title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1268 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: New tracheal stainless steel stent pilot study: twelve month follow-up in a rabbit model link: https://peerj.com/articles/7797 last-modified: 2019-10-08 description: BackgroundCanine tracheal collapse is a complex airway pathology without promising treatment results. Currently nitinol stents are the best surgical option; however, some professionals are doubting if stent placement is the best option due to the associated complications.ObjectiveDetermine the technical feasibility, safety, and long-term follow-up after the implantation of a new tracheal stent designed for canine tracheal collapse.MethodsThirteen healthy, adult female New Zealander rabbits were involved in this pilot study.A new intra-tracheal device (Reference number 902711 patent registered as CasMin-Twine) was implanted in ten animals. Deployment was performed under general anesthesia, making a puncture incision via a 21 Gauge needle in the intra-tracheal space where the stent was introduced with a screwing process. The device was fixed to the tracheal wall with a non-absorbable suture. Computerized Tomography (CT) and an endoscopy to study structural abnormalities were performed after 30, 90 and 365 days after stent placement.ResultsTechnical and clinical success was 100%. There was no significant change in behavior or respiratory disorders. CT studies showed no significant alterations. After the 30 days, 60% of the animals showed partial endothelization in the endoscopy study, and only one animal still presented partial endothelization after 12 months. Mucus accumulation was only present in 40% of cases and classified as low, without respiratory consequences. Only one animal presented a single granuloma at caudal stent tip.ConclusionsThis new tracheal stent (CasMin-Twine) is an effective and safe procedure with promising results, and also shows the possibility of removing the device after endothelization has been produced. New studies should be carried out to evaluate the effectiveness in patients with tracheomalacia.Clinical Significance/ImpactThis new product can give veterinarians a new option of treatment for this complicated pathology. Minimizing specific equipment for its deployment, CasMin-Twine will be more accessible for all professionals. creator: Sandra Lopez-Minguez creator: Carolina Serrano-Casorran creator: Jose A. Guirola creator: Sergio Rodriguez-Zapater creator: Cristina Bonastre creator: Miguel Angel De Gregorio uri: https://doi.org/10.7717/peerj.7797 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lopez-Minguez et al. title: MicroRNA-205-5p inhibits three-dimensional spheroid proliferation of ErbB2-overexpressing breast epithelial cells through direct targeting of CLCN3 link: https://peerj.com/articles/7799 last-modified: 2019-10-08 description: We previously reported that microRNA-205-5p (miR-205-5p) is significantly decreased in the ErbB2-overexpressing breast epithelial cell line MCF10A-ErbB2 compared with control cells. In this study, we identified a direct target of miR-205-5p, chloride voltage-gated channel 3 (CLCN3). CLCN3 expression was induced by ErbB2 overexpression; this induced expression was then reduced to control levels by the transfection of the miR-205-5p precursor. In RNA-binding protein immunoprecipitation with Ago1/2/3 antibody, CLCN3 was significantly enriched in 293T embryonic kidney cells with miR-205-5p mimic transfection compared with negative control mimic transfection. In luciferase reporter assays using CLCN3 3′-UTR constructs, the miR-205-5p mimic significantly decreased reporter activity of both wild-type and partial mutant constructs in MCF10A-ErbB2 cells. In contrast, no inhibitory effects of the miR-205-5p mimic were detected using the complete mutant constructs. Since miR-205-5p expression in exosomes derived from MCF10A-neo cells was substantially higher than in exosomes derived from MCF10A-ErbB2 cells, we next investigated whether an exosome-mediated miR-205-5p transfer could control CLCN3 expression. To this end, exosomal miR-205-5p derived from MCF10A-neo cells was functionally transferred to MCF10A-ErbB2 cells, which served to decrease the expression of CLCN3. To assess the roles of CLCN3 in breast cancer, we next performed three-dimensional (3D) spheroid proliferation analyses using MCF10A-ErbB2 cells treated with MCF10A-neo-derived exosomes or CLCN3 shRNA stably expressing SKBR3 and