title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1119 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L. link: https://peerj.com/articles/9315 last-modified: 2020-06-16 description: Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of R. integrifolia and one each of R. ovata from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level. creator: Craig F. Barrett uri: https://doi.org/10.7717/peerj.9315 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Barrett title: Keraphyton gen. nov., a new Late Devonian fern-like plant from Australia link: https://peerj.com/articles/9321 last-modified: 2020-06-16 description: The first plants related to the ferns are represented by several extinct groups that emerged during the Devonian. Among them, the iridopterids are closely allied to the sphenopsids, a group represented today by the genus Equisetum. They have been documented in Middle to early Late Devonian deposits of Laurussia and the Kazakhstan plate. Their Gondwanan record is poor, with occurrences limited to Venezuela and Morocco. Here we describe a new genus from a late Late Devonian locality of New South Wales. It is represented by a single anatomically preserved large stem characterized by a star-shaped vascular system with protoxylem strands located at rib tips, and by a lack of secondary tissues. Within the first fern-like plants, this stem shares the largest number of characters with iridopterid axes but differs by the pattern of its vascular system. Keraphyton mawsoniae gen. et sp. nov. adds a new record of early fern-like plants in eastern Gondwana. It provides new insights into the anatomical diversity within this key group of plants and supports the distinctiveness of the Australian flora in the latest Devonian. creator: Antoine Champreux creator: Brigitte Meyer-Berthaud creator: Anne-Laure Decombeix uri: https://doi.org/10.7717/peerj.9321 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Champreux et al. title: Reversal of glucocorticoid resistance in Acute Lymphoblastic Leukemia cells by miR-145 link: https://peerj.com/articles/9337 last-modified: 2020-06-16 description: ObjectiveTo analyze the expression levels of miR-145 in ALL children and their effects on the prognosis of ALL and to explore the mechanism of miR-145 in reversing the resistance of ALL cells to glucocorticoids.MethodsA GEO database dataset was used to analyze the expression levels of miR-145 in ALL children. The association between miR-145 and childhood prognosis was analyzed by the TARGET database data. The expression levels of miR-145 in the glucocorticoid-resistant ALL cell line CEM-C1 were increased by lipofectamine 2000-mediated transfection. Cell proliferation inhibition experiments were performed to detect the effect of miR-145 on the response of CEM-C1 cell line to glucocorticoids. The expression levels of the apoptotic, autophagic and drug resistance-associated genes and proteins were detected by qPCR and western blot analysis.ResultsThe expression levels of miR-145 were decreased in ALL patients (P < 0.001) and the prognosis of ALL in children with high miR-145 expression was significantly improved (P < 0.001). Increased miR-145 expression can improve the sensitivity of CEM-C1 cells to glucocorticoids. The expression levels of the proapoptotic and the anti-apoptotic genes Bax and Bcl-2 were increased and decreased, respectively, whereas the expression levels of the autophagicgenes Beclin 1 and LC were increased. In addition, the expression levels of the drug resistance gene MDR1 were decreased.ConclusionThe expression levels of miR-145 in ALL children were decreased and they were associated with disease prognosis. The data indicated that miR-145 can reverse cell resistance by regulating apoptosis of CEM-C1 cells and autophagy. creator: Sili Long creator: Danwei Ren creator: Fangfang Zhong creator: Yana Niu creator: Xiang Qin creator: Dan Mu creator: Wenjun Liu uri: https://doi.org/10.7717/peerj.9337 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Long et al. title: Visualization and quantification of mimetic musculature via DiceCT link: https://peerj.com/articles/9343 last-modified: 2020-06-16 description: The muscles of facial expression are of significant interest to studies of communicative behaviors. However, due to their small size and high integration with other facial tissues, the current literature is largely restricted to descriptions of the presence or absence of specific muscles. Using diffusible iodine-based contrast-enhanced computed tomography (DiceCT) to stain and digitally