title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1230 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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 title: The effect of voluntary head movements on postural kinetics in the standing cat link: https://peerj.com/articles/8186 last-modified: 2019-12-12 description: BackgroundAlthough the postural instability accompanying bilateral vestibular loss in human and quadrupeds during lateral head movements are well-known, it is still unclear whether or not lateral head turns would indeed activate the postural control system to maintain balance. This study aimed to examine the kinetic parameters in freely standing intact cats during head movements in order to further answer the above question.MethodsSix intact cats were trained to stand, unrestrained on a force plate and perform voluntary head movements to the left and right positions in response to visual cues. Each trial was divided into two phases, quiet standing with the cat’s head maintaining a straight forward and lateral head position after voluntary head movements. Kinetic parameters including peak pressure and contact area under each limb as well as center of pressure (COP) displacements of the whole body were measured.ResultsCompared to the neutral head position, peak pressure and contact area of the left head position were significantly smaller for the left forelimb while greatly larger for the right forelimb. An exact opposite case of peak pressure and contact area in the forelimbs was found between the right and neutral head positions. In addition, the COP displacements altered oppositely to the head movements, and presented a significantly right shift in the left position and a significantly left shift in the right position.ConclusionThese results demonstrate that the lateral displacement of the head in standing intact cats does activate the postural adjustment to maintain balance, which is consistent with the concept that vestibular input can contribute to postural balance during voluntary head turns. creator: Yang Song creator: Meizi Wang creator: Julien Steven Baker creator: Yaodong Gu uri: https://doi.org/10.7717/peerj.8186 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Song et al. title: Identification of key genes in non-small cell lung cancer by bioinformatics analysis link: https://peerj.com/articles/8215 last-modified: 2019-12-12 description: BackgroundNon-small cell lung cancer (NSCLC) is one of the most common malignant tumors in the world, and it has become the leading cause of death of malignant tumors. However, its mechanisms are not fully clear. The aim of this study is to investigate the key genes and explore their potential mechanisms involving in NSCLC.MethodsWe downloaded gene expression profiles GSE33532, GSE30219 and GSE19804 from the Gene Expression Omnibus (GEO) database and analyzed them by using GEO2R. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for the functional and pathway enrichment analysis. We constructed the protein-protein interaction (PPI) network by STRING and visualized it by Cytoscape. Further, we performed module analysis and centrality analysis to find the potential key genes. Finally, we carried on survival analysis of key genes by GEPIA.ResultsIn total, we obtained 685 DEGs. Moreover, GO analysis showed that they were mainly enriched in cell adhesion, proteinaceous extracellular region, heparin binding. KEGG pathway analysis revealed that transcriptional misregulation in cancer, ECM-receptor interaction, cell cycle and p53 signaling pathway were involved in. Furthermore, PPI network was constructed including 249 nodes and 1,027 edges. Additionally, a significant module was found, which included eight candidate genes with high centrality features. Further, among the eight candidate genes, the survival of NSCLC patients with the seven high expression genes were significantly worse, including CDK1, CCNB1, CCNA2, BIRC5, CCNB2, KIAA0101 and MELK. In summary, these identified genes should play an important role in NSCLC, which can provide new insight for NSCLC research. creator: Li Zhang creator: Rui Peng creator: Yan Sun creator: Jia Wang creator: Xinyu Chong creator: Zheng Zhang uri: https://doi.org/10.7717/peerj.8215 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Fossil fern rhizomes as a model system for exploring epiphyte community structure across geologic time: evidence from Patagonia link: https://peerj.com/articles/8244 last-modified: 2019-12-12 description: BackgroundIn extant ecosystems, complex networks of ecological interactions between organisms can be readily studied. In contrast, understanding of such interactions in ecosystems of the geologic past is incomplete. Specifically, in past terrestrial ecosystems we know comparatively little about plant biotic interactions besides saprotrophy, herbivory, mycorrhizal associations, and oviposition. Due to taphonomic biases, epiphyte communities are particularly rare in the plant-fossil record, despite their prominence in modern ecosystems. Accordingly, little is known about how terrestrial epiphyte communities have changed across geologic time. Here, we describe a tiny in situ fossil epiphyte community that sheds light on plant-animal and plant-plant interactions more than 50 million years ago.MethodsA single silicified Todea (Osmundaceae) rhizome from a new locality of the early Eocene (ca. 52 Ma) Tufolitas Laguna del Hunco (Patagonia, Argentina) was studied in serial thin sections using light microscopy. The community of organisms colonizing the tissues of the rhizome was characterized by identifying the organisms and mapping and quantifying their distribution. A 200 × 200 µm grid was superimposed onto the rhizome cross section, and the colonizers present at each node of the grid were tallied.ResultsPreserved in situ, this community offers a rare window onto aspects of ancient ecosystems usually lost to time and taphonomic processes. The community is surprisingly diverse and includes the first fossilized leafy liverworts in South America, also marking the