title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=780 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Multiple comparisons of precipitation variations in different areas using simultaneous confidence intervals for all possible ratios of variances of several zero-inflated lognormal models link: https://peerj.com/articles/12659 last-modified: 2021-12-20 description: Flash flooding and landslides regularly cause injury, death, and homelessness in Thailand. An advancedwarning system is necessary for predicting natural disasters, and analyzing the variability of daily precipitation might be usable in this regard. Moreover, analyzing the differences in precipitation data among multiple weather stations could be used to predict variations in meteorological conditions throughout the country. Since precipitation data in Thailand follow a zero-inflated lognormal (ZILN) distribution, multiple comparisons of precipitation variation in different areas can be addressed by using simultaneous confidence intervals (SCIs) for all possible pairwise ratios of variances of several ZILN models. Herein, we formulate SCIs using Bayesian, generalized pivotal quantity (GPQ), and parametric bootstrap (PB) approaches. The results of a simulation study provide insight into the performances of the SCIs. Those based on PB and the Bayesian approach via probability matching with the beta prior performed well in situations with a large amount of zero-inflated data with a large variance. Besides, the Bayesian based on the reference-beta prior and GPQ SCIs can be considered as alternative approaches for small-to-large and medium-to-large sample sizes from large population, respectively. These approaches were applied to estimate the precipitation variability among weather stations in lower southern Thailand to illustrate their efficacies. creator: Patcharee Maneerat creator: Sa-Aat Niwitpong uri: https://doi.org/10.7717/peerj.12659 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Maneerat and Niwitpong title: miR-15a-5p regulates myocardial fibrosis in atrial fibrillation by targeting Smad7 link: https://peerj.com/articles/12686 last-modified: 2021-12-20 description: BackgroundAt present, there is no effective treatment for myocardial fibrosis in atrial fibrillation (AF). It is reported that miR-15a-5p is abnormally expressed in AF patients but its specific role remains unclear. This study aims to investigate the effect of miR-15a-5p in myocardial fibrosis.MethodsLeft atrial appendage (LAA) tissues were collected from AF and non-AF patients. In lipopolysaccharide (LPS) stimulated H9C2 cells, miR-15a-5p mimic, inhibitor, pcDNA3.1-Smad7 and small interfering RNA-Smad7 (siRNA-Smad7) were respectively transfected to up-regulate or down-regulate the intracellular expression levels of miR-15a-5p and Smad7. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot (WB) were used to determine the expression levels of miR-15a-5p, Smad7, transforming growth factor β1 (TGF-β1) and collagen I. Cell counting kit-8 (CCK-8) and ethylene deoxyuridine (EdU) were used to determine cell viability and proliferation capacity, respectively. Dual-luciferase was used to detect whether miR-15a-5p interacted with Smad7, hydroxyproline (HYP) and Hematoxylin-Eosin (HE) staining were used to detect tissue fibrosis.ResultsThe expression levels of miR-15a-5p, TGF-β1 and collagen I were up-regulated, while Smad7 was down-regulated in AF tissues and LPS-stimulated cells. MiR-15a-5p mimic can inhibit the expression of Smad7, and the dual-luciferase experiment confirmed their interaction. MiR-15a-5p inhibitor or pcDNA3.1-Smad7 can inhibit LPS-induced fibrosis and cell proliferation, while siRNA-Smad7 can reverse the changes caused by miR-15a-5p inhibitor.ConclusionWe combined clinical studies with LPS-stimulated H9C2 cell model to validate the role of miR-15a-5p in the regulation of Smad7 and fibrosis. Taken together, the miR-15a-5p/Smad7 pathway might be a potential target for AF therapy. creator: Dan He creator: Zhong-bao Ruan creator: Gui-xian Song creator: Ge-cai Chen creator: Fei Wang creator: Mei-xiang Wang creator: Mao-kun Yuan creator: Li Zhu uri: https://doi.org/10.7717/peerj.12686 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 He et al. title: Light intensity drives different growth strategies in two duckweed species: Lemna minor L. and Spirodela polyrhiza (L.) Schleiden link: https://peerj.com/articles/12698 last-modified: 2021-12-20 description: Duckweed species Lemna minor and Spirodela polyrhiza are clonal plants with vegetative organs reduced to a frond and a root in L. minor or a frond and several roots in S. polyrhiza. They reproduce vegetatively by relatively rapid multiplication of their fronds. The habit of S. polyrhiza (large fronds with up to 21 roots) makes it a strong competitor among representatives of the family Lemnaceae, probably due to different resource-use strategies compared to small duckweed. In our study, light was the resource that affected the plants before and during the laboratory experiment. We sampled the plants from natural habitats differing in light conditions (open and shady) and grew them for 16 days in a thermostatic growth room at 22 °C under a 16:8 photoperiod and three light intensities (125, 236, 459 µmol photons m–2 s–1) to investigate the trade-off between frond enlargement and multiplication. Both species from the open habitat had higher growth rates based on the frond numbers and on surface area of fronds compared to plants from the shady habitat. They adopted different species-specific strategies in response to the experimental light conditions. The species size affected the growth rates in L. minor and S. polyrhiza. Spirodela polyrhiza grew slower than L. minor, but both species grew fastest at medium light intensity (236 µmol m–2 s–1). Lemna minor maintained the growth rates at high light intensity, while S. polyrhiza slowed down. Spirodela polyrhiza responded to deteriorating light conditions by increasing its frond surface area, thus optimising light capture. Lemna minor from the shady habitat enhanced light harvest by increasing chlorophyll a concentration, but did not invest more in frond enlargement than L. minor from the open habitat. Under shady conditions, S. polyrhiza is likely to achieve an advantage over L. minor due to the larger frond size of the former. Our findings suggest the existence of a trade-off between size and number in duckweed. creator: Małgorzata Strzałek creator: Lech Kufel uri: https://doi.org/10.7717/peerj.12698 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Strzałek et al. title: Palatal mucosa thickness and palatal neurovascular bundle position evaluation by cone-beam computed tomography—retrospective study on relationships with palatal vault anatomy link: https://peerj.com/articles/12699 last-modified: 2021-12-20 description: BackgroundMeasuring the thickness of the palatal mucosa at the planning of the surgical procedure is an important step in order to obtain the maximum width and thickness of the graft from the appropriate area. The aim of this study is to determine whether there is a relationship between palatal angle (PA) or palatal depth (PD) and palatal mucosa thickness (PMT) or palatal neurovascular bundle distance (PNBD).MethodsPMT, PNBD, PD and PA were measured on cone-beam computed tomography (CBCT) images of maxillary posterior region of 200 male and 200 female patients. The mean of all parameters according to gender was compared and the significance of the difference detected between groups was evaluated. Potential relationship between PMT or PNBD and PA or PD was also evaluated.ResultsIn females, the palatal mucosa was significantly thinner at all tooth regions (p < 0.005), and PNBD was lower only at the level of the second molar (p < 0.001). In addition, it was found that there was a significant inverse correlation between the palatal depth value and the palatal mucosal thickness, and palatal depth was correlated with the palatal neurovascular bundle distance (p ≤ 0.001).DiscussionConsistent with previous studies, it was observed that the thickest mucosa in the palatal region was located in the region of the premolar teeth, and women had thinner palatal mucosa. In addition, in patients with a deeper palate vault, the palatal mucosa was thinner, but the palatal neurovascular bundle was more distant from the cemento-enamel junction. creator: Ilkim Karadag creator: Hasan Guney Yilmaz uri: https://doi.org/10.7717/peerj.12699 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Karadag and Yilmaz title: Methodological recommendations for assessing scleractinian and octocoral recruitment to settlement tiles link: https://peerj.com/articles/12549 last-modified: 2021-12-17 description: Quantifying recruitment of corals is important for evaluating their capacity to recover after disturbances through natural processes, yet measuring