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: 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. title: Organ health and development in larval kingfish are unaffected by ocean acidification and warming link: https://peerj.com/articles/8266 last-modified: 2019-12-12 description: Anthropogenic CO2 emissions are causing global ocean warming and ocean acidification. The early life stages of some marine fish are vulnerable to elevated ocean temperatures and CO2 concentrations, with lowered survival and growth rates most frequently documented. Underlying these effects, damage to different organs has been found as a response to elevated CO2 in larvae of several species of marine fish, yet the combined effects of acidification and warming on organ health are unknown. Yellowtail kingfish, Seriola lalandi, a circumglobal subtropical pelagic fish of high commercial and recreational value, were reared from fertilization under control (21 °C) and elevated (25 °C) temperature conditions fully crossed with control (500 µatm) and elevated (1,000 µatm) pCO2 conditions. Larvae were sampled at 11 days and 21 days post hatch for histological analysis of the eye, gills, gut, liver, pancreas, kidney and liver. Previous work found elevated temperature, but not elevated CO2, significantly reduced larval kingfish survival while increasing growth and developmental rate. The current histological analysis aimed to determine whether there were additional sublethal effects on organ condition and development and whether underlying organ damage could be responsible for the documented effects of temperature on survivorship. While damage to different organs was found in a number of larvae, these effects were not related to temperature and/or CO2 treatment. We conclude that kingfish larvae are generally vulnerable during organogenesis of the digestive system in their early development, but that this will not be exacerbated by near-future ocean warming and acidification. creator: Andrea Y. Frommel creator: Colin J. Brauner creator: Bridie J.M. Allan creator: Simon Nicol creator: Darren M. Parsons creator: Steve M.J. Pether creator: Alvin N. Setiawan creator: Neville Smith creator: Philip L. Munday uri: https://doi.org/10.7717/peerj.8266 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Frommel et al. title: Effect of temperature on pollen germination for several Rosaceae species: influence of freezing conservation time on germination patterns link: https://peerj.com/articles/8195 last-modified: 2019-12-11 description: Between February 2018 and April 2018, flowers were collected from eight Rosaceae species. Flowers were kept in a freezer at −20 °C for three freezing times (Treatment 1, two months; Treatment 2, four months; Treatment 3, six months). After extracting pollen, in vitro germination was induced in a culture medium and incubated at six different temperatures for 72 h. The percentage of pollen germination, average pollen tube length and maximum pollen tube length were measured. Pollen germination was maximum for all species between 15 °C and 30 °C. Cydonia oblonga, Malus sylvestris, Prunus avium, Prunus domestica, Prunus dulcis, Prunus persica and Pyrus communis obtained 30–52% pollen germination between 15 °C and 20 °C. Prunus cerasifera had 40% pollen germination at 30 °C. All species studied reached the maximum pollen tube length between 10 °C and 25 °C. Germination did not change significantly for any of the species with freezing time, but we found significant differences in the three parameters measured between treatments. The highest germination percentages were obtained in Treatment 2 (four months frozen at −20 °C), while the maximum pollen tube length was reached in Treatment 1 (two months frozen at −20 °C). According to our results, freezing time affected the germination-temperature patterns. This could indicate that studies on the effect of temperature on pollen germination should always be carried out with fresh pollen to obtain more conclusive data. creator: Roberto Beltrán creator: Aina Valls creator: Nuria Cebrián creator: Carlos Zornoza creator: Francisco García Breijo creator: José Reig Armiñana creator: Alfonso Garmendia creator: Hugo Merle uri: https://doi.org/10.7717/peerj.8195 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Beltrán et al. title: Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands link: https://peerj.com/articles/8047 last-modified: 2019-12-11 description: Acidobacteria is found to be dominant and abundant in forest soil, and performs specific ecological functions (such as cellulose decomposition and photosynthetic capacity, etc.). However, relative limited is known about its changing patterns after a fire interruption. In this study, the response of soil Acidobacteria to a wildfire disturbance was investigated using the Illumina MiSeq sequencing system. The research area was classified by different severities of fire damage (high, moderate, and low severity, and an unburnt area), and samples were collected from various soil layers (0–10 cm as topsoil; 10–20 cm as subsoil). We obtained a total of 986,036 sequence reads; 31.77% of them belonged to Acidobacteria. Overall, 18 different Acidobacteria subgroups were detected, with subgroups 4, 6, 1, 3, and 2 the most abundant, accounting for 31.55%, 30.84%, 17.42%, 6.02%, and 5.81% of acidobacterial sequences across all samples, respectively. Although no significant differences in acidobacterial diversity were found in the same soil layer across different fire severities, we observed significantly lower numbers of reads, but higher Shannon and Simpson indices, in the topsoil of the high-severity fire area than in the subsoil. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) also revealed significant differences in the acidobacterial community structure between the two soil layers. Soil pH, total nitrogen, NH4+-N, the Shannon index of understory vegetation and canopy density were the major drivers for acidobacterial community structure in the topsoil, while soil pH and organic matter were significant factors in the subsoil. A variance partitioning analysis (VPA) showed that edaphic factors explained the highest variation both in the topsoil (15.6%) and subsoil (56.3%). However, there are large gaps in the understanding of this field of research that still need to be explored in future studies. creator: Weike Li creator: Xiaodong Liu creator: Shukui Niu uri: https://doi.org/10.7717/peerj.8047 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Response of colonial Peruvian guano birds to flying UAVs: effects and feasibility for implementing new population monitoring methods link: https://peerj.com/articles/8129 last-modified: 2019-12-11 description: BackgroundDrones are reliable tools for estimating colonial seabird numbers. Although most research has focused on methods of improving the accuracy of bird counts, few studies have evaluated the impacts of these methods on bird behavior. In this study, we examined the effects of the DJI Phantom 3 drone approach (altitude, horizontal and vertical descent speeds) on changes in the intensity of behavioral response of guano birds: guanay cormorants (Phalacrocorax bougainvilli), Peruvian boobies (Sula variegata) and Peruvian pelicans (Pelecanus thagus). The breeding and non-breeding condition was also evaluated.MethodsEleven locations along the Peruvian coast were visited in 2016–2017. Drone flight tests considered an altitude range from 5 to 80 m from the colony level, a horizontal speed range from 0.5 to 15 m/s, and a vertical descent speed range from 0.5 to 3 m/s. The intensity of the behavioral response of birds was scored and categorized as: 0-no reacting, 1-head pointing to the drone (HP), 2-wing flapping (WF), 3-walking/running (WR) and 4-taking-off/flying (TK). Drone noise at specific altitudes was recorded with a sound meter close to the colony to discriminate visual from auditory effects of the drone.ResultsIn 74% of all test flights (N = 507), guano birds did not react to the presence of the drone, whereas in the remaining flights, birds showed a sign of discomfort: HP (47.7%, N = 130), WF (18.5%), WR (16.9%) and TK (16.9%). For the drone approach tests, only flight altitude had a significant effect in the intensity of the behavioral response of guano birds (intensity behavioral response <2). No birds reacted at drone altitudes above 50 m from the colony. Birds, for all species either in breeding or non-breeding condition, reacted more often at altitudes of 5 and 10 m. Chick-rearing cormorants and pelicans were less sensitive than their non-breeding counterparts in the range of 5–30 m of drone altitude, but boobies reacted similarly irrespective of their condition. At 5 m above the colony, cormorants were more sensitive to the drone presence than the other two species. Horizontal and vertical flights at different speeds had negligible effects (intensity behavioral response <1). At 2 m above the ground, the noise of the cormorant colony was in average 71.34 ± 4.05 dB (N = 420). No significant differences were observed in the drone noise at different flight altitudes because the background noise of the colony was as loud as the drone.ConclusionsIt is feasible to use the drone DJI Phantom 3 for surveys on the guano islands of Peru. We recommend performing drone flights at altitudes greater than 50 m from guano bird colonies and to select take-off spots far from gulls. Likewise, this study provides a first step to develop guidelines and protocols of drone use for other potential activities on the Peruvian guano islands and headlands such as surveys of other seabirds and pinnipeds, filming and surveillance. creator: Cinthia Irigoin-Lovera creator: Diana M. Luna creator: Diego A. Acosta creator: Carlos B. Zavalaga uri: https://doi.org/10.7717/peerj.8129 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Irigoin-Lovera et al.