title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2020-12 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: DHA content in milk and biohydrogenation pathway in rumen: a review link: https://peerj.com/articles/10230 last-modified: 2020-12-22 description: Docosahexaenoic acid (DHA) is an essential human nutrient that may promote neural health and development. DHA occurs naturally in milk in concentrations that are influenced by many factors, including the dietary intake of the cow and the rumen microbiome. We reviewed the literature of milk DHA content and the biohydrogenation pathway in rumen of dairy cows aim to enhance the DHA content. DHA in milk is mainly derived from two sources: α-linolenic acid (ALA) occurring in the liver and consumed as part of the diet, and overall dietary intake. Rumen biohydrogenation, the lymphatic system, and blood circulation influence the movement of dietary intake of DHA into the milk supply. Rumen biohydrogenation reduces DHA in ruminal environmental and limits DHA incorporation into milk. The fat-1 gene may increase DHA uptake into the body but this lacks experimental confirmation. Additional studies are needed to define the mechanisms by which different dietary sources of DHA are associated with variations of DHA in milk, the pathway of DHA biohydrogenation in the rumen, and the function of the fat-1 gene on DHA supply in dairy cows. creator: Guoxin Huang creator: Yangdong Zhang creator: Qingbiao Xu creator: Nan Zheng creator: Shengguo Zhao creator: Kaizhen Liu creator: Xueyin Qu creator: Jing Yu creator: Jiaqi Wang uri: https://doi.org/10.7717/peerj.10230 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Lack of guilt, shame, and remorse following weight stigma expression: a real-time assessment pilot study link: https://peerj.com/articles/10294 last-modified: 2020-12-22 description: ObjectiveWeight stigma is pervasive and is associated with negative health and psychological outcomes. Few studies have examined weight stigma perpetration or the emotions individuals experience after perpetrating weight stigma. This study used experience sampling to explore the nature and frequency of weight stigma behaviors and cognitions and moral emotions (shame, guilt, remorse, pride) in the perpetrator following weight stigma perpetration.MethodsParticipants were college students (N = 31, 77.1% female). Participants completed baseline measures of anti-fat attitudes and one week of experience sampling phone prompts assessing: (1) weight stigma behaviors and cognitions and (2) moral emotions. Generalized estimating equation analyses were used to model trajectories of moral emotions after weight stigma events.ResultsThirty-one participants reported 1,008 weight stigma events over 7.5 days. Feelings of guilt, shame, and remorse decreased after weight stigma perpetration. Individuals also reported feeling less proud after engaging in weight stigma.ConclusionsWeight stigma occurs frequently as reported by perpetrators. A lack of remorse, guilt, and shame is evident in undergraduates after they express weight stigma; however, individuals in this study also reported feeling less pride after perpetration. This study highlights the need for future studies to explore the expression of weight stigma from the perspective of perpetrators instead of targets. Results highlight the pervasiveness and normative nature of weight stigma perpetration in everyday life and the need to better understand the emotional response following weight stigma perpetration as a potential mechanism of its perpetuation. creator: Paige J. Trojanowski creator: Lauren Breithaupt creator: Sonakshi Negi creator: Joseph Wonderlich creator: Sarah Fischer uri: https://doi.org/10.7717/peerj.10294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Trojanowski et al. title: The relationship between anti-Müllerian hormone (AMH) levels and pregnancy outcomes in patients undergoing assisted reproductive techniques (ART) link: https://peerj.com/articles/10390 last-modified: 2020-12-22 description: A variety of predictors are available for ovarian stimulation cycles in assisted reproductive technology (ART) forecasting ovarian response and reproductive outcome in women including biomarkers such as anti- Müllerian hormone (AMH). The aim of our present study was to compare the relationship between AMH levels and pregnancy outcomes in patients undergoing intra-cytoplasmic sperm injection (ICSI). Overall, fifty patients (n = 50), aged 20–45 years were recruited for the present prospective study. Three AMH levels were presented with high often poly cystic ovarian syndrome (PCOS) amongst 52.4% patients, 40.5% in normal and 7.1% in low to normal, correspondingly. There was statistically significant relationship between AMH and day of embryo transfer (p < 0.05). The Pearson analysis between AMH, age, E2 and FSH displayed no statistically significant relationship between E2 and AMH (p < 0.05) and negative correlation between FSH and age (p > 0.05). The area under the receiver operating characteristic curve for E2 was 0.725 and for AMH levels as predictors of CPR was 0.497 indicating E2 as better predictor than AMH. The number of oocytes, mature oocytes and fertilized oocytes all presented a weak positive relationship to AMH. Our results confirm the clinical significance of AMH to accurately predict ovarian reserve as a marker and its limitations to use as predictor for a positive pregnancy outcome. Additional prospective studies should be conducted to validate the predictive capability of AMH levels for the outcome of clinical pregnancy. creator: Shalini Umarsingh creator: Jamila Khatoon Adam creator: Suresh Babu Naidu Krishna uri: https://doi.org/10.7717/peerj.10390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Umarsingh et al. title: Supraspecific units in correlative niche modeling improves the prediction of geographic potential of biological invasions link: https://peerj.com/articles/10454 last-modified: 2020-12-22 description: BackgroundBiological invasions rank among the most significant threats to biodiversity and ecosystems. Correlative ecological niche modeling is among the most frequently used tools with which to estimate potential distributions of invasive species. However, when areas accessible to the species across its native distribution do not represent the full spectrum of environmental conditions that the species can tolerate, correlative studies often underestimate fundamental niches.MethodsHere, we explore the utility of supraspecific modeling units to improve the predictive ability of models focused on biological invasions. Taking into account phylogenetic relationships in correlative ecological niche models, we studied the invasion patterns of three species (Aedes aegypti, Pterois volitans and Oreochromis mossambicus).ResultsUse of supraspecific modeling units improved the predictive ability of correlative niche models in anticipating potential distributions of three invasive species. We demonstrated that integrating data on closely related species allowed a more complete characterization of fundamental niches. This approach could be used to model species with invasive potential but that have not yet invaded new regions. creator: Sandra Castaño-Quintero creator: Jazmín Escobar-Luján creator: Luis Osorio-Olvera creator: A Townsend Peterson creator: Xavier Chiappa-Carrara creator: Enrique Martínez-Meyer creator: Carlos Yañez-Arenas uri: https://doi.org/10.7717/peerj.10454 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Castaño-Quintero et al. title: BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis link: https://peerj.com/articles/10469 last-modified: 2020-12-22 description: BackgroundRNA sequencing is an indispensable research tool used in a broad range of transcriptome analysis studies. The most common application of RNA Sequencing is differential expression analysis and it is used to determine genetic loci with distinct expression across different conditions. An emerging field called single-cell RNA sequencing is used for transcriptome profiling at the individual cell level. The standard protocols for both of these approaches include the processing of sequencing libraries and result in the generation of count matrices. An obstacle to these analyses and the acquisition of meaningful results is that they require programing expertise. Although some effort has been directed toward the development of user-friendly RNA-Seq analysis analysis tools, few have the flexibility to explore both Bulk and single-cell RNA sequencing.ImplementationBingleSeq was developed as an intuitive application that provides a user-friendly solution for the analysis of count matrices produced by both Bulk and Single-cell RNA-Seq experiments. This was achieved by building an interactive dashboard-like user interface which incorporates three state-of-the-art software packages for each type of the aforementioned analyses. Furthermore, BingleSeq includes additional features such as visualization techniques, extensive functional annotation analysis and rank-based consensus for differential gene analysis results. As a result, BingleSeq puts some of the best reviewed and most widely used packages and tools for RNA-Seq analyses at the fingertips of biologists with no programing experience.AvailabilityBingleSeq is as an easy-to-install R package available on GitHub at https://github.com/dbdimitrov/BingleSeq/. creator: Daniel Dimitrov creator: Quan Gu uri: https://doi.org/10.7717/peerj.10469 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dimitrov and Gu title: Expression of the neurotrophic tyrosine kinase receptors, ntrk1 and ntrk2a, precedes expression of other ntrk genes in embryonic zebrafish link: https://peerj.com/articles/10479 last-modified: 2020-12-22 description: BackgroundThe neurotrophic tyrosine kinase receptor (Ntrk) gene family plays a critical role in the survival of somatosensory neurons. Most vertebrates have three Ntrk genes each of which encode a Trk receptor: TrkA, TrkB, or TrkC. The function of the Trk receptors is modulated by the p75 neurotrophin receptors (NTRs). Five ntrk genes and one p75 NTR gene (ngfrb) have been discovered in zebrafish. To date, the expression of these genes in the initial stages of neuron specification have not been investigated.PurposeThe present work used whole mount in situ hybridization to analyze expression of the five ntrk genes and ngfrb in zebrafish at a timepoint when the first sensory neurons of the zebrafish body are being established (16.5 hpf). Because expression of multiple genes were not found at this time point, we also checked expression at 24 hpf to ensure the functionality of our six probes.ResultsAt 16.5 hpf, we found tissue specific expression of ntrk1 in cranial ganglia, and tissue specific expression of ntrk2a in cranial ganglia and in the spinal cord. Other genes analyzed at 16.5 hpf were either diffuse or not detected. At 24 hpf, we found expression of both ntrk1 and ntrk2a in the spinal cord as well as in multiple cranial ganglia, and we identified ngfrb expression in cranial ganglia at 24 hpf. ntrk2b, ntrk3a and ntrk3b were detected in the developing brain at 24 hpf.ConclusionThese data are the first to demonstrate that ntrk1 and ntrk2a are the initial neurotrophic tyrosine kinase receptors expressed in sensory neurons during the development of the zebrafish body, and the first to establish expression patterns of ngfrb during early zebrafish development. Our data indicate co-expression of ntrk1, ntrk2a and ngfrb, and we speculate that these overlapping patterns indicate relatedness of function. creator: Katie Hahn creator: Paul Manuel creator: Cortney Bouldin uri: https://doi.org/10.7717/peerj.10479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hahn et al. title: The ecomorphology of the shell of extant turtles and its applications for fossil turtles link: https://peerj.com/articles/10490 last-modified: 2020-12-22 description: Turtles are a successful clade of reptiles that originated in the Late Triassic. The group adapted during its evolution to different types of environments, ranging from dry land to ponds, rivers, and the open ocean, and survived all Mesozoic and Cenozoic extinction events. The body of turtles is characterized by a shell, which has been hypothesized to have several biological roles, like protection, thermal and pH regulation, but also to be adapted in its shape to the ecology of the animal. However, only few studies have investigated the relationships between shell shape and ecology in a global context or clarified if shape can be used to diagnose habitat preferences in fossil representatives. Here, we assembled a three-dimensional dataset of 69 extant turtles and three fossils, in particular, the Late Triassic Proganochelys quenstedtii and Proterochersis robusta and the Late Jurassic Plesiochelys bigleri to test explicitly for a relationship between shell shape and ecology. 