title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1355 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Expression of ICOSL is associated with decreased survival in invasive breast cancer link: https://peerj.com/articles/6903 last-modified: 2019-05-16 description: BackgroundInducible co-stimulator (ICOS) is a CD28-related molecule exclusively expressed on activated T cells and plays a critical role in modulating the immune response in breast cancer. The blockage of ICOS pathway has been shown to inhibit the activity of Type 2 T helper cells, thus potentially protecting against cancer growth. The current study aims to investigate the correlation between inducible co-stimulator ligand (ICOSL) expression in tumor tissues and the prognoses of patients with invasive breast cancer.MethodsTumor samples from 562 Chinese patients with invasive breast carcinomas were collected between 2003 and 2010. The expression of ICOSL on breast tumor and adjacent non-cancerous tissue was determined via immunohistochemistry. The overall survival (OS) of patients with positive and negative ICOSL expression were described using Kaplan–Meier curves, respectively. Parametric correlation method was used to analyze the correlation between ICOSL expression and other clinicopathological parameters. ICOSL was selected as a dependent variable for multivariate analysis.ResultsPositive ICOSL expression was identified on the plasma membrane in both cytoplasm and the nucleus of breast cancer cells. Membrane-expressed ICOSL is determined as an independent prognostic factor for OS in breast cancer but without significantly correlating with other clinicopathologic parameters such as age, menopausal status, depth of invasion, lymph node metastasis status, histologic classification, etc.ConclusionOur study suggests that the up-regulated expression of ICOSL protein in breast tumor cells can be associated with poor prognoses in invasive breast carcinomas. creator: Bin Wang creator: Huayong Jiang creator: Tingyang Zhou creator: Ning Ma creator: Wei Liu creator: Yajie Wang creator: Li Zuo uri: https://doi.org/10.7717/peerj.6903 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Phylogeography of Dictyota fasciola and Dictyota mediterranea (Dictyotales, Phaeophyceae): unexpected patterns on the Atlantic-Mediterranean marine transition and taxonomic implications link: https://peerj.com/articles/6916 last-modified: 2019-05-16 description: The Atlantic-Mediterranean marine transition is a fascinating biogeographic region, but still very poorly studied from the point of view of seaweed phylogeography. Dictyota fasciola and D. mediterranea (Dictyotales, Phaeophyceae) are two currently recognized sister species that share a large part of their distribution along the Mediterranean Sea and the Atlantic Ocean, representing a unique study model to understand the diversification processes experienced by macroalgae during and after Messinian at this marine region. In this study, we sampled 102 individuals of D. fasciola and D. mediterranea from 32 localities along their distribution range and sequenced the mitochondrial cox1 and the chloroplast rbcL-rbcS DNA regions for all the samples. Our data do not support the occurrence of two sister species but a morphologically variable and highly genetic diverse species or a complex of species. Most of the observed genetic diversity corresponds to the Mediterranean populations, whereas the Atlantic ones are much more homogeneous. The early-diverged lineages inferred from both mtDNA and cpDNA phylogenetic reconstructions were constituted by samples from the Mediterranean Sea. Together, these results suggest that the Mediterranean Sea acted as a refugium for the D. fasciola–D. mediterranea lineage during the geologic and climatic changes occurred on the region since the Miocene, subsequently dispersing to the Atlantic Ocean. creator: Daniel Vitales creator: Joana Aragay creator: Teresa Garnatje creator: Amelia Gómez Garreta creator: Jordi Rull Lluch uri: https://doi.org/10.7717/peerj.6916 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Vitales et al. title: Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain link: https://peerj.com/articles/6931 last-modified: 2019-05-16 description: Forests and woodlands worldwide are being severely impacted by invasive Phytophthora species, with initial outbreaks in some cases occurring on host trees located in public parks and gardens. These highly disturbed sites with diverse planting practices may indeed act as harbours for invasive Phytophthora pathogens which are particularly well adapted to surviving in soil. High throughput Illumina sequencing was used to analyse Phytophthora species diversity in soil samples collected from 14 public garden/amenity woodland sites in northern Britain. Bioinformatic analyses revealed some limitations to using internal transcribed spacer as the barcode region; namely reporting of false positives and ambiguous species matches. Taking this into account, 35 distinct sequences were amplified across the sites, corresponding to 23 known Phytophthora species as well as twelve oomycete sequences with no match to any known Phytophthora species. Phytophthora pseudosyringae and P. austrocedri, both of which cause serious damage to trees and are regarded as fairly recent introductions to Britain, were the two most abundant Phytophthora species detected. There was no evidence that any of the detected Phytophthora species were more associated with any one type of host, healthy or otherwise. This study has demonstrated the ubiquity and diversity of Phytophthora species endemic in highly managed, extensively planted soil environments in Britain. Suggested improvements to the methodology and the practical implications of the findings in terms of mitigating Phytophthora spread and impact are discussed. creator: Carolyn E. Riddell creator: Debbie Frederickson-Matika creator: April C. Armstrong creator: Matt Elliot creator: Jack Forster creator: Pete E. Hedley creator: Jenny Morris creator: Peter Thorpe creator: David EL Cooke creator: Leighton Pritchard creator: Paul M. Sharp creator: Sarah Green uri: https://doi.org/10.7717/peerj.6931 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Riddell et al. title: Vehicle emission and atmospheric pollution in China: problems, progress, and prospects link: https://peerj.com/articles/6932 last-modified: 2019-05-16 description: China has been the largest vehicle market in the world since 2009. The stalemate between the rapid development of the vehicle industry and delayed vehicle emission control has become increasingly prominent. Vehicle emission has become a significant source of air pollution in China’s cities. Understanding the current barriers in the vehicle industry is necessary for the development of effective and sustainable measures and policy to manage vehicle-induced air pollution. This review provides insight into the circumstances and causes of vehicle-induced air pollution and outlines recent progress in policy-makers’ long-term strategies and regulations. The development of an integrated mechanism of social participation, technical revolution, and regulatory innovation in vehicles, fuel, and roads is suggested to break the stalemate between air pollution and the automobile boom in China; the implications of this review extend to other countries facing the similar atmospheric pollution problems. creator: Jin Wang creator: Qiuxia Wu creator: Juan Liu creator: Hong Yang creator: Meiling Yin creator: Shili Chen creator: Peiyu Guo creator: Jiamin Ren creator: Xuwen Luo creator: Wensheng Linghu creator: Qiong Huang uri: https://doi.org/10.7717/peerj.6932 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Identification of RyR2-PBmice and the effects of transposon insertional mutagenesis of the RyR2 gene on cardiac function in mice link: https://peerj.com/articles/6942 last-modified: 2019-05-16 description: Ryanodine receptor 2 (RyR2) plays an important role in maintaining the normal heart function, and mutantions can lead to arrhythmia, heart failure and other heart diseases. In this study, we successfully identified a piggyBac translocated RyR2 gene heterozygous mouse model (RyR2-PBmice) by tracking red fluorescent protein (RFP) and genotyping PCR. Cardiac function tests showed that there was no significant difference between the RyR2-PBmice and corresponding wild-type mice (WTmice), regardless of whether they were in the basal state or injected with epinephrine and caffeine. However, the sarcoplasmic reticulum Ca2+ content was significantly reduced in the cardiomyocytes of RyR2-PBmice as assessed by measuring caffeine-induced [Ca2+]i transients; the cardiac muscle tissue of RyR2-PBmice displayed significant mitochondrial swelling and focal dissolution of mitochondrial cristae, and the tissue ATP content in the RyR2-PBmice heart was significantly reduced. To further analyze the molecular mechanism behind these changes, we tested the expression levels of related proteins using RT-PCR and Western blot analyses. The mRNA level of RyR2 in RyR2-PBmice cardiac tissue decreased significantly compared with the WTmice, and the protein expression associated with the respiratory chain was also downregulated. These results suggested that the piggyBac transposon inserted into the RyR2 gene substantively affected the structure and function of mitochondria in the mouse cardiomyocytes, leading to disorders of energy metabolism. creator: Qianqian Wang creator: Chao Wang creator: Bo Wang creator: Qirui Shen creator: Leilei Qiu creator: Shuaijun Zou creator: Tao Wang creator: Guoyan Liu creator: Beilei Wang creator: Liming Zhang uri: https://doi.org/10.7717/peerj.6942 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Comparison of the National Early Warning Score (NEWS) and the Modified Early Warning Score (MEWS) for predicting admission and in-hospital mortality in elderly patients in the pre-hospital setting and in the emergency department link: https://peerj.com/articles/6947 last-modified: 2019-05-16 description: The aim of this study is to evaluate the usefulness of the pre-hospital National Early Warning Score (pNEWS) and the pre-hospital Modified Early Warning Score (pMEWS) for predicting admission and in-hospital mortality in elderly patients presenting to the emergency department (ED). We also compare the value of the pNEWS with that of the ED NEWS (eNEWS) and ED MEWS (eMEWS) for predicting admission and in-hospital mortality. This retrospective, single-centre observational study was carried out in the ED of Jikei University Kashiwa Hospital, in Chiba, Japan, from 1st April 2017 to 31st March 2018. All patients aged 65 years or older were included in this study. The pNEWS/eNEWS were derived from seven common physiological vital signs: respiratory rate, peripheral oxygen saturation, the presence of inhaled oxygen parameters, body temperature, systolic blood pressure, pulse rate and Alert, responds to Voice, responds to Pain, Unresponsive (AVPU) score, whereas the pMEWS/eMEWS were derived from six common physiological vital signs: respiratory rate, peripheral oxygen saturation, body temperature, systolic blood pressure, pulse rate and AVPU score. Discrimination was assessed by plotting the receiver operating characteristic (ROC) curve and calculating the area under the ROC curve (AUC). The median pNEWS, pMEWS, eNEWS and eMEWS were significantly higher at admission than at discharge (p < 0.001). The median pNEWS, pMEWS, eNEWS and eMEWS of non-survivors were significantly higher than those of the survivors (p < 0.001). The AUC for predicting admission was 0.559 for the pNEWS and 0.547 for the pMEWS. There was no significant difference between the AUCs of the pNEWS and the pMEWS for predicting admission (p = 0.102). The AUCs for predicting in-hospital mortality were 0.678 for the pNEWS and 0.652 for the pMEWS. There was no significant difference between the AUCs of the pNEWS and the pMEWS for predicting in-hospital mortality (p = 0.081). The AUC for predicting admission was 0.628 for the eNEWS and 0.591 for the eMEWS. The AUC of the eNEWS was significantly greater than that of the eMEWS for predicting admission (p < 0.001). The AUC for predicting in-hospital mortality was 0.789 for the eNEWS and 0.720 for the eMEWS. The AUC of the eNEWS was significantly greater than that of the eMEWS for predicting in-hospital mortality (p < 0.001). For admission and in-hospital mortality, the AUC of the eNEWS was significantly greater than that of the pNEWS (p < 0.001, p < 0.001), and the AUC of the eMEWS was significantly greater than that of the pMEWS (p < 0.01, p < 0.05). Our single-centre study has demonstrated the low utility of the pNEWS and the pMEWS as predictors of admission and in-hospital mortality in elderly patients, whereas the eNEWS and the eMEWS predicted admission and in-hospital mortality more accurately. Evidence from multicentre studies is needed before introducing pre-hospital versions of risk-scoring systems. creator: Toshiya Mitsunaga creator: Izumu Hasegawa creator: Masahiko Uzura creator: Kenji Okuno creator: Kei Otani creator: Yuhei Ohtaki creator: Akihiro Sekine creator: Satoshi Takeda uri: https://doi.org/10.7717/peerj.6947 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mitsunaga et al. title: Biochemical changes throughout early- and middle-stages of embryogenesis in lobsters (Homarus americanus) under different thermal regimes link: https://peerj.com/articles/6952 last-modified: 2019-05-16 description: Most marine crustacean eggs contain the full complement of nutritional resources required to fuel their growth and development. Given the propensity of many ovigerous (egg-bearing) American lobsters (Homarus americanus) to undergo seasonal inshore-to-offshore migrations, thereby potentially exposing their eggs to varying thermal regimes, the goal of this study was to determine the impact of water temperature on egg quality over their course of development. This was accomplished by documenting changes in total lipids, proteins, and size (volume) of eggs subjected to one of three thermal regimes: inshore, offshore, and constant (16 °C) conditions. Total egg lipids showed a marked decrease over time, while protein levels increased over the same period. Although there were no significant differences in total lipids, proteins, or egg sizes between eggs exposed to inshore and offshore temperatures, they differed from values for eggs exposed to a constant temperature, which also hatched almost three months sooner. This is most likely due to the fact that eggs held at a constant temperature did not experience a period of slow development during the colder months from November to March that are important for synchronizing egg hatch and may be compromised by elevated seawater temperatures. creator: Jason S. Goldstein creator: Winsor H. Watson III uri: https://doi.org/10.7717/peerj.6952 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Goldstein and Watson III title: Dissection of three quantitative trait loci for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.) link: https://peerj.com/articles/6966 last-modified: 2019-05-16 description: BackgroundThousand grain weight is a key component of grain yield in rice, and a trait closely related to grain length (GL) and grain width (GW) that are important traits for grain quality. Causal genes for 16 quantitative trait loci (QTL) affecting these traits have been cloned, but more QTL remain to be characterized for establishing a genetic regulating network. A QTL controlling grain size in rice, qGS10, was previously mapped in the interval RM6100–RM228 on chromosome 10. This study aimed to delimitate this QTL to a more precise location.MethodA total of 12 populations were used. The ZC9 population comprised 203 S1:2 families derived from a residual heterozygous (RH) plant in the F9 generation of the indica rice cross Teqing (TQ)/IRBB52, segregating the upper region of RM6100–RM228 and three more regions on chromosomes 1, 9, and 11. The Ti52-1 population comprised 171 S1 plants derived from one RH plant in F7 of TQ/IRBB52, segregating a single interval that was in the lower portion of RM6100–RM228. The other ten populations were all derived from Ti52-1, including five S1 populations with sequential segregating regions covering the target region and five near isogenic line (NIL) populations maintaining the same segregating pattern. QTL analysis for 1,000-grain weight, GL, and GW was performed using QTL IciMapping and SAS procedure GLM.ResultThree QTL were separated in the original qGS10 region. The qGL10.1 was located in the upper region RM6704–RM3773, shown to affect GL only. The qGS10.1 was located within a 207.1-kb interval flanked by InDel markers Te20811 and Te21018, having a stable and relatively high effect on all the three traits analyzed. The qGS10.2 was located within a 1.2-Mb interval flanked by simple sequence repeat markers RM3123 and RM6673. This QTL also affected all the three traits but the effect was inconsistent across different experiments. QTL for grain size were also detected in all the other three segregating regions.ConclusionThree QTL for grain size that were tightly linked on the long arm of chromosome 10 of rice were separated using NIL populations with sequential segregating regions. One of them, qGS10.1, had a stable and relatively high effect on grain weight, GL, and GW, providing a good candidate for gene cloning. Another QTL, qGS10.2, had a significant effect on all the three traits but the effect was inconsistent across different experiments, providing an example of genotype-by-environmental interaction. creator: Yu-Jun Zhu creator: Zhi-Chao Sun creator: Xiao-Jun Niu creator: Jie-Zheng Ying creator: Ye-Yang Fan creator: Tong-Min Mou creator: Shao-Qing Tang creator: Jie-Yun Zhuang uri: https://doi.org/10.7717/peerj.6966 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhu et al. title: Retrospective correlation analysis of plasma Immunoglobulin G and clinical performance in CIDP link: https://peerj.com/articles/6969 last-modified: 2019-05-16 description: BackgroundChronic inflammatory demyelinating polyneuropathy (CIDP) can be successfully treated with immunoglobulin either intravenously (IVIG) or