title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=992 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species link: https://peerj.com/articles/10237 last-modified: 2020-12-18 description: Research on the gut microbiome of host organisms has rapidly advanced with next generation sequencing (NGS) and high-performance computing capabilities. Nonetheless, gut microbiome research has focused on mammalian organisms in laboratory settings, and investigations pertaining to wild fish gut microbiota remain in their infancy. We applied a procedure (available at https://github.com/bngallo1994) for sampling of the fish gut for use in NGS to describe microbial community structure. Our approach allowed for high bacterial OTU diversity coverage (>99.7%, Good’s Coverage) that led to detection of differences in gut microbiota of an invasive (Round Goby) and native (Yellow Bullhead) fish species and collected from the upper St. Lawrence River, an environment where the gut microbiota of fish had not previously been tested. Additionally, results revealed habitat level differences in gut microbiota using two distance metrics (Unifrac, Bray–Curtis) between nearshore littoral and offshore profundal collections of Round Goby. Species and habitat level differences in intestinal microbiota may be of importance in understanding individual and species variation and its importance in regulating fish health and physiology. creator: Benjamin D. Gallo creator: John M. Farrell creator: Brian Leydet uri: https://doi.org/10.7717/peerj.10237 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gallo et al. title: Ischemic infarct detection, localization, and segmentation in noncontrast CT human brain scans: review of automated methods link: https://peerj.com/articles/10444 last-modified: 2020-12-18 description: Noncontrast Computed Tomography (NCCT) of the brain has been the first-line diagnosis for emergency evaluation of acute stroke, so a rapid and automated detection, localization, and/or segmentation of ischemic lesions is of great importance. We provide the state-of-the-art review of methods for automated detection, localization, and/or segmentation of ischemic lesions on NCCT in human brain scans along with their comparison, evaluation, and classification. Twenty-two methods are (1) reviewed and evaluated; (2) grouped into image processing and analysis-based methods (11 methods), brain atlas-based methods (two methods), intensity template-based methods (1 method), Stroke Imaging Marker-based methods (two methods), and Artificial Intelligence-based methods (six methods); and (3) properties of these groups of methods are characterized. A new method classification scheme is proposed as a 2 × 2 matrix with local versus global processing and analysis, and density versus spatial sampling. Future studies are necessary to develop more efficient methods directed toward deep learning methods as well as combining the global methods with a high sampling both in space and density for the merged radiologic and neurologic data. creator: Wieslaw L. Nowinski creator: Jerzy Walecki creator: Gabriela Półtorak-Szymczak creator: Katarzyna Sklinda creator: Bartosz Mruk uri: https://doi.org/10.7717/peerj.10444 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nowinski et al. title: Antimicrobial activity of Streptomyces spp. isolated from Apis dorsata combs against some phytopathogenic bacteria link: https://peerj.com/articles/10512 last-modified: 2020-12-18 description: The aim of this study was to investigate the antimicrobial potential of actinomycetes isolated from combs of the giant honey bee, Apis dorsata. In total, 25 isolates were obtained from three different media and were screened for antimicrobial activity against four plant pathogenic bacteria (Ralstonia solanacearum, Xanthomonas campestris pv. campestris, Xanthomonas oryzae pv. oryzae and Pectobacterium carotovorum). Following screening using a cross-streaking method, three isolates showed the potential to inhibit the growth of plant pathogenic bacteria. Based on a 96-well microtiter assay, the crude extract of DSC3-6 had minimum inhibitory concentration (MIC) values against X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum of 16, 32, 32 and 64 mg L−1, respectively. The crude extract of DGA3-20 had MIC values against X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum of 32, 32, 32 and 64 mg L−1, respectively. The crude extract of DGA8-3 at 32 mgL−1 inhibited the growth of X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum. Based on their 16S rRNA gene sequences, all isolates were identified as members of the genus Streptomyces. The analysis of 16S rRNA gene sequence similarity and of the phylogenetic tree based on the maximum likelihood algorithm showed that isolates DSC3-6, DGA3-20 and DGA8-3 were closely related to Streptomyces ramulosus (99.42%), Streptomyces axinellae (99.70%) and Streptomyces drozdowiczii (99.71%), respectively. This was the first report on antibacterial activity against phytopathogenic bacteria from actinomycetes isolated from the giant honey bee. creator: Yaowanoot Promnuan creator: Saran Promsai creator: Sujinan Meelai uri: https://doi.org/10.7717/peerj.10512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Promnuan et al. title: Peripheral-physiological and neural correlates of the flow experience while playing video games: a comprehensive review link: https://peerj.com/articles/10520 last-modified: 2020-12-18 description: The flow state is defined by intense involvement in an activity with high degrees of concentration and focused attention accompanied by a sense of pleasure. Video games are effective tools for inducing flow, and keeping players in this state is considered to be one of the