title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1093 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: RdRp mutations are associated with SARS-CoV-2 genome evolution link: https://peerj.com/articles/9587 last-modified: 2020-07-21 description: COVID-19, caused by the novel SARS-CoV-2 virus, started in China in late 2019, and soon became a global pandemic. With the help of thousands of viral genome sequences that have been accumulating, it has become possible to track the evolution of the viral genome over time as it spread across the world. An important question that still needs to be answered is whether any of the common mutations affect the viral properties, and therefore the disease characteristics. Therefore, we sought to understand the effects of mutations in RNA-dependent RNA polymerase (RdRp), particularly the common 14408C>T mutation, on mutation rate and viral spread. By focusing on mutations in the slowly evolving M or E genes, we aimed to minimize the effects of selective pressure. Our results indicate that 14408C>T mutation increases the mutation rate, while the third-most common RdRp mutation, 15324C>T, has the opposite effect. It is possible that 14408C>T mutation may have contributed to the dominance of its co-mutations in Europe and elsewhere. creator: Doğa Eskier creator: Gökhan Karakülah creator: Aslı Suner creator: Yavuz Oktay uri: https://doi.org/10.7717/peerj.9587 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Eskier et al. title: Pedagogic prestidigitation: using magic tricks to enhance educational videos link: https://peerj.com/articles/9610 last-modified: 2020-07-21 description: Previous research suggests that magic tricks can be employed within an educational context to enhance attention, engagement, critical thinking and recall. This study builds on this work by examining the impact of incorporating magic tricks into an online educational video. Adult participants (N = 198) completed a need for cognition scale and then watched a video containing either several bespoke card tricks that had been specially devised to help tell the story of the Apollo Moon landings (Magic Video), or an almost identical video that did not contain any magic tricks (Control Video). All participants rated their levels of engagement, absorption and recall. Compared to the Control Video, the Magic Video was rated as significantly more interesting, informative and absorbing. There was no difference between the groups for recall. There was a positive correlation between participants’ need for cognition scores, and the degree to which they found the Magic Video interesting, and were willing to share it with others. The theoretical, methodological and practical implications of these results are discussed, along with recommendations for future work. creator: Richard Wiseman creator: William Houstoun creator: Caroline Watt uri: https://doi.org/10.7717/peerj.9610 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wiseman et al. title: The timing mega-study: comparing a range of experiment generators, both lab-based and online link: https://peerj.com/articles/9414 last-modified: 2020-07-20 description: Many researchers in the behavioral sciences depend on research software that presents stimuli, and records response times, with sub-millisecond precision. There are a large number of software packages with which to conduct these behavioral experiments and measure response times and performance of participants. Very little information is available, however, on what timing performance they achieve in practice. Here we report a wide-ranging study looking at the precision and accuracy of visual and auditory stimulus timing and response times, measured with a Black Box Toolkit. We compared a range of popular packages: PsychoPy, E-Prime®, NBS Presentation®, Psychophysics Toolbox, OpenSesame, Expyriment, Gorilla, jsPsych, Lab.js and Testable. Where possible, the packages were tested on Windows, macOS, and Ubuntu, and in a range of browsers for the online studies, to try to identify common patterns in performance. Among the lab-based experiments, Psychtoolbox, PsychoPy, Presentation and E-Prime provided the best timing, all with mean precision under 1 millisecond across the visual, audio and response measures. OpenSesame had slightly less precision across the board, but most notably in audio stimuli and Expyriment had rather poor precision. Across operating systems, the pattern was that precision was generally very slightly better under Ubuntu than Windows, and that macOS was the worst, at least for visual stimuli, for all packages. Online studies did not deliver the same level of precision as lab-based systems, with slightly more variability in all measurements. That said, PsychoPy and Gorilla, broadly the best performers, were achieving very close to millisecond precision on several browser/operating system combinations. For response times (measured using a high-performance button box), most of the packages achieved precision at least under 10 ms in all browsers, with PsychoPy achieving a precision under 