title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1013 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Estimating salt content of vegetated soil at different depths with Sentinel-2 data link: https://peerj.com/articles/10585 last-modified: 2020-12-21 description: The accurate and timely monitoring of the soil salt content (SSC) at different depths is the prerequisite for the solution to salinization in the arid and semiarid areas. Sentinel-2 has demonstrated significant superiority in SSC inversion for its higher temporal, spatial and spectral resolution, but previous research on SSC inversion with Sentinel-2 mainly focused on the unvegetated surface soil. Based on Sentinel-2 data, this study aimed to build four machine learning models at five depths (0∼20 cm, 20∼40 cm, 40∼60 cm, 0∼40 cm, and 0∼60 cm) in the vegetated area, and evaluate the sensitivity of Sentinel-2 to SSC at different depths and the inversion capability of the models. Firstly, 117 soil samples were collected from Jiefangzha Irrigation Area (JIA) in Hetao Irrigation District (HID), Inner Mongolia, China during August, 2019. Then a set of independent variables (IVs, including 12 bands and 32 spectral indices) were obtained based on the Sentinel-2 data (released by the European Space Agency), and the full subset selection was used to select the optimal combination of IVs at five depths. Finally, four machine learning algorithms, back propagation neural network (BPNN), support vector machine (SVM), extreme learning machine (ELM) and random forest (RF), were used to build inversion models at each depth. The model performance was assessed using adjusted coefficient of determination (R2adj), root mean square error (RMSE) and mean absolute error (MAE). The results indicated that 20∼40 cm was the optimal depth for SSC inversion. All the models at this depth demonstrated a good fitting (R2adj≈ 0.6) and a good control of the inversion errors (RMSE < 0.16%, MAE < 0.12%). At the depths of 40∼60 cm and 0∼20 cm the inversion performance showed a slight and a great decrease respectively. The sensitivity of Sentinel-2 to SSC at different depths was as follows: 20∼40 cm > 40∼60 cm > 0∼40 cm > 0∼60 cm > 0∼20 cm. All four machine learning models demonstrated good inversion performance (R2adj > 0.46). RF was the best model with high fitting and inversion accuracy. Its R2adj at five depths were between 0.5 to 0.68. The SSC inversion capabilities of all the four models were as follows: RF model > ELM model > SVM model > BPNN model. This study can provide a reference for soil salinization monitoring in large vegetated area. creator: Yinwen Chen creator: Yuanlin Qiu creator: Zhitao Zhang creator: Junrui Zhang creator: Ce Chen creator: Jia Han creator: Dan Liu uri: https://doi.org/10.7717/peerj.10585 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Sevoflurane preconditioning attenuates hypoxia/reoxygenation injury of H9c2 cardiomyocytes by activation of the HIF-1/PDK-1 pathway link: https://peerj.com/articles/10603 last-modified: 2020-12-21 description: BackgroundSevoflurane preconditioning (SPC) can provide myocardial protective effects similar to ischemic preconditioning (IPC). However, the underlying molecular mechanism of SPC remains unclear. Studies confirm that hypoxia-inducible factor-1 (HIF-1) can transform cells from aerobic oxidation to anaerobic glycolysis by activating the switch protein pyruvate dehydrogenase kinase-1 (PDK-1), thus providing energy for the normal life activities of cells under hypoxic conditions. The purpose of this study was to investigate whether the cardioprotective effects of SPC are associated with activation of the HIF-1a/PDK-1 signal pathway.MethodsThe H9c2 cardiomyocytes hypoxia/reoxygenation model was established and treated with 2.4% sevoflurane at the end of equilibration. Lactate dehydrogenase (LDH) level, cell viability, cell apoptosis, mitochondrial membrane potential, key enzymes of glycolysis, ATP concentration of glycolysis were assessed after the intervention. Apoptosis related protein(Bcl-2, Bax), HIF-1a protein, and PDK-1 protein were assessed by western blot.ResultsCompared with the H/R group, SPC significantly increased the expression of HIF-1a, PDK-1, and Bcl-2 and reduced the protein expression of Bax, which markedly decreased the apoptosis ratio and Lactate dehydrogenase (LDH) level, increasing the cell viability, content of key enzymes of glycolysis, ATP concentration of glycolysis and stabilizing the mitochondrial membrane potential. However, the cardioprotective effects of SPC were