness. In this study, we present evidence that the Neotropical liana Marcgravia longifolia (Marcgraviaceae) infests host trees non-randomly. We identified host trees to species or genus level for 87 of the 100 M. longifolia individuals found in the study area of the Estación Biológica Quebrada Blanco (EBQB) in north-eastern Peruvian Amazonia. Data on host availability were taken from two 1-ha plots sampled at EBQB as part of a large-scale tree inventory in western Amazonia. Of the total of 88 tree genera with two or more individuals present in the inventory, 18 were represented amongst hosts. Host genera with a probability of colonization higher than expected by chance were Eschweilera (Lecythidaceae), Pouteria (Sapotaceae), Brosimum (Moraceae), and Hymenaea (Fabaceae). These findings suggest that M. longifolia exerts some level of host selectivity, but the mechanisms for this are completely unknown. Given the large number of animal species (41 bird species, three primate species) that are dispersing the seeds of M. longifolia and that have diverse ecological strategies, directed seed dispersal is unlikely to account for the observed patterns of host infestation. creator: Eckhard W. Heymann creator: Sarina Thiel creator: Filipa Paciência creator: Milagros N. Rimachi Taricuarima creator: Ricardo Zárate Gómez creator: Ney Shahuano Tello creator: Katrin Heer creator: Holger Sennhenn-Reulen creator: Roger Mundry uri: https://doi.org/10.7717/peerj.14535 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Heymann et al. title: The long-term dynamics of serum antibodies against SARS-CoV-2 link: https://peerj.com/articles/14547 last-modified: 2022-12-15 description: ObjectiveTo analyze the long-term dynamics of antibodies against SARS-CoV-2 and understand the impact of age, gender, and viral load on patients’ immunological response.MethodsSerum samples were obtained from 231 COVID-19 positive patients from Macaé, in Rio de Janeiro state, in Brazil, from June 2020 until January 2021. The production of IgA, IgM, IgG, and IgE against S glycoprotein was analyzed using the S-UFRJ assay, taking into account the age, gender, and viral load.ResultsAnalysis of antibody production over 7 months revealed that IgA positivity gradually decreased after the first month. Additionally, the highest percentage of IgM positivity occurred in the first month (97% of patients), and declined after this period, while IgG positivity remained homogeneous for all 7 months. The same analysis for IgE revealed that almost all samples were negative. The comparison of antibody production between genders showed no significant difference. Regarding the age factor and antibody production, patients aged ≥60 years produced almost twice more IgA than younger ones (17–39 years old). Finally, a relationship between viral load and antibody production was observed only for older patients.ConclusionsOur work provides an overview of long-term production of antibodies against SARS-CoV-2, suggesting prolonged production of IgA and IgM antibodies for 3 months and continued IgG production for over 7 months. In addition, it identified a correlation between viral load and IgM titers in the older group and, finally, different IgA production between the age groups. creator: Graziele Fonseca de Sousa creator: Thuany da Silva Nogueira creator: Lana Soares de Sales creator: Fernanda Ferreira Maissner creator: Odara Araújo de Oliveira creator: Hellade Lopes Rangel creator: Daniele das Graças dos Santos creator: Rodrigo Nunes-da-Fonseca creator: Jackson de Souza-Menezes creator: Jose Luciano Nepomuceno-Silva creator: Flávia Borges Mury creator: Raquel de Souza Gestinari creator: Amilcar Tanuri creator: Orlando da Costa Ferreira Jr creator: Cintia Monteiro-de-Barros uri: https://doi.org/10.7717/peerj.14547 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 de Sousa et al.