title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2021-06 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Taxonomic revision of the Temnothorax salvini clade (Hymenoptera: Formicidae), with a key to the clades of New World Temnothorax link: https://peerj.com/articles/11514 last-modified: 2021-06-30 description: Temnothorax is a large myrmicine ant genus with a range spanning the northern hemisphere, including the northern half of the Neotropics. Many of the Neotropical species were originally placed in the now defunct genus Macromischa. Recent molecular work has revealed that distinct lineages of Neotropical Temnothorax have arrived by evolutionary convergenceat a morphological syndrome with characteristics that were used to diagnose the former genus Macromischa. One such lineage is the salvini clade, which in this study is redefined to contain 63 species, 35 of which are described as new. A key to all species of the salvini clade based on the worker caste is provided; additionally, a worker-based key to all clades of the New World is provided. The following species are redescribed: T. albispinus (Wheeler), T. androsanus (Wheeler), T. annexus (Baroni Urbani), T. augusti (Baroni Urbani), T. aztecus (Wheeler), T. ciferrii (Menozzi & Russo), T. flavidulus (Wheeler & Mann), T. fuscatus (Mann), T. goniops (Baroni Urbani), T. huehuetenangoi (Baroni Urbani), T. ixili (Baroni Urbani), T. leucacanthus (Baroni Urbani), T. nigricans (Baroni Urbani), T. ocarinae (Baroni Urbani), T. pastinifer (Emery), T. pergandei (Emery), T. politus (Smith), T. pulchellus (Emery), T. rugosus (Mackay), T. salvini (Forel), T. schwarzi (Mann), T. skwarrae (Wheeler), T. subditivus (Wheeler), T. tenuisculptus (Baroni Urbani), T. terricola (Mann), T. terrigena (Wheeler), T. torrei (Aguayo). The gynes of T. ciferrii, T. fuscatus, T. ixili, T. politus, T. rugosus, T. salvini, T. tenuisculptus and T. torrei are described. The males of T. albispinus and T. fuscatus are described. Lectotypes are designated for T. androsanus, T. annexus, T. augusti, T. aztecus, T. flavidulus, T. fuscatus, T. nigricans, T. pastinifer, T. pergandei, T. politus, T. pulchellus, T. salvini, T. skwarrae, T. subditivus, T. terricola, and T. terrigena. A neotype for Temnothorax salvini obscurior (Forel) is designated, the taxon is raised to species, and a replacement name is designated: T. longicaulisstat. nov., nom. nov. The following species are described as new: T. achiisp. nov., T. acuminatussp. nov., T. acutispinosussp. nov., T. agavicolasp. nov., T. altinodussp. nov., T. arbustussp. nov., T. aureussp. nov., T. aztecoidessp. nov., T. bahorucosp. nov., T. balaclavasp. nov., T. balneariussp. nov., T. bisonsp. nov., T. casanovaisp. nov., T. fortispinosussp. nov., T. harlequinasp. nov., T. hippolytussp. nov., T. laticrussp. nov., T. leucacanthoidessp. nov., T. longinoisp. nov., T. magnabullasp. nov., T. misomoschussp. nov., T. nebliselvasp. nov., T. obtusigastersp. nov., T. paraztecussp. nov., T. parralensissp. nov., T. parvidentatussp. nov., T. pilicornissp. nov., T. quercicolasp. nov., T. quetzalsp. nov., T. rutabulafersp. nov., T. terraztecussp. nov., T. tuxtlanussp. nov., T. wettererisp. nov., T. wilsonisp. nov., T. xincaisp. nov. creator: Matthew M. Prebus uri: https://doi.org/10.7717/peerj.11514 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Prebus title: The impact of PIT tags on the growth and survival of pythons is insignificant in randomised controlled trial link: https://peerj.com/articles/11531 last-modified: 2021-06-30 description: Individual identification is fundamental to the study of captive and wild animals but can have adverse impacts if the method of identification is inappropriate for the species or question of interest. We conducted a randomised controlled trial to test whether passive integrated transponder (PIT) tags reduced the growth or survival of pythons. We randomly allocated 200 captive-bred Burmese python (Python bivittatus) hatchlings into two groups, tagged versus untagged. Hatchlings were individually identified using a combination of PIT tags and unique colour patterns, and their mass, snout-vent length (SVL) and body condition measured at 9, 73, 134, 220, 292 and 385 days of age. We recorded the date of all mortalities. Python morphometrics and their rate of change increased or fluctuated non-linearly with age. The impact of PIT tagging on python body mass and body mass growth over the 376 day study period was insignificant. PIT tagging additionally had an insignificant impact on python survival. However, we found minor differences in SVL growth between tagged and untagged pythons. These differences peaked at approximately 0.5 mm/day and appeared to drive similar, but more pronounced, differences between tagged and untagged pythons in their rate of change in body condition; peaking at approximately 3–4 g/day. While we cannot be certain that these small differences are, or are not, biologically meaningful, they nonetheless appear to be short-term and readily resolved. Unsurprisingly, the strongest driver of python growth was their age, with growth rapidly increasing or highest amongst younger snakes for all measures of size. Python sex was associated with their body mass and survival, with higher mass but lower survival amongst females. Python size at hatching did not impact on their growth or survival. Our results confirm that PIT tags are a valuable and effective tool for the identification and tracking of captive pythons, and snakes generally, and meet high safety and animal welfare standards. creator: Patrick L. Taggart creator: Stephen Morris creator: Charles G.B. Caraguel uri: https://doi.org/10.7717/peerj.11531 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Taggart et al. title: Whole blood fatty acid concentrations in the San Cristóbal Galápagos tortoise (Chelonoidis chathamensis) link: https://peerj.com/articles/11582 last-modified: 2021-06-30 description: To continue releasing San Cristóbal Galápagos tortoises housed in managed-care facilities at the Giant Tortoise Breeding Center of Galápagos National Park (Galapaguera de Cerro Colorado) to the Otoy Ecological Farm, health assessments and physical examinations were conducted. As a part of these wellness examinations, blood was drawn from 11 tortoises to analyze fatty acid concentrations. Fatty acid levels can provide insight into the nutritional profiles, immune status, and reproductive health of vertebrates. To the co-author’s knowledge, there is no current information about fatty acids in this species. It was hypothesized that there would be inherent differences based on the different geographic ranges, diets, sex, and age of turtles. It was noted that the ω-6/ω-3 ratio was higher for the breeding center than for the ecological farm and that overall polyunsaturated fatty acids (PUFAs) did not have any significant differences. The ω-6/ω-3 findings can contribute to a global picture of these fatty acids across taxa, as reptiles are underrepresented in this area of research. Additional results are a resourceful starting point for future investigations into how fatty acids are affected in Galápagos tortoises. creator: Khushboo Dass creator: Gregory A. Lewbart creator: Juan Pablo Muñoz-Pérez creator: Maryuri I. Yépez creator: Andrea Loyola creator: Emile Chen creator: Diego Páez-Rosas uri: https://doi.org/10.7717/peerj.11582 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dass et al. title: Effects of mannan oligosaccharides on growth performance, nutrient digestibility, ruminal fermentation and hematological parameters in sheep link: https://peerj.com/articles/11631 last-modified: 2021-06-30 description: BackgroundMannan oligosaccharides (MOS) are a promising feed additive in animal husbandry due to mainly improving animal health status. The purpose of this study was to investigate the effects of MOS on growth performance, nutrient digestibility, ruminal fermentation, and twelve hematological parameters in sheep.MethodsNinety-six healthy Hu rams with similar body weights were chosen and divided into four treatment groups (twenty-four rams in each group), in which four different doses of MOS were tested: 0%, 0.8%, 1.6% and 2.4% of the basal diet (on an as-fed basis).ResultsThe results showed that supplementation dietary MOS did not affect feed intake, body weight, average daily weight gain, or ruminal short-chain fatty acids (SCFAs) concentration; the ratio of individual fatty acids to total SCFAs, the C2/C3 ratio, and the hematological parameters in the sheep were also unaltered (P > 0.05). Conversely, supplementation dietary MOS increased the dry matter, organic matter, crude protein, neutral detergent fiber, acid detergent fiber, and ash apparent digestibility (P < 0.05), and decreased the ruminal ammonia concentration in the sheep (P < 0.05), especially at a dose of 1.6%.ConclusionsThis indicates that supplementation dietary MOS improved nutrient utilization by the sheep and nitrogen metabolism in the rumen; however, the effects are too slight to interfere with the basal metabolism in the sheep. creator: Chen Zheng creator: Juwang Zhou creator: Yanqin Zeng creator: Ting Liu uri: https://doi.org/10.7717/peerj.11631 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zheng et al. title: Heterogeneity of gut microbial responses in healthy household dogs transitioning from an extruded to a mildly cooked diet link: https://peerj.com/articles/11648 last-modified: 2021-06-30 description: BackgroundThe gut microbiota (GM) is associated with canine health and can be impacted by diet. Dog owners in the U.S. have increasingly shown an interest in feeding their dogs a mildly cooked (MC) diet. However, its impact on canine GM and health remains largely unknown.MethodsHealthy household dogs were tracked upon switching from various brands of extruded to MC diets for four weeks. A health assessment was completed and stool samples were collected by each owner before (day 0) and after the diet transition (day 28). Shotgun metagenomic sequencing was performed at both time points to characterize the GM.ResultsDogs completed the study by either completing the health assessments (n = 31) or providing stool samples at both time points (n = 28). All owners reported either better or no change in overall health at the end of the study (61% and 39%, respectively), and none reported worse overall health. Defecation frequency was also reported to be lower (58%) or about the same (35%). Principal coordinate (PCo) analysis showed a significant shift (p = 0.004) in the β-diversity of the GM upon diet transition (34.2% and 10.3% explained by the first two axes). The abundances of 70 species increased after the diet change (adjusted p < 0.05), 67% and 24% of which belonged to the Lactobacillales and the Enterobacterales orders respectively. The abundances of 28 species decreased (adjusted p < 0.05), 46%, 18%, and 11% of which belonged to the Clostridiales, Bacillales, and Bacteroidales orders, respectively. Lower Lactobacillales and Enterobacterales, and higher Bacteroidales at baseline were associated with a greater shift along the PCo1 axis. Protein content of the baseline diet was correlated with the shift along the PCo1 axis (ρ = 0.67, p = 0.006).ConclusionOwners reported either improvement or no change in health in dogs transitioning from extruded kibble to MC diets for 4 weeks, but this report of health perception requires further exploration in a controlled trial. Diet change also led to a significant shift in the GM profile of healthy dogs. The magnitude of shift was associated with baseline GM and dietary protein, and warrants further examination of individualized responses and personalized nutrition in companion dogs. These results also support future investigation of the impact of a MC diet on health maintenance given its increasing popularity. creator: Jirayu Tanprasertsuk creator: Justin Shmalberg creator: Heather Maughan creator: Devon E. Tate creator: LeeAnn M. Perry creator: Aashish R. Jha creator: Ryan W. Honaker uri: https://doi.org/10.7717/peerj.11648 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2021 Tanprasertsuk et al. title: Biosynthesized selenium nanoparticles: characterization, antimicrobial, and antibiofilm activity against Enterococcus faecalis link: https://peerj.com/articles/11653 last-modified: 2021-06-30 description: BackgroundControl over microbial growth is a crucial factor in determining the success of endodontic therapy. Enterococcus faecalis is the most resistant biofilm-forming species leading to endodontic failure. Hence, the current researches are directed towards discovering materials with superior disinfection properties and lesser cytotoxicity. This study aimed to synthesize and characterize biogenically produced Selenium Nanoparticles, and to evaluate the antimicrobial and antibiofilm efficacy, against Enterococcus Faecalis, for the following test groups: Group I: Distilled water (control), Group II: SeNPs (1 mg/ml), Group III: Calcium hydroxide (1 mg/ml), Group IV: 2% Chlorhexidine gluconate (CHX), Group V: 5.25% Sodium hypochlorite (NaOCl).Materials and MethodsSelenium nanoparticles were derived using fresh guava leaves (Psidium guajava) and were characterized. The antibacterial efficacy against E. faecalis was evaluated by agar well diffusion method. The antibiofilm efficacy of the test groups was observed by viable cell count, antibiofilm assay, and Anthrone and Bradford’s tests. The morphology of the biofilms was analysed using the Scanning Electron Microscope and Fourier Transform Infrared spectroscopy.ResultsAntibacterial and antibiofilm efficacy of all tested solutions showed superior antibacterial and antibiofilm efficacy when compared to the control group. Overall, SeNPs (Group II) was the most effective against E. faecalis biofilm, followed by NaOCl (Group V), CHX (Group IV), and Ca(OH)2 (Group III).ConclusionBiogenically produced SeNPs emerged as a novel antibacterial and antibiofilm agent against E. faecalis. This nano-formulation demonstrates the potential to be developed as a root canal disinfectant combating bacterial biofilm in endodontics after the results have been clinically extrapolated. creator: Sanjay Miglani creator: Nobuyuki Tani-Ishii uri: https://doi.org/10.7717/peerj.11653 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Miglani and Tani-Ishii title: New austrolimulid from Russia supports role of Early Triassic horseshoe crabs as opportunistic taxa link: https://peerj.com/articles/11709 last-modified: 2021-06-30 description: Horseshoe crabs are extant marine euchelicerates that have a fossil record extending well into the Palaeozoic. Extreme xiphosurid morphologies arose during this evolutionary history. These forms often reflected the occupation of freshwater or marginal conditions. This is particularly the case for Austrolimulidae—a xiphosurid family that has recently been subject to thorough taxonomic examination. Expanding the austrolimulid record, we present new material from the Olenekian-aged Petropavlovka Formation in European Russia and assign this material to Attenborolimulus superspinosus gen. et sp. nov. A geometric morphometric analysis of 23 horseshoe crab genera illustrates that the new taxon is distinct from limulid and paleolimulid morphologies, supporting the assignment within Austrolimulidae. In considering Triassic austrolimulids, we suggest that the hypertrophy or reduction in exoskeletal sections illustrate how species within the family evolved as opportunistic taxa after the end-Permian extinction. creator: Russell D.C. Bicknell creator: Dmitry E. Shcherbakov uri: https://doi.org/10.7717/peerj.11709 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bicknell and Shcherbakov title: Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms link: https://peerj.com/articles/11721 last-modified: 2021-06-30 description: The impacts of climate change on the Arctic Ocean are manifesting throughout the ecosystem at an unprecedented rate. Of global importance are the impacts on heat and freshwater exchange between the Arctic and North Atlantic Oceans. An expanding Atlantic influence in the Arctic has accelerated sea-ice decline, weakened water column stability and supported the northward shift of temperate species. The only deep-water gateway connecting the Arctic and North Atlantic and thus, fundamental for these exchange processes is the Fram Strait. Previous research in this region is extensive, however, data on the ecology of microbial communities is limited, reflecting the wider bias towards temperate and tropical latitudes. Therefore, we present 14 metagenomes, 11 short-read from Illumina and three long-read from PacBio Sequel II, of the 0.2–3 µm fraction to help alleviate such biases and support future analyses on changing ecological patterns. Additionally, we provide 136 species-representative, manually refined metagenome-assembled genomes which can be used for comparative genomics analyses and addressing questions regarding functionality or distribution of taxa. creator: Taylor Priest creator: Luis H. Orellana creator: Bruno Huettel creator: Bernhard M. Fuchs creator: Rudolf Amann uri: https://doi.org/10.7717/peerj.11721 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Priest et al. title: Space-filling and benthic competition on coral reefs link: https://peerj.com/articles/11213 last-modified: 2021-06-29 description: Reef-building corals are ecosystem engineers that compete with other benthic organisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the exposure to competitors. This predicted an association between these two geometric properties of corals and the competitive outcome against other benthic organisms. To test the prediction, fifty coral colonies from the Caribbean island of Curaçao were rendered using digital 3D and 2D reconstructions. The surface areas, perimeters, box-counting dimensions (as a proxy of surface and perimeter space-filling), and other geometric properties were extracted and analyzed with respect to the percentage of the perimeter losing or winning against competitors based on the coral tissue apparent growth or damage. The increase in surface space-filling dimension was the only significant single indicator of coral winning outcomes, but the combination of surface space-filling dimension with perimeter length increased the statistical prediction of coral competition outcomes. Corals with larger surface space-filling dimensions (Ds > 2) and smaller perimeters displayed more winning outcomes, confirming the initial hypothesis. We propose that the space-filling property of coral surfaces complemented with other proxies of coral competitiveness, such as life history traits, will provide a more accurate quantitative characterization of coral competition outcomes on coral reefs. This framework also applies to other organisms or ecological systems that rely on complex surfaces to obtain energy for competition. creator: Emma E. George creator: James A. Mullinix creator: Fanwei Meng creator: Barbara A. Bailey creator: Clinton Edwards creator: Ben Felts creator: Andreas F. Haas creator: Aaron C. Hartmann creator: Benjamin Mueller creator: Ty N.F. Roach creator: Peter Salamon creator: Cynthia Silveira creator: Mark J.A. Vermeij creator: Forest Rohwer creator: Antoni Luque uri: https://doi.org/10.7717/peerj.11213 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 George et al. title: Evolutionary relationships among the snakelike pygopodid lizards: a review of phylogenetic studies of an enigmatic Australian adaptive radiation link: https://peerj.com/articles/11502 last-modified: 2021-06-29 description: Here, I review phylogenetic studies of the lizard family Pygopodidae, a group of 47 extant species that diversified in Australia and New Guinea. The goal of this study was to examine published phylogenetic and phylogenomic hypotheses on pygopodids to identify the strengths and weaknesses in our understanding of their phylogeny. Many parts of the pygopodid family tree are well established by multiple independent tree inferences including: (1) all multispecies genera (i.e., Aprasia, Delma, Lialis, Pletholax, and Pygopus) are monophyletic groups; (2) the root of the pygopodid tree is located along the branch leading to the Delma clade, thus showing that Delma is the sister group to all other pygopodid genera; (3) the Aprasia repens group, Delma tincta group, and several other groups of closely related species are demonstrated to be monophyletic entities; and (4) the monotypic Paradelma orientalis is the sister lineage to the Pygopus clade. Based on accumulated phylogenetic evidence, two taxonomic recommendations are given: Paradelma merits generic status rather than being subsumed into Pygopus as some earlier studies had suggested, and the monotypic Aclys concinna should be recognized as a member of Delma (following current practice) until future studies clarify its placement inside or outside the Delma clade. One chronic problem with phylogenetic studies of pygopodids, which has limited the explanatory power of many tree hypotheses, concerns the undersampling of known species. Although the continual addition of newly described species, especially over the past two decades, has been a major reason for these taxon sampling gaps, deficits in species sampling for ingroups and/or outgroups in several studies of pygopodid species complexes has confounded the testing of some ingroup monophyly hypotheses. Ancient hybridization between non-sister lineages may also be confounding attempts to recover the relationships among pygopodids using molecular data. Indeed, such a phenomenon can explain at least five cases of mito-nuclear discordance and conflicts among trees based on nuclear DNA datasets. Another problem has been the lack of consensus on the relationships among most pygopodid genera, an issue that may stem from rapid diversification of these lineages early in the group’s history. Despite current weaknesses in our understanding of pygopodid phylogeny, enough evidence exists to clarify many major and minor structural parts of their family tree. Accordingly, a composite tree for the Pygopodidae was able to be synthesized. This novel tree hypothesis contains all recognized pygopodid species and reveals that about half of the clades are corroborated by multiple independent tree hypotheses, while the remaining clades have less empirical support. creator: W. Bryan Jennings uri: https://doi.org/10.7717/peerj.11502 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Jennings title: Forecasting the COVID-19 transmission in Italy based on the minimum spanning tree of dynamic region network link: https://peerj.com/articles/11603 last-modified: 2021-06-29 description: BackgroundItaly surpassed 1.5 million confirmed Coronavirus Disease 2019 (COVID-19) infections on November 26, as its death toll rose rapidly in the second wave of COVID-19 outbreak which is a heavy burden on hospitals. Therefore, it is necessary to forecast and early warn the potential outbreak of COVID-19 in the future, which facilitates the timely implementation of appropriate control measures. However, real-time prediction of COVID-19 transmission and outbreaks is usually challenging because of its complexity intertwining both biological systems and social systems.MethodsBy mining the dynamical information from region networks and the short-term time series data, we developed a data-driven model, the minimum-spanning-tree-based dynamical network marker (MST-DNM), to quantitatively analyze and monitor the dynamical process of COVID-19 spreading. Specifically, we collected the historical information of daily cases caused by COVID-19 infection in Italy from February 24, 2020 to November 28, 2020. When applied to the region network of Italy, the MST-DNM model has the ability to monitor the whole process of COVID-19 transmission and successfully identify the early-warning signals. The interpretability and practical significance of our model are explained in detail in this study.ResultsThe study on the dynamical changes of Italian region networks reveals the dynamic of COVID-19 transmission at the network level. It is noteworthy that the driving force of MST-DNM only relies on small samples rather than years of time series data. Therefore, it is of great potential in public surveillance for emerging infectious diseases. creator: Min Dong creator: Xuhang Zhang creator: Kun Yang creator: Rui Liu creator: Pei Chen uri: https://doi.org/10.7717/peerj.11603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dong et al. title: Comparative analysis of carbon footprint between conventional smallholder operation and innovative largescale farming of urban agriculture in Beijing, China link: https://peerj.com/articles/11632 last-modified: 2021-06-29 description: The sustainable development of agriculture is one of the key issues of ensuring food security and mitigating climate change. Since innovative large-scale agriculture is gaining popularity in cities in China, where the agricultural landscape is dominated by conventional smallholder farming, it is necessary to investigate the difference in carbon emissions between conventional smallholder operation and innovative largescale agriculture. This study evaluated the carbon footprint (CF) of conventional and innovative urban agriculture in Beijing using the cradle-to-consumption Life Cycle Assessment (LCA). Two modes of greenhouse vegetable and fruit production were analyzed and compared respectively: conventional smallholder operated vegetable farms that sell in local markets versus largescale home-delivery agriculture (HDA) that deliver vegetables to consumers’ home directly, conventional smallholder operated fruit farms that sell in farm shops versus largescale pick-your-own (PYO) initiatives. Results showed that HDA and PYO can reduce CF per area in on-farm cultivation compared to smallholder operation, while may bring an increase in CF per product weight unit and the gap was wider if the supply chain was considered. This is mainly because innovative large-scale farming consumes fewer agricultural inputs (e.g., fertilizer, pesticides) and obtains lower yields than conventional smallholder operations. Plastic materials with high carbon emission, fossil energy dependence and transportation efficiency are CF hotspots of both modes and therefore can be prioritized and targeted for carbon reduction adjustment. The results of this work further advance understanding of how innovative largescale agriculture and conventional smallholder operation compare and which particular inputs and activities should be prioritized to effectively reduce the CF in China during agricultural transformation. creator: Yingjie Hu creator: Jin Sun creator: Ji Zheng uri: https://doi.org/10.7717/peerj.11632 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hu et al. title: What do alexithymia items measure? A discriminant content validity study of the Toronto-alexithymia-scale–20 link: https://peerj.com/articles/11639 last-modified: 2021-06-29 description: BackgroundQuestions have been raised about whether items of alexithymia scales assess the construct alexithymia and its key features, and no other related constructs. This study assessed the (discriminant) content validity of the most widely used alexithymia scale, i.e., the Toronto Alexithymia Scale (TAS-20).MethodsParticipants (n = 81) rated to what extent TAS-20 items and items of related constructs were relevant for assessing the constructs ‘alexithymia’, ‘difficulty identifying feelings’, ‘difficulty describing feelings’, ‘externally-oriented thinking’, ‘limited imaginal capacity’, ‘anxiety’, ‘depression’, and ‘health anxiety’.ResultsResults revealed that, overall, the TAS-20 did only partly measure ‘alexithymia’. Only the subscales ‘difficulty identifying feelings’ and ‘difficulty describing feelings’ represented ‘alexithymia’ and their intended construct, although some content overlap between these subscales was found. In addition, some items assessed (health) anxiety equally well or even better.ConclusionsRevision of the TAS-20 is recommended to adequately assess all key features of alexithymia. Findings with the TAS-20 need to be interpreted with caution in people suffering from medical conditions. creator: Elke Veirman creator: Dimitri M.L. Van Ryckeghem creator: Gregory Verleysen creator: Annick L. De Paepe creator: Geert Crombez uri: https://doi.org/10.7717/peerj.11639 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Veirman et al. title: Vertical zonation of the Siberian Arctic benthos: bathymetric boundaries from coastal shoals to deep-sea Central Arctic link: https://peerj.com/articles/11640 last-modified: 2021-06-29 description: The bathymetric distribution of species of Annelida, Crustacea and Echinodermata from the region including the Kara, Laptev and East Siberian seas and the adjacent region of the deep-sea Central Arctic was analysed. We focused on vertical species ranges revealing zones of crowding of upper and lower species range limits. Using published data and in part the material obtained during the expeditions of the P.P. Shirshov Institute of Oceanology, we evaluated species vertical distribution from 0 m to the maximum depth of the Central Arctic (~4,400 m). The entire depth range was divided into smaller intervals; number of upper and lower limits of species depth ranges was counted and plotted to visualize the range limits crowding. Several zones of crowding of vertical species range limits were found for all analysed macrotaxa. The most significant zones occurred at depths of 450–800 m and 1,800–2,000 m. The first depth zone corresponds to the boundary between the sublittoral and bathyal faunas. The last one marks the boundary between the bathyal and abyssal faunas. Depths of these boundaries differ from those reported from other Ocean regions; possible explanations of these differences are discussed. creator: Andrey Vedenin creator: Sergey Galkin creator: Alexander N. Mironov creator: Andrey Gebruk uri: https://doi.org/10.7717/peerj.11640 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Vedenin et al. title: Taxonomic relevance of petiole anatomical and micro-morphological characteristics of Clematis L. (Ranunculaceae) taxa from South Korea link: https://peerj.com/articles/11669 last-modified: 2021-06-29 description: We assessed the micro-morphological and anatomical structures of the petioles of 19 Clematis taxa from South Korea. The petiole surface features were observed with the help of stereomicroscopy and scanning electron microscopy, and the anatomical features are studied via microtomy and light microscopy. The results of this study showed that the presence/absence and abundance of trichomes, petiole cross-section outlines, upper surface wings and grooves, and the number of vascular bundles were useful for species discrimination in Clematis. Among the studied taxa, C. hexapetala was the only species with a glabrous petiole surface. Two types of trichomes were observed in the other 18 taxa: long, non-glandular and flagelliform trichomes and short, glandular capitate trichomes. We found four to six major vascular bundles and a maximum of eight interfascicular vascular bundles (C. heracleifolia and C. urticifolia) in the 19 taxa. A cluster analysis based on UPGMA identified six clusters with 18 nodes. Although the number of taxa investigated was limited, taxa from the sections Tubulosae, Viorna, and Astragene clustered with each other in the UPGMA phenogram due to the overall similarity of petiole features. Based on this observation, we can conclude that most of the petiole features are limited to the species level, and thus, the data obtained could be used as descriptive and/or diagnostic features for particular taxa, which may be useful for the investigation of problematic taxa in the genus. creator: Beom Kyun Park creator: Dong Chan Son creator: Balkrishna Ghimire uri: https://doi.org/10.7717/peerj.11669 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Park et al. title: Integrated mRNA-seq and miRNA-seq analysis of goat fibroblasts response to Brucella Melitensis strain M5-90 link: https://peerj.com/articles/11679 last-modified: 2021-06-29 description: Brucellosis is a globally zoonotic bacterial disease of humans and various animals including goats, sheep, and cattle. Brucella melitensis M5-90, a live attenuated vaccine strain, has been widely used to prevent brucellosis in goats and sheep. However, the molecular mechanisms governing protective immunity response in non-professional phagocytes infected with B. melitensis M5-90 have not been fully investigated, especially in goats. In our research, goat fibroblasts were used as in vitro models to determine these mechanisms by transcriptome analysis. After incubating with B. melitensis M5-90 3 h, the infected goat fibroblasts were collected at 0 h, 4 h, 24 h, 48 h and 72 h for RNA-seq. The results indicated that there were totally 11,819 differentially expressed genes (DEGs) and 777 differentially expressed (DE) miRNAs found in experiment groups compared with the control groups (|log2(Foldchange)|≥1, FDR<0.05). GO and KEGG enrichment analyses revealed that down-regulated genes were involved in the riboflavin metabolism and positive regulation of IL-8 secretion pathway. The up-regulated genes were mainly involved in adaptive immunity, including TNF signaling pathway, MAPK signaling pathway and JAK/STAT pathway. Additionally, cytokine-cytokine receptor interaction, natural killer cell mediated cytotoxicity and toll-like receptor signaling pathway, which associated with innate immunity pathways, were also induced. Based on the Pearson correlation coefficients and prediction results of TargetScan and miRanda, the miRNA-mRNA networks of NFKB1, IFNAR2 and IL10RB were constructed and verified in goat fibroblasts by qPCR, which demonstrated that goat fibroblasts displayed immunomodulatory properties. Our findings provide a deeper insight into the host miRNA-driven B. melitensis defense mechanism and reveal the transcriptome changes involved in the innate and adaptive immune response of the goats to B. melitensis infection. creator: Baobao Li creator: Si Chen creator: Chengqiang Wang creator: Qiaoling Chen creator: Churiga Man creator: Qi An creator: Zhenxing Zhang creator: Zhiyong Liu creator: Li Du creator: Fengyang Wang uri: https://doi.org/10.7717/peerj.11679 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Oral function in patients with myasthenia gravis link: https://peerj.com/articles/11680 last-modified: 2021-06-29 description: Myasthenia Gravis (MG) is characterised by muscle weakness and increased fatigability. The aim of this pilot study was to investigate if patients with MG demonstrate different functional chewing patterns and report more complaints related to mastication as compared with healthy controls. Twelve patients (median 60 years Q1–Q3: 46–70) with generalised MG and nine healthy controls (median 57 years Q1–Q3: 55–63) participated. All participants underwent dental and oral examination and were asked to fill in a questionnaire concerning oral health. Static maximum bite force was measured with a bite force transducer, electromyography in the masseter, temporalis, and suprahyoid muscles were recorded, and jaw movement was tracked, during a 5-minute gum chewing test. The patients had more oral complaints (oral health impact profile total score 22.6 vs 7.5 P < 0.01) and had lower peak bite force than controls (18.8kgf (11.1;26.4) (95% CI) vs 29.5 kgf (21.6; 37.4) (P = 0.04)). In contrast, fatigability of the masticatory muscles, as defined by number of chewing cycles during the gum-chewing test, did not differ between patients and controls (P = 0.10). In conclusion, patients had more oral complaints and lower bite force than controls, but did not show significantly different functional chewing patterns. Future studies should aim at integrating measurement of peak force into functional tests. Attention should be given to oral complaints of patients with MG. creator: Agnete Overgaard Donskov creator: Akiko Shimada creator: Lotte Vinge creator: Peter Svensson creator: Henning Andersen uri: https://doi.org/10.7717/peerj.11680 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Donskov et al. title: Depression and low physical activity are related to sarcopenia in hemodialysis: a single-center study link: https://peerj.com/articles/11695 last-modified: 2021-06-29 description: BackgroundThe number of patients who suffer from chronic renal failure (CRF) has widely increased worldwide. Patients with advanced stages of CRF experience a gradual and progressive loss of muscle and fat mass leading to decreased physical activity and mental health problems. The loss of muscle mass in CRF might contribute to the development of sarcopenia. Therefore, this study aimed to explore the prevalence of sarcopenia and to determine the relationship of physical activity and mental state of depression with sarcopenia in hemodialysis patients.MethodsA cross-sectional study was designed with a total of 104 male and female with a minimum age of 35 years. Based on the guidelines of the Asian Working Group for Sarcopenia in 2019, gait speed, muscle mass, and handgrip were used to define sarcopenia. In addition, participants were requested to perform a set of questionnaires to evaluate their physical activity and state of depression. Logistic regression analyses were used to explore the risk factors of sarcopenia.ResultsThirty-four (32.69%) of 104 participants had sarcopenia. Compared to the 70 individuals without sarcopenia, they had a low physical activity and a high depression score (ps < .05). Furthermore, low physical activity and high depression scores in combination with sarcopenia were associated with an increased mortality risk. Low physical activity and high depression scores were also independently associated with sarcopenia in hemodialysis patients after controlling for age (odds ratio = 3.23, and 4.92, respectively). creator: Kornanong Yuenyongchaiwat creator: Sasikan Jongritthiporn creator: Kasarn Somsamarn creator: Oranat Sukkho creator: Sasipim Pairojkittrakul creator: Opas Traitanon uri: https://doi.org/10.7717/peerj.11695 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yuenyongchaiwat et al. title: Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study link: https://peerj.com/articles/11699 last-modified: 2021-06-29 description: BackgroundEarly and accurate diagnosis of microorganism(s) is important to optimize antimicrobial therapy. Shotgun metagenomic sequencing technology, an unbiased and comprehensive method for pathogen identification, seems to potentially assist or even replace conventional microbiological methodology in the diagnosis of infectious diseases. However, evidence in clinical application of this platform is relatively limited.MethodsTo evaluate the capability of shotgun metagenomic sequencing technology in clinical practice, both shotgun metagenomic sequencing and conventional culture were performed in the PCR-positive body fluid specimens of 20 patients with suspected infection. The sequenced data were then analyzed for taxonomic identification of microbes and antibiotic resistance gene prediction using bioinformatics pipeline.ResultsShotgun metagenomic sequencing results showed a concordance of 17/20 compared with culture results in bacterial detection, and a concordance of 20/20 compared with culture results in fungal detection. Besides, drug-resistant types annotated from antibiotic resistance genes showed much similarity with antibiotic classes identified by susceptibility tests, and more than half of the specimens had consistent drug types between shotgun metagenomic sequencing and culture results.ConclusionsPathogen identification and antibiotic resistance gene prediction by shotgun metagenomic sequencing identification had the potential to diagnose microorganisms in infectious diseases, and it was especially helpful for multiple microbial co-infections and for the cases where standard culture approached failed to identify microorganisms. creator: Huan Chen creator: Jun Li creator: Shanshan Yan creator: Hui Sun creator: Chuyi Tan creator: Meidong Liu creator: Ke Liu creator: Huali Zhang creator: Mingxiang Zou creator: Xianzhong Xiao uri: https://doi.org/10.7717/peerj.11699 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: Identification of a three-gene-based prognostic model in multiple myeloma using bioinformatics analysis link: https://peerj.com/articles/11320 last-modified: 2021-06-28 description: BackgroundMultiple myeloma (MM), the second most hematological malignancy, has high incidence and remains incurable till now. The pathogenesis of MM is poorly understood. This study aimed to identify novel prognostic model for MM on gene expression profiles.MethodsGene expression datas of MM (GSE6477, GSE136337) were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in GSE6477 between case samples and normal control samples were screened by the limma package. Meanwhile, enrichment analysis was conducted, and a protein-protein interaction (PPI) network of these DEGs was established by STRING and cytoscape software. Co-expression modules of genes were built by Weighted Correlation Network Analysis (WGCNA). Key genes were identified both from hub genes and the DEGs. Univariate and multivariate Cox congression were performed to screen independent prognostic genes to construct a predictive model. The predictive power of the model was evaluated by Kaplan–Meier curve and time-dependent receiver operating characteristic (ROC) curves. Finally, univariate and multivariate Cox regression analyse were used to investigate whether the prognostic model could be independent of other clinical parameters.ResultsGSE6477, including 101 case and 15 normal control, were screened as the datasets. A total of 178 DEGs were identified, including 59 up-regulated and 119 down-regulated genes. In WGCNA analysis, module black and module purple were the most relevant modules with cancer traits, and 92 hub genes in these two modules were selected for further analysis. Next, 47 genes were chosen both from the DEGs and hub genes as key genes. Three genes (LYVE1, RNASE1, and RNASE2) were finally screened by univariate and multivariate Cox regression analyses and used to construct a risk model. In addition, the three-gene prognostic model revealed independent and accurate prognostic capacity in relation to other clinical parameters for MM patients.ConclusionIn summary, we identified and constructed a three-gene-based prognostic model that could be used to predict overall survival of MM patients. creator: Ying Pan creator: Ye Meng creator: Zhimin Zhai creator: Shudao Xiong uri: https://doi.org/10.7717/peerj.11320 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pan et al. title: Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum link: https://peerj.com/articles/11461 last-modified: 2021-06-28 description: BackgroundSugarcane is a crop of global importance and has been expanding to areas with soils containing high levels of exchangeable aluminum (Al), which is a limiting factor for crop development in acidic soils. The study of the sugarcane physiological and nutritional behavior together with patterns of gene expression in response to Al stress may provide a basis for effective strategies to increase crop productivity in acidic soils.MethodsSugarcane cultivars were evaluated for physiological parameters (photosynthesis, stomatal conductance, and transpiration), nutrient (N, P, K, Ca, Mg, and S) and Al contents in leaves and roots and gene expression, of the genes MDH, SDH by qPCR, both related to the production of organic acids, and SOD, related to oxidative stress.ResultsBrazilian sugarcane RB867515, RB928064, and RB935744 cultivars exhibited very different responses to induced stress by Al. Exposure to Al caused up-regulation (SOD and MDH) or down-regulation (SDH, MDH, and SOD), depending on the cultivar, Al level, and plant tissue. The RB867515 cultivar was the most Al-tolerant, showing no decline of nutrient content in plant tissue, photosynthesis, transpiration, and stomatal conductance after exposure to Al; it exhibited the highest Al content in the roots, and showed important MDH and SOD gene expression in the roots. RB928064 only showed low expression of SOD in roots and leaves, while RB935744 showed important expression of the SOD gene only in the leaves. Sugarcane cultivars were classified in the following descending Al-tolerance order: RB867515 > RB928064 = RB935744. These results may contribute to the obtention of Al-tolerant cultivars that can play their genetic potential in soils of low fertility and with low demand for agricultural inputs; the selection of potential plants for breeding programs; the elucidation of Al detoxification mechanisms employed by sugarcane cultivars. creator: Mariane de Souza Oliveira creator: Sâmara Vieira Rocha creator: Vanessa Karine Schneider creator: Flavio Henrique-Silva creator: Marcio Roberto Soares creator: Andrea Soares-Costa uri: https://doi.org/10.7717/peerj.11461 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Oliveira et al. title: Effects of biotransport and hydro-meteorological conditions on transport of trace elements in the Scott River (Bellsund, Spitsbergen) link: https://peerj.com/articles/11477 last-modified: 2021-06-28 description: The shaping of surface water chemistry in the Svalbard Archipelago is strongly dependent on the geology of the catchment and the process of long-range transport of atmospheric pollutants (LRATP). It was found that the dissolved trace elements in the Scott River, which catchment is characterized by a decreasing degree of glaciation, were of the natural origin (i.a. weathering and dissolution of local geological substratum). The exception was Zn originated from LRATP. The paper describe the influence changes in hydro-meteorological conditions and the presence of a seabird colony on the variability in the transport of trace elements within the Scott River catchment. The work assesses long-time fluctuations in the concentration of twenty five trace elements (i.a. Al, Cr, Cu, Pb, Sr, and Zn) from eighty-four surface water samples and their relation to changes in water discharge (Q), precipitation (P), pH, and dissolved organic carbon (DOC) at two river sites (with one being under the influence of the biotransport factor). Based on the results of matrix correlation and cluster analysis it was found that the additional load of DOC