title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=633 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: RFfiller: a robust and fast statistical algorithm for gap filling in draft genomes link: https://peerj.com/articles/14186 last-modified: 2022-10-14 description: Numerous published genomes contain gaps or unknown sequences. Gap filling is a critical final step in de novo genome assembly, particularly for large genomes. While certain computational approaches partially address the problem, others have shortcomings regarding the draft genome’s dependability and correctness (high rates of mis-assembly at gap-closing sites and high error rates). While it is well established that genomic repeats result in gaps, many sequence reads originating from repeat-related gaps are typically missed by existing approaches. A fast and reliable statistical algorithm for closing gaps in a draft genome is presented in this paper. It utilizes the alignment statistics between scaffolds, contigs, and paired-end reads to generate a Markov chain that appropriately assigns contigs or long reads to scaffold gap regions (only corrects candidate regions), resulting in accurate and efficient gap closure. To reconstruct the missing component between the two ends of the same insert, the RFfiller meticulously searches for valid overlaps (in repeat regions) and generates transition tables for similar reads, allowing it to make a statistical guess at the missing sequence. Finally, in our experiments, we show that the RFfiller’s gap-closing accuracy is better than that of other publicly available tools when sequence data from various organisms are used. Assembly benchmarks were used to validate RFfiller. Our findings show that RFfiller efficiently fills gaps and that it is especially effective when the gap length is longer. We also show that the RFfiller outperforms other gap closing tools currently on the market. creator: Firaol Dida Midekso creator: Gangman Yi uri: https://doi.org/10.7717/peerj.14186 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Midekso and Yi title: Automated mapping of Portulacaria afra canopies for restoration monitoring with convolutional neural networks and heterogeneous unmanned aerial vehicle imagery link: https://peerj.com/articles/14219 last-modified: 2022-10-14 description: Ecosystem restoration and reforestation often operate at large scales, whereas monitoring practices are usually limited to spatially restricted field measurements that are (i) time- and labour-intensive, and (ii) unable to accurately quantify restoration success over hundreds to thousands of hectares. Recent advances in remote sensing technologies paired with deep learning algorithms provide an unprecedented opportunity for monitoring changes in vegetation cover at spatial and temporal scales. Such data can feed directly into adaptive management practices and provide insights into restoration and regeneration dynamics. Here, we demonstrate that convolutional neural network (CNN) segmentation algorithms can accurately classify the canopy cover of Portulacaria afra Jacq. in imagery acquired using different models of unoccupied aerial vehicles (UAVs) and under variable light intensities. Portulacaria afra is the target species for the restoration of Albany Subtropical Thicket vegetation, endemic to South Africa, where canopy cover is challenging to measure due to the dense, tangled structure of this vegetation. The automated classification strategy presented here is widely transferable to restoration monitoring as its application does not require any knowledge of the CNN model or specialist training, and can be applied to imagery generated by a range of UAV models. This will reduce the sampling effort required to track restoration trajectories in space and time, contributing to more effective management of restoration sites, and promoting collaboration between scientists, practitioners and landowners. creator: Nicholas C. Galuszynski creator: Robbert Duker creator: Alastair J. Potts creator: Teja Kattenborn uri: https://doi.org/10.7717/peerj.14219 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Galuszynski et al. title: Coral reef fish assemblages exhibit signs of depletion in two protected areas from the eastern of Los Canarreos archipelago (Cuba, Caribbean Sea) link: https://peerj.com/articles/14229 last-modified: 2022-10-14 description: Understanding the impact of marine protected areas on the distribution and