3D models were obtained using surface scanning and photogrammetry. The general shape of the shells was captured using geometric morphometrics. The habitat ecology of extant turtles was classified using the webbing of their forelimbs as a proxy. Principal component analysis (PCA) highlights much overlap between habitat groups. Discriminant analyses suggests significant differences between extant terrestrial turtles, extant fully aquatic (i.e., marine and riverine) turtles, and an unspecialized assemblage that includes extant turtles from all habitats, mostly freshwater aquatic forms. The paleoecology of the three fossil species cannot be determined with confidence, as all three fall within the unspecialized category, even if Plesiochelys bigleri plots closer to fully aquatic turtles, while the two Triassic species group closer to extant terrestrial forms. Although the shape of the shell of turtles indeed contains an ecological signal, it is overall too weak to uncover using shell shape in paleoecological studies, at least with the methods we selected. creator: Ilya Dziomber creator: Walter G. Joyce creator: Christian Foth uri: https://doi.org/10.7717/peerj.10490 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dziomber et al. title: SKP1-like protein, CrSKP1-e, interacts with pollen-specific F-box proteins and assembles into SCF-type E3 complex in ‘Wuzishatangju’ (Citrus reticulata Blanco) pollen link: https://peerj.com/articles/10578 last-modified: 2020-12-22 description: S-ribonuclease (S-RNase)-based self-incompatibility (SI) mechanisms have been extensively studied in Solanaceae, Rosaceae and Plantaginaceae. S-RNase-based SI is controlled by two closely related genes, S-RNase and S-locus F-box (SLF), located at a polymorphic S-locus. In the SI system, the SCF-type (SKP1-CUL1-F-box-RBX1) complex functions as an E3 ubiquitin ligase complex for ubiquitination of non-self S-RNase. Pummelo (Citrus grandis) and several mandarin cultivars are suggested to utilize an S-RNase-based SI system. However, the molecular mechanism of the non-S-factors involved in the SI reaction is not straightforward in Citrus. To investigate the SCF-type E3 complex responsible for the SI reaction in mandarin, SLF, SKP1-like and CUL1 candidates potentially involved in the SI reaction of ‘Wuzishatangju’ (Citrus reticulata Blanco) were identified based on the genome-wide identification and expression analyses. Sixteen pollen-specific F-box genes (CrFBX1-CrFBX16), one pollen-specific SKP1-like gene (CrSKP1-e) and two CUL1 genes (CrCUL1A and CrCUL1B) were identified and cloned from ‘Wuzishatangju’. Yeast two-hybrid (Y2H) and in vitro binding assays showed that five CrFBX proteins could bind to CrSKP1-e, which is an ortholog of SSK1 (SLF-interacting-SKP1-like), a non-S-factor responsible for the SI reaction. Luciferase complementation imaging (LCI) and in vitro binding assays also showed that CrSKP1-e interacts with the N-terminal region of both CrCUL1A and CrCUL1B. These results indicate that CrSKP1-e may serve as a functional member of the SCF-type E3 ubiquitin ligase complex in ‘Wuzishatangju’. creator: Yi Ren creator: Qingzhu Hua creator: Jiayan Pan creator: Zhike Zhang creator: Jietang Zhao creator: Xinhua He creator: Yonghua Qin creator: Guibing Hu uri: https://doi.org/10.7717/peerj.10578 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ren et al. title: The effect of brewery spent grain application on biogas yields and kinetics in co-digestion with sewage sludge link: https://peerj.com/articles/10590 last-modified: 2020-12-22 description: The present study examines the effect of introducing dried brewery spent grain (BSG), known as the main solid by-product of the brewery industry on biogas yields and kinetics in co-digestion with sewage sludge (SS). The experiment was conducted in semi-continuous anaerobic reactors (supplied once a day) operating under mesophilic conditions (35°C) at different hydraulic retention times (HRT) of 18 and 20 d. In co-digestion runs, the BSG mass to the feed volume ratio was constant and maintained 1:10.The results indicated that the addition of BSG did not influence the biogas production, by comparison with SS mono-digestion (control run). At HRT of 18 d, in the co-digestion run, the average methane yield was 0.27 m3 kg/VSadded, while in the control run the higher value of 0.29 m3 kg/VSaddedwas observed. However, there was no difference in terms of statistical significance. At HRT of 20 d, the methane yield was 0.21 m3 kg/VSadded for both mono- and co-digestion runs. In the BSG presence, the decrease in kinetic constant values was observed. As compared to SS mono-digestion, reductions by 21 and 35% were found at HRT of 20 and 18 d, respectively. However, due to the supplementation of the feedstock with BSG rich in organic compounds, the significantly enhanced energy profits were achieved with the highest value of approx. 40% and related to the longer HRT of 20 d. Importantly, the mono- and co-digestion process proceeded in stable manner. Therefore, the anaerobic co-digestion of SS and BSG might be considered as a cost-effective solution that could contribute to the energy self-efficiency of wastewater treatment plants (WWTPs) and sustainable waste management for breweries. creator: Aleksandra Szaja creator: Agnieszka Montusiewicz creator: Magdalena Lebiocka creator: Marta Bis uri: https://doi.org/10.7717/peerj.10590 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Szaja et al. title: Diversification and selection pattern of CYP6B genes in Japanese Papilio butterflies and their association with host plant spectra link: https://peerj.com/articles/10625 last-modified: 2020-12-22 description: Herbivorous insects are thought to have evolved counteradaptations to conquer chemical defenses in their host plants in a stepwise co-evolutionary process. Papilio butterflies use CYP6B gene family members to metabolize furanocoumarins in their Rutaceae or Apiaceae host plants. CYP6Bs have functionally diverged among Papilio species to be able to metabolite diverse types of furanocoumarins in their host plants. In this study, we examined the diversification and selection patterns of CYP6B among nine Papilio species in Japan (eight Rutaceae specialists and one Apiaceae specialist) and their association with host plant spectra and furanocoumarin profiles. We compared host plant spectrum of eight Rutaceae feeding Papilio species and also performed a furanocoumarin profiling of their host plants. In addition, we reconstructed CYP6B gene phylogeny and performed selection analysis based on the transcriptome data of those nine Papilio species. Among Rutaceae-feeding Papilio species, host plant spectrum differences were correlated with their furanocoumarin profiles. However, all tested Papilio species had similar duplicated sets of CYP6B, with no apparent lineage-specific or host plant-specific pattern of CYP6B diversification. Selection analysis showed a signature of positive selection on a CYP6B branch. The positively selected sites located at predicted substrate recognition sites and we also found that these CYP6B genes were observed only in Rutaceae-feeding species. These findings indicate that most CYP6B diversification occurred in ancestral species of these Papilio species, possibly in association with specific host plant chemical defenses and subsequent gene loss due to host specialization. These processes would have shaped the complex diversification patterns of the CYP6B gene family in Papilio butterflies. Our results also show potentially important CYP6B clades among Papilio species which likely to have diverged functions and associated with host plant phytochemicals in ancestral Papilio species. creator: Ai Sato creator: Yu Okamura creator: Masashi Murakami uri: https://doi.org/10.7717/peerj.10625 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sato et al. title: Viscoelastic characteristics of the canine cranial cruciate ligament complex at slow strain rates link: https://peerj.com/articles/10635 last-modified: 2020-12-22 description: Ligaments including the cruciate ligaments support and transfer loads between bones applied to the knee joint organ. The functions of these ligaments can get compromised due to changes to their viscoelastic material properties. Currently there are discrepancies in the literature on the viscoelastic characteristics of knee ligaments which are thought to be due to tissue variability and different testing protocols.The aim of this study was to characterise the viscoelastic properties of healthy cranial cruciate ligaments (CCLs), from the canine knee (stifle) joint, with a focus on the toe region of the stress-strain properties where any alterations in the extracellular matrix which would affect viscoelastic properties would be seen. Six paired CCLs, from skeletally mature and disease-free Staffordshire bull terrier stifle joints were retrieved as a femur-CCL-tibia complex and mechanically tested under uniaxial cyclic loading up to 10 N at three strain rates, namely 0.1%, 1% and 10%/min, to assess the viscoelastic property of strain rate dependency. The effect of strain history was also investigated by subjecting contralateral CCLs to an ascending (0.1%, 1% and 10%/min) or descending (10%, 1% and 0.1%/min) strain rate protocol. The differences between strain rates were not statistically significant. However, hysteresis and recovery of ligament lengths showed some dependency on strain rate. Only hysteresis was affected by the test protocol and lower strain rates resulted in higher hysteresis and lower recovery. These findings could be explained by the slow process of uncrimping of collagen fibres and the contribution of proteoglycans in the ligament extracellular matrix to intra-fibrillar gliding, which results in more tissue elongations and higher energy dissipation. This study further expands our understanding of canine CCL behaviour, providing data for material models of femur-CCL-tibia complexes, and demonstrating the challenges for engineering complex biomaterials such as knee joint ligaments. creator: Rosti Readioff creator: Brendan Geraghty creator: Ahmed Elsheikh creator: Eithne Comerford uri: https://doi.org/10.7717/peerj.10635 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Readioff et al. title: Australia’s prehistoric ‘swamp king’: revision of the Plio-Pleistocene crocodylian genus Pallimnarchus de Vis, 1886 link: https://peerj.com/articles/10466 last-modified: 2020-12-21 description: The crocodylian fossil record from the Cenozoic of Australasia is notable for its rich taxonomic diversity, and is primarily represented by members of the clade Mekosuchinae. Reports of crocodylian fossils from Australia date back to the late nineteenth century. In 1886, Charles Walter de Vis proposed the name Pallimnarchus pollens for crocodylian fossils from southeast Queensland—the first binomen given to an extinct crocodylian taxon from Australia. Pallimnarchus has come to be regarded as a large, broad-snouted crocodylian from Australia’s Plio-Pleistocene, and numerous specimens, few of which are sufficiently complete, have been assigned to it by several authors throughout the twentieth century. In the late 1990s, the genus was expanded to include a second species, Pallimnarchus gracilis. Unfortunately, the original syntype series described as Pallimnarchus pollens is very fragmentary and derives from more than one taxon, while a large part of the subsequently selected lectotype specimen is missing. Because descriptions and illustrations of the complete lectotype do not reveal any autapomorphic features, we propose that Pallimnarchus pollens should be regarded as a nomen dubium. Following this decision, the fossil material previously referred to Pallimnarchus is of uncertain taxonomic placement. A partial skull, formerly assigned to Pallimnarchus pollens and known as ‘Geoff Vincent’s specimen’, possesses many features of diagnostic value and is therefore used as basis to erect a new genus and species—Paludirex vincenti gen. et sp. nov. A comprehensive description is given for the osteology of ‘Geoff Vincent’s specimen’ as well as aspects of its palaeoneurology, the latter being a first for an extinct Australian crocodyliform. The newly named genus is characterized by a unique combination of premaxillary features such as a distinctive arching of the anterior alveolar processes of the premaxillae, a peculiar arrangement of the first two premaxillary alveoli and a large size disparity between the 3rd and 4th premaxillary alveoli. These features presently allow formal recognition of two species within the genus, Paludirex vincenti and Paludirex gracilis comb. nov., with the former having comparatively more robust rostral proportions than the latter. The Paludirex vincenti holotype comes from the Pliocene Chinchilla Sand of the Darling Downs, south-eastern Queensland, whereas the material assigned to Paludirex gracilis is from the Pleistocene of Terrace Site Local Fauna, Riversleigh, northwest Queensland. Phylogenetic analyses recover Paludirex vincenti as a mekosuchine, although further cladistic assessments are needed to better understand the relationships within the clade. creator: Jorgo Ristevski creator: Adam M. Yates creator: Gilbert J. Price creator: Ralph E. Molnar creator: Vera Weisbecker creator: Steven W. Salisbury uri: https://doi.org/10.7717/peerj.10466 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ristevski et al. title: The Aichi Biodiversity Targets: achievements for marine conservation and priorities beyond 2020 link: https://peerj.com/articles/9743 last-modified: 2020-12-21 description: In 2010 the Conference of the Parties (COP) for the Convention on Biological Diversity revised and updated a Strategic Plan for Biodiversity 2011–2020, which included the Aichi Biodiversity Targets. Here a group of early career researchers mentored by senior scientists, convened as part of the 4th World Conference on Marine Biodiversity, reflects on the accomplishments and shortfalls under four of the Aichi Targets considered highly relevant to marine conservation: target 6 (sustainable fisheries), 11 (protection measures), 15 (ecosystem restoration and resilience) and 19 (knowledge, science and technology). We conclude that although progress has been made towards the targets, these have not been fully achieved for the marine environment by the 2020 deadline. The progress made, however, lays the foundations for further work beyond 2020 to work towards the 2050 Vision for Biodiversity. We identify key priorities that must be addressed to better enable marine biodiversity conservation efforts moving forward. creator: Hannah Carr creator: Marina Abas creator: Loubna Boutahar creator: Olivia N. Caretti creator: Wing Yan Chan creator: Abbie S.A. Chapman creator: Sarah N. de Mendonça creator: Abigail Engleman creator: Filippo Ferrario creator: Kayelyn R. Simmons creator: Jana Verdura creator: Anna Zivian uri: https://doi.org/10.7717/peerj.9743 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Carr et al. title: The effects of the recombinant YeaZ of Vibrio harveyi on the resuscitation and growth of soil bacteria in extreme soil environment link: https://peerj.com/articles/10342 last-modified: 2020-12-21 description: Numerous bacteria entered the viable but non-culturable state due to the stresses of dry and salt in soils. YeaZ of Gram-negative bacteria is a resuscitation promoting factor (Rpf) homologous protein could resuscitate bacteria of natural environment in VBNC state. To investigate the promoting effect of YeaZ on the isolation of viable but non-culturable (VBNC) bacteria from soil samples in extreme environments, the recombinant YeaZ of Vibrio harveyi was prepared and added to the soil samples from volcanic soil and saline soil in Northwest China. The study has shown that YeaZ can