from the nesting site of Larus Argentatus in the mouth section of the river drastically changed the hydro-geochemical cycle of Co, Ni, Zn, Ga, Sr, Rb, Ba and U (0.30 < r < 0.51). Furthermore, the results of cluster analysis confirmed that the bird colony’s nesting site was strongly responsible for the presence of U, Rb, Zn, Ni and marine-derived nutrients (e.g. Se and Li). The discharge of glacier meltwater and the alkaline character of water have a negative effect on the dissolution of Li and Mn (−0.31 < r < −0.51), but positively affect the level of Rb and U (r = 0.31 and 0.35, respectively) due to it being washing out a seabird nesting colony in the mouth section of the Scott River. It was observed that the event of rises in air temperature and rain, which results in increased water discharge, caused an intense transport of the trace elements load. Moreover, results of the precipitation sensitivity coefficient factor (CF) proved that precipitation effect the occurrence of Li, Sr and U in the Scott River. creator: Sara Lehmann-Konera creator: Waldemar Kociuba creator: Stanisław Chmiel creator: Łukasz Franczak creator: Żaneta Polkowska uri: https://doi.org/10.7717/peerj.11477 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Lehmann-Konera et al. title: Characterization of the microbiome of the invasive Asian toad in Madagascar across the expansion range and comparison with a native co-occurring species link: https://peerj.com/articles/11532 last-modified: 2021-06-28 description: Biological invasions are on the rise, with each invader carrying a plethora of associated microbes. These microbes play important, yet poorly understood, ecological roles that can include assisting the hosts in colonization and adaptation processes or as possible pathogens. Understanding how these communities differ in an invasion scenario may help to understand the host’s resilience and adaptability. The Asian common toad, Duttaphrynus melanostictus is an invasive amphibian, which has recently established in Madagascar and is expected to pose numerous threats to the native ecosystems. We characterized the skin and gut bacterial communities of D. melanostictus in Toamasina (Eastern Madagascar), and compared them to those of a co-occurring native frog species, Ptychadena mascareniensis, at three sites where the toad arrived in different years. Microbial composition did not vary among sites, showing that D. melanostictus keeps a stable community across its expansion but significant differences were observed between these two amphibians. Moreover, D. melanostictus had richer and more diverse communities and also harboured a high percentage of total unique taxa (skin: 80%; gut: 52%). These differences may reflect the combination of multiple host-associated factors including microhabitat selection, skin features and dietary preferences. creator: Bárbara Santos creator: Molly C. Bletz creator: Joana Sabino-Pinto creator: Walter Cocca creator: Jean Francois Solofoniaina Fidy creator: Karen LM Freeman creator: Sven Kuenzel creator: Serge Ndriantsoa creator: Jean Noel creator: Tsanta Rakotonanahary creator: Miguel Vences creator: Angelica Crottini uri: https://doi.org/10.7717/peerj.11532 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Santos et al. title: Helicobacter pylori prevalence in healthy Mexican children: comparison between two non-invasive methods link: https://peerj.com/articles/11546 last-modified: 2021-06-28 description: BackgroundHelicobacter pylori detection in asymptomatic children with suspected infection or with symptoms that suggest gastric pathology is problematic, since most of the methods depend on the endoscopic study, an invasive and expensive method. Non-invasive methods can be a feasible alternative but must be validated. The purpose of this study was to evaluate the concordance between H. pylori DNA detection in saliva and dental plaque by PCR, with antigen detection in stool by immunochromatography, among asymptomatic children in the state of Guerrero, Mexico.MethodsDental plaque, saliva, and stool samples were obtained from 171 children between 6 and 12 years old. H. pylori detection in saliva and dental plaque was performed by PCR using specific primers for the 16S rRNA gene, while the detection in stool samples was performed by immunochromatography using the CerTest kit.ResultsWe found an overall H. pylori prevalence of 59.6% (102/171). Of the H. pylori positive children 18% (20/111) were positive in saliva samples, 28.1% (34/121) in dental plaque samples, and 50.4% (71/141) in stool samples. A higher prevalence was found in girls (64.7%, p = 0.002). Although some of the children declared some dyspeptic symptoms, these were no related to H. pylori. In conclusion, we found a high prevalence of H. pylori in asymptomatic children and the highest proportion was detected by stool antigen test, which was the most feasible method to detect H. pylori infection. creator: Verónica I. Martínez-Santos creator: Manuel Hernández Catalán creator: Luis Octavio Ojeda Salazar creator: Octavio Andrei Orozco Gómez creator: Sandra Ines Lorenzo creator: Rayver Santos Gómez creator: Norma S. Romero-Castro creator: Roxana Reyes Ríos creator: Dinorah Nashely Martinez Carrillo creator: Gloria Fernández-Tilapa uri: https://doi.org/10.7717/peerj.11546 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Martínez-Santos et al. title: Iron deficiency anemia among children aged 2–5 years in southern Ethiopia: a community-based cross-sectional study link: https://peerj.com/articles/11649 last-modified: 2021-06-28 description: BackgroundIron-deficiency anemia (IDA) is a common type of nutritional anemia in low-income countries, including Ethiopia. However, there is limited data on iron deficiency anemia prevalence and associated factors in Ethiopia, particularly for children aged 2 to 5 years.ObjectivesTo establish the prevalence of iron deficiency anemia and associated risk factors, focusing on iron-rich food consumption among children aged 2 to 5 years in southern Ethiopia.MethodsA community-based cross-sectional study was conducted in southern Ethiopia in 2017, involving 331 randomly selected children aged 2 to 5 years old. A structured questionnaire was used to collect information about the children and the households. Venous blood was collected from each child in a test tube to measure hemoglobin, ferritin, and C-reactive protein (CRP). Hemoglobin levels were determined using Hemocue®301 and adjusted for altitude. Anemia was defined as hemoglobin levels <11 g/dl. Ferritin was adjusted for inflammation based on CRP concentration and low ferritin concentration defined as adjusted ferritin concentration <12 µg/L. IDA was considered when a child had both hemoglobin level <11g/dl and low ferritin concentration. Bi-variable and multivariable logistic regression models were performed to identify factors associated with IDA and iron-rich food consumption.ResultsThe prevalence of iron deficiency anemia was 25%, and the total anemia prevalence was 32%. Only 15% of children consumed iron-rich foods in the preceding 24 h, and 30% of children consumed iron-rich foods at least once in the preceding week. IDA decreased as the height for age z-score increased (Adjusted Odds Ratio 0.7; 95% CI [0.5–0.9]). Mothers with increased educational level (AOR 1.1; 1.0–1.2) and households with increased dietary diversity (AOR 1.4; 1.2–1.6) consumed more iron-rich foods.ConclusionsIron deficiency anaemia was a moderate public health problem in southern Ethiopia, and the iron-rich food consumption was low. Interventions should focus on food supplementation and fortification, food diversification and nutritional education, and promoting women’s education. creator: Alemselam Zebdewos Orsango creator: Wossene Habtu creator: Tadesse Lejisa creator: Eskindir Loha creator: Bernt Lindtjørn creator: Ingunn Marie S. Engebretsen uri: https://doi.org/10.7717/peerj.11649 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Orsango et al. title: Combination of ferulic acid, ligustrazine and tetrahydropalmatine inhibits invasion and metastasis through MMP/TIMP signaling in endometriosis link: https://peerj.com/articles/11664 last-modified: 2021-06-28 description: BackgroundThe design of the combination of ferulic acid, ligustrazine and tetrahydropalmatine (FLT) is inspired by the Chinese herbal prescription Foshou San. Previous work has shown that FLT inhibited endometriosis growth in rat autograft models. However, the mechanism behind this is unclear. MMP/TIMP signaling is considered as the vital pathway of metastasis and invasion in endometriosis. In this study, we aim to disclose effects of FLT on MMP/TIMP signaling in invasion and metastasis during endometrial cells and xenograft endometriosis.MethodsIn vivo, effect of FLT on endometriosis was evaluated in a xenogeneic mice model. In vitro, cell viability assay was performed with an IC50 measurement of FLT in hEM15A and HEC1-B cells. The effect of FLT on invasion and metastasis was analyzed in scratch wound and transwell assay. Gene and protein expression of MMP/TIMP signaling were detected by qPCR and Western blotting.ResultsIn xenograft endometriosis, FLT reduced ectopic volume without effect on weight. FLT inhibitory effects on cell growth exhibited a dose-dependent manner in hEM15A and HEC1-B cells. IC50s of FLT in hEM15A cells were 839.30 ± 121.11 or 483.53 ±156.91 μg·ml−1 after the treatment for 24 or 48 h, respectively. In HEC1-B cells, IC50 values of 24 or 48 h were 625.20 ± 59.52 or 250.30 ± 68.12 μg·ml−1. In addition, FLT significantly inhibited invasion and metastasis in scratch wound and transwell assay. Furthermore, FLT inactivated MMP/TIMP signaling with decreasing expression of MMP-2/9, and an enhancing expression of TIMP-1.ConclusionsMMP/TIMP inactivation is a reasonable explanation for the inhibition of FLT on invasion and metastasis in endometriosis. This result reveals a potential mechanism on the role of FLT in endometriosis and may benefit for its further application. creator: Yi Tan creator: Chengling Zhang creator: Ying Zhang creator: Xueshan Dai creator: Qinghua Wei creator: Jiahui Wei creator: Pingli Xu creator: Yi Chen uri: https://doi.org/10.7717/peerj.11664 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Tan et al. title: Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize link: https://peerj.com/articles/11707 last-modified: 2021-06-28 description: As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P < 2.03 ×  10-6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize. creator: Yinchao Zhang creator: Peng Liu creator: Chen Wang creator: Na Zhang creator: Yuxiao Zhu creator: Chaoying Zou creator: Guangsheng Yuan creator: Cong Yang creator: Shibin Gao creator: Guangtang Pan creator: Langlang Ma creator: Yaou Shen uri: https://doi.org/10.7717/peerj.11707 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Farming practices affect the amino acid profiles of the aquaculture Chinese mitten crab link: https://peerj.com/articles/11605 last-modified: 2021-06-25 description: Farming operation and amino acid profiles of pond-reared Chinese mitten crabs, Eriocheir sinensis (Milne Edwards, 1853), collected from different areas in Jiangsu Province, China were investigated and compared with the aim to elucidate how farming practices affected the nutritional values of three edible tissues (muscle, hepatopancreas and gonad) of crab. The crab pond aquaculture practices including snail input, macrophytes coverage, total commercial feed, the ratio of trash fish to total feed, were much higher in Gaochun and Jintan than that in other sites (having larger pond size), which leads to higher average individual body weight and commercial yields. Further, the mean body weight, muscle weight, carapace length and width, and the ratio of gonad to hepatopancreas were significantly higher in Jintan, Suzhou and Gaochun areas than in other regions. Amino acid assessment showed that all crabs collected delivered high-quality protein (Amino acid score >1 except Valine), the main amino acids being glutamic acid, aspartic acid, and alanine. Significant differences in amino acid profiles were observed between sites, tissues and sexes. Muscles were rich in total amino acids, essential amino acids, and delicious amino acids, followed by gonads and hepatopancreas. The contents of essential amino acids in crab muscles from Gaochun, Jintan, Suzhou and Guannan were significantly higher than those from Suqian, Sihong and Xinghua. All the amino acids except Serine and Glycine were significantly higher in gonads from males than from females. The redundancy analysis revealed that the snail input, trash fish ratio to the total feed, macrophytes coverage and total trash fish supply explained 84.3% of the variation in the amino acid content and structure in crabs from Gaochun, Jintan and Suzhou. Overall, our results show that mitten crabs collected in Jiangsu province had good nutritional quality suitable for human dietary needs, and that farming practices, especially degree of fish-source protein feeding, influence the amino acids composition of crabs. creator: Qingfei Zeng creator: Yuxia Xu creator: Erik Jeppesen creator: Xiaohong Gu creator: Zhigang Mao creator: Huihui Chen uri: https://doi.org/10.7717/peerj.11605 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zeng et al. title: Insect taxonomy can be difficult: a noctuid moth (Agaristinae: Aletopus imperialis) and a geometrid moth (Sterrhinae: Cartaletis dargei) combined into a cryptic species complex in eastern Africa (Lepidoptera) link: https://peerj.com/articles/11613 last-modified: 2021-06-25 description: The systematic position of a large and strikingly coloured reddish-black moth, Cartaletis dargeiHerbulot, 2003 (Geometridae: Sterrhinae) from Tanzania, has remained questionable since its description. Here we present molecular and morphological evidence showing that Cartaletis dargei only superficially resembles true Cartaletis Warren, 1894 (the relative name currently considered a junior synonym of Aletis Hübner, 1820), which are unpalatable diurnal moths superficially resembling butterflies, and that it is misplaced in the family Geometridae. We transfer it to Noctuidae: Agaristinae, and combine it with the genus AletopusJordan, 1926, from Tanzania, as Aletopus dargei (Herbulot, 2003) (new combination). We revise the genus Aletopus to contain three species, but find that it is a cryptic species complex that needs to be revised with more extensive taxon sampling. Our results demonstrate the difficulties in interpreting and classifying biological diversity. We discuss the problems in species delimitation and the potential drivers of evolution in eastern Africa that led to phenotypic similarity in unrelated lepidopteran lineages. creator: Pasi Sihvonen creator: Leidys Murillo-Ramos creator: Niklas Wahlberg creator: Axel Hausmann creator: Alberto Zilli creator: Michael Ochse creator: Hermann S. Staude uri: https://doi.org/10.7717/peerj.11613 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sihvonen et al. title: Knowledge gaps hamper understanding the relationship between fragmentation and biodiversity loss: the case of Atlantic Forest fruit-feeding butterflies link: https://peerj.com/articles/11673 last-modified: 2021-06-25 description: BackgroundA key challenge for conservation biology in the Neotropics is to understand how deforestation affects biodiversity at various levels of landscape fragmentation. Addressing this challenge requires expanding the coverage of known biodiversity data, which remain to date restricted to a few well-surveyed regions. Here, we assess the sampling coverage and biases in biodiversity data on fruit-feeding butterflies at the Brazilian Atlantic Forest, discussing their effect on our understanding of the relationship between forest fragmentation and biodiversity at a large-scale. We hypothesize that sampling effort is biased towards large and connected fragments, which occur jointly in space at the Atlantic forest.MethodsWe used a comprehensive dataset of Atlantic Forest fruit-feeding butterfly communities to test for sampling biases towards specific geographical areas, climate conditions and landscape configurations.ResultsWe found a pattern of geographical aggregation of sampling sites, independently of scale, and a strong sampling bias towards large and connected forest fragments, located near cities and roads. Sampling gaps are particularly acute in small and disconnected forest fragments and rare climate conditions. In contrast, currently available data can provide a fair picture of fruit-feeding butterfly communities in large and connected Atlantic Forest remnants.DiscussionBiased data hamper the inference of the functional relationship between deforestation and biodiversity at a large-scale, since they are geographically clustered and have sampling gaps in small and disconnected fragments. These data are useful to inform decision-makers regarding conservation efforts to curb biodiversity loss in the Atlantic Forest. Thus, we suggest to expand sampling effort to small and disconnected forest fragments, which would allow more accurate evaluations of the effects of landscape modification. creator: Thadeu Sobral-Souza creator: Juliana Stropp creator: Jessie Pereira Santos creator: Victor Mateus Prasniewski creator: Neucir Szinwelski creator: Bruno Vilela creator: André Victor Lucci Freitas creator: Milton Cezar Ribeiro creator: Joaquín Hortal uri: https://doi.org/10.7717/peerj.11673 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sobral-Souza et al. title: Feasibility of melting fingerprint obtained from ISSR-HRM curves for marine mammal species identification link: https://peerj.com/articles/11689 last-modified: 2021-06-25 description: Currently, species identification of stranded marine mammals mostly relies on morphological features, which has inherent challenges. The use of genetic information for marine mammal species identification remains limited, therefore, new approaches that can contribute to a better monitoring of stranded species are needed. In that context, the ISSR-HRM method we have proposed offers a new approach for marine mammal species identification. Consequently, new approaches need to be developed to identify individuals at the species level. Eight primers of the ISSR markers were chosen for HRM analysis resulting in ranges of accuracy of 56.78–75.50% and 52.14–75.93% in terms of precision, while a degree of sensitivity of more than 80% was recorded when each single primer was used. The ISSR-HRM primer combinations revealed a success rate of 100% in terms of discrimination for all marine mammals included in this study. Furthermore, ISSR-HRM analysis was successfully employed in determining marine mammal discrimination among varying marine mammal species. Thus, ISSR-HRM analysis could serve as an effective alternative tool in the species identification process. This option would offer researchers a heightened level of convenience in terms of its performance and success rate. It would also offer field practice to veterinarians, biologists and other field-related people a greater degree of ease with which they could interpret results when effectively classifying stranded marine mammals. However, further studies with more samples and with a broader geographical scope will be required involving distinct populations to account for the high degree of intraspecific variability in cetaceans and to demonstrate the range of applications of this approach. creator: Wannapimol Kriangwanich creator: Kittisak Buddhachat creator: Anocha Poommouang creator: Siriwadee Chomdej creator: Chatchote Thitaram creator: Patcharaporn Kaewmong creator: Kongkiat Kittiwattanawong creator: Korakot Nganvongpanit uri: https://doi.org/10.7717/peerj.11689 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kriangwanich et al., title: Comparative phylogeography uncovers evolutionary past of Holarctic dragonflies link: https://peerj.com/articles/11338 last-modified: 2021-06-24 description: Here, we investigate the evolutionary history of five northern dragonfly species to evaluate what role the last glaciation period may have played in their current distributions. We look at the population structure and estimate divergence times for populations of the following species: Aeshna juncea (Linnaeus), Aeshna subarctica Walker, Sympetrum danae (Sulzer), Libellula quadrimaculata Linnaeus and Somatochlora sahlbergi Trybom across their Holarctic range. Our results suggest a common phylogeographic pattern across all species except for S. sahlbergi. First, we find that North American and European populations are genetically distinct and have perhaps been separated for more than 400,000 years. Second, our data suggests that, based on genetics, populations from the Greater Beringian region (Beringia, Japan and China) have haplotypes that cluster with North America or Europe depending on the species rather than having a shared geographic affinity. This is perhaps a result of fluctuating sea levels and ice sheet coverage during the Quaternary period that influenced dispersal routes and refugia. Indeed, glacial Beringia may have been as much a transit zone as a refugia for dragonflies. Somatochlora sahlbergi shows no genetic variation across its range and therefore does not share the geographic patterns found in the other circumboreal dragonflies studied here. Lastly, we discuss the taxonomic status of Sympetrum danae, which our results indicate is a species complex comprising two species, one found in Eurasia through Beringia, and the other in North America east and south of Beringia. Through this study we present a shared history among different species from different families of dragonflies, which are influenced by the climatic fluctuations of the past. creator: Manpreet Kohli creator: Marie Djernæs creator: Melissa Sanchez Herrera creator: Göran Sahlen creator: Erik Pilgrim creator: Thomas J. Simonsen creator: Kent Olsen creator: Jessica Ware uri: https://doi.org/10.7717/peerj.11338 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kohli et al. title: Comprehensive transcriptome analysis of peripheral blood unravels key lncRNAs implicated in ABPA and asthma link: https://peerj.com/articles/11453 last-modified: 2021-06-24 description: Allergic bronchopulmonary aspergillosis (ABPA) is a complex hypersensitivity lung disease caused by a fungus known as Aspergillus fumigatus. It complicates and aggravates asthma. Despite their potential associations, the underlying mechanisms of asthma developing into ABPA remain obscure. Here we performed an integrative transcriptome analysis based on three types of human peripheral blood, which derived from ABPA patients, asthmatic patients and health controls, aiming to identify crucial lncRNAs implicated in ABPA and asthma. Initially, a high-confidence dataset of lncRNAs was identified using a stringent filtering pipeline. A comparative mutational analysis revealed no significant difference among these samples. Differential expression analysis disclosed several immune-related mRNAs and lncRNAs differentially expressed in ABPA and asthma. For each disease, three sub-networks were established using differential network analysis. Many key lncRNAs implicated in ABPA and asthma were identified, respectively, i.e., AL139423.1-201, AC106028.4-201, HNRNPUL1-210, PUF60-218 and SREBF1-208. Our analysis indicated that these lncRNAs exhibits in the loss-of-function networks, and the expression of which were repressed in the occurrences of both diseases, implying their important roles in the immune-related processes in response to the occurrence of both diseases. Above all, our analysis proposed a new point of view to explore the relationship between ABPA and asthma, which might provide new clues to unveil the pathogenic mechanisms for both diseases. creator: Chen Huang creator: Dongliang Leng creator: Peiyan Zheng creator: Min Deng creator: Lu Li creator: Ge Wu creator: Baoqing Sun creator: Xiaohua Douglas Zhang uri: https://doi.org/10.7717/peerj.11453 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Huang et al. title: Alpha- and beta- adrenergic receptors regulate inflammatory responses to acute and chronic sleep fragmentation in mice link: https://peerj.com/articles/11616 last-modified: 2021-06-24 description: Sleep is a recuperative process, and its dysregulation has cognitive, metabolic, and immunological effects that are largely deleterious to human health. Epidemiological and empirical studies have suggested that sleep fragmentation (SF) as result of obstructive sleep apnea (OSA) and other sleep abnormalities leads to pronounced inflammatory responses, which are influenced by the sympathetic nervous system (SNS). However, the underlying molecular mechanisms contributing to SNS regulation of SF-induced inflammation are not fully understood. To assess the effects of the SNS upon inflammatory responses to SF, C57BL/6j female mice were placed in automated SF chambers with horizontally moving bars across the bottom of each cage at specified intervals to disrupt sleep. Mice were first subjected to either control (no bar movement), acute sleep fragmentation (ASF), or chronic sleep fragmentation (CSF) on a 12:12-h light/dark schedule. ASF involved a bar sweep every 120 s for 24 h, whereas CSF involved a bar sweep every 120 s for 12 h (during 12 L; resting period) over a period of 4 weeks. After exposure to these conditions, mice received an intraperitoneal injection of either phentolamine (5 mg/kg BW; an α-adrenergic receptor blocker), propranolol (5 mg/kg BW; a β-adrenergic receptor blocker), or vehicle (saline). Serum corticosterone concentration, brain and peripheral cytokine (IL1β, TNFα, and TGFβ) mRNA expression, and body mass were assessed. ASF and CSF significantly elevated serum corticosterone concentrations as well as cytokine mRNA expression levels compared with controls, and mice subjected to CSF had decreased body mass relative to controls. Mice subjected to CSF and treated with phentolamine or propranolol had a greater propensity for a decrease in cytokine gene expression compared with ASF, but effects were tissue-specific. Taken together, these results suggest that both α- and β-adrenergic receptors contribute to the SNS mediation of inflammatory responses, and adrenergic antagonists may effectively mitigate tissue-specific SF-mediated inflammation. creator: Nicholas D. Wheeler creator: David C. Ensminger creator: Megan M. Rowe creator: Zachary S. Wriedt creator: Noah T. Ashley uri: https://doi.org/10.7717/peerj.11616 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wheeler et al. title: Using an integrative taxonomic approach to delimit a sibling species, Mycetomoellerius mikromelanos sp. nov. (Formicidae: Attini: Attina) link: https://peerj.com/articles/11622 last-modified: 2021-06-24 description: The fungus-growing ant Mycetomoellerius (previously Trachymyrmex) zeteki (Weber 1940) has been the focus of a wide range of studies examining symbiotic partners, garden pathogens, mating frequencies, and genomics. This is in part due to the ease of collecting colonies from creek embankments and its high abundance in the Panama Canal region. The original description was based on samples collected on Barro Colorado Island (BCI), Panama. However, most subsequent studies have sampled populations on the mainland 15 km southeast of BCI. Herein we show that two sibling ant species live in sympatry on the mainland: Mycetomoellerius mikromelanos Cardenas, Schultz, & Adams and M. zeteki. This distinction was originally based on behavioral differences of workers in the field and on queen morphology (M. mikromelanos workers and queens are smaller and black while those of M. zeteki are larger and red). Authors frequently refer to either species as “M. cf. zeteki,” indicating uncertainty about identity. We used an integrative taxonomic approach to resolve this, examining worker behavior, chemical profiles of worker volatiles, molecular markers, and morphology of all castes. For the latter, we used conventional taxonomic indicators from nine measurements, six extrapolated indices, and morphological characters. We document a new observation of a Diapriinae (Hymenoptera: Diapriidae) parasitoid wasp parasitizing M. zeteki. Finally, we discuss the importance of vouchering in dependable, accessible museum collections and provide a table of previously published papers to clarify the usage of the name T. zeteki. We found that most reports of M. zeteki or M. cf. zeteki—including a genome—actually refer to the new species M. mikromelanos. creator: Cody Raul Cardenas creator: Amy Rongyan Luo creator: Tappey H. Jones creator: Ted R. Schultz creator: Rachelle M.M. Adams uri: https://doi.org/10.7717/peerj.11622 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cardenas et al. title: Expression of thermophilic two-domain laccase from Catenuloplanes japonicus in Escherichia coli and its activity against triarylmethane and azo dyes link: https://peerj.com/articles/11646 last-modified: 2021-06-24 description: BackgroundTwo-domain laccases are copper-containing oxidases found in bacteria in the beginning of 2000ths. Two-domain laccases are known for their thermal stability, wide substrate specificity and, the most important of all, their resistance to so-called «strong inhibitors» of classical fungal laccases (azides, fluorides). Low redox potential was found to be specific for all the two-domain laccases, due to which these enzymes lost the researchers’ interest as potentially applicable for various biotechnological purposes, such as bioremediation. Searching, obtaining and studying the properties of novel two-domain laccases will help to obtain an enzyme with high redox-potential allowing its practical application.MethodsA gene encoding two-domain laccase was identified in Catenuloplanes japonicus genome, cloned and expressed in an Echerichia coli strain. The protein was purified to homogeneity by immobilized metal ion affinity chromatography. Its molecular properties were studied using electrophoresis in native and denaturing conditions. Physico-chemical properties, kinetic characteristics, substrate specificity and decolorization ability of laccase towards triphenylmethane dyes were measured spectrophotometrically.ResultsA novel two-domain recombinant laccase CjSL appeared to be a multimer with a subunit molecular mass of 37 kDa. It oxidized a wide range of phenolic substrates (ferulic acid, caffeic acid, hydroquinone, catechol, etc.) at alkaline pH, while oxidizing of non phenolic substrates (K4[Fe(CN)6], ABTS) was optimal at acidic pH. The UV-visible absorption spectrum of the purified enzyme was specific for all two-domain laccases with peak of absorption at 600 nm and shoulder at 340 nm. The pH optima of CjSL for oxidation of ABTS and 2, 6-DMP substrates were 3.6 and 9.2 respectively. The temperature optimum was 70 °C. The enzyme was most stable in neutral-alkaline conditions. CjSL retained 53% activity after pre-incubation at 90 °C for 60 min. The enzyme retained 26% activity even after 60 min of boiling. The effects of NaF, NaN3, NaCl, EDTA and 1,10-phenanthroline on enzymatic activity were investigated. Only 1,10-phenanthroline reduced laccase activity under both acidic and alkaline conditions. Laccase was able to decolorize triphenylmethane dyes and azo-dyes. ABTS and syringaldehyde were effective mediators for decolorization. The efficacy of dye decolorization depended on pH of the reaction medium. creator: Liubov Igorevna Trubitsina creator: Azat Vadimovich Abdullatypov creator: Anna Petrovna Larionova creator: Ivan Vasilyevich Trubitsin creator: Sergey Valerievich Alferov creator: Olga Nikolaevna Ponamoreva creator: Alexey Arkadyevich Leontievsky uri: https://doi.org/10.7717/peerj.11646 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Trubitsina et al. title: Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum link: https://peerj.com/articles/11647 last-modified: 2021-06-24 description: BackgroundThe dehydration responsive element-binding (DREB) gene family plays a crucial role as transcription regulators and enhances plant tolerance to abiotic stresses. Although the DREB gene family has been identified and characterized in many plants, knowledge about it in Solanum tuberosum (Potato) is limited.ResultsIn the present study, StDREB gene family was comprehensively analyzed using bioinformatics approaches. We identified 66 StDREB genes through genome wide screening of the Potato genome based on the AP2 domain architecture and amino acid conservation analysis (Valine at position 14th). Phylogenetic analysis divided them into six distinct subgroups (A1–A6). The categorization of StDREB genes into six subgroups was further supported by gene structure and conserved motif analysis. Potato DREB genes were found to be distributed unevenly across 12 chromosomes. Gene duplication proved that StDREB genes experienced tandem and segmental duplication events which led to the expansion of the gene family. The Ka/Ks ratios of the orthologous pairs also demonstrated the StDREB genes were under strong purification selection in the course of evolution. Interspecies synteny analysis revealed 45 and 36 StDREB genes were orthologous to Arabidopsis and Solanum lycopersicum, respectively. Moreover, subcellular localization indicated that StDREB genes were predominantly located within the nucleus and the StDREB family’s major function was DNA binding according to gene ontology (GO) annotation.ConclusionsThis study provides a comprehensive and systematic understanding of precise molecular mechanism and functional characterization of StDREB genes in abiotic stress responses and will lead to improvement in Solanum tuberosum. creator: Nida Mushtaq creator: Faiza Munir creator: Alvina Gul creator: Rabia Amir creator: Rehan Zafar Paracha uri: https://doi.org/10.7717/peerj.11647 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Mushtaq et al. title: Prediction model of emergency mortality risk in patients with acute upper gastrointestinal bleeding: a retrospective study link: https://peerj.com/articles/11656 last-modified: 2021-06-24 description: BackgroundUpper gastrointestinal bleeding is a common presentation in emergency departments and carries significant morbidity worldwide. It is paramount that treating physicians have access to tools that can effectively evaluate the patient risk, allowing quick and effective treatments to ultimately improve their prognosis. This study aims to establish a mortality risk assessment model for patients with acute upper gastrointestinal bleeding at an emergency department.MethodsA total of 991 patients presenting with acute upper gastrointestinal bleeding between July 2016 and June 2019 were enrolled in this retrospective single-center cohort study. Patient demographics, parameters assessed at admission, laboratory test, and clinical interventions were extracted. We used the least absolute shrinkage and selection operator regression to identify predictors for establishing a nomogram for death in the emergency department or within 24 h after leaving the emergency department and a corresponding nomogram. The area under the curve of the model was calculated. A bootstrap resampling method was used to internal validation, and decision curve analysis was applied for evaluate the clinical utility of the model. We also compared our predictive model with other prognostic models, such as AIMS65, Glasgow-Blatchford bleeding score, modified Glasgow-Blatchford bleeding score, and Pre-Endoscopic Rockall Score.ResultsAmong 991 patients, 41 (4.14%) died in the emergency department or within 24 h after leaving the emergency department. Five non-zero coefficient variables (transfusion of plasma, D-dimer, albumin, potassium, age) were filtered by the least absolute shrinkage and selection operator regression analysis and used to establish a predictive model. The area under the curve for the model was 0.847 (95% confidence interval [0.794–0.900]), which is higher than that of previous models for mortality of patients with acute upper gastrointestinal bleeding. The decision curve analysis indicated the clinical usefulness of the model.ConclusionsThe nomogram based on transfusion of plasma, D-dimer, albumin, potassium, and age effectively assessed the prognosis of patients with acute upper gastrointestinal bleeding presenting at the emergency department. creator: Lan Chen creator: Han Zheng creator: Saibin Wang uri: https://doi.org/10.7717/peerj.11656 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: Intra-subject sample size effects in plantar pressure analyses link: https://peerj.com/articles/11660 last-modified: 2021-06-24 description: BackgroundRecent work using large datasets (>500 records per subject) has demonstrated seemingly high levels of step-to-step variation in peak plantar pressure within human individuals during walking. One intuitive consequence of this variation is that smaller sample sizes (e.g., 10 steps per subject) may be quantitatively and qualitatively inaccurate and fail to capture the variance in plantar pressure of individuals seen in larger data sets. However, this remains quantitatively unexplored reflecting a lack of detailed investigation of intra-subject sample size effects in plantar pressure analysis.MethodsHere we explore the sensitivity of various plantar pressure metrics to intra-subject sample size (number of steps per subject) using a random subsampling analysis. We randomly and incrementally subsample large data sets (>500 steps per subject) to compare variability in three metric types at sample sizes of 5–400 records: (1) overall whole-record mean and maximum pressure; (2) single-pixel values from five locations across the foot; and (3) the sum of pixel-level variability (measured by mean square error, MSE) from the whole plantar surface.ResultsOur results indicate that the central tendency of whole-record mean and maximum pressure within and across subjects show only minor sensitivity to sample size >200 steps. However, <200 steps, and particularly <50 steps, the range of overall mean and maximum pressure values yielded by our subsampling analysis increased considerably resulting in potential qualitative error in analyses of pressure changes with speed within-subjects and in comparisons of relative pressure magnitudes across subjects at a given speed. Our analysis revealed considerable variability in the absolute and relative response of the single pixel centroids of five regions to random subsampling. As the number of steps analysed decreased, the absolute value ranges were highest in the areas of highest pressure (medial forefoot and hallux), while the largest relative changes were seen in areas of lower pressure (the midfoot). Our pixel-level measure of variability by MSE across the whole-foot was highly sensitive to our manipulation of sample size, such that the range in MSE was exponentially larger in smaller subsamples. Random subsampling showed that the range in pixel-level MSE only came within 5% of the overall sample size in subsamples of >400 steps. The range in pixel-level MSE at low subsamples (<50) was 25–75% higher than that of the full datasets of >500 pressure records per subject. Overall, therefore, we demonstrate a high probability that the very small sample sizes (n < 20 records), which are routinely used in human and animal studies, capture a relatively low proportion of variance evident in larger plantar pressure data set, and thus may not accurately reflect the true population mean. creator: Juliet McClymont creator: Russell Savage creator: Todd C. Pataky creator: Robin Crompton creator: James Charles creator: Karl T. Bates uri: https://doi.org/10.7717/peerj.11660 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 McClymont et al. title: Genomic evidence of adaptive evolution in the reptilian SOCS gene family link: https://peerj.com/articles/11677 last-modified: 2021-06-24 description: The suppressor of the cytokine signaling (SOCS) family of proteins play an essential role in inhibiting cytokine receptor signaling by regulating immune signal pathways. Although SOCS gene functions have been examined extensively, no comprehensive study has been performed on this gene family’s molecular evolution in reptiles. In this study, we identified eight canonical SOCS genes using recently-published reptilian genomes. We used phylogenetic analysis to determine that the SOCS genes had highly conserved evolutionary dynamics that we classified into two types. We identified positive SOCS4 selection signals in whole reptile lineages and SOCS2 selection signals in the crocodilian lineage. Selective pressure analyses using the branch model and Z-test revealed that these genes were under different negative selection pressures compared to reptile lineages. We also concluded that the nature of selection pressure varies across different reptile lineages on SOCS3, and the crocodilian lineage has experienced rapid evolution. Our results may provide a theoretical foundation for further analyses of reptilian SOCS genes’ functional and molecular mechanisms, as well as their roles in reptile growth and development. creator: Tian Xia creator: Lei Zhang creator: Guolei Sun creator: Xiufeng Yang creator: Honghai Zhang uri: https://doi.org/10.7717/peerj.11677 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Xia et al. title: Malagasy Polka Dot Moths (Noctuoidea: Erebidae: Arctiinae: Syntomini) of Ambohitantely—endemism in the most important relict of Central Plateau rainforest in Madagascar link: https://peerj.com/articles/11688 last-modified: 2021-06-24 description: Malagasy Syntomini (Polka Dot Moths) are one of the largest endemic lineages of Lepidoptera on the island, belonging to the Tiger Moth subfamily (Arctiinae). This diverse radiation comprises nearly 100 valid described species that share a single ancestor. Despite a monograph in 1964 by Paul Griveaud, systematics of the group greatly needs modern revision, and their distribution on the island is still poorly known. This contribution concerns the diversity of Syntomini of the Réserve Spéciale d’Ambohitantely, which protects the largest remaining, but already highly fragmented, vestige of Central Plateau rainforest in Madagascar. Here we provide an annotated checklist of the eight species occurring in the Reserve. Two species are recorded from the forest for the first time, while five endemics are until now known only from Ambohitantely. We also describe for the first time the female of Thyrosticta vestigii Griveaud, 1964 and of Maculonaclia tampoketsya Griveaud, 1969, as well as a yellow morphotype of Thyrosticta dilata Griveaud, 1964, and we redescribe and illustrate the genitalia of the remaining species. The significance of such colour pattern variation in aposematic moths and the role of this Reserve as a local centre of diversity of Malagasy Syntomini together with its importance in the protection of the biodiversity of Madagascar are discussed. creator: Marcin Wiorek creator: Kamila Malik creator: David Lees creator: Łukasz Przybyłowicz uri: https://doi.org/10.7717/peerj.11688 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wiorek et al. title: Application of blended learning approach in clinical skills to stimulate active learning attitudes and improve clinical practice among medical students link: https://peerj.com/articles/11690 last-modified: 2021-06-24 description: BackgroundThe recent application of blended educational methods has impacted medical education and has drawn attention to a new teaching method. This teaching style presents unique opportunities and challenges. We investigated the effects of blended learning and traditional teaching methods on clinical skill development.MethodsWe sorted 200 medical students from Tongji Medical College at Huazhong University of Science and Technology into a control or experimental group. The control group was taught with a traditional lecture-based learning method and the experimental group was taught using a blended learning method. The two groups were compared after training to assess their theoretical and practical differences. A student satisfaction survey was given to participants in both groups.ResultsThe results of the experimental group’s theoretical and practical assessments were found to be significantly higher (p < 0.05) than that of the control group. The student satisfaction survey showed that blended learning was significantly more effective for acquiring relevant knowledge, enhancing student-centered learning and improving clinical practice.ConclusionsBlended learning may address deficiencies in clinical skills, make up for limited time and space, and ensure learning efficiency and quality. creator: Jie Gong creator: Manzhen Ruan creator: Wen Yang creator: Miao Peng creator: Zhen Wang creator: Lichen Ouyang creator: Guangyao Yang uri: https://doi.org/10.7717/peerj.11690 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gong et al. title: Effects of nitrogen application on phytochemical component levels and anticancer and antioxidant activities of Allium fistulosum link: https://peerj.com/articles/11706 last-modified: 2021-06-24 description: BackgroundAllium fistulosum L. has good nutritional value and is cultivated worldwide as an efficacious traditional medicinal plant. Its biological activities are attributable to its phytochemicals. Nitrogen is an essential nutrient for plant growth and development; however, the effect of nitrogen levels on the level of active components in this species is not well understood.MethodsIn this study, using urea fertilizer, we investigated the effects of different nitrogen levels (N0, N1, and N2 at 0, 130, and 260 kg/ha, respectively) on the phytochemical constituents , and antioxidant and anticancer properties of A. fistulosum.ResultsThe results suggested that nitrogen fertilizers have a significant effect on the level of total phenols and flavonoids. The analysis of the antioxidant capacity revealed that the lowest IC50 values corresponded to plants treated with the highest nitrogen concentration. Anticancer activity was investigated against cancer cell lines (HeLa and HepG2), and the extracts of A. fistulosum treated with a high nitrogen level showed the highest antiproliferative effect. Collectively, our results suggest that nitrogen fertilizer application enhanced the quality of A. fistulosum, particularly its health benefits. creator: Chen Zhao creator: Zhongjian Wang creator: Rongzong Cui creator: Le Su creator: Xin Sun creator: Orlando Borras-Hidalgo creator: Kunlun Li creator: Jianlin Wei creator: Qiulin Yue creator: Lin Zhao uri: https://doi.org/10.7717/peerj.11706 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhao et al. title: Predicting judging-perceiving of Myers-Briggs Type Indicator (MBTI) in online social forum link: https://peerj.com/articles/11382 last-modified: 2021-06-23 description: The Myers-Briggs Type Indicator (MBTI) is a well-known personality test that assigns a personality type to a user by using four traits dichotomies. For many years, people have used MBTI as an instrument to develop self-awareness and to guide their personal decisions. Previous researches have good successes in predicting Extraversion-Introversion (E/I), Sensing-Intuition (S/N) and Thinking-Feeling (T/F) dichotomies from textual data but struggled to do so with Judging-Perceiving (J/P) dichotomy. J/P dichotomy in MBTI is a non-separable part of MBTI that have significant inference on human behavior, perception and decision towards their surroundings. It is an assessment on how someone interacts with the world when making decision. This research was set out to evaluate the performance of the individual features and classifiers for J/P dichotomy in personality computing. At the end, data leakage was found in dataset originating from the Personality Forum Café, which was used in recent researches. The results obtained from the previous research on this dataset were suggested to be overly optimistic. Using the same settings, this research managed to outperform previous researches. Five machine learning algorithms were compared, and LightGBM model was recommended for the task of predicting J/P dichotomy in MBTI personality computing. creator: En Jun Choong creator: Kasturi Dewi Varathan uri: https://doi.org/10.7717/peerj.11382 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Choong and Varathan title: Identification and expression pattern analysis of miRNAs in pectoral muscle during pigeon (Columba livia) development link: https://peerj.com/articles/11438 last-modified: 2021-06-23 description: MicroRNAs (miRNAs) are a group of crucial regulators in the process of animal growth and development. However, little is known about the expression and function of miRNAs in pigeon muscles. To identify the miRNAs participating in the rapid development of pigeon pectoral muscles and quantitate their expression levels of pectoral muscles in different age stages, we performed miRNA transcriptome analysis in pigeon pectoral muscles by sequencing small RNAs over three different age stages (1-day old, 28 days old, and 2 years old). Dual-luciferase reporter assay was applied to validate the interaction between miRNA and its target gene. We identified 304 known miRNAs, 201 conserved miRNAs, and 86 novel miRNAs in pigeon pectoral muscles. 