disappeared by treatment with a HIF-1a selective inhibitor.ConclusionThis study demonstrates that the cardioprotective effects of SPC are associated with the activation of the HIF-1a/PDK-1 signaling pathway. The mechanism may be related to increasing the content of key enzymes and ATP of glycolysis in the early stage of hypoxia. creator: Tianliang Hou creator: Haiping Ma creator: Haixia Wang creator: Chunling Chen creator: Jianrong Ye creator: Ahmed Mohamed Ahmed creator: Hong Zheng uri: https://doi.org/10.7717/peerj.10603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hou et al. title: Improved plaque assay for human coronaviruses 229E and OC43 link: https://peerj.com/articles/10639 last-modified: 2020-12-21 description: In light of the COVID-19 pandemic, studies that work to understand SARS-CoV-2 are urgently needed. In turn, the less severe human coronaviruses such as HCoV-229E and OC43 are drawing newfound attention. These less severe coronaviruses can be used as a model to facilitate our understanding of the host immune response to coronavirus infection. SARS-CoV-2 must be handled under biosafety level 3 (BSL-3) conditions. Therefore, HCoV-229E and OC43, which can be handled at BSL-2 provide an alternative to SARS-CoV-2 for preclinical screening and designing of antivirals. However, to date, there is no published effective and efficient method to titrate HCoVs other than expensive indirect immunostaining. Here we present an improved approach using an agarose-based conventional plaque assay to titrate HCoV 229E and OC43 with mink lung epithelial cells, Mv1Lu. Our results indicate that titration of HCoV 229E and OC43 with Mv1Lu is consistent and reproducible. The titers produced are also comparable to those produced using human rhabdomyosarcoma (RD) cells. More importantly, Mv1Lu cells display a higher tolerance for cell-cell contact stress, decreased temperature sensitivity, and a faster growth rate. We believe that our improved low-cost plaque assay can serve as an easy tool for researchers conducting HCoV research. creator: Nicole Bracci creator: Han-Chi Pan creator: Caitlin Lehman creator: Kylene Kehn-Hall creator: Shih-Chao Lin uri: https://doi.org/10.7717/peerj.10639 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bracci et al. title: Uncovering the hidden diversity of Mississippian crinoids (Crinoidea, Echinodermata) from Poland link: https://peerj.com/articles/10641 last-modified: 2020-12-21 description: Partial crinoid crowns and aboral cups are reported from the Mississippian of Poland for the first time. Most specimens are partially disarticulated or isolated plates, which prevent identification to genus and species, but regardless these remains indicate a rich diversity of Mississippian crinoids in Poland during the Mississippian, especially during the late Viséan. Lanecrinus? sp. is described from the late Tournaisian of the Dębnik Anticline region. A high crinoid biodiversity occurred during late Viséan of the Holy Cross Mountains, including the camerate crinoids Gilbertsocrinus? sp., Platycrinitidae Indeterminate; one flexible crinoid; and numerous eucladid crinoids, including Cyathocrinites mammillaris (Phillips), three taxa represented by partial cups left in open nomenclature, and numerous additional taxa known only from isolated radial plates, brachial plates, and columnals. To date, the youngest occurrence of Gilbertsocrinus was the early Viséan of the United States, thus the present finding in upper Viséan extends this genus range. Furthermore, the occurrence of Lanecrinus? sp. expands the Western European range of this genus into the Tournaisian. A single partially disarticulated crown, Crinoidea Indeterminate B, is described from the Serpukhovian of the Upper Silesian Coal Basin. In addition, several echinoid test plates and spines are also reported. creator: Mariusz A. Salamon creator: William I. Ausich creator: Tomasz Brachaniec creator: Bartosz J. Płachno creator: Przemysław Gorzelak uri: https://doi.org/10.7717/peerj.10641 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Salamon et al. title: Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes link: https://peerj.com/articles/9859 last-modified: 2020-12-18 description: Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level. creator: Tingting Song creator: Yingyue Shen creator: Qunli Jin creator: Weilin Feng creator: Lijun Fan creator: Weiming Cai uri: https://doi.org/10.7717/peerj.9859 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Song et al. 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.