promote the recovery and growth of soil microorganisms, and the number of cultivable bacteria in volcanic and saline soil has increased from 0.17 × 103 and 2.03 × 103 cfu⋅ml−1 to 1.00 × 103 and 5.55 × 103 cfu⋅ml−1, respectively. The 16S rDNA gene sequencing and phylogenetic analysis showed that YeaZ played an essential role in the increase of composition and diversity of bacteria. A total of 13 bacterial strains were isolated from the volcanic soil samples, which belong to phyla Actinobacteria, Firmicutes and Gamma-proteobacteria. Four species, including Ornithinimicrobium kibberense, Agrococcus citreus, Stenotrophomonas rhizophila and Pseudomonas zhaodongensis were found in the control group, while Micrococcus antarcticus, Kocuria rose, Salinibacterium xinjiangense, Planococcus antarcticus, Ornithinimicrobium kibberense and Pseudomonas zhaodongensis were isolated from the treatment groups (addition of YeaZ). Twenty-one strains were isolated from the saline soil samples, including eight species from the control group and thirteen species from the treatment groups, among which nine species were only found, including Bacillus oceanisediminis, Brevibacillus brevis, Paenibacillus xylanilyticus, Microbacterium maritypicum, B. subtilis, B. alcalophilus, B. niabensis, Oceanimonas doudoroffii and Zobellella taiwanensis. The results suggest that addition of YeaZ to soil samples can promote the recovery of VBNC. This method has the implications for the discovery of VBNC bacteria that have potential environmental functions. creator: Yanlin Li creator: Jixiang Chen creator: Yonggang Wang creator: Dan Ma creator: Wenhong Rui uri: https://doi.org/10.7717/peerj.10342 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Complexities of assessing palaeocave stratigraphy: reconstructing site formation of the ∼2.61 Ma Drimolen Makondo fossil site link: https://peerj.com/articles/10360 last-modified: 2020-12-21 description: Palaeocave sites in South Africa are world renowned repositories for palaeontological and archaeological material, dating from the terminal Pliocene to the Early Pleistocene. Due to their antiquity, complex karstification history and multifaceted infilling phases, palaeocave sites are notoriously difficult to contextualise. Further to this, 19th century lime-mining and diverse excavation and sampling techniques, have complicated stratigraphic interpretations of fossil-bearing deposits within the region. Locating and assessing newly discovered, minimally disturbed palaeocave sites allow for contextual information to be gathered with greater confidence and can aid in constructing a more robust understanding of the South African fossil record. Here, we use Drimolen Makondo; a minimally lime-mined ∼2.61 Ma palaeontological site, to apply a series of in-depth stratigraphic and micromorphological studies. Contextual data presented within this study, testifies to a relatively rapid infill with greater fluvial activity when compared to adjacent deposits at the younger ∼2.04–1.95 Ma Drimolen Main Quarry. The quantity of articulated macromammalian remains, high density of micromammalian remains and pollen identified, also highlights Drimolen Makondo as a key site for ongoing palaeoenvironmental studies at the Pliocene to Pleistocene transition in South Africa. creator: Ashleigh Murszewski creator: Giovanni Boschian creator: Andy I.R. Herries uri: https://doi.org/10.7717/peerj.10360 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Murszewski et al. title: Synoptic revision of the fern genus Elaphoglossum Schott ex J.Sm. (Dryopteridaceae) in Madagascar, with the description of 23 new taxa, all but one endemic link: https://peerj.com/articles/10484 last-modified: 2020-12-21 description: After 15 years of field studies in Madagascar, especially focused on the overlooked fern genus Elaphoglossum (Dryopteridaceae), a synoptic revision of the genus is here presented. Based on more than 2,600 herbarium specimens including collections over 200 years, Elaphoglossum is the second most diversified fern genus in Madagascar, with 52 species and three subspecies (with 76% of endemism). It is to be compared to the 34 species treated by Tardieu-Blot in 1960 for the “Flore de Madagascar et des Comores” or the 38 species listed by Roux in 2009 in the seminal “Synopsis of the Lycopodiophyta and Pteridophyta of Africa, Madagascar and neighboring islands”. The 55 taxa represent five out of seven existing generic sections (sect. Amygdalifolia and sect. Wrightiana being monotypic and Neotropical): sect. Lepidoglossa (29 spp. and three subspp.), sect. Elaphoglossum (17 spp.), sect. Setosa (3 spp.), sect. Squamipedia (2 spp.), and sect. Polytrichia (1 sp.). Distribution is given for each species and subspecies, and detailed for each island or archipelago in the Western Indian Ocean (La Réunion, Mauritius, Seychelles, and Comoros). Twenty species and three subspecies are newly described, all but one endemic to Madagascar: Elaphoglossum ambrense Rouhan, Elaphoglossum andohahelense Rouhan, Elaphoglossum anjanaharibense Rouhan, Elaphoglossum approximatum Rouhan, Elaphoglossum brachymischum Rouhan, Elaphoglossum cerussatum Tardieu subsp. brunneum Rouhan, Elaphoglossum coracinolepis Rouhan, Elaphoglossum desireanum Rouhan, Elaphoglossum glabricaule Rouhan, Elaphoglossum gladiifolium Rouhan, Elaphoglossum leucolepis (Baker) Krajina ex Tardieu subsp. nanolepis Rouhan, Elaphoglossum leucolepis (Baker) Krajina ex Tardieu subsp. nigricans Rouhan, Elaphoglossum longiacuminatum Rouhan, Elaphoglossum patriceanum Rouhan, Elaphoglossum perangustum Rouhan, Elaphoglossum prominentinervulum Rouhan, Elaphoglossum rakotondrainibeae Rouhan, Elaphoglossum repandum Rouhan, Elaphoglossum sabineanum Rouhan, Elaphoglossum sinensiumbrarum Rouhan, Elaphoglossum subglabricaule Rouhan, Elaphoglossum tsaratananense Rouhan, and Elaphoglossum viridicaule Rouhan. Morphological description, distribution map, and original illustrations are provided for each new taxon. Novel identification keys to the sections and all species from Madagascar are also presented. creator: Germinal Rouhan uri: https://doi.org/10.7717/peerj.10484 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Rouhan title: Plasma BCAA concentrations during exercise of varied intensities in young healthy men—the impact of endurance training link: https://peerj.com/articles/10491 last-modified: 2020-12-21 description: BackgroundBranched-chain amino acids (BCAA) i.e., leucine (Leu), isoleucine (Ile) and valine (Val) are important amino acids, which metabolism play a role in maintaining system energy homeostasis at rest and during exercise. As recently shown lowering of circulating BCAA level improves insulin sensitivity and cardiac metabolic health. However, little is known concerning the impact of a single bout of incremental exercise and physical training on the changes in blood BCAA. The present study aimed to determine the impact of a gradually increasing exercise intensity—up to maximal oxygen uptake (VO2max) on the changes of the plasma BCAA [∑BCAA]pl, before and after 5-weeks of moderate-intensity endurance training (ET).MethodsTen healthy young, untrained men performed an incremental cycling exercise test up to exhaustion to reach VO2max, before and after ET.ResultsWe have found that exercise of low-to-moderate intensity (up to ∼50% of VO2max lasting about 12 min) had no significant effect on the [∑BCAA]pl, however the exercise of higher intensity (above 70% of VO2max lasting about 10 min) resulted in a pronounced decrease (p < 0.05) in [∑BCAA]pl. The lowering of plasma BCAA when performing exercise of higher intensity was preceded by a significant increase in plasma lactate concentration, showing that a significant attenuation of BCAA during incremental exercise coincides with exercise-induced acceleration of glycogen utilization. In addition, endurance training, which significantly increased power generating capabilities at VO2max (p = 0.004) had no significant impact on the changes of [∑BCAA]pl during this incremental exercise.ConclusionWe have concluded that an exercise of moderate intensity of relatively short duration generally has no effect on the [∑BCAA]pl in young, healthy men, whereas significant decrease in [∑BCAA]pl occurs when performing exercise in heavy-intensity domain. The impact of exercise intensity on the plasma BCAA concentration seems to be especially important for patients with cardiometabolic risk undertaken cardiac rehabilitation or recreational activity. creator: Anna Gawedzka creator: Marcin Grandys creator: Krzysztof Duda creator: Justyna Zapart-Bukowska creator: Jerzy A. Zoladz creator: Joanna Majerczak uri: https://doi.org/10.7717/peerj.10491 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gawedzka et al. title: Effect of a HIIT protocol on the lower limb muscle power, ankle dorsiflexion and dynamic balance in a sedentary type 1 diabetes mellitus population: a pilot study link: https://peerj.com/articles/10510 last-modified: 2020-12-21 description: BackgroundType 1 diabetes mellitus (T1DM) is commonly associated with premature loss of muscle function, ankle dorsiflexion and dynamic balance. Those impairments, usually, lead to physical functionality deterioration. High-intensity interval training is an efficient and safety methodology since it prevents hypoglycemia and not requires much time, which are the main barriers for this population to practice exercise and increase physical conditioning. We hypothesized that a 6-week HIIT program performed on a cycle ergometer would increase lower limb muscle power, ankle dorsiflexion range of motion and dynamic balance without hypoglycemic situations.MethodsA total of 19 diagnosed T1DM subjects were randomly assigned to HIIT group (n = 11; 6-week HIIT protocol) or Control group (n = 8; no treatment). Lower limb strength was evaluated through velocity execution in squat with three different overloads. Weight bearing lunge test (WBLT) was performed to test ankle dorsiflexion range of motion and Y-Balance test (YBT) was the test conducted to analyze dynamic balance performance.ResultsVelocity in squat improved a 11.3%, 9.4% and 10.1% (p < 0.05) with the 50%, 60% and 70% of their own body mass overload respectively, WBLT performance increased a 10.43% in the right limb and 15.45% in the left limb. YBT showed improvements in all directions (right limb-left limb): Anterior (4.3–6.1%), Posteromedial (1.8–5.2%) and Posterolateral (3.4–4.5%) in HIIT group (p < 0.05), unlike control group that did not experience any significant change in any of the variables (p > 0.05).ConclusionA 6-week HIIT program is safe and effective to improve execution velocity in squat movement, a fundamental skill in daily living activities, as well as ankle dorsiflexion range of motion and dynamic balance to reduce foot ulcers, risk falls and functional impairments. HIIT seems an efficient and safety training methodology not only for overcome T1DM barriers for exercising but also for improving functional capacities in T1DM people. creator: Jesús Alarcón-Gómez creator: Fernando Martin Rivera creator: Joaquin Madera creator: Iván Chulvi-Medrano uri: https://doi.org/10.7717/peerj.10510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Alarcón-Gómez et al. title: A methodology for examining the association between plasma volume and micronutrient biomarker mass and concentration in healthy eumenorrheic women link: https://peerj.com/articles/10535 last-modified: 2020-12-21 description: BackgroundAccurate estimation and interpretation of nutritional biomarker concentrations are important in nutritional research, clinical care, and public health surveillance. Plasma volume (PV) may affect the interpretation of plasma biomarkers but is rarely measured. We aimed to examine the association between plasma volume (PV) and micronutrient biomarker concentrations and mass as part of pilot work to develop methods.MethodsNine healthy women with regular menstrual cycles provided fasting blood samples to measure micronutrient biomarkers. Indocyanine green was injected, and five timed blood draws were taken from 2 to 5 min to measure PV. Visits were scheduled around menstrual cycle day 2. Retinol, 25-hydroxyvitamin D, riboflavin, alpha-tocopherol, zinc, copper, magnesium, manganese, cobalt, iron, and ferritin concentrations were measured in serum. Total circulating micronutrient biomarker mass was calculated from PV and concentration.ResultsThe mean PV was 2067 ±  470 mL. PV correlated positively with concentration of iron (r = 0.87, P = 0.005); other correlations were weaker with p > 0.05. PV and total mass of retinol (r = 0.90), 25(OH)D (r = 0.75), zinc (r = 0.88), copper (r = 0.83), magnesium (r = 0.93), manganese (r = 0.72), and iron (r = 0.92) were strongly correlated (all p < 0.05). PV was positively correlated with circulating micronutrient mass for most biomarkers, implying that concentrations are maintained at different volumes of plasma. Larger studies are needed to further examine these relationships.ConclusionThough there appear to be some association between micronutrient biomarker mass and plasma volume, we are unable to draw a firm conclusion about any relationship from these results because of the small sample size. We consider these findings as a preliminary analysis to establish methods for future studies. creator: Sixtus Aguree creator: Alison D. Gernand uri: https://doi.org/10.7717/peerj.10535 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Aguree and Gernand title: The positive effect of coexisting ecosystem engineers: a unique seaweed-mussel association provides refuge for native mud crabs against a non-indigenous predator link: https://peerj.com/articles/10540 last-modified: 2020-12-21 description: In marine sedimentary bottoms, mussels and macroalgae have long been recognized as important autogenic engineers that create habitat and modify abiotic conditions. The structural complexity added by bivalves and macroalgae may also mediate intraguild predation amongst marine decapod crustaceans. While spatial distributions of these ecosystem engineers frequently overlap, there is limited understanding of compounded effects when more than one engineer is present. Here we demonstrate that the coexistence of two ecosystem engineers may create habitat valuable for the survival of a small native species, the Atlantic mud crab (Panopeus herbstii), in