image the mimetic mask of Eulemur flavifrons (the blue-eyed black lemur), we demonstrate—for the first time—the ability to visualize these muscles in three-dimensional space and to measure their relative volumes. Comparing these data to earlier accounts of mimetic organization with the face of lemuroidea, we demonstrate several novel configurations within this taxon, particularly in the superior auriculolabialis and the posterior auricularis. We conclude that DiceCT facilitates the study these muscles in closer detail than has been previously possible, and offers significant potential for future studies of this anatomy. creator: Edwin Dickinson creator: Emily Atkinson creator: Antonio Meza creator: Shruti Kolli creator: Ashley R. Deutsch creator: Anne M. Burrows creator: Adam Hartstone-Rose uri: https://doi.org/10.7717/peerj.9343 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dickinson et al. title: Hiding in plain sight: DNA barcoding suggests cryptic species in all ‘well-known’ Australian flower beetles (Scarabaeidae: Cetoniinae) link: https://peerj.com/articles/9348 last-modified: 2020-06-16 description: DNA barcode data is presented for Australian cetoniine flower beetles to aid with species discovery and guide revisionary taxonomy. Sequences of the COI gene’s DNA barcode region were acquired from 284 cetoniine specimens, covering 68 described species and 33 genera. This equates to 48% of the known species and 83% of the genera which occur in Australia. Results suggest up to 27 putative undescribed species in our sample, only 11 of which were suspected to be undescribed before this study, leaving 16 unexpected (“cryptic”) species. The Australian cetoniine fauna may hence be increased by up to 19%. An unanticipated result of the work is that each of the five most visible and commonly collected Australian cetoniine species, Eupoecila australasiae (Donovan, 1805), Neorrhina punctatum (Donovan, 1805), Glycyphana (Glycyphaniola) stolata (Fabricius, 1781), Chondropyga dorsalis (Donovan, 1805) and Bisallardiana gymnopleura (Fischer, 1823), have unexpectedly high diversity in DNA barcode sequences and were consequently split into multiple clusters, possibly indicating the presence of cryptic species. creator: Andrew Mitchell creator: Christian H. Moeseneder creator: Paul M. Hutchinson uri: https://doi.org/10.7717/peerj.9348 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mitchell et al. title: A retrospective study on the prognostic value of preoperative C-reactive protein to albumin ratio in patients with oral cavity squamous cell carcinoma link: https://peerj.com/articles/9361 last-modified: 2020-06-16 description: BackgroundAlthough the C-reactive protein-to-albumin ratio (CAR) can predict poor outcomes in assorted cancers, its prognostic value in oral cavity squamous cell carcinoma (OSCC) remains unclear. We explored the value of preoperative CAR in predicting clinical outcomes in OSCC patients treated with radical surgery.MethodsAll the recommended cutoff values were defined analyzing receiver operating characteristic curves or overall survival (OS). Dichotomization was performed on the basis of optimal CAR cutoff, and we compared the clinicopathological features between groups. Kaplan–Meier analysis was also performed to compare OS curves between the two groups. Univariate and multivariate analyses using the Cox proportional hazards model were conducted to find the clinical characteristics that were most closely correlated with disease free survival (DFS) and overall survival (OS). A nomogram incorporated CAR and several clinicopathological factors was established to predict prognosis and its accuracy was evaluated using concordance index (c-index).ResultsIn this retrospective study, a total of 326 patients with newly diagnosis of OSCC and received primary surgery between 2008 and 2017 were enrolled. Through the executed ROC curve analyses, the optimal CAR cutoff derived was 0.195 (area under the curve = 0.718, p < 0.001), with this cutoff exhibiting a discrimination ability superior to that of other inflammation-based prognostic scores after comparing the area under curves. Multivariate analysis demonstrated that CAR (≥0.195/<0.195) was associated with OS (hazard ratio 3.614; 95% CI [1.629–8.018]; p = 0.002) and DFS (hazard ratio 1.917; 95% CI [1.051–3.863]; p = 0.029). Kaplan–Meier analysis and log rank test revealed a significant difference in DFS and OS curves between patients with low CAR (<0.195) and those with high CAR (≥0.195; both p < 0.001). The c-index of the nomogram based