189 differentially expressed (DE) miRNAs were screened out during pigeon development. A short time-series expression miner (STEM) analysis indicated 89 DE miRNAs were significantly clustered in a progressively decreasing expression profile, and mainly enriched in biosynthesis-related GO categories and signaling pathways for MAPK and TGF-β. Dual-luciferase reporter assay indicated that a progressively down-regulated miRNA (miR-20b-5p) could directly target Krüppel-like factor 3 (KLF3) gene. To sum-up, our data expand the repertoire of pigeon miRNAs and enhance understanding of the mechanisms underlying rapid development in squabs. creator: Xun Wang creator: Peiqi Yan creator: Siyuan Feng creator: Yi Luo creator: Jiyuan Liang creator: Ling Zhao creator: Haifeng Liu creator: Qianzi Tang creator: Keren Long creator: Long Jin creator: Jideng Ma creator: Anan Jiang creator: Surong Shuai creator: Mingzhou Li uri: https://doi.org/10.7717/peerj.11438 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Comparison of fruit morphology and nutrition metabolism in different cultivars of kiwifruit across developmental stages link: https://peerj.com/articles/11538 last-modified: 2021-06-23 description: Kiwifruit (Actinidia) is becoming increasingly popular worldwide due to its favorable flavour and high vitamin C content. However, quality parameters vary among cultivars. To determine the differences in quality and metabolic parameters of kiwifruit, we monitored the growth processes of ‘Kuilv’ (Actinidia arguta), ‘Hongyang’ (Actinidia chinensis) and ‘Hayward’ (Actinidia deliciosa). We found that ‘Kuilv’ required the shortest time for fruit development, while ‘Hayward’ needed the longest time to mature. The fruit size of ‘Hayward’ was the largest and that of ‘Kuilv’ was the smallest. Furthermore, ‘Hongyang’ showed a double-S shape of dry matter accumulation, whereas ‘Kuilv’ and ‘Hayward’ showed a linear or single-S shape pattern of dry matter accumulation during development. The three cultivars demonstrated the same trend for total soluble solids accumulation, which did not rise rapidly until 90–120 days after anthesis. However, the accumulation of organic acids and soluble sugars varied among the cultivars. During later fruit development, the content of glucose, fructose and quinic acid in ‘Kuilv’ fruit was far lower than that in ‘Hongyang’ and ‘Hayward’. On the contrary, ‘Kuilv’ had the highest sucrose content among the three cultivars. At maturity, the antioxidative enzymatic systems were significantly different among the three kiwifruit cultivars. ‘Hongyang’ showed higher activities of superoxide dismutase than the other cultivars, while the catalase content of ‘Hayward’ was significantly higher than that of ‘Hongyang’ and ‘Kuilv’. These results provided knowledge that could be implemented for the marketing, handling and post-harvest technologies of the different kiwifruit cultivars. creator: Yu-fei Li creator: Weijia Jiang creator: Chunhong Liu creator: Yuqi Fu creator: Ziyuan Wang creator: Mingyuan Wang creator: Cun Chen creator: Li Guo creator: Qi-guo Zhuang creator: Zhi-bin Liu uri: https://doi.org/10.7717/peerj.11538 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Rare evidence for ‘gnawing-like’ behavior in a small-bodied theropod dinosaur link: https://peerj.com/articles/11557 last-modified: 2021-06-23 description: Mammalian carnivores show a higher degree of prey bone utilization relative to non-avian theropod dinosaurs, with this major ecological difference reflected in the frequency and morphology of tooth marks in modern and Cenozoic assemblages relative to Mesozoic ones. As such, prey bone utilization (i.e., gnawing, bone-breaking, osteophagy) may represent a key ecological strategy repeatedly exploited by mammalian carnivores but rarely in theropod dinosaurs. Here we describe an isolated adult-sized hadrosaurid pedal ungual (III-4) from the Dinosaur Park Formation (Campanian) of southern Alberta which shows a unique pattern of bite marks from a small- to medium-sized theropod dinosaur. Thirteen distinct tooth marks occur in a restricted area of the ungual, and the pattern suggests up to six repeated, high-power bites delivered to the bone. The tracemaker cannot be definitively identified, but was likely a dromaeosaurid or very young tyrannosaurid. Tooth marks on at least four other Dinosaur Park Formation hadrosaur pedal unguals are reported, but the overall frequency of occurrence in unguals (< 1%) is much lower than that reported for other bones. The pattern of tooth marks on this specimen deviates from most described theropods tooth marks, and given the low volume of meat associated with the ungual, may represent theropod prey bone utilization as part of late-stage carcass consumption, and a behavior similar to mammalian gnawing. creator: Caleb M. Brown creator: Darren H. Tanke creator: David W.E. Hone uri: https://doi.org/10.7717/peerj.11557 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Brown et al. title: Discrete simulation analysis of COVID-19 and prediction of isolation bed numbers link: https://peerj.com/articles/11629 last-modified: 2021-06-23 description: BackgroundThe outbreak of COVID-19 has been defined by the World Health Organization as a pandemic, and containment depends on traditional public health measures. However, the explosive growth of the number of infected cases in a short period of time has caused tremendous pressure on medical systems. Adequate isolation facilities are essential to control outbreaks, so this study aims to quickly estimate the demand and number of isolation beds.MethodsWe established a discrete simulation model for epidemiology. By adjusting or fitting necessary epidemic parameters, the effects of the following indicators on the development of the epidemic and the occupation of medical resources were explained: (1) incubation period, (2) response speed and detection capacity of the hospital, (3) disease healing time, and (4) population mobility. Finally, a method for predicting the number of isolation beds was summarized through multiple linear regression. This is a city level model that simulates the epidemic situation from the perspective of population mobility.ResultsThrough simulation, we show that the incubation period, response speed and detection capacity of the hospital, disease healing time, degree of population mobility, and infectivity of cured patients have different effects on the infectivity, scale, and duration of the epidemic. Among them, (1) incubation period, (2) response speed and detection capacity of the hospital, (3) disease healing time, and (4) population mobility have a significant impact on the demand and number of isolation beds (P <0.05), which agrees with the following regression equation: N = P × (−0.273 + 0.009I + 0.234M + 0.012T1 + 0.015T2) × (1 + V). creator: Xinyu Li creator: Yufeng Cai creator: Yinghe Ding creator: Jia-Da Li creator: Guoqing Huang creator: Ye Liang creator: Linyong Xu uri: https://doi.org/10.7717/peerj.11629 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Simultaneous confidence intervals for all pairwise differences between the coefficients of variation of rainfall series in Thailand link: https://peerj.com/articles/11651 last-modified: 2021-06-23 description: The delta-lognormal distribution is a combination of binomial and lognormal distributions, and so rainfall series that include zero and positive values conform to this distribution. The coefficient of variation is a good tool for measuring the dispersion of rainfall. Statistical estimation can be used not only to illustrate the dispersion of rainfall but also to describe the differences between rainfall dispersions from several areas simultaneously. Therefore, the purpose of this study is to construct simultaneous confidence intervals for all pairwise differences between the coefficients of variation of delta-lognormal distributions using three methods: fiducial generalized confidence interval, Bayesian, and the method of variance estimates recovery. Their performances were gauged by measuring their coverage probabilities together with their expected lengths via Monte Carlo simulation. The results indicate that the Bayesian credible interval using the Jeffreys’ rule prior outperformed the others in virtually all cases. Rainfall series from five regions in Thailand were used to demonstrate the efficacies of the proposed methods. creator: Noppadon Yosboonruang creator: Sa-Aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.11651 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yosboonruang et al. title: The characteristics of host lipid body biogenesis during coral-dinoflagellate endosymbiosis link: https://peerj.com/articles/11652 last-modified: 2021-06-23 description: Intracellular lipid body (LB) biogenesis depends on the symbiosis between coral hosts and their Symbiodinaceae. Therefore, understanding the mechanism(s) behind LB biosynthesis in corals can portentially elucide the drivers of cellular regulation during endosymbiosis. This study assessed LB formation in the gastrodermal tissue layer of the hermatypic coral Euphyllia glabrescens. Diel rhythmicity in LB size and distribution was observed; solar irradiation onset at sunrise initiated an increase in LB formation, which continued throughout the day and peaked after sunset at 18:00. The LBs migrated from the area near the mesoglea to the gastrodermal cell border near the coelenteron. Micro-LB biogenesis occurred in the endoplasmic reticulum (ER) of the host gastrodermal cells. A transcriptomic analysis of genes related to lipogenesis indicated that binding immunoglobulin protein (BiP) plays a key role in metabolic signaling pathways. The diel rhythmicity of LB biogenesis was correlated with ER-localized BiP expression. BiP expression peaked during the period with the largest increase in LB formation, thereby indicating that the chaperoning reaction of abnormal protein folding inside the host ER is likely involved in LB biosynthesis. These findings suggest that the host ER, central to LB formation, potentially facilitates the regulation of endosymbiosis between coral hosts and Symbiodiniaceae. creator: Hung-Kai Chen creator: Sabrina L. Rosset creator: Li-Hsueh Wang creator: Chii-Shiarng Chen uri: https://doi.org/10.7717/peerj.11652 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Improving maize’s N uptake and N use efficiency by strengthening roots’ absorption capacity when intercropped with legumes link: https://peerj.com/articles/11658 last-modified: 2021-06-23 description: Maize’s nitrogen (N) uptake can be improved through maize-legume intercropping. N uptake mechanisms require further study to better understand how legumes affect root growth and to determine maize’s absorptive capacity in maize-legume intercropping. We conducted a two-year field experiment with two N treatments (zero N (N0) and conventional N (N1)) and three planting patterns (monoculture maize (Zea mays L.) (MM), maize-soybean (Glycine max L. Merr.) strip intercropping (IMS), and maize-peanut (Arachis hypogaea L.) strip intercropping (IMP)). We sought to understand maize’s N uptake mechanisms by investigating root growth and distribution, root uptake capacity, antioxidant enzyme activity, and the antioxidant content in different maize-legume strip intercropping systems. Our results showed that on average, the N uptake of maize was significantly greater by 52.5% in IMS and by 62.4% in IMP than that in MM. The average agronomic efficiency (AE) of maize was increased by 110.5 % in IMS and by 163.4 % in IMP, compared to MM. The apparent recovery efficiency (RE) of maize was increased by 22.3% in IMS. The roots of intercropped maize were extended into soybean and peanut stands underneath the space and even between the inter-rows of legume, resulting in significantly increased root surface area density (RSAD) and total root biomass. The root-bleeding sap intensity of maize was significantly increased by 22.7–49.3% in IMS and 37.9–66.7% in IMP, compared with the MM. The nitrate-N content of maize bleeding sap was significantly greater in IMS and IMP than in MM during the 2018 crop season. The glutathione (GSH) content, superoxide dismutase (SOD), and catalase (CAT) activities in the root significantly increased in IMS and IMP compared to MM. Strip intercropping using legumes increases maize’s aboveground N uptake by promoting root growth and spatial distribution, delaying root senescence, and strengthening root uptake capacity. creator: Benchuan Zheng creator: Xiaona Zhang creator: Ping Chen creator: Qing Du creator: Ying Zhou creator: Huan Yang creator: Xiaochun Wang creator: Feng Yang creator: Taiwen Yong creator: Wenyu Yang uri: https://doi.org/10.7717/peerj.11658 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zheng et al. title: Particularities of the changes in young swimmers’ body adaptation to the stimuli of physical and mental stress in sports training process link: https://peerj.com/articles/11659 last-modified: 2021-06-23 description: BackgroundA factor favoring the swimming performance increase is the adaptation and readaptation of body energetic and functional systems to the physical and mental stress stimuli in training and competitions. The efficiency of monitoring the young swimmers’ training is based on a precise determination of the changes in the specific adaptations. The evaluation and control of the biochemical, mental and motor changes ensure the knowledge of the particularities of body adaptation in different training stages.MethodsSix young swimmers aged 12–16 years specialized in 100 m event participated in this study, conducted in four stages (E1–general, E2–specific, E3–pre-competitive and E4–competitive). The distress occurrence during adaptation to training and competition stimuli was studied in 3 levels: mental (Cohen & Williamson Test (CWT), Cohen Perceived Stress Test (CPST), Competition Anxiety Test (SCAT), Crăciun Test (CT)), motor (workouts monitoring, planning of means on training areas, anaerobic threshold assessment and average training speed calculation) and biochemical (blood lactate (La) and blood glucose (Glu) before and after effort—5 and 15 minutes; level of metabolic biochemical parameters, lymphocytes and blood glucose, and also hormonal parameters—norepinephrine, prolactin and cortisol—before and after competition effort).ResultsQuantity results of the mental, motor and biochemical tests were analyzed in groups; the quality results for each subject in dynamics were analyzed by comparison and correlation. Psychological tests showed increases in athletes’ mental behavior by 34% at CWT (p < 0.05), by 37.5% at CPST (p < 0.05), average stress level at SCAT and 70% stress in self-confidence at CT (p < 0.01). Biochemical tests revealed an ascending dynamics of La accumulated after specific effort, with peaks in E2 period (p < 0.05) and decreases in E3 compared to E2 (p < 0.05), revealing the adaptation to specific effort and the increase in anaerobic capacity. The Glu values decrease in pre-effort and increase in minute 5 and 15 post-effort (p < 0.05) in E2 and decrease in pre- and post- effort in E3 (p < 0.05), showing the effort impact on body and ability to recover after effort. Athletes’ individual metabolic results were 50% above maximum values, mainly post-effort (42%); hormonal results were 17% over maximum values, mainly post-effort (14%). Spearman’s correlative analysis of the induced-stress stimuli in workouts revealed 6.06% significant correlations at p < 0.05 and 9.1% strong connections in competitions: 4.67% significant correlations at p < 0.05 and 6.4% strong connections.ConclusionThe research demonstrated that the mental and biochemical tests results correlation with the specific motor tests facilitated the correct individualization of effort orientation in training and recovery and contributed to the knowledge of the particularities of young swimmers’ body adaptation to training and competition effort. creator: Liliana Mihailescu creator: Nicoleta Dubiţ creator: Liviu Emanuel Mihailescu creator: Vladimir Potop uri: https://doi.org/10.7717/peerj.11659 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Mihailescu et al. title: Digital mapping of soil texture in ecoforest polygons in Quebec, Canada link: https://peerj.com/articles/11685 last-modified: 2021-06-23 description: Texture strongly influences the soil’s fundamental functions in forest ecosystems. In response to the growing demand for information on soil properties for environmental modeling, more and more studies have been conducted over the past decade to assess the spatial variability of soil properties on a regional to global scale. These investigations rely on the acquisition and compilation of numerous soil field records and on the development of statistical methods and technology. Here, we used random forest machine learning algorithms to model and map particle size composition in ecoforest polygons for the entire area of managed forests in the province of Quebec, Canada. We compiled archived laboratory analyses of 29,570 mineral soil samples (17,901 sites) and a set of 33 covariates, including 22 variables related to climate, five related to soil characteristics, three to spatial position or spatial context, two to relief and topography, and one to vegetation. After five repeats of 5-fold cross-validation, results show that models that include two functionally independent values regarding particle size composition explain 60%, 34%, and 78% of the variance in sand, silt and clay fractions, respectively, with mean absolute errors ranging from 4.0% for the clay fraction to 9.5% for the sand fraction. The most important model variables are those observed in the field and those interpreted from aerial photography regarding soil characteristics, followed by those regarding elevation and climate. Our results compare favorably with those of previous soil texture mapping studies for the same territory, in which particle size composition was modeled mainly from rasterized climatic and topographic covariates. The map we provide should meet the needs of provincial forest managers, as it is compatible with the ecoforest map that constitutes the basis of information for forest management in Quebec, Canada. creator: Louis Duchesne creator: Rock Ouimet uri: https://doi.org/10.7717/peerj.11685 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Duchesne and Ouimet title: Neuroticism vulnerability factors of anxiety symptoms in adolescents and early adults: an analysis using the bi-factor model and multi-wave longitudinal model link: https://peerj.com/articles/11379 last-modified: 2021-06-22 description: BackgroundNeuroticism and stress are important vulnerability factors in the development and outcome of anxiety symptoms. However, as neuroticism is a heterogeneity trait, it is still unclear how different neuroticism factors contribute to anxiety symptoms independently or in conjunction with stress. Thus, different factors of neuroticism were extracted in the present longitudinal study using the bi-factor model. The prediction effect of these different factors on anxiety symptoms and their combined effects with stress in both adolescent and adult samples were examined.MethodParticipants (592 adolescents and 638 young adults) in Hunan China were included. In the initial assessment in our longitudinal study, participants were asked to complete measurements that assessed neuroticism, stress, and anxiety symptoms. Next, a monthly assessment of stress and anxiety symptoms was completed for the subsequent 6 months. The bi-factor model was used to extract different factors of neuroticism. The hierarchical linear model was used to analyze longitudinal multi-wave data.ResultSeveral model fit indices were used to evaluate the bi-factor model fit for neuroticism (adolescent: Tucker-Lewis index (TLI) = 0.957, comparative fit index (CFI) = 0.973, RMSEA = 0.040, Chi-Square = 80.471; early adults: TLI = 0.957, CFI = 0.973, RMSEA = 0.042, Chi-Square = 88.465). The results of hierarchical linear modeling analyses indicated that the general factor of neuroticism possessed a predictive effect on anxiety symptoms (adolescents: F = 36.77, p < 0.0001, early adults: F = 30.44, p < 0.0001); The negative effect factor only had the prediction effect on anxiety symptoms in early adults (adolescents: F = 0.65, p > 0.05; early adults: F = 4.84, p < 0.05); No prediction of self-reproach factor was found on anxiety symptoms (adolescents: F = 3.79, p > 0.05; early adults: F = 0.02, p > 0.05); the interactive effects of the general factor and stress on anxiety symptoms were only found in early adulthood (adolescents: F = 0.13, p > 0.05; early adults: F = 11.55, p < 0.01).ConclusionOur results suggested that the bi-factor model achieved a satisfactory fit for neuroticism measurement and supported that the anxiety symptoms were induced by the main effects of the general factor in both age samples and the negative factor only in adults. The general factor of neuroticism, but not the negative factor could make an additive effect for anxiety symptoms in face of stress, which meant that the homogeneity of neuroticism played a more significant role in further anxiety symptoms than heterogeneity when coping with stress. creator: Yini He creator: Ang Li creator: Kaixin Li creator: Jing Xiao uri: https://doi.org/10.7717/peerj.11379 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 He et al. title: Therapeutic effect of and mechanisms underlying the effect of miR-195-5p on subarachnoid hemorrhage-induced vasospasm and brain injury in rats link: https://peerj.com/articles/11395 last-modified: 2021-06-22 description: ObjectivesThere is much evidence suggesting that inflammation contributes majorly to subarachnoid hemorrhage (SAH)-induced cerebral vasospasm and brain injury. miRNAs have been found to modulate inflammation in several neurological disorders. This study investigated the effect of miR-195-5p on SAH-induced vasospasm and early brain injury in experimental rats.MethodsNinety-six Sprague-Dawley male rats were randomly and evenly divided into a control group (no SAH, sham surgery), a SAH only group, a SAH + NC-mimic group, and a SAH + miR-195-5p group. SAH was induced using a single injection of blood into the cisterna magna. Suspensions containing NC-mimic and miR-195-5p were intravenously injected into rat tail 30 mins after SAH was induced. We determined degree of vasospasm by averaging areas of cross-sections the basilar artery 24h after SAH. We measured basilar artery endothelial nitric oxide synthase (eNOS), inducible nitric oxide synthase (iNOS), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κ B), phosphorylated NF-κ B (p-NF-κ B), inhibitor of NF-κ B (Iκ Bα) and phosphorylated-Iκ Bα (p-Iκ Bα). Cell death assay was used to quantify the DNA fragmentation, an indicator of apoptotic cell death, in the cortex, hippocampus, and dentate gyrus. Tumor necrosis factor alpha (TNF-α) levels were measured using sample protein obtained from the cerebral cortex, hippocampus and dentate gyrus.ResultsPrior to fixation by perfusion, there were no significant physiological differences among the control and treatment groups. SAH successfully induced vasospasm and early brain injury. MiR-195-5p attenuated vasospasam-induced changes in morphology, reversed SAH-induced elevation of iNOS, p-NF-κ B, NF-κ B, and p-Iκ Bα and reversed SAH-induced suppression of eNOS in the basilar artery. Cell death assay revealed that MiR-195-5p significantly decreased SAH-induced DNA fragmentation (apoptosis) and restored TNF-α level in the dentate gyrus.ConclusionIn conclusion, MiRNA-195-5p attenuated SAH-induced vasospasm by up-regulating eNOS, down-regulating iNOS and inhibiting the NF-κ B signaling pathway. It also protected neurons by decreasing SAH-induced apoptosis-related cytokine TNF-α expression in the dentate gyrus. Further study is needed to elucidate the detail mechanism underlying miR-195-5p effect on SAH-induced vasospasm and cerebral injury. We believe that MiR-195-5p can potentially be used to manage SAH-induced cerebral vasospasm and brain injury. creator: Tai-Hsin Tsai creator: Chih-Hui Chang creator: Szu-Huai Lin creator: Yu-Feng Su creator: Yi-Cheng Tsai creator: Sheau-Fang Yang creator: Chih-Lung Lin uri: https://doi.org/10.7717/peerj.11395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tsai et al. title: Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations link: https://peerj.com/articles/11402 last-modified: 2021-06-22 description: BackgroundThe phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera.MethodsMitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups.ResultsAmong these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata. creator: Dan-Na Yu creator: Pan-Pan Yu creator: Le-Ping Zhang creator: Kenneth B. Storey creator: Xin-Yan Gao creator: Jia-Yong Zhang uri: https://doi.org/10.7717/peerj.11402 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yu et al. title: Characterization of auxin transporter AUX, PIN and PILS gene families in pineapple and evaluation of expression profiles during reproductive development and under abiotic stresses link: https://peerj.com/articles/11410 last-modified: 2021-06-22 description: Polar auxin transport in plant is mediated by influx and efflux transporters, which are encoded by AUX/LAX, PIN and PILS genes, respectively. The auxin transporter gene families have been characterized in several species from monocots and eudicots. However, a genome-wide overview of auxin transporter gene families in pineapple is not yet available. In this study, we identified a total of threeAcAUX genes, 12 AcPIN genes, and seven AcPILS genes in the pineapple genome, which were variably located on 15 chromosomes. The exon-intron structure of these genes and properties of deduced proteins were relatively conserved within the same family. Most protein motifs were widespread in the AUX, PIN or PILS proteins, whereas a few motifs were absent in only one or two proteins. Analysis of the expression profiles of these genes elucidated that several genes exhibited either preferential or tissue-specific expression patterns in vegetative and/or reproductive tissues. AcAUX2 was specifically expressed in the early developmental ovules, while AcPIN1b and AcPILS2 were strongly expressed in stamens and ovules. AcPIN9b, AcPILS1, AcPILS6a, 6b and 6c were abundantly expressed in stamens. Furthermore, qRT-PCR results showed that several genes in these families were responsive to various abiotic stresses. Comparative analysis indicated that the genes with close evolutionary relationships among pineapple, rice and Arabidopsis exhibited similar expression patterns. Overexpression of the AcAUX1 in Arabidopsis rescued the phenotype in aux1-T, and resulted in increased lateral roots in WT. These results will provide new insights into auxin transporter genes of pineapple and facilitate our understanding of their roles in pineapple growth and development. creator: Heming Zhao creator: Yan Maokai creator: Han Cheng creator: Mingliang Guo creator: Yanhui Liu creator: Lulu Wang creator: Shi Chao creator: Minqian Zhang creator: Linyi Lai creator: Yuan Qin uri: https://doi.org/10.7717/peerj.11410 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhao et al. title: Spatial-temporal variability of Mytilus galloprovincialis Lamarck 1819 populations and their accumulated sediment in northern Portugal link: https://peerj.com/articles/11499 last-modified: 2021-06-22 description: Mytilus galloprovincialis is an ecosystem engineer that provides habitat and generates environmental heterogeneity, increasing local biodiversity. Moreover, it is an economically important species representing 14% of the global production of marine bivalves. Natural drivers and the increase of anthropogenic pressures, such as sediment stress, influence its populations on rocky shores. The objective of this study was to explore the spatial-temporal patterns of different M. galloprovincialis attributes along the north of Portugal. For that purpose, six rocky shores were selected and sampled six times along the year 2019. The percentage of cover, density, spat density, condition index, clump thickness, size classes and clump sediment content were considered. Results showed the lack of seasonality in M. galloprovincialis along the north coast of Portugal. However, density, spat stage, clump thickness, condition index and size classes showed some variability among dates and shores. The percentage cover and sediment content only significantly differed among shores. Our results indicated an absence of seasonality for all the studied variables, probably because temperature was always within the optimum range for this species and the abundance of food supply in the study area independently of the season. The accumulated sediment on mussel clumps did not show any temporal variability with only significant differences among shores. The accumulated sediment was composed mainly by medium and coarse sand and it was correlated with mussel average size, condition index, but especially with the mussel clump thickness. creator: Catarina Ramos-Oliveira creator: Leandro Sampaio creator: Marcos Rubal creator: Puri Veiga uri: https://doi.org/10.7717/peerj.11499 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ramos-Oliveira et al. title: Methylation of CYP1A1 and VKORC1 promoter associated with stable dosage of warfarin in Chinese patients link: https://peerj.com/articles/11549 last-modified: 2021-06-22 description: ObjectiveTo investigate the association between DNA methylation and the stable warfarin dose through genome-wide DNA methylation analysis and pyrosequencing assay.MethodThis study included 161 patients and genome-wide DNA methylation analysis was used to screen potential warfarin dose-associated CpGs through Illumina Infinium HumanMethylation 450 K BeadChip; then, the pyrosequencing assay was used to further validate the association between the stable warfarin dose and alterations in the methylation of the screened CpGs. GenomeStudio Software and R were used to analyze the differentially methylated CpGs.ResultsThe methylation levels of CpGs surrounding the xenobiotic response element (XRE) within the CYP1A1 promoter, differed significantly between the different dose groups (P < 0.05), and these CpGs presented a positive correlation (r> 0, P < 0.05) with an increase in the stable dose of warfarin. At the VKORC1 promoter, two CpGs methylation levels were significantly different between the differential dose groups (P < 0.05), and one CpG (Chr16: 31106793) presented a significant negative correlation (r <  0, P <  0.05) among different dose (low, medium, and high) groups.ConclusionThis is a novel report of the methylation levels of six CpGs surrounding the XRE within the CYP1A1 promoter and one differential CpG at the VKORC1 promoter associated with stable warfarin dosage; these methylation levels might be applied as molecular signatures for warfarin. creator: Shiwei He creator: Yuan Wu creator: Shuidi Yan creator: Jumei Liu creator: Li Zhao creator: Huabin Xie creator: Shengxiang Ge creator: Huiming Ye uri: https://doi.org/10.7717/peerj.11549 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 He et al. title: Host migration and environmental temperature influence avian haemosporidians prevalence: a molecular survey in a Brazilian Atlantic rainforest link: https://peerj.com/articles/11555 last-modified: 2021-06-22 description: Avian haemosporidians are parasites with great capacity to spread to new environments and new hosts, being considered a good model to host-parasite interactions studies. Here, we examine avian haemosporidian parasites in a protected area covered by Restinga vegetation in northeastern Brazil, to test the hypothesis that haemosporidian prevalence is related to individual-level traits (age and breeding season), species-specific traits (diet, foraging strata, period of activity, species body weight, migratory status, and nest shape), and climate factors (temperature and rainfall). We screened DNA from 1,466 birds of 70 species captured monthly from April 2013 to March 2015. We detected an overall prevalence (Plasmodium/Haemoproteus infection) of 22% (44 host species) and parasite’s lineages were identified by mitochondrial cyt b gene. Our results showed that migration can be an important factor predicting the prevalence of Haemoproteus (Parahaemoproteus), but not Plasmodium, in hosts. Besides, the temperature, but not rainfall, seems to predict the prevalence of Plasmodium in this bird community. Neither individual-level traits analyzed nor the other species-specific traits tested were related to the probability of a bird becoming infected by haemosporidians. Our results point the importance of conducting local studies in particular environments to understand the degree of generality of factors impacting parasite prevalence in bird communities. Despite our attempts to find patterns of infection in this bird community, we should be aware that an avian haemosporidian community organization is highly complex and this complexity can be attributed to an intricate net of factors, some of which were not observed in this study and should be evaluated in future studies. We evidence the importance of looking to host-parasite relationships in a more close scale, to assure that some effects may not be obfuscated by differences in host life-history. creator: Raquel A. Rodrigues creator: Gabriel M.F. Felix creator: Mauro Pichorim creator: Patricia A. Moreira creator: Erika M. Braga uri: https://doi.org/10.7717/peerj.11555 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Rodrigues et al. title: The protective effect of Moringa oleifera plant extract against glutamate-induced DNA damage and reduced cell viability in a primary retinal ganglion cell line link: https://peerj.com/articles/11569 last-modified: 2021-06-22 description: BackgroundGlutamate excitotoxicity can cause DNA damage and is linked to many retinal and neurological disorders. In mammals, the visual signal from the eyes to the brain is conducted only by retinal ganglion cells (RGCs), which can be damaged by overstimulation of glutamate receptors.MethodologyWe examined the protective effects of Moringa oleifera seed extract against glutamate-induced DNA damage in RGCs. RGCs cells were treated with 5, 10, 50, or 100 µg/ml of M. oleifera seed extract and glutamate separately and then assessed for DNA damage using the comet assay. We also evaluated the viability of the RGCs after both treatments using the MTT test. Additionally, RGCs were pretreated with M. oleifera seed extract (50 or 100 µg/ml) for 2 h before glutamate treatment (100 µg/ml) to determine the potential protective effects of M. oleifera. We performed a phytochemical analysis of the M. oleifera seed extract using standard reactions.ResultsThe M. oleifera seed extract was found to be rich in many phytochemicals. We observed a significant dose-dependent elevation in all comet assay variables in glutamate-treated RGCs, whereas M. oleifera seed extract treatments did not show any significant change in DNA integrity.ConclusionM. oleifera seed extract demonstrates neuroprotective effects, which suggests it may help to prevent the development of many neurodegenerative disorders. creator: Musarat Amina creator: Ramesa Shafi Bhat creator: Abeer M. Al-Dbass creator: Nawal M. Musayeib creator: Rania Fahmy creator: Leen Alhadlaq creator: Afaf El-Ansary uri: https://doi.org/10.7717/peerj.11569 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Amina et al. title: Comparative anatomical and transcriptomic analyses of the color variation of leaves in Aquilaria sinensis link: https://peerj.com/articles/11586 last-modified: 2021-06-22 description: Color variation in plant tissues is a common phenomenon accompanied with a series of biological changes. In this study, a special-phenotype Aquilaria sinensis (GS) with color variation of leaf was firstly reported, and DNA barcode sequences showed GS samples could not be discriminated clearly with the normal A. sinensis sample (NS), which suggested that the variety was not the cause of the GS formation. To reveal the characteristics of GS compared to NS, the anatomical and transcriptome sequencing studies were carried out. In microscopic observation, the leaves of golden-vein-leaf sample (LGS) and normal-vein-leaf sample (LNS) showed significant differences including the area of the included phloem in midrib and the thickness parameters of palisade and spongy tissues; the stems of golden-vein-leaf sample (SGS) and normal-vein-leaf sample (SNS) were also different in many aspects such as the area of vessels and included phloem. In addition, the structure of chloroplast was more complete in the midrib of LNS than that of LGS, and some particles suspected as virus were found through transmission electron microscope as well. Genes upregulated in LGS in contrast with LNS were mainly enriched in photosynthesis. As for stems, most of the genes upregulated in SGS compared to SNS were involved in translation and metabolism processes. The pathways about photosynthesis and chlorophyll metabolism as well as some important transcription factors may explain the molecular mechanism of the unique phenotypes of leaves and the genes related to suberin biosynthesis may result in the difference of stems. In addition, the genes about defense response especially biotic stress associated with numerous pathogenesis-related (PR) genes upregulated in LGS compared to LNS indicated that the pathogen may be the internal factor. Taken together, our results reveal the macro- and micro-phenotype variations as well as gene expression profiles between GS and NS, which could provide valuable clues for elucidating the mechanism of the color variation of Aquilaria. creator: Jiaqi Gao creator: Tong Chen creator: Chao Jiang creator: Tielin Wang creator: Ou Huang creator: Xiang Zhang creator: Juan Liu uri: https://doi.org/10.7717/peerj.11586 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gao et al. title: Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.) link: https://peerj.com/articles/11593 last-modified: 2021-06-22 description: Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs. creator: Vipin Tomar creator: Guriqbal Singh Dhillon creator: Daljit Singh creator: Ravi Prakash Singh creator: Jesse Poland creator: Arun Kumar Joshi creator: Budhi Sagar Tiwari creator: Uttam Kumar uri: https://doi.org/10.7717/peerj.11593 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tomar et al. title: Continued nucleic acid tests for SARS-CoV-2 following discharge of patients with COVID-19 in Lu’an, China link: https://peerj.com/articles/11617 last-modified: 2021-06-22 description: BackgroundStudies have shown that discharged Coronavirus disease 2019 (COVID-19) patients have retested positive for SARS-CoV-2 during a follow-up RT-PCR test. We sought to assess the results of continued nucleic acid testing for SARS-CoV-2 patients in COVID-19 patients after they were discharged in Lu’an, China.MethodsWe conducted RT-PCR tests on sputum, throat swabs, fecal or anal swabs, and urine samples collected from 67 COVID-19 patients following discharge. Samples were collected on the 7th and 14th days following discharge. Patients testing positive on the 7th or 14th day were retested after 24 hours until they tested negative twice.ResultsSeventeen (17/67, 25.4%) discharged COVID-19 patients had a positive RT-PCR retest for SARS-CoV-2. Among them, 14 (82.4%) were sputum positive, five (29.4%) were throat swab positive, seven (41.2%) were fecal or anal swab positive, one (5.9%) was urine sample positive, five (29.4%) were both sputum and throat swab positive, four (23.5%) were both sputum and fecal test positive, and one (5.9%) was positive of all four specimens. The shortest period of time between discharge and the last positive test was 7 days, the longest was 48 days, and the median was 16 days. The proportion of positive fecal or anal swab tests increased from the third week. The median Cq cut-off values after onset were 26.7 after the first week, 37.7 the second to sixth week, and 40 after the sixth week. There were no significant differences between the RT-PCR retest positive group and the unrecovered positive group.ConclusionsThere was a high proportion of patients who retested positive for COVID-19. Discharge criteria have remained fairly consistent so we encourage regions affected by COVID-19 to appropriately amend their current criteria. creator: Yong Lyu creator: Danni Wang creator: Xiude Li creator: Tianqi Gong creator: Pengpeng Xu creator: Lei Liu creator: Jie Sun uri: https://doi.org/10.7717/peerj.11617 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lyu et al. title: Potency of bisresorcinol from Heliciopsis terminalis on skin aging: in vitro bioactivities and molecular interactions link: https://peerj.com/articles/11618 last-modified: 2021-06-22 description: BackgroundA bisresorcinol was isolated as the main constituent of Heliciopsis terminalis’s trunk (Proteaceae). Recently, resorcinol is applied as an active whitening agent in various cosmetic products. Because of the structural mimic to resorcinol, benefits of the bisresorcinol as an aging-enzyme antagonist were demonstrated in this study.MethodsThe bisresorcinol was purified from the crude ethanolic extract of H. terminalis’s trunk by solvent extraction and preparative chromatography, respectively. Inhibitory activity on collagenase, elastase, and tyrosinase of the compound was investigated by using a different spectroscopic technique. Molecular docking was carried out to predict possible interactions of the substance around the enzyme active sites.ResultsThe IC50 values on collagenase of the bisresorcinol and caffeic acid were 156.7 ± 0.7 and 308.9 ± 1.6 µmole L−1, respectively. For elastase activity, the IC50 of 33.2 ± 0.5 and 34.3 ± 0.3 µmole L−1 was respectively determined for the bisresorcinol and ursolic acid. The bisresorcinol was inhibitory to tyrosinase by exhibiting the IC50 of 22.8 µmole L−1, and that of 78.4 µmole L−1 was present for β-arbutin. The bisresorcinol bound to collagenase, elastase, and tyrosinase with the respective binding energies of −5.89, −5.69, and −6.57 kcal mol−1. These binding energies were in the same ranges of tested inhibitors. The aromatic phenol groups in the structure were responsible for principle as well as supporting binding interactions with enzymes. Hydrogen binding due to hydroxyl groups and π-related attractive forces from an aromatic ring(s) provided binding versatility to bisresorcinol.ConclusionThe bisresorcinol purified from H. terminalis might be useful for inclusion in cosmetic products as an aging-enzyme antagonist. creator: Charinrat Saechan creator: Uyen Hoang Nguyen creator: Zhichao Wang creator: Sachiko Sugimoto creator: Yoshi Yamano creator: Katsuyoshi Matsunami creator: Hideaki Otsuka creator: Giang Minh Phan creator: Viet Hung Pham creator: Varomyalin Tipmanee creator: Jasadee Kaewsrichan uri: https://doi.org/10.7717/peerj.11618 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Saechan et al. title: Evaluating active versus passive sources of human brucellosis in Jining City, China link: https://peerj.com/articles/11637 last-modified: 2021-06-22 description: Human brucellosis (HB) remains a serious public health concern owing to its resurgence across the globe and specifically in China. The timely detection of this disease is the key to its prevention and control. We sought to describe the differences in the demographics of high-risk populations with detected cases of HB contracted from active versus