title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1228 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps link: https://peerj.com/articles/8027 last-modified: 2019-12-13 description: Growing pressures linked to global warming are prompting governments to put policies in place to find alternatives to fossil fuels. In this study, we compared the impact of tree-length harvesting to more intensive full-tree harvesting on the composition of fungi residing in residual stumps 5 years after harvest. In the tree-length treatment, a larger amount of residual material was left around the residual stumps in contrast to the full-tree treatment where a large amount of woody debris was removed. We collected sawdust from five randomly selected residual stumps in five blocks in each of the tree-length and full-tree treatments, yielding a total of 50 samples (25 in each treatment). We characterized the fungal operational taxonomic units (OTUs) present in each stump using high-throughput DNA sequencing of the fungal ITS region. We observed no differences in Shannon diversity between tree-length and full-tree harvesting. Likewise, we observed few differences in the composition of fungal OTUs among tree-length and full-tree samples using non-metric multidimensional scaling. Using the differential abundance analysis implemented with DESeq2, we did, however, detect several associations between specific fungal taxa and the intensity of residual biomass harvest. For example, Peniophorella pallida (Bres.) KH Larss. and Tephromela sp. were found mainly in the full-tree treatment, while Phlebia livida (Pers.) Bres. and Cladophialophora chaetospira (Grove) Crous & Arzanlou were found mainly in the tree-length treatment. While none of the 20 most abundant species in our study were identified as pathogens we did identify one conifer pathogen species Serpula himantioides (Fr.) P. Karst found mainly in the full-tree treatment. creator: Cédric Boué creator: Tonia DeBellis creator: Lisa A. Venier creator: Timothy T. Work creator: Steven W. Kembel uri: https://doi.org/10.7717/peerj.8027 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Boué et al. title: Invasive alien plants in Polish national parks—threats to species diversity link: https://peerj.com/articles/8034 last-modified: 2019-12-13 description: Due to the relevance of protected areas to the conservation of native biota, the magnitude of invasions and threats posed by alien plants are currently important issues for the preservation of these areas. The paper summarises data on invasive alien plant species presence in the most valuable protected areas in Poland, i.e. national parks (NPs). We investigated the distribution of invasive alien plant species and management attempts concerning those species. We analysed data obtained from 23 national parks originating from published and unpublished sources. Invasive plants were present in all protected areas analysed, from two to 42 species in a particular national park, and 68 in total. The most widely distributed species were: Impatiens parviflora (present in 19 NPs), I. glandulifera (17), Solidago gigantea (17), Reynoutria japonica (17), and Robinia pseudoacacia (16). The conducted analyses showed that the number of invasive species decreased with the higher altitude (asl) of the national park. The most often managed species were Impatiens glandulifera (being removed in seven NPs), I. parviflora (six), Padus serotina (four) and Quercus rubra (four). In the majority of NPs, control activities are limited to small areas and singular species, thus having an incidental character. Only in five objects (Białowieża NP, Biebrza NP, Kampinos NP, Tuchola NP, Wigry NP), management has been focused on several species. We conclude that a lack of comprehensive management of invasive plant species in the majority of national parks currently limits the effectiveness of IAS (invasive alien species) eradication. Exchange of expertise among protected areas, documenting best practice examples, synthesising lessons learnt in IAS management, as well as the development of minimum standards for invasive plants surveillance and management are pivotal. creator: Anna Bomanowska creator: Wojciech Adamowski creator: Izabella Kirpluk creator: Anna Otręba creator: Agnieszka Rewicz uri: https://doi.org/10.7717/peerj.8034 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bomanowska et al. title: Embryo aggregation regulates in vitro stress conditions to promote developmental competence in pigs link: https://peerj.com/articles/8143 last-modified: 2019-12-13 description: Embryo aggregation is a useful method to produce blastocysts with high developmental competence to generate more offspring in various mammals, but the underlying mechanism(s) regarding the beneficial effects are largely unknown. In this study, we investigated the effects of embryo aggregation using 4-cell stage embryos in in vitro developmental competence and the relationship of stress conditions in porcine early embryogenesis. We conducted aggregation using the well of the well system and confirmed that aggregation using two or three embryos was useful for obtaining blastocysts. Aggregated embryos significantly improved developmental competence, including blastocyst formation