title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1115 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness link: https://peerj.com/articles/8824 last-modified: 2020-06-09 description: Active commuting to and from school (ACS) has been recognized as a potential tool to improve physical fitness. Thus, this study aims to test the relationships between the average slope in the ACS and physical fitness, as well as to verify the mediator role of fatness in the relationship between average slope and physical fitness. A total of 257 participants, 137 boys and 120 girls, from 22 schools belonged to first and second High School grades participated in this study. Based on self-reported measure and Google Earth, participants were grouped into the active commuter (number of trips was ≥5, and the time of the trip was ≥15 min), mixed commuter (number of weekly trips was <5, and the time spent on the trip was <15 min) and passive commuter groups (those who reported traveling regularly by car, motorcycle, or bus). Specifically, in the active commuter group, a positive association between the average slope in the ACS with fatness was found, which in turn was positively related to strength lower limbs and cardiorrespiratory fitness. The average slope was not significantly associated with physical fitness indicators. Furtheremore, fatness did not mediate the relathionship between average slope and physical fitness. This research concluded positive associations between average slope and the body fat in the ACS. The tendency of findings signal that the average slope should be taken into account along with the distance, time and frequency of the active commuting. creator: Pedro Antonio Sánchez Miguel creator: David Sánchez Oliva creator: Mikel Vaquero Solís creator: J. J. Pulido creator: Miguel Angel Tapia Serrano uri: https://doi.org/10.7717/peerj.8824 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sánchez Miguel et al. title: Plastome of the mycoheterotrophic eudicot Exacum paucisquama (Gentianaceae) exhibits extensive gene loss and a highly expanded inverted repeat region link: https://peerj.com/articles/9157 last-modified: 2020-06-09 description: Mycoheterotrophic plants are highly specialized species able to acquire organic carbon from symbiotic fungi, with relaxed dependence on photosynthesis for carbon fixation. The relaxation of the functional constraint of photosynthesis and thereby the relaxed selective pressure on functional photosynthetic genes usually lead to substantial gene loss and a highly degraded plastid genome in heterotrophs. In this study, we sequenced and analyzed the plastome of the eudicot Exacum paucisquama, providing the first plastid genome of a mycoheterotroph in the family Gentianaceae to date. The E. paucisquama plastome was 44,028 bp in length, which is much smaller than the plastomes of autotrophic eudicots. Although the E. paucisquama plastome had a quadripartite structure, a distinct boundary shift was observed in comparison with the plastomes of other eudicots. We detected extensive gene loss and only 21 putative functional genes (15 protein-coding genes, four rRNA genes and two tRNA genes). Our results provide valuable information for comparative evolutionary analyses of plastomes of heterotrophic species belonging to different phylogenetic groups. creator: Zhanghai Li creator: Xiao Ma creator: Yi Wen creator: Sisi Chen creator: Yan Jiang creator: Xiaohua Jin uri: https://doi.org/10.7717/peerj.9157 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Validation of a general subjective well-being factor using Classical Test Theory link: https://peerj.com/articles/9193 last-modified: 2020-06-09 description: BackgroundSubjective Well-Being (SWB) is usually conceptualized in terms of an affective (i.e., judgements of biological emotional reactions and experiences) and a cognitive component (i.e., judgements of life satisfaction in relation to a psychological self-imposed ideal). Recently, researchers have suggested that judgements of harmony in life can replace or at least complement the cognitive component of SWB. Here, however, we go beyond that suggestion and propose that harmony in life should be seen as SWB’s social component since it is the sense of balance between the individual and the world around her—a process that comprises acceptance, adaptation, and balance. By adding judgements of one’s social interactions (i.e., harmony in life) to judgments of one’s life satisfaction (psycho) and judgements of one’s emotional reactions (bio), we propose a tentatively biopsychosocial model of SWB. As a first step, we used different factorial models in order to determine if both a general