title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1226 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: The association between mental rotation capacity and motor impairment in children with obesity—an exploratory study link: https://peerj.com/articles/8150 last-modified: 2019-12-11 description: BackgroundMotor impairments are relatively common in children with obesity and evidence suggests that these difficulties go beyond those expected based on the extra weight. This study aimed to investigate the mental rotation capacity in children with obesity, i.e., the ability to mentally view and rotate spatial information, which is a function of both visual-spatial and action representation processes. In particular, we examined whether children with obesity solved mental hand rotation tasks using an egocentric perspective (i.e., motor imagery) and if performance was related to their motor competence.MethodsFifty children (age range: 7–11 y) of which 19 with obesity and motor impairments (OB-) as assessed by the Movement Assessment Battery for Children (2nd version), 13 with obesity without motor impairments (OB+) and 18 control children with a healthy weight (HW) and normal motor competence, were submitted to a classic hand rotation task. Sitting at a desk the children were instructed to indicate the laterality of a picture of a hand displayed on a monitor as quickly and as accurately as possible.ResultsThe results indicate no differences in response time between groups (2,648 ms, 2,558 ms, 2,664 ms for OB-, OB+ and HW respectively). The OB- group, however, had significantly lower accuracy rates and inverse efficiency scores than the HW group (Accuracy: 72% vs. 89%; Inverse efficiency: 4,428 vs. 3,238). No difference was observed in accuracy and inverse efficiency between the OB+ and HW group (Accuracy: 86%; Inverse efficiency: 3,432). In all groups, slower and more error-prone responses were observed when the angle of rotation was larger and when the hand on display was incongruent with the posture of the participants, which indicates that judgments were made from an egocentric perspective and involved motor imagery.ConclusionAll children, including those with obesity, appear to engage in motor imagery. This notion needs to be investigated further in children with obesity and motor impairments, given their generally lower accuracy and decreased efficiency, which may indicate a reduced mental rotation capacity. creator: Frederik J.A. Deconinck creator: Eva D’Hondt creator: Karen Caeyenberghs creator: Matthieu Lenoir creator: Mireille J.C.M. Augustijn uri: https://doi.org/10.7717/peerj.8150 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Deconinck et al. title: Prosaposin in seminal plasma on the day of oocyte retrieval is associated with normal fertilization and embryo development in in vitro fertilization cycles link: https://peerj.com/articles/8177 last-modified: 2019-12-11 description: The prospective study including 166 participants aims to evaluate the association between seminal prosaposin and the outcomes of in vitro fertilization (IVF) cycles in humans. The generalized linear model (GLM) was used to analyze the associations between seminal prosaposin concentrations and normal fertilization rates and good embryos proportion. The generalized estimating equation (GEE) was used to evaluate the association between embryo parameters and the prosaposin concentrations. Each model was adjusted for age of the couples, female basal FSH, AFC and BMI, starting dose and oocyte yield of IVF cycles and smoker. GLM models suggested that prosaposin was significantly associated with fertilization rate (P = 0.005) and good embryo proportion (P = 0.038) while none of the semen parameters (sperm concentration, motility, progressive motility, normal morphology rate, postwash sperm concentration and motility) was significantly associated with the parameters in the cohort. Using GEE, it was also shown that prosaposin was positively associated with the occurrence of early cleavage and negatively associated with uneven cleavage pattern on day 3. In both the overall population and the normozoospermia patients, the prosaposin was significantly associated with pregnancy with adjustment with covariates. In conclusion, our data suggested that seminal prosaposin concentration could provide more information regarding normal fertilization and embryo development in IVF than traditional semen parameters. creator: Chun Xu creator: Jiali Cai creator: Lanlan Liu creator: Jianzhi Ren uri: https://doi.org/10.7717/peerj.8177 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xu et al. title: Soil and plant phytoliths from the Acacia-Commiphora mosaics at Oldupai Gorge (Tanzania) link: https://peerj.com/articles/8211 last-modified: 2019-12-11 description: This article studies soil and plant phytoliths from the Eastern Serengeti Plains, specifically the Acacia-Commiphora mosaics from Oldupai Gorge, Tanzania, as present-day analogue for the environment that was contemporaneous with the emergence of the genus Homo. We investigate whether phytolith assemblages from recent soil surfaces reflect plant community structure and composition with fidelity. The materials