passive sources. We collected data from a large sample population from January to December 2018, in Jining City, China. We recruited patients that were at high-risk for brucellosis from three hospitals and Centers of Disease Control and Prevention (CDCs). These patients were classified into two groups: the active detection group was composed of individuals receiving brucellosis counseling at the CDCs; the passive detection group came from hospitals and high-risk HB groups. We tested a total of 2,247 subjects and 13.3% (299) presented as positive for HB. The positive rates for active and passive detection groups were 20.5% (256/1,249) and 4.3% (43/998), respectively (p < 0.001). The detection rate of confirmed HB cases varied among all groups but was higher in the active detection group than in the passive detection group when controlled for age, sex, ethnicity, education, career, and contact history with sheep or cattle (p < 0.05). Males, farmers, those with four types of contact history with sheep or cattle, and those presenting fever, hyperhidrosis and muscle pain were independent factors associated with confirmed HB cases in multivariate analysis of the active detection group. Active detection is the most common method used to detect brucellosis cases and should be applied to detect HB cases early and avoid misdiagnosis. We need to improve our understanding of brucellosis for high-risk populations. Passive HB detection can be supplemented with active detection when the cognitive changes resulting from brucellosis are low. It is important that healthcare providers understand and emphasis the timely diagnosis of HB. creator: Xihong Sun creator: Wenguo Jiang creator: Yan Li creator: Xiuchun Li creator: Qingyi Zeng creator: Juan Du creator: Aitian Yin creator: Qing-Bin Lu uri: https://doi.org/10.7717/peerj.11637 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sun et al. title: Accuracy of triggering receptor expressed on myeloid cells 1 in diagnosis and prognosis of acute myocardial infarction: a prospective cohort study link: https://peerj.com/articles/11655 last-modified: 2021-06-22 description: BackgroundAcute myocardial infarction (AMI) is one of the fatal cardiac emergencies. The detection of triggering receptor expressed on myeloid cells 1 (TREM1), a cell surface immunoglobulin that amplifies pro-inflammatory responses, screened by bioinformatics was shown to be significant in diagnosing and predicting the prognosis of AMI.MethodsGSE66360, GSE61144 and GSE60993 were downloaded from the Gene Expression Omnibus (GEO) database to explore the differentially expressed genes (DEGs) between AMI and control groups using R software. A total of 147 patients in total were prospectively enrolled from October 2018 to June 2019 and divided into two groups, the normal group (n = 35) and the AMI group (n = 112). Plasma was collected from each patient at admission and all patients received 6-month follow-up care.ResultsAccording to bioinformatic analysis, TREM1 was an important DEG in patients with AMI. Compared with the normal group, TREM1 expression was markedly increased in the AMI group (p < 0.001). TREM1 expression was positively correlated with fasting plasma glucose (FPG), glycosylated hemoglobin (HbAC), and the number of lesion vessels, although it had no correlation with Gensini score. TREM1 expression in the triple-vessels group was significantly higher than that of the single-vessel group (p < 0.05). Multiple linear regression showed that UA and HbAC were two factors influencing TREM1 expression. The ROC curve showed that TREM1 had a diagnostic significance in AMI (p < 0.001), especially in AMI patients without diabetes. Cox regression showed increased TREM1 expression was closely associated with 6-month major adverse cardiac events (MACEs) (p < 0.001).ConclusionsTREM1 is a potentially significant biomarker for the diagnosis of AMI and may be closely associated with the severity of coronary lesions and diabetes. TREM1 may also be helpful in predicting the 6-month MACEs after AMI. creator: Zhenjun Ji creator: Rui Zhang creator: Mingming Yang creator: Wenjie Zuo creator: Yuyu Yao creator: Yangyang Qu creator: Yamin Su creator: Zhuyuan Liu creator: Ziran Gu creator: Genshan Ma uri: https://doi.org/10.7717/peerj.11655 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ji et al. title: Similar seed dispersal systems by local frugivorous birds in native and alien plant species in a coastal seawall forest link: https://peerj.com/articles/11672 last-modified: 2021-06-22 description: Frugivorous birds play an important role in seed dispersal. Alien plant species’ seeds are dispersed by local birds in order to establish populations in new habitats. Alien plant species that produce fruits similar to that of native species have the potential to attract local birds, creating new mutualistic systems that are similar to the local ones. In autumn 2018 and 2019, we studied the seed dispersal systems of an alien plant species, Phytolacca americana, and a native species, Cayratia japonica, in a coastal seawall forest. Both plant species’ fruit, frugivorous bird foraging behaviors, seed germination rates, and seedling microhabitats were examined to determine whether the alien species had a similar seed dispersal system to that of the native species. Our results showed that P. americana and C. japonica had similar fruit type, color, and ripening period. There was a positive correlation between the percentage rate of fruit ripening and the percentage rate of fruit missing for both plant species, indicating that local frugivorous birds have the potential to sufficiently disperse the alien seeds to enable its spread in the coastal seawall forest (simple linear regression, P. americana: β = 0.863 ± 0.017, R2adj = 0.978, P < 0.01; C. japonica: β = 0.787 ± 0.034, R2adj = 0.898, P < 0.01). Eleven bird species consumed the fruits of the alien species or native species during the study period. Similar results were shown across alien and native species in bird foraging behavior (feeding frequency, feeding duration and first stop distance) indicating that a similar seed dispersal relationship had been established between local frugivorous and both plant species. The alien plant had a higher number of fruits carried by birds, suggesting that P. americana had a slightly higher fruit consumption than that of C. japonica (t-test, P < 0.01). Alien plant seedlings grow more abundant in forest gap microhabitat (t-test, P < 0.01). Our results confirmed that bird digestion promotes seed germination success in both plant species. Our study suggests that in a narrow coastal seawall forest, alien plant species can successfully establish their populations by relying on similar seed dispersal systems as the local species. creator: Bin Liu creator: Guohai Wang creator: Yuting An creator: Dandan Xue creator: Libo Wang creator: Changhu Lu uri: https://doi.org/10.7717/peerj.11672 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Clinical, serological and epidemiological features of hepatitis A in León, Nicaragua link: https://peerj.com/articles/11516 last-modified: 2021-06-21 description: Background and ObjectivesTo monitor and document the endemicity and disease burden of acute hepatitis A in the area of an ongoing vaccine effectiveness study in León, Nicaragua.MethodsAt community health centres in León, all children, adolescents and young adults presenting with jaundice and/or other clinical signs of hepatitis were offered free serologic screening (hepatitis A, B and C) and blood tests for liver enzymes and bilirubin. Clinical and socioeconomic data were collected with a structured questionnaire. Diagnosis of acute hepatitis A was confirmed by anti-HAV IgM testing. Using logistic regression we compared the characteristics and living conditions of acute hepatitis A cases with those of non-cases.ResultsOf 557 eligible subjects enrolled between May 2006 and March 2010, 315 (56.6%) were diagnosed with hepatitis A, 80.6% of them ≤10 years and five >18 years of age. No severe cases were encountered. Apart from jaundice (95.6%) and other signs of hepatitis A (fever, pale stool, dark urine, nausea, vomiting, anorexia), two thirds of patients had moderately raised liver enzymes. Cases occurred throughout the year, with highest incidences from August to March. Poor sanitary conditions and crowding were the main risk factors.ConclusionsIn the study area, hepatitis A is still highly endemic in young and school age children living in low socioeconomic conditions. There are, however, first indications that the endemicity level is shifting from high to high-intermediate. creator: Sophie Jaisli creator: Orlando Mayorga creator: Nadia Flores creator: Sandra de Berti creator: Gustav Frösner creator: Christian Herzog creator: Marcel Zwahlen creator: Sereina A. Herzog uri: https://doi.org/10.7717/peerj.11516 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jaisli et al. title: Clostridium butyricum relieve the visceral hypersensitivity in mice induced by Citrobacter rodentium infection with chronic stress link: https://peerj.com/articles/11585 last-modified: 2021-06-21 description: BackgroundVisceral hypersensitivity is a common symptom in patients with post-infectious irritable bowel syndrome (PI-IBS), and change of the microbiota is a vital etiological factor of it. Clostridium butyricum (C. butyricum) is one of the probiotics which is reported as the active components in the treatment of IBS, especially IBS with diarrhea. Citrobacter rodentium (C. rodentium) is an enteropathogenic bacteria which can produce self-limiting colitis in mice, which have been used to produce a PI-IBS-like mice model. Whether C. butyricum could influence the visceral hypersensitivity and gut microbiota of PI-IBS is still unknown. Our study aimed to examine whether the intervention of C. butyricum or antibiotics could affect the etiology of visceral hypersensitivity.MethodsC57BL/6 male mice were gavaged with the C. rodentium to induce a infective colitis. The C. butyricum and antibiotic compound were used to intervene the infected mice 3 days later. A 9-day chronic water avoidance stress (WAS) process was implemented to help induce the visceral hypersensitivity. The abdominal withdrawal reflex (AWR) score was assayed to indicate the visceral hypersensitivity of different groups. On the 7th, 14th, and 30th days after infection, mice feces were collected and high-throughput sequencing was carried out to analyze their gut microbiota.ResultsCombined, the C. rodentium infection plus chronic stress (WAS) could induce the visceral hypersensitivity in mice. Treatment of the C. butyricum after C. rodentium infection could relieve visceral hypersensitivity of mice, while no difference was observed in the antibiotic treatment group. The gut microbiota diversity of C. rodentium infected mice was similar to the uninfected mice, while there were different microbial communities structure between them. The Shannon and Chao indexes significantly decreased in the antibiotic treatment group compared to other groups at 7th, 14th, and 30th days post-infection, while treatment of C. butyricum could maintain the indexes within normal range. At day 14 after infection, the structure of microbiota headed towards normality after the C. butyricum treatment. After the WAS, the Shannon and Chao indexes of the control group decreased and the structure of microbiota changed. The C. butyricum treatment could prevent these changes of the gut microbiota induced by WAS.ConclusionC. butyricum could relieve the visceral hypersensitivity in mice induced by C. rodentium infection plus chronic stress. It could also remodel the microbiota change caused by the infection and chronic stress. It may be a more effective treatment strategy for PI-IBS than antibiotics. creator: Tengfei Wang creator: Lixiang Li creator: Shiyang Li creator: Hongyu Zhao creator: Junyan Qu creator: Yanan Xia creator: Yanqing Li uri: https://doi.org/10.7717/peerj.11585 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding link: https://peerj.com/articles/11619 last-modified: 2021-06-21 description: Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological identification. Here, we used data from a North Sea benthic sampling station to investigate to what extent metabarcoding data is affected by sampling bias and spatial heterogeneity. Using three grab parallels, we sampled five separate sediment samples from each grab. We then made five DNA extraction replicates from each sediment sample. Each extract was amplified targeting both the 18S SSU rRNA V1–V2 region for total eukaryotic composition, and the cytochrome c oxidase subunit I (COI) gene for metazoans only. In both datasets, extract replicates from the same sediment sample were significantly more similar than different samples from the same grab. Further, samples from different grabs were less similar than those from the same grab for 18S. Interestingly, this was not true for COI metabarcoding, where the differences within the same grab were similar to the differences between grabs. We also investigated how much of the total identified richness could be covered by extract replicates, individual sediment samples and all sediment samples from a single grab, as well as the variability of Shannon diversity and, for COI, macrofaunal biotic indices indicating environmental status. These results were largely consistent with the beta diversity findings, and show that total eukaryotic diversity can be well represented using 18S metabarcoding with a manageable number of biological replicates. Based on these results, we strongly recommend the combination of different parts of the surface of single grabs for eDNA extraction as well as several grab replicates, or alternatively box cores or similar. This will dilute the effects of dominating species and increase the coverage of alpha diversity. COI-based metabarcoding consistency was found to be lower compared to 18S, but COI macrofauna-based indices were more consistent than direct COI alpha diversity measures. creator: Jon T. Hestetun creator: Anders Lanzén creator: Thomas G. Dahlgren uri: https://doi.org/10.7717/peerj.11619 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hestetun et al. title: Recovery of antimicrobial susceptibility in methicillin-resistant Staphylococcus aureus (MRSA): a retrospective, epidemiological analysis in a secondary care hospital, Sapporo, Japan link: https://peerj.com/articles/11644 last-modified: 2021-06-21 description: Anti-methicillin-resistant Staphylococcus aureus (MRSA) drugs are critical final options for treating MRSA infection. This study investigated the percentage of all S. aureus isolates that are resistant to methicillin and also MRSA susceptibility to other antimicrobial agents in the JR Sapporo Hospital inpatient service. The inpatient service MRSA percentages for Japan, Hokkaido, and JR Sapporo Hospital from 2010–2019 were compared, exploring the annual rate of change in the MRSA percentage. We also investigated the antimicrobial use density (AUD) and its relationship with MRSA antimicrobial susceptibility in the JR Sapporo Hospital during 2019. The MRSA percentage in JR Sapporo Hospital was 61.5% (95% CI [52.6–69.7]) in 2010 but was only 51.6% (95% CI [41.6–61.5]) in 2019, which is a 1.43% (95% CI [0.42–2.43]) annual decrease (p = 0.05). Regarding the MRSA antimicrobial susceptibility rate in JR Sapporo Hospital, the highest rates of annual increase were seen for minocycline (3.11% (95% CI [2.25–3.94])) followed by fosfomycin (2.85% (95% CI [1.83–3.85])). Positive correlations with the AUD of anti-MRSA drugs were identified for susceptibility to erythromycin (p < 0.01), clindamycin (p = 0.002), and levofloxacin (p = 0.0005). A recovery of MRSA antimicrobial susceptibility was observed in our antibiogram dataset. Our study supports the potential for appropriate antimicrobial agent use in reviving MRSA antimicrobial susceptibility. creator: Yuji Koike creator: Hiroshi Nishiura uri: https://doi.org/10.7717/peerj.11644 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Koike and Nishiura title: Retinal dysfunction induced in a mouse model of unilateral common carotid artery occlusion link: https://peerj.com/articles/11665 last-modified: 2021-06-21 description: BackgroundRetinal ischemic stresses are associated with the pathogenesis of various retinal vascular diseases. To investigate pathological mechanisms of retinal ischemia, reproducible, robust and clinically significant experimental rodent models are highly needed. Previously, we established a stable murine model of chronic hypoperfusion retinal injuries by permanent unilateral common carotid artery occlusion (UCCAO) and demonstrated chronic pathological processes in the ischemic retina after the occlusion; however, retinal functional deficits and other acute retinal ischemic injuries by UCCAO still remain obscure. In this study, we attempted to examine retinal functional changes as well as acute retinal ischemic alterations such as retinal thinning, gliosis and cell death after UCCAO.MethodsAdult mice (male C57BL/6, 6–8 weeks old) were subjected to UCCAO in the right side, and retinal function was primarily measured using electroretinography for 14 days after the surgery. Furthermore, retinal thinning, gliosis and cell death were investigated using optical coherence tomography, immunohistochemistry and TUNEL assay, respectively.ResultsFunctional deficits in the unilateral right retina started to be seen 7 days after the occlusion. Specifically, the amplitude of b-wave dramatically decreased while that of a-wave was slightly affected. 14 days after the occlusion, the amplitudes of both waves and oscillatory potentials were significantly detected decreased in the unilateral right retina. Even though a change in retinal thickness was not dramatically observed among all the eyes, retinal gliosis and cell death in the unilateral right retina were substantially observed after UCCAO.ConclusionsAlong with previous retinal ischemic results in this model, UCCAO can stimulate retinal ischemia leading to functional, morphological and molecular changes in the retina. This model can be useful for the investigation of pathological mechanisms for human ischemic retinopathies and furthermore can be utilized to test new drugs for various ischemic ocular diseases. creator: Deokho Lee creator: Heonuk Jeong creator: Yukihiro Miwa creator: Ari Shinojima creator: Yusaku Katada creator: Kazuo Tsubota creator: Toshihide Kurihara uri: https://doi.org/10.7717/peerj.11665 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lee et al. title: Chemical defense in developmental stages and adult of the sea star Echinaster (Othilia) brasiliensis link: https://peerj.com/articles/11503 last-modified: 2021-06-18 description: To date, evidence regarding the performance of secondary metabolites from larval stages of sea stars as an anti-predation defense relates only to a few species/specimens from a few geographic ranges. Unfortunately, this hinders a comprehensive global understanding of this inter-specific predator-prey interaction. Here, we present laboratory experimental evidence of chemical defense action in the early developmental stages and adults of the sea star Echinaster (Othilia) brasiliensis from Brazil against sympatric and allopatric invertebrate consumers. Blastulae, early and late brachiolarias of E. (O.) brasiliensis were not consumed by the sympatric and allopatric crabs Mithraculus forceps. Blastulae were also avoided by the sympatric and allopatric individuals of the anemone Anemonia sargassensis, but not the larval stages. Extracts from embryos (blastula) and brachiolarias of E. (O.) brasiliensis from one sampled population (João Fernandes beach) significantly inhibited the consumption by sympatric M. forceps, but not by allopatric crabs and A. sargassensi anemone. In this same site, extracts from adults E. (O.) brasiliensis significantly inhibited the consumption by sympatric and allopatric specimens of the crab in a range of concentrations. Whereas equivalent extract concentrations of E. (O.) brasiliensis from other population (Itaipu beach)inhibited the predation by allopatric M. forceps, while sympatric individuals of this crab avoided the only the higher level tested. Then, early stages and adult specimens of E. (O.) brasiliensis can be chemically defended against consumers, but this action is quite variable, depending on the type (anemone or crab) and the origin of the consumer (sympatric or allopatric). creator: Renato Crespo Pereira creator: Daniela Bueno Sudatti creator: Thaise S.G. Moreira creator: Carlos Renato R. Ventura uri: https://doi.org/10.7717/peerj.11503 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pereira et al. title: Dynamics of rumen bacterial composition of yak (Bos grunniens) in response to dietary supplements during the cold season link: https://peerj.com/articles/11520 last-modified: 2021-06-18 description: This study aimed to explore the rumen bacterial community of yak in response to dietary supplements during the cold season. In addition, the rumen fermentation products were also analyzed. Twenty-one female domestic yaks were randomly divided into three groups i.e., pure grazing (GG) group, grazing plus oats hay supplement (OG) group, and grazing plus concentrate supplement group (CG). Rumen contents were collected after 90 days to assess rumen fermentation parameters and bacterial community. The GC group presented higher concentrations of ammonia nitrogen (P < 0.001), and total volatile fatty acids (TVFA) (P < 0.001), and lower rumen pH (P < 0.001) compared to other experimental groups. The CG group displayed higher proportions of propionate, butyrate, isobutyrate, and isovalerate while lower A/P ratio compared to other experimental groups. Shannon, Chao1, and ACE values were significantly lower in the OG group compared to GG and CG groups. Anosim test showed significant differences in bacterial community structure between groups but the PCA plot was not very informative to see these differences. Bacteroidetes, Proteobacteria, and Firmicutes were the three dominant phyla in all groups. The genera Oscillospira was more abundant in GG and OG groups. Higher relative abundance of Ruminococcus and Clostridium was observed in the GG group, while Ruminobacter, Corynebacterium, and Selenomonas were more abundant in the CG group. These findings will help in improving our understanding of rumen bacteria in yaks in response to changes in diet. creator: Anum Ali Ahmad creator: Jian Bo Zhang creator: Zeyi Liang creator: Chao Yang creator: Qudratullah Kalwar creator: Tariq Shah creator: Mei Du creator: Ishaq Muhammad creator: Juanshan Zheng creator: Ping Yan creator: Xue-Zhi Ding creator: Ruijun Long uri: https://doi.org/10.7717/peerj.11520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ahmad et al. title: Evolutionary and ecological processes influencing chemical defense variation in an aposematic and mimetic Heliconius butterfly link: https://peerj.com/articles/11523 last-modified: 2021-06-18 description: Chemical defences against predators underlie the evolution of aposematic coloration and mimicry, which are classic examples of adaptive evolution. Surprisingly little is known about the roles of ecological and evolutionary processes maintaining defence variation, and how they may feedback to shape the evolutionary dynamics of species. Cyanogenic Heliconius butterflies exhibit diverse warning color patterns and mimicry, thus providing a useful framework for investigating these questions. We studied intraspecific variation in de novo biosynthesized cyanogenic toxicity and its potential ecological and evolutionary sources in wild populations of Heliconius erato along environmental gradients, in common-garden broods and with feeding treatments. Our results demonstrate substantial intraspecific variation, including detectable variation among broods reared in a common garden. The latter estimate suggests considerable evolutionary potential in this trait, although predicting the response to selection is likely complicated due to the observed skewed distribution of toxicity values and the signatures of maternal contributions to the inheritance of toxicity. Larval diet contributed little to toxicity variation. Furthermore, toxicity profiles were similar along steep rainfall and altitudinal gradients, providing little evidence for these factors explaining variation in biosynthesized toxicity in natural populations. In contrast, there were striking differences in the chemical profiles of H. erato from geographically distant populations, implying potential local adaptation in the acquisition mechanisms and levels of defensive compounds. The results highlight the extensive variation and potential for adaptive evolution in defense traits for aposematic and mimetic species, which may contribute to the high diversity often found in these systems. creator: Anniina L. K. Mattila creator: Chris D. Jiggins creator: Øystein H. Opedal creator: Gabriela Montejo-Kovacevich creator: Érika C. Pinheiro de castro creator: W. Owen McMillan creator: Caroline Bacquet creator: Marjo Saastamoinen uri: https://doi.org/10.7717/peerj.11523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Mattila et al. title: The impact of mental and somatic stressors on physical activity and sedentary behaviour in adults with type 2 diabetes mellitus: a diary study link: https://peerj.com/articles/11579 last-modified: 2021-06-18 description: BackgroundAdopting an active lifestyle is key in the management of type 2 diabetes mellitus (T2DM). Nevertheless, the majority of individuals with T2DM fails to do so. Additionally, individuals with T2DM are likely to experience mental (e.g., stress) and somatic (e.g., pain) stressors. Research investigating the link between these stressors and activity levels within this group is largely lacking. Therefore, current research aimed to investigate how daily fluctuations in mental and somatic stressors predict daily levels of physical activity (PA) and sedentary behaviour among adults with T2DM.MethodsIndividuals with T2DM (N = 54) were instructed to complete a morning diary assessing mental and somatic stressors and to wear an accelerometer for 10 consecutive days. The associations between the mental and somatic stressors and participants’ levels of PA and sedentary behaviour were examined using (generalized) linear mixed effect models.ResultsValid data were provided by 38 participants. We found no evidence that intra-individual increases in mental and somatic stressors detrimentally affected participants’ activity levels. Similarly, levels of sedentary behaviour nor levels of PA were predicted by inter-individual differences in the mental and somatic stressors. creator: Louise Poppe creator: Annick L. De Paepe creator: Dimitri M.L. Van Ryckeghem creator: Delfien Van Dyck creator: Iris Maes creator: Geert Crombez uri: https://doi.org/10.7717/peerj.11579 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Poppe et al. title: Design and analysis of statistical probability distribution and non-parametric trend analysis for reference evapotranspiration link: https://peerj.com/articles/11597 last-modified: 2021-06-18 description: Accurate estimates of reference evapotranspiration are critical for water-resource management strategies such as irrigation scheduling and operation. Therefore, knowledge of events such as spatial and temporal reference evapotranspiration (ETo) and their related principle of statistical probability theory plays a vital role in amplifying sustainable irrigation planning. Spatiotemporal statistical probability distribution and its associated trends have not yet has explored in Pakistan. In this study, we have two objectives: (1) to determine the most appropriate statistical probability distribution that better describes ETo on mean monthly and seasons wise estimates for the design of irrigation system in Khyber Pakhtunkhwa, and (2) to check the trends in ETo on a monthly, seasonal, and annual basis. To check the ETo trends, we used the modified version of the Mann-Kendall and Sen Slope. We used Bayesian Kriging for spatial interpolation and propose a practical approach to the design and study of statistical probability distributions for the irrigation system and water supplies management. Also, the scheme preeminent explains ETo, on a monthly and seasonal basis. The statistical distribution that showed the best fit ETo result occupying 58.33% and 25% performance for the design of irrigation scheme in the entire study region on the monthly level was Johnson SB and Generalized Pareto, respectively. However, according to the Anderson-Darling (AD) and Kolmogorov–Smirnov (KS) goodness of fit measure, seasonal ETo estimates were preferably suited to the Burr, Johnson SB & Generalized Extreme Value. More research work must be conduct to assess the significance of this study to other fields. In conclusion, these findings might be helpful for water resource management and policymaker in future operations. creator: Sajid Gul creator: Jingli Ren creator: Neal Xiong creator: Muhammad Asif Khan uri: https://doi.org/10.7717/peerj.11597 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gul et al. title: Phytocenosis biodiversity at various water levels in mesotrophic Lake Arakhley, Lake Baikal basin, Russia link: https://peerj.com/articles/11628 last-modified: 2021-06-18 description: Small lakes have lower water levels during dry years as was the case in 2000–2020. We sought to show the biodiversity of plant communities at various water levels in Lake Arakhley. Changes in moisture content are reflected in the cyclical variations of the water level in the lake, which decreased approximately 2 m in 2017–2018. These variations affect the biological diversity of the aquatic ecosystems. We present the latest data on the state of the plant communities in this mesotrophic lake located in the drainage basin of Lake Baikal. Lake Arakhley is a freshwater lake with low mineral content and a sodium hydrocarbonate chemical composition. Changes in the nutrient concentration were related to precipitation; inflow volume and organic matter were autochtonous at low water levels. The most diverse groups of phytoplankton found in the lake were Bacillariophyta, Chlorophyta, and Chrysophyta. High biodiversity values indicate the complexity and richness of the lake’s phytoplankton community. A prevalence of Lindavia comta was observed when water levels were low and Asterionella formosa dominated in high-water years. The maximum growth depth of lacustrine vegetation decreased from 11.0 m to 4.0 m from 1967 to 2018. Decreasing water levels were accompanied by a reduction in the littoral zone, altering the communities of aquatic plants. The hydrophyte communities were monodominant in the dry years and were represented by Ceratophyllum demersum. The vegetation cover of the lake was more diverse in high-water years and variations in the lake’s water content altered the composition of biogenic substances. These changes were reflected in the lake’s phytocenosis. creator: Gazhit Ts. Tsybekmitova creator: Larisa D. Radnaeva creator: Natalya A. Tashlykova creator: Valentina G. Shiretorova creator: Balgit B. Bazarova creator: Arnold K. Tulokhonov creator: Marina O. Matveeva uri: https://doi.org/10.7717/peerj.11628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tsybekmitova et al. title: Determinants of pro-environmental behavior among excessive smartphone usage children and moderate smartphone usage children in Taiwan link: https://peerj.com/articles/11635 last-modified: 2021-06-18 description: IntroductionAlthough there is evidence linking the relationships between smartphone usage with health, stress, and academic performance, there is still inadequate knowledge about the influence on pro-environmental behaviors. This study seeks to bridge this gap by adapting the theory of attribution framework to examine the effects of personal norms, social norms, perceived behavioral control on pro-environmental behavior of smartphone usage in children.MethodsA total of 225 children aged between 11 to 12 from eight selected public primary schools at the Hsinchu Science and Industrial Park in Taiwan were surveyed. Two distinct groups (excessive versus moderate usage) were purposefully selected for comparison, of which 96 participants were excessive smartphone users while the remaining 129 were moderate smartphone users.ResultsFindings revealed significant differences between excessive and moderate smartphone usage children groups in personal norms (p < 0.001), social norms (p = 0.002), perceived behavioral control (p = 0.001), and pro-environmental behavior (p = 0.001). Findings for excessive smartphone usage children showed that social norms (β = 0.428, t = 4.096***, p < 0.001) had a direct predictive impact on pro-environmental behavior. In contrast, while there was no direct path established between personal norms and pro-environmental behavior (β = 0.177, t = 1.580, p > 0.05), as well as social norms and pro-environmental behavior for moderate smartphone usage children (β = 0.181, t = 1.924, p > 0.05), but such a relationship could be developed through the mediating effect of perceived behavioral control (β = 0.497, t = 4.471***, p < 0.001).DiscussionThe results suggested that excessive smartphone usage children lack positive perceived behavioral control, and their pro-environmental behavior could only be predicted through explicit social norms, whereas pro-environmental behavior of moderate smartphone usage children was implicitly influenced by personal norms through perceived behavioral control. creator: Wei-Ta Fang creator: Eric Ng creator: Shu-Mei Liu creator: Yi-Te Chiang creator: Mei-Chuan Chang uri: https://doi.org/10.7717/peerj.11635 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Fang et al. title: Association of heat shock protein polymorphisms with patient susceptibility to coronary artery disease comorbid depression and anxiety in a Chinese population link: https://peerj.com/articles/11636 last-modified: 2021-06-18 description: BackgroundCoronary artery disease (CAD) is one of the severe diseases that threaten human health worldwide. In addition, the associated rate of comorbidity with depression and anxiety is extremely high. Heat shock proteins (HSPs) are a group of proteins that possesses cardiovascular and psychological protection properties. The objective of this study is to determine the association of the two most widely studied HSPs, namely, HSP70 and HSP90, with CAD comorbid depression and anxiety in a Chinese population.MethodsA case-control study involving 271 CAD patients and 113 healthy individuals was conducted. The 271 CAD patients include individuals with (123) and without depression (148) and individuals with (57) and without anxiety (214). Ten single nucleotide polymorphisms (SNPs) for HSP70 and seven SNPs for HSP90 were selected and genotyped.ResultsResults revealed that the HSP70 rs10892958 C allele and HSP70 rs2236658 T allele were associated with a decreased risk of CAD (P < 0.05), whereas the G allele of the rs11218941 polymorphism was associated with an increased risk of CAD. The haplotype analysis results indicated that the haplotype TGGGC of the HSPA8 gene (coded the HSP70 family, rs4936770/rs4802/rs10892958/rs11218941/rs2236658) significantly increased the risk of CAD (P = 0.008). Among the patients with CAD, the carriers of the CC genotype for the HSP90 rs1042665 showed higher risks of anxiety than the carriers of another genotypes. However, no significant relationships were found among the CAD with depression and CAD without depression groups for the selected SNPs. These findings suggested that the genetic polymorphisms in the HSP gene, especially the HSPA8 of HSP70, contribute to CAD susceptibility and rs1042665 genetic polymorphisms might have an effect on the anxiety incidence among CAD patients. creator: Haidong Wang creator: Yudong Ba creator: Wenxiu Han creator: Haixia Zhang creator: Laiqing Zhu creator: Pei Jiang uri: https://doi.org/10.7717/peerj.11636 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Nurse educators perceptions of simulation teaching in Chinese context: benefits and barriers link: https://peerj.com/articles/11519 last-modified: 2021-06-17 description: BackgroundAlthough simulated teaching was introduced to China in the 1990s, it remains underused in nursing education. Determining how Chinese nurse educators feel about using simulation in their institutions is very important for faculty training and has the potential to influence simulation implementation.MethodThis cross-sectional descriptive study was undertaken to identify the nurse educators’ experiences in the use of simulation from various regions of China. One hundred and thirty-six nurse educators provided demographic data and information about simulation implementation within their institutions and explored the perceived barriers and benefits of simulation usage.ResultsThe survey data shows that 108 participants have used simulation in their work, but less than 92 (67.6%) of the respondents had used this teaching strategy more than ten times in last year. The study identified four factors hindering nurse faculty from simulation adoption: (1) concerns with student readiness; (2) the need for faculty team-building for simulation teaching; (3) lack of adequate simulation resources; and (4) thoughtful integration of simulation into nursing curricula.ConclusionsStudy data suggest that faculty training programs for simulation should be based on the nurse educators’ training needs, including systematically designed training topics, and the provision of hands-on learning simulation activities with expert feedback to help nurse educators achieve the competencies required for effective simulation-based education. creator: Dan Luo creator: Bing-Xiang Yang creator: Qian Liu creator: Aijing Xu creator: Yaxuan Fang creator: Ailing Wang creator: Sihong Yu creator: Ting Li uri: https://doi.org/10.7717/peerj.11519 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Luo et al. title: Application of a multilayer perceptron artificial neural network for identification of peach cultivars based on physical characteristics link: https://peerj.com/articles/11529 last-modified: 2021-06-17 description: In the fresh fruit industry, identification of fruit cultivars and fruit quality is of vital importance. In the current study, nine peach cultivars (Dixon, Early Grande, Flordaprince, Flordastar, Flordaglo, Florda 834, TropicSnow, Desertred, and Swelling) were evaluated for differences in skin color, firmness, and size. Additionally, a multilayer perceptron (MLP) artificial neural network was applied for identification of the cultivars according to these attributes. The MLP was trained with an input layer including six input nodes, a single hidden layer with six hidden nodes, and an output layer with nine output nodes. A hyperbolic tangent activation function was used in the hidden layer and the cross entropy error was given because the softmax activation function was functional to the output layer. Results showed that the cross entropy error was 0.165. The peach identification process was significantly affected by the following variables in order of contribution (normalized importance): polar diameter (100%), L∗ (89.0), b∗ (88.0%), a∗ (78.5%), firmness (71.3%), and cross diameter (37.5.3%). The MLP was found to be a viable method of peach cultivar identification and classification because few identifying attributes were required and an overall classification accuracy of 100% was achieved in the testing phase. Measurements and quantitative discrimination of peach properties are provided in this research; these data may help enhance the processing efficiency and quality of processed peaches. creator: Adel M. Al-Saif creator: Mahmoud Abdel-Sattar creator: Abdulwahed M. Aboukarima creator: Dalia H. Eshra uri: https://doi.org/10.7717/peerj.11529 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Al-Saif et al. title: A diverse Late Cretaceous vertebrate tracksite from the Winton Formation of Queensland, Australia link: https://peerj.com/articles/11544 last-modified: 2021-06-17 description: The Upper Cretaceous ‘upper’ Winton Formation of Queensland, Australia is world famous for hosting Dinosaur Stampede National Monument at Lark Quarry Conservation Park, a somewhat controversial tracksite that preserves thousands of tridactyl dinosaur tracks attributed to ornithopods and theropods. Herein, we describe the Snake Creek Tracksite, a new vertebrate ichnoassemblage from the ‘upper’ Winton Formation, originally situated on Karoola Station but now relocated to the Australian Age of Dinosaurs Museum of Natural History. This site preserves the first sauropod tracks reported from eastern Australia, a small number of theropod and ornithopod tracks, the first fossilised crocodyliform and ?turtle tracks reported from Australia, and possible lungfish and actinopterygian feeding traces. The sauropod trackways are wide-gauge, with manus tracks bearing an ungual impression on digit I, and anteriorly tapered pes tracks with straight or concave forward posterior margins. These tracks support the hypothesis that at least one sauropod taxon from the ‘upper’ Winton Formation retained a pollex claw (previously hypothesised for Diamantinasaurus matildae based on body fossils). Many of the crocodyliform trackways indicate underwater walking. The Snake Creek Tracksite reconciles the sauropod-, crocodyliform-, turtle-, and lungfish-dominated body fossil record of the ‘upper’ Winton Formation with its heretofore ornithopod- and theropod-dominated ichnofossil record. creator: Stephen F. Poropat creator: Matt A. White creator: Tim Ziegler creator: Adele H. Pentland creator: Samantha L. Rigby creator: Ruairidh J. Duncan creator: Trish Sloan creator: David A. Elliott uri: https://doi.org/10.7717/peerj.11544 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Poropat et al. title: Marathon race performance increases the amount of particulate matter deposited in the respiratory system of runners: an incentive for “clean air marathon runs” link: https://peerj.com/articles/11562 last-modified: 2021-06-17 description: BackgroundIn the last decades, marathon running has become a popular form of physical activity among people around the world. It should be noticed that the main marathon races are performed in large cities, where air quality varies considerably. It is well established that breathing polluted air results in a number of harmful effects to the human body. However, there have been no studies to show the impact of marathon run performance on the amount of the deposition of varied fractions of airborne particulate matter (PM) in the respiratory tract of runners. This is why the present study sought to determine the impact of marathon run performance in the air of varying quality on the deposition of the PM1, PM2.5, PM10 in the respiratory tract in humans.MethodsThe PM1, PM2.5 and PM10 deposition was determined in an “average runner” (with marathon performance time 4 h: 30 min) and in an “elite marathon runner” (with marathon performance time 2 h: 00 min) at rest, and during a marathon race, based on own measurements of the PM content in the air and the size-resolved DF(d) profile concept.ResultsWe have shown that breathing air containing 50 µg m−3 PM10 (a borderline value according to the 2006 WHO standard - still valid) at minute ventilation (VE) equal to 8 L min−1 when at rest, resulted in PM10deposition rate of approximately 9 µg h−1, but a marathon run of an average marathon runner with the VE = 62 L min−1 increased the deposition rate up to 45 µg h−1. In the elite runner, marathon run with the VE= 115 L min−1 increased PM10 deposition rate to 83 µg h−1. Interestingly, breathing the air containing 50 µg m−3of PM10 at the VE = 115 L min−1by the elite marathon runner during the race resulted in the same PM10deposition rate as the breathing highly polluted air containing as much as 466 µg m−3 of PM10 when at rest. Furthermore, the total PM10 deposition in the respiratory tract during a marathon race in average runners is about 22% greater (203 / 166 = 1.22) than in elite runners. According to our calculations, the concentration of PM10in the air during a marathon race that would allow one not to exceed the PM10 deposition rate of 9 µg h−1should be lower than 10 µg m−3 in the case of an average runner, and it should be lower than 5.5 µg m−3 in the case of an elite runner.ConclusionsWe conclude that a marathon run drastically increases the rate of deposition of the airborne PM in the respiratory tract of the runners, as a consequence of the huge VE generated during the race. A decrease of the PM content in the air attenuates this rate. Based on our calculations, we postulate that the PM10 content in the air during a “clean air marathon run”, involving elite marathon runners, should be below 5.5 µg m−3. creator: Jerzy A. Zoladz creator: Zenon Nieckarz uri: https://doi.org/10.7717/peerj.11562 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zoladz and Nieckarz title: HPV molecular detection from urine versus cervical samples: an alternative for HPV screening in indigenous populations link: https://peerj.com/articles/11564 last-modified: 2021-06-17 description: BackgroundCervical cancer (CC) is the fourth leading cause of death from neoplasms in women and is caused by the human papilloma virus (HPV). Several methods have been developed for the screening of cervical lesions and HPV; however, some socio-cultural factors prevent women from undergoing gynecological inspection, which results in a higher risk of mortality from cervical cancer in certain population groups as indigenous communities. This study aimed to compare the concordance in HPV detection from urine and cervical samples, to propose an alternative to cervical scraping, which is commonly used in the cervical cancer screening.MethodologyThe DNA from cervical scrapings and urine samples was extracted using the proteinase K method followed by precipitation with alcohol, phenol andchloroform; a modification of the proteinase K method was developed in the management of urine sediment. Viral genotyping was performed using INNOLipa.ResultsThe study population consisted of 108 patients from an indigenous population at southern Mexico, 32 without squamous intraepithelial lesions (NSIL) and 76 with low squamous intraepithelial lesions (LSIL). The majority of NSIL cervical scrapes were negative for HPV (90.63%), whereas more than half of LSIL cases were high-risk HPV positive (51.32%), followed by multiple infection by HR-HPV (17.11%), and multiple infection by LR- and HR-HPV (9.21%). No statistically significant relationship between the cytological diagnosis and the HPV genotypes detected in the urine samples was observed. A concordance of 68.27% for HPV positivity from urine and cervical samples was observed. Similarly, a concordance of 64.52% was observed in the grouping of HPVs by oncogenic risk. HR-HPV was detected in 71% of the urine samples from women with LSIL diagnosis, which suggests that HR-HPV detected in a urine sample could indicate the presence or risk of developing SIL.ConclusionHR-HPV detection in urine samples could be an initial approach for women at risk of developing LSIL and who, for cultural reasons, refuse to undergo a gynecological inspection. creator: Francisco I. Torres-Rojas creator: Miguel A. Mendoza-Catalán creator: Luz del C. Alarcón-Romero creator: Isela Parra-Rojas creator: Sergio Paredes-Solís creator: Marco A. Leyva-Vázquez creator: Jair E. Cortes-Arciniega creator: Carlos J. Bracamontes-Benítez creator: Berenice Illades-Aguiar uri: https://doi.org/10.7717/peerj.11564 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Torres-Rojas et al. title: Shifts in gut and vaginal microbiomes are associated with cancer recurrence time in women with ovarian cancer link: https://peerj.com/articles/11574 last-modified: 2021-06-17 description: Many studies investigating the human microbiome-cancer interface have focused on the gut microbiome and gastrointestinal cancers. Outside of human papillomavirus driving cervical cancer, little is known about the relationship between the vaginal microbiome and other gynecological cancers, such as ovarian cancer. In this retrospective study, we investigated the relationship between ovarian cancer, platinum-free interval (PFI) length, and vaginal and gut microbiomes. We observed that Lactobacillus-dominated vaginal communities were less common in women with ovarian cancer, as compared to existing datasets of similarly aged women without cancer. Primary platinum-resistance (PPR) disease is strongly associated with survivability under one year, and we found over one-third of patients with PPR (PFI < 6 months, n = 17) to have a vaginal microbiome dominated by Escherichia (>20% relative abundance), while only one platinum super-sensitive (PFI > 24 months, n = 23) patient had an Escherichia-dominated microbiome. Additionally, L. iners was associated with little, or no, gross residual disease, while other Lactobacillus species were dominant in women with >1 cm gross residual disease. In the gut microbiome, we found patients with PPR disease to have lower phylogenetic diversity than platinum-sensitive patients. The trends we observe in women with ovarian cancer and PPR disease, such as the absence of Lactobacillus and presence of Escherichia in the vaginal microbiome as well as low gut microbiome phylogenetic diversity have all been linked to other diseases and/or pro-inflammatory states, including bacterial vaginosis and autoimmune disorders. Future prospective studies are necessary to explore the translational potential and underlying mechanisms driving these associations. creator: David Jacobson creator: Kathleen Moore creator: Camille Gunderson creator: Michelle Rowland creator: Rita Austin creator: Tanvi Prasad Honap creator: Jiawu Xu creator: Christina Warinner creator: Krithivasan Sankaranarayanan creator: Cecil M. Lewis Jr uri: https://doi.org/10.7717/peerj.11574 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Jacobson et al. title: A seven-lncRNA signature for predicting Ewing’s sarcoma link: https://peerj.com/articles/11599 last-modified: 2021-06-17 description: BackgroundLong non-coding RNAs (lncRNAs) are a class of non-coding RNAs with unique characteristics. These RNA can regulate cancer cells’ survival, proliferation, invasion, metastasis, and angiogenesis and are potential diagnostic and prognostic markers. We identified a seven-lncRNA signature related to the overall survival (OS) of patients with Ewing’s sarcoma (EWS).MethodsWe used an expression profile from the Gene Expression Omnibus (GEO) database as a training cohort to screen out the OS-associated lncRNAs in EWS and further established a seven-lncRNA signature using univariate Cox regression, the least absolute shrinkage, and selection operator (LASSO) regression analysis. The prognostic lncRNA signature was validated in an external dataset from the International Cancer Genome Consortium (ICGC) as a validation cohort.ResultsWe obtained 10 survival-related lncRNAs from the Kaplan-Meier and ROC curve analysis (log-rank test P < 0.05; AUC >0.6). Univariate Cox regression and LASSO regression analyses confirmed seven key lncRNAs and we established a lncRNA signature to predict an EWS prognosis. EWS patients in the training cohort were categorized into a low-risk group or a high-risk group based on their median risk score. The high-risk group’s survival time was significantly shorter than the low-risk group’s. This seven-lncRNA signature was further confirmed by the validation cohort. The area under the curve (AUC) for this lncRNA signature was up to 0.905 in the training group and 0.697 in the 3-year validation group. The nomogram’s calibration curves demonstrated that EWS probability in the two cohorts was consistent between the nomogram prediction and actual observation.ConclusionWe screened a seven-lncRNA signature to predict the EWS patients’ prognosis. Our findings provide a new reference for the current prognostic evaluation of EWS and new direction for the diagnosis and treatment of EWS. creator: Zhihui Chen creator: Xinyu Wang creator: Guozhu Wang creator: Bin Xiao creator: Zhe Ma creator: Hongliang Huo creator: Weiwei Li uri: https://doi.org/10.7717/peerj.11599 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Knowledge about cervical cancer and awareness about human papillomavirus vaccination among medical students in Jordan link: https://peerj.com/articles/11611 last-modified: 2021-06-17 description: ObjectivesTo assess the knowledge about cervical cancer and HPV infection and the awareness towards and perceived barriers of HPV vaccination amid medical students in Jordan.MethodsThe present study is a cross-sectional survey that was conducted for a period of three months in the College of Medicine at six different universities in Jordan. Third-year to sixth-year students from these medical colleges in Jordan were invited to participate in the study.ResultsThere were 504 students that took part in the study with 42.3% being males and 57.7% females. The mean knowledge score of students in our survey was 21.4 ± 4.4 out of 34, which was categorized as a moderate level of knowledge regarding cervical cancer and HPV. Only 40.5% knew about the availability of the HPV vaccine in Jordan, and 65.9% accepted the idea that it is necessary to introduce the HPV vaccine for school girls in Jordan.ConclusionsThis study highlights that there is inadequate knowledge about cervical cancer and its screening among medical students in Jordan. Despite the limited awareness about the HPV vaccine among the study’s participants, there is a favorable opinion towards the introduction of the vaccine for school girls in Jordan. The data provide a benchmark on the level of knowledge about cervical cancer and awareness about HPV, which can be used to formulate an effective awareness program. creator: Mervat M. Alsous creator: Ahlam Ali creator: Sayer Al-Azzam creator: Reema Karasneh creator: Haneen Amawi uri: https://doi.org/10.7717/peerj.11611 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Alsous et al. title: Shifting cultivation and hunting across the savanna-forest mosaic in the Gran Sabana, Venezuela: facing changes link: https://peerj.com/articles/11612 last-modified: 2021-06-17 description: BackgroundHuman encroachment and overexploitation of natural resources in the Neotropics is constantly increasing. Indigenous communities all across the Amazon, are trapped between a population rise and a hot debate about the sustainability of hunting rates. The Garden Hunting hypothesis states that shifting cultivation schemes (conucos) used by Amazon indigenous communities may generate favorable conditions, increasing abundance of small and medium wildlife species close to the ‘gardens’ providing game for indigenous hunters.MethodsHere, we combined camera trap surveys and spatially explicit interview dataset on Pemón indigenous hunting scope and occurrence in a mosaic of savanna and forest in the Gran Sabana, Venezuela to evaluate to what extent the wildlife resource use corresponds to Garden Hunting hypothesis. We applied the Royle–Nichols model and binomial regression in order to: (1) assess whether abundance of small and medium wildlife species is higher close to conucos and (2) evaluate whether hunters select hunting localities based on accessibility to wildlife resources (closeness to conuco) more than wildlife abundance.ResultsWe find mixed evidence supporting the Garden Hunting hypothesis predictions. Abundance of small and medium species was high close to conucos but the pattern was not statistically significant for most of them. Pemón seem to hunt in locations dominated by forest, where species abundance was predicted to be higher, than in close vicinity to conucos. Hunting scope was focused on the most abundant species located close to the conuco (Cuniculus paca), but also in less abundant and unavailable species (Crax alector, Tapirus terrestris and Odocoileus virginianus).ConclusionsOur research provided the first attempt of a systematic sampling survey in the Gran Sabana, generating a quantitative dataset that not only describes the current pattern of wildlife abundance, but sets the base-line to monitor temporal and spatial change in this region of highland Amazon. We discuss the applicability of the estimates generated as a baseline as well as, environmental challenges imposed by economic, social and cultural changes such as mining encroachment for wildlife management. creator: Izabela Stachowicz creator: José R. Ferrer-Paris creator: Ada Sanchez-Mercado uri: https://doi.org/10.7717/peerj.11612 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Stachowicz et al. title: Embryonic development and perinatal skeleton in a limbless, viviparous lizard, Anguis fragilis (Squamata: Anguimorpha) link: https://peerj.com/articles/11621 last-modified: 2021-06-17 description: Despite the long history of embryological studies of squamates, many groups of this huge clade have received only limited attention. One such understudied group is the anguimorphs, a clade comprising morphologically and ecologically very diverse lizards. We describe several stages of embryonic development of Anguis fragilis, a limbless, viviparous anguimorph. Interestingly, in several clutches we observe high morphological variation in characters traditionally important in classifying embryos into developmental stages. The causes of this variation remain unknown but environmental factors do not seem to be very important. Additionally, we describe the state of ossification in several perinatal specimens of A. fragilis. The cranial skeleton is relatively poorly ossified around the time of birth, with all of the bones constituting the braincase unfused. On the other hand, the vertebral column is well ossified, with the neurocentral sutures closed and the neural arches fused in all postatlantal vertebrae. Such an advanced state of ossification may be related to the greater importance of the vertebral column in locomotion in limbless species than in ones with fully-developed limbs. Numerous factors seem to affect the state of ossification at the time of hatching or birth in squamates, including phylogenetic position, mode of reproduction and, potentially, limblessness. However, data from a greater number of species are needed to reach firmer conclusions about the relative importance of these variables in certain clades. creator: Tomasz Skawiński creator: Grzegorz Skórzewski creator: Bartosz Borczyk uri: https://doi.org/10.7717/peerj.11621 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Skawiński et al. title: Methyl jasmonate effects on sugarbeet root responses to postharvest dehydration link: https://peerj.com/articles/11623 last-modified: 2021-06-17 description: BackgroundSugarbeet (Beta vulgaris L.) roots are stored under conditions that cause roots to dehydrate, which increases postharvest losses. Although exogenous jasmonate applications can reduce drought stress in intact plants, their ability to alleviate the effects of dehydration in postharvest sugarbeet roots or other stored plant products is unknown. Research was conducted to determine whether jasmonate treatment could mitigate physiological responses to dehydration in postharvest sugarbeet roots.MethodsFreshly harvested sugarbeet roots were treated with 10 µM methyl jasmonate (MeJA) or water and stored under dehydrating and non-dehydrating storage conditions. Changes in fresh weight, respiration rate, wound healing, leaf regrowth, and proline metabolism of treated roots were investigated throughout eight weeks in storage.ResultsDehydrating storage conditions increased root weight loss, respiration rate, and proline accumulation and prevented leaf regrowth from the root crown. Under dehydrating conditions, MeJA treatment reduced root respiration rate, but only in severely dehydrated roots. MeJA treatment also hastened wound-healing, but only in the late stages of barrier formation. MeJA treatment did not impact root weight loss or proline accumulation under dehydrating conditions or leaf regrowth under non-dehydrating conditions. Both dehydration and MeJA treatment affected expression of genes involved in proline metabolism. In dehydrated roots, proline dehydrogenase expression declined 340-fold, suggesting that dehydration-induced proline accumulation was governed by reducing proline degradation. MeJA treatment altered proline biosynthetic and catabolic gene expression, with greatest effect in non-dehydrated roots. Overall, MeJA treatment alleviated physiological manifestations of dehydration stress in stored roots, although the beneficial effects were small. Postharvest jasmonate applications, therefore, are unlikely to significantly reduce dehydration-related storage losses in sugarbeet roots. creator: Fernando L. Finger creator: John D. Eide creator: Abbas M. Lafta creator: Mohamed F.R. Khan creator: Munevver Dogramaci creator: Karen K. Fugate uri: https://doi.org/10.7717/peerj.11623 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Cranial anatomy of Bolotridon frerensis, an enigmatic cynodont from the Middle Triassic of South Africa, and its phylogenetic significance link: https://peerj.com/articles/11542 last-modified: 2021-06-16 description: The cynodont fauna of the Trirachodon-Kannemeyeria Subzone of the Middle Triassic Cynognathus Assemblage Zone (AZ) is almost exclusively represented by taxa belonging to the clade Eucynodontia. However, there is one basal (non-eucynodont) cynodont known to have survived into this assemblage: the enigmatic Bolotridon frerensis. BSPG 1934-VIII-7 represents by far the most extensive specimen of B. frerensis, consisting of a partial skull with occluded lower jaw. The specimen was initially described by Broili & Schröder (1934), but their description was limited to surface details of the skull and the dental morphology. Here, by using a computed tomographic (CT) reconstruction, we redescribe this specimen, providing novel information on its palatal and internal anatomy. New endocranial characters recognized for this taxon include ridges in the nasal cavity indicating the presence of cartilaginous respiratory turbinals. New data obtained from the CT scan were incorporated into the most recently published data matrix of early non-mammalian cynodonts to test the previously unstable phylogenetic position of Bolotridon. Our phylogenetic analyses recovered Bolotridon as the sister-taxon of Eucynodontia, a more crownward position than previously hypothesized. creator: Luisa C. Pusch creator: Christian F. Kammerer creator: Jörg Fröbisch uri: https://doi.org/10.7717/peerj.11542 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pusch et al. title: Factors affecting livestock depredation by snow leopards (Panthera uncia) in the Himalayan region of Nepal link: https://peerj.com/articles/11575 last-modified: 2021-06-16 description: The snow leopard (Panthera uncia) found in central Asia is classified as vulnerable species by the International Union for Conservation of Nature (IUCN). Every year, large number of livestock are killed by snow leopards in Nepal, leading to economic loss to local communities and making human-snow leopard conflict a major threat to snow leopard conservation. We conducted formal and informal stakeholder’s interviews to gather information related to livestock depredation with the aim to map the attack sites by the snow leopard. These sites were further validated by district forest office staffs to assess sources of bias. Attack sites older than 3 years were removed from the survey. We found 109 attack sites and visited all the sites for geo location purpose (GPS points of all unique sites were taken). We maintained at least a 100 m distance between attack locations to ensure that each attack location was unique, which resulted in 86 unique locations. A total of 235 km2 was used to define livestock depredation risk zone during this study. Using Maximum Entropy (MaxEnt) modeling, we found that distance to livestock sheds, distance to paths, aspect, and distance to roads were major contributing factors to the snow leopard’s attacks. We identified 13.64 km2 as risk zone for livestock depredation from snow leopards in the study area. Furthermore, snow leopards preferred to attack livestock near livestock shelters, far from human paths and at moderate distance from motor roads. These identified attack zones should be managed both for snow leopard conservation and livestock protection in order to balance human livelihoods while protecting snow leopards and their habitats. creator: Ajay Karki creator: Saroj Panthi uri: https://doi.org/10.7717/peerj.11575 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Karki et al. title: Confirmation of age-related alterations in inhibitory control using a modified minimally delayed oculomotor response (MDOR) task link: https://peerj.com/articles/11610 last-modified: 2021-06-16 description: Considerable effort has been made to measure and understand the effects of ageing on inhibitory control using a range of behavioural tasks. In the minimally delayed oculomotor response (MDOR) task, participants are presented with a simple visual target step with variable target display duration (TDD), and instructed to saccade to the target not when it appears (a prosaccade response), but when it disappears (i.e., on target offset). Using this task, we recently found higher error rates and longer latencies for correct responses in older compared to younger participants. Here we have used a modified MDOR task, in which participants were presented with static placeholders identifying potential target positions (increasing spatial information), and three TDDs rather than two (reducing temporal predictability). We found that the yield of analysable trials was generally higher with this modified task and in 28 older (mean ± SD age: 65 ± 7 y) and 25 younger (26 ± 7 y) participants the total overall error rate was again higher in the older group (30 ± 18% vs. 16 ± 11%). An analysis of the temporal distribution of responses demonstrated a pronounced peak in error production around 150 ms (young) or 200 ms (old) after target onset. When we recalculated the error rate focusing on these errors, it was again significantly higher in the older group. The latency of correct responses (to offsets) was significantly increased in the older group, although much of this increase was accounted for by expected age-related visuomotor slowing. However, both latency and distribution data suggested that while older participants could generate increased levels of inhibition, they could not maintain these levels as efficiently as the younger participants. In 24 participants (15 old, 9 young) who completed both versions of the MDOR task, neither latency nor error rates differed significantly between versions. These results confirm an inhibitory control deficit in healthy older participants, and suggest that the dynamics of inhibitory control are also affected by ageing. The modified MDOR task yields more data while not altering basic performance parameters. creator: Paul C. Knox creator: Dongmei Liang uri: https://doi.org/10.7717/peerj.11610 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Knox and Liang title: Effects of fragrance compounds on growth of the silkworm Bombyx mori link: https://peerj.com/articles/11620 last-modified: 2021-06-16 description: Due to the contamination and biological toxicity of some fragrance compounds, the environmental and ecological problems of such compounds have attracted more and more attention. However, studies of the toxicity of fragrance compounds for insects have been limited. The toxicity of 48 fragrance compounds for the silkworm Bombyx mori were investigated in this study. All of the fragrance compounds examined had no acute toxicity for B. mori larvae, but eight of them (menthol, maltol, musk xylene, musk tibeten, dibutyl sulfide, nerolidol, ethyl vanillin, and α-amylcinnamaldehyde) exhibited chronic and lethal toxicity with LC50 values from 20 to 120 µM. In a long-term feeding study, musk tibeten, nerolidol, and musk xylene showed significant growth regulatory activity. They were also extremely harmful to the cocooning of B. mori, resulting in small, thin, and loose cocoons. Two important insect hormones, namely, juvenile hormone (JH) and 20-hydroxyecdysone (20-E), were quantified in hemolymph following chronic exposure to musk tibeten, nerolidol, and musk xylene, respectively. Musk tibeten significantly increased JH titer and decreased the 20-E titer in hemolymph, and musk xylene had a significant inhibitory effect on JH titer and increased 20-E titer. Although nerolidol had no effect on hormone levels, exogenous JH mimic nerolidol increased the physiological effects of JH and significantly slowed the growth rate of B. mori larvae. The results showed that these fragrance compounds could interfere with the insect endocrine system, leading to death and abnormal growth. The risk to insects of residual fragrance compounds in the environment is worthy of attention. creator: Zhen-peng Kai creator: Yanwei Qiu creator: Xue-wei Zhang creator: Shan-shan Chen uri: https://doi.org/10.7717/peerj.11620 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kai et al. title: Distribution of soil nutrients and erodibility factor under different soil types in an erosion region of Southeast China link: https://peerj.com/articles/11630 last-modified: 2021-06-16 description: BackgroundSoil erosion can affect the distribution of soil nutrients, which restricts soil productivity. However, it is still a challenge to understand the response of soil nutrients to erosion under different soil types.MethodsThe distribution of soil nutrients, including soil organic carbon (SOC), soil organic nitrogen (SON), and soil major elements (expressed as Al2O3, CaO, Fe2O3, K2O, Na2O, MgO, TiO2, and SiO2), were analyzed in the profiles from yellow soils, red soils, and lateritic red soils in an erosion region of Southeast China. Soil erodibility K factor calculated on the Erosion Productivity Impact Calculator (EPIC) model was used to indicate erosion risk of surface soils (0∼30 cm depth). The relationships between these soil properties were explored by Spearman’s rank correlation analysis, further to determine the factors that affected the distribution of SOC, SON, and soil major elements under different soil types.ResultsThe K factors in the red soils were significantly lower than those in the yellow soils and significantly higher than those in the lateritic red soils. The SON concentrations in the deep layer of the yellow soils were twice larger than those in the red soils and lateritic red soils, while the SOC concentrations between them were not significantly different. The concentrations of most major elements, except Al2O3 and SiO2, in the yellow soils, were significantly larger than those in the red soils and lateritic red soils. Moreover, the concentrations of major metal elements positively correlated with silt proportions and SiO2 concentrations positively correlated with sand proportions at the 0∼80 cm depth in the yellow soils. Soil major elements depended on both soil evolution and soil erosion in the surface layer of yellow soils. In the yellow soils below the 80 cm depth, soil pH positively correlated with K2O, Na2O, and CaO concentrations, while negatively correlated with Fe2O3 concentrations, which was controlled by the processes of soil evolution. The concentrations of soil major elements did not significantly correlate with soil pH or particle distribution in the red soils and lateritic red soils, likely associated with intricate factors.ConclusionsThese results suggest that soil nutrients and soil erodibility K factor in the yellow soils were higher than those in the lateritic red soils and red soils. The distribution of soil nutrients is controlled by soil erosion and soil evolution in the erosion region of Southeast China. creator: Man Liu creator: Guilin Han uri: https://doi.org/10.7717/peerj.11630 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Tropane alkaloids and terpenes synthase genes of Datura stramonium (Solanaceae) link: https://peerj.com/articles/11466 last-modified: 2021-06-15 description: BackgroundPlants have evolved physical–chemical defense to prevent/diminish damage by their enemies. Chemical defense involves the synthesis’ pathways of specialized toxic, repellent, or anti-nutritive metabolites to herbivores. Molecular evolutionary studies have revealed the origin of new genes, acquisition and functional diversification along time in different plant lineages.MethodsUsing bioinformatic tools we analyze gene divergence of tropane alkaloids (TAs) and terpene synthases (TPSs) in Datura stramonium and other species of Solanaceae; compared gene and amino acids sequence of TAs and TPSs on genomes, cDNA and proteins sequences of Viridiplantae. We analyzed two recently assembled genomes of D. stramonium (Ticumán and Teotihuacán), transcriptomes of Datura metel and genomes of other Solanaceae. Hence, we analyzed variation of TAs and TPSs to infer genes involved in plant defense and plant responses before stress. We analyzed protein modeling and molecular docking to predict interactions between H6H and ligand; we translated the sequences (Teo19488, Tic8550 and Tic8549) obtained from the two genomes of D. stramonium by using Swiss-Model and Ramachandran plot and MolProbity structure validation of Teo19488 protein model.ResultsFor TAs, we detected an expansion event in the tropinone reductase II (TRII) and the ratio synonymous/non-synonymous substitutions indicate positive selection. In contrast, a contraction event and negative selection was detected in tropinone reductase I (TRI). In Hy-oscyamine 6 b-hydroxylase (H6H), enzyme involved in the production of tropane alkaloids atropine and scopolamine, the synonymous/non-synonymous substitution ratio in its dominion indicates positive selection. For terpenes (TPS), we found 18 DsTPS in D. stramomiun and seven in D. metel; evolutionary analyses detected positive selection in TPS10.1 and TPS10.2 of D. stramonium and D. metel. Comparison of copies of TPSs in D. stramonium detected variation among them in the binding site. Duplication events and differentiation of TAs and TPSs of D. stramonium, as compared to other Solanaceae, suggest their possible involvement on adaptive evolution of defense to herbivores. Protein modeling and docking show that the three protein structures obtained of DsH6H from Teo19488, Tic-8550 and Tic8549 maintain the same interactions and the union site of 2OG-FeII_Oxy with the Hy-o ligand as in 6TTM of D. metel.ConclusionOur results indicate differences in the number of gene copies involved in the synthesis of tropane alkaloids, between the genomes of D. stramonium from two Mexican populations. More copies of genes related to the synthesis of tropane alkaloids (TRI, TRII, H6H, PMT) are found in D. stramonium as compared to Viridiplantae. Likewise, for terpene synthases (TPS), TPS-10 is duplicated in D. stramonium and D. metel. Further studies should be directed to experimentally assess gain (overexpression) or loss (silencing) of function of duplicated genes. creator: Sabina Velázquez-Márquez creator: Iván M. De-la-Cruz creator: Rosalinda Tapia-López creator: Juan Núñez-Farfán uri: https://doi.org/10.7717/peerj.11466 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Velázquez-Márquez et al. title: AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change link: https://peerj.com/articles/11534 last-modified: 2021-06-15 description: BackgroundAt any particular location, frequencies of alleles that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline frequencies of alleles across environmental gradients can act as a predictor of patterns in changed climates (typically future but possibly paleo-climates), a methodology is provided by AlleleShift of predicting changes in allele frequencies at the population level.MethodsThe prediction procedure involves a first calibration and prediction step through redundancy analysis (RDA), and a second calibration and prediction step through a generalized additive model (GAM) with a binomial family. As such, the procedure is fundamentally different to an alternative approach recently proposed to predict changes in allele frequencies from canonical correspondence analysis (CCA). The RDA step is based on the Euclidean distance that is also the typical distance used in Analysis of Molecular Variance (AMOVA). Because the RDA step or CCA approach sometimes predict negative allele frequencies, the GAM step ensures that allele frequencies are in the range of 0 to 1.ResultsAlleleShift provides data sets with predicted frequencies and several visualization methods to depict the predicted shifts in allele frequencies from baseline to changed climates. These visualizations include ‘dot plot’ graphics (function shift.dot.ggplot), pie diagrams (shift.pie.ggplot), moon diagrams (shift.moon.ggplot), ‘waffle’ diagrams (shift.waffle.ggplot) and smoothed surface diagrams of allele frequencies of baseline or future patterns in geographical space (shift.surf.ggplot). As these visualizations were generated through the ggplot2 package, methods of generating animations for a climate change time series are straightforward, as shown in the documentation of AlleleShift and in the supplemental videos.AvailabilityAlleleShift is available as an open-source R package from https://cran.r-project.org/package=AlleleShift and https://github.com/RoelandKindt/AlleleShift. Genetic input data is expected to be in the adegenet::genpop format, which can be generated from the adegenet::genind format. Climate data is available from various resources such as WorldClim and Envirem. creator: Roeland Kindt uri: https://doi.org/10.7717/peerj.11534 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kindt title: Genome-wide identification and characterization of UBP gene family in wheat (Triticum aestivum L.) link: https://peerj.com/articles/11594 last-modified: 2021-06-15 description: Ubiquitination is essential for plant growth and development. Deubiquitination cooperates with ubiquitination to regulate the ubiquitination levels of target proteins. The ubiquitin-specific protease (UBP) family is the largest group of deubiquitinases (DUBs), which perform extensive and significant roles in eukaryotic organisms. However, the UBP genes in wheat (TaUBPs) are not identified, and the functions of TaUBPs are unknown. The present study identified 97 UBP genes in the whole genome of T. aestivum. These genes were divided into 15 groups and non-randomly distributed on chromosomes of T. aestivum. Analyses of evolutionary patterns revealed that TaUBPs mainly underwent purification selection. The studies of cis-acting regulatory elements indicated that they might be involved in response to hormones. Quantitative real-time PCR (qRT-PCR) results showed that TaUBPs were differentially expressed in different tissues. Besides, several TaUBPs were significantly up-regulated when plants were treated with salicylic acid (SA), implying that these DUBs may play a role in abiotic stress responses in plants and few TaUBPs displayed differential expression after viral infection. Furthermore, TaUBP1A.1 (TraesCS1A02G432600.1) silenced by virus-induced gene silencing (VIGS) facilitates Chinese wheat mosaic virus (CWMV) infection in wheat, indicating that TaUBP1A.1 may be involved in a defense mechanism against viruses. This study comprehensively analyzed the UBP gene family in wheat and provided a basis for further research of TaUBPs functions in wheat plant response to viral infection. creator: Miaoze Xu creator: Peng Jin creator: Tingting Liu creator: Shiqi Gao creator: Tianye Zhang creator: Fan Zhang creator: Xiaolei Han creator: Long He creator: Jianping Chen creator: Jian Yang uri: https://doi.org/10.7717/peerj.11594 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: Denouncing the use of field-specific effect size distributions to inform magnitude link: https://peerj.com/articles/11383 last-modified: 2021-06-14 description: An effect size (ES) provides valuable information regarding the magnitude of effects, with the interpretation of magnitude being the most important. Interpreting ES magnitude requires combining information from the numerical ES value and the context of the research. However, many researchers adopt popular benchmarks such as those proposed by Cohen. More recently, researchers have proposed interpreting ES magnitude relative to the distribution of observed ESs in a specific field, creating unique benchmarks for declaring effects small, medium or large. However, there is no valid rationale whatsoever for this approach. This study was carried out in two parts: (1) We identified articles that proposed the use of field-specific ES distributions to interpret magnitude (primary articles); and (2) We identified articles that cited the primary articles and classified them by year and publication type. The first type consisted of methodological papers. The second type included articles that interpreted ES magnitude using the approach proposed in the primary articles. There has been a steady increase in the number of methodological and substantial articles discussing or adopting the approach of interpreting ES magnitude by considering the distribution of observed ES in that field, even though the approach is devoid of a theoretical framework. It is hoped that this research will restrict the practice of interpreting ES magnitude relative to the distribution of ES values in a field and instead encourage researchers to interpret such by considering the specific context of the study. creator: Emily Panzarella creator: Nataly Beribisky creator: Robert A. Cribbie uri: https://doi.org/10.7717/peerj.11383 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Panzarella et al. title: Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation link: https://peerj.com/articles/11447 last-modified: 2021-06-14 description: BackgroundViruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs).ResultsThe in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k-mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k-mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ∼5% for virome and ∼75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. For viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from ∼95% (whole genomes) down to ∼80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes.ConclusionTogether, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses ‘hidden’ in diverse sequence datasets. creator: Akbar Adjie Pratama creator: Benjamin Bolduc creator: Ahmed A. Zayed creator: Zhi-Ping Zhong creator: Jiarong Guo creator: Dean R. Vik creator: Maria Consuelo Gazitúa creator: James M. Wainaina creator: Simon Roux creator: Matthew B. Sullivan uri: https://doi.org/10.7717/peerj.11447 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pratama et al. title: Chemistry of enzymatic browning in longan fruit as a function of pericarp pH and dehydration and its prevention by essential oil, an alternative approach to SO2 fumigation link: https://peerj.com/articles/11539 last-modified: 2021-06-14 description: BackgroundLongan fruit is a rich source of bioactive compounds; however, enzymatic browning of pericarp and microbial decay have limited its postharvest life. SO2 has widely been used to overcome these limitations; however, due to safety and regulatory concerns, alternative means should be identified. In this study, antioxidant and antimicrobial properties of thymol (TH) essential oil were investigated against the enzymatic browning and decay of longan fruit.MethodsFruits were coated with TH (4%) for 5 min, sealed in polyethylene (PE) packages and stored at 4 °C for 42 d. Fruits immersed in distilled water (DW) and stored in PE were used as control.ResultsTH extended the postharvest life of longan to 42 d than 28 d in DW. TH residues decreased from 142 to 11.17 mg kg–1, while no residues were found at day 42. TH significantly (P ≤ 0.05) reduced the respiration rate, inhibited polyphenol oxidase (PPO) and peroxidase (POD) enzyme activities, sustained high phenols/flavonoids and prevented pericarp browning (BI) than DW. TH also effectively (P ≤ 0.05) maintained the color values, firmness of peel and aril, total soluble solids (TSS), titratable acidity (TA), inhibited decay incidence (DI) and resulted in lower ethanol content than DW. BI as a function of pericarp pH was highly correlated; pH and BI (r = 0. 97), with PPO (r = 0.93) and with water loss (r = 0.99). A high coefficient of correlation of BI was found with the pericarp pH, enzymes, phenolic, water loss and decay incidence with ethanol. TH could be the best alternative to SO2 and other synthetic preservatives. creator: Muhammad Rafiullah Khan creator: Chongxing Huang creator: Yasser Durrani creator: Ali Muhammad uri: https://doi.org/10.7717/peerj.11539 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Khan et al. title: Genetic connectivity between Atlantic bluefin tuna larvae spawned in the Gulf of Mexico and in the Mediterranean Sea link: https://peerj.com/articles/11568 last-modified: 2021-06-14 description: The highly migratory Atlantic bluefin tuna (ABFT) is currently managed as two distinct stocks, in accordance with natal homing behavior and population structuring despite the absence of barriers to gene flow. Larval fish are valuable biological material for tuna molecular ecology. However, they have hardly been used to decipher the ABFT population structure, although providing the genetic signal from successful breeders. For the first time, cooperative field collection of tuna larvae during 2014 in the main spawning area for each stock, the Gulf of Mexico (GOM) and the Mediterranean Sea (MED), enabled us to assess the ABFT genetic structure in a precise temporal and spatial frame exclusively through larvae. Partitioning of genetic diversity at nuclear microsatellite loci and in the mitochondrial control region in larvae spawned contemporarily resulted in low significant fixation indices supporting connectivity between spawners in the main reproduction area for each population. No structuring was detected within the GOM after segregating nuclear diversity in larvae spawned in two hydrographically distinct regions, the eastern GOM (eGOM) and the western GOM (wGOM), with the larvae from eGOM being more similar to those collected in the MED than the larvae from wGOM. We performed clustering of genetically characterized ABFT larvae through Bayesian analysis and by Discriminant Analysis of Principal Components (DAPC) supporting the existence of favorable areas for mixing of ABFT spawners from Western and Eastern stocks, leading to gene flow and apparent connectivity between weakly structured populations. Our findings suggest that the eastern GOM is more prone for the mixing of breeders from the two ABFT populations. Conservation of this valuable resource exploited for centuries calls for intensification of tuna ichthyoplankton research and standardization of genetic tools for monitoring population dynamics. creator: Carolina Johnstone creator: Montse Pérez creator: Estrella Malca creator: José María Quintanilla creator: Trika Gerard creator: Diego Lozano-Peral creator: Francisco Alemany creator: John Lamkin creator: Alberto García creator: Raúl Laiz-Carrión uri: https://doi.org/10.7717/peerj.11568 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Johnstone et al. title: Biological control of important fungal diseases of potato and raspberry by two Bacillus velezensis strains link: https://peerj.com/articles/11578 last-modified: 2021-06-14 description: Stem canker and black scurf caused by Rhizoctonia solani are the important diseases in potato, while spur blight caused by Didymella applanata is a major disease in red raspberry. In Western Siberia, both crops are grown predominantly in small-scale farming that requires maximal usage of biological products for plant protection instead of chemicals. We evaluated two promising Bacillus velezensis strains BZR 336 g and BZR 517 isolated in the south of Russia (45°1′N, 38°59′E) for their biological control potentials against the potato and red raspberry diseases under the more severe weather conditions of Western Siberia (55°1′N, 82°55′ E). We tested two techniques to apply biocontrol agents: (1) coating the seeds (potato tubers) and (2) spraying over the plants (raspberry canes). In each case, we estimated B. velezensis strains on two plant cultivars differed by the disease resistance. The degree of B. velezensis influence on disease incidence and severity depended on the bacterial strain, the protected plant, and its cultivar. We also demonstrated that two B. velezensis strains significantly stimulated plant growth of potato, which contributed to the plant productivity on both cultivars. The BZR 336 g strain affected the potato productivity more than the BZR 517 strain. Under the influence of both bacterial strains, raspberry yield was significantly higher compared to the control on the susceptible cultivar. These findings indicated that two southern B. velezensis strains had proved their efficacy as biological control agents in the control of the serious fungal infection of potato and raspberry plants under the more severe ecological conditions of Western Siberia. For the first time, we demonstrated B. velezensis strains potential for use as biological control agents against R. solani on potato, and against D. applanata on red raspberry. creator: Anzhela Asaturova creator: Margarita Shternshis creator: Vera Tsvetkova creator: Tatyana Shpatova creator: Vladislava Maslennikova creator: Natalya Zhevnova creator: Anna Homyak uri: https://doi.org/10.7717/peerj.11578 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Asaturova et al. title: Developing new lines of Japonica rice for higher quality and yield under arid conditions link: https://peerj.com/articles/11592 last-modified: 2021-06-14 description: Rice is the world’s largest food crop, and its production needs to be doubled by 2050 to cope with population growth and associated demand. In addition to the value of improving yields, quality is also important for breeders and consumers, but it pays less attention in arid regions. During two successive summer growing seasons, the experimental material focused on 34 genotypes developed from different crosses on Fn generation after fixation as well as six of the most recent commercial cultivars used for comparisons. The results showed that a high yield of grain followed by high milling and grain quality characteristics were observed among the 34 genotypes used in this analysis. Highly important and positive correlations between the percentage of hulling and the percentage of milling (0.424) and the yield ability could be accomplished by choosing the number of panicles per plant and the weight of the panicles. Selection criteria for good quality should be met by the percentage of head rice and many mineral elements, particularly zinc and iron. As a consequence, the genotypes M.J 5460S/SK105-1, M.J 5460S/GZ7768-1, M.J 5460S/G177-1, M.J 5460S/SK105-3 and M.J 5460S/SK106-4 had desirable high yield and quality characteristics and could be used as promising accessions to the rice breeding program in arid regions. In addition to commercial genotypes, improved Japonica rice genotypes could be produced in arid conditions for higher yield and quality, leading to an increase in total production, supporting food security and nutrition. creator: Mahmoud A.A. El Sayed creator: Ahmed M.S. Kheir creator: Fatma A. Hussein creator: Esmat F. Ali creator: Mahmoud E. Selim creator: Ali Majrashi creator: Essam A.Z. El Shamey uri: https://doi.org/10.7717/peerj.11592 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 El Sayed et al. title: Transcriptome analysis associated with polysaccharide synthesis and their antioxidant activity in Cyclocarya paliurus leaves of different developmental stages link: https://peerj.com/articles/11615 last-modified: 2021-06-14 description: BackgroundCyclocarya paliurus (Batal.) Iljinskaja is a common endemic tree species and used as a Chinese medicine. The main active components in the leaves of this plant are polysaccharides. However, the temporal patterns of gene expression underlying the synthesis of polysaccharides in C. paliurus at different leaf developmental stages and its relationship with the polysaccharide content and antioxidant activities has not been reported to date.MethodsRNA-seq was used to investigate the biosynthesis pathway of polysaccharides at the four developmental stages of C. paliurus leaves. The content and the antioxidant activities of polysaccharides were measured with typical biochemical methods and the identified