factor and specific sub-factors contribute to the biopsychosocial model of SWB.MethodA total of 527 participants responded to the Positive Affect Negative Affect Schedule (PANAS; 20 items), the Satisfaction with Life Scale (SWLS; five items), and the Harmony in life Scale (HILS; five items). We conducted exploratory and confirmatory factor analyses to validate the biopsychosocial model of subjective well-being and a general factor (SWBS).ResultsThe 20 PANAS items reflected a mixture of general latent structure saturation and specific latent structure saturation, but contributed to their respective specific latent factor (PA: 48%; NA: 49%) more than to the general latent SWBS factor (positive affect: 25%; negative affect: 32%). The five SWLS items contributed to a larger degree to the general SWBS factor (72%) than to life satisfaction itself (22%), while the five HILS items contributed to even a larger degree to the general SWBS factor (98%) than to harmony in life (0%). The bifactor model was the best model compared with all other models we tested (χ2 = 1,660.78, df = 375, p < 0.001); Satorra Bentler χ2 = 1,265.80, df = 375, p < 0.001; CFI = 0.92; Tucker–Lewis Index = 0.91; RMSEA = 0.067. This model of a general SWBS factor explained about 64% of the total variance in the model, while specific SWBS components together explained 15% of the total variance.ConclusionOur study suggests SWB as a general factor in a multidimensional biopsychosocial model. Indeed, as much as 64% of the variance of SWB was explained by this general factor. The SWB components, however, contributed to a different degree to each corresponding factor in the model. For instance, while the affective and cognitive components seem to be their own constructs and also part of the general SWB factor, the social component tested here contributed 0% to its own variance but 98% to the general factor. creator: Ali Al Nima creator: Kevin M. Cloninger creator: Franco Lucchese creator: Sverker Sikström creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.9193 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nima et al. title: Silicon induces hormetic dose-response effects on growth and concentrations of chlorophylls, amino acids and sugars in pepper plants during the early developmental stage link: https://peerj.com/articles/9224 last-modified: 2020-06-09 description: BackgroundSilicon (Si) is a beneficial element that has been proven to influence plant responses including growth, development and metabolism in a hormetic manner.MethodsIn the present study, we evaluated the effect of Si on the growth and concentrations of chlorophylls, total amino acids, and total sugars of pepper plants (Capsicum annuum L.) during the early developmental stage in a hydroponic system under conventional (unstressed) conditions. We tested four Si concentrations (applied as calcium silicate): 0, 60, 125 and 250 mg L−1, and growth variables were measured 7, 14, 21 and 28 days after treatment (dat), while biochemical variables were recorded at the end of the experiment, 28 dat.ResultsThe application of 125 mg L−1 Si improved leaf area, fresh and dry biomass weight in leaves and stems, total soluble sugars, and concentrations of chlorophylls a and b in both leaves and stems. The amino acids concentration in leaves and roots, as well as the stem diameter were the highest in plants treated with 60 mg L−1 Si. Nevertheless, Si applications reduced root length, stem diameter and total free amino acids in leaves and stems, especially when applied at the highest concentration (i.e., 250 mg L−1 Si).ConclusionThe application of Si has positive effects on pepper plants during the early developmental stage, including stimulation of growth, as well as increased concentrations of chlorophylls, total free amino acids and total soluble sugars. In general, most benefits from Si applications were observed in the range of 60–125 mg L−1 Si, while some negative effects were observed at the highest concentration applied (i.e., 250 mg L−1 Si). Therefore, pepper is a good candidate crop to benefit from Si application during the early developmental stage under unstressed conditions. creator: Libia Iris Trejo-Téllez creator: Atonaltzin García-Jiménez creator: Hugo Fernando Escobar-Sepúlveda creator: Sara Monzerrat Ramírez-Olvera creator: Jericó Jabín Bello-Bello creator: Fernando Carlos Gómez-Merino uri: https://doi.org/10.7717/peerj.9224 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Trejo-Téllez et al. title: Bacterial communities associated with cell phones and shoes link: https://peerj.com/articles/9235 last-modified: 2020-06-09 description: BackgroundEvery