3.5 ms in all. There was considerable variability between OS/browser combinations, especially in audio-visual synchrony which is the least precise aspect of the browser-based experiments. Nonetheless, the data indicate that online methods can be suitable for a wide range of studies, with due thought about the sources of variability that result. The results, from over 110,000 trials, highlight the wide range of timing qualities that can occur even in these dedicated software packages for the task. We stress the importance of scientists making their own timing validation measurements for their own stimuli and computer configuration. creator: David Bridges creator: Alain Pitiot creator: Michael R. MacAskill creator: Jonathan W. Peirce uri: https://doi.org/10.7717/peerj.9414 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bridges et al. title: Raccoon roundworm prevalence (Baylisascaris procyonis) at the North Carolina Zoo, USA link: https://peerj.com/articles/9426 last-modified: 2020-07-20 description: Baylisascaris procyonis is an important zoonotic nematode of raccoons (Procyon lotor). Infection with this parasite has important health implications for humans, zoo animals, and free-ranging wildlife. As a large, natural habitat zoo, the North Carolina Zoo (NC Zoo) coexists with native wildlife. Raccoons are abundant at the NC Zoo and the prevalence of B. procyonis is unknown. Raccoon latrines were located through employee reporting and systematic searching throughout the zoo and sampled for B. procyonis in October and November of 2018 and 2019. Parasite prevalence, latrine location, substrate category and latrine persistence were recorded. Thirty-three latrines were located in 2018 and eight new latrines in 2019 while four latrines from the prior year were no longer available to be sampled. Of the 29 latrines sampled over the two years, 16 (55%) persisted for at least one year. The majority of the latrines were found on natural substrate with rock showing the highest preference. Just over half (n = 21 of 41 total) of the active latrines in the study were in or immediately adjacent to animal enclosures. Two latrines were found in public areas including one contaminating children’s play equipment. Additionally, fresh fecal samples were collected from five adult raccoons presented to the zoo’s veterinary clinic in 2018 and 2019. All fecal samples tested by centrifugal flotation for both years were negative for B. procyonis. The results of this study show the value of field sampling to properly assess risk and enable informed decision-making regarding public health and wildlife management. creator: Meghan M. Louis creator: Larry J. Minter creator: James R. Flowers creator: Michael K. Stoskopf creator: Suzanne Kennedy-Stoskopf uri: https://doi.org/10.7717/peerj.9426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Louis et al. title: Detecting the outbreak of influenza based on the shortest path of dynamic city network link: https://peerj.com/articles/9432 last-modified: 2020-07-20 description: The influenza pandemic causes a large number of hospitalizations and even deaths. There is an urgent need for an efficient and effective method for detecting the outbreak of influenza so that timely, appropriate interventions can be made to prevent or at least prepare for catastrophic epidemics. In this study, we proposed a computational method, the shortest-path-based dynamical network marker (SP-DNM), to detect the pre-outbreak state of influenza epidemics by monitoring the dynamical change of the shortest path in a city network. Specifically, by mapping the real-time information to a properly constructed city network, our method detects the early-warning signal prior to the influenza outbreak in both Tokyo and Hokkaido for consecutive 9 years, which demonstrate the effectiveness and robustness of the proposed method. creator: Yingqi Chen creator: Kun Yang creator: Jialiu Xie creator: Rong Xie creator: Zhengrong Liu creator: Rui Liu creator: Pei Chen uri: https://doi.org/10.7717/peerj.9432 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Quantifying local ecological knowledge to model historical abundance of long-lived, heavily-exploited fauna link: https://peerj.com/articles/9494 last-modified: 2020-07-20 description: Deriving robust historical population trends for long-lived species subject to human exploitation is challenging in scenarios where long-term scientific data are scarce or unavailable, as often occurs for species affected by small-scale fisheries and subsistence hunting. The importance of Local Ecological Knowledge (LEK) in data-poor scenarios is increasingly recognized in conservation, both in terms of uncovering historical trends and for engaging community stewardship of historic information. Building on previous work in marine historical ecology and local ecological knowledge, we propose a mixed socio-ecological framework to reliably document and quantify LEK to reconstruct historical population trends. Our method can be adapted by interdisciplinary teams to study various long-lived taxa with a