rate, blastomere number, ICM/TE ratio, and cellular survival rate, compared to non-aggregated embryos. Investigation into the relationship between embryo aggregation and stress conditions revealed that mitochondrial function increased, and oxidative and endoplasmic reticulum (ER)-stress decreased compared to 1X (non-aggregated embryos) blastocysts. In addition, 3X (three-embryo aggregated) blastocysts increased the expression of pluripotency, anti-apoptosis, and implantation related genes, and decreased expression of pro-apoptosis related genes. Therefore, these findings indicate that embryo aggregation regulates in vitro stress conditions to increase developmental competence and contributes to the in vitro production of high-quality embryos and the large-scale production of transgenic and chimeric pigs. creator: Pil-Soo Jeong creator: Seung-Bin Yoon creator: Mun-Hyeong Lee creator: Hee-Chang Son creator: Hwal-Yong Lee creator: Sanghoon Lee creator: Bon-Sang Koo creator: Kang-Jin Jeong creator: Jong-Hee Lee creator: Yeung Bae Jin creator: Bong-Seok Song creator: Ji-Su Kim creator: Sun-Uk Kim creator: Deog-Bon Koo creator: Bo-Woong Sim uri: https://doi.org/10.7717/peerj.8143 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jeong et al. title: Resident microbes of lactation rooms and daycares link: https://peerj.com/articles/8168 last-modified: 2019-12-13 description: Dedicated lactation rooms are a modern development as mothers return to work while still providing breastmilk to their absent infants. This study describes the built environment microbiome of lactation rooms and daycares, and explores the influence of temperature and humidity on the microbiome of lactation rooms. Sterile swabs were used to collect samples from five different sites in lactation rooms at University of California, Davis and from five different sites in daycares located in Davis, California. DNA from the swabs was extracted and the V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Temperature and relative humidity data were collected on a subset of the lactation rooms. Sampled lactation rooms could be either dedicated lactation rooms or could also serve other functions (e.g., combined lactation room and restroom lounge). The majority of sequence reads were identified as belonging to family Moraxellaceae, with 73% of all reads included in analysis identified as an unknown species of Acinetobacter. Alpha diversity was analyzed using the Shannon index, while beta diversity was analyzed using unweighted and weighted UniFrac distance. The Jaccard distance was used to measure amount of change at sampling locations between time points for analysis of the impact of temperature and humidity on the microbiome. There were significant differences in the beta diversity of the microbiome of lactation rooms by room type. There were also significant differences in the beta diversity of the microbiome by sample collection location. There were no significant differences in either alpha or beta diversity associated with room temperature or humidity. Additional studies are needed to understand if the differences in lactation room type may result in differences in the breastmilk microbiome of milk collected in those rooms, and to what extent any such differences may influence the infant microbiome. creator: Diana H. Taft creator: Samir Akre creator: Nicolas Madrid creator: Andre Knoesen creator: David A. Mills creator: Zachery T. Lewis uri: https://doi.org/10.7717/peerj.8168 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Taft et al. title: consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction link: https://peerj.com/articles/8206 last-modified: 2019-12-13 description: Extensive evaluation of RNA-seq methods have demonstrated that no single algorithm consistently outperforms all others. Removal of unwanted variation (RUV) has also been proposed as a method for stabilizing differential expression (DE) results. Despite this, it remains a challenge to run multiple RNA-seq algorithms to identify significant differences common to multiple algorithms, whilst also integrating and assessing the impact of RUV into all algorithms. consensusDE was developed to automate the process of identifying significant DE by combining the results from multiple algorithms with minimal user input and with the option to automatically integrate RUV. consensusDE only requires a table describing the sample groups, a directory containing BAM files or preprocessed count tables and an optional transcript database for annotation. It supports merging of technical replicates, paired analyses and outputs a compendium of plots to guide the user in subsequent analyses. Herein, we assess the ability of RUV to improve DE stability when combined with multiple algorithms and between algorithms, through application to real and simulated data. We find that, although RUV increased fold change stability between algorithms, it demonstrated improved FDR in a setting of low replication for the intersect, the effect was algorithm specific and diminished with increased replication, reinforcing increased replication for recovery of true DE genes. We finish by offering some rules and considerations for the application of RUV in a consensus-based setting. consensusDE