on TNM system alone was 0.684 and could be increased to 0.801 if CAR and other clinicopathological factors were included.ConclusionsPreoperative CAR could constitute an independent prognostic indicator for OS and DFS prediction in OSCC patients treated with curative surgery. The established nomogram that incorporated CAR and prognostic factors might increase the accuracy of prognostic prediction for patients with OSCC. creator: Ku-Hao Fang creator: Chia-Hsuan Lai creator: Cheng-Ming Hsu creator: Ethan Huang creator: Ming-Shao Tsai creator: Geng-He Chang creator: Yi-Chan Lee creator: Yao-Te Tsai uri: https://doi.org/10.7717/peerj.9361 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fang et al. title: Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China link: https://peerj.com/articles/9376 last-modified: 2020-06-16 description: As a polymicrobial disease, sour rot decreases grape berry yield and wine quality. The diversity of microbial communities in sour rot-affected grapes depends on the cultivation site, but the microbes responsible for this disease in eastern coastal China, has not been reported. To identify the microbes that cause sour grape rot in this important grape-producing region, the diversity and abundance of bacteria and fungi were assessed by metagenomic analysis and cultivation-dependent techniques. A total of 15 bacteria and 10 fungi were isolated from sour rot-affected grapes. High-throughput sequencing of PCR-amplicons generated from diseased grapes revealed 1343 OTUs of bacteria and 1038 OTUs of fungi. Proteobacteria and Firmicutes were dominant phyla among the 19 bacterial phyla identified. Ascomycota was the dominant fungal phylum and the fungi Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa represented the vast majority ofmicrobial species associated with sour rot-affected grapes. An in vitro spoilage assay confirmed that four of the isolated bacteria strains (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) and five of the isolated fungi strains (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum) spoiled grapes. These microorganisms, which appear responsible for spoiling grapes in eastern China, appear closely related to microbes that cause this plant disease around the world. creator: Huanhuan Gao creator: Xiangtian Yin creator: Xilong Jiang creator: Hongmei Shi creator: Yang Yang creator: Chaoping Wang creator: Xiaoyan Dai creator: Yingchun Chen creator: Xinying Wu uri: https://doi.org/10.7717/peerj.9376 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gao et al. title: State-space modeling of the dynamics of temporal plant cover using visually determined class data link: https://peerj.com/articles/9383 last-modified: 2020-06-16 description: A lot of vegetation-related data have been collected as an ordered plant cover class that can be determined visually. However, they are difficult to analyze numerically as they are in an ordinal scale and have uncertainty in their classification. Here, I constructed a state-space model to estimate unobserved plant cover proportions (ranging from zero to one) from such cover class data. The model assumed that the data were measured longitudinally, so that the autocorrelations in the time-series could be utilized to estimate the unobserved cover proportion. The model also assumed that the quadrats where the data were collected were arranged sequentially, so that the spatial autocorrelations also could be utilized to estimate the proportion. Assuming a beta distribution as the probability distribution of the cover proportion, the model was implemented with a regularized incomplete beta function, which is the cumulative density function of the beta distribution. A simulated dataset and real datasets, with one-dimensional spatial structure and longitudinal survey, were fit to the model, and the parameters were estimated using the Markov chain Monte Carlo method. Then, the validity was examined using posterior predictive checks. As a result of the fitting, the Markov chain successfully converged to the stationary distribution, and the posterior predictive checks did not show large discrepancies. For the simulated dataset, the estimated values were close to the values used for the data generation. The estimated values for the real datasets also seemed to be reasonable. These results suggest that the proposed state-space model was able to successfully estimate the unobserved cover proportion. The present model is applicable to similar types of plant cover class data, and has the possibility to be expanded, for