MDA-MB-453 breast cancer cells. Our results showed that both treatment with MCF10A-neo-derived exosome and CLCN3 shRNA expression suppressed 3D spheroid proliferation. Collectively, these novel findings suggest that CLCN3 may be a novel direct target of miR-205-5p and this CLCN3/miR-205-5p interaction may serve a pivotal role in regulating breast cancer cellular proliferation under physiological conditions. creator: Takayoshi Takeno creator: Takuya Hasegawa creator: Hiroki Hasegawa creator: Yasuyuki Ueno creator: Ryo Hamataka creator: Aya Nakajima creator: Junji Okubo creator: Koji Sato creator: Toshiyuki Sakamaki uri: https://doi.org/10.7717/peerj.7799 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Takeno et al. title: Spatio-temporal variation in oxidative status regulation in a small mammal link: https://peerj.com/articles/7801 last-modified: 2019-10-08 description: Life-history allocation trade-offs are dynamic over time and space according to the ecological and demographical context. Fluctuations in food availability can affect physiological trade-offs like oxidative status regulation, reflecting the balance between pro-oxidant production and antioxidant capacity. Monitoring the spatio-temporal stability of oxidative status in natural settings may help understanding its importance in ecological and evolutionary processes. However, few studies have yet conducted such procedures in wild populations. Here, we monitored individual oxidative status in a wild eastern chipmunk (Tamias striatus) population across the 2017 summer active period and over three study sites. Oxidative damage (MDA: Malondialdehyde levels) and non-enzymatic antioxidant levels (FRAP: Ferric reducing antioxidant power and HASC: Hypochlorous acid shock capacity) were quantified across time and space using assays optimized for small blood volumes. Our results showed an increase in oxidative damage mirrored by a decrease in FRAP throughout the season. We also found different antioxidant levels among our three study sites for both markers. Our results also revealed the effects of sex and body mass on oxidative status. Early in the active season, females and individuals with a greater body mass had higher oxidative damage. Males had higher HASC levels than females throughout the summer. This study shows that oxidative status regulation is a dynamic process that requires a detailed spatial and temporal monitoring to yield a complete picture of possible trade-offs between pro-oxidant production and antioxidant capacity. creator: Vincent Lemieux creator: Dany Garant creator: Denis Reale creator: Patrick Bergeron uri: https://doi.org/10.7717/peerj.7801 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lemieux et al. title: Effect on hand kinematics when using assistive devices during activities of daily living link: https://peerj.com/articles/7806 last-modified: 2019-10-08 description: Assistive devices (ADs) are products intended to overcome the difficulties produced by the reduction in mobility and grip strength entailed by ageing and different pathologies. Nevertheless, there is little information about the effect that the use of these devices produces on hand kinematics. Thus, the aim of this work is to quantify this effect through the comparison of kinematic parameters (mean posture, ROM, median velocity and peak velocity) while performing activities of daily living (ADL) using normal products and ADs. Twelve healthy right-handed subjects performed 11 ADL with normal products and with 17 ADs wearing an instrumented glove on their right hand, 16 joint angles being recorded. ADs significantly affected hand kinematics, although the joints affected differed according to the AD. Furthermore, some pattern effects were identified depending on the characteristics of the handle of the ADs, namely, handle thickening, addition of a handle to products that initially did not have one, extension of existing handles or addition of handles to apply higher torques. An overview of the effects of these design characteristics on hand kinematics is presented as a basis for the selection of the most suitable AD depending on the patient’s impairments. creator: Alba Roda-Sales creator: Margarita Vergara creator: Joaquín L. Sancho-Bru creator: Verónica Gracia-Ibáñez creator: Néstor J. Jarque-Bou uri: https://doi.org/10.7717/peerj.7806 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Roda-Sales et al. title: Fluctuation and diversity of Hydromedusae (Hydrozoa, Cnidaria) in a highly