the presence of the invasive green crab (Carcinus maenas). Using laboratory and field habitat mimics, we measured mud crab survival rates as a proxy for refuge quality. We compared the refuge provided by a unique association between shells of blue mussels (Mytilus edulis) and the giant strain of Irish moss (Chondrus crispus) to that provided by bare substrate, and by each engineer alone. These experiments revealed that the association of giant Irish moss with blue mussel shells positively and non-additively increased mud crab survival compared to the other less complex habitat mimics. In contrast, parallel experiments revealed that high habitat complexity was less important for young green crabs to survive predation from large conspecifics. These results suggest that the impact of ecosystem engineers on trophic dynamics should be considered in a broader, whole-community context encompassing multiple habitat-forming species present. creator: Paula Tummon Flynn creator: Keegan McCarvill creator: K. Devon Lynn creator: Pedro A. Quijón uri: https://doi.org/10.7717/peerj.10540 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tummon Flynn et al. title: Cinnamtannin B1 attenuates rosacea-like signs via inhibition of pro-inflammatory cytokine production and down-regulation of the MAPK pathway link: https://peerj.com/articles/10548 last-modified: 2020-12-21 description: BackgroundRosacea is a common inflammatory disease of facial skin. Dysregulation of innate immunity with enhanced inflammation and increased abundance of LL-37 at the epidermal site is a characteristic feature of rosacea. Cinnamtannin B1 (CB1) is a condensed tannin with anti-inflammatory and anti-microbial activities. The aims of the study were to evaluate the potential of CB1 as a therapy for rosacea and to characterize the potential mechanisms of action.MethodsWe intraperitoneally administered 20 mg/kg CB1 once daily for 2 days into the LL-37-induced mouse model of rosacea. The effects of CB1 in vivo were evaluated by the observations of lesions, histology, immunohistochemistry, and the transcription and translation of pro-inflammatory cytokines and chemokines. Human keratinocyte HaCaT and monocyte THP-1 were used to characterize the effects of CB1 on LL-37-induced inflammation in vitro. The changes in pro-inflammatory chemokine interleukin-8 (IL-8) were quantitated by enzyme-linked immunosorbent assay (ELISA), and the expressions of genes involved were determined by Western blotting.ResultsCB1 attenuated local redness, inflammation, and neutrophil recruitment in the mouse model of rosacea in vivo. CB1 suppressed myeloperoxidase (MPO) and macrophage inflammatory protein 2 (MIP-2) production, a functional homolog of interleukin-8 (IL-8), at the lesions. In vitro experiments confirmed that CB1 reversed the LL-37-induced IL-8 production in human keratinocytes HaCaT and monocyte THP-1 cells. CB1 inhibited IL-8 production through downregulating the phosphorylation of extracellular signal-regulated kinase (ERK) in the mitogen-activated protein kinase (MAPK) pathway.ConclusionCB1 attenuated LL-37-induced inflammation, specifically IL-8 production, through inhibiting the phosphorylation of ERK. CB1 has potential as a treatment for rosacea. creator: Hung-Lin Kan creator: Chia-Chi Wang creator: Yin-Hua Cheng creator: Chi-Lung Yang creator: Hsun-Shuo Chang creator: Ih-Sheng Chen creator: Ying-Chi Lin uri: https://doi.org/10.7717/peerj.10548 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kan et al. title: Responses of branching reef corals Acropora digitifera and Montipora digitata to elevated temperature and pCO2 link: https://peerj.com/articles/10562 last-modified: 2020-12-21 description: Anthropogenic emission of CO2 into the atmosphere has been increasing exponentially, causing ocean acidification (OA) and ocean warming (OW). The “business-as-usual” scenario predicts that the atmospheric concentration of CO2 may exceed 1,000 µatm and seawater temperature may increase by up to 3 °C by the end of the 21st century. Increases in OA and OW may negatively affect the growth and survival of reef corals. In the present study, we separately examined the effects of OW and OA on the corals Acropora digitifera and Montipora digitata, which are dominant coral species occurring along the Ryukyu Archipelago, Japan, at three temperatures (28 °C, 30 °C, and 32 °C) and following four pCO2 treatments (400, 600, 800, and 1,000 µatm) in aquarium experiments. In the OW experiment, the calcification rate (p = 0.02), endosymbiont density, and maximum photosynthetic efficiency (Fv/Fm) (both p < 0.0001) decreased significantly at the highest temperature (32 °C) compared to those at the lower temperatures (28 °C and 30 °C) in both species. In the OA experiment, the calcification rate decreased significantly as pCO2 increased (p < 0.0001), whereas endosymbiont density, chlorophyll content, and Fv/Fm were not affected. The calcification rate of A. digitifera showed greater decreases from 30 °C to 32 °C than that of M. digitata. The calcification of the two species responded differently to OW and OA. These results suggest that A. digitifera is more sensitive to OW than M. digitata, whereas M. digitata is more sensitive to OA. Thus, differences in the sensitivity of the two coral species to OW and OA might be attributed to differences in the endosymbiont species and high calcification rates, respectively. creator: Cristiana Manullang creator: Intan Herwindra Millyaningrum creator: Akira Iguchi creator: Aika Miyagi creator: Yasuaki Tanaka creator: Yukihiro Nojiri creator: Kazuhiko Sakai uri: https://doi.org/10.7717/peerj.10562 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Manullang et al. title: Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia link: https://peerj.com/articles/10575 last-modified: 2020-12-21 description: BackgroundRecently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (n = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia.MethodsWhole genome sequencing (WGS) was performed using next-generation sequencing (NGS) applied in the Illumina MiSeq instrument. Full-length virus genomes were annotated using the reference genome of hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2) and then visualized in UGENE v. 1.30. For phylogenetic analysis, a dataset of 88 available SARS-CoV-2 complete genomes from different countries, including Indonesia, was retrieved from GISAID.ResultsAll patients were hospitalized with various severities of COVID-19. Phylogenetic analysis revealed that one and three virus samples belong to clade L and GH. These three clade GH virus samples (EPI_ISL_525492, EPI_ISL_516800 and EPI_ISL_516829) were not only located in a cluster with SARS-CoV-2 genomes from Asia but also those from Europe, whereas the clade L virus sample (EPI_ISL_516806) was located amongst SARS-CoV-2 genomes from Asia. Using full-length sequences available in the GISAID EpiCoV Database, 39 of 60 SARS-CoV-2 (65%) from Indonesia harbor the D614G mutation.ConclusionThese findings indicate that SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, concurrent with the COVID-19 situation worldwide. creator: Gunadi creator: Hendra Wibawa creator: Marcellus creator: Mohamad Saifudin Hakim creator: Edwin Widyanto Daniwijaya creator: Ludhang Pradipta Rizki creator: Endah Supriyati creator: Dwi Aris Agung Nugrahaningsih creator: Afiahayati creator: Siswanto creator: Kristy Iskandar creator: Nungki Anggorowati creator: Alvin Santoso Kalim creator: Dyah Ayu Puspitarani creator: Kemala Athollah creator: Eggi Arguni creator: Titik Nuryastuti creator: Tri Wibawa uri: https://doi.org/10.7717/peerj.10575 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gunadi et al. title: Dnajb8, a target gene of SOX30, is dispensable for male fertility in mice link: https://peerj.com/articles/10582 last-modified: 2020-12-21 description: BackgroundThe DNAJ family of molecular chaperones maintains protein homeostasis in mitotic and postmeiotic cells, especially germ cells. Recently, we found that the transcription factor SOX30 initiates transcription of Dnajb8 during late meiosis and spermiogenesis in mouse testes.MethodsWe used the CRISPR/Cas9 system to generate Dnajb8 mutant mice and analyze the phenotype of the Dnajb8 mutants.ResultsAlthoughDnajb8 is an evolutionarily conserved gene, it is not essential for spermatogenesis and male fertility. We provide this phenotypic information, which could prevent duplicative work by other groups. creator: Fengsong Wang creator: Shuai Kong creator: Xuechun Hu creator: Xin Li creator: Bo Xu creator: Qiuling Yue creator: Kaiqiang Fu creator: Lan Ye creator: Shun Bai uri: https://doi.org/10.7717/peerj.10582 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Estimating salt content of vegetated soil at different depths with Sentinel-2 data link: https://peerj.com/articles/10585 last-modified: 2020-12-21 description: The accurate and timely monitoring of the soil salt content (SSC) at different depths is the prerequisite for the solution to salinization in the arid and semiarid areas. Sentinel-2 has demonstrated significant superiority in SSC inversion for its higher temporal, spatial and spectral resolution, but previous research on SSC inversion with Sentinel-2 mainly focused on the unvegetated surface soil. Based on Sentinel-2 data, this study aimed to build four machine learning models at five depths (0∼20 cm, 20∼40 cm, 40∼60 cm, 0∼40 cm, and 0∼60 cm) in the vegetated area, and evaluate the sensitivity of Sentinel-2 to SSC at different depths and the inversion capability of the models. Firstly, 117 soil samples were collected from Jiefangzha Irrigation Area (JIA) in Hetao Irrigation District (HID), Inner Mongolia, China during August, 2019. Then a set of independent variables (IVs, including 12 bands and 32 spectral indices) were obtained based on the Sentinel-2 data (released by the European Space Agency), and the full subset selection was used to select the optimal combination of IVs at five depths. Finally, four machine learning algorithms, back propagation neural network (BPNN), support vector machine (SVM), extreme learning machine (ELM) and random forest (RF), were used to build inversion models at each depth. The model performance was assessed using adjusted coefficient of determination (R2adj), root mean square error (RMSE) and mean absolute error (MAE). The results indicated that 20∼40 cm was the optimal depth for SSC inversion. All the models at this depth demonstrated a good fitting (R2adj≈ 0.6) and a good control of the inversion errors (RMSE < 0.16%, MAE < 0.12%). At the depths of 40∼60 cm and 0∼20 cm the inversion performance showed a slight and a great decrease respectively. The sensitivity of Sentinel-2 to SSC at different depths was as follows: 20∼40 cm > 40∼60 cm > 0∼40 cm > 0∼60 cm > 0∼20 cm. All four machine learning models demonstrated good inversion performance (R2adj > 0.46). RF was the best model with high fitting and inversion accuracy. Its R2adj at five depths were between 0.5 to 0.68. The SSC inversion capabilities of all the four models were as follows: RF model > ELM model > SVM model > BPNN model. This study can provide a reference for soil salinization monitoring in large vegetated area. creator: Yinwen Chen creator: Yuanlin Qiu creator: Zhitao Zhang creator: Junrui Zhang creator: Ce Chen creator: Jia Han creator: Dan Liu uri: https://doi.org/10.7717/peerj.10585 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Sevoflurane preconditioning attenuates hypoxia/reoxygenation injury of H9c2 cardiomyocytes by activation of the HIF-1/PDK-1 pathway link: https://peerj.com/articles/10603 last-modified: 2020-12-21 description: BackgroundSevoflurane preconditioning (SPC) can provide myocardial protective effects similar to ischemic preconditioning (IPC). However, the underlying molecular mechanism of SPC remains unclear. Studies confirm that hypoxia-inducible factor-1 (HIF-1) can transform cells from aerobic oxidation to anaerobic glycolysis by activating the switch protein pyruvate dehydrogenase kinase-1 (PDK-1), thus providing energy for the normal life activities of cells under hypoxic conditions. The purpose of this study was to investigate whether the cardioprotective effects of SPC are associated with activation of the HIF-1a/PDK-1 signal pathway.MethodsThe H9c2 cardiomyocytes hypoxia/reoxygenation model was established and treated with 2.4% sevoflurane at the end of equilibration. Lactate dehydrogenase (LDH) level, cell viability, cell apoptosis, mitochondrial membrane potential, key enzymes of glycolysis, ATP concentration of glycolysis were assessed after the intervention. Apoptosis related protein(Bcl-2, Bax), HIF-1a protein, and PDK-1 protein were assessed by western blot.ResultsCompared with the H/R group, SPC significantly increased the expression of HIF-1a, PDK-1, and Bcl-2 and reduced the protein expression of Bax, which markedly decreased the apoptosis ratio and Lactate dehydrogenase (LDH) level, increasing the cell viability, content of key enzymes of glycolysis, ATP concentration of glycolysis and stabilizing the mitochondrial membrane potential. However, the cardioprotective effects of SPC were disappeared by treatment with a HIF-1a selective inhibitor.ConclusionThis study demonstrates that the cardioprotective effects of SPC are associated with the activation of the HIF-1a/PDK-1 signaling pathway. The mechanism may be related to increasing the content of key enzymes and ATP of glycolysis in the early stage of hypoxia. creator: Tianliang Hou creator: Haiping Ma creator: Haixia Wang creator: Chunling Chen creator: Jianrong Ye creator: Ahmed Mohamed Ahmed creator: Hong Zheng uri: https://doi.org/10.7717/peerj.10603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hou et al. title: Improved plaque assay for human coronaviruses 229E and OC43 link: https://peerj.com/articles/10639 last-modified: 2020-12-21 description: In light of the COVID-19 pandemic, studies that work to understand SARS-CoV-2 are urgently needed. In turn, the less severe human coronaviruses such as HCoV-229E and OC43 are drawing newfound attention. These less severe coronaviruses can be used as a model to facilitate our understanding of the host immune response to coronavirus infection. SARS-CoV-2 must be handled under biosafety level 3 (BSL-3) conditions. Therefore, HCoV-229E and OC43, which can be handled at