correlations were statistically evaluated.ResultsSixty-nine differentially expressed genes were found in the leaves during different developmental stages of C. paliurus. These are associated with glycosyltransferases and belong to 18 families. During different developmental stages of C. paliurus, the polysaccharide content first increased and then decreased, and the UDP-glucose 4-epimerase gene was found to be significantly positively correlated with the polysaccharide content. The clearance rates of DPPH radicals, superoxide anion radicals, hydroxyl radicals, and the reducing power of polysaccharides in the leaves of C. paliurus at different developmental stages showed a dose-dependent relationship with the concentration of polysaccharides.ConclusionsThe smallest fully expanded leaves are suitable for high-quality tea, and leaves with sizes below the largest fully expanded leaves are suitable for industrial production of polysaccharides. creator: Weida Lin creator: Huanwei Chen creator: Jianmei Wang creator: Yongli Zheng creator: Qiuwei Lu creator: Ziping Zhu creator: Na Li creator: Zexin Jin creator: Junmin Li creator: Hongfei Lu uri: https://doi.org/10.7717/peerj.11615 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Lin et al. title: Wnt signaling related transcripts and their relationship to energy metabolism in C2C12 myoblasts under temperature stress link: https://peerj.com/articles/11625 last-modified: 2021-06-14 description: Temperature stress is one of the main environmental stressors affecting the welfare, health and productivity of livestock. Temperature changes can modify cell membrane components, disrupting the crosstalk between the cell and its surroundings by affecting signaling pathways including Wnt signaling pathway, which subsequently disrupts cell energy metabolism. The present study aims to understand the effect of temperature stress on the expression of genes involved in Wnt signaling pathways, and their interaction with energy metabolism in C2C12 myoblasts cells. The C2C12 cells were exposed to cold stress (35 °C), mild heat stress (39 °C) and severe heat stress (41 °C), whereas 37 °C was used as control temperature. Transcript levels of important genes involved in Wnt signaling including Axin2, Tnks2, Sfrp1, Dkk1, Dact1, Cby1, Wnt5a, Wnt7a, Wnt11, Porcn, Ror2, Daam1, and Ppp3ca were significantly altered under severe heat stress (41 °C), whereas eight Wnt signaling-related transcripts (Daam1, Ppp3ca, Fzd7, Wnt5a, Porcn, Tnks2, Lrp6, and Aes) were significantly altered under cold stress (35 °C) compared to control. Under heat stress transcripts of the Wnt/β-catenin inhibitors (Sfrp1, Dkk1, and Cby1) and negative regulators (Dact1 and Axin2) are activated. A positive correlation between oxidative phosphorylation and Wnt-related transcripts was found under high temperatures. Transcripts of the cell membrane receptors, including Lrp6 and Fzd7, and the members of Wnt/Ca+2 signaling pathway, including Ppp3ca and Porcn were downregulated under cold stress. Many Wnt signaling-related transcripts were positively correlated with glycolysis under cold stress. These findings indicate a cross-talk between Wnt signaling and energy metabolism under thermal stress. creator: Marua Abu Risha creator: Asghar Ali creator: Puntita Siengdee creator: Nares Trakooljul creator: Fiete Haack creator: Dirk Dannenberger creator: Klaus Wimmers creator: Siriluck Ponsuksili uri: https://doi.org/10.7717/peerj.11625 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Risha et al. title: Development and validation of ferroptosis-related lncRNAs signature for hepatocellular carcinoma link: https://peerj.com/articles/11627 last-modified: 2021-06-11 description: BackgroundHepatocellular carcinoma (HCC) with high heterogeneity is one of the most frequent malignant tumors throughout the world. However, there is no research to establish a ferroptosis-related lncRNAs (FRlncRNAs) signature for the patients with HCC. Therefore, this study was designed to establish a novel FRlncRNAs signature to predict the survival of patients with HCC.MethodThe expression profiles of lncRNAs were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. FRlncRNAs co-expressed with ferroptosis-related genes were utilized to establish a signature. Cox regression was used to construct a novel three FRlncRNAs signature in the TCGA cohort, which was verified in the GEO validation cohort.ResultsThree differently expressed FRlncRNAs significantly associated with prognosis of HCC were identified, which composed a novel FRlncRNAs signature. According to the FRlncRNAs signature, the patients with HCC could be divided into low- and high-risk groups. Patients with HCC in the high-risk group displayed shorter overall survival (OS) contrasted with those in the low-risk group (P < 0.001 in TCGA cohort and P = 0.045 in GEO cohort). This signature could serve as a significantly independent predictor in Cox regression (multivariate HR > 1, P < 0.001), which was verified to a certain extent in the GEO cohort (univariate HR > 1, P < 0.05). Meanwhile, it was also a useful tool in predicting survival among each stratum of gender, age, grade, stage, and etiology,etc. This signature was connected with immune cell infiltration (i.e., Macrophage, Myeloid dendritic cell, and Neutrophil cell, etc.) and immune checkpoint blockade targets (PD-1, CTLA-4, and TIM-3).ConclusionThe three FRlncRNAs might be potential therapeutic targets for patients, and their signature could be utilized for prognostic prediction in HCC. creator: Jiaying Liang creator: Yaofeng Zhi creator: Wenhui Deng creator: Weige Zhou creator: Xuejun Li creator: Zheyou Cai creator: Zhijian Zhu creator: Jinxiang Zeng creator: Wanlan Wu creator: Ying Dong creator: Jin Huang creator: Yuzhuo Zhang creator: Shichao Xu creator: Yixin Feng creator: Fuping Ding creator: Jin Zhang uri: https://doi.org/10.7717/peerj.11627 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liang et al. title: Methylmercury-induced cytotoxicity and oxidative biochemistry impairment in dental pulp stem cells: the first toxicological findings link: https://peerj.com/articles/11114 last-modified: 2021-06-10 description: BackgroundMethylmercury (MeHg) is a potent toxicant able to harm human health, and its main route of contamination is associated with the consumption of contaminated fish and other seafood. Moreover, dental amalgams are also associated with mercury release on human saliva and may contribute to the accumulation of systemic mercury. In this way, the oral cavity seems to be the primary location of exposure during MeHg contaminated food ingestion and dental procedures but there is a lack of literature about its effects on dental tissues and the impact of this toxicity on human health. In this way, this study aimed to analyze the effects of different doses of MeHg on human dental pulp stem cells after short-term exposure.MethodsDental pulp stem cells from human exfoliated deciduous teeth (SHED) were treated with 0.1, 2.5 and 5 µM of MeHg during 24 h. The MeHg effects were assessed by evaluating cell viability with Trypan blue exclusion assay. The metabolic viability was indirectly assessed by MTT reduction assay. In order to evaluate an indicative of antioxidant defense impairment, cells exposed to 0.1 and 5 µM MeHg were tested by measuring glutathione (GSH) level.ResultsIt was observed that cell viability decreased significantly after exposure to 2.5 and 5 µM of MeHg, but the metabolic viability only decreased significantly at 5 µM MeHg exposure, accompanied by a significant decrease in GSH levels. These results suggest that an acute exposure of MeHg in concentrations higher than 2.5 µM has cytotoxic effects and reduction of antioxidant capacity on dental pulp stem cells. creator: Renata Duarte de Souza-Rodrigues creator: Bruna Puty creator: Laís Bonfim creator: Lygia Sega Nogueira creator: Priscila Cunha Nascimento creator: Leonardo Oliveira Bittencourt creator: Roberta Souza D’Almeida Couto creator: Carlos Augusto Galvão Barboza creator: Edivaldo Herculano Corrêa de Oliveira creator: Marcia Martins Marques creator: Rafael Rodrigues Lima uri: https://doi.org/10.7717/peerj.11114 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Souza-Rodrigues et al. title: nCov2019: an R package for studying the COVID-19 coronavirus pandemic link: https://peerj.com/articles/11421 last-modified: 2021-06-10 description: BackgroundThe global spreading of the COVID-19 coronavirus is still a serious public health challenge. Although there are a large number of public resources that provide statistics data, tools for retrospective historical data and convenient visualization are still valuable. To provide convenient access to data and visualization on the pandemic we developed an R package, nCov2019 (https://github.com/YuLab-SMU/nCov2019).MethodsWe collect stable and reliable data of COVID-19 cases from multiple authoritative and up-to-date sources, and aggregate the most recent and historical data for each country or even province. Medical progress information, including global vaccine development and therapeutics candidates, were also collected and can be directly accessed in our package. The nCov2019 package provides an R language interfaces and designed functions for data operation and presentation, a set of interfaces to fetch data subset intuitively, visualization methods, and a dashboard with no extra coding requirement for data exploration and interactive analysis.ResultsAs of January 14, 2021, the global health crisis is still serious. The number of confirmed cases worldwide has reached 91,268,983. Following the USA, India has reached 10 million confirmed cases. Multiple peaks are observed in many countries. Under the efforts of researchers, 51 vaccines and 54 drugs are under development and 14 of these vaccines are already in the pre-clinical phase.DiscussionThe nCov2019 package provides detailed statistics data, visualization functions and the Shiny web application, which allows researchers to keep abreast of the latest epidemic spread overview. creator: Tianzhi Wu creator: Erqiang Hu creator: Xijin Ge creator: Guangchuang Yu uri: https://doi.org/10.7717/peerj.11421 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wu et al. title: Molecular characterization and phylogenetic analyses of Lophodermella needle pathogens (Rhytismataceae) on Pinus species in the USA and Europe link: https://peerj.com/articles/11435 last-modified: 2021-06-10 description: Increasing prevalence of conifer needle pathogens globally have prompted further studies on pathogen identification and a better understanding of phylogenetic relationships among needle pathogens. Several Lophodermella species can be aggressive pathogens causing needle cast in natural pine forests in the USA and Europe. However, their relationships with other Rhytismataceae species have historically been based on similarities of only limited phenotypic characters. Currently, no molecular studies have been completed to elucidate their relationships with other Lophodermella needle pathogens. This study collected and sequenced three gene loci, namely: internal transcribed spacer, large ribosomal subunit, and translation elongation factor 1-alpha, from five Lophodermella needle pathogens from North America (L. arcuata, L. concolor, L. montivaga) and Europe (L. conjuncta and L. sulcigena) to distinguish phylogeny within Rhytismatacaeae, including Lophophacidium dooksii. Phylogenetic analyses of the three loci revealed that all but L. conjuncta that were sampled in this study consistently clustered in a well-supported clade within Rhytismataceae. The multi-gene phylogeny also confirmed consistent nesting of L. dooksii, a needle pathogen of Pinus strobus, within the clade. Potential synapomorphic characters such as ascomata position and ascospore shape for the distinct clade were also explored. Further, a rhytismataceous species on P. flexilis that was morphologically identified as L. arcuata was found to be unique based on the sequences at the three loci. This study suggests a potential wider range of host species within the genus and the need for genetic characterization of other Lophodermella and Lophophacidium species to provide a higher phylogenetic resolution. creator: Jessa P. Ata creator: Kelly S. Burns creator: Suzanne Marchetti creator: Isabel A. Munck creator: Ludwig Beenken creator: James J. Worrall creator: Jane E. Stewart uri: https://doi.org/10.7717/peerj.11435 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: ©2021 Ata et al. title: Relationship between age, category and experience with the soccer referee’s self-efficacy link: https://peerj.com/articles/11472 last-modified: 2021-06-10 description: Soccer referees (SRs) encounter stressful situations during competitions and sometimes even outside them, which may affect their decision making. Therefore, it is important that they possess or acquire optimal levels of self-efficacy, since it is related to less stress during competition, also guaranteeing sports performance and prevent sports abandonment. The objectives of this study were to characterize the profile, in terms of self-efficacy, of SRs depending on their category, age, and experience and to determine the relationship of these factors on SR self-efficacy. Two-hundred fifty-six Spanish referees participated in this study and Referee Self-Efficacy Scale was administered and completed. The results indicated that the SRs older than 25 years, of national category, and with experience greater than or equal to 8 years, have higher levels of self-efficacy than those with the least (p < .01). Likewise, moderate positive correlations were also observed between global self-efficacy and the category, age, and experience of the SRs. In conclusion, age, category and experience factors relate the self-efficacy of the SR, which can explain up to 17% of the variance, affecting decision-making and other decisive behaviors in the competition. These findings are of interest to delegations and referee committees seeking to implement psychological intervention programs to prevent burnout and abandonment of sports practice due to the consequences of low self-efficacy. creator: José López Aguilar creator: Alfonso Castillo-Rodriguez creator: José L. Chinchilla-Minguet creator: Wanesa Onetti-Onetti uri: https://doi.org/10.7717/peerj.11472 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 López Aguilar et al. title: Comparative sera proteomics analysis of differentially expressed proteins in oral squamous cell carcinoma link: https://peerj.com/articles/11548 last-modified: 2021-06-10 description: BackgroundOral squamous cell carcinoma (OSCC) has increased in incidence from 1990 to 2017, especially in South and Southeast Asia. It is often diagnosed at an advanced stage with a poor prognosis. Therefore, early detection of OSCC is essential to improve the prognosis of OSCC. This study aims to identify the differentially expressed serum proteins as potential biomarkers for oral squamous cell carcinoma (OSCC).MethodsComparative proteomics profiling of serum samples from OSCC patients, oral potentially malignant disorder (OPMD) patients, and healthy individuals were performed using two-dimensional gel electrophoresis (2-DE) coupled with mass spectrometry (MS) (n = 60) and bioinformatics analysis. The enzyme-linked immunosorbent assay (ELISA) (n = 120) and immunohistochemistry (IHC) (n = 70) were used to confirm our findings.ResultsThe 2-DE analysis revealed that 20 differentially expressed proteins were detected in OPMD and OSCC (p < 0.05). Bioinformatics analysis indicated that the activation of classical complement, liver X receptor/retinoid X receptor (LXR/RXR) activation, and acute phase response signaling pathway are associated with the development and progression of OSCC. Most of the detected proteins are acute-phase proteins and were related to inflammation and immune responses, including apolipoprotein A-I (APOA1), complement C3 (C3), clusterin (CLU), and haptoglobin (HP). The expression levels of CLU and HP in ELISA are consistent with the findings from the 2-DE analysis, except for the mean serum level of HP in OPMD, whereby it was slightly higher than that in control. IHC results demonstrated that CLU and HP are significantly decreased in OSCC tissues.ConclusionDecreased expression of CLU and HP could serve as complementary biomarkers of OSCC. These proteins may assist in predicting the outcomes of OSCC patients. However, a larger cohort is needed for further investigation. creator: Yin-Ling Wong creator: Anand Ramanathan creator: Kar Mun Yuen creator: Wan Mahadzir Wan Mustafa creator: Mannil Thomas Abraham creator: Keng Kiong Tay creator: Zainal Ariff Abdul Rahman creator: Yeng Chen uri: https://doi.org/10.7717/peerj.11548 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wong et al. title: Maximization of information transmission influences selection of native phosphorelay architectures link: https://peerj.com/articles/11558 last-modified: 2021-06-10 description: Phosphorelays are signal transduction circuits that sense environmental changes and adjust cellular metabolism. Five different circuit architectures account for 99% of all phosphorelay operons annotated in over 9,000 fully sequenced genomes. Here we asked what biological design principles, if any, could explain selection among those architectures in nature. We began by studying kinetically well characterized phosphorelays (Spo0 of Bacillus subtilis and Sln1 of Saccharomyces cerevisiae). We find that natural circuit architecture maximizes information transmission in both cases. We use mathematical models to compare information transmission among the architectures for a realistic range of concentration and parameter values. Mapping experimentally determined phosphorelay protein concentrations onto that range reveals that the native architecture maximizes information transmission in sixteen out of seventeen analyzed phosphorelays. These results suggest that maximization of information transmission is important in the selection of native phosphorelay architectures, parameter values and protein concentrations. creator: Rui Alves creator: Baldiri Salvadó creator: Ron Milo creator: Ester Vilaprinyo creator: Albert Sorribas uri: https://doi.org/10.7717/peerj.11558 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Alves et al. title: First record of Trichinella in Leopardus guigna (Carnivora, Felidae) and Galictis cuja (Carnivora, Mustelidae): new hosts in Chile link: https://peerj.com/articles/11601 last-modified: 2021-06-10 description: BackgroundTrichinellosis is a zoonotic disease with a worldwide distribution. It is caused by several species of nematodes in the genus Trichinella. Trichinella spp. are transmitted through predation or carrion consumption and occur in domestic and sylvatic cycles. In humans trichinellosis occurs due to the consumption of raw or undercooked, infected meat and is mainly associated with the household slaughter of pigs or the consumption of game animals without veterinary inspection, a cultural practice that is difficult to resolve. Therefore, knowledge of this parasite’s reservoir is relevant for better implementing public health strategies. The aim of this study was to assess the presence of Trichinella sp. in several carnivore and omnivore vertebrates in central-southern Chile.MethodsWe collected muscle tissue from a total of 53 animals from 15 species and were digested to detect Trichinella larvae which were further identified to species level using molecular techniques.ResultsWe detected Trichinella larvae in Leopardus guigna (Felidae) and Galictis cuja (Mustelidae). We identified the larvae collected from L. guigna as Trichinella spiralis, but we were unable to molecularly characterize the larvae from G. cuja. This is the first record of Trichinella in a native mustelid of South America and the first record of T. spiralis in L. guigna. This study identified two novel hosts; however, further work is needed to identify the role that these and other hosts play in the cycle of Trichinella in Chile. creator: Diana Maritza Echeverry creator: AnaLía Henríquez creator: Pablo Oyarzún-Ruiz creator: Maria Carolina Silva-de la Fuente creator: Rene Ortega creator: Daniel Sandoval creator: Carlos Landaeta-Aqueveque uri: https://doi.org/10.7717/peerj.11601 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Echeverry et al. title: Antiviral efficacy of short-hairpin RNAs and artificial microRNAs targeting foot-and-mouth disease virus link: https://peerj.com/articles/11227 last-modified: 2021-06-09 description: RNA interference (RNAi) is a well-conserved mechanism in eukaryotic cells that directs post-transcriptional gene silencing through small RNA molecules. RNAi has been proposed as an alternative approach for rapid and specific control of viruses including foot-and-mouth disease virus (FMDV), the causative agent of a devastating animal disease with high economic impact. The aim of this work was to assess the antiviral activity of different small RNA shuttles targeting the FMDV RNA-dependent RNA polymerase coding sequence (3D). Three target sequences were predicted within 3D considering RNA accessibility as a major criterion. The silencing efficacy of short-hairpin RNAs (shRNAs) and artificial microRNAs (amiRNAs) targeting the selected sequences was confirmed in fluorescent reporter assays. Furthermore, BHK-21 cells transiently expressing shRNAs or amiRNAs proved 70 to >95% inhibition of FMDV growth. Interestingly, dual expression of amiRNAs did not improve FMDV silencing. Lastly, stable cell lines constitutively expressing amiRNAs were established and characterized in terms of antiviral activity against FMDV. As expected, viral replication in these cell lines was delayed. These results show that the target RNA-accessibility-guided approach for RNAi design rendered efficient amiRNAs that constrain FMDV replication. The application of amiRNAs to complement FMDV vaccination in specific epidemiological scenarios shall be explored further. creator: Anabella Currá creator: Marco Cacciabue creator: María José Gravisaco creator: Sebastián Asurmendi creator: Oscar Taboga creator: María I. Gismondi uri: https://doi.org/10.7717/peerj.11227 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Currá et al. title: The transition to agricultural cultivation of neo-crops may fail to account for wild genetic diversity patterns: insights from the Cape Floristic Region link: https://peerj.com/articles/11462 last-modified: 2021-06-09 description: AimThe global increase in the cultivation of native wild plants has raised concerns regarding potential risks associated with translocating genetic lineages beyond their natural range. This study aimed to investigate whether agricultural cultivation of neo-crops (a) accounts for the levels of genetic diversity present in wild populations, and whether (b) cultivated populations are genetically divergent from wild populations and thus pose a potential threat to wild genetic diversity.LocationThe Cape Floristic Region (CFR), located along the southern Cape of South Africa.MethodsHigh Resolution Melt analysis (HRM) coupled with Sanger sequencing was used to screen three non-coding chloroplast DNA loci in Cyclopia Vent. (Fabaceae), a CFR endemic neo-crop cultivated for the production of a herbal infusion referred to as Honeybush tea. Wild and cultivated populations for three of three widely cultivated Honeybush species (C. intermedia, C. longifolia, and C. subternata) were screened. Genetic diversity and differentiation were measured and compared between wild and cultivated groups.ResultsAcross all asseccions, a total of 17 haplotypes were detected, four of which were shared between wild and cultivated populations, while the remaining 13 were only detected in wild populations. Genetic diversity and differentiation was significantly higher in wild populations than in cultivated populations.ConclusionsIf no guidelines exist to facilitate the introduction of native wild plant taxa to a cultivated setting, wild genetic diversity patterns are likely to be compromised by cultivated populations. In the case presented here, cultivation represents a genetic bottleneck, failing to account for rare haplotypes, and may have disrupted species boundaries by initiating interspecific hybridization. More empirical work is required to evaluate the extent to which neo-crop cultivation poses a risk to wild genetic resources in the CFR and globally. creator: Nicholas C. Galuszynski uri: https://doi.org/10.7717/peerj.11462 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Galuszynski title: Sunburns among beachgoers in the northern coast of Peru: frequency and factors associated link: https://peerj.com/articles/11473 last-modified: 2021-06-09 description: BackgroundOverexposure to ultraviolet (UV) radiation has increased skin cancer incidence and the risk of sunburns, especially during the summer months.ObjectiveIdentify the frequency and factors associated with sunburns in a sample of beachgoers in the northern coast of Peru.MethodsWe conducted a secondary data analysis of a previous study that assessed the awareness, behavior and attitudes concerning sun exposure among beachgoers. We included adults between 18 and 59 years who went to a beach in northern Peru during summer (March 2018). Three generalized linear models of the Poisson family were constructed to evaluate the factors associated with having had at least one sunburn last summer. All regression models reported the adjusted prevalence ratio (aPR) with their respective 95% confidence interval (95% CI).ResultsOf a total of 402 participants, 225 (56.0%) had one to five sunburns and 25 (6.2%) had six or more. Beachgoers who were 1–15 days (aPR: 1.16, 95% CI [1.05–1.27]) or more than 15 days (aPR: 1.22, 95% CI [1.09–1.36]) exposed to the sun on the beach had a higher frequency of at least one sunburn. The non-regular wearing of a hat or cap also increased the frequency of sunburns (aPR: 1.06, 95% CI [1.01–1.12]). In contrast, those who had Skin Phototype III (aPR: 0.94, 95% CI [0.88–0.99]) or IV (aPR: 0.69, 95% CI [0.63–0.75]) had a lower frequency of sunburns.ConclusionThree out of five beachgoers had one or more sunburns in the last summer. The factors associated with a higher frequency were the time of sun exposure at the beach and the non-regular use of a hat or cap. Type III–IV skin phototypes were associated with a lower sunburn frequency. creator: Eliana L. Fernandez-Quiroz creator: Lizeth Gonzales-Chachapoyas creator: Ana L. Alcantara-Diaz creator: Binz Bulnes-Villalta creator: Zulmy Ayala-Porras creator: Carlos J. Toro-Huamanchumo uri: https://doi.org/10.7717/peerj.11473 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Fernandez-Quiroz et al. title: Current status of Helicobacter pylori resistance to Clarithromycin and Levofloxacin in Malaysia—findings from a molecular based study link: https://peerj.com/articles/11518 last-modified: 2021-06-09 description: BackgroundResistance to clarithromycin and levofloxacin in Helicobacter pylori which resulted in treatment failures has become a major challenge for physicians worldwide. The resistance is mainly mediated by mutations in a specific domain of the 23S rRNA, gyrA and gyrB genes for clarithromycin and levofloxacin respectively. Hence in this study, we aimed to investigate the current status of H. pylori resistance in our hospital to these two antibiotics based on the molecular approach.Materials and MethodsGastric biopsy samples were obtained from treatment-naïve patients. Bacterial genomic DNA was extracted using a commercial kit and continued with DNA amplification using polymerase chain reaction (PCR) with specific primers. The PCR amplicons were subjected to sequencing on 23S rRNA gene targeting nucleotide positions at 2,146, 2,147, 2,186 and amino acids at gyrA positions 87 and 91 and gyrB positions 436, 438, 481, 484 to investigate the possible mutations or polymorphisms of genes that lead to clarithromycin and levofloxacin resistance respectively.ResultsSixty-one urease-positive gastric biopsy samples were studied. The findings revealed the primary resistance rates to clarithromycin was 14.8% and to levofloxacin was 3.3% in our current scenario based on detection of reported resistance-related mutations of A2147G and D91N in 23S rRNA and gyrA genes, respectively. Interestingly, we found a high rate of silent mutations of the gyrA codon 87Asn (32.8%, 20/61) and two polymorphisms of the gyrB D481E (16.4%, 10/61) and R484K (21.3%, 13/61). The role of these polymorphisms in gyrB remained to be elucidated whether the levels of levofloxacin resistance are related to the position/amino acid.ConclusionThe primary resistance rate of H. pylori to clarithromycin has increased compared to the previous report in Malaysia. Therefore, molecular screening could aid and is important for the selection of antibiotics for H. pylori eradication therapies. creator: Suat Moi Puah creator: Khean Lee Goh creator: Heng Kang Ng creator: Kek Heng Chua uri: https://doi.org/10.7717/peerj.11518 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Puah et al. title: Increased microRNA-30a levels in bronchoalveolar lavage fluid as a diagnostic biomarker for lung cancer link: https://peerj.com/articles/11528 last-modified: 2021-06-09 description: BackgroundMicroRNA-30a (miRNA-30a) levels have been shown to increase in the plasma of lung cancer patients. Herein, we evaluated the miRNA-30a levels in the bronchoalveolar lavage fluid (BALF) of lung cancer patients as a potential biomarker for lung cancer diagnosis.MethodsBALF miRNA-30a expression of 174 subjects was quantified using quantitative real-time reverse transcription-polymerase chain reaction and compared between lung cancer patients and control patients with benign lung diseases. Moreover, its diagnostic value was evaluated by performing receiver operating characteristic (ROC) curve analysis.ResultsThe relative BALF miRNA-30a expression was significantly higher in the lung cancer patients than in the controls (0.74 ±  0.55 versus 0.07 ±  0.48, respectively, p < 0.001) as well as in lung cancer patients with stage I–IIA disease than in those with stage IIB–IV disease (0.98 ±  0.64 versus 0.66 ±  0.54, respectively, p < 0.05). Additionally, miRNA-30a distinguished benign lung diseases from lung cancers, with an area under the ROC curve (AUC) of 0.822. ROC analysis also revealed an AUC of 0.875 for the Youden index-based optimal cut-off points for stage I–IIA adenocarcinoma. Thus, increased miRNA-30a levels in BALF may be a useful biomarker for non-small-cell lung cancer diagnosis. creator: Wen-Jun Zhu creator: Bo-Jiang Chen creator: Ying-Ying Zhu creator: Ling Sun creator: Yu-Chen Zhang creator: Huan Liu creator: Feng-Ming Luo uri: https://doi.org/10.7717/peerj.11528 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhu et al. title: Assessing of evapotranspiration models using limited climatic data in Southeast Anatolian Project Region of Turkey link: https://peerj.com/articles/11571 last-modified: 2021-06-09 description: Evapotranspiration carries vital importance in areas with arid and semi-arid climate properties for many issues, including the planning of irrigation water as a scarce resource, the establishment of irrigation programs and conducting project design for drainage. The empirical equations used for determining plant water consumption are classified subject to the diversity of the utilized data. The Penman–Monteith method used frequently in many parts of the world as a standard method needs more climate data. Models that yield results that are similar to those of the standard method with less climate parameters are preferred due to their ease of use and wide impact. Temperature, relative humidity and radiation data for the years 2008–2017 were utilized to analyze the usability of the Hargreaves–Samani and Turc-1961 equations with regard to the estimation of reference evapotranspiration in four provinces located in Southeastern Anatolia Region. Results obtained via models were compared in pairs by way of the standard method in order to define the performance of the models. While the best performances were obtained from the comparison with the standard method and Hargreaves–Samani value pair, the comparison of the standard model with Turc displayed the lowest performance. Based on the study data, ETo-Turc values were higher in the provinces analyzed, thus displaying a lower performance. While maximum long term annual monthly average ETo-HS value was identified as 7.6 mm at Diyarbakır in July, whereas the lowest value was determined at Kilis with 5.8 mm; the highest and lowest ETo-Turc values were obtained in the same month at Diyarbakır and Kilis with 13.3 and 10.3 mm respectively. It was calculated based on the long term average annual total ETo values that while highest ETo-HS was calculated at Diyarbakır with 1,500 mm, whereas the lowest value was calculated at Batman with 1,183 mm. The highest value for ETo-Turc was obtained at Diyarbakır with 2,365 mm while Mardin had the lowest ETo value with 1,920 mm. Accordingly, based on the ETo values calculated at both cities studies based on both models, Diyarbakır had the highest values, whereas Kilis had the lowest ETo values. According to the standard method known as PM, lowest daily ETo values were calculated in all provinces, which displayed the highest performance among the models. As a result of this study, it is possible to use the Hargreaves-Samani model instead of the standard model in the absence of reliable climatic data. creator: Yusuf Aydın uri: https://doi.org/10.7717/peerj.11571 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Aydın title: Expression of autophagy and apoptosis-related factors in the periodontal tissue of experimental diabetic rats: a histomorphometric, microtomographic and immunohistochemical study link: https://peerj.com/articles/11577 last-modified: 2021-06-09 description: ObjectiveThis study aimed to investigate the expression of autophagy-related factors microtubule-associated protein l light chain 3 (LC3) and the apoptosis-related factors BCL2-associated X protein (Bax) and B cell lymphoma-2 (Bcl-2) in the periodontal tissue of experimental diabetic rats. These data were used to explore the potential mechanism in diabetes-induced periodontal tissue lesions.MethodsA total of 32 Sprague Dawley (SD) rats were randomly assigned into diabetes (group D, n = 16) and control groups (group N, n = 16). The diabetic group was induced by intraperitoneal injection of 1% streptozotocin (STZ, 60 mg/kg) and the control group was injected with citrate buffer (0.1mol/L). Rats were sacrificed after 4 and 8 weeks of feeding and collected as D1, N1 groups and D2, N2 groups, and the maxilla were retained for analysis. The changes in periodontal tissue structure were observed by hematoxylin-eosin (HE) staining. The expression and distribution of LC3, Bax and Bcl-2 in the periodontium of the rats was detected by immunohistochemical (SP) staining.ResultsDiabetic rats showed several changes compared to control animals including sparse alveolar bone trabecular structure, loss of the lamina dura and absorption of the local alveolar bone. The positive expression level of LC3 in the gingival epithelial, periodontal ligament and alveolar bone of group D1 was significantly higher than in the N1, N2 and D2 groups (P < 0.05). The level of Bax expression in the group D2 rats was significantly higher than those in the N1, N2 and D1 groups (P < 0.05), while the positive degree of Bcl-2 was significantly lower than those of other groups (P < 0.001). LC3 was negatively correlated with Bax and was irrelevant with Bcl-2; Bcl-2 was not correlated with Bax.ConclusionsThe expression of LC3, Bax and Bcl-2 changes in the periodontal tissue of diabetic rats may indicate that autophagy and apoptotic are involved in the process of periodontal tissue damage in diabetic rats. These changes may be one of the mechanisms of periodontal tissue lesions. creator: Youmin Mei creator: Xiang Shen creator: Xiaoqian Wang creator: Min Zhang creator: Qiao Li creator: Junyi Yan creator: Jiali Xu creator: Yan Xu uri: https://doi.org/10.7717/peerj.11577 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Mei et al. title: Validity and reliability of the DiCI for the measurement of shoulder flexion and abduction strength in asymptomatic and symptomatic subjects link: https://peerj.com/articles/11600 last-modified: 2021-06-09 description: BackgroundA higher risk of shoulder injury in the athletic and non-athletic population is frequently associated with strength deficits. Therefore, shoulder strength assessment can be clinically useful to identify and to quantify the magnitude of strength deficit. Thus, the aim of this study was to evaluate the validity and reliability of a DiCI (a new hand-held dynamometer) for the measurement of shoulder flexion and abduction strength in asymptomatic and symptomatic subjects.MethodsForty-three recreational athletes (29 males and 14 females; age: 22.1 ± 0.47 years; body mass: 68.7 ± 13.1 kg; height = 173.3 ± 9.7 cm) and 40 symptomatic subjects (28 males and 12 females; age: 49.9 ± 8.1 years; body mass: 70.6 ± 14.3 kg; height = 171.7 ± 9.0 cm) completed shoulder flexion and abduction strength tests in two identical sessions one-week apart. Both types of movement were evaluated at 45º and 90º.ResultsRelative reliability analysis showed excellent intra-class correlation coefficients (ICC) for all evaluated movements (ICC range = 0.90 to 0.99). Absolute reliability analysis showed a standard error of measurement (SEM) ranging from 1.36% to 2.25%, and minimal detectable change (MDC) ranging from 3.93% to 6.25%. In conclusion, the DiCI is a valid and reliable device for assessing shoulder strength both in recreational athletes and in subjects with restricted mobility and loss of strength. creator: Javier González-Rosalén creator: Alba Cuerda-Del Pino creator: Mariana Sánchez-Barbadora creator: Rodrigo Martín-San Agustín uri: https://doi.org/10.7717/peerj.11600 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 González-Rosalén et al. title: Meta-analysis of the effect of expression of MYB transcription factor genes on abiotic stress link: https://peerj.com/articles/11268 last-modified: 2021-06-08 description: BackgroundMYB proteins are a large group of transcription factors. The overexpression of MYB genes has been reported to improve abiotic stress tolerance in plant. However, due to the variety of plant species studied and the types of gene donors/recipients, along with different experimental conditions, it is difficult to interpret the roles of MYB in abiotic stress tolerance from published data.MethodsUsing meta-analysis approach, we investigated the plant characteristics involved in cold, drought, and salt stress in MYB-overexpressing plants and analyzed the degrees of influence on plant performance by experimental variables.ResultsThe results show that two of the four measured plant parameters in cold-stressed plants, two of the six in drought-stressed, and four of the 13 in salt-stressed were significantly impacted by MYB overexpression by 22% or more, and the treatment medium, donor/recipient species, and donor type significantly influence the effects of MYB-overexpression on drought stress tolerance. Also, the donor/recipient species, donor type, and stress duration all significantly affected the extent of MYB-mediated salt stress tolerance. In summary, this study compiles and analyzes the data across studies to help us understand the complex interactions that dictate the efficacy of heterologous MYB expression designed for improved abiotic stress tolerance in plants. creator: Zhaolan Han creator: Xiaowen Shang creator: Lingxia Shao creator: Ya Wang creator: Xujun Zhu creator: Wanping Fang creator: Yuanchun Ma uri: https://doi.org/10.7717/peerj.11268 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Han et al. title: Sex- and age-specific variation of gut microbiota in Brandt’s voles link: https://peerj.com/articles/11434 last-modified: 2021-06-08 description: BackgroundGut microbiota plays a key role in the survival and reproduction of wild animals which rely on microbiota to break down plant compounds for nutrients. As compared to laboratory animals, wild animals face much more threat of environmental changes (e.g. food shortages and risk of infection). Therefore, studying the gut microbiota of wild animals can help us better understand the mechanisms animals use to adapt to their environment.MethodsWe collected the feces of Brandt’s voles in the grassland, of three age groups (juvenile, adult and old), in both sexes. We studied the gut microbiota by 16S rRNA sequencing.ResultsThe main members of gut microbiota in Brandt’s voles were Firmicutes, Bacteroidetes and Proteobacteria. As voles get older, the proportion of Firmicutes increased gradually, and the proportion of Bacteroides decreased gradually. The diversity of the microbiota of juveniles is lower, seems like there is still a lot of space for colonization, and there are large variations in the composition of the microbiome between individuals. In adulthood, the gut microbiota tends to be stable, and the diversity is highest. In adult, the abundances of Christensenellaceae and Peptococcus of female were significantly higher than male voles.ConclusionsThe gut microbiota of Brandt’s vole was influenced by sex and age, probably due to growth needs and hormone levels. Gut microbiota of wild animals were much influenced by their life-history reflected by their age and sex. Future studies will be directed to identify functions of these “wild microbiota” in regulating physiological or behavioral processes of wild animals in different life stage or sexes. creator: Xiaoming Xu creator: Zhibin Zhang uri: https://doi.org/10.7717/peerj.11434 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu and Zhang title: Characterization of the gut microbiota in Chinese children with overweight and obesity using 16S rRNA gene sequencing link: https://peerj.com/articles/11439 last-modified: 2021-06-08 description: BackgroundChildhood obesity constitutes a worldwide health problem, and the gut microbiota play extremely important roles in obesity. Herein, we aimed to characterize the gut microbiota in children of normal weight, overweight, and obesity.MethodsThirty children of normal weight, 35 who were overweight, and 35 with obesity were enrolled from Nanjing, China. We isolated DNA from fecal samples, and employed 16S rRNA gene sequencing to explore the diversity and composition of gut microbiota.ResultsThe operational taxonomic unit (OTU) numbers exhibited a reduction in the gut microbiota abundance with the increase in the body weight. Alpha diversity analysis revealed a sharp decrease in the mean microbial abundance among the three groups (Chao1: F = 5.478, P = 0.006; observed species: F = 7.271, P = 0.001; PD whole tree: F = 8.735, P < 0.001). Beta diversity analysis indicated notable differences in the gut microbial composition between children of normal weight and obesity. However, overweight children had little difference in gut microbiota compared to either children of normal weight or obesity. At the genus level, Oscillospira decreased among the three groups (χ2 = 10.062, P = 0.001), and Sutterella increased (F = 4.052, P = 0.020). There were many remarkably increased species of gut bacteria in the comparison among three groups, 31 in the normal weight group, 32 in the obese group, and only three species of bacteria were identified in the overweight group. These significantly increased species of gut bacteria may have a close relationship with the progression of obesity.ConclusionsThe abundance of species decreased significantly as the BMI increased. Although the gut microbial composition between children of normal weight and obesity was notably different, due to the changing ratio of some microbial communities, gut microbiota in overweight children showed similarities to that of children with normal weight and obesity. creator: Xiaowei Chen creator: Dawei Zhang creator: Haixiang Sun creator: Fei Jiang creator: Yan Shen creator: Pingmin Wei creator: Xiaobing Shen uri: https://doi.org/10.7717/peerj.11439 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: Exploring the differential stages of the pigment metabolism by pre-harvest bagging and post-harvest ethylene de-greening of Eureka lemon peel link: https://peerj.com/articles/11504 last-modified: 2021-06-08 description: Pre-harvest bagging or post-harvest ethylene treatments on lemons are commonly applied to change the surface color from green to favorable yellow. In this study, the differential mechanisms of the pigment metabolism by the two treatments were investigated by pigments contents and related genetic expression. The results showed that both treatments reduced the number of chloroplasts and the content of chlorophyll. The differential expression of PSY1 and PSY2 were observed, causing the different accumulation of the main carotenoid phytoene content. The differential expression of NYC resulted in altered contents of chlorophyll a and chlorophyll b, and further led to the difference in a* value. More interestingly, the degradation of chlorophyll uncovered the color of carotenoids, leading to the color changed from green to yellow. creator: Anjun Chen creator: Lu Liu creator: Xiaoping Liu creator: Yunyun Fu creator: Jie Li creator: Jianglin Zhao creator: Xiaoyan Hou uri: https://doi.org/10.7717/peerj.11504 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Anjun et al. title: Unsupervised learning of satellite images enhances discovery of late Miocene fossil sites in the Urema Rift, Gorongosa, Mozambique link: https://peerj.com/articles/11573 last-modified: 2021-06-08 description: BackgroundPaleoanthropological research focus still devotes most resources to areas generally known to be fossil rich instead of a strategy that first maps and identifies possible fossil sites in a given region. This leads to the paradoxical task of planning paleontological campaigns without knowing the true extent and likely potential of each fossil site and, hence, how to optimize the investment of time and resources. Yet to answer key questions in hominin evolution, paleoanthropologists must engage in fieldwork that targets substantial temporal and geographical gaps in the fossil record. How can the risk of potentially unsuccessful surveys be minimized, while maximizing the