only fossil record of leafy bryophyte epiphytes outside of amber deposits; as well as several types of fungal hyphae and spores; microsclerotia with possible affinities in several ascomycete families; and evidence for oribatid mites.DiscussionThe community associated with the Patagonian rhizome enriches our understanding of terrestrial epiphyte communities in the distant past and adds to a growing body of literature on osmundaceous rhizomes as important hosts for component communities in ancient ecosystems, just as they are today. Because osmundaceous rhizomes represent an ecological niche that has remained virtually unchanged over time and space and are abundant in the fossil record, they provide a paleoecological model system that could be used to explore epiphyte community structure through time. creator: Alexander C. Bippus creator: Ignacio H. Escapa creator: Peter Wilf creator: Alexandru M.F. Tomescu uri: https://doi.org/10.7717/peerj.8244 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bippus et al. title: Unprofessional peer reviews disproportionately harm underrepresented groups in STEM link: https://peerj.com/articles/8247 last-modified: 2019-12-12 description: BackgroundPeer reviewed research is paramount to the advancement of science. Ideally, the peer review process is an unbiased, fair assessment of the scientific merit and credibility of a study; however, well-documented biases arise in all methods of peer review. Systemic biases have been shown to directly impact the outcomes of peer review, yet little is known about the downstream impacts of unprofessional reviewer comments that are shared with authors.MethodsIn an anonymous survey of international participants in science, technology, engineering, and mathematics (STEM) fields, we investigated the pervasiveness and author perceptions of long-term implications of receiving of unprofessional comments. Specifically, we assessed authors’ perceptions of scientific aptitude, productivity, and career trajectory after receiving an unprofessional peer review.ResultsWe show that survey respondents across four intersecting categories of gender and race/ethnicity received unprofessional peer review comments equally. However, traditionally underrepresented groups in STEM fields were most likely to perceive negative impacts on scientific aptitude, productivity, and career advancement after receiving an unprofessional peer review.DiscussionStudies show that a negative perception of aptitude leads to lowered self-confidence, short-term disruptions in success and productivity and delays in career advancement. Therefore, our results indicate that unprofessional reviews likely have and will continue to perpetuate the gap in STEM fields for traditionally underrepresented groups in the sciences. creator: Nyssa J. Silbiger creator: Amber D. Stubler uri: https://doi.org/10.7717/peerj.8247 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Silbiger and Stubler title: Quantitative estimation of wastewater quality parameters by hyperspectral band screening using GC, VIP and SPA link: https://peerj.com/articles/8255 last-modified: 2019-12-12 description: Water pollution has been hindering the world’s sustainable development. The accurate inversion of water quality parameters in sewage with visible-near infrared spectroscopy can improve the effectiveness and rational utilization and management of water resources. However, the accuracy of spectral models of water quality parameters is usually prone to noise information and high dimensionality of spectral data. This study aimed to enhance the model accuracy through optimizing the spectral models based on the sensitive spectral intervals of different water quality parameters. To this end, six kinds of sewage water taken from a biological sewage treatment plant went through laboratory physical and chemical tests. In total, 87 samples of sewage water were obtained by adding different amount of pure water to them. The raw reflectance (Rraw) of the samples were collected with analytical spectral devices. The Rraw-SNV were obtained from the Rraw processed with the standard normal variable. Then, the sensitive spectral intervals of each of the six water quality parameters, namely, chemical oxygen demand (COD), biological oxygen demand (BOD), NH3-N, the total dissolved substances (TDS), total hardness (TH) and total alkalinity (TA), were selected using three different methods: gray correlation (GC), variable importance in projection (VIP) and set pair analysis (SPA). Finally, the performance of both extreme learning machine (ELM) and partial least squares regression (PLSR) was investigated based on the sensitive spectral intervals. The results demonstrated that the model accuracy based on the sensitive spectral ranges screened through different methods appeared different. The GC method had better performance in reducing the redundancy and the VIP method was better in information preservation. The SPA method could make the optimal trade-offs between information preservation and redundancy reduction and it could retain maximal spectral band intervals with good response to the inversion parameters. The accuracy of the models based on varied sensitive spectral ranges selected by the three analysis methods was different: the GC was the highest, the SPA came next and the VIP was the lowest. On the whole, PLSR and ELM both achieved satisfying model accuracy, but the prediction accuracy of the latter was higher than the former. Great differences existed among the optimal inversion accuracy of different water quality parameters: COD, BOD and TN were very high; TA relatively high; and TDS and TH relatively low. These findings can provide a new way to optimize the spectral model of wastewater biochemical parameters and thus improve its prediction precision. creator: Zheng Xing creator: Junying Chen creator: Xiao Zhao creator: Yu Li creator: Xianwen Li creator: Zhitao Zhang creator: Congcong Lao creator: Haifeng Wang uri: https://doi.org/10.7717/peerj.8255 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xing et al.