BSL-2 provide an alternative to SARS-CoV-2 for preclinical screening and designing of antivirals. However, to date, there is no published effective and efficient method to titrate HCoVs other than expensive indirect immunostaining. Here we present an improved approach using an agarose-based conventional plaque assay to titrate HCoV 229E and OC43 with mink lung epithelial cells, Mv1Lu. Our results indicate that titration of HCoV 229E and OC43 with Mv1Lu is consistent and reproducible. The titers produced are also comparable to those produced using human rhabdomyosarcoma (RD) cells. More importantly, Mv1Lu cells display a higher tolerance for cell-cell contact stress, decreased temperature sensitivity, and a faster growth rate. We believe that our improved low-cost plaque assay can serve as an easy tool for researchers conducting HCoV research. creator: Nicole Bracci creator: Han-Chi Pan creator: Caitlin Lehman creator: Kylene Kehn-Hall creator: Shih-Chao Lin uri: https://doi.org/10.7717/peerj.10639 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bracci et al. title: Uncovering the hidden diversity of Mississippian crinoids (Crinoidea, Echinodermata) from Poland link: https://peerj.com/articles/10641 last-modified: 2020-12-21 description: Partial crinoid crowns and aboral cups are reported from the Mississippian of Poland for the first time. Most specimens are partially disarticulated or isolated plates, which prevent identification to genus and species, but regardless these remains indicate a rich diversity of Mississippian crinoids in Poland during the Mississippian, especially during the late Viséan. Lanecrinus? sp. is described from the late Tournaisian of the Dębnik Anticline region. A high crinoid biodiversity occurred during late Viséan of the Holy Cross Mountains, including the camerate crinoids Gilbertsocrinus? sp., Platycrinitidae Indeterminate; one flexible crinoid; and numerous eucladid crinoids, including Cyathocrinites mammillaris (Phillips), three taxa represented by partial cups left in open nomenclature, and numerous additional taxa known only from isolated radial plates, brachial plates, and columnals. To date, the youngest occurrence of Gilbertsocrinus was the early Viséan of the United States, thus the present finding in upper Viséan extends this genus range. Furthermore, the occurrence of Lanecrinus? sp. expands the Western European range of this genus into the Tournaisian. A single partially disarticulated crown, Crinoidea Indeterminate B, is described from the Serpukhovian of the Upper Silesian Coal Basin. In addition, several echinoid test plates and spines are also reported. creator: Mariusz A. Salamon creator: William I. Ausich creator: Tomasz Brachaniec creator: Bartosz J. Płachno creator: Przemysław Gorzelak uri: https://doi.org/10.7717/peerj.10641 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Salamon et al. title: Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes link: https://peerj.com/articles/9859 last-modified: 2020-12-18 description: Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level. creator: Tingting Song creator: Yingyue Shen creator: Qunli Jin creator: Weilin Feng creator: Lijun Fan creator: Weiming Cai uri: https://doi.org/10.7717/peerj.9859 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Song et al. title: Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species link: https://peerj.com/articles/10237 last-modified: 2020-12-18 description: Research on the gut microbiome of host organisms has rapidly advanced with next generation sequencing (NGS) and high-performance computing capabilities. Nonetheless, gut microbiome research has focused on mammalian organisms in laboratory settings, and investigations pertaining to wild fish gut microbiota remain in their infancy. We applied a procedure (available at https://github.com/bngallo1994) for sampling of the fish gut for use in NGS to describe microbial community structure. Our approach allowed for high bacterial OTU diversity coverage (>99.7%, Good’s Coverage) that led to detection of differences in gut microbiota of an invasive (Round Goby) and native (Yellow Bullhead) fish species and collected from the upper St. Lawrence River, an environment where the gut microbiota of fish had not previously been tested. Additionally, results revealed habitat level differences in gut microbiota using two distance metrics (Unifrac, Bray–Curtis) between nearshore littoral and offshore profundal collections of Round Goby. Species and habitat level differences in intestinal microbiota may be of importance in understanding individual and species variation and its importance in regulating fish health and physiology. creator: Benjamin D. Gallo creator: John M. Farrell creator: Brian Leydet uri: https://doi.org/10.7717/peerj.10237 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gallo et al. title: Ischemic infarct detection, localization, and segmentation in noncontrast CT human brain scans: review of automated methods link: https://peerj.com/articles/10444 last-modified: 2020-12-18 description: Noncontrast Computed Tomography (NCCT) of the brain has been the first-line diagnosis for emergency evaluation of acute stroke, so a rapid and automated detection, localization, and/or segmentation of ischemic lesions is of great importance. We provide the state-of-the-art review of methods for automated detection, localization, and/or segmentation of ischemic lesions on NCCT in human brain scans along with their comparison, evaluation, and classification. Twenty-two methods are (1) reviewed and evaluated; (2) grouped into image processing and analysis-based methods (11 methods), brain atlas-based methods (two methods), intensity template-based methods (1 method), Stroke Imaging Marker-based methods (two methods), and Artificial Intelligence-based methods (six methods); and (3) properties of these groups of methods are characterized. A new method classification scheme is proposed as a 2 × 2 matrix with local versus global processing and analysis, and density versus spatial sampling. Future studies are necessary to develop more efficient methods directed toward deep learning methods as well as combining the global methods with a high sampling both in space and density for the merged radiologic and neurologic data. creator: Wieslaw L. Nowinski creator: Jerzy Walecki creator: Gabriela Półtorak-Szymczak creator: Katarzyna Sklinda creator: Bartosz Mruk uri: https://doi.org/10.7717/peerj.10444 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nowinski et al. title: Antimicrobial activity of Streptomyces spp. isolated from Apis dorsata combs against some phytopathogenic bacteria link: https://peerj.com/articles/10512 last-modified: 2020-12-18 description: The aim of this study was to investigate the antimicrobial potential of actinomycetes isolated from combs of the giant honey bee, Apis dorsata. In total, 25 isolates were obtained from three different media and were screened for antimicrobial activity against four plant pathogenic bacteria (Ralstonia solanacearum, Xanthomonas campestris pv. campestris, Xanthomonas oryzae pv. oryzae and Pectobacterium carotovorum). Following screening using a cross-streaking method, three isolates showed the potential to inhibit the growth of plant pathogenic bacteria. Based on a 96-well microtiter assay, the crude extract of DSC3-6 had minimum inhibitory concentration (MIC) values against X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum of 16, 32, 32 and 64 mg L−1, respectively. The crude extract of DGA3-20 had MIC values against X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum of 32, 32, 32 and 64 mg L−1, respectively. The crude extract of DGA8-3 at 32 mgL−1 inhibited the growth of X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum. Based on their 16S rRNA gene sequences, all isolates were identified as members of the genus Streptomyces. The analysis of 16S rRNA gene sequence similarity and of the phylogenetic tree based on the maximum likelihood algorithm showed that isolates DSC3-6, DGA3-20 and DGA8-3 were closely related to Streptomyces ramulosus (99.42%), Streptomyces axinellae (99.70%) and Streptomyces drozdowiczii (99.71%), respectively. This was the first report on antibacterial activity against phytopathogenic bacteria from actinomycetes isolated from the giant honey bee. creator: Yaowanoot Promnuan creator: Saran Promsai creator: Sujinan Meelai uri: https://doi.org/10.7717/peerj.10512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Promnuan et al. title: Peripheral-physiological and neural correlates of the flow experience while playing video games: a comprehensive review link: https://peerj.com/articles/10520 last-modified: 2020-12-18 description: The flow state is defined by intense involvement in an activity with high degrees of concentration and focused attention accompanied by a sense of pleasure. Video games are effective tools for inducing flow, and keeping players in this state is considered to be one of the central goals of game design. Many studies have focused on the underlying physiological and neural mechanisms of flow. Results are inconsistent when describing a unified mechanism underlying this mental state. This paper provides a comprehensive review of the physiological and neural correlates of flow and explains the relationship between the reported physiological and neural markers of the flow experience. Despite the heterogeneous results, it seems possible to establish associations between reported markers and the cognitive and experiential aspects of flow, particularly regarding arousal, attention control, reward processing, automaticity, and self-referential processing. creator: Shiva Khoshnoud creator: Federico Alvarez Igarzábal creator: Marc Wittmann uri: https://doi.org/10.7717/peerj.10520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Khoshnoud et al. title: Archosauriform footprints in the Lower Triassic of Western Alps and their role in understanding the effects of the Permian-Triassic hyperthermal link: https://peerj.com/articles/10522 last-modified: 2020-12-18 description: The most accepted killing model for the Permian-Triassic mass extinction (PTME) postulates that massive volcanic eruption (i.e., the Siberian Traps Large Igneous Province) led to geologically rapid global warming, acid rain and ocean anoxia. On land, habitable zones were drastically reduced, due to the combined effects of heating, drought and acid rains. This hyperthermal had severe effects also on the paleobiogeography of several groups of organisms. Among those, the tetrapods, whose geographical distribution across the end-Permian mass extinction (EPME) was the subject of controversy in a number of recent papers. We here describe and interpret a new Early Triassic (?Olenekian) archosauriform track assemblage from the Gardetta Plateau (Briançonnais, Western Alps, Italy) which, at the Permian-Triassic boundary, was placed at about 11° North. The tracks, both arranged in trackways and documented by single, well-preserved imprints, are assigned to Isochirotherium gardettensis ichnosp. nov., and are here interpreted as produced by a non-archosaurian archosauriform (erytrosuchid?) trackmaker. This new discovery provides further evidence for the presence of archosauriformes at low latitudes during the Early Triassic epoch, supporting a model in which the PTME did not completely vacate low-latitude lands from tetrapods that therefore would have been able to cope with the extreme hot temperatures of Pangaea mainland. creator: Fabio Massimo Petti creator: Heinz Furrer creator: Enrico Collo creator: Edoardo Martinetto creator: Massimo Bernardi creator: Massimo Delfino creator: Marco Romano creator: Michele Piazza uri: https://doi.org/10.7717/peerj.10522 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Petti et al. title: The p53 signaling pathway of the large yellow croaker (Larimichthys crocea) responds to acute cold stress: evidence via spatiotemporal expression analysis of p53, p21, MDM2, IGF-1, Gadd45, Fas, and Akt link: https://peerj.com/articles/10532 last-modified: 2020-12-18 description: The p53 activation is induced by stressors, such as DNA damage, oxidative stress, and activated oncogenes, and can promote cell cycle arrest, cellular senescence, and apoptosis. The large yellow croaker (Larimichthys crocea) is an important warm temperate marine fish in the Chinese aquiculture industry. However, few studies have investigated the role of p53 in the response of L. crocea to environmental stressors. Therefore, the aim of the present study was to assess the spatiotemporal mRNA expression levels of genes involved in the p53 signaling pathway of the large yellow croaker in response to cold stress. The results showed significant changes in the expression levels of p53, p21, MDM2, IGF-1, Gadd45, Fas, and Akt in various tissues of the large yellow croaker in response to cold stress for different times. As compared to the control group, p53 mRNA expression was upregulated in most of the examined tissues at 24 h with the exception of the gill. In the liver, the expression levels of p53 and Fas were significantly decreased at 12 h, while those of p21, MDM2, IGF-1, Gadd45 were dramatically increased. Akt expression was notably changed in response to cold in several tissues. These results suggested that p53 was potentially a key gene in the large yellow croaker response to cold and possibly other environmental stressors. creator: Baoying Qian creator: Xin Qi creator: Yi Bai creator: Yubo Wu uri: https://doi.org/10.7717/peerj.10532 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Qian et al. title: Individual differences show that only some bats can cope with noise-induced masking and distraction link: https://peerj.com/articles/10551 last-modified: 2020-12-18 description: Anthropogenic noise is a widespread pollutant that has received considerable recent attention. While alarming effects on wildlife have been documented, we have limited understanding of the perceptual mechanisms of noise disturbance, which are required to understand potential mitigation measures. Likewise, individual differences in response to noise (especially via perceptual mechanisms) are likely widespread, but lacking in empirical data. Here we use the echolocating bat Phyllostomus discolor, a trained discrimination task, and experimental noise playback to explicitly test