history of human use. We demonstrate the validity of our approach by reconstructing long-term abundance data for the heavily-exploited East Pacific green turtle (Chelonia mydas) in Baja California, Mexico, which was driven to near extinction by a largely unregulated fishery from the early 1950s to the 1980s. No scientific baseline abundance data were available for this time-frame because recent biological surveys started in 1995 after all green turtle fisheries in the area were closed. To fill this data gap, we documented LEK among local fishers using ethnographic methods and obtained verified, qualitative data to understand the socio-environmental complexity of the green turtle fishery. We then established an iterative framework to synthesize and quantify LEK using generalized linear models (GLMs) and nonlinear regression (NLR) to generate a standardized, LEK-derived catch-per-unit-effort (CPUE) time-series. CPUE is an index of abundance that is compatible with contemporary scientific survey data. We confirmed the accuracy of LEK-derived CPUE estimates via comparisons with fisheries statistics available for 1962–1982. We then modeled LEK-derived abundance trends prior to 1995 using NLR. Our model established baseline abundance and described historical declines, revealing that the most critical (exponential) decline occurred between 1960 and 1980. This robust integration of LEK data with ecological science is of critical value for conservation and management, as it contributes to a holistic view of a species’ historic and contemporary conservation status. creator: Michelle-María Early-Capistrán creator: Elena Solana-Arellano creator: F. Alberto Abreu-Grobois creator: Nemer E. Narchi creator: Gerardo Garibay-Melo creator: Jeffrey A. Seminoff creator: Volker Koch creator: Andrea Saenz-Arroyo uri: https://doi.org/10.7717/peerj.9494 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Early-Capistrán et al. title: Engineering of HN3 increases the tumor targeting specificity of exosomes and upgrade the anti-tumor effect of sorafenib on HuH-7 cells link: https://peerj.com/articles/9524 last-modified: 2020-07-20 description: Safe, efficient and cancer cell targeted delivery of CRISPR/Cas9 is important to increase the effectiveness of available cancer treatments. Although cancer derived exosomes offer significant advantages, the fact that it carries cancer related/inducing signaling molecules impedes them from being used as a reliable drug delivery vehicle. In this study, we report that normal epithelial cell-derived exosomes engineered to have HN3 (HN3LC9-293exo), target tumor cells as efficiently as that of the cancer cell-derived exosomes (C9HuH-7exo). HN3LC9-293exo were quickly absorbed by the recipient cancer cell in vitro. Anchoring HN3 to the membrane of the exosomes using LAMP2, made HN3LC9-293exo to specifically enter the GPC3+ HuH-7 cancer cells than the GPC3− LO2 cells in a co-culture model. Further, sgIQ 1.1 plasmids were loaded to exosomes and surprisingly, in combination with sorafenib, synergistic anti-proliferative and apoptotic effect of loaded HN3LC9-293exo was more than the loaded C9HuH-7exo. While cancer-derived exosomes might induce the drug resistance and tumor progression, normal HEK-293 cells-derived exosomes with modifications for precise cancer cell targeting like HN3LC9-293exo can act as better, safe and natural delivery systems to improve the efficacy of the cancer treatments. creator: Cong He creator: Doulathunnisa Jaffar Ali creator: Yumin Li creator: Yanliang Zhu creator: Bo Sun creator: Zhongdang Xiao uri: https://doi.org/10.7717/peerj.9524 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 He et al. title: The importance of open science for biological assessment of aquatic environments link: https://peerj.com/articles/9539 last-modified: 2020-07-20 description: Open science principles that seek to improve science can effectively bridge the gap between researchers and environmental managers. However, widespread adoption has yet to gain traction for the development and application of bioassessment products. At the core of this philosophy is the concept that research should be reproducible and transparent, in addition to having long-term value through effective data preservation and sharing. In this article, we review core open science concepts that have recently been adopted in the ecological sciences and emphasize how adoption can benefit the field of bioassessment for both prescriptive condition assessments and proactive applications that inform environmental management. An example from the state of California demonstrates effective adoption of open science principles through data stewardship, reproducible research, and engagement of stakeholders with multimedia applications. We also discuss technical, sociocultural, and institutional challenges for adopting open science, including practical approaches for overcoming these hurdles in bioassessment applications. creator: Marcus W. Beck creator: Casey O’Hara creator: Julia S. Stewart Lowndes creator: Raphael D. Mazor creator: Susanna