potential for successful surveys?MethodsHere we present a simple and effective solution for finding fossil sites based on clustering by unsupervised learning of satellite images with the k-means algorithm and pioneer its testing in the Urema Rift, the southern termination of the East African Rift System (EARS). We focus on a relatively unknown time period critical for understanding African apes and early hominin evolution, the early part of the late Miocene, in an overlooked area of southeastern Africa, in Gorongosa National Park, Mozambique. This clustering approach highlighted priority targets for prospecting that represented only 4.49% of the total area analysed.ResultsApplying this method, four new fossil sites were discovered in the area, and results show an 85% accuracy in a binary classification. This indicates the high potential of a remote sensing tool for exploratory paleontological surveys by enhancing the discovery of productive fossiliferous deposits. The relative importance of spectral bands for clustering was also determined using the random forest algorithm, and near-infrared was the most important variable for fossil site detection, followed by other infrared variables. Bands in the visible spectrum performed the worst and are not likely indicators of fossil sites.DiscussionWe show that unsupervised learning is a useful tool for locating new fossil sites in relatively unexplored regions. Additionally, it can be used to target specific gaps in the fossil record and to increase the sample of fossil sites. In Gorongosa, the discovery of the first estuarine coastal forests of the EARS fills an important paleobiogeographic gap of Africa. These new sites will be key for testing hypotheses of primate evolution in such environmental settings. creator: João d’Oliveira Coelho creator: Robert L. Anemone creator: Susana Carvalho uri: https://doi.org/10.7717/peerj.11573 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 d’Oliveira Coelho et al. title: Dental health care providers’ concerns, perceived impact, and preparedness during the COVID-19 pandemic in Saudi Arabia link: https://peerj.com/articles/11584 last-modified: 2021-06-08 description: BackgroundDental health care providers (DHCPs)are at high risk of cross-infection during clinical practice therefore, the aim of the study was to evaluate the DHCPs Covid-19 related concerns, its perceived impact, and their preparedness in Saudi Arabia.MethodsThis cross-sectional study on DHCPs was carried out at five dental teaching hospitals/colleges in four provinces of Saudi Arabia from October to December 2020. A 35-item valid and reliable questionnaire was used to assess the concerns, perceived impact, and preparedness of DHCPs in the COVID-19 pandemic. Chi-square tests and logistic regression were used to compare parameters between the clinical and non-clinical staff.ResultsA total of 320 DHCPs participated in this study with proportion of clinical staff (57.5%) surpassing the non-clinical staff (42.5%). The clinical DHCPs felt greater odds of falling ill with COVID-19 than non-clinical workers (OR, 2.61) and willing to look for another job (OR, 3.50). The higher proportion in both groups was worried that people close to them would be at higher exposure risk (96.3%) however, slightly more clinical DHCPs were concerned for their children than a non-clinical worker (OR, 3.57). The clinical DHCPs have greater odds of worrying that people would avoid them and their family members because of their job (OR, 2.75). A higher proportion in both groups (75.0%, 63.2%) felt that they would feel stress at work. More non-clinical DHCPs (94.1%) had received training for infection control than clinical (94.1% vs 63.0%: OR 0.10). Similarly, more DHCPs in the nonclinical group received adequate personal protective equipment training (88.2%; OR, 0.48). Most participants practiced self-preparation such as buying masks and disinfection (94.4%, 96.9%).ConclusionThe majority of DHCPs felt concerned about their risk of exposure and falling ill from infection and infecting friends/family. These concerns could potentially affect the working of DHCPs during this pandemic. Measures to improve protection for DHCPs, minimize psychological implications, and potential social stigmatization should be identified at the planning phase before any pandemic. creator: Muhammad Qasim Javed creator: Farooq Ahmad Chaudhary creator: Syed Fareed Mohsin creator: Mustafa Hussein AlAttas creator: Hadeel Yaseen Edrees creator: Syed Rashid Habib creator: Arham Riaz uri: https://doi.org/10.7717/peerj.11584 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Javed et al. title: Effects of short-term grazing prohibition on soil physical and chemical properties of meadows in Southwest China link: https://peerj.com/articles/11598 last-modified: 2021-06-08 description: BackgroundGrassland plays an important role in the ecosystem, but overgrazing harms the grassland system in many places. Grazing prohibition is an effective method to restore grassland ecosystems, and it plays a great role in realizing the sustainable development of grassland systems. Therefore, it is necessary to carry out research on the influence of regional grazing prohibition on the physical and chemical properties of different grassland systems.MethodsIn Potatso National Park, Southwest China, we selected experimental plots in the artificial grazing meadow area to study the effects of grazing prohibition on plant and soil indexes in subalpine meadows and swamp meadows. We investigated the biomass and species diversity of grazing prohibition treatment and grazing treatment plots and sampled and tested the soil index. The variation percentage was used to remove the original heterogeneity and yearly variation, allowing us to compare differences in plant index and soil index values between grazing prohibition and grazing treatments.ResultsGrazing prohibition increased the aboveground biomass, total biomass, total meadow coverage, average height, richness index, Shannon diversity index and evenness index and reduced the belowground biomass and root/shoot ratio in the subalpine meadow and swamp meadow. Additionally, grazing prohibition reduced the pH and soil bulk density and increased the soil total carbon, soil organic carbon, soil total nitrogen, soil hydrolyzable nitrogen, soil total phosphorus and soil available phosphorus in the subalpine meadow and swamp meadow. Nonmetric multidimensional scaling (NMDS) analysis showed that both plant indexes and soil indexes were significantly different between grazing and grazing prohibition treatments and between meadow types. Short-term grazing prohibition had a great impact on improving the fertility of meadow soil in the study area. We suggest that long-term and extensive research should be carried out to promote the restoration and sustainable development of regional grassland systems. creator: Guiqing Zhu creator: Chaoxiang Yuan creator: Hede Gong creator: Yanling Peng creator: Changjiang Huang creator: Chuansheng Wu creator: Huachao Duan uri: https://doi.org/10.7717/peerj.11598 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhu et al. title: A new giant sauropod, Australotitan cooperensis gen. et sp. nov., from the mid-Cretaceous of Australia link: https://peerj.com/articles/11317 last-modified: 2021-06-07 description: A new giant sauropod, Australotitan cooperensis gen. et sp. nov., represents the first record of dinosaurs from the southern-central Winton Formation of the Eromanga Basin, Australia. We estimate the type locality to be 270–300 m from the base of the Winton Formation and compare this to the semi-contemporaneous sauropod taxa, Diamantinasaurus matildaeHocknull et al., 2009, Wintonotitan wattsiHocknull et al., 2009 and Savannasaurus elliottorumPoropat et al., 2016. The new titanosaurian is the largest dinosaur from Australia as represented by osteological remains and based on limb-size comparisons it reached a size similar to that of the giant titanosaurians from South America. Using 3-D surface scan models we compare features of the appendicular skeleton that differentiate Australotitan cooperensis gen. et sp. nov. as a new taxon. A key limitation to the study of sauropods is the inability to easily and directly compare specimens. Therefore, 3-D cybertypes have become a more standard way to undertake direct comparative assessments. Uncoloured, low resolution, and uncharacterized 3-D surface models can lead to misinterpretations, in particular identification of pre-, syn- and post-depositional distortion. We propose a method for identifying, documenting and illustrating these distortions directly onto the 3-D geometric surface of the models using a colour reference scheme. This new method is repeatable for researchers when observing and documenting specimens including taphonomic alterations and geometric differences. A detailed comparative and preliminary computational phylogenetic assessment supports a shared ancestry for all four Winton Formation taxa, albeit with limited statistical support. Palaeobiogeographical interpretations from these resultant phylogenetic hypotheses remain equivocal due to contrary Asian and South American relationships with the Australian taxa. Temporal and palaeoenvironmental differences between the northern and southern-central sauropod locations are considered to explain the taxonomic and morphological diversity of sauropods from the Winton Formation. Interpretations for this diversity are explored, including an eco-morphocline and/or chronocline across newly developed terrestrial environments as the basin fills. creator: Scott A. Hocknull creator: Melville Wilkinson creator: Rochelle A. Lawrence creator: Vladislav Konstantinov creator: Stuart Mackenzie creator: Robyn Mackenzie uri: https://doi.org/10.7717/peerj.11317 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hocknull et al. title: Airborne transmission pathway for coastal water pollution link: https://peerj.com/articles/11358 last-modified: 2021-06-07 description: Each year, over one hundred million people become ill and tens of thousands die from exposure to viruses and bacteria from sewage transported to the ocean by rivers, estuaries, stormwater, and other coastal discharges. Water activities and seafood consumption have been emphasized as the major exposure pathways to coastal water pollution. In contrast, relatively little is known about the potential for airborne exposure to pollutants and pathogens from contaminated seawater. The Cross Surfzone/Inner-shelf Dye Exchange (CSIDE) study was a large-scale experiment designed to investigate the transport pathways of water pollution along the coast by releasing dye into the surfzone in Imperial Beach, CA. Additionally, we leveraged this ocean-focused study to investigate potential airborne transmission of coastal water pollution by collecting complementary air samples along the coast and inland. Aerial measurements tracked sea surface dye concentrations along 5+ km of coast at 2 m × 2 m resolution. Dye was detected in the air over land for the first 2 days during two of the three dye releases, as far as 668 m inland and 720 m downwind of the ocean. These coordinated water/air measurements, comparing dye concentrations in the air and upwind source waters, provide insights into the factors that lead to the water-to-air transfer of pollutants. These findings show that coastal water pollution can reach people through an airborne pathway and this needs to be taken into account when assessing the full impact of coastal ocean pollution on public health. This study sets the stage for further studies to determine the details and importance of airborne exposure to sewage-based pathogens and toxins in order to fully assess the impact of coastal pollution on public health. creator: Matthew A. Pendergraft creator: Derek J. Grimes creator: Sarah N. Giddings creator: Falk Feddersen creator: Charlotte M. Beall creator: Christopher Lee creator: Mitchell V. Santander creator: Kimberly A. Prather uri: https://doi.org/10.7717/peerj.11358 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pendergraft et al. title: Estimation of the probability of daily fluctuations of incidence of COVID-19 according to official data link: https://peerj.com/articles/11049 last-modified: 2021-06-04 description: When studying the dynamics of morbidity and mortality, one should not limit ourselves to analyzing general trends. Interesting information can be obtained from the analysis of deviations in morbidity and mortality from the general dynamics. Comparison of the cases of morbidity or death for adjacent time intervals allows us to find out whether the changes in conditions were for short periods of time and whether the cases of morbidity or death were independent. The article consists of two parts: Study of the probability distribution (CDF) of the difference between two independent observations of the Poisson distribution; Application of the results to analyze the morbidity and mortality trends by day for the new coronavirus infection. For the distribution function of the module of difference between two independent observations of the Poisson distribution, an analytical expression has been obtained that allows to get an exact solution. A program has been created, whose software can be downloaded at http://1mgmu.com/nau/DeltaPoisson/DeltaPoisson.zip. An approximate solution that does not require complex calculations has also been obtained, which can be used for an average of more than 20. If real difference is greater than expected, it may be in the following cases: morbidity or mortality varies considerably during the day. That could happen, for example, if the registered number of morbidity on Saturday and Sunday is less than on weekdays due to the management model of the health system, or if the cases are not independent; for example, due to the active identification of infected people among those who have come into contact with the patient. If the difference is less than expected, it may be due to external limiting factors, such as a shortage of test systems for making a diagnosis, a limited number of pathologists to determine the cause of death, and so on. In the analysis of the actual data for COVID-19 it was found that for Poland and Russia, excluding Moscow, the difference in the number of cases and deaths is greater than expected, while for Moscow—less than expected. This may be due to the information policy—the effort to somehow reassure Moscow’s population, which in the spring of 2020 had a high incidence rate of the new coronavirus infection. creator: Andrey Gerasimov creator: Elena Galkina creator: Elena Danilova creator: Irina Ikonnikova creator: Tamara Novoselova creator: Yuriy L. Orlov creator: Irina Senenycheva uri: https://doi.org/10.7717/peerj.11049 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Gerasimov et al. title: Development and validation of the Health Promoting Behaviour for Bloating (HPB-Bloat) scale link: https://peerj.com/articles/11444 last-modified: 2021-06-04 description: BackgroundHealth management strategies may help patients with abdominal bloating (AB), but there are currently no tools that measure behaviour and awareness. This study aimed to validate and verify the dimensionality of the newly-developed Health Promoting Behaviour for Bloating (HPB-Bloat) scale.MethodsBased on previous literature, expert input, and in-depth interviews, we generated new items for the HPB-Bloat. Its content validity was assessed by experts and pre-tested across 30 individuals with AB. Construct validity and dimensionality were first determined using exploratory factor analysis (EFA) and Promax rotation analysis, and then using confirmatory factor analysis (CFA).ResultsDuring the development stage, 35 items were generated for the HPB-Bloat, and were maintained following content validity assessment and pre-testing. One hundred and fifty-two participants (mean age of 31.27 years, 68.3% female) and 323 participants (mean age of 27.69 years, 59.4% male) completed the scale for EFA and CFA, respectively. Using EFA, we identified 20 items that we divided into five factors: diet (five items), health awareness (four items), physical activity (three items), stress management (four items), and treatment (four items). The total variance explained by the EFA model was 56.7%. The Cronbach alpha values of the five factors ranged between 0.52 and 0.81. In the CFA model, one problematic latent variable (treatment) was identified and three items were removed. In the final measurement model, four factors and 17 items fit the data well based on several fit indices (root mean square error of approximation (RMSEA) = 0.044 and standardized root mean squared residual (SRMR) = 0.052). The composite reliability of all factors in the final measurement model was above 0.60, indicating acceptable construct reliability.ConclusionThe newly developed HPB-Bloat scale is valid and reliable when assessing the awareness of health-promoting behaviours across patients with AB. Further validation is needed across different languages and populations. creator: Nurzulaikha Abdullah creator: Yee Cheng Kueh creator: Garry Kuan creator: Mung Seong Wong creator: Fatan Hamamah Yahaya creator: Nor Aslina Abd Samat creator: Khairil Khuzaini Zulkifli creator: Yeong Yeh Lee uri: https://doi.org/10.7717/peerj.11444 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Abdullah et al. title: Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress link: https://peerj.com/articles/11463 last-modified: 2021-06-04 description: Many agricultural regions in arid and semiarid climate zone need to deal with increased soil salinity. Legumes are classified as salt-sensitive crops. A field experiment was performed to examine the application of phosphorus (P) fertilizer source and rate on growth, chlorophylls and carotenoid content, DNA and RNA content and ion accumulation in common bean (Phaseolus vulgaris L.) cultivated under salinity stress. An experimental design was split-plot with three replicates. The main plots included two P sources, namely single superphosphate (SP) and urea phosphate (UP). The sub-plots covered four P rates, i.e., 0.0, 17.5, 35.0, and 52.5 kg P ha–1. All applied P fertilization rates, in both forms, increased plant height, leaf area, dry weight of shoots and roots per plant, and total dry weight (TDW) in t ha−1. The highest accumulation of N, P, K+, Mg2+, Mn2+, Zn2+, and Cu2+ was determined in the shoot and root of common bean, while 35 kg of P per ha−1 was used compared to the other levels of P fertilizer. The highest P rate (52.5 kg ha−1) resulted in a significant reduction in Na+ in shoot and root of common bean. The response curve of TDW (t ha–1) to different rates of P (kg ha–1) proved that the quadratic model fit better than the linear model for both P sources. Under SP, the expected TDW was 1.675 t ha–1 if P was applied at 51.5 kg ha–1, while under UP, the maximum expected TDW was 1.875 t ha–1 if P was supplied at 42.5 kg ha–1. In conclusion, the 35.0 kg P ha–1 could be considered the best effective P level imposed. The application of P fertilizer as urea phosphate is generally more effective than single superphosphate in enhancing plant growth and alleviating common bean plants against salinity stress. creator: Heba I. Mohamed creator: Adel A. El-Sayed creator: Mostafa M. Rady creator: Gianluca Caruso creator: Agnieszka Sekara creator: Magdi T. Abdelhamid uri: https://doi.org/10.7717/peerj.11463 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Mohamed et al. title: Spondias mombin as a reservoir of fruit fly parasitoid populations in the Eastern Amazon: an undervalued ecosystem service link: https://peerj.com/articles/11530 last-modified: 2021-06-04 description: Fruit flies are economically important pests that infest a wide variety of host trees. The environmental damage caused by traditional pesticide-based control methods has prompted scientists to seek less damaging alternatives such as biological control by native species. Parasitoids, especially Braconidae species, have excellent potential as biological control agents for fruit flies, being both generalists and well distributed geographically. Native fruit trees that support medium or high levels of these parasitoids could therefore play an important role in biological control strategies. A good potential example is Spondias mombin L. in the Brazilian Amazon, which hosts several species of fruit flies and associated parasitoids. Here, we provide a unique synthesis of over nearly two decades of data from the east Amazon, clearly demonstrating the potential of S. mombin to act as a source and reservoir of fruit fly parasitoids. This important ecosystem service (biological control) provided by the parasitoids and supported by S. mombin could be further enhanced through conservation of this plant species in its natural environment. creator: Maria do Socorro Miranda de Sousa creator: Ezequiel de Deus creator: Adilson Lopes Lima creator: Cristiane Ramos de Jesus creator: Salustiano Vilar da Costa Neto creator: Lailson do Nascimento Lemos creator: Ana Claudia Mendes Malhado creator: Richard J. Ladle creator: Ricardo Adaime uri: https://doi.org/10.7717/peerj.11530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sousa et al. title: Characteristics of the pediatric patients diagnosed with SARS-CoV-2 infection in a Romanian children’s hospital: a retrospective study link: https://peerj.com/articles/11560 last-modified: 2021-06-04 description: BackgroundTo date, information on COVID-19 pediatric patients is still sparse. We aimed to highlight the epidemiological and clinical data regarding SARS-CoV-2 infection in children and adolescents to improve the understanding of the disease in this age group and inform physicians during the ongoing COVID-19 pandemic.MethodsWe conducted a retrospective, observational study in “Marie Curie” Emergency Children’s Hospital from Bucharest, Romania. We analyzed clinical and epidemiological characteristics of the patients confirmed with SARS-CoV-2 infection, between April 1, 2020–October 31, 2020.ResultsA total of 172 patients aged 0–18 years were included, 79 (45.93%) female and 93 (54.07%) male patients. 28 (16.28%) patients had co-morbidities (more often identified in asymptomatic group; p < 0.0001). 47 (27.32%) had exposure to an identified source. 30 (17.44%) patients were asymptomatic; 142 (85.56%) had mild or moderate disease. The most frequent symptoms were: pyrexia (78.87%), digestive symptoms (50%), cough (40.14%). Chest X-ray was performed in 50 patients and it was abnormal in half of them, all being symptomatic. About 2/3 of the evaluated patients had normal leukocytes. The most common hematological change was lymphopenia; monocytes tended to be higher in symptomatic patients. About 40% of the patients were admitted; none required admission to ICU. No significant differences were found between symptomatic and asymptomatic patients regarding gender, age distribution, and exposure to a source.ConclusionsAll the patients had asymptomatic, mild or moderate disease. Patients with comorbidities, classically considered high risk patients, presented the same pattern of disease. creator: Liana-Cătălina Gavriliu creator: Carmen Murariu creator: Vladimir Potop creator: Radu Spătaru uri: https://doi.org/10.7717/peerj.11560 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Gavriliu et al. title: The m6A-related gene signature for predicting the prognosis of breast cancer link: https://peerj.com/articles/11561 last-modified: 2021-06-04 description: N6-methyladenosine (m6A) modification has been shown to participate in tumorigenesis and metastasis of human cancers. The present study aimed to investigate the roles of m6A RNA methylation regulators in breast cancer. We used LASSO regression to identify m6A-related gene signature predicting breast cancer survival with the datasets downloaded from Gene Expression Omnibus and The Cancer Genome Atlas (TCGA). RNA-Seq data of 3409 breast cancer patients from GSE96058 and 1097 from TCGA were used in present study. A 10 m6A-related gene signature associated with prognosis was identified from 22 m6A RNA methylation regulators. The signature divided patients into low- and high-risk group. High-risk patients had a worse prognosis than the low-risk group. Further analyses indicated that IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer. Survival analysis showed that IGF2BP1 is an independent prognostic factor of breast cancer, and higher expression level of IGF2BP1 is associated with shorter overall survival of breast cancer patients. In conclusion, we identified a 10 m6A-related gene signature associated with overall survival of breast cancer. IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer. creator: Shanliang Zhong creator: Zhenzhong Lin creator: Huanwen Chen creator: Ling Mao creator: Jifeng Feng creator: Siying Zhou uri: https://doi.org/10.7717/peerj.11561 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhong et al. title: Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from Bacillus cereus RSA1 link: https://peerj.com/articles/11570 last-modified: 2021-06-04 description: Microbial fibrinolytic proteases are therapeutic enzymes responsible to ameliorate thrombosis, a fatal cardiac-disorder which effectuates due to excessive fibrin accumulation in blood vessels. Inadequacies such as low fibrin specificity, lethal after-effects and short life-span of available fibrinolytic enzymes stimulates an intensive hunt for novel, efficient and safe substitutes. Therefore, we herewith suggest a novel and potent fibrinolytic enzyme RFEA1 from Bacillus cereus RSA1 (MK288105). Although, attributes such as in-vitro purification, characterization and thrombolytic potential of RFEA1 were successfully accomplished in our previous study. However, it is known that structure-function traits and mode of action significantly aid to commercialization of an enzyme. Also, predicting structural model of a protein from its amino acid sequence is challenging in computational biology owing to intricacy of energy functions and inspection of vast conformational space. Our present study thus reports In-silico structural-functional analysis of RFEA1. Sequence based modelling approaches such as—Iterative threading ASSEmbly Refinement (I-TASSER), SWISS-MODEL, RaptorX and Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) were employed to model three-dimensional structure of RFEA1 and the modelled RFEA1 was validated by structural analysis and verification server (SAVES v6.0). The modelled crystal structure revealed the presence of high affinity Ca1 binding site, associated with hydrogen bonds at Asp147, Leu181, Ile185 and Val187residues. RFEA1 is structurally analogous to Subtilisin E from Bacillus subtilis 168. Molecular docking analysis using PATCH DOCK and FIRE DOCK servers was performed to understand the interaction of RFEA1 with substrate fibrin. Strong RFEA1-fibrin interaction was observed with high binding affinity (−21.36 kcal/mol), indicating significant fibrinolytic activity and specificity of enzyme RFEA1. Overall, the computational research suggests that RFEA1 is a subtilisin-like serine endopeptidase with proteolytic potential, involved in thrombus hydrolysis. creator: Chhavi Sharma creator: Arti Nigam creator: Rajni Singh uri: https://doi.org/10.7717/peerj.11570 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sharma et al. title: Response of the characteristics of organic carbon mineralization of soft rock and soil composed of sand to soil depth link: https://peerj.com/articles/11572 last-modified: 2021-06-04 description: The addition of soft rock to aeolian sandy soil can improve the level of fertility and ability of the soil to sequester carbon, which is of substantial significance to improve the ecological environment of the Mu Us sandy land and supplement newly added cultivated land. S oft rock and sand were combined using the ratio (v/v) of 0:1 (CK), 1:5 (S1), 1:2 (S2), and 1:1 (S3). The process of mineralization of organic carbon at different depths (0–10 cm, 10–20 cm, and 20–30 cm) in the combined soil was studied by 58 days of incubation indoors at a constant temperature. The content of soil nutrient s increased significantly under the S2 and S3 treatments and was higher in the 0–10 cm soil depth. The mineralization of rate of soil organic carbon (SOC) of different combination ratios can be divided into three time periods: the stress mineralization stage (1–7 d), the rapid mineralization stage (7–9 d) and the slow mineralization stage (9–58 d). At the end of incubation, the rates of mineralization of SOC and accumulated mineralization amount (Ct) were relatively large in the 0–10 cm soil depth, followed by the 10–20 cm and 20–30 cm soil layers , indicating that the stability of SOC in the surface layer was poor, which is not conducive to the storage of carbon. The content of potentially mineralizable organic carbon (C0) in the soil was consistent with the trend of change of Ct. Compared with the CK treatment, the cumulative organic carbon mineralization rate (Cr) of the S2 and S3 treatment s decreased by 7.77% and 6.05%, respectively; and the C0/SOC decreased by 22.84% and 15.55%, respectively. Moreover, the Cr and C0/SOC values in the 10–20 cm soil depth were small, which indirectly promoted the storage of organic carbon. With the process of SOC mineralization, the contents of soil microbial biomass carbon (SMBC) and dissolved organic carbon (DOC) tended to decrease compared with the initial contents, with larger amplitudes in the 20–30 cm and 10–20 cm soil depth s, respectively. SOC, total nitrogen, available potassium, SMBC and DOC were all closely related to the process of mineralization of organic carbon. Therefore, the accumulation of soil carbon could be enhanced when the proportion of soft rock and sand composite soil was between 1:2 and 1:1, and the 10–20 cm soil depth was relatively stable. These results provide a theoretical basis for the improvement of desertified land. creator: Wanying Li creator: Zhen Guo creator: Juan Li creator: Jichang Han uri: https://doi.org/10.7717/peerj.11572 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats link: https://peerj.com/articles/11498 last-modified: 2021-06-03 description: Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure. creator: Imogene A. Cancellare creator: Elizabeth M. Kierepka creator: Jan Janecka creator: Byron Weckworth creator: Richard T. Kazmaier creator: Rocky Ward uri: https://doi.org/10.7717/peerj.11498 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cancellare et al. title: Transcriptome analysis of Sonneratia caseolaris seedlings under chilling stress link: https://peerj.com/articles/11506 last-modified: 2021-06-03 description: Sonneratia caseolaris is a native mangrove species found in China. It is fast growing and highly adaptable for mangrove afforestation, but suffered great damage by chilling event once introduced to high latitude area. To understand the response mechanisms under chilling stress, physiological and transcriptomic analyses were conducted. The relative electrolyte conductivity, malondialdehyde (MDA) content, soluble sugar content and soluble protein content increased significantly under chilling stress. This indicated that S. caseolaris suffered great damage and increased the levels of osmoprotectants in response to the chilling stress. Gene expression comparison analysis of S. caseolaris leaves after 6 h of chilling stress was performed at the transcriptional scale using RNA-Seq. A total of 168,473 unigenes and 3,706 differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analyses showed that the DEGs were mainly involved in carbohydrate metabolism, antioxidant enzyme, plant hormone signal transduction, and transcription factors (TFs). Sixteen genes associated with carbohydrate metabolism, antioxidant enzyme, phytohormones and TFs were selected for qRT-PCR verification, and they indicated that the transcriptome data were reliable. Our work provided a comprehensive review of the chilling response of S. caseolaris at both physiological and transcriptomic levels, which will prove useful for further studies on stress-responses in mangrove plants. creator: Yong Yang creator: Chunfang Zheng creator: Cairong Zhong creator: Tianxi Lu creator: Juma Gul creator: Xiang Jin creator: Ying Zhang creator: Qiang Liu uri: https://doi.org/10.7717/peerj.11506 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: iTRAQ-based quantitative proteomic analysis of heat stress-induced mechanisms in pepper seedlings link: https://peerj.com/articles/11509 last-modified: 2021-06-03 description: BackgroundAs one of the most important vegetable crops, pepper has rich nutritional value and high economic value. Increasing heat stress due to the global warming has a negative impact on the growth and yield of pepper.MethodsTo understand the heat stress response mechanism of pepper, an iTRAQ-based quantitative proteomic analysis was employed to identify possible heat-responsive proteins and metabolic pathways in 17CL30 and 05S180 pepper seedlings under heat stress.ResultIn the present study, we investigated the changes of phenotype, physiology, and proteome in heat-tolerant (17CL30) and heat-sensitive (05S180) pepper cultivars in response to heat stress. Phenotypic and physiological changes showed that 17CL30 had a stronger ability to resist heat stress compared with 05S180. In proteomic analysis, a total of 3,874 proteins were identified, and 1,591 proteins were considered to participate in the process of heat stress response. According to bioinformatic analysis of heat-responsive proteins, the heat tolerance of 17CL30 might be related to a higher ROS scavenging, photosynthesis, signal transduction, carbohydrate metabolism, and stress defense, compared with 05S180. creator: Jing Wang creator: Chengliang Liang creator: Sha Yang creator: Jingshuang Song creator: Xuefeng Li creator: Xiongze Dai creator: Fei Wang creator: Niran Juntawong creator: Fangjun Tan creator: Xilu Zhang creator: Chunhai Jiao creator: Xuexiao Zou creator: Wenchao Chen uri: https://doi.org/10.7717/peerj.11509 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Spatial patterns and associations of tree species at different developmental stages in a montane secondary temperate forest of northeastern China link: https://peerj.com/articles/11517 last-modified: 2021-06-03 description: BackgroundSecondary forests have become the major forest type worldwide. Research on spatial patterns and associations of tree species at different developmental stages may be informative in understanding the structure and dynamic processes of secondary forests.MethodsIn this study, we used point pattern analysis to analyze the spatial patterns and associations of tree species at seedling, sapling and adult stages in a 4ha plot in the montane secondary temperate forest of northeastern China.ResultsWe found that species showed similar patterns at seedling, sapling and adult stages, and aggregation was the dominant pattern. The spatial patterns of tree species were mainly affected by habitat heterogeneity. In addition, the strength of positive or negative associated pattern among tree species would decrease with developmental stages, which attributed to neighborhood competition and plant size increasing.ConclusionsOur results indicated that the spatial patterns and associations of tree species at seedling and sapling stages partly reflected that at adult stage; habitat heterogeneity and neighborhood competition jointly contributed to species coexistence in this secondary forest. creator: Jia Liu creator: Xuejiao Bai creator: You Yin creator: Wenguang Wang creator: Zhiqiang Li creator: Pengyu Ma uri: https://doi.org/10.7717/peerj.11517 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Liu et al. title: Freshwater-adapted sea bass Dicentrarchus labrax feeding frequency impact in a lettuce Lactuca sativa aquaponics system link: https://peerj.com/articles/11522 last-modified: 2021-06-03 description: The aim of this study is to investigate the effect of three daily fish feeding frequencies, two, four and eight times per day (FF2, FF4, and FF8, respectively) on growth performance of sea bass (Dicentrarchus labrax)and lettuce plants (Lactuca sativa) reared in aquaponics. 171 juvenile sea bass with an average body weight of 6.80 ± 0.095 g were used, together with 24 lettuce plants with an average initial height of 11.78 ± 0.074 cm over a 45-day trial period. FF2 fish group showed a significantly lower final weight, weight gain and specific growth rate than the FF4 and FF8 groups. Voluntary feed intake was similar for all the three feeding frequencies treatmens (p > 0.05). No plant mortality was observed during the 45-day study period. All three aquaponic systems resulted in a similar leaf fresh weight and fresh and dry aerial biomass. The results of the present study showed that the FF4 or FF8 feeding frequency contributes to the more efficient utilization of nutrients for better growth of sea bass adapted to fresh water while successfully supporting plant growth to a marketable biomass. creator: Paraskevi Stathopoulou creator: Panagiotis Berillis creator: Nikolaos Vlahos creator: Eleni Nikouli creator: Konstantinos A. Kormas creator: Efi Levizou creator: Nikolaos Katsoulas creator: Eleni Mente uri: https://doi.org/10.7717/peerj.11522 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Stathopoulou et al. title: Effects of maternal taurine supplementation on maternal dietary intake, plasma metabolites and fetal growth and development in cafeteria diet fed rats link: https://peerj.com/articles/11547 last-modified: 2021-06-03 description: BackgroundMaternal obesity may disrupt the developmental process of the fetus during gestation in rats. Recent evidence suggests that taurine can exert protective role against detrimental influence of obesogenic diets. This study aimed to examine the effect of maternal cafeteria diet and/or taurine supplementation on maternal dietary intake, plasma metabolites, fetal growth and development.MethodsFemale Wistar rats were fed a control diet (CON), CON supplemented with 1.5% taurine in drinking water (CONT), cafeteria diet (CAF) or CAF supplemented with taurine (CAFT) from weaning. After 8 weeks all animals were mated and maintained on the same diets during pregnancy and lactation.ResultsDietary intakes were significantly different between the groups. Both CAF and CAFT fed dams consumed less water in comparison to CON and CONT dams. Taurine supplementation only increased plasma taurine concentrations in CONT group. Maternal plasma adiponectin concentrations increased in CAF and CAFT fed dams compared to CON and CONT fed dams and there was no effect of taurine. Hyperleptinemia was observed in CAF fed dams but not in CAFT fed dams. Malondialdehyde was significantly increased only in CAF fed dams. Litter size, sex ratio and birth weight were similar between the groups. There was an increase in neonatal mortality in CONT group.DiscussionThis study showed that maternal taurine supplementation exerted modest protective effects on cafeteria diet induced maternal obesity. The increased neonatal mortality in CONT neonates indicates possible detrimental effects of taurine supplementation in the setting of normal pregnancy. Therefore, future studies should investigate the optimal dose of taurine supplementation and long term potential effects on the offspring. creator: Arzu Kabasakal Çetin creator: Tuǧba Alkan Tuğ creator: Atila Güleç creator: Aslı Akyol uri: https://doi.org/10.7717/peerj.11547 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kabasakal Çetin et al. title: No significant association of repeated messages with changes in health compliance in the COVID-19 pandemic: a registered report on the extended parallel process model link: https://peerj.com/articles/11559 last-modified: 2021-06-03 description: When people are confronted with health proposals during the coronavirus disease 2019 (COVID-19) pandemic, it has been suggested that fear of COVID-19 can serve protective functions and ensure public health compliance. However, health proposal repetition and its perceived efficacy also influence the behavior intention toward the proposal, which has not yet been confirmed in the COVID-19 context. The present study examined whether the extended parallel process model (EPPM) could be generalized to a naturalistic context like the COVID-19 pandemic. Additionally, we explored how repetition of a health proposal is involved with the EPPM. In this study, two groups of participants were exposed to the same health proposal related to COVID-19, where one group was exposed once and another group twice. Participants then filled out a questionnaire consisting of items concerning behavior intention and adapted from the Risk Behavior Diagnosis Scale. Structural equation modeling was used to determine the multivariate associations between the variables. Although the results showed that behavior intention is predicted by perceived efficacy, no significant influence of perceived threat was detected. Furthermore, no significant effect of repetition was found toward either response efficacy or perceived susceptibility. These findings indicate that to promote health compliance during the COVID-19 pandemic, it is more efficient to focus on health proposals’ perceived efficacy rather than the disease’s perceived threat. For future health communication research, the present study suggests improved analysis strategies and repeated manipulation of messages. creator: Jingwen Yang creator: Xue Wu creator: Kyoshiro Sasaki creator: Yuki Yamada uri: https://doi.org/10.7717/peerj.11559 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang et al. title: Characterisation of secretome-based immune responses of human leukocytes infected with various Mycobacterium tuberculosis lineages link: https://peerj.com/articles/11565 last-modified: 2021-06-03 description: BackgroundDifferences in immune responses against different lineages of Mycobacterium tuberculosis (Mtb), and by different types of immune cell, are still poorly understood. We aimed to compare the secretome-based immune responses among three Mtb lineages and among immune-cell types. The immune responses were also investigated during infection and when the bacilli had been eliminated from the immune cells.MethodsHuman primary leukocytes were infected with strains representing three lineages of Mtb (East-Asian, Indo-Oceanic and Euro-American). Label-free GeLC MS/MS proteomic analysis of secretomes was performed. The response of each immune-cell type was compared with the appropriate interactome database for each.ResultsThe expression pattern of proteins secreted by Mtb-infected leukocytes differed among Mtb lineages. The ancestral lineage (IO lineage) had a greater ability to activate MMP14 (associated with leukocyte migration) than did the more recent lineages (EA and EuA). During infection, proteins secreted by macrophages, dendritic cells, neutrophils and B-cells were associated with cell proliferation. Following clearance of Mtb, proteins associated with interferon signaling were found in macrophages, dendritic cells and neutrophils: proteins associated with antigen processing were found in B-cells and regulatory T-cells. Expression of immune response-related proteins from many immune-cell types might be suppressed by Mtb infection. Our study has provided a better insight into the host-pathogen interaction and immune response against different Mtb lineages. creator: Benjawan Kaewseekhao creator: Sittiruk Roytrakul creator: Yodying Yingchutrakul creator: Marut Laohaviroj creator: Kanin Salao creator: Kiatichai Faksri uri: https://doi.org/10.7717/peerj.11565 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kaewseekhao et al. title: Bite force estimates in juvenile Tyrannosaurus rex based on simulated puncture marks link: https://peerj.com/articles/11450 last-modified: 2021-06-02 description: BackgroundBite marks attributed to adult Tyrannosaurus rex have been subject to numerous studies. However, few bite marks attributed to T. rex have been traced to juveniles, leaving considerable gaps in understanding ontogenetic changes in bite mechanics and force, and the paleoecological role of juvenile tyrannosaurs in the late Cretaceous.MethodsHere we present bite force estimates for a juvenile Tyrannosaurus rex based on mechanical tests designed to replicate bite marks previously attributed to a T. rex of approximately 13 years old. A maxillary tooth of the juvenile Tyrannosaurus specimen BMR P2002.4.1 was digitized, replicated in dental grade cobalt chromium alloy, and mounted to an electromechanical testing system. The tooth was then pressed into bovine long bones in various locations with differing cortical bone thicknesses at varying speeds for a total of 17 trials. Forces required to replicate punctures were recorded and puncture dimensions were measured.ResultsOur experimentally derived linear models suggest bite forces up to 5,641.19 N from cortical bone thickness estimated from puncture marks on an Edmontosaurus and a juvenile Tyrannosaurus. These findings are slightly higher than previously estimated bite forces for a juvenile Tyrannosaurus rex of approximately the same size as BMR P2002.4.1 but fall within the expected range when compared to estimates of adult T. rex.DiscussionThe results of this study offer further insight into the role of juvenile tyrannosaurs in late Cretaceous ecosystems. Furthermore, we discuss the implications for feeding mechanisms, feeding behaviors, and ontogenetic niche partitioning. creator: Joseph E. Peterson creator: Z. Jack Tseng creator: Shannon Brink uri: https://doi.org/10.7717/peerj.11450 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Peterson et al. title: Air pollutants and outpatient visits for influenza-like illness in Beijing, China link: https://peerj.com/articles/11397 last-modified: 2021-06-02 description: BackgroundAir pollution leads to many adverse health conditions, mainly manifested by respiratory or cardiac symptoms. Previous studies are limited as to whether air pollutants were associated to influenza-like illness (ILI). This study aimed to explore the association between air pollutants and outpatient visits for ILI, especially during an outbreak of influenza.MethodsDaily counts of hospital visits for ILI were obtained from Peking University Third Hospital between January 1, 2015, and March 31, 2018. A