perceptual mechanisms of noise disturbance. We demonstrate high individual variability in response to noise treatments and evidence for multiple perceptual mechanisms. Additionally, we highlight that only some individuals were able to cope with noise, while others were not. We tested for changes in echolocation call duration, amplitude, and peak frequency as possible ways of coping with noise. Although all bats strongly increased call amplitude and showed additional minor changes in call duration and frequency, these changes could not explain the differences in coping and non-coping individuals. Our understanding of noise disturbance needs to become more mechanistic and individualistic as research knowledge is transformed into policy changes and conservation action. creator: Dylan G.E. Gomes creator: Holger R. Goerlitz uri: https://doi.org/10.7717/peerj.10551 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gomes and Goerlitz title: Macrel: antimicrobial peptide screening in genomes and metagenomes link: https://peerj.com/articles/10555 last-modified: 2020-12-18 description: MotivationAntimicrobial peptides (AMPs) have the potential to tackle multidrug-resistant pathogens in both clinical and non-clinical contexts. The recent growth in the availability of genomes and metagenomes provides an opportunity for in silico prediction of novel AMP molecules. However, due to the small size of these peptides, standard gene prospection methods cannot be applied in this domain and alternative approaches are necessary. In particular, standard gene prediction methods have low precision for short peptides, and functional classification by homology results in low recall.ResultsHere, we present Macrel (for metagenomic AMP classification and retrieval), which is an end-to-end pipeline for the prospection of high-quality AMP candidates from (meta)genomes. For this, we introduce a novel set of 22 peptide features. These were used to build classifiers which perform similarly to the state-of-the-art in the prediction of both antimicrobial and hemolytic activity of peptides, but with enhanced precision (using standard benchmarks as well as a stricter testing regime). We demonstrate that Macrel recovers high-quality AMP candidates using realistic simulations and real data.AvailabilityMacrel is implemented in Python 3. It is available as open source at https://github.com/BigDataBiology/macrel and through bioconda. Classification of peptides or prediction of AMPs in contigs can also be performed on the webserver: https://big-data-biology.org/software/macrel. creator: Célio Dias Santos-Júnior creator: Shaojun Pan creator: Xing-Ming Zhao creator: Luis Pedro Coelho uri: https://doi.org/10.7717/peerj.10555 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Santos-Júnior et al. title: Quality of urban parks in the perception of city residents with mobility difficulties link: https://peerj.com/articles/10570 last-modified: 2020-12-18 description: Urban parks should be inclusive for all. Availability and accessibility of urban parks determine the quality of life in cities. The importance of access increases for residents with limited mobility who, facing obstacles due to inadequate adjustment of the surrounding physical space, are exposed to social exclusion. Five groups of respondents completed a survey questionnaire revealing their attitudes towards green areas and indicating barriers to parks’ accessibility. The groups were designed to include blind and vision impaired people, those who use a wheelchair, have a physical disability of any kind, their carers/assistants and parents pushing strollers. The results revealed more similarities than differences among the five groups (the differences included preferences towards the neighbourhood and destination parks, physical barriers in parks, as well as using assistive technology devices and mobile assistive applications). Overall, city residents with mobility difficulties find those green public spaces as an important element of their life quality. creator: Magdalena Błaszczyk creator: Marzena Suchocka creator: Magdalena Wojnowska-Heciak creator: Magdalena Muszyńska uri: https://doi.org/10.7717/peerj.10570 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Błaszczyk et al. title: Optimizing the amount of pig manure in the vermicomposting of spent mushroom (Lentinula) substrate link: https://peerj.com/articles/10584 last-modified: 2020-12-18 description: BackgroundThe mushroom industry produces a large amount of spent mushroom substrate (SMS), which requires a large geographical footprint and causes pollution.MethodsWe sought to optimize the C:N ratio of the initial feedstock used in vermicomposting of SMS by adding pig manure additions. We applied five treatments to the initial feedstock (S0, S1, S2, S3, and S4) with different C:N ratio of approximately 35, 30, 25, 20, and 15, respectively.ResultsOur results showed that lignin and cellulose in SMS were degraded after 56 days vermicomposting, especially in S2 (77.05% and 45.29%, respectively) and S3 (65.05% and 48.37%, respectively) treatments. We observed the degradation of the fibrous structure in SMS using pig manure treatments after vermicomposting by microscope and scanning electron microscope. Cellulase and polyphenol oxidase (PPO) were enhanced in pig manure treatments during vermicomposting, especially in the S2 and S3 treatments. The biomass of earthworms in the S2 treatments was at its highest level among all treatments at 28 to 56 days. The high level of PPO activity in the S2 treatment may protect cellulase and earthworms against the aromatic toxicity that is a byproduct of lignin degradation, particularly at 28 to 56 days of vermicomposting. Conclusively, it indicated that the C/N ratio of 25 in the S2 treatment was the optimal for SMS vermicomposting with the addition of pig manure. Our results provide a positive application for the recycling of both SMS and pig manure. creator: Yajing Shi creator: Zhenyu Wang creator: Yurong Wang uri: https://doi.org/10.7717/peerj.10584 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shi et al. title: Previous oil exposure alters Gulf Killifish Fundulus grandis oil avoidance behavior link: https://peerj.com/articles/10587 last-modified: 2020-12-18 description: Oil spills threaten the structure and function of ecological communities. The Deepwater Horizon spill was predicted to have catastrophic consequences for nearshore fishes, but field studies indicate resilience in populations and communities. Previous research indicates many marsh fishes exhibit avoidance of oil contaminated areas, representing one potential mechanism for this resilience. Here, we test whether prior oil exposure of Gulf killifish Fundulus grandis alters this avoidance response. Using choice tests between unoiled and oiled sediments at one of three randomized concentrations (low: 0.1 L oil m−2, medium: 0.5 L oil m−2, or high: 3.0 L oil m−2), we found that, even at low prior exposure levels, killifish lose recognition of oiled sediments compared to control, unexposed fish. Preference for unoiled sediments was absent across all oil concentrations after oil exposure, and some evidence for preference of oiled sediments at high exposure was demonstrated. These results highlight the lack of response to toxic environments in exposed individuals, indicating altered behavior despite organism survival. Future research should document additional sublethal consequences that affect ecosystem and food web functioning. creator: Charles W. Martin creator: Ashley M. McDonald creator: Guillaume Rieucau creator: Brian J. Roberts uri: https://doi.org/10.7717/peerj.10587 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Martin et al. title: Time of night and moonlight structure vertical space use by insectivorous bats in a Neotropical rainforest: an acoustic monitoring study link: https://peerj.com/articles/10591 last-modified: 2020-12-18 description: BackgroundPrevious research has shown diverse vertical space use by various taxa, highlighting the importance of forest vertical structure. Yet, we know little about vertical space use of tropical forests, and we often fail to explore how this three-dimensional space use changes over time.MethodsHere we use canopy tower systems in French Guiana and passive acoustic monitoring to measure Neotropical bat activity above and below the forest canopy throughout nine nights. We use a Bayesian generalized linear mixed effect model and kernel density estimates to demonstrate patterns in space-use over time.ResultsWe found that different bats use both canopy and understory space differently and that these patterns change throughout the night. Overall, bats were more active above the canopy (including Cormura brevirostris, Molossus molossus, Peropteryx kappleri and Peropteryx macrotis), but multiple species or acoustic complexes (when species identification was impossible) were more active in the understory (such as Centronycteris maximiliani, Myotis riparius, Pteronotus alitonus and Pteronotus rubiginosus). We also found that most bats showed temporally-changing preferences in hourly activity. Some species were less active (e.g., P. kappleri and P. macrotis), whereas others were more active (Pteronotus gymnonotus, C. brevirostris, and M. molossus) on nights with higher moon illuminance.DiscussionHere we show that Neotropical bats use habitat above the forest canopy and within the forest understory differently throughout the night. While bats generally were more active above the forest canopy, we show that individual groups of bats use space differently over the course of a night, and some prefer the understory. This work highlights the need to consider diel cycles in studies of space use, as animals use different habitats during different periods of the day. creator: Dylan G.E. Gomes creator: Giulliana Appel creator: Jesse R. Barber uri: https://doi.org/10.7717/peerj.10591 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gomes et al. title: Sesamoids in Caudata and Gymnophiona (Lissamphibia): absences and evidence link: https://peerj.com/articles/10595 last-modified: 2020-12-18 description: An integrative definition of sesamoid bones has been recently proposed, highlighting their relationship with tendons and ligaments, their genetic origin, the influence of epigenetic stimuli on their development, and their variable tissue composition. Sesamoid bones occur mainly associated with a large number of mobile joints in vertebrates, most commonly in the postcranium. Here, we present a survey of the distribution pattern of sesamoids in 256 taxa of Caudata and Gymnophiona and 24 taxa of temnospondyls and lepospondyls, based on dissections, high-resolution X-ray computed tomography from digital databases and literature data. These groups have a pivotal role in the interpretation of the evolution of sesamoids in Lissamphibia and tetrapods in general. Our main goals were: (1) to contribute to the knowledge of the comparative anatomy of sesamoids in Lissamphibia; (2) to assess the evolutionary history of selected sesamoids. We formally studied the evolution of the observed sesamoids by optimizing them in the most accepted phylogeny of the group. We identified only three bony or cartilaginous sesamoids in Caudata: the mandibular sesamoid, which is adjacent to the jaw articulation; one located on the mandibular symphysis; and one located in the posterior end of the maxilla. We did not observe any cartilaginous or osseous sesamoid in Gymnophiona. Mapping analyses of the sesamoid dataset of urodeles onto the phylogeny revealed that the very conspicuous sesamoid in the mandibular symphysis of Necturus beyeri and Amphiuma tridactylum is an independent acquisition of these taxa. On the contrary, the sesamoid located between the maxilla and the lower jaw is a new synapomorphy that supports the node of Hydromantes platycephalus and Karsenia coreana. The absence of a mandibular sesamoid is plesiomorphic to Caudata, whereas it is convergent in seven different families. The absence of postcranial sesamoids in salamanders might reveal a paedomorphic pattern that would be visible in their limb joints. creator: María Laura Ponssa creator: Virginia Abdala uri: https://doi.org/10.7717/peerj.10595 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ponssa and Abdala title: Utilizing sponge spicules in taxonomic, ecological and environmental reconstructions: a review link: https://peerj.com/articles/10601 last-modified: 2020-12-18 description: Most sponges produce skeletons formed by spicules, structural elements that develop in a wide variety of sizes and tridimensional shapes. The morphologies of spicules are often unique to clade- or even species-level taxa which makes them particularly useful in taxonomic assignments. When dead sponge bodies disintegrate, spicules become incorporated into sediments and sometimes accumulate into enormous agglomerations called spicule mats or beds, or fossilize to form special type of rocks called the spiculites. The record of fossil and subfossil sponge spicules is extraordinarily rich and often serves as a basis for far-reaching reconstructions of sponge communities, though spicules are also bearers of significant ecological and environmental information. Specific requirements and preferences of sponges can be used to interpret the environment in which they lived, and reconstruct oscillations in water depths, pH, temperatures, and other parameters, providing snapshots of past climate conditions. In turn, the silicon isotope compositions in spicules (δ30Si) are being increasingly often used to estimate the level of silicic acid in the marine settings throughout the geological history, which enables to reconstruct the past silica cycle and ocean circulation. This contribution provides a review of the use of sponge spicules in reconstructions of sponge communities, their ecology, and environments, and aims to detect the pertinent gaps in their utilization. Even though spicules are well known for their significance as bearers of taxonomic, ecological, and environmental data, their potential remains to be fully exploited. creator: Magdalena Łukowiak uri: https://doi.org/10.7717/peerj.10601 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Łukowiak title: Mutational spectra of SARS-CoV-2 isolated from animals link: https://peerj.com/articles/10609 last-modified: 2020-12-18 