recruitment rates in situ is challenging due to the minute size of the study organism and the complexity of benthic communities. Settlement tiles are widely used in studies of coral recruitment because they can be viewed under a microscope to enhance accuracy, but methodological choices such as the rugosity of tiles used and when and how to scan tiles for recruits post-collection may cause inconsistencies in measured recruitment rates. We deployed 2,880 tiles with matching rugosity on top and bottom surfaces to 30 sites along the Florida Reef Tract for year-long saturations during a three year study. We scanned the top and bottom surfaces of the same tiles for scleractinian recruits before (live scans) and after treating tiles with sodium hypochlorite (corallite scans). Recruit counts were higher in corallite than live scans, indicating that scleractinian recruitment rates should not be directly compared between studies using live scans and those scanning tiles which have been processed to remove fouling material. Recruit counts also were higher on tile tops in general, but the proportion of settlement to the top and bottom surfaces varied significantly by scleractinian family. Thus, biases may be introduced in recruitment datasets by differences in tile rugosity or by only scanning a subset of tile surfaces. Finally, we quantified octocoral recruitment during live scans and found they preferentially settled to tile tops. We recommend that recruitment tile studies include corallite scans for scleractinian skeletons, deploy tiles with matching rugosity on top and bottom surfaces, and scan all tile surfaces. creator: Leah M. Harper creator: Lindsay K. Huebner creator: Elijah D. O’Cain creator: Rob Ruzicka creator: Daniel F. Gleason creator: Nicole D. Fogarty uri: https://doi.org/10.7717/peerj.12549 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Harper et al. title: Inhibition of LINK-A lncRNA overcomes ibrutinib resistance in mantle cell lymphoma by regulating Akt/Bcl2 pathway link: https://peerj.com/articles/12571 last-modified: 2021-12-17 description: Ibrutinib, a bruton tyrosine kinase (BTK) inhibitor which suppresses B-cell receptor signaling, has remarkably improved the outcome of patients with mantle cell lymphoma (MCL). However, approximately 33% of MCL patients have primary Ibrutinib resistance, and acquired Ibrutinib resistance is nearly universal. Long intergenic non-coding RNA for kinase activation (LINK-A) exerts oncogenic role in different types of tumors, but the role of LINK-A in intrinsic ibrutinib resistance in MCL is still unclear. Here, LINK-A expression level was first assessed using quantitative Real-time PCR (qPCR) and immunofluorescence analysis in five MCL cell lines. The effect of LINK-A on regulating MCL cells viability and apoptosis was assayed using CCK-8 and TdT-mediated dUTP nick end labeling (TUNEL) assay, respectively. The association of LINK-A with AKT activation and B cell lymphoma 2 (Bcl2)expression was evaluated using qPCR and western blot analysis. We found that LINK-A level was elevated in Ibrutinib-resistant MCL cell lines (Mino, REC-1, MAVER-1, and Granta-519) compared to Ibrutinib-sensitive MCL cell lines (Jeko-1). Functionally, LINK-A overexpression in Jeko-1 cells enhanced cell viability and repressed Ibrutinib-induced cell apoptosis. LINK-A knockdown in MAVER-1 cells decreased cell viability and further accelerated Ibrutinib-induced cell apoptosis. LINK-A overexpression enhanced Bcl2 expression in Jeko-1 cells, and Bcl2 inhibition blocked the effect of LINK-A on increasing cell viability in the presence of Ibrutinib. On the contrary, LINK-A knockdown reduced Bcl2 expression in MAVER-1 cells, and Bcl2 overexpression damaged the role of LINK-A inhibition in regulating cell viability. Mechanistically, LINK-A positively regulated the activation of AKT signaling, and inhibition of AKT signaling destroyed LINK-A-induced increased of Bcl2 and resulted in a subsequent suppression of cell viability. Taken together, the current results demonstrate that LINK-A inhibition overcomes Ibrutinib resistance in MCL cells by regulating AKT/Bcl2 pathway. creator: Ye Zhang creator: Peng Lu creator: Yan Zhou creator: Lifei Zhang uri: https://doi.org/10.7717/peerj.12571 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Characterizing the Type 6 Secretion System (T6SS) and its role in the virulence of avian pathogenic Escherichia coli strain APECO18 link: https://peerj.com/articles/12631 last-modified: 2021-12-17 description: Avian pathogenic E. coli is the causative agent of extra-intestinal infections in birds known as colibacillosis, which can manifest as localized or systemic infections. The disease affects all stages of poultry production, resulting in economic losses that occur due to morbidity, carcass condemnation and increased mortality of the birds. APEC strains have a diverse virulence trait repertoire, which includes virulence factors involved in adherence to and invasion of the host cells, serum resistance factors, and toxins. However, the pathogenesis of APEC infections remains to be fully elucidated. The Type 6 secretion (T6SS) system has recently gained attention due to its role in the infection process and protection of bacteria from host defenses in human and animal pathogens. Previous work has shown that T6SS components are involved in the adherence to and invasion of host cells, as well as in the formation of biofilm, and intramacrophage bacterial replication. Here, we analyzed the frequency of T6SS genes hcp, impK, evpB, vasK and icmF in a collection of APEC strains and their potential role in virulence-associated phenotypes of APECO18. The T6SS genes were found to be significantly more prevalent in APEC than in fecal E. coli isolates from healthy birds. Expression of T6SS genes was analyzed in culture media and upon contact with host cells. Mutants were generated for hcp, impK, evpB, and icmF and characterized for their impact on virulence-associated phenotypes, including adherence to and invasion of host model cells, and resistance to predation by Dictyostelium discoideum. Deletion of the aforementioned genes did not significantly affect adherence and invasion capabilities of APECO18. Deletion of hcp reduced resistance of APECO18 to predation by D. discoideum, suggesting that T6SS is involved in the virulence of APECO18. creator: Aline L. de Oliveira creator: Nicolle L. Barbieri creator: Darby M. Newman creator: Meaghan M. Young creator: Lisa K. Nolan creator: Catherine M. Logue uri: https://doi.org/10.7717/peerj.12631 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 de Oliveira et al. title: Metabarcoding prey DNA from fecal samples of adult dragonflies shows no predicted sex differences, and substantial inter-individual variation, in diets link: https://peerj.com/articles/12634 last-modified: 2021-12-17 description: Sexes often differ in foraging and diet, which is associated with sex differences in size, trophic morphology, use of habitats, and/or life history tactics. Herein, strikingly similar diets were found for adult sexes of a dragonfly (Leucorrhinia intacta), based on comparing 141 dietary taxa identified from the metabarcoding of mitochondrial DNA archived in feces. Arthropods in > 5% of samples included five species of dipterans, two hemipterans, two spider species and one parasitic mite. The mite was not traditional prey as its presence was likely due to DNA contamination of samples arising through parasitism or possibly via accidental consumption during grooming, and therefore the mite was excluded from diet characterizations. Common prey species were found with statistically indistinguishable frequencies in male and female diets, with one exception of an aphid more often found in male diets, although this pattern was not robust to corrections for multiple statistical tests. While rare prey species were often found in diets of only one sex, instances of this were more frequent in the more oft-sampled females, suggesting sampling artefact. Sexes did not differ in the mean prey species richness in their diets. Overall, sexes showed statistically indistinguishable diets both on a prey species-by-species basis and in terms of multivariate characterizations of diet composition, derived from presence-absence data of prey species analyzed via PERMANOVA and accumulation curves. Males and females may have similar diets by being both opportunistic and generalist predators of arthropods, using the same foraging habitats and having similar sizes and flight agilities. Notably, similarities in diet between sexes occur alongside large interindividual differences in diet, within sexes. Researchers intending on explaining adaptive sex differences in diet should consider characteristics of species whose sexes show similar diets. creator: André Morrill creator: Kari M. Kaunisto creator: Julia J. Mlynarek creator: Ella Sippola creator: Eero J. Vesterinen creator: Mark R. Forbes uri: https://doi.org/10.7717/peerj.12634 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Morrill et al. title: Novel visual analytics approach for chromosome territory analysis link: https://peerj.com/articles/12661 last-modified: 2021-12-17 description: This document presents a new and improved, more intuitive version of a novel method for visually representing the location of objects relative to each other in 3D. The motivation and inspiration for developing this new method came from the necessity for objective chromosome territory (CT) adjacency analysis. The earlier version, Distance Profile Chart (DPC), used octants for 3D orientation. This approach did not provide the best 3D space coverage since space was divided into just eight cones and was not intuitive with regard to orientation in 3D. However, the version presented in this article, called DPC12, allows users to achieve better space coverage during conification since space is now divided into twelve cones. DPC12 is faster than DPC and allows for a more precise determination of the location of objects in 3D. In this article a short introduction about the conification idea is presented. Then we explain how DPC12 is designed and created. After that, we show DPC12 on an instructional dataset to make it easier to understand and demonstrate how they appear and how to read them. Finally, using DPC12 we present an example of an adjacency analysis (AA) using the model of Chromosome Territories (CTs) distribution in the rice nucleus. creator: Magdalena A. Tkacz creator: Kornel Chromiński creator: Dominika Idziak-Helmcke creator: Ewa Robaszkiewicz uri: https://doi.org/10.7717/peerj.12661 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tkacz et al. title: Quantifying the association of natal household wealth with women’s early marriage in Nepal link: https://peerj.com/articles/12324 last-modified: 2021-12-16 description: BackgroundWomen’s early marriage (<18 years) is a critical global health issue affecting 650 million women worldwide. It is associated with a range of adverse maternal physical and mental health outcomes, including early childbearing, child undernutrition and morbidity. Poverty is widely asserted to be the key risk factor driving early marriage. However, most studies do not measure wealth in the natal household, but instead, use marital household wealth as a proxy for natal wealth. Further research is required to understand the key drivers of early marriage.MethodsWe investigated whether natal household poverty was associated with marrying early, independently of women’s lower educational attainment and broader markers of household disadvantage. Data on natal household wealth (material asset score) for 2,432 women aged 18–39 years was used from the cluster-randomized Low Birth Weight South Asia Trial in lowland rural Nepal. Different early marriage definitions (<15, <16, <17 and <18 years) were used because most of our population marries below the conventional 18-year cut-off. Logistic mixed-effects models were fitted to estimate the probabilities, derived from adjusted Odds Ratios, of (a) marrying at different early ages for the full sample and for the uneducated women, and (b) being uneducated in the first place.ResultsWomen married at median age 15 years (interquartile range 3), and only 18% married ≥18 years. Two-thirds of the women were entirely uneducated. We found that, rather than poverty, women’s lower education was the primary factor associated with early marriage, regardless of how ‘early’ is defined. Neither poverty nor other markers of household disadvantage were associated with early marriage at any age in the uneducated women. However, poverty was associated with women being uneducated.ConclusionWhen assets are measured in the natal household in this population, there is no support for the conventional hypothesis that household poverty is associated with daughters’ early marriage, but it is associated with not going to school. We propose that improving access to free education would both reduce early marriage and have broader benefits for maternal and child health and gender equality. creator: Akanksha A. Marphatia creator: Naomi M. Saville creator: Dharma S. Manandhar creator: Mario Cortina-Borja creator: Jonathan C. K. Wells creator: Alice M. Reid uri: https://doi.org/10.7717/peerj.12324 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Marphatia et al.