productive region of the Gulf of Mexico inferred from high frequency plankton sampling link: https://peerj.com/articles/7848 last-modified: 2019-10-08 description: Hydrozoa medusae undergo blooms and seasonal fluctuations; however the drivers of such fluctuations are unknown. To understand how medusa populations fluctuate in response to seasonal factors such as temperature, salinity, dissolved oxygen, and chlorophyll a, and to enhance our taxonomic knowledge of Hydrozoa in Galveston Bay (TX), we performed frequent plankton sampling from September 2015 to September 2016. We collected 1,321 medusae in 190 sampling days. Using molecular barcoding and morphological analyses we identified 25 species, of which 21 are a first record for Galveston Bay and eight for the Gulf of Mexico. Daily medusa abundance is non-linearly related to temperature, with peak abundance estimated with multivariate regression analysis at approximately 21C. The role that temperature plays in driving medusa abundance has implications for future climate change scenarios, given that temperature in the Gulf of Mexico is expected to rise 4 °C by the end of the century. We also show that the biodiversity of the Galveston Bay and the Gulf of Mexico is underestimated and that molecular barcoding is an important and efficient tool to identify large number of medusae. We conclude that dense plankton sampling is necessary to capture both diversity and abundance of planktonic medusae. creator: Sarah Pruski creator: Maria Pia Miglietta uri: https://doi.org/10.7717/peerj.7848 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pruski and Miglietta title: Endemism and diversity of small mammals along two neighboring Bornean mountains link: https://peerj.com/articles/7858 last-modified: 2019-10-08 description: Mountains offer replicated units with large biotic and abiotic gradients in a reduced spatial scale. This transforms them into well-suited scenarios to evaluate biogeographic theories. Mountain biogeography is a hot topic of research and many theories have been proposed to describe the changes in biodiversity with elevation. Geometric constraints, which predict the highest diversity to occur in mid-elevations, have been a focal part of this discussion. Despite this, there is no general theory to explain these patterns, probably because of the interaction among different predictors with the local effects of historical factors. We characterize the diversity of small non-volant mammals across the elevational gradient on Mount (Mt.) Kinabalu (4,095 m) and Mt. Tambuyukon (2,579 m), two neighboring mountains in Borneo, Malaysia. We documented a decrease in species richness with elevation which deviates from expectations of the geometric constraints and suggests that spatial factors (e.g., larger diversity in larger areas) are important. The lowland small mammal community was replaced in higher elevations (from above ~1,900 m) with montane communities consisting mainly of high elevation Borneo endemics. The positive correlation we find between elevation and endemism is concordant with a hypothesis that predicts higher endemism with topographical isolation. This supports lineage history and geographic history could be important drivers of species diversity in this region. creator: Miguel Camacho-Sanchez creator: Melissa T.R. Hawkins creator: Fred Tuh Yit Yu creator: Jesus E. Maldonado creator: Jennifer A. Leonard uri: https://doi.org/10.7717/peerj.7858 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Camacho-Sanchez et al. title: Identification of crucial genes in abdominal aortic aneurysm by WGCNA link: https://peerj.com/articles/7873 last-modified: 2019-10-08 description: BackgroundAbdominal aortic aneurysm (AAA) is the full thickness dilation of the abdominal aorta. However, few effective medical therapies are available. Thus, elucidating the molecular mechanism of AAA pathogenesis and exploring the potential molecular target of medical therapies for AAA is of vital importance.MethodsThree expression datasets (GSE7084, GSE47472 and GSE57691) were downloaded from the Gene Expression Omnibus (GEO). These datasets were merged and then normalized using the “sva” R package. Differential expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were conducted. We compared the co-expression patterns between AAA and normal conditions, and hub genes of each functional module were identified. DEGs were mapped to co-expression network under AAA condition and a DEG co-expression network was