is freely available, implemented in R and available as a Bioconductor package, under the GPL-3 license, along with a comprehensive vignette describing functionality: http://bioconductor.org/packages/consensusDE/. creator: Ashley J. Waardenberg creator: Matthew A. Field uri: https://doi.org/10.7717/peerj.8206 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Waardenberg and Field title: Vegetation dynamic analysis based on multisource remote sensing data in the east margin of the Qinghai-Tibet Plateau, China link: https://peerj.com/articles/8223 last-modified: 2019-12-13 description: This study focuses on the vegetation dynamic caused by global environmental change in the eastern margin of the Qinghai-Tibet Plateau (EMQTP). The Qinghai–Tibet Plateau (QTP) is one of the most sensitive areas responding to global environmental change, particularly global climate change, and has been recognized as a hotspot for coupled studies on changes in global terrestrial ecosystems and global climates. An important component of terrestrial ecosystems, vegetation dynamic has become a key issue in global environmental change, and numerous case studies have been conducted on vegetation dynamic trends using multi-source data and multi-scale methods across different study periods. The EMQTP is regarded as a transitional area located between the QTP and the Sichuan basin, and has special geographical and climatic conditions. Although this area is ecologically fragile and sensitive to climate change, few studies about vegetation dynamics have been carried out in this area. Thus, in this study, we used long-term series datasets of GIMMS 3g NDVI and VGT/PROBA-V NDVI to analyze the vegetation dynamics and phenological changes from 1982 to 2018. Validation was performed based on Landsat NDVI and Vegetation Index & Phenology (VIP) data. The results reveal that the year 1998 was a vital turning point in the start of growing season (SGS) in vegetation ecosystems. Before this turning point, the SGS had an average slope of 9.2 days/decade, and after, the average slope was 3.9 days/decade. The length of growing season (LGS) was slightly prolonged between 1982 to 2015. Additionally, the largest national alpine wetland grassland experienced significant vegetation degradation; in autumn, the degraded area accounted for 63.4%. Vegetation degradation had also appeared in the arid valleys of the Yalong River and the Jinsha River. Through validation analysis, we found that the main causes of vegetation degradation are the natural degradation of wetland grassland and human activities, specifically agricultural development and residential area expansion. creator: Haijun Wang creator: Peihao Peng creator: Xiangdong Kong creator: Tingbin Zhang creator: Guihua Yi uri: https://doi.org/10.7717/peerj.8223 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Development and characterization of a multiplex panel of microsatellite markers for the Reunion free-tailed bat Mormopterus francoismoutoui link: https://peerj.com/articles/8036 last-modified: 2019-12-12 description: The ecology and conservation status of many island-restricted bats remain largely unexplored. The free-tailed bat Mormopterus francoismoutoui is a small insectivorous tropical bat, endemic to Reunion Island (Indian Ocean). Despite being widely distributed on the island, the fine-scale genetic structure and evolutionary ecology of M. francoismoutoui remain under-investigated, and therefore its ecology is poorly known. Here, we used Illumina paired-end sequencing to develop microsatellite markers for M. francoismoutoui, based on the genotyping of 31 individuals from distinct locations all over the island. We selected and described 12 polymorphic microsatellite loci with high levels of heterozygosity, which provide novel molecular markers for future genetic population-level studies of M. francoismoutoui. creator: Muriel Dietrich creator: Gildas Le Minter creator: Magali Turpin creator: Pablo Tortosa uri: https://doi.org/10.7717/peerj.8036 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dietrich et al. title: Body height and waist circumference of young Swiss men as assessed by 3D laser-based photonic scans and by manual anthropometric measurements link: https://peerj.com/articles/8095 last-modified: 2019-12-12 description: Overweight and obesity are considered among the major health concerns worldwide. The body mass index is a frequently used measure for overweight and obesity and is associated with common non-communicable diseases such as diabetes type II, cardiovascular diseases and certain cancers. However, the body mass index does not account for the distribution of body fat and relative fat to muscle mass. 3D laser-based photonic full body scans provide detailed information on various body circumferences, surfaces, and volumes as well as body height and weight (using an integrated scale). In the literature, body scans showed good feasibility, reliability, and validity, while also demonstrating a good correlation with health parameters linked to the metabolic syndrome. However, systematic differences between body scan derived measurements and manual measurements remain an issue. This study aimed to assess these systematic differences for body height, waist circumference, and