central goals of game design. Many studies have focused on the underlying physiological and neural mechanisms of flow. Results are inconsistent when describing a unified mechanism underlying this mental state. This paper provides a comprehensive review of the physiological and neural correlates of flow and explains the relationship between the reported physiological and neural markers of the flow experience. Despite the heterogeneous results, it seems possible to establish associations between reported markers and the cognitive and experiential aspects of flow, particularly regarding arousal, attention control, reward processing, automaticity, and self-referential processing. creator: Shiva Khoshnoud creator: Federico Alvarez Igarzábal creator: Marc Wittmann uri: https://doi.org/10.7717/peerj.10520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Khoshnoud et al. title: Archosauriform footprints in the Lower Triassic of Western Alps and their role in understanding the effects of the Permian-Triassic hyperthermal link: https://peerj.com/articles/10522 last-modified: 2020-12-18 description: The most accepted killing model for the Permian-Triassic mass extinction (PTME) postulates that massive volcanic eruption (i.e., the Siberian Traps Large Igneous Province) led to geologically rapid global warming, acid rain and ocean anoxia. On land, habitable zones were drastically reduced, due to the combined effects of heating, drought and acid rains. This hyperthermal had severe effects also on the paleobiogeography of several groups of organisms. Among those, the tetrapods, whose geographical distribution across the end-Permian mass extinction (EPME) was the subject of controversy in a number of recent papers. We here describe and interpret a new Early Triassic (?Olenekian) archosauriform track assemblage from the Gardetta Plateau (Briançonnais, Western Alps, Italy) which, at the Permian-Triassic boundary, was placed at about 11° North. The tracks, both arranged in trackways and documented by single, well-preserved imprints, are assigned to Isochirotherium gardettensis ichnosp. nov., and are here interpreted as produced by a non-archosaurian archosauriform (erytrosuchid?) trackmaker. This new discovery provides further evidence for the presence of archosauriformes at low latitudes during the Early Triassic epoch, supporting a model in which the PTME did not completely vacate low-latitude lands from tetrapods that therefore would have been able to cope with the extreme hot temperatures of Pangaea mainland. creator: Fabio Massimo Petti creator: Heinz Furrer creator: Enrico Collo creator: Edoardo Martinetto creator: Massimo Bernardi creator: Massimo Delfino creator: Marco Romano creator: Michele Piazza uri: https://doi.org/10.7717/peerj.10522 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Petti et al. title: The p53 signaling pathway of the large yellow croaker (Larimichthys crocea) responds to acute cold stress: evidence via spatiotemporal expression analysis of p53, p21, MDM2, IGF-1, Gadd45, Fas, and Akt link: https://peerj.com/articles/10532 last-modified: 2020-12-18 description: The p53 activation is induced by stressors, such as DNA damage, oxidative stress, and activated oncogenes, and can promote cell cycle arrest, cellular senescence, and apoptosis. The large yellow croaker (Larimichthys crocea) is an important warm temperate marine fish in the Chinese aquiculture industry. However, few studies have investigated the role of p53 in the response of L. crocea to environmental stressors. Therefore, the aim of the present study was to assess the spatiotemporal mRNA expression levels of genes involved in the p53 signaling pathway of the large yellow croaker in response to cold stress. The results showed significant changes in the expression levels of p53, p21, MDM2, IGF-1, Gadd45, Fas, and Akt in various tissues of the large yellow croaker in response to cold stress for different times. As compared to the control group, p53 mRNA expression was upregulated in most of the examined tissues at 24 h with the exception of the gill. In the liver, the expression levels of p53 and Fas were significantly decreased at 12 h, while those of p21, MDM2, IGF-1, Gadd45 were dramatically increased. Akt expression was notably changed in response to cold in several tissues. These results suggested that p53 was potentially a key gene in the large yellow croaker response to cold and possibly other environmental stressors. creator: Baoying Qian creator: Xin Qi creator: Yi Bai creator: Yubo Wu uri: https://doi.org/10.7717/peerj.10532 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Qian et al. title: Individual differences show that only some bats can cope with noise-induced masking and distraction link: https://peerj.com/articles/10551 last-modified: 2020-12-18 description: Anthropogenic noise is a widespread pollutant that has received considerable recent attention. While alarming effects on wildlife have been documented, we have limited understanding of the perceptual mechanisms of noise disturbance, which are required to understand potential mitigation measures. Likewise, individual differences in response to noise (especially via perceptual mechanisms) are likely widespread, but lacking in empirical data. Here we use the echolocating bat Phyllostomus discolor, a trained discrimination task, and experimental noise playback to explicitly test perceptual mechanisms of noise disturbance. We demonstrate high individual variability in response to noise treatments and evidence for multiple perceptual mechanisms. Additionally, we highlight that only some individuals were able to cope with noise, while others were not. We tested for changes in echolocation call duration, amplitude, and peak frequency as possible ways of coping with noise. Although all bats strongly increased call amplitude and showed additional minor changes in call duration and frequency, these changes could not explain the differences in coping and non-coping individuals. Our understanding of noise disturbance needs to become more mechanistic and individualistic as research knowledge is transformed into policy changes and conservation action. creator: Dylan G.E. Gomes creator: Holger R. Goerlitz uri: https://doi.org/10.7717/peerj.10551 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gomes and Goerlitz title: Macrel: antimicrobial peptide screening in genomes and metagenomes link: https://peerj.com/articles/10555 last-modified: 2020-12-18 description: MotivationAntimicrobial peptides (AMPs) have the potential to tackle multidrug-resistant pathogens in both clinical and non-clinical contexts. The recent growth in the availability of genomes and metagenomes provides an opportunity for in silico prediction of novel AMP molecules. However, due to the small size of these peptides, standard gene prospection methods cannot be applied in this domain and alternative approaches are necessary. In particular, standard gene prediction methods have low precision for short peptides, and functional classification by homology results in low recall.ResultsHere, we present Macrel (for metagenomic AMP classification and retrieval), which is an end-to-end pipeline for the prospection of high-quality AMP candidates from (meta)genomes. For this, we introduce a novel set of 22 peptide features. These were used to build classifiers which perform similarly to the state-of-the-art in the prediction of both antimicrobial and hemolytic activity of peptides, but with enhanced precision (using standard benchmarks as well as a stricter testing regime). We demonstrate that Macrel recovers high-quality AMP candidates using realistic simulations and real data.AvailabilityMacrel is implemented in Python 3. It is available as open source at https://github.com/BigDataBiology/macrel and through bioconda. Classification of peptides or prediction of AMPs in contigs can also be performed on the webserver: https://big-data-biology.org/software/macrel. creator: Célio Dias Santos-Júnior creator: Shaojun Pan creator: Xing-Ming Zhao creator: Luis Pedro Coelho uri: https://doi.org/10.7717/peerj.10555 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Santos-Júnior et al. title: Quality of urban parks in the perception of city residents with mobility difficulties link: https://peerj.com/articles/10570 last-modified: 2020-12-18 description: Urban parks should be inclusive for all. Availability and accessibility of urban parks determine the quality of life in cities. The importance of access increases for residents with limited mobility who, facing obstacles due to inadequate adjustment of the surrounding physical space, are exposed to social exclusion. Five groups of respondents completed a survey questionnaire revealing their attitudes towards green areas and indicating barriers to parks’ accessibility. The groups were designed to include blind and vision impaired people, those who use a wheelchair, have a physical disability of any kind, their carers/assistants and parents pushing strollers. The results revealed more similarities than differences among the five groups (the differences included preferences towards the neighbourhood and destination parks, physical barriers in parks, as well as using assistive technology devices and mobile assistive applications). Overall, city residents with mobility difficulties find those green public spaces as an important element of their life quality. creator: Magdalena Błaszczyk creator: Marzena Suchocka creator: Magdalena Wojnowska-Heciak creator: Magdalena Muszyńska uri: https://doi.org/10.7717/peerj.10570 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Błaszczyk et al. title: Optimizing the amount of pig manure in the vermicomposting of spent mushroom (Lentinula) substrate link: https://peerj.com/articles/10584 last-modified: 2020-12-18 description: BackgroundThe mushroom industry produces a large amount of spent mushroom substrate (SMS), which requires a large geographical footprint and causes pollution.MethodsWe sought to optimize the C:N ratio of the initial feedstock used in vermicomposting of SMS by adding pig manure additions. We applied five treatments to the initial feedstock (S0, S1, S2, S3, and S4) with different C:N ratio of approximately 35, 30, 25, 20, and 15, respectively.ResultsOur results showed that lignin and cellulose in SMS were degraded after 56 days vermicomposting, especially in S2 (77.05% and 45.29%, respectively) and S3 (65.05% and 48.37%, respectively) treatments. We observed the degradation of the fibrous structure in SMS using pig manure treatments after vermicomposting by microscope and scanning electron microscope. Cellulase and polyphenol oxidase (PPO) were enhanced in pig manure treatments during vermicomposting, especially in the S2 and S3 treatments. The biomass of earthworms in the S2 treatments was at its highest level among all treatments at 28 to 56 days. The high level of PPO activity in the S2 treatment may protect cellulase and earthworms against the aromatic toxicity that is a byproduct of lignin degradation, particularly at 28 to 56 days of vermicomposting. Conclusively, it indicated that the C/N ratio of 25 in the S2 treatment was the optimal for SMS vermicomposting with the addition of pig manure. Our results provide a positive application for the recycling of both SMS and pig manure. creator: Yajing Shi creator: Zhenyu Wang creator: Yurong Wang uri: https://doi.org/10.7717/peerj.10584 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shi et al.