generalized additive Poisson model was applied to examine the associations between air pollutants concentrations and daily outpatient visits for ILI when adjusted for the meteorological parameters.ResultsThere were 35862 outpatient visits at the fever clinic for ILI cases. Air quality index (AQI), PM2.5, PM10, CO and O3 on lag0 days, as well as nitrogen dioxide (NO2) and sulfur dioxide (SO2) on lag1 days, were significantly associated with an increased risk of outpatient visits for ILI from January 2015 to November 2017. From December 2017 to March 2018, on lag0 days, air pollutants PM2.5 [risk ratio (RR) = 0.971, 95% CI: 0.963-0.979], SO2 (RR = 0.892, 95% CI: 0.840–0.948) and CO (RR = 0.306, 95% CI: 0.153–0.612) were significantly associated with a decreased risk of outpatient visits for ILI. Interestingly, on the lag2 days, all the pollutants were significantly associated with a reduced risk of outpatient visits for ILI except for O3. We did not observe the linear correlations between the outpatient visits for ILI and any of air pollutants, which were instead associated via a curvilinear relationship.ConclusionsWe found that the air pollutants may be associated with an increased risk of outpatient visits for ILI during the non-outbreak period and with a decreased risk during the outbreak period, which may be linked with the use of disposable face masks and the change of outdoor activities. These findings expand the current knowledge of ILI outpatient visits correlated with air pollutants during an influenza pandemic. creator: Xiaoguang Li creator: Jie Xu creator: Wei Wang creator: Jing-Jin Liang creator: Zhong-Hua Deng creator: Juan Du creator: Ming-Zhu Xie creator: Xin-Rui Wang creator: Yaqiong Liu creator: Fuqiang Cui creator: Qing-Bin Lu uri: https://doi.org/10.7717/peerj.11397 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Li et al. title: Expression and gene regulation network of TYMS and BCL2L1 in colorectal cancer based on data mining link: https://peerj.com/articles/11368 last-modified: 2021-06-02 description: BackgroundThe purpose of this study was to study the role of thymidylate synthetase (TYMS) and B-cell lymphoma-2 like 1 (BCL2L1) in the occurrence and development of colorectal cancer and its potential regulatory mechanism.MethodsThe Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to examine the expression and prognostic value of TYMS and BCL2L1 in colorectal cancer. C-BioPortal analysis was used to detect the TYMS and BCL2L1 alterations. Through The Human Protein Atlas (THPA), the TYMS and BCL2L1 protein levels were also assessed. The protein protein interaction (PPI) network was built using GeneMANIA analysis, while co-expression genes correlated with TYMS and BCL2L1 were identified using LinkedOmics analysis. Finally, we collected clinical samples to verify the expressions of TYMS and BCL2L1 in colorectal cancer.ResultsTYMS and BCL2L1 were up-regulated, and TYMS and BCL2L1 genomic alterations were not associated with the occurrence of colorectal cancer. TYMS and BCL2L1 were significantly connected with the prognosis of colorectal cancer patients. The genes interacted with TYMS and BCL2L1 were linked to functional networks involving pathway of apoptosis, apoptosis-multiple species, colorectal cancer, platinum drug resistance and p53 signaling pathway. qRT-PCR verification results of TYMS were consistent with the result of TCGA and GEO analysis.ConclusionsThis study display that data mining can efficiently provide information on expression of TYMS and BCL2L1, correlated genes of TYMS and BCL2L1, core pathways and potential functional networks in colorectal cancer, suggesting that TYMS and BCL2L1 may become new prognostic and therapeutic targets for colorectal cancer. creator: Yanghua Jie creator: Xiaobei Yang creator: Weidong Chen uri: https://doi.org/10.7717/peerj.11368 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jie et al. title: Optimized nitrogen fertilizer application strategies under supplementary irrigation improved winter wheat (Triticum aestivum L.) yield and grain protein yield link: https://peerj.com/articles/11467 last-modified: 2021-06-02 description: BackgroundExploring suitable split nitrogen management is essential for winter wheat production in the Huang-Huai-Hai Plain of China (HPC) under water-saving irrigation conditions, which can increase grain and protein yields by improving nitrogen translocation, metabolic enzyme activity and grain nitrogen accumulation.MethodsTherefore, a 2-year field experiment was conducted to investigate these effects in HPC. Nitrogen fertilizer was applied at a constant total rate (240 kg/ha), split between the sowing and at winter wheat jointing growth stage in varying ratios, N1 (0% basal and 100% dressing fertilizer), N2 (30% basal and 70% dressing fertilizer), N3 (50% basal and 50% dressing fertilizer), N4 (70% basal and 30% dressing fertilizer), and N5 (100% basal and 0% dressing fertilizer).ResultsWe found that the N3 treatment significantly increased nitrogen accumulation post-anthesis and nitrogen translocation to grains. In addition, this treatment significantly increased flag leaf free amino acid levels, and nitrate reductase and glutamine synthetase activities, as well as the accumulation rate, active accumulation period, and accumulation of 1000-grain nitrogen. These factors all contributed to high grain nitrogen accumulation. Finally, grain yield increase due to N3 ranging from 5.3% to 15.4% and protein yield from 13.7% to 31.6%. The grain and protein yields were significantly and positively correlated with nitrogen transport parameters, nitrogen metabolic enzyme activity levels, grain nitrogen filling parameters.ConclusionsTherefore, the use of split nitrogen fertilizer application at a ratio of 50%:50% basal-topdressing is recommended for supporting high grain protein levels and strong nitrogen translocation, in pursuit of high-quality grain yield. creator: Zhen Zhang creator: Zhenwen Yu creator: Yongli Zhang creator: Yu Shi uri: https://doi.org/10.7717/peerj.11467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Nicotine smoking is associated with impaired cognitive performance in Pakistani young people link: https://peerj.com/articles/11470 last-modified: 2021-06-02 description: Nicotine smoking is the most common mode of tobacco smoking among young people. It affects the areas of the brain associated with memory, attention, and learning. This study has investigated the effect of nicotine smoking on cognitive performance. One hundred male volunteers (50 nicotine smokers and 50 nonsmokers) aged 18–30 years with similar socioeconomic backgrounds were recruited for this study. Clinical history of participants was obtained using a questionnaire. Their brain health and handedness were determined using the Mini Mental State Examination (MMSE) and the Edinburgh Handedness Inventory (EHI), respectively. The dependent variables examined in the study were attention-switching tasks (AST), pattern recognition memory (PRM), and choice reaction time (CRT). These parameters were assessed using the Cambridge Neuropsychological Automated Battery (CANTAB). The average ages of participating smokers and nonsmokers were 24.02 ± 3.41 years (mean ± standard deviation) and 22.68 ± 1.87 years, respectively. MMSE and EHI scores of smokers were 28.42 ± 1.09 and 99.75 ± 1.77, respectively; for nonsmokers, these scores were 28.54 ± 1.34 and 98 ± 1.91, respectively. The mean score for AST correct latency/delay was significantly higher (p = 0.050) in smokers (620.26 ± 142.03) than in nonsmokers (570.11 ± 108.39). The percentage of correct AST trials was significantly higher (p = 0.000) in nonsmokers (96.95 ± 2.18) than in smokers (83.75 ± 11.22). The PRM percent correct were significantly higher (p = 0.000) of nonsmokers (93.42 ± 8.34) than of smokers (79.75 ± 13.44). The mean correct latency for CRT was significantly higher (p = 0.009) in smokers (509.87 ± 129.83) than in nonsmokers (455.20 ± 65.73). From this data, it can be concluded that nicotine smoking is linked with impaired cognitive functions in smokers. creator: Tuba Riaz creator: Ghulam Murtaza creator: Areej Arif creator: Shahid Mahmood creator: Razia Sultana creator: Fawaz Al-Hussain creator: Shahid Bashir uri: https://doi.org/10.7717/peerj.11470 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Riaz et al. title: Involvement of plasminogen activator inhibitor-1 and its related molecules in atrial fibrosis in patients with atrial fibrillation link: https://peerj.com/articles/11488 last-modified: 2021-06-02 description: Atrial fibrillation is the most common form of cardiac arrhythmia. Atrial fibrosis is a significant feature of atrial fibrillation though its mechanism is not well understood. We searched the Gene Expression Omnibus database to compare mRNA expression patterns between atrial fibrillation and sinus rhythm samples; one hundred and forty eight differentially expressed genes were identified. Most of these genes were significantly enriched in the extracellular matrix organization process and collagen-activated tyrosine kinase receptor signaling pathway. To screen hub genes involved in atrial fibrosis, we constructed a protein-protein interaction network and found that three hub genes (SERPINE1/plasminogen activator inhibitor-1/PAI-1, TIMP Metallopeptidase Inhibitor 3/TIMP3 and decorin/DCN) play vital roles in atrial fibrosis, especially plasminogen activator inhibitor-1. Elevated plasminogen activator inhibitor-1 expression was positively correlated with the p53 signaling pathway. Plasminogen activator inhibitor-1 and p53 protein expression levels were verified in patients with sinus rhythm and atrial fibrillation by Western blot analysis. Compared with the sinus rhythm controls, p53 and plasminogen activator inhibitor-1 protein expressions were upregulated in the atrial tissues of patients with atrial fibrillation. p53 was also found to regulate plasminogen activator inhibitor-1 based on the results of cellular and molecular experiments. Thus, the p53/plasminogen activator inhibitor-1 signaling axis may participate in the pathophysiological processes of atrial fibrillation, and plasminogen activator inhibitor-1 may serve as a new therapeutic biomarker in atrial fibrillation. creator: Qiaoqiao Li creator: Yingyu Lai creator: Xiaoyan Gao creator: Xin Li creator: Chun-Yu Deng creator: Huiming Guo creator: Junfei Zhao creator: Hui Yang creator: Yuwen Xu creator: Shulin Wu creator: Yumei Xue creator: Fang Rao uri: https://doi.org/10.7717/peerj.11488 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: The gut microbiome of the Sunda pangolin (Manis javanica) reveals its adaptation to specialized myrmecophagy link: https://peerj.com/articles/11490 last-modified: 2021-06-02 description: BackgroundThe gut microbiomes of mammals are closely related to the diets of their hosts. The Sunda pangolin (Manis javanica) is a specialized myrmecophage, but its gut microbiome has rarely been studied.MethodsUsing high-throughput Illumina barcoded 16S rRNA amplicons of nine fecal samples from nine captive Sunda pangolins, we investigated their gut microbiomes.ResultsThe detected bacteria were classified into 14 phyla, 24 classes, 48 orders, 97 families, and 271 genera. The main bacterial phyla were Firmicutes (73.71%), Proteobacteria (18.42%), Actinobacteria (3.44%), and Bacteroidetes (0.51%). In the PCoA and neighbor-net network (PERMANOVA: pangolins vs. other diets, weighted UniFrac distance p < 0.01, unweighted UniFrac distance p < 0.001), the gut microbiomes of the Sunda pangolins were distinct from those of mammals with different diets, but were much closer to other myrmecophages, and to carnivores, while distant from herbivores. We identified some gut microbiomes related to the digestion of chitin, including Lactococcus, Bacteroides, Bacillus, and Staphylococcus species, which confirms that the gut microbiome of pangolins may help them to digest chitin.SignificanceThe results will aid studies of extreme dietary adaption and the mechanisms of diet differentiation in mammals, as well as metagenomic studies, captive breeding, and ex situ conservation of pangolins. creator: Fuhua Zhang creator: Na Xu creator: Wenhua Wang creator: Yishuang Yu creator: Shibao Wu uri: https://doi.org/10.7717/peerj.11490 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Zhang et al. title: Reliability of hip muscle strength measured in principal and intermediate planes of movement link: https://peerj.com/articles/11521 last-modified: 2021-06-02 description: BackgroundMuscle strength testing is widely used in clinical and athletic populations. Commercially available dynamometers are designed to assess strength in three principal planes (sagittal, transverse, frontal). However, the anatomy of the hip suggests muscles may only be recruited submaximally during tasks performed in these principal planes.ObjectiveTo evaluate the inter-session reliability of maximal isometric hip strength in the principal planes and three intermediate planes.MethodsTwenty participants (26.1 ± 2.7 years, 50% female) attended two testing sessions 6.2 ± 1.8 days apart. Participants completed 3-5 maximal voluntary isometric contractions for hip abduction, adduction, flexion, extension, and internal and external rotation measured using a fixed uniaxial load cell (custom rig) and commercial dynamometer (Biodex). Three intermediate hip actions were also tested using the custom rig: extension with abduction, extension with external rotation, and extension with both abduction and external rotation.ResultsModerate-to-excellent intraclass correlation coefficients were observed for all principal and intermediate muscle actions using the custom rig (0.72–0.95) and the Biodex (0.85–0.95). The minimum detectable change was also similar between devices (custom rig = 11–31%; Biodex = 9–20%). Bland-Altman analysis revealed poor agreement between devices (range between upper and lower limits of agreement = 77–131%).ConclusionsAlthough the custom rig and Biodex showed similar reliability, both devices may lack the sensitivity to detect small changes in hip strength commonly observed following intervention. creator: Basilio A.M. Goncalves creator: David J. Saxby creator: Adam Kositsky creator: Rod S. Barrett creator: Laura E. Diamond uri: https://doi.org/10.7717/peerj.11521 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Goncalves et al. title: Effects of thiourea on the skull of Triturus newts during ontogeny link: https://peerj.com/articles/11535 last-modified: 2021-06-02 description: BackgroundIn amphibians, thyroid hormone (TH) has a profound role in cranial development, especially in ossification of the late-appearing bones and remodeling of the skull. In the present study, we explored the influence of TH deficiency on bone ossification and resulting skull shape during the ontogeny of Triturus newt hybrid larvae obtained from interspecific crosses between T. ivanbureschi and T. macedonicus.MethodsLarvae were treated with two concentrations of thiourea (an endocrine disruptor that chemically inhibits synthesis of TH) during the midlarval and late larval periods. Morphological differences of the cranium were assessed at the end of the midlarval period (ontogenetic stage 62) and the metamorphic stage after treatment during the late larval period.ResultsThere was no difference in the ossification level and shape of the skull between the experimental groups (control and two treatment concentrations) at stage 62. During the late larval period and metamorphosis, TH deficit had a significant impact on the level of bone ossification and skull shape with no differences between the two treatment concentrations of thiourea. The most pronounced differences in bone development were: the palatopterygoid failed to disintegrate into the palatal and pterygoid portions, retardation was observed in development of the maxilla, nasal and prefrontal bones and larval organization of the vomer was retained in thiourea-treated larvae.ConclusionsThis implies that deficiency of TH caused retardation in development and arrested metamorphic cranium skeletal reorganization, which resulted in divergent cranial shape compared to the control group. Our results confirmed that skull remodeling and ossification of late-appearing bones is TH–dependent, as in other studied Urodela species. Also, our results indicate that TH plays an important role in the establishment of skull shape during the ontogeny of Triturus newts, especially during the late larval period and metamorphosis, when TH concentrations reach their maximum. creator: Maja Ajduković creator: Tijana Vučić creator: Milena Cvijanović uri: https://doi.org/10.7717/peerj.11535 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ajduković et al. title: Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus link: https://peerj.com/articles/11552 last-modified: 2021-06-02 description: BackgroundOseltamivir (OTV)-resistant influenza virus exhibits His-to-Tyr mutation at residue 274 (H274Y) in N1 neuraminidase (NA). However, the molecular mechanisms by which the H274Y mutation in NA reduces its binding affinity to OTV have not been fully elucidated.MethodsIn this study, we used dynamic residue interaction network (dRIN) analysis based on molecular dynamics simulation to investigate the correlation between the OTV binding site of NA and its H274Y mutation site.ResultsdRIN analysis revealed that the OTV binding site and H274Y mutation site of NA interact via the three interface residues connecting them. H274Y mutation significantly enhanced the interaction between residue 274 and the three interface residues in NA, thereby significantly decreasing the interaction between OTV and its surrounding loop 150 residues. Thus, we concluded that such changes in residue interactions could reduce the binding affinity of OTV to NA, resulting in drug resistant influenza viruses. Using dRIN analysis, we succeeded in understanding the characteristic changes in residue interactions due to H274Y mutation, which can elucidate the molecular mechanism of reduction in OTV binding affinity to influenza NA. Finally, the dRIN analysis used in this study can be widely applied to various systems such as individual proteins, protein-ligand complexes, and protein-protein complexes, to characterize the dynamic aspects of the interactions. creator: Mohini Yadav creator: Manabu Igarashi creator: Norifumi Yamamoto uri: https://doi.org/10.7717/peerj.11552 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yadav et al. title: Alien plants of Europe: introduction pathways, gateways and time trends link: https://peerj.com/articles/11270 last-modified: 2021-06-01 description: The Convention on Biological Diversity (CBD) pathways classification framework used in the implementation of the European Union’s (EU) Regulation 1143/2014 on invasive alien species (IAS Regulation) has recently been adopted by the European Alien Species Information Network (EASIN), the official information system supporting the implementation of the IAS Regulation. In the current paper, the result of an alignment of the primary introduction pathways of all alien plants in Europe included in the EASIN catalogue is presented, based on the CBD framework. In total, 6,250 alien plant taxa (marine plants excluded), both alien to Europe (native range outside Europe) and alien in Europe (native range partially in Europe) are reported. Altogether 5,175 plant taxa had their primary introduction pathway aligned based on the CBD framework, while for the rest the pathway remains unknown. In addition, the taxonomy, year and country of its first record in the wild are provided for each taxon. Our analyses reveal that the main primary introduction pathways of alien plants into Europe are linked to accidental escapes from ornamental and horticultural activities. Northwestern European countries seem to act as the main gateway areas of alien plants into Europe. Recent first observations of new alien taxa growing spontaneously exhibit a contemporary accelerating trend for plants alien to Europe, particularly linked to ornamental and horticultural activities. On the other hand, the number of new plants alien in Europe seems to have stabilized over the last few decades. The present work can assist in the prioritization of introduction pathways control, with the target of slowing down the rate of alien plants introductions into Europe, following also the requirements of the IAS Regulation. creator: Margarita Arianoutsou creator: Ioannis Bazos creator: Anastasia Christopoulou creator: Yannis Kokkoris creator: Andreas Zikos creator: Sevasti Zervou creator: Pinelopi Delipetrou creator: Ana Cristina Cardoso creator: Ivan Deriu creator: Eugenio Gervasini creator: Konstantinos Tsiamis uri: https://doi.org/10.7717/peerj.11270 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Arianoutsou et al. title: A new pterosaur tracksite from the Lower Cretaceous of Wuerho, Junggar Basin, China: inferring the first putative pterosaur trackmaker link: https://peerj.com/articles/11361 last-modified: 2021-06-01 description: We report the discovery of 114 small pterosaur footprints preserved in a greyish-green fine sandstone slab comprising 57 manus imprints and 57 pes imprints. Due to the chaotic distribution of footprints, the trackways are difficult to recognize. The pes imprints are sub-triangular and enlongate, the metatarsal part is roughly subequal to the digital part. The manus imprints are asymmetrical, longer than wide, and the lengths of digits I–III gradually increase. According to the diagnostic features of the Wuerho small pterosaur tracks, the present set was classified as Pteraichnus and is different from the nine reported valid ichnospecies of Pteraichnus. We therefore propose a new ichnospecies, Pteraichnus wuerhoensis isp. nov. The description is based on the anatomical characteristics (lengths of digits I–IV, length of digital part, length of metatarsal part) extracted from the pes imprints and comparisons with the pes bone fossils of Noripterus complicidens. We infer that the footprints were probably left by N. complicidens and the total width of the wings was presumably 2–2.3 m. In addition, the high density (365 per square meter) and varied sizes of the Wuerho small pterosaur tracks suggest that many pterosaurs of different ages lived in Huangyangquan Reservoir tracksite 1 area. Thus the trackmakers may have had gregarious behavior. creator: Yang Li creator: Xiaolin Wang creator: Shunxing Jiang uri: https://doi.org/10.7717/peerj.11361 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Early maternal separation is not associated with changes in telomere length in domestic kittens (Felis catus) link: https://peerj.com/articles/11394 last-modified: 2021-06-01 description: ObjectiveStudies of multiple species have found that adverse early life experiences, including childhood trauma and maternal separation, can result in accelerated telomere shortening. The objective of this study was to determine if premature separation from the mother affected telomere length in domestic kittens (Felis catus). Subjects were 42 orphaned kittens and 10 mother-reared kittens from local animal rescue groups and shelters. DNA was extracted from whole blood collected from kittens at approximately 1 week and 2 months of age. Telomere length was assessed by qPCR (quantitative polymerase chain reaction) from a total of 86 samples and expressed as a ratio of telomere PCR relative to a single copy gene PCR (T/S).ResultsA generalized linear mixed model found there were no detectable differences in telomere length based on survival (F1, 76.2 = 3.35, p = 0.07), orphan status (F1, 56.5 = 0.44, p = 0.51), time point (F1, 43.5 = 0.19, p = 0.67), or the interaction between orphan status and time (F1, 43.5 = 0.86, p = 0.36). Although in other species telomere shortening is commonly associated with aging, even early in life, we did not find evidence for telomere shortening by two months of age. Our results suggest that the experience of early maternal separation in domestic cats who are subsequently hand-reared by humans does not accelerate telomere shortening compared to mother-reared kittens, at least in the first few months of life. creator: Mikel Delgado creator: C.A. Tony Buffington creator: Melissa Bain creator: Dana L. Smith creator: Karen Vernau uri: https://doi.org/10.7717/peerj.11394 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Delgado et al. title: Guiclupea superstes, gen. et sp. nov., the youngest ellimmichthyiform (clupeomorph) fish to date from the Oligocene of South China link: https://peerj.com/articles/11418 last-modified: 2021-06-01 description: A new ellimmichthyiform, Guiclupea superstes, gen. et sp. nov., from the Oligocene Ningming Formation of Ningming Basin, Guangxi Zhuang Autonomous Region, South China is described herein. With relatively large body size, parietals meeting at the midline, anterior ceratohyal with a beryciform foramen in the center, a complete predorsal scutes series of very high number and about equally-size scutes with radiating ridges on dorsal surface, first preural centrum unfused with first uroneural but fused with the parhypural, and first ural centrum of roughly the same size as the preural centrum, Guiclupea superstes cannot be assigned to the order Clupeiformes. The phylogenetic analyses using parsimony and Bayesian inference methods with Chanos/Elops as outgroup respectively suggests that the new form is closer to ellimmichthyiform genus Diplomystus than to any other fishes, although there are some discrepancies between the two criteria and different outgroups used. It shares with Diplomystus the high supraoccipital crest, pelvic-fin insertion in advance of dorsal fin origin, and the number of predorsal scutes more than 20. The new form represents the youngest ellimmichthyiform fish record in the world. Its discovery indicates that the members of the Ellimmichthyiformes had a wider distribution range and a longer evolutional history than previously known. creator: Gengjiao Chen creator: Mee-mann Chang creator: Feixiang Wu creator: Xiaowen Liao uri: https://doi.org/10.7717/peerj.11418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data link: https://peerj.com/articles/11425 last-modified: 2021-06-01 description: Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation. creator: Sofia G. Seabra creator: Ana S.B. Rodrigues creator: Sara E. Silva creator: Ana Carina Neto creator: Francisco Pina-Martins creator: Eduardo Marabuto creator: Vinton Thompson creator: Michael R. Wilson creator: Selçuk Yurtsever creator: Antti Halkka creator: Maria Teresa Rebelo creator: Paulo A.V. Borges creator: José A. Quartau creator: Chris D. Jiggins creator: Octávio S. Paulo uri: https://doi.org/10.7717/peerj.11425 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Seabra et al. title: Development of landscape conservation value map of Jeju island, Korea for integrative landscape management and planning using conservation value of landscape typology link: https://peerj.com/articles/11449 last-modified: 2021-06-01 description: Understanding landscape as a socio-ecological system where systematic interactions occur among diverse ecosystems and human society is necessary for a sustainable landscape and resource management. However, many countries with rapid economic growth, including South Korea, depend on conventional planning and policy decisions to meet increasing demands for the use of specific natural resources. Such resource-oriented planning and policy which neglect considerations for the surrounding landscape can result in conflicts of interest and regulation. We designed a landscape conservation value (LCV) map of Jeju Island, Korea to overcome rising managerial and policy issues with the provision of systematic perspectives of landscape. With a consideration for natural and human-modified characteristics of the landscape, we used landform and land cover data to create fundamental landscape types. Then, the LCV was assigned to each type by a board of landscape experts. Within a study region, we observed relatively high values in registered protected areas and unique landscapes, and areas where high and low values are aligned. The resultant LCV map can identify areas that potentially require an integrated approach to prevent adverse effects caused by a conventional approach. creator: Baysok Jun creator: Ilkwon Kim creator: Jihoon Shin creator: Hyuksoo Kwon uri: https://doi.org/10.7717/peerj.11449 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Jun et al. title: Oyster farms are the main spawning grounds of the black sea bream Acanthopagrus schlegelii in Hiroshima Bay, Japan link: https://peerj.com/articles/11475 last-modified: 2021-06-01 description: Understanding the anthropogenic impact of oyster farms is essential for the management and conservation of marine fishes. In Japan, Hiroshima Bay is the region with the most intense oyster farming and thus suitable to study the impact of these farms. Here, we surveyed spherical planktonic eggs of the black sea bream Acanthopagrus schlegelii, one of the most abundant fish in the Bay. Our survey was performed at fourteen stations which included places with oyster farms and historical spawning grounds. We found the highest egg densities in four stations, one with historical spawning aggregations and three with major oyster farms. Besides, surveys at the innermost part of Hiroshima Bay, where two major rivers discharge, showed a low density of eggs indicating that black sea bream avoids spawning in low salinity areas. Our study suggests that oyster farms benefit spawners of black sea bream by providing more food sources than historical spawning grounds for efficient spawning. Yet, whether oyster farms represent a full advantage for the species remains unclear, particularly because they are known to host jellyfishes that prey on eggs and limit water flow that can influence the survival of fish eggs. creator: Kentaro Kawai creator: Hiroki Fujita creator: Gustavo Sanchez creator: Tetsuya Umino uri: https://doi.org/10.7717/peerj.11475 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kawai et al. title: Myocardial contrast echocardiography assessment of mouse myocardial infarction: comparison of kinetic parameters with conventional methods link: https://peerj.com/articles/11500 last-modified: 2021-06-01 description: This study explores the use of a minimally invasive assessment of myocardial infarction (MI) in mice using myocardial contrast echocardiography (MCE). The technique uses existing equipment and software readily available to the average researcher. C57/BL6 mice were randomized to either MI or sham surgery and evaluated using MCE at 1- or 2-weeks post-surgery. Size-isolated microbubbles were injected via retro-orbital catheter where their non-linear characteristics were utilized to produce the two-dimensional parameters of Wash-in-Rate and the Peak Enhancement, indicative of relative myocardial perfusion and blood volume, respectively. Three-dimensional cardiac reconstructions allowed the calculation of the Percent Agent, interpreted as the vascularity of the entire myocardium. These MCE parameters were compared to conventional assessments including M-Mode, strain analysis, and 2,3,5-Triphenyltetrazolium chloride (TTC) staining. Except for the Wash-in-Rate 2-week cohort, all MCE parameters were able to differentiate sham-operated versus MI animals and correlated with TTC staining (P < 0.05). MCE parameters were also able to identify MI group animals which failed to develop infarctions as determined by TTC staining. This study provides basic validation of these MCE parameters to detect MI in mice complementary to conventional methods while providing additional hemodynamic information in vivo. creator: Nicholas T. Thielen creator: Adison A. Kleinsasser creator: Jessica L. Freeling uri: https://doi.org/10.7717/peerj.11500 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Thielen et al. title: Neuromedin U and neurotensin may promote the development of the tumour microenvironment in neuroblastoma link: https://peerj.com/articles/11512 last-modified: 2021-06-01 description: Stage 4S neuroblastoma, as defined by the International Neuroblastoma Staging System committee (INSS), is known to regress spontaneously and have a more favourable outcome compared with stage 4 tumours. Comparing the molecular differences between these two stages may provide insights into the progression of neuroblastoma. Our study aimed to explore the molecular differences in the tumour microenvironment (TME) between INSS stage 4S and stage 4 tumours to provide an insight into the mechanisms underlying the biological processes of neuroblastoma. We downloaded the datasets GSE120572 and GSE73517 from the GEO database and pre-processed them using the limma package. CIBERSORT deconvolution agorithm was applied to analyse the differences in 22 infiltrating immune leukocyte subsets between the two stages. We used gene ontology (GO) enrichment analysis to determine the biological process (BP) annotation of differentially expressed genes (DEGs) using the online WebGestalt tool. Hub genes were determined in the STRING database and Cytoscape, and the expression of these genes was verified in the Oncomine database. Then these critical genes were performed survival analysis in TARGET database. We further validated the hub genes using a transwell assay and wound healing assay to detect the function of the genes in the neuroblastoma cell line SK-N-BE(2). GO analysis revealed that the 216 DEGs between stage 4S and stage 4 were enriched in aggressive biological processes. Neuromedin U (NMU) and neurotensin (NTS), which were significantly associated with patients’ overall survival rate, were verified to be elevated in stage 4, and to promote the proliferation and invasion of the SK-N-BE(2) cell. Tumour infiltrating leukocyte analysis showed a high infiltration of regulatory T cells and type 2 tumour-associated macrophages in stage 4 but not in stage 4S. Results of gene co-expression correlation, and the results of previous studies, suggest that NMU and NTS may play certain roles in modulating TME, thus facilitating the progression of neuroblastoma. creator: Daheng Yang creator: Xianwei Zhang creator: Zheqian Li creator: Fei Xu creator: Chenjie Tang creator: Hongbing Chen uri: https://doi.org/10.7717/peerj.11512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Promoting effect of rapamycin on osteogenic differentiation of maxillary sinus membrane stem cells link: https://peerj.com/articles/11513 last-modified: 2021-06-01 description: BackgroundStem cells located in the maxillary sinus membrane can differentiate into osteocytes. Our study aimed to evaluate the effect of rapamycin (RAPA) on the osteogenic differentiation of maxillary sinus membrane stem cells (MSMSCs).MethodsColony-forming unit assay, immunophenotype identification assay, and multi-differentiation assay confirmed characteristics of MSMSCs obtained from SD rats. Transmission electron microscopy (TEM) and flow cytometry (FCM) identified the initial autophagic level of MSMSCs induced by RAPA. Real-time quantitative PCR (qPCR) evaluated subsequent autophagic levels and osteogenic differentiation. Alkaline phosphatase (ALP) activity assay and alizarin red staining (ARS) evaluated subsequent osteogenic differentiation. We performed a histological examination to clarify in vivo osteogenesis with ectopic bone mass from BALB/c nude mice.ResultsMSMSCs possessed an active proliferation and multi-differentiation capacity, showing a phenotype of mesenchymal stem cells. The autophagic level increased with increasing RAPA (0, 10, 100, 1,000 nM) and decreased over time. ALP activity and calcium nodules forming in four RAPA-treated groups on three-time points (7, 14, 21 d) showed significant differences. Col1a1, Runx2, and Spp1 expressed most in 100 nM RAPA group on 7 and 14 d. Osteogenesis-related genes except for Ibsp expression between four groups tended to be consistent on 21 d. 100 nM and 10 nM RAPA-treated groups showed more bone formation in vivo.ConclusionRAPA can promote osteogenic differentiation of MSMSCs, indicating a possible relationship between osteogenic differentiation and autophagy. creator: Yanjun Lin creator: Min Zhang creator: Lin Zhou creator: Xuxi Chen creator: Jiang Chen creator: Dong Wu uri: https://doi.org/10.7717/peerj.11513 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lin et al. title: Structural variation and evolution of chloroplast tRNAs in green algae link: https://peerj.com/articles/11524 last-modified: 2021-06-01 description: As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the Ψ-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. Based on the constructed phylogenetic tree, mutations were found to accompany the evolution of the Green algae chloroplast tRNA. Moreover, chloroplast tRNAs of Chlorophyceae are consistent with those of monocotyledons and gymnosperms in terms of evolutionary patterns, sharing a common multi-phylogenetic pattern and rooted in a rich common ancestor. Sequence alignment and systematic analysis of tRNA in chloroplast genome of Chlorophyceae, clarified the characteristics and rules of tRNA changes, which will promote the evolutionary relationship of tRNA and the origin and evolution of chloroplast. creator: Fangbing Qi creator: Yajing Zhao creator: Ningbo Zhao creator: Kai Wang creator: Zhonghu Li creator: Yingjuan Wang uri: https://doi.org/10.7717/peerj.11524 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Qi et al. title: T-complex protein 1 subunit zeta-2 (CCT6B) deficiency induces murine teratospermia link: https://peerj.com/articles/11545 last-modified: 2021-06-01 description: BackgroundThe CCT complex is an important mediator of microtubule assembly and intracellular protein folding. Owing to its high expression in spermatids, CCT knockdown can disrupt spermatogenesis. In the present report, we therefore evaluated the in vivo functionality of the testis-specific CCT complex component CCT6B using a murine knockout model system.MethodsA CRISPR/Cas9 approach was used to generate Cct6b−/− mice, after which candidate gene expression in these animals was evaluated via qPCR and Western blotting. Testicular and epididymal phenotypes were assessed through histological and immunofluorescent staining assays, while a computer-assisted sperm analyzer was employed to assess semen quality.ResultsCct6b−/− mice were successfully generated, and exhibited no differences in development, fertility, appearance, testis weight, or sperm counts relative to control littermates. In addition, no differences in spermatogenesis were detected when comparingCct6b+/+ and Cct6b−/− testes. However, when progressive motility was analyzed, the ratio of normal sperm was significantly decreased in Cct6b−/− male mice, with nuclear base bending being the primary detected abnormality. In addition, slight decreases in Cct4 and Cct7 expression were detected.ConclusionThese data indicated that CCT6B is an important regulator of murine spermatogenesis, with the loss of this protein resulting in CCT complex dysfunction, providing a foundation for further studies. creator: Peiyin Yang creator: Wenjing Tang creator: Huiling Li creator: Rong Hua creator: Yan Yuan creator: Yue Zhang creator: Yunfei Zhu creator: Yiqiang Cui creator: Jiahao Sha uri: https://doi.org/10.7717/peerj.11545 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: High PHD Finger Protein 19 (PHF19) expression predicts poor prognosis in colorectal cancer: a retrospective study link: https://peerj.com/articles/11551 last-modified: 2021-06-01 description: BackgroundColorectal cancer (CRC) is the third most common cancer all around the world, and it seriously threats human health. PHF19 has been proved to be closely related to the prognosis of patients in a variety of malignant tumors, but the effect of PHF19 on the prognosis evaluation of CRC patients has not been confirmed.MethodsIn our study, we used GEO, TCGA database and IHC to verify the PHF19 expression in CRC samples. Survival analysis of PHF19 based on TCGA, GEO series, and our own CRC sample were performed. Cox regression was performed to reveal the relationship between PHF19 and prognosis. Co-expression was performed to find genes related to PHF19 expression. GO/KEGG enrichment analysis and GSEA analysis were used to confirm the most relevant signal pathway to PHF19. Next, cell experiments were performed to verify the effect of PHF19 on the proliferation, invasion and metastasis of CRC. Then, Western blot was used to verify the protein expression of the above two phenotypes. Finally, tumor formation experiments in nude mice were used to verify the role of PHF19 of tumor proliferation in vivo.ResultsWe found that PHF19 was significantly over-expressed in tumors compared with normal tissues. Kaplan–Meier (K–M) analysis indicated that high PHF19 in CRC associated with poor overall survival (OS) in CRC patients. Clinical correlation analysis showed that high expression of PHF19 was closely related to t umor progression in CRC patients, especially infiltration and metastasis. Bioinformatics revealed that PHF19 might affect tumor malignant phenotype by regulating the cell cycle in CRC. CCK-8 and clonal formation experiment showed that the proliferative ability of tumor cells was promoted. Flow cytometry showed that the cell cycle accelerated the transition from G1 to S phase. Western blot found that Cyclin D1, CDK4, and CDK6 expression were up-regulated. Transwell and wound-healing experiment found that invasive and migratory abilities was promoted after the over-expression of PHF19. Western blot showed that the expression of key proteins of Epithelial-Mesenchymal Transition (EMT) changed. Tumor formation experiments in nude mice showed that overexpression of PHF19 could promote tumor proliferation in vivo.ConclusionOur research proved that PHF19 could be an independent prognostic factor for CRC, PHF19 promoted the proliferative ability and the invasion and metastasis of CRC by up-regulating the expression of key molecules related to cell cycle and EMT pathway in vitro, promoting tumor proliferation in vivo. creator: Pengfei Li creator: Jie Sun creator: Yuanyuan Ruan creator: Lujun Song uri: https://doi.org/10.7717/peerj.11551 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Changes in the stoichiometry of Castanopsis fargesii along an elevation gradient in a Chinese subtropical forest link: https://peerj.com/articles/11553 last-modified: 2021-06-01 description: Elevation is important for determining the nutrient biogeochemical cycle in forest ecosystems. Changes in the ecological stoichiometry of nutrients along an elevation gradient can be used to predict how an element cycle responds in the midst of global climate change. We investigated changes in concentrations of and relationships between nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) in the leaves and roots of the dominant tree species, Castanopsis fargesii, along an elevation gradient (from 500 to 1,000 m above mean sea level) in a subtropical natural forest in China. We analyzed correlations between C. fargesii’s above-ground biomass and stoichiometry with environmental factors. We also analyzed the soil and plant stoichiometry of this C. fargesii population. Our results showed that leaf N decreased while leaf K and Ca increased at higher elevations. Meanwhile, leaf P showed no relationship with elevation. The leaf N:P indicated that C. fargesii was limited by N. Elevation gradients contributed 46.40% of the total variance of ecological stoichiometry when assessing environmental factors. Our research may provide a theoretical basis for the biogeochemical cycle along with better forest management and fertilization for this C. fargesii population. creator: Danping Liu creator: Dexiang Zheng creator: Yaoyao Xu creator: Yifei Chen creator: Hesong Wang creator: Ku Wang creator: Xiaoli Liao creator: Changxiong Chen creator: Jiangjiang Xia creator: Shaofei Jin uri: https://doi.org/10.7717/peerj.11553 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Vibrio alginolyticus influences quorum sensing-controlled phenotypes of acute hepatopancreatic necrosis disease-causing Vibrio parahaemolyticus link: https://peerj.com/articles/11567 last-modified: 2021-06-01 description: BackgroundAcute hepatopancreatic necrosis syndrome (AHPND) caused by Vibrio parahaemolyticus strain (VPAHPND) impacts the shrimp industry worldwide. With the increasing problem of antibiotic abuse, studies on quorum sensing (QS) system and anti-QS compounds bring potential breakthroughs for disease prevention and treatment.MethodsIn this study, the cell-free culture supernatant (CFCS) and its extract of V. alginolyticus BC25 were investigated for anti-QS activity against a reporter bacteria, Chromobacterium violaceum DMST46846. The effects of CFCS and/ or extract on motility, biofilm formation and extracellular polymeric substances (EPSs) of VPAHPND PSU5591 were evaluated. Moreover, the effects of V. alginolyticus BC25 on virulence of VPAHPND PSU5591 were investigated by shrimp challenge test. The potentially active anti-QS compounds presented in the extract and effect on gene expression of VPAHPND PSU5591 were identified.ResultsThe CFCS of V. alginolyticus BC25 and its extract showed a significant anti-QS activity against the reporter bacteria as well as swimming and swarming motilities, biofilms, and EPSs production by VPAHPND PSU5591. Transcriptome analysis revealed that V. alginolyticus BC25 extract significantly reduced the flagella genes involved in biofilm formation and iron-controlled virulence regulatory gene of VPAHPND PSU5591. Whereas, the LuxR family transcriptional regulator gene, c-factor, a cell-cell signaling gene, and capsular polysaccharide were up-regulated. The potentially active anti-QS compounds identified in extract were Cyclo-(L-Leu-L-Pro), and Cyclo-(L-Phe-L-Pro). Furthermore, V. alginolyticus BC25 enhanced disease resistance against VPAHPND PSU5591 in tested shrimp larvae.ConclusionThese findings suggest that V. alginolyticus BC25 could provide natural anti-QS and anti-biofilms compounds and has great ability to be used as biocontrol agent against VPAHPND infection in shrimp aquaculture. creator: Panida Paopradit creator: Natta Tansila creator: Komwit Surachat creator: Pimonsri Mittraparp-arthorn uri: https://doi.org/10.7717/peerj.11567 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Paopradit et al.