description: Coronaviruses are ubiquitous and infect a wide spectrum of animals and humans. The newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a worldwide pandemic. To address the role that animals may play in the evolution of SARS-CoV-2, the full genome sequences of SARS-CoV-2 isolated from animals were compared with SARS-CoV-2 human isolates from the same clade and geographic region. Phylogenetic analysis of SARS-CoV-2 isolated from the cat, dog, mink, mouse, and tiger revealed a close relationship with SARS-CoV-2 human isolates from the same clade and geographic region with sequence identities of 99.94–99.99%. The deduced amino acid sequence of spike (S) protein revealed the presence of a furin cleavage site (682RRAR▾685), which did not differ among all SARS-CoV-2 isolates from animals and humans. SARS-CoV-2 isolates from minks exhibited two amino acid substitutions (G261D, A262S) in the N-terminal domain of S protein and four (L452M, Y453F, F486L, N501T) in the receptor-binding motif (RBM). In the mouse, the S protein had two amino acid substitutions, one in the RBM (Q498H) and the other (N969S) in the heptad repeat 1. SARS-CoV-2 isolated from minks furtherly exhibited three unique amino acid substitutions in the nucleocapsid (N)protein. In the cat, two unique amino acid substitutions were discovered in the N (T247I) and matrix (T175M) proteins. Additionally, SARS-CoV-2 isolated from minks possessed sixteen, four, and two unique amino acid substitutions in the open reading frame 1ab (ORF1ab), ORF3a, and ORF6, respectively. Dog and cat SARS-CoV-2 isolates showed one and seven unique amino acid substitutions in ORF1ab, respectively. Further studies may be necessary to determine the pathogenic significance of these amino acid substitutions to understand the molecular epidemiology and evolution of SARS-CoV-2. creator: Ahmed Elaswad creator: Mohamed Fawzy creator: Shereen Basiouni creator: Awad A. Shehata uri: https://doi.org/10.7717/peerj.10609 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Elaswad et al. title: Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians link: https://peerj.com/articles/10611 last-modified: 2020-12-18 description: BackgroundIn 2020, to limit the spread of Coronavirus (COVID-19), many countries, including Italy, have issued a lengthy quarantine period for the entire population. For this reason lifestyle has changed, bringing inevitable repercussions to the Quality of Life (QoL). The present study aims to identify which psychosocial variables predict behaviors capable of affecting the QoL during the lockdown period, potentially highlighting factors that might promote well-being and health in the Italian population during the epidemic.MethodsBetween 27 April 2020 and 11 May 2020, we administered a web-survey to a sample of young Italian people (age M = 21.2; SD = 3.5; female = 57.7% of the sample). Employing variance-based structural equation modeling, we attempted to identify whether social connectedness, social support, and loneliness were variables predictive of the QoL of young Italians. We also sought to identify specific psychological factors, such as symbolic threat, realistic threat, and the threat from potentially contaminated objects, was correlated to COVID-19 fear and whether engaging in particular behaviors was likely to improve the QoL.ResultsOur results suggest that social connectedness and loneliness are significant predictors of QoL, while social support did not have a significant effect on QoL. Furthermore, we observed that symbolic and realistic threats and the threat from potentially contaminated objects are significant and positive predictors of COVID-19 fear. Moreover, COVID-19 fear had significant and positive relationships with the carrying out of specific behaviors, such as creative activities during the isolation period and that this related to affirming individuals’ country-specific identity. Finally, COVID-19 fear is a significant predictor of behavioral factors related to the adherence to public health advice in line with national guidance regarding the containment of COVID-19; this factor, however, did not correlate with QoL.ConclusionOur results suggest the importance of social context and psychological factors to help devise intervention strategies to improve the QoL during lockdown from epidemic events and, in particular, support the importance of promoting social communication and accurate information about the transmission of the virus. creator: Anna Lardone creator: Pierpaolo Sorrentino creator: Francesco Giancamilli creator: Tommaso Palombi creator: Trevor Simper creator: Laura Mandolesi creator: Fabio Lucidi creator: Andrea Chirico creator: Federica Galli uri: https://doi.org/10.7717/peerj.10611 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lardone et al. title: Optimal voluntary and mandatory insect repellent usage and emigration strategies to control the chikungunya outbreak on Reunion Island link: https://peerj.com/articles/10151 last-modified: 2020-12-17 description: In 2005, a chikungunya virus outbreak devastated the tropical island of Reunion, infecting a third of the total population. Motivated by the Reunion Island case study, we investigate the theoretic potential for two intervention measures under both voluntary and mandatory protocols to control a vector-borne disease when there is risk of the disease becoming endemic. The first measure uses insect repellent to prevent mosquito bites, while the second involves emigrating to the neighboring Mauritius Island to avoid infection. There is a threshold on the cost of using repellent above which both voluntary and mandatory regimes find it optimal to forgo usage. Below that threshold, mandatory usage protocols will eradicate the disease; however, voluntary adoption leaves the disease at a small endemic level. Emigrating from the island to avoid infection results in a tragedy-of-the-commons effect: while being potentially beneficial to specific susceptible individuals, the remaining islanders paradoxically face a higher risk of infection. Mandated relocation of susceptible individuals away from the epidemic is viable only if the cost of this relocation is several magnitudes lower than the cost of infection. Since this assumption is unlikely to hold for chikungunya, it is optimal to discourage such emigration for the benefit of the entire population. An underlying assumption about the conservation of human-vector encounter rates in mosquito biting behavior informs our conclusions and may warrant additional experimental verification. creator: Sylvia R.M. Klein creator: Alex O. Foster creator: David A. Feagins creator: Jonathan T. Rowell creator: Igor V. Erovenko uri: https://doi.org/10.7717/peerj.10151 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Klein et al. title: A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment link: https://peerj.com/articles/10338 last-modified: 2020-12-17 description: BackgroundThe importance of the inland fisheries sector in food security as a provider of much-needed protein and income supplier has been highlighted. This is especially the case in poor rural communities in developing countries. Inland capture fisheries in Thailand are in place nationwide in rivers, lakes, swamps and reservoirs. The clown featherback (Chitala ornata) is popularly consumed and is an economically important fish in Thailand which is often used in food products such as fish balls and fish cakes. Along with other fish species, the clown featherback is one of fish of inland fisheries at Phayao Lake. Recent fish surveys from 2016-2018 at Phayao Lake using netting and electrofishing found that the number of clown featherback have been reducing since 2016 and could not be detected at all by 2018. This is despite the fact that there are still reports of their presence in the lake from locals.MethodsWe developed an eDNA-based method for detection of the clown featherback in Phayao Lake as an alternative tool. Water samples were collected in three different sampling months (February, June and September) at six sites located in the lake. Species-specific primers and the probe were designed to amplify a 183 bp fragment of the cytB region of the clown featherback.ResultseDNA of the clown featherback can be detected in all different sampling months and sites. Concentration of the clown featherback found in Prayao Lake showed no difference over sampling month but between collecting sites. This proves that eDNA based survey is a sensitive and useful tool for monitoring and surveying the clown featherback at any time of the year. creator: Maslin Osathanunkul creator: Toshifumi Minamoto uri: https://doi.org/10.7717/peerj.10338 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Osathanunkul and Minamoto title: The effect of decay and lexical uncertainty on processing long-distance dependencies in reading link: https://peerj.com/articles/10438 last-modified: 2020-12-17 description: To make sense of a sentence, a reader must keep track of dependent relationships between words, such as between a verb and its particle (e.g. turn the music down). In languages such as German, verb-particle dependencies often span long distances, with the particle only appearing at the end of the clause. This means that it may be necessary to process a large amount of intervening sentence material before the full verb of the sentence is known. To facilitate processing, previous studies have shown that readers can preactivate the lexical information of neighbouring upcoming words, but less is known about whether such preactivation can be sustained over longer distances. We asked the question, do readers preactivate lexical information about long-distance verb particles? In one self-paced reading and one eye tracking experiment, we delayed the appearance of an obligatory verb particle that varied only in the predictability of its lexical identity. We additionally manipulated the length of the delay in order to test two contrasting accounts of dependency processing: that increased distance between dependent elements may sharpen expectation of the distant word and facilitate its processing (an antilocality effect), or that it may slow processing via temporal activation decay (a locality effect). We isolated decay by delaying the particle with a neutral noun modifier containing no information about the identity of the upcoming particle, and no known sources of interference or working memory load. Under the assumption that readers would preactivate the lexical representations of plausible verb particles, we hypothesised that a smaller number of plausible particles would lead to stronger preactivation of each particle, and thus higher predictability of the target. This in turn should have made predictable target particles more resistant to the effects of decay than less predictable target particles. The eye tracking experiment provided evidence that higher predictability did facilitate reading times, but found evidence against any effect of decay or its interaction with predictability. The self-paced reading study provided evidence against any effect of predictability or temporal decay, or their interaction. In sum, we provide evidence from eye movements that readers preactivate long-distance lexical content and that adding neutral sentence information does not induce detectable decay of this activation. The findings are consistent with accounts suggesting that delaying dependency resolution may only affect processing if the intervening information either confirms expectations or adds to working memory load, and that temporal activation decay alone may not be a major predictor of processing time. creator: Kate Stone creator: Titus von der Malsburg creator: Shravan Vasishth uri: https://doi.org/10.7717/peerj.10438 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Stone et al. title: Digitizing abdominal palpation with a pressure measurement and positioning device link: https://peerj.com/articles/10511 last-modified: 2020-12-17 description: An abdominal physical examination is one of the most important tools in evaluating patients with acute abdominal pain. We focused on palpation, in which assessment is made according to the patient’s response and force feedback. Since palpation is performed manually by the examiner, the uniformity of force and location is difficult to achieve during examinations. We propose an integrated system to quantify palpation pressure and location. A force sensor continuously collects pressure data, while a camera locates the precise position of contact. The system recorded, displayed average and maximum pressure by creating a pressure/time curve for computer-aided diagnosis. Compared with previous work on pressure sensors of quantifying abdominal palpation, our proposed system is the integrated approach to measure palpation force and track the corresponding position at the same time, for further diagnosis. In addition, we only make use of a sensing device and a general web camera, rather than commercial algometry and infrared cameras used in the previous work. Based on our clinical trials, the statistics of palpation pressure values and the corresponding findings are also reported. We performed abdominal palpation with our system for twenty-three healthy participants, including fourteen males and nine females. We applied two grades of force on the abdomen (light and deep) by four-quadrant and nine-region schemes, record the value of pressure and location. In the four-quadrant scheme, the average pressures of abdominal palpation with light and deep force levels were 0.506(N) and 0.552(N), respectively. In the nine-region scheme, the average pressures were 0.496(N) and 0.577(N), respectively. Two episodes of contact dermal reaction were identified. According to our experiment statistics, there is no significant difference in the force level between the four-quadrant and nine-region scheme. Our results have the potential to be used as a reference guide while designing digital abdominal palpation devices. creator: Jia-Lien Hsu creator: Chia-Hui Lee creator: Chung-Ho Hsieh uri: https://doi.org/10.7717/peerj.10511 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hsu et al. title: Distribution and species diversity of the floating green macroalgae and micro-propagules in the Subei Shoal, southwestern Yellow Sea link: https://peerj.com/articles/10538 