human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively.FindingsWe report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States.ConclusionsWe place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects. creator: David A. Coil creator: Russell Y. Neches creator: Jenna M. Lang creator: Guillaume Jospin creator: Wendy E. Brown creator: Darlene Cavalier creator: Jarrad Hampton-Marcell creator: Jack A. Gilbert creator: Jonathan A. Eisen uri: https://doi.org/10.7717/peerj.9235 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Coil et al. title: Effectiveness of topical antibiotics in treating corals affected by Stony Coral Tissue Loss Disease link: https://peerj.com/articles/9289 last-modified: 2020-06-09 description: Since 2014, Stony Coral Tissue Loss Disease (SCTLD) has led to mass mortality of the majority of hard coral species on the Florida Reef Tract. Following the successful treatment of SCTLD lesions on laboratory corals using water dosed with antibiotics, two topical pastes were developed as vehicles to directly apply antibiotic treatments to wild corals. These pastes were tested as placebos and with additions of amoxicillin on active SCTLD lesions on multiple coral species. The effectiveness of the pastes without antibiotics (placebo treatments) was 4% and 9%, no different from untreated controls. Adding amoxicillin to both pastes significantly increased effectiveness to 70% and 84%. Effectiveness with this method was seen across five different coral species, with success rates of the more effective paste ranging from 67% (Colpophyllia natans) to 90% (Orbicella faveolata and Montastraea cavernosa). Topical antibiotic application is a viable and effective tool for halting disease lesions on corals affected by SCTLD. creator: Karen L. Neely creator: Kevin A. Macaulay creator: Emily K. Hower creator: Michelle A. Dobler uri: https://doi.org/10.7717/peerj.9289 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Neely et al. title: Within-person structures of daily cognitive performance differ from between-person structures of cognitive abilities link: https://peerj.com/articles/9290 last-modified: 2020-06-09 description: Over a century of research on between-person differences has resulted in the consensus that human cognitive abilities are hierarchically organized, with a general factor, termed general intelligence or “g,” uppermost. Surprisingly, it is unknown whether this body of evidence is informative about how cognition is structured within individuals. Using data from 101 young adults performing nine cognitive tasks on 100 occasions distributed over six months, we find that the structures of individuals’ cognitive abilities vary among each other, and deviate greatly from the modal between-person structure. Working memory contributes the largest share of common variance to both between- and within-person structures, but the g factor is much less prominent within than between persons. We conclude that between-person structures of cognitive abilities cannot serve as a surrogate for within-person structures. To reveal the development and organization of human intelligence, individuals need to be studied over time. creator: Florian Schmiedek creator: Martin Lövdén creator: Timo von Oertzen creator: Ulman Lindenberger uri: https://doi.org/10.7717/peerj.9290 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Schmiedek et al. title: Shade effects on growth, photosynthesis and chlorophyll fluorescence parameters of three Paeonia species link: https://peerj.com/articles/9316 last-modified: 2020-06-09 description: Insufficient light intensity inhibits the growth of cultivated herbaceous peony and decreases its economic value. Owing to the increased demand for shade-tolerant herbaceous peony, the selection of appropriate parents for hybridization is essential. Paeonia anomala, Paeonia intermedia and Paeonia veitchii can grow under shade conditions in their natural habitats; however, their photosynthetic capacities under shade have not been studied. In this study, we simulated low light intensity (30% sunlight) and evaluated the morphological, photosynthetic and chlorophyll fluorescence parameters of these three species. Moreover, the shade tolerance of these species as well as two common cultivars (Paeonia lactiflora ‘Da Fugui’, which is suitable for solar greenhouse cultivation, and P. lactiflora ‘Qiao Ling’, which is not suitable for solar greenhouse cultivation) was evaluated. The results showed that under shade, the leaf area of P. anomala and P. intermedia increased, the single flowering period of P. intermedia and P. veitchii was prolonged, and the flower color of P. veitchii faded. With respect to P. anomala, P. intermedia and P. veitchii, shade eliminated the photosynthetic ‘lunch break’ phenomenon and decreased photoinhibition at midday. Furthermore, the maximum photochemical efficiency (Fv/Fm) and maximum primary photochemical yield (Fv/Fo) of photosystem II (PSII) in the three species improved significantly, and their changes in light dissipation were different. The shade tolerance of the tested accessions was in the order P. veitchii > P. intermedia > P. anomala > ‘Da Fugui’ > ‘Qiao Ling’, showing that the three wild species were better adapted to low light intensity than the cultivars. Thus, P. anomala, P. intermedia and P. veitchii could potentially be used in the development of shade-tolerant herbaceous peony cultivars. creator: Yingling Wan creator: Yixuan Zhang creator: Min Zhang creator: Aiying Hong creator: HuiYan Yang creator: Yan Liu uri: https://doi.org/10.7717/peerj.9316 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wan et al. title: SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera link: https://peerj.com/articles/9320 last-modified: 2020-06-09 description: The white-backed planthopper Sogatella furcifera is an economically important rice pest distributed throughout Asia. It damages rice crops by sucking phloem sap, resulting in stunted growth and plant virus transmission. We aimed to obtain the full-length transcriptome data of S. furcifera using PacBio single-molecule real-time (SMRT) sequencing. Total RNA extracted from S. furcifera at various developmental stages (egg, larval, and adult stages) was mixed and used to generate a full-length transcriptome for SMRT sequencing. Long non-coding RNA (lncRNA) identification, full-length coding sequence prediction, full-length non-chimeric (FLNC) read detection, simple sequence repeat (SSR) analysis, transcription factor detection, and transcript functional annotation were performed. A total of 12,514,449 subreads (15.64 Gbp, clean reads) were generated, including 630,447 circular consensus sequences and 388,348 FLNC reads. Transcript cluster analysis of the FLNC reads revealed 251,109 consensus reads including 29,700 high-quality reads. Additionally, 100,360 SSRs and 121,395 coding sequences were identified using SSR analysis and ANGEL software, respectively. Furthermore, 44,324 lncRNAs were annotated using four tools and 1,288 transcription factors were identified. In total, 95,495 transcripts were functionally annotated based on searches of seven different databases. To the best of our knowledge, this is the first study of the full-length transcriptome of the white-backed planthopper obtained using SMRT sequencing. The acquired transcriptome data can facilitate further studies on the ecological and viral-host interactions of this agricultural pest. creator: Jing Chen creator: Yaya Yu creator: Kui Kang creator: Daowei Zhang uri: https://doi.org/10.7717/peerj.9320 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: COVID-19: Taiwan’s epidemiological characteristics and public and hospital responses link: https://peerj.com/articles/9360 last-modified: 2020-06-09 description: BackgroundCoronavirus disease 19 (COVID-19) is a global health threat with significant medical, economic, social and political implications. The optimal strategies for combating COVID-19 have not been fully determined and vary across countries.MethodsBy the end of February 2020 in Taiwan, 2,150 patients received diagnostic COVID-19 testing and 39 confirmed cases were detected. This is a relatively lower rate of infection compared to other Asian countries. In this article, we summarize the epidemiological characteristics of the 39 infected patients as well as public and hospital responses to COVID-19.ResultsThirty-nine COVID-19 cases and one death have been confirmed in Taiwan. Seventeen of these patients were infected by family members or in hospital wards, emphasizing how COVID-19 is mostly spread by close contact. We examined how hospital have responded to COVID-19, including their implementation of patient route control, outdoor clinics, hospital visit restrictions and ward and staff modifications. We also studied the public’s use of face masks in response to COVID-19. These strategies may reduce the spread of COVID-19 in other countries.ConclusionThe emergence and spread of COVID-19 is a threat to health worldwide. Taiwan has reported lower infected cases and its strategies may contribute to further disease prevention and control. creator: Chih-Ming Chang creator: Ting-Wan Tan creator: Tai-Cheng Ho creator: Chung-Chu Chen creator: Tsung-Hsien Su creator: Chien-Yu Lin uri: https://doi.org/10.7717/peerj.9360 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chang et al.