included 35 topsoil samples and 29 plant species (20 genera, 15 families). Phytoliths were extracted from both soil and botanical samples. Quantification aimed at discovering relationships amongst the soil and plant phytoliths relative distributions through Chi–square independence tests, establishing the statistical significance of the relationship between categorical variables within the two populations. Soil assemblages form a spectrum, or cohort of co-ocurring phytolith classes, that will allow identifying environments similar to those in the Acacia-Commiphora ecozone in the fossil record. creator: Julio Mercader creator: Siobhán Clarke creator: Mariam Bundala creator: Julien Favreau creator: Jamie Inwood creator: Makarius Itambu creator: Fergus Larter creator: Patrick Lee creator: Garnet Lewiski-McQuaid creator: Neduvoto Mollel creator: Aloyce Mwambwiga creator: Robert Patalano creator: María Soto creator: Laura Tucker creator: Dale Walde uri: https://doi.org/10.7717/peerj.8211 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mercader et al. title: Identification of miRNA precursors in the phloem of Cucurbita maxima link: https://peerj.com/articles/8269 last-modified: 2019-12-11 description: Plant development and responses to environmental cues largely depend on mobile signals including microRNAs (miRNAs) required for post-transcriptional silencing of specific genes. Short-range cell-to-cell transport of miRNA in developing tissues and organs is involved in transferring positional information essential for determining cell fate. Among other RNA species, miRNAs are found in the phloem sap. Long-distance transport of miRNA via the phloem takes a part in regulation of physiological responses to changing environmental conditions. As shown for regulation of inorganic phosphorus and sulfate homeostasis, mature miRNAs rather than miRNAs precursors are transported in the phloem as signaling molecules. Here, a bioinformatics analysis of transcriptomic data for Cucurbita maxima phloem exudate RNAs was carried out to elucidate whether miRNA precursors could also be present in the phloem. We demonstrated that the phloem transcriptome contained a subset of C. maxima pri-miRNAs that differed from a subset of pri-miRNA sequences abundant in a leaf transcriptome. Differential accumulation of pri-miRNA was confirmed by PCR analysis of C. maxima phloem exudate and leaf RNA samples. Therefore, the presented data indicate that a number of C. maxima pri-miRNAs are selectively recruited to the phloem translocation pathway. This conclusion was validated by inter-species grafting experiments, in which C. maxima pri-miR319a was found to be transported across the graft union via the phloem, confirming the presence of pri-miR319a in sieve elements and showing that phloem miRNA precursors could play a role in long-distance signaling in plants. creator: Eugeny Tolstyko creator: Alexander Lezzhov creator: Andrey Solovyev uri: https://doi.org/10.7717/peerj.8269 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tolstyko et al. title: The landscape and prognostic value of tumor-infiltrating immune cells in gastric cancer link: https://peerj.com/articles/7993 last-modified: 2019-12-10 description: BackgroundGastric cancer (GC) is the fourth most frequently diagnosed malignancy and the second leading cause of cancer-associated mortality worldwide. The tumor microenvironment, especially tumor-infiltrating immune cells (TIICs), exhibits crucial roles both in promoting and inhibiting cancer growth. The aim of the present study was to evaluate the landscape of TIICs and develop a prognostic nomogram in GC.Materials and MethodsA gene expression profile obtained from a dataset from The Cancer Genome Atlas (TCGA) was used to quantify the proportion of 22 TIICs in GC by the CIBERSORT algorithm. LASSO regression analysis and multivariate Cox regression were applied to select the best survival-related TIICs and develop an immunoscore formula. Based on the immunoscore and clinical information, a prognostic nomogram was built, and the predictive accuracy of it was evaluated by the area under the curve (AUC) of the receiver operating characteristic curve (ROC) and the calibration plot. Furthermore, the nomogram was validated by data from the International Cancer Genome Consortium (ICGC) dataset.ResultsIn the GC samples, macrophages (25.3%), resting memory CD4 T cells (16.2%) and CD8 T cells (9.7%) were the most abundant among 22 TIICs. Seven TIICs were filtered out and used to develop an immunoscore formula. The AUC of the prognostic nomogram in the TCGA set was 0.772, similar to that in the ICGC set (0.730) and whole set (0.748), and significantly superior to that of TNM staging alone (0.591). The calibration plot demonstrated an outstanding consistency between the prediction and actual observation. Survival analysis revealed that patients with GC in the high-immunoscore group exhibited a poor clinical outcome. The result of multivariate analysis revealed that the immunoscore was an independent prognostic factor.DiscussionThe immunoscore could be used to reinforce the clinical outcome prediction ability of the TNM staging system and provide a convenient tool for risk