composition of fishes is key to the protection and management of coral reef ecosystems, and especially for fish-based activities such as SCUBA diving and recreational fishing. The aim of this research is to compare the ichthyofauna structure in three areas in the eastern part of Los Canarreos archipelago in Cuba with different management schemes: Cayo Campos-Cayo Rosario Fauna Refuge (CCCR), Cayo Largo Ecological Reserve (CL) and non-protected area (nMPA), and considering habitat differences and depth variation. A total of 131 video transects were conducted using diver operated stereo-video (stereo-DOV) in November, 2015 in backreef and forereef along the CCCR, CL and the adjacent nMPA. We recorded 84 species and 27 functional groups suggesting high complementarity of functions. Several multispecies schools were observed along surveys, which explain the biomass peaks in some sites, mainly for Lutjanidae, Haemulidae and Carangidae. A concerning issue was the bare representation of critical functional groups and threatened species. The effect of sites nested within habitats was significant and the most important driver structuring fish assemblages, while MPA condition was not evident. Favorable habitat features (habitat heterogeneity and surrounding coastal ecosystems) are likely enhancing fish assemblages and counteracting the effects of pouching derived from insufficient management. We recommend immediate actions within a strategy of precautionary management including, but not limited to, the appointment of staff for the administration of CL, frequent monitoring and effective enforcement. creator: Zenaida María Navarro-Martínez creator: Maickel Armenteros creator: Leonardo Espinosa creator: Patricia González-Díaz creator: Amy Apprill uri: https://doi.org/10.7717/peerj.14229 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Navarro-Martínez et al. title: Postpartum depression and health-related quality of life: a Saudi Arabian perspective link: https://peerj.com/articles/14240 last-modified: 2022-10-14 description: Background and ObjectivesThe mental and physical functioning of an individual is partly determined by their health-related quality of life (HRQOL), which is a multifaceted component. Women who have recently given birth must have a good quality of life to provide proper care and development for their infant. The purpose of this study was to assess the relationship between postpartum depression (PPD) and HRQOL in Saudi Arabian women and to identify potential risk factors that could influence them.MethodsThis study comprised 253 mothers aged 1–24 weeks postpartum from several health centers in Saudi Arabia, recruited by random purposive sampling. The study’s questionnaire featured three sections: the first section had demographic information; the second and third sections contained the Edinburgh Postnatal Depression Scale (EPDS) scale and the HRQOL scale (SF-12), respectively. Data were analyzed using descriptive statistics, chi square analyses, independent samples t-tests and binary logistic regression analysis using IBM SPSS 25.ResultsResults of current study indicate that 59.68% of the patients exhibited probable post-partum depression symptoms. Participants who were depressed had significantly lower mental component (MCS) and physical component scores than participants who were in good health. When compared to non-smokers, smokers have a 21-fold higher risk of developing depression. Similar to this, mothers who worked had a 3.98 times higher risk of depression, and patients with a history of depression had a 3.6 times higher chance of getting PPD. The probability of developing PPD was also significantly higher in those who lived outside the Riyadh region, had given birth more than twice before this time, and had experienced undesired pregnancies.ConclusionOur study demonstrated an inverse correlation between postpartum depression and health-related quality of life scores. Treatment for depression, particularly among mothers, is crucial for improving their quality of life and, as a result, creating a favorable environment for the development of newborn babies. creator: Mansour Almuqbil creator: Nora Kraidiye creator: Hatoun Alshmaimri creator: Amerah Ali kaabi creator: Atheer Almutiri creator: Abeer Alanazi creator: Ayat Hjeij creator: Abdulhakeem S. Alamri creator: Wala F. Alsanie creator: Majid Alhomrani creator: Syed Mohammed Basheeruddin Asdaq uri: https://doi.org/10.7717/peerj.14240 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Almuqbil et al. title: Ribovirus classification by a polymerase barcode sequence link: https://peerj.com/articles/14055 last-modified: 2022-10-13 description: RNA viruses encoding a polymerase gene (riboviruses) dominate the known eukaryotic virome. High-throughput sequencing is revealing a wealth of new riboviruses known only from sequence, precluding classification by traditional taxonomic methods. Sequence classification is often based on polymerase sequences, but standardised methods to support this approach are currently lacking. To address this need, we describe the polymerase palmprint, a segment of the palm sub-domain robustly delineated by well-conserved catalytic motifs. We present an algorithm, Palmscan, which identifies palmprints in nucleotide and amino acid sequences; PALMdb, a collection of palmprints derived from public sequence databases; and palmID, a public website implementing palmprint identification, search, and annotation. Together, these methods demonstrate a proof-of-concept workflow for high-throughput characterisation of RNA viruses, paving the path for the continued rapid growth in RNA virus discovery anticipated in the coming decade. creator: Artem Babaian creator: Robert Edgar uri: https://doi.org/10.7717/peerj.14055 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Babaian and Edgar title: Planting Cyperus esculentus augments soil microbial biomass and diversity, but not enzymatic activities link: https://peerj.com/articles/14199 last-modified: 2022-10-13 description: The planting of Cyperus esculentus, a member of the grass family Cyperaceae which includes nut sedge weeds, is being increasingly promoted in northern China’s semi-arid and arid regions. Yet the effects of planting C. esculentus upon soil quality and soil microbial characteristics of sandy land remain unclear. This study examined the short-term (1 year) impact of this grass species on soil microbial biomass indices, enzymatic activities, and microbiome characteristics in the Horqin Sandy Land area of China. The results show that planting C. esculentus could increase microbial biomass in the form of carbon (MBC), nitrogen (MBN), and phosphorus (MBP), but it negligibly influenced the enzymatic activities of soil β-1,4-glucosidase (BG), cellobiohydrolase (CBH), leucine aminopeptidase (LAP), and β-1,4-N-acetaminoglycosidase (NAG). Over 1 year, we found that planting C. esculentus significantly increased the soil bacterial richness and diversity of sandy land, yet also altered community composition of soil bacteria and eukaryotes in way that could promote their homogenization. In this respect, the relative abundances of Acidobacteria and Proteobacteria significantly decreased and increased, respectively; hence, they may be considered for use as important indicators of soil nutrient-rich conditions. Overall, the results could be explained by greater soil organic carbon (SOC) and total nitrogen (TN), mainly derived from cumulative plant litter input to soils, which then increased the sandy soil’s C:N ratio. Future research should focus on exploring the long-term effects of planting C. esculentus on soil quality and soil microbial characteristics of sandy lands in China and abroad. creator: Yulong Duan creator: Wei Ren creator: Jianhua Zhao creator: Chun Luo creator: Yang Liu uri: https://doi.org/10.7717/peerj.14199 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Duan et al. title: Revision of the Late Triassic metoposaurid “Metoposaurus” bakeri (Amphibia: Temnospondyli) from Texas, USA and a phylogenetic analysis of the Metoposauridae link: https://peerj.com/articles/14065 last-modified: 2022-10-12 description: Metoposaurids are a clade of large-bodied temnospondyls commonly found in non-marine Late Triassic deposits across northern Pangea. Three taxa are known from North America: Anaschisma browni, Apachesaurus gregorii, and “Metoposaurus” bakeri. While the osteology of most metoposaurids has been recently revised, that of a few taxa, including “Metoposaurus” bakeri remains poorly characterized. This taxon was formally described in 1931 as “Buettneria bakeri,” and its taxonomy has remained in flux ever since then. “Metoposaurus” bakeri is the earliest appearing metoposaurid in North America (Carnian of Texas), and Metoposaurus has frequently been utilized as an index taxon of the Otischalkian estimated holochron (‘land vertebrate faunachron’) and for biostratigraphic correlations with other geographic regions. The taxonomy of this species is therefore relevant for both taxonomic experts and biostratigraphers. Here we redescribe all material from the type locality of “M.” bakeri, the Elkins Place bone bed, and perform a phylogenetic analysis using a revised matrix assembled from several previous studies. Anatomical comparisons and phylogenetic analyses do not support placement in either Metoposaurus, a taxon otherwise only found in Europe, or Anaschisma, the only other large-bodied taxon from North America. Therefore, we erect a new genus, Buettnererpeton gen. nov., to accommodate this species. Metoposaurus is consequently absent from North America, and this genus cannot be used in global biostratigraphy. Phylogenetic analyses provide evidence that the phylogeny of the Metoposauridae remains extremely labile, with drastic differences in topological resolution and structure being linked to just a handful of characters and scores. Metoposaurids’ morphological conservatism and the increased recognition of intraspecific variation thus continue to be major confounds to elucidating the evolutionary history of this clade. creator: Bryan M. Gee creator: Aaron M. Kufner uri: https://doi.org/10.7717/peerj.14065 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gee and Kufner title: Prevalence and associated risk factors of avian influenza A virus subtypes H5N1 and H9N2 in LBMs of East Java province, Indonesia: a cross-sectional study link: https://peerj.com/articles/14095 last-modified: 2022-10-12 description: BackgroundAvian influenza A virus subtypes H5N1 and H9N2 are contagious zoonotic diseases that are circulating in Indonesia and have raised increasing concern about their potential impacts on poultry and public health. A cross-sectional study was carried out to investigate the prevalence and associated risk factors of avian influenza A virus subtypes H5N1 and H9N2 among poultry in the live bird markets of four cities in East Java province, Indonesia.MethodsA total of 600 tracheal and cloacal swabs (267 from backyards, 179 from broilers, and 154 from layers) from healthy birds were collected. The samples were inoculated into specific pathogenic-free embryonated eggs at 9-day-old via the allantoic cavity. qRT-PCR was used for further identification of avian influenza.ResultsThe overall prevalence of circulating influenza A virus subtypes H5N1 and H9N2 was 3.8% (23/600, 95%CI [0.0229–0.0537]). Prevalence was higher in backyards at 5.99% (16/267) followed by broilers (2.23% (4/179)) and layers (1.68% (3/154)). The final multivariable model revealed five risk factors for H9N2 infections: presence of ducks (p = 0.003, OR = 38.2), turkeys (p = 0.017 OR = 0.032), and pheasants in the stall (p = 0.04, OR = 18.422), dry (p = 0.006) and rainy season (p < 0.001), and household birds (p = 0.002) and seven factors for H5N1 infections including: observing rodents (p = 0.036, OR = 0.005), stray dogs access (p = 0.004 OR ≤ 0.001), presence of turkeys (p = 0.03 OR = 0.007), chukars/partridges (p = 0.024 OR = 2500), and peafowls in the stalls (p = 0.0043 OR ≤ 0.001), rainy season (p = 0.001) and birds from the household sources (p = 0.002) in the live bird markets.ConclusionsThe findings of the current study illustrate the recurring infection and presence of both avian influenza viruses and associated risk factors in the surveyed marketplaces. Effective protective measures and mitigation strategies for risks outlined in this study could help to reduce the burden of H5N1 and H9N2 AI subtypes into the live bird markets of Indonesia. creator: Saifur Rehman creator: Mustofa Helmi Effendi creator: Aamir Shehzad creator: Attaur Rahman creator: Jola Rahmahani creator: Adiana Mutamsari Witaningrum creator: Muhammad Bilal uri: https://doi.org/10.7717/peerj.14095 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rehman et al. title: Telomerase activity, relative telomere length, and longevity in alfalfa (Medicago sativa L.) link: https://peerj.com/articles/14102 last-modified: 2022-10-12 description: BackgroundMedicago sativa L. ‘Qingshui’ is a valuable rhizomatous forage germplasm resource. We previously crossed Qingshui with the high-yielding Medicago sativa L. ‘WL168’ and obtained novel rhizomatous hybrid strains (RSA-01, RSA-02, and RSA-03). Telomere dynamics are more accurate predictors of survival and mortality than chronological age. Based on telomere analyses, we aimed to identify alfalfa varieties with increased stamina and longevity for the establishment of artificial grazing grasslands.MethodsIn this study, we performed longitudinal analysis of telomerase activity and relative telomere length in five alfalfa varieties (Qingshui, WL168, RSA-01, RSA-02, and RSA-03) at the age of 1 year and 5 years to examine the relationship among telomerase activity, rate of change in relative telomere length, and longevity. We further aimed to evaluate the longevity of the examined varieties. Telomerase activity and relative telomere length were measured using enzyme-linked immunosorbent assay and real-time polymerase chain reaction, respectively.ResultsWe observed significant differences in telomerase activity between plants aged 1 year and those aged 5 years in all varieties except WL168, and the rate of change in telomerase activity does not differ reliably with age. As telomerase activity and relative telomere length are complex phenomena, further studies examining the molecular mechanisms of telomere-related proteins are needed. Relative telomere lengths of Qingshui, WL168, RSA-01, RSA-02, and RSA-03 in plants aged 5 years were higher than those aged 1 year by 11.41, 11.24, 9.21, 10.23, and 11.41, respectively. Relative telomere length of alfalfa tended to increase with age. Accordingly, alfalfa varieties can be classified according to rate of change in relative telomere length as long-lived (Qingshui, WL168, and RSA-03), medium-lived (RSA-02) and short-lived (RSA-01). The differences in relative telomere length distances of Qingshui, WL168, RSA-01, RSA-02, and RSA-03 between plants aged 1 and 5 years were 10.40, 13.02, 12.22, 11.22, and 13.25, respectively. The largest difference in relative telomere length was found between Qingshui and RSA-02 at 2.20. Our findings demonstrated that relative telomere length in alfalfa is influenced by genetic variation and age, with age exerting a greater effect. creator: Yun A creator: Shangli Shi creator: Shoujiang Sun creator: Yuanyuan Jing creator: Zili Li creator: Xiaoyan Zhang creator: Xiaolong Li creator: Fang Wu uri: https://doi.org/10.7717/peerj.14102 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 A et al. title: Glycyrrhizic acid Poly(D,L-lactide-co-glycolide) nanoparticles: anti-aging cosmeceutical formulation for topical applications link: https://peerj.com/articles/14139 last-modified: 2022-10-12 description: Glycyrrhizic acid (GA) is one of the components of licorice roots (Glycyrrhiza glabra L.). GA is a triterpenoid saponin can be used as a medicinal plant with its antiallergic, antiviral, anti-inflammatory, anti-ulcer, hepatoprotective, anticancer, anti-oxidation activities and several other therapeutic properties. The aim of this study is to develop an anti-aging formulation for topical application containing GA. In this context, GA-loaded Poly (D,L-lactide-co-glycolide) (PLGA) nanoparticles (NPs) were prepared using the double emulsion method, and were characterized by various spectroscopic methods. The efficacy of GA-PLGA NPs was evaluated with in vitro and in silico methods. The encapsulation efficiency and loading capacity were calculated. The in vitro release study was conducted, and the GA release profile was determined. The genotoxic activity of GA and GA-PLGA NPs was evaluated by the Ames test using TA98 and TA100 mutant strains of Salmonella typhimurium. The cytotoxic potential of GA-PLGA NPs was evaluated on the HaCaT cell line using the MTT assay. According to the genotoxicity and cytotoxicity results, it was found that the GA-PLGA NP formulation did not exhibit genotoxic and cytotoxic effects. Moreover, the efficacy of GA in preventing UVB-induced photo-aging in HaCaT cells and the clarification of the molecular mechanism of GA binding to MMPs were revealed by molecular docking analysis. In addition, through molecular dynamics (MD) analysis, the binding interaction of GA with MMPs in a dynamic system, and protein-ligand stability were predicted as a result of 50 ns MD simulation studies considering various analysis parameters. Finally, it was evaluated that GA-PLGA nanoformulation might be used as an alternative anti-aging skin care product candidate via topical application. creator: Cigdem Cetin Aluc creator: Bahar Gok creator: Serda Kecel-Gunduz creator: Yasemin Budama-Kilinc uri: https://doi.org/10.7717/peerj.14139 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cetin Aluc et al.