subcutaneously (SCIG). Measurement of plasma immunoglobulin G levels (P-IgG) and its correlation to clinical improvement has shown conflicting results. This study aims to clarify whether changes in P-IgG are related to clinical development in patients with CIDP treated with IVIG or SCIG.MethodsPatients from five previous studies treated with either IVIG or SCIG with evaluation at baseline and re-evaluation after two or 10/12 weeks, respectively were included. At evaluation and re-evaluation, the following tests were done: combined isokinetic muscle strength (cIKS), grip strength, 9-hole-peg test (9-HPT), 40-meter-walk test (40-MWT), clinical examination of muscle strength score by the Medical Research Council (MRC) and measurement of plasma immunoglobulin G (P-IgG).ResultsFifty-five patients were included in the IVIG group and 41 in the SCIG group. There was no correlation between the changes in P-IgG and cIKS in neither the IVIG group (r = 0.137, p = 0.32) nor the SCIG group (r =  − 0.048, p = 0.77). Similarly, no correlations could be demonstrated between P-IgG and grip strength, 9-HPT, 40-MWT or MRC.ConclusionsIn patients with CIDP receiving SCIG or IVIG, changes in P-IgG during treatment did not correlate with changes in muscle strength or other motor performance skills. creator: Lars Kjøbsted Markvardsen creator: Stine Bruun-Sørensen creator: Ingelise Christiansen creator: Henning Andersen uri: https://doi.org/10.7717/peerj.6969 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Markvardsen et al. title: Fish nursery value of algae habitats in temperate coastal reefs link: https://peerj.com/articles/6797 last-modified: 2019-05-15 description: The nursery function of coastal habitats is one of the most frequently mentioned and recognized ecosystem services in the valuation of coastal ecosystems. Despite its importance our understanding of the precise habitat parameters and mechanisms that make a habitat important as a nursery area is still limited for many species. The study aimed to establish the importance of different algae morphotypes in providing shelter and food for juvenile coastal fish during the main settlement peaks, in early spring and late summer, in littoral rocky reef systems in the Northwestern Mediterranean. The results of our study showed strong seasonal differences in algae cover, composition and height between the two sampling periods. Overall, during spring the algae were well developed, while in late summer, both density and height, of most algae decreased considerably. Equally, prey biomass, in form of suitable sized invertebrate fauna associated to the algae, decreased. Accordingly, the shelter and food for the fish settling in this habitat during late summer were less abundant, indicating a mismatch between the observed presence of juvenile fish and optimal habitat conditions. Differences in prey densities were detected between algae morphotypes, with structurally more complex algae, such as Cystoseira spp. and Halopteris spp. consistently containing more prey, independent of season, compared to simpler structured morphotypes such as Dictoytales. The study furthermore related juvenile fish density to habitats dominated by different algae morphotypes. Out of the three-study species (Diplodus vulgaris, Symphodus ocellatus, Coris julis) only S. ocellatus showed a significant association with an algae habitat. S. ocellatus related positively to habitats dominated by Dictoytales which provided the highest cover during late summer but had the lowest prey densities. A strong association of this species with Cystoseira, as reported by other studies, could not be confirmed. Cystoseira was abundant within the study area but in a state of dieback, showing loss and reduced height of foliage, typical for the time of year within the study area. It is therefore likely that algae-fish associations are context-dependent and that several algae species may fulfil similar functions. We also discovered that prey biomass did not appear to have an important effect on juvenile abundances. Nevertheless, the availability of prey may influence juvenile fish condition, growth performance and ultimately long-term survival. We therefore suggest that future studies on habitat quality should also include, besides abundance, indicators related to the condition and growth of juveniles. creator: Hilmar Hinz creator: Olga Reñones creator: Adam Gouraguine creator: Andrew F. Johnson creator: Joan Moranta uri: https://doi.org/10.7717/peerj.6797 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hinz et al.