assessment and treatment selection for patients with GC. creator: Linhai Li creator: Yiming Ouyang creator: Wenrong Wang creator: Dezhi Hou creator: Yu Zhu uri: https://doi.org/10.7717/peerj.7993 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Cellular components in tumor microenvironment of neuroblastoma and the prognostic value link: https://peerj.com/articles/8017 last-modified: 2019-12-10 description: BackgroundTumor microenvironment (TME) contributes to tumor development, progression, and treatment response. In this study, we detailed the cell composition of the TME in neuroblastoma (NB) and constructed a cell risk score model to predict the prognosis of NB.MethodsxCell score was calculated through transcriptomic data from the datasets GSE49711 and GSE45480 based on the xCell algorithm. The random forest method was employed to select important features and the coefficient was obtained via multivariate cox regression analysis to construct a prognostic model, and the performance was validated in another two independent datasets, GSE16476 and TARGET-NBL.ResultsWe found that both immune and non-immune cells varies significantly in different prognostic groups, and were correlated with survival time. The proposed prognostic cell risk score (pCRS) model we constructed can be an independent prognostic indicator for overall survival (OS) and event-free survival (EFS) (training: OS, HR 1.579, EFS, HR 1.563; validation: OS, HR 1.665, 3.848, EFS, HR 2.203, all p-values < 0.01) and only independent prognostic factor in International Neuroblastoma Risk Group high risk patients (HR 1.339, 3.631; p-value 1.76e–2, 3.71e–5), rather than MYCN amplification. Besides, pCRS model showed good performance in grouping, in discriminating MYCN status, the area under the curve (AUC) was 0.889, 0.933, and 0.861 in GSE49711, GSE45480, and GSE16476, respectively. In separating high risk groups, the AUC was 0.904 in GSE49711.ConclusionThis study details the cellular components in the TME of NB through gene expression data, the proposed pCRS model might provide a basis for treatment selection of high risk patients or targeting cellular components of TME in NB. creator: Xiaodan Zhong creator: Yutong Zhang creator: Linyu Wang creator: Hao Zhang creator: Haiming Liu creator: Yuanning Liu uri: https://doi.org/10.7717/peerj.8017 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhong et al. title: motoRneuron: an open-source R toolbox for time-domain motor unit analyses link: https://peerj.com/articles/7907 last-modified: 2019-12-10 description: Motor unit synchronization is the tendency of motor neurons and their associated muscle fibers to discharge near-simultaneously. It has been theorized as a control mechanism for force generation by common excitatory inputs to these motor neurons. Magnitude of synchronization is calculated from peaks in cross-correlation histograms between motor unit discharge trains. However, there are many different methods for detecting these peaks and even more indices for calculating synchronization from them. Methodology is diverse, typically laboratory-specific and requires expensive software, like Matlab or LabView. This lack of standardization makes it difficult to draw definitive conclusions about motor unit synchronization. A free, open-source toolbox, “motoRneuron”, for the R programming language, has been developed which contains functions for calculating time domain synchronization using different methods found in the literature. The objective of this paper is to detail the toolbox’s functionality and present a case study showing how the same synchronization index can differ when different methods are used to compute it. A pair of motor unit action potential trains were collected from the forearm during a isometric finger flexion task using fine wire electromyography. The motoRneuron package was used to analyze the discharge time of the motor units for time-domain synchronization. The primary function “mu_synch” automatically performed the cross-correlation analysis using three different peak detection methods, the cumulative sum method, the z-score method, and a subjective visual method. As function parameters defined by the user, only first order recurrence intervals were calculated and a 1 ms bin width was used to create the cross correlation histogram. Output from the function were six common synchronization indices, the common input strength (CIS), k′, k′ − 1, E, S, and Synch Index. In general, there was a high degree of synchronization between the two motor units. However, there was a varying degree of synchronization between methods. For example, the widely used CIS index, which represents a rate of synchronized discharges, shows a 45% difference between the visual and z-score methods. This singular example demonstrates how a lack of consensus in motor unit synchronization methodologies may lead to substantially differing results between studies. The motoRneuron toolbox provides researchers with a standard interface and software to examine time-domain motor unit synchronization. creator: Andrew J. Tweedell creator: Matthew S. Tenan uri: https://doi.org/10.7717/peerj.7907 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: