title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1026
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Clonal versus non-clonal milkweeds (Asclepias spp.) respond differently to stem damage, affecting oviposition by monarch butterflies
link: https://peerj.com/articles/10296
last-modified: 2020-11-03
description: BackgroundOviposition decisions are critical to the fitness of herbivorous insects and are often impacted by the availability and condition of host plants. Monarch butterflies (Danaus plexippus) rely on milkweeds (Asclepias spp.) for egg-laying and as food for larvae. Previous work has shown that monarchs prefer to oviposit on recently regrown plant tissues (after removal of above-ground biomass) while larvae grow poorly on plants previously damaged by insects. We hypothesized that these effects may depend on the life-history strategy of plants, as clonal and non-clonal milkweed species differ in resource allocation and defense strategies.Methodology/Principal FindingsWe first confirmed butterfly preference for regrown tissue in a field survey of paired mowed and unmowed plots of the common milkweed A. syriaca. We then experimentally studied the effects of plant damage (comparing undamaged controls to plants clipped and regrown, or damaged by insects) on oviposition choice, larval performance, and leaf quality of two closely related clonal and non-clonal species pairs: (1) A. syriaca and A. tuberosa, and (2) A. verticillata and A. incarnata. Clonal and non-clonal species displayed different responses to plant damage, impacting the proportions of eggs laid on plants. Clonal species had similar mean proportions of eggs on regrown and control plants (≈35–40% each), but fewer on insect-damaged plants (≈20%). Meanwhile non-clonal species had similar oviposition on insect-damaged and control plants (20–30% each) but more eggs on regrown plants (40–60%). Trait analyses showed reduced defenses in regrown plants and we found some evidence, although variable, for negative effects of insect damage on subsequent larval performance.Conclusions/SignificanceOverall, non-clonal species are more susceptible and preferred by monarch butterflies following clipping, while clonal species show tolerance to clipping and induced defense to insect herbivory. These results have implications for monarch conservation strategies that involve milkweed habitat management by mowing. More generally, plant life-history may mediate growth and defense strategies, explaining species-level variation in responses to different types of damage.
creator: Elise He
creator: Anurag A. Agrawal
uri: https://doi.org/10.7717/peerj.10296
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 He and Agrawal

title: A case against default effect sizes in sport and exercise science
link: https://peerj.com/articles/10314
last-modified: 2020-11-03
description: Recent discussions in the sport and exercise science community have focused on the appropriate use and reporting of effect sizes. Sport and exercise scientists often analyze repeated-measures data, from which mean differences are reported. To aid the interpretation of these data, standardized mean differences (SMD) are commonly reported as a description of effect size. In this manuscript, we hope to alleviate some confusion. First, we provide a philosophical framework for conceptualizing SMDs; that is, by dichotomizing them into two groups: magnitude-based and signal-to-noise SMDs. Second, we describe the statistical properties of SMDs and their implications. Finally, we provide high-level recommendations for how sport and exercise scientists can thoughtfully report raw effect sizes, SMDs, or other effect sizes for their own studies. This conceptual framework provides sport and exercise scientists with the background necessary to make and justify their choice of an SMD.
creator: Aaron Caldwell
creator: Andrew D. Vigotsky
uri: https://doi.org/10.7717/peerj.10314
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Caldwell and Vigotsky

title: Projection of premature mortality from noncommunicable diseases for 2025: a model based study from Hunan Province, China, 1990–2016
link: https://peerj.com/articles/10298
last-modified: 2020-11-03
description: BackgroundIn 2011, the United Nations set a target to reduce premature mortality from non-communicable diseases (NCDs) by 25% by 2025. While studies have reported the target in some countries, no studies have been done in China. This study aims to project the ability to reach the target in Hunan Province, China, and establish the priority for future interventions.MethodsWe conducted the study during 2019–2020. From the Global Burden of Disease Study 2016, we extracted death data for Hunan during 1990–2016 for four main NCDs, namely cancer, cardiovascular disease (CVD), chronic respiratory diseases, and diabetes. We generated estimates for 2025 by fitting a linear regression to the premature mortality over the most recent trend identified by a joinpoint regression model. We also estimated excess premature mortality attributable to unfavorable changes over time.ResultsThe rate of premature mortality from all NCDs in Hunan will be 19.5% (95% CI [19.0%–20.1%]) by 2025, with the main contributions being from CVD (8.2%, 95% CI [7.9%–8.5%]) and cancer (7.9%, 95% CI [7.8%–8.1%]). Overall, it will be impossible to achieve the target, with a relative reduction of 16.4%. Women may be able to meet the target except with respect to cancer, and men will not except with respect to chronic respiratory diseases. Most of the unfavorable changes have occurred since 2008–2009.DiscussionMore urgent efforts, especially for men, should be exerted in Hunan by integrating population-wide interventions into a stronger health-care system. In the post lock-down COVID-19 era in China, reducing the NCD risk factors can also lower the risk of death from COVID-19.
creator: Qiaohua Xu
creator: Maigeng Zhou
creator: Donghui Jin
creator: Xinying Zeng
creator: Jinlei Qi
creator: Li Yin
creator: Yuan Liu
creator: Lei Yin
creator: Yuelong Huang
uri: https://doi.org/10.7717/peerj.10298
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Xu et al.

title: Identification and functional characterization of SlDronc in Spodoptera littoralis
link: https://peerj.com/articles/10329
last-modified: 2020-11-03
description: BackgroundApoptosis is responsible for eliminating damaged and virus-infected cells, regulating normal cell turnover, and maintaining the immune system’s development and function. Caspases play a vital role in both mammal and invertebrate apoptosis. Spodoptera littoralis is a generalist insect herbivore that is one of the most destructive pests in tropical and subtropical areas and attacks a wide range of commercially important crops. Although S. littoralis is a model organism in the study of baculovirus infection, its apoptotic pathway has not been explored.MethodsWe cloned a new caspase gene named sldronc in S. littoralis using Rapid Amplification of cDNA Ends (RACE). We then measured caspase activity on synthetic caspase substrates and S. littoralis’ effector caspase. SlDronc’s function in the apoptotic pathway and its interaction with caspase inhibitors were also tested in SL2 cells.ResultsWe found that the initiator caspase SlDronc cleaved and activated effector caspase in S. littoralis. SlDronc overexpression induced apoptosis in SL2 cells, and Sldronc knockdown decreased apoptosis induced by UV irradiation in SL2 cells. Our results indicate that SlDronc acts as an apoptotic initiator caspase in S. littoralis. Additionally, we found that processed forms of SlDronc increased in the presence of N-terminally truncated S. littoralis inhibitors of apoptosis (SlIAP) and that SlDronc was inhibited by P49. This study contributes to the further understanding of S. littoralis’ apoptotic pathway and may facilitate future studies on baculovirus infection-induced apoptosis.
creator: Hao Liu
creator: Ke Zhou
creator: Zhouning Yang
uri: https://doi.org/10.7717/peerj.10329
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Liu et al.

title: Genome-wide discovery and characterization of long noncoding RNAs in African oil palm (Elaeis guineensis Jacq.)
link: https://peerj.com/articles/9585
last-modified: 2020-11-02
description: Long noncoding RNAs (lncRNAs) are an important class of genes and play important roles in a range of biological processes. However, few reports have described the identification of lncRNAs in oil palm. In this study, we applied strand specific RNA-seq with rRNA removal to identify 1,363 lncRNAs from the equally mixed tissues of oil palm spear leaf and six different developmental stages of mesocarp (8–24 weeks). Based on strand specific RNA-seq data and 18 released oil palm transcriptomes, we systematically characterized the expression patterns of lncRNA loci and their target genes. A total of 875 uniq target genes for natural antisense lncRNAs (NAT-lncRNA, 712), long intergenic noncoding RNAs (lincRNAs, 92), intronic-lncRNAs (33), and sense-lncRNAs (52) were predicted. A majority of lncRNA loci (77.8%–89.6%) had low expression in 18 transcriptomes, while only 89 lncRNA loci had medium to high expression in at least one transcriptome. Coexpression analysis between lncRNAs and their target genes indicated that 6% of lncRNAs had expression patterns positively correlated with those of target genes. Based on single nucleotide polymorphism (SNP) markers derived from our previous research, 6,882 SNPs were detected for lncRNAs and 28 SNPs belonging to 21 lncRNAs were associated with the variation of fatty acid contents. Moreover, seven lncRNAs showed expression patterns positively correlated expression pattern with those of genes in de novo fatty acid synthesis pathways. Our study identified a collection of lncRNAs for oil palm and provided clues for further research into lncRNAs that may regulate mesocarp development and lipid metabolism.
creator: Wei Xia
creator: Yajing Dou
creator: Rui Liu
creator: Shufang Gong
creator: Dongyi Huang
creator: Haikuo Fan
creator: Yong Xiao
uri: https://doi.org/10.7717/peerj.9585
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Xia et al.

title: Static and dynamic alterations in the amplitude of low-frequency fluctuation in patients with amyotrophic lateral sclerosis
link: https://peerj.com/articles/10052
last-modified: 2020-11-02
description: BackgroundStatic changes in local brain activity in patients suffering from amyotrophic lateral sclerosis (ALS) have been studied. However, the dynamic characteristics of local brain activity are poorly understood. Whether dynamic alterations could differentiate patients with ALS from healthy controls (HCs) remains unclear.MethodsA total of 54 patients with ALS (mean age = 48.71 years, male/female = 36/18) and 54 (mean age = 48.30 years, male/female = 36/18) HCs underwent magnetic resonance imaging scans. To depict static alterations in cortical activity, amplitude of low-frequency fluctuations (ALFF) which measures the total power of regional activity was computed. Dynamic ALFF (d-ALFF) from all subjects was calculated using a sliding-window approach. Statistical differences in ALFF and d-ALFF between both groups were used as features to explore whether they could differentiate ALS from HC through support vector machine method.ResultsIn contrast with HCs, patients with ALS displayed increased ALFF in the right inferior temporal gyrus and bilateral frontal gyrus and decreased ALFF in the left middle occipital gyrus and left precentral gyrus. Furthermore, patients with ALS demonstrated lower d-ALFF in widespread regions, including the right lingual gyrus, left superior temporal gyrus, bilateral precentral gyrus, and left paracentral lobule by comparison with HCs. In addition, the ALFF in the left superior orbitofrontal gyrus had a tendency of correlation with ALSFRS-R score and disease progression rate. The classification performance in distinguishing ALS was higher with both features of ALFF and d-ALFF than that with a single approach.ConclusionsDecreased dynamic brain activity in the precentral gyrus, paracentral gyrus, lingual gyrus, and temporal regions was found in the ALS group. The combined ALFF and d-ALFF could distinguish ALS from HCs with a higher accuracy than ALFF and d-ALFF alone. These findings may provide important evidence for understanding the neuropathology underlying ALS.
creator: Xujing Ma
creator: Fengmei Lu
creator: Heng Chen
creator: Caihong Hu
creator: Jiao Wang
creator: Sheng Zhang
creator: Shuqin Zhang
creator: Guiran Yang
creator: Jiuquan Zhang
uri: https://doi.org/10.7717/peerj.10052
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Ma et al.

title: In vitro anti-diabetic effects and phytochemical profiling of novel varieties of Cinnamomum zeylanicum (L.) extracts
link: https://peerj.com/articles/10070
last-modified: 2020-11-02
description: BackgroundDiabetes mellitus type 2 (DMT2) is a leading metabolic disorder in the world. Anti-diabetic actions of phytochemicals from various medicinal herbs have been explored as an alternative therapy in the management of DMT2 due to adverse effects of synthetic drugs used in allopathic medicine. α-amylase and α-glucosidase inhibitory potential and phytochemical profiling were investigated in aqueous extracts of two new Cinnamomum zeylanicum accessions, namely C. zeylanicum Sri Wijaya (SW), C. zeylanicum Sri Gemunu (SG) and commercially available C. zeylanicum (CC).MethodsMicrowave Digestion (MD), Pressurized Water Extraction (PWE), Steam Distillation (SD), Solvent Extraction (SE), Decoction Water Extraction (DWE) and Infusion Water Extraction (IWE) methods were used to prepare Cinnamon quill extracts. Total phenolic content (TPC, Folin-Ciocalteu method) and Proanthocyanidin content (PC, vanillin assay), α-amylase and α-glucosidase inhibition of Cinnamon extracts were determined spectrophotometrically. The α-amylase and α-glucosidase inhibition were reported in terms of IC50 value. The phytochemical profiling was accomplished by GC-MS technique.Results and DiscussionLowest IC50 values were observed in PWE and DWE of SW. The highest PC and TPC were also observed in PWE and DWE of SW. Pressured water and decoctions are promising methods for the extraction of antidiabetic constituents from cinnamon. Benzoic acid, cinnamyl alcohol, benzyl alcohol, and 4-Allyl-2,6-dimethoxyphenol were identified as major compounds in SW extracts. These compounds are believed to be responsible for strong enzyme inhibitory activity of the extracts.ConclusionsThis is the first study to explore the use of pressured and decoctions water to extract anti-diabetic phytochemicals from cinnamon. The extensive metabolite profiling of novel SW and SG extracts and comparison of that with commercially available CC are reported for the first time in this study. The C. zeylanicum, SW accession holds some promise in the management of diabetes.
creator: W.A. Niroshani M. Wariyapperuma
creator: Sagarika Kannangara
creator: Yasanandana S. Wijayasinghe
creator: Sri Subramanium
creator: Bimali Jayawardena
uri: https://doi.org/10.7717/peerj.10070
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Wariyapperuma et al.

title: Assessment of autonomous nerve system through non-linear heart rate variability outcomes in sedentary healthy adults
link: https://peerj.com/articles/10178
last-modified: 2020-11-02
description: BackgroundHeart rate variability (HRV) is a psycho-physiological phenomenon with broad health implications. Different data analysis methods have been used to assess the autonomic nervous system activity, but the validation of new indexes that accurately describe its balance through non-invasive methods (i.e., HRV analysis) is of clinical interest. This study aimed: (i) to evaluate the association of the Stress Score (SS) and the Sympathetic/Parasympathetic Ratio (S/PS) with time domain and frequency domain analysis of HRV, and (ii) to set reference values of SS and S/PS in sedentary healthy adults.MethodsA total of 156 sedentary healthy adults (38.4 ± 15.57 years old, 81 women), aged were involved in this study. HRV was measured for 15 min in a supine position at rest. SS and S/PS were calculated from the non-linear HRV analyses based on Poincare Plot.ResultsStress Score showed a non-linear negative power-law relationship with SDNN (β = −0.969; R2 = 0.963; P < 0.001), RMSSD (β = −0.867; R2 = 0.722; P < 0.001), high frequency (β = −0.834; R2 = 0.752; P =< 0.001), low frequency (β = −0.627; R2 = 0.330; P < 0.001), SD1 (β = −0.867; R2 = 0.722; P < 0.001) and SD2 (β = −1.000; R2 > 0.999; P < 0.001). There was observed a negative cubic relationship between SS with PNN50 (β = −1.972; R2 = 0.644; P < 0.001). A linear regression model was conducted between SS with Ratio Low/High Frequency (β = 0.026; R2 < 0.001; P = 0.750). Non-linear power-law regression models were built between S/PS and SDNN (β = −0.990; R2 = 0.981; P < 0.001), RMSSD (β = −0.973; R2 = 0.939; P < 0.001), high frequency (β = −0.928; R2 = 0.970; P < 0.001), low frequency (β = −2.344; R2 = 0.557; P < 0.001), SD1 (β = −0.973; R2 = 0.939; P < 0.001) and SD2 (β = −0.611; R2 = 0.908; P < 0.001). A non-linear negative regression model was built between S/PS and PNN50 (β = −3.412; R2 = 0.868; P < 0.001). A linear regression model was conducted between S/PS and SD2/SD1 (β = 0.075; R2 = 0.006; P < 0.001).ConclusionOur results support the use of SS as a sympathetic activity marker, and S/PS as an indicator of the sympathetic and parasympathetic activity of the autonomic nervous system in sedentary healthy adults.
creator: Gines Navarro-Lomas
creator: Alejandro De-la-O
creator: Lucas Jurado-Fasoli
creator: Manuel J. Castillo
creator: Pedro Femia
creator: Francisco J. Amaro-Gahete
uri: https://doi.org/10.7717/peerj.10178
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Navarro-Lomas et al.

title: Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages
link: https://peerj.com/articles/10223
last-modified: 2020-11-02
description: BackgroundRed palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control.MethodsIn this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest.ResultsSequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus.
creator: Hongjun Yang
creator: Danping Xu
creator: Zhihang Zhuo
creator: Jiameng Hu
creator: Baoqian Lu
uri: https://doi.org/10.7717/peerj.10223
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Yang et al.

title: Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections
link: https://peerj.com/articles/10246
last-modified: 2020-11-02
description: BackgroundIn December 2019, an ongoing outbreak of pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/ 2019-nCoV) infection was initially reported in Wuhan, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be a Public Health Emergency of International Concern (PHEIC). Cellular co-infection is a critical determinant of viral fitness and infection outcomes and plays a crucial role in shaping the host immune response to infections.MethodsIn this study, 68 public next-generation sequencing data from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Data screening was performed using an alignment-free method based on k-mer mapping and extension, fastv. Taxonomic classification was performed using Kraken 2 on all reads containing one or more virus sequences other than SARS-CoV-2.ResultsSARS-CoV-2 was identified in all except three patients. Influenza type A (H7N9) virus, human immunodeficiency virus, rhabdovirus, human metapneumovirus, Human adenovirus, Human herpesvirus 1, coronavirus NL63, parvovirus, simian virus 40, and hepatitis virus genomes sequences were detected in SARS-CoV-2 infected patients. Besides, a very diverse group of bacterial populations were observed in the samples.
creator: Mohamed A. Abouelkhair
uri: https://doi.org/10.7717/peerj.10246
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Abouelkhair