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: 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 title: Retrospective clinical study of renin-angiotensin system blockers in lung cancer patients with hypertension link: https://peerj.com/articles/8188 last-modified: 2019-12-10 description: PurposeRenin-angiotensin system blockers (RASBs), which include angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin-2 receptor 1 blockers (ARBs), have been reported to be associated with lung cancer metastasis, radiotherapy and chemotherapy. Until now, very limited clinical data for RASBs’ diagnostic and prognostic effects has existed for lung cancer chemotherapy in Chinese patients.MethodsThere were a total of 678 lung cancer patients with hypertension, of which 461 (68%) were in the non-RASBs group and 217 (32%) were in the RASBs group. Patients’ gender, age, smoking status, histologic differentiation, tumor size, pathological grade, lymph node metastasis, pathological stage and progression-free survival (PFS) were retrospectively analyzed between these two groups. The clinical effects of ACEIs and ARBs in lung cancer patients were compared via t tests, and χ2 test, and potential prognostic factors for progression-free survival (PFS) were evaluated by Kaplan–Meier analysis.ResultsSignificant differences were observed in lymph node metastasis between the RASBs and non-RASBs groups. The RASBs group (62.8% vs 71.7%, p = 0.037) and ARBs group (60.0% vs 71.7%, p = 0.030) had lower lymph node metastasis, and patients with RASBs had a lower pathological stage than those in non-RASBs groups (67.1% vs 77.4%, p = 0.044 ). The PFS of the RASBs (10.7 vs. 6.7 months, p = 0.040) and ACEIs (12.9 vs 6.7 months, p = 0.021) groups were longer than that of the non-RASBs group, while no statistical difference was shown between the ACEIs and ARBs groups. Moreover, the significant results of PFS were further confirmed in pathological stage III–IV patients. In the non-RASB group, 55% of patients took calcium channel blockers (CCBs), and the ACEIs group have a significantly longer PFS compared to the non-CCBs group (6.4 vs 12.9 months, p = 0.036).ConclusionIn this study, we showed that the use of RASBs is a positive factor for pathological stage and prognosis of lung cancer patients. Therefore, it is necessary to actively evaluate medical history, especially the use of anti-hypertension medication, in patients with lung cancer and reflect medical history in the treatment and management plans of these patients. creator: Jie Wei creator: Zhiyang Zhou creator: Zhijie Xu creator: Shuangshuang Zeng creator: Xi Chen creator: Xiang Wang creator: Wanli Liu creator: Min Liu creator: Zhicheng Gong creator: Yuanliang Yan uri: https://doi.org/10.7717/peerj.8188 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wei et al.