example, to incorporate a two-dimensional spatial structure and/or zero-inflation. creator: Hiroki Itô uri: https://doi.org/10.7717/peerj.9383 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Itô title: Smoking cessation interventions on health-care workers: a systematic review and meta-analysis link: https://peerj.com/articles/9396 last-modified: 2020-06-16 description: ObjectiveThe authors carried out a systematic review and a meta-analysis on smoking cessation interventions on health -care workers to clarify the state of the art interventions and to identify the best one.Materials and MethodsThis review was registered with PROSPERO: CRD42019130117. The databases PubMed, Scopus, Web of Science and CINAHL were searched until December 2018. Quality of all studies included in the systematic review was assessed according to the Newcastle-Ottawa Scale (NOS) on cohort or cross-sectional studies and to the Cochrane Risk of Bias Tool for Randomized Controlled Trials. Meta-analysis and meta-regression analyses were also carried out for cohort studies (quasi-experimental or a before-after studies design) and clinical trials.ResultsTwenty–four studies have been included in the analysis: four before-after, 13 cross-sectional, three quasi-experimental studies and four clinical trials. Articles were heterogeneous (P for homogeneity <0.01), but they have all shown positive results since they reached the goal of smoking cessation among health-care workers, even if with different proportions. Meta-analysis was performed on 10 studies (six cohort studies and four clinical trials), showing a 21% of success rate from the application of smoking cessation interventions, either pharmacological or behavioral ones. The resulted pooled RR (Risk Ratio) was 1.21 (95% CI [1.06–1.38]), being 24% of success rate from clinical trials (pooled RR 1.244; 95% CI [1.099–1.407]) and 19% of success rate from cohort studies (pooled RR 1.192; 0.996–1.426). However, two studies have confidence intervals which include unity and one study has a wide confidence interval; as a consequence, the meta-analysis for its results depends heavily on one single study. Meta-regression analysis revealed that results were influenced by the number of participants.ConclusionBoth policy and pharmaceutical interventions can obtain positive results in quitting smoking among health-care workers. However, as shown by our review, combination approaches can produce better results in terms of cessation percentages and smoking abstinence. creator: Giuseppe La Torre creator: Generosa Tiberio creator: Alessandro Sindoni creator: Barbara Dorelli creator: Vittoria Cammalleri uri: https://doi.org/10.7717/peerj.9396 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 La Torre et al. title: Prevalence and correlates of depressive symptoms among Chinese patients with cataracts treated in tertiary general hospitals link: https://peerj.com/articles/9397 last-modified: 2020-06-16 description: BackgroundPrevious studies recruited unrepresentative samples of Chinese patients with cataract and reported a wide range of prevalence of depressive symptoms in this patient population (18.0–89.7%). The present study determined the prevalence and correlates of depressive symptoms among a consecutive sample of Chinese patients with cataract treated in tertiary general hospitals.MethodsA total of 339 patients with cataract were consecutively selected from ophthalmology departments of two large general hospitals in Wuhan, China. Depressive symptoms were assessed with the Chinese Hospital Anxiety and Depression Scale. Logistic regression was used to identify factors that were associated with depression.ResultsThe prevalence of depressive symptoms was 23.9% (95% CI [19.4–28.4]%) among patients with cataract. Correlates for depressive symptoms include an education level of primary school and below (OR = 1.93, P = 0.038), marital status of “others” (OR =3.15, P < 0.001), poor family economic status (OR = 2.26, P = 0.010), nuclear cataract (OR =4.32, P < 0.001), and mixed cataract (OR = 2.76, P = 0.017).ConclusionsDepressive symptoms are common among Chinese patients with cataract treated in large general hospitals. Patients who are poorly educated, have a marital status other than “married”, have poor family economic status, and suffer from nuclear and mixed cataracts are at greater risk for depressive symptoms. creator: Zhong-Hua Liu creator: Chang-Zheng Chen creator: Cong Gao creator: De-Yi Zhou uri: https://doi.org/10.7717/peerj.9397 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al.