generated. Crucial genes were identified using molecular complex detection (MCODE) (a plugin in Cytoscape).ResultsIn our study, 6 and 10 gene modules were detected for the AAA and normal conditions, respectively, while 143 DEGs were screened. Compared to the normal condition, genes associated with immune response, inflammation and muscle contraction were clustered in three gene modules respectively under the AAA condition; the hub genes of the three modules were MAP4K1, NFIB and HPK1, respectively. A DEG co-expression network with 102 nodes and 303 edges was identified, and a hub gene cluster with 10 genes from the DEG co-expression network was detected. YIPF6, RABGAP1, ANKRD6, GPD1L, PGRMC2, HIGD1A, GMDS, MGP, SLC25A4 and FAM129A were in the cluster. The expression levels of these 10 genes showed potential diagnostic value.ConclusionBased on WGCNA, we detected 6 modules under the AAA condition and 10 modules in the normal condition. Hub genes of each module and hub gene clusters of the DEG co-expression network were identified. These genes may act as potential targets for medical therapy and diagnostic biomarkers. Further studies are needed to elucidate the detailed biological function of these genes in the pathogenesis of AAA. creator: Siliang Chen creator: Dan Yang creator: Chuxiang Lei creator: Yuan Li creator: Xiaoning Sun creator: Mengyin Chen creator: Xiao Wu creator: Yuehong Zheng uri: https://doi.org/10.7717/peerj.7873 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chen et al. title: Bees may drive the reproduction of four sympatric cacti in a vanishing coastal mediterranean-type ecosystem link: https://peerj.com/articles/7865 last-modified: 2019-10-07 description: BackgroundSympatric congeneric plants might share pollinators, or each species might avoid competition by evolving specialized traits that generate partitions in pollinator assemblages. In both cases, pollen limitation (a decrease in the quality and quantity of compatible reproductive pollen) can occur, driving the plant mating system to autogamy as a mechanism of reproductive assurance. We assessed the relationships between pollinator assemblages and mating systems in a group of sympatric congeneric plants. We attempted to answer the following questions: (i) How similar are pollinator assemblages among sympatric cactus species? (ii) Which mating systems do sympatric cactus species use?MethodsWe studied sympatric Eriosyce taxa that inhabit a threatened coastal strip in a mediterranean-type ecosystem in central Chile. We performed field observations on four taxa and characterized pollinators during the years 2016 and 2017. We estimated differences in the pollinator assemblages using the Bray–Curtis index. To elucidate the mating systems, we conducted hand-pollination experiments using three treatments: manual cross-pollination, automatic self-pollination, and control (unmanipulated individuals). We tested differences in seed production for statistical significance using Kruskal–Wallis analysis.ResultsEriosyce subgibbosa showed a distinctive pollinator assemblage among the sympatric species that we studied (similarity ranged from 0% to 8%); it was visited by small bees and was the only species that was visited by the giant hummingbird Patagona gigas. Pollinator assemblages were similar between E. chilensis (year 2016 = 4 species; 2017 = 8) and E. chilensis var. albidiflora (2016 = 7; 2017 = 4); however, those of E. curvispina var. mutabilis (2016 = 7; 2017 = 6) were less similar to those of the aforementioned species. E. curvispina var. mutabilis showed the highest interannual variation in its pollinator assemblage (18% similarity). Reproduction in E. subgibbosa largely depends on pollinators, although it showed some degree of autogamy. Autonomous pollination was unfeasible in E. chilensis, which depended on flower visitors for its reproductive success. Both E. chilensis var. albidiflora and E. curvispina var. mutabilis showed some degree of autogamy.DiscussionWe observed differences in pollinator assemblages between E. subgibbosa and the remaining Eriosyce taxa, which depend on hymenopterans for pollen transfer. Pollinator assemblages showed considerable interannual variation, especially those of E. subgibbosa (ornithophilous syndrome) and E. curvispina var. mutabilis (melitophilous syndrome). Autogamous reproduction in these taxa may act as a reproductive assurance mechanism when pollinator availability is unpredictable. Our study contributes to improving our