title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1229
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

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: 

title: Species recovery and recolonization of past habitats: lessons for science and conservation from sea otters in estuaries
link: https://peerj.com/articles/8100
last-modified: 2019-12-10
description: Recovering species are often limited to much smaller areas than they historically occupied. Conservation planning for the recovering species is often based on this limited range, which may simply be an artifact of where the surviving population persisted. Southern sea otters (Enhydra lutris nereis) were hunted nearly to extinction but recovered from a small remnant population on a remote stretch of the California outer coast, where most of their recovery has occurred. However, studies of recently-recolonized estuaries have revealed that estuaries can provide southern sea otters with high quality habitats featuring shallow waters, high production and ample food, limited predators, and protected haul-out opportunities. Moreover, sea otters can have strong effects on estuarine ecosystems, fostering seagrass resilience through their consumption of invertebrate prey. Using a combination of literature reviews, population modeling, and prey surveys we explored the former estuarine habitats outside the current southern sea otter range to determine if these estuarine habitats can support healthy sea otter populations. We found the majority of studies and conservation efforts have focused on populations in exposed, rocky coastal habitats. Yet historical evidence indicates that sea otters were also formerly ubiquitous in estuaries. Our habitat-specific population growth model for California’s largest estuary—San Francisco Bay—determined that it alone can support about 6,600 sea otters, more than double the 2018 California population. Prey surveys in estuaries currently with (Elkhorn Slough and Morro Bay) and without (San Francisco Bay and Drakes Estero) sea otters indicated that the availability of prey, especially crabs, is sufficient to support healthy sea otter populations. Combining historical evidence with our results, we show that conservation practitioners could consider former estuarine habitats as targets for sea otter and ecosystem restoration. This study reveals the importance of understanding how recovering species interact with all the ecosystems they historically occupied, both for improved conservation of the recovering species and for successful restoration of ecosystem functions and processes.
creator: Brent B. Hughes
creator: Kerstin Wasson
creator: M. Tim Tinker
creator: Susan L. Williams
creator: Lilian P. Carswell
creator: Katharyn E. Boyer
creator: Michael W. Beck
creator: Ron Eby
creator: Robert Scoles
creator: Michelle Staedler
creator: Sarah Espinosa
creator: Margot Hessing-Lewis
creator: Erin U. Foster
creator: Kathryn M. Beheshti
creator: Tracy M. Grimes
creator: Benjamin H. Becker
creator: Lisa Needles
creator: Joseph A. Tomoleoni
creator: Jane Rudebusch
creator: Ellen Hines
creator: Brian R. Silliman
uri: https://doi.org/10.7717/peerj.8100
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Hughes et al.

title: Exploring profile and potential influencers of vaginal microbiome among asymptomatic pregnant Chinese women
link: https://peerj.com/articles/8172
last-modified: 2019-12-10
description: BackgroundThis study was designed to explore the profile and potential influencers of the vaginal microbiome (VMB) among asymptomatic pregnant Chinese women and its possible association with pregnancy outcomes.MethodsA prospective study was conducted among pregnant Chinese women receiving regular prenatal care at a hospital in Shanghai, China from March 2017 to March 2018. Vaginal swabs were obtained from 113 asymptomatic pregnant women in mid-pregnancy and sequenced by the V3–V4 region of 16S rRNA on an Ion S5™ XL platform. Demographic characteristics and major pregnancy outcomes were collected through questionnaires and electronic medical records.ResultsThe predominant vaginal community state types (CSTs) were CST I (45.1%) and CST III (31.9%). Participants were divided into a lactobacilli-dominant group (LD, CST I/II/III/I–III/V, n = 100, 88.5%) and a less lactobacilli-dominant group (LLD, CST IV-A/B, n = 13, 11.5%). Women in the LLD group showed an increased alpha diversity [median (interquartile range, IQR): 2.41 (1.67, 2.49) vs. 0.30 (0.17, 0.59), P < 0.001], which was related to a lower pre-pregnancy body mass index (BMI) (P = 0.012), and a greater instance of passive smoking (P = 0.033). The relative abundance of Lactobacillus was correlated positively with the pre-pregnancy BMI (r = 0.177, P = 0.041), but negatively with passive smoking (r =  − 0.204, P = 0.030).ConclusionThe vaginal flora of asymptomatic pregnant Chinese women was mostly dominated by Lactobacillus crispatus and L. iners. A lower BMI and greater instance of passive smoking may contribute to a less lactobacilli-dominant VMB. However, a larger sample size is needed.
creator: Yining He
creator: Yun Huang
creator: Zhengyin Zhang
creator: Fengping Yu
creator: Yingjie Zheng
uri: https://doi.org/10.7717/peerj.8172
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 He et al.

title: The accumulation of Mn and Cu in the morphological parts of Solidago canadensis under different soil conditions
link: https://peerj.com/articles/8175
last-modified: 2019-12-10
description: Solidago canadensis L. is a drought-tolerant, invasive plant, characterized by a large biomass of underground and aboveground parts. The aim of this study was to assess the accumulation of manganese (Mn) and copper (Cu) in the roots and rhizomes and the stems, leaves, and inflorescence parts in S. canadensis from two locations that differed in soil pH, organic carbon, and Mn and Cu concentrations. The concentration of the metals in the samples was determined by the AAS method; the pH was determined by the potentiometric method; and the content of organic carbon was determined using Tiurin’s method. The concentration of Mn and Cu in the roots of S. candensis correlated with the concentrations of the metals in the soil without regard to the soil condition or its organic carbon content. With a low soil pH and organic carbon content, Mn accumulation per 1 ramet in the aboveground parts of S. canadensis consisted over 50% of the total Mn content in the plant. In neutral or alkaline soils, the amount of Mn per 1 ramet accumulated in underground parts was over 60%. Regardless of the soil conditions, about 35% of Mn accumulated in rhizomes. Approximately 60% of copper accumulated in the underground parts of S. candensis (45% in rhizomes) without regard to the soil reaction or organic carbon content. The ability of the plant to accumulate large amounts of metals disposes Solidago canadensis as a candidate for the phytoremediation of soils contaminated with heavy metals.
creator: Aleksandra Bielecka
creator: Elżbieta Królak
uri: https://doi.org/10.7717/peerj.8175
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Bielecka and Królak