body mass index using cross-sectional data from a homogenous sample of 52 young Swiss male volunteers. In addition to 3D laser-based photonic full body scans and correlative manual measurements, body fat distribution was assessed through bioelectrical impedance analysis. Overall, an excellent correlation was found between measurements of waist circumference and body mass index, and good correlation between body mass index and total fat mass, as well as between waist circumference and visceral fat mass as assessed by bioelectrical impedance analysis. Volunteers were shorter in height measured by body scan when compared to manual measurements. This systematic difference became smaller when volunteers stood in the scanner in a completely upright position with their feet together. Waist circumference was slightly smaller for manual measurements than for body scan derived values. This systematic difference was larger in overweight volunteers compared to leaner volunteers. creator: Claudia Beckmann creator: Lafi Aldakak creator: Patrick Eppenberger creator: Frank Rühli creator: Kaspar Staub creator: Nicole Bender uri: https://doi.org/10.7717/peerj.8095 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Beckmann et al. title: Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences link: https://peerj.com/articles/8158 last-modified: 2019-12-12 description: BackgroundSpecies in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional ITS sequences, ITS pseudogenes show higher sequence diversity, so they can provide useful phylogenetic information.MethodsWe sequenced the ITS regions and the chloroplast DNA regions TrnL-TrnF and TrnT-TrnL from 33 mulberry accessions, and performed phylogenetic analyses to explore the evolution of mulberry.ResultsWe found ITS pseudogenes in 11 mulberry accessions. In the phylogenetic tree constructed from ITS sequences, clade B was separated into short-type sequence clades (clades 1 and 2), and a long-type sequence clade (clade 3). Pseudogene sequences were separately clustered into two pseudogroups, designated as pseudogroup 1 and pseudogroup 2. The phylogenetic tree generated from cpDNA sequences also separated clade B into two clades.ConclusionsTwo species were separated in clade B. The existence of three connection patterns and incongruent distribution patterns between the phylogenetic trees generated from cpDNA and ITS sequences suggested that the ITS pseudogene sequences connect with genetic information from the female progenitor. Hybridization has played important roles in the evolution of mulberry, resulting in low resolution of the phylogenetic analysis based on ITS sequences. An evolutionary pattern illustrating the evolution history of mulberry is proposed. These findings have significance for the conservation of local mulberry resources. Polyploidy, hybridization, and concerted evolution have all played the roles in the evolution of ITS sequences in mulberry. This study will expand our understanding of mulberry evolution. creator: Yahui Xuan creator: Yue Wu creator: Peng Li creator: Ruiling Liu creator: Yiwei Luo creator: Jianglian Yuan creator: Zhonghuai Xiang creator: Ningjia He uri: https://doi.org/10.7717/peerj.8158 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xuan et al. title: MemCat: a new category-based image set quantified on memorability link: https://peerj.com/articles/8169 last-modified: 2019-12-12 description: Images differ in their memorability in consistent ways across observers. What makes an image memorable is not fully understood to date. Most of the current insight is in terms of high-level semantic aspects, related to the content. However, research still shows consistent differences within semantic categories, suggesting a role for factors at other levels of processing in the visual hierarchy. To aid investigations into this role as well as contributions to the understanding of image memorability more generally, we present MemCat. MemCat is a category-based image set, consisting of 10K images representing five broader, memorability-relevant categories (animal, food, landscape, sports, and vehicle) and further divided into subcategories (e.g., bear). They were sampled from existing source image sets that offer bounding box annotations or more detailed segmentation masks. We collected memorability scores for all 10 K images, each score based on the responses of on average 99 participants in a repeat-detection memory task. Replicating previous research, the collected memorability scores show high levels of consistency across observers. Currently, MemCat is the second largest memorability image set and the largest offering a category-based structure. MemCat can be used to study the factors underlying the variability in image memorability, including the variability within semantic categories. In addition, it offers a new benchmark dataset for the automatic prediction of memorability scores (e.g., with convolutional neural networks). Finally, MemCat allows the study of neural and behavioral correlates of memorability while controlling for semantic category. creator: Lore Goetschalckx creator: Johan Wagemans uri: https://doi.org/10.7717/peerj.8169 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Goetschalckx and Wagemans