last-modified: 2020-12-17 description: Massive floating green macroalgae have formed harmful green tides in the Yellow Sea since 2007. To study the early development and the associated environmental factors for the green tide, a field survey was carried out in the Subei Shoal, southwestern Yellow Sea. Multiple species were identified in both floating green macroalgae and micro-propagules , while their abundances showed distinct spatial variations. The floating macroalgal biomass was widespread in the northern Subei Shoal and most abundant at 34°N. Ulva prolifera dominated (91.2% in average) the floating macroalgae, and the majority (88.5%) of U. prolifera was the ‘floating type’. In comparison, the micro-propagules were most abundant around the aquaculture rafts, and decreased significantly with the distance to the rafts. The dominant species of micro-propagules was U. linza (48.5%), followed by U. prolifera (35.1%). Their distinct distribution patterns and species diversity suggested little direct contribution of micro-propagules for the floating macroalgae. The spatial variation of the floating macroalgae was probably a combined result from the biomass source and environmental factors, while the abundance of micro-propagules was closely associated with the rafts. A positive correlation between the floating macroalgae and DO was observed and suggested active photosynthesis of the initial biomass in Subei Shoal. This study revealed specific distributional pattern and relationships among the floating macroalgae, micro-propagules and the environmental factors in the source region, which helps understanding the early blooming dynamics of the green tides in Yellow Sea. creator: Xiaoxiang Miao creator: Jie Xiao creator: Qinzeng Xu creator: Shiliang Fan creator: Zongling Wang creator: Xiao Wang creator: Xuelei Zhang uri: https://doi.org/10.7717/peerj.10538 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Miao et al. title: Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery link: https://peerj.com/articles/10554 last-modified: 2020-12-17 description: BackgroundPanulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region.MethodsThis study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus.ResultsUsing a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5′ ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3′ ETS (287 bp). A total of 1,281 SSRs were identified. creator: J. Antonio Baeza uri: https://doi.org/10.7717/peerj.10554 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Baeza title: bmd: an R package for benchmark dose estimation link: https://peerj.com/articles/10557 last-modified: 2020-12-17 description: The benchmark dose (BMD) methodology is used to derive a hazard characterization measure for risk assessment in toxicology or ecotoxicology. The present paper’s objective is to introduce the R extension package bmd, which facilitates the estimation of BMD and the benchmark dose lower limit for a wide range of dose-response models via the popular package drc. It allows using the most current statistical methods for BMD estimation, including model averaging. The package bmd can be used for BMD estimation for binomial, continuous, and count data in a simple set up or from complex hierarchical designs and is introduced using four examples. While there are other stand-alone software solutions available to estimate BMDs, the package bmd facilitates easy estimation within the established and flexible statistical environment R. It allows the rapid implementation of available, novel, and future statistical methods and the integration of other statistical analyses. creator: Signe M. Jensen creator: Felix M. Kluxen creator: Jens C. Streibig creator: Nina Cedergreen creator: Christian Ritz uri: https://doi.org/10.7717/peerj.10557 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jensen et al. title: Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas link: https://peerj.com/articles/10646 last-modified: 2020-12-17 description: Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism. creator: Timothy P. Driscoll creator: Victoria I. Verhoeve creator: Cassia Brockway creator: Darin L. Shrewsberry creator: Mariah Plumer creator: Spiridon E. Sevdalis creator: John F. Beckmann creator: Laura M. Krueger creator: Kevin R. Macaluso creator: Abdu F. Azad creator: Joseph J. Gillespie uri: https://doi.org/10.7717/peerj.10646 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Driscoll et al. title: Observing animals and humans: dogs target their gaze to the biological information in natural scenes link: https://peerj.com/articles/10341 last-modified: 2020-12-16 description: BackgroundThis study examines how dogs observe images of natural scenes containing living creatures (wild animals, dogs and humans) recorded with eye gaze tracking. Because dogs have had limited exposure to wild animals in their lives, we also consider the natural novelty of the wild animal images for the dogs.MethodsThe eye gaze of dogs was recorded while they viewed natural images containing dogs, humans, and wild animals. Three categories of images were used: naturalistic landscape images containing single humans or animals, full body images containing a single human or an animal, and full body images containing a pair of humans or animals. The gazing behavior of two dog populations, family and kennel dogs, were compared.ResultsAs a main effect, dogs gazed at living creatures (object areas) longer than the background areas of the images; heads longer than bodies; heads longer than background areas; and bodies longer than background areas. Dogs gazed less at the object areas vs. the background in landscape images than in the other image categories. Both dog groups also gazed wild animal heads longer than human or dog heads in the images. When viewing single animal and human images, family dogs focused their gaze very prominently on the head areas, but in images containing a pair of animals or humans, they gazed more at the body than the head areas. In kennel dogs, the difference in gazing times of the head and body areas within single or paired images failed to reach significance.DiscussionDogs focused their gaze on living creatures in all image categories, also detecting them in the natural landscape images. Generally, they also gazed at the biologically informative areas of the images, such as the head, which supports the importance of the head/face area for dogs in obtaining social information. The natural novelty of the species represented in the images as well as the image category affected the gazing behavior of dogs. Furthermore, differences in the gazing strategy between family and kennel dogs was obtained, suggesting an influence of different social living environments and life experiences. creator: Heini Törnqvist creator: Sanni Somppi creator: Miiamaaria V. Kujala creator: Outi Vainio uri: https://doi.org/10.7717/peerj.10341 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Törnqvist et al. title: Transcriptome profiling reveals Silibinin dose-dependent response network in non-small lung cancer cells link: https://peerj.com/articles/10373 last-modified: 2020-12-16 description: Silibinin (SIL), a natural flavonolignan from the milk thistle (Silybum marianum), is known to exhibit remarkable hepatoprotective, antineoplastic and EMT inhibiting effects in different cancer cells by targeting multiple molecular targets and pathways. However, the predominant majority of previous studies investigated effects of this phytocompound in a one particular cell line. Here, we carry out a systematic analysis of dose-dependent viability response to SIL in five non-small cell lung cancer (NSCLC) lines that gradually differ with respect to their intrinsic EMT stage. By correlating gene expression profiles of NSCLC cell lines with the pattern of their SIL IC50 response, a group of cell cycle, survival and stress responsive genes, including some prominent targets of STAT3 (BIRC5, FOXM1, BRCA1), was identified. The relevancy of these computationally selected genes to SIL viability response of NSCLC cells was confirmed by the transient knockdown test. In contrast to other EMT-inhibiting compounds, no correlation between the SIL IC50 and the intrinsic EMT stage of NSCLC cells was observed. Our experimental results show that SIL viability response of differently constituted NSCLC cells is linked to a subnetwork of tightly interconnected genes whose transcriptomic pattern can be used as a benchmark for assessment of individual SIL sensitivity instead of the conventional EMT signature. Insights gained in this study pave the way for optimization of customized adjuvant therapy of malignancies using Silibinin. creator: Jagan Mohan Kaipa creator: Vytaute Starkuviene creator: Holger Erfle creator: Roland Eils creator: Evgeny Gladilin uri: https://doi.org/10.7717/peerj.10373 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kaipa et al. title: Muscle strength and inflammatory response to the training load in rowers link: https://peerj.com/articles/10355 last-modified: 2020-12-16 description: BackgroundRegular exercise leads to changes in muscle metabolism. The consequence of this is the adaptation to higher training loads.The aim of this study was to evaluate biomechanical and biochemical parameters describing the functions of skeletal muscles in periods when changes in training forms were introduced.MethodsSeventeen male sweep-oar rowers, members of the Polish national rowing team, participated. The study was carried out at the beginning and at the end of the preparatory period. In the first and second examination measurements of torques of selected muscle groups and blood biochemical analysis were performed.ResultsThere was observed a statistically significant decrease in the relative global force of the right lower limb between both terms of examination. A statistically significant increase in maximum torque was found for torso flexors. In the case of muscles responsible for torso rotation, a statistically significant decrease in the torque values of right torso rotators was observed. A significant difference was found with respect to creatine kinase activity, total testosterone concentration, total testosterone to cortisol ratio and total phenolics concentration (p < 0.05).ConclusionThe study shows that the rowers’ training should be more focused on building the strength of lower limbs to prevent the overload of lumbar spine and that the amount of force developed may be significantly affected by the antioxidant potential of rowers. creator: Tomasz Podgórski creator: Alicja Nowak creator: Katarzyna Domaszewska creator: Jacek Mączyński creator: Magdalena Jabłońska creator: Jarosław Janowski creator: Małgorzata B. Ogurkowska uri: https://doi.org/10.7717/peerj.10355 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Podgórski et al. title: Dysregulated levels of glycogen synthase kinase-3β (GSK-3β) and miR-135 in peripheral blood samples of cases with nephrotic syndrome link: https://peerj.com/articles/10377 last-modified: 2020-12-16 description: BackgroundGlycogen synthase kinase-3 (GSK-3β) is a serine/threonine kinase with multifunctions in various physiological procedures. Aberrant level of GSK-3β in kidney cells has a harmful role in podocyte injury.MethodsIn this article, the expression levels of GSK-3β and one of its upstream regulators, miR-135a-5p, were measured in peripheral blood mononuclear cells (PBMCs) of cases with the most common types of nephrotic syndrome (NS); focal segmental glomerulosclerosis (FSGS) and membranous glomerulonephritis (MGN). In so doing, fifty-two cases along with twenty-four healthy controls were included based on the strict criteria.ResultsLevels of GSK-3β mRNA and miR-135 were measured with quantitative real-time PCR. There were statistically significant increases in GSK-3β expression level in NS (P = 0.001), MGN (P = 0.002), and FSGS (P = 0.015) groups compared to the control group. Dysregulated levels of miR-135a-5p in PBMCs was not significant between the studied groups. Moreover, a significant decrease was observed in the expression level of miR-135a-5p in the plasma of patients with NS (P = 0.020), MGN (P = 0.040), and FSGS (P = 0.046) compared to the control group. ROC curve analysis approved a diagnostic power of GSK-3β in discriminating patients from healthy controls (AUC: 0.72, P = 0.002) with high sensitivity and specificity.ConclusionsDysregulated levels of GSK-3β and its regulator miR-135a may participate in the pathogenesis of NS with different etiology. Therefore, more research is needed for understanding the relationship between them. creator: Mohammadreza Ardalan creator: Seyyedeh Mina Hejazian creator: Hassan Fazlazar Sharabiyani creator: Farahnoosh Farnood creator: Amirhossein Ghafari Aghdam creator: Milad Bastami creator: Elham Ahmadian creator: Sepideh Zununi Vahed creator: Magali Cucchiarini uri: https://doi.org/10.7717/peerj.10377 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Ardalan et al. title: Long-term administration of vitamin B12 and adenosine triphosphate for idiopathic sudden sensorineural hearing loss: a retrospective study link: https://peerj.com/articles/10406 last-modified: 2020-12-16 description: BackgroundIn idiopathic sudden sensorineural hearing loss (ISSNHL), the relationship between the administration duration of vitamin B12 (vit B12) with adenosine triphosphate (ATP) and their therapeutic effect is not fully understood.ObjectiveTo investigate the therapeutic effect of long-term 16 (≥weeks) administration of vit B12 with ATP on the prognosis of ISSNHL patients and compare it with those of short-term (<8 weeks) and middle-term (≥8 weeks, <16 weeks) administration.MethodsWe retrospectively reviewed the medical records of 117 patients with ISSNHL treated between 2015 and 2018.ResultsThe overall recovery rate was 32.5%. Initial higher hearing threshold and initial higher grade of hearing loss (HL) were associated with a poor prognosis. However, the administration duration of vit B12 and ATP did not influence the overall hearing improvement. With regard to the time course of hearing recovery, there was no significant difference in hearing recovery among the long-, middle-, and short-term administration groups until 16 weeks after treatment. However, at 16–24 weeks after initial treatment, the short-term administration group exhibited significantly lower