Theroux creator: David J. Gillett creator: Belize Lane creator: Gregory Gearheart uri: https://doi.org/10.7717/peerj.9539 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Beck et al. title: Application of material from used car tyres in geotechnics—an environmental impact analysis link: https://peerj.com/articles/9546 last-modified: 2020-07-20 description: This work begins with a literature-based discussion of the hazardous-waste problem represented by car tyres as hazardous waste, along with possible ways in which they might be utilised or managed. The impact of the material on the environment is characterised in the process, not least in the context of pollutants leached to the aquatic environment. Input in terms of new research results concerns the impact on water and soil of material from used car tyres being used in geotechnics. Specifically, tyre bales comprising 100–140 car vehicle tyres compressed into a lightweight block and secured by galvanised steel tie wires running around the length and depth of the bale, were researched, having been immersed in basins with alkaline and acidic water following initial preparation and pre-washing. The aim was to in some sense simulate—respectively—conditions in which rain and surface/ground water are involved, or else acid rain. To do that, the tyre bales were placed in the water for 120 days, with emerging leachate analysed after set intervals of time, with a view to changes in key physicochemical parameters of water being noted, as well as signs of the leaching of both undesirable components and priority substances, from tyres into the aqueous medium. Washing of the tyre bales was shown to induce slight pollution of water, with limited exceedance of normative values in respect of OWO content. However, this increase was not due to leaching of the Persistent Organic Pollutants tested for, but may rather have reflected contamination of tyres used, e.g., of soil at the place of previous storage. In general, waste water arising does not therefore contain substances that would stand in the way (legally) of its being discharged into a combined sewer system. Similar conclusions were arrived at through analysis of the leaching of pollutants from tyre bales exposed in the aforementioned pools of water of neutral and acidic reaction. Wastewater arising was not enriched significantly in impurities (be these metals, PAHs, phthalates, selected anions or cations), and there were therefore no exceedances of standards imposed for wastewater discharged to either waters or soil. creator: Aleksander Duda creator: Małgorzata Kida creator: Sabina Ziembowicz creator: Piotr Koszelnik uri: https://doi.org/10.7717/peerj.9546 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Duda et al. title: Pots vs trammel nets: a catch comparison study in a Mediterranean small-scale fishery link: https://peerj.com/articles/9287 last-modified: 2020-07-17 description: Passive bottom-set nets are the most widely used fishing gears in Mediterranean small-scale fisheries (SSFs). Trammel nets, in particular, have key advantages such as their ease of use and handling and high capture efficiency for numerous commercial species. However, they entail high discard rates (5–44% of the total catch) connected to high mortality, thus exerting an adverse impact on benthic communities, besides catching individuals of commercial species under the minimum conservation reference size (MCRS) and specimens of protected species. Fish pots are seen as alternative and a more sustainable gear type that allow reducing discards in SSFs. In this study, a collapsible pot was tested at three coastal sites in the north-western Adriatic Sea (GFCM GSA 17) to compare its catch efficiency with that of the local traditional trammel nets. Data analysis demonstrated a similar catch efficiency for the commercial species, both among sites and as a whole. Moreover, the trammel net caught a larger amount of discards, both in terms of species number and of CPUEW. The catch comparison study involved the two most abundant landed species, common cuttlefish Sepia officinalis and annular sea bream Diplodus annularis. The pots were more effective for S. officinalis, whereas the trammel net was more effective for the shorter length classes for D. annularis, which were mostly under the MCRS (12 cm). The innovative pots could provide a valuable alternative to the trammel nets traditionally used in the Adriatic Sea, at least in certain areas and periods. Their main advantages include that they do not require a different rigging and they can be used without bait, while their foldable design allows large numbers to be easily loaded on board SSF vessels. The results of this pilot study indicate that pots can achieve the objectives of reducing discards and bycatch in SSFs without penalizing the catch of commercial species. creator: Andrea Petetta creator: Claudio Vasapollo creator: Massimo Virgili creator: Giada Bargione creator: Alessandro Lucchetti uri: https://doi.org/10.7717/peerj.9287 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Petetta et al.