understanding of the reproductive systems of ecological interactions between threatened species in a Chilean mediterranean-type ecosystem. creator: Pablo C. Guerrero creator: Claudia A. Antinao creator: Beatriz Vergara-Meriño creator: Cristian A. Villagra creator: Gastón O. Carvallo uri: https://doi.org/10.7717/peerj.7865 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guerrero et al. title: Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China link: https://peerj.com/articles/7853 last-modified: 2019-10-07 description: Labriocimbex sinicus Yan & Wei gen. et sp. nov. of Cimbicidae is described. The new genus is similar to Praia Andre and Trichiosoma Leach. A key to extant Holarctic genera of Cimbicinae is provided. To identify the phylogenetic placement of Cimbicidae, the mitochondrial genome of L. sinicus was annotated and characterized using high-throughput sequencing data. The complete mitochondrial genome of L. sinicus was obtained with a length of 15,405 bp (GenBank: MH136623; SRA: SRR8270383) and a typical set of 37 genes (22 tRNAs, 13 PCGs, and two rRNAs). The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. Remarkably, the secondary structures of the rrnS and rrnL of L. sinicus were much different from those of Corynis lateralis. Phylogenetic analyses verified the monophyly and positions of the three Cimbicidae species within the superfamily Tenthredinoidea and demonstrated a relationship as (Tenthredinidae + Cimbicidae) + (Argidae + Pergidae) with strong nodal supports. Furthermore, we found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters. Phylogenetic tree based on two methods shows that L. sinicus is the sister group of Praia with high support values. We suggest that Labriocimbex belongs to the tribe Trichiosomini of Cimbicinae based on adult morphology and molecular data. Besides, we suggest to promote the subgenus Asitrichiosoma to be a valid genus. creator: Yuchen Yan creator: Gengyun Niu creator: Yaoyao Zhang creator: Qianying Ren creator: Shiyu Du creator: Bocheng Lan creator: Meicai Wei uri: https://doi.org/10.7717/peerj.7853 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yan et al. title: Integrative transcriptome data mining for identification of core lncRNAs in breast cancer link: https://peerj.com/articles/7821 last-modified: 2019-10-07 description: BackgroundCumulative evidence suggests that long non-coding RNAs (lncRNAs) play an important role in tumorigenesis. This study aims to identify lncRNAs that can serve as new biomarkers for breast cancer diagnosis or screening.MethodsFirst, the linear fitting method was used to identify differentially expressed genes from the breast cancer RNA expression profiles in The Cancer Genome Atlas (TCGA). Next, the diagnostic value of all differentially expressed lncRNAs was evaluated using a receiver operating characteristic (ROC) curve. Then, the top ten lncRNAs with the highest diagnostic value were selected as core genes for clinical characteristics and prognosis analysis. Furthermore, core lncRNA-mRNA co-expression networks based on weighted gene co-expression network analysis (WGCNA) were constructed, and functional enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The differential expression level and diagnostic value of core lncRNAs were further evaluated by using independent data set from Gene Expression Omnibus (GEO). Finally, the expression status and prognostic value of core lncRNAs in various tumors were analyzed based on Gene Expression Profiling Interactive Analysis (GEPIA).ResultsSeven core lncRNAs (LINC00478, PGM5-AS1, AL035610.1, MIR143HG, RP11-175K6.1, AC005550.4, and MIR497HG) have good single-factor diagnostic value for breast cancer. AC093850.2 has a prognostic value for breast cancer. AC005550.4 and MIR497HG can better distinguish breast cancer patients in early-stage from the advanced-stage. Low expression of MAGI2-AS3, LINC00478, AL035610.1, MIR143HG, and MIR145 may be associated with lymph node metastasis in breast cancer.ConclusionOur study provides candidate biomarkers for the diagnosis and prognosis of breast cancer, as well as a bioinformatics basis for the further elucidation of the molecular pathological mechanism of breast cancer. creator: Xiaoming Zhang creator: Jing Zhuang creator: Lijuan Liu creator: Zhengguo He creator: Cun Liu creator: Xiaoran Ma creator: Jie Li creator: Xia Ding creator: Changgang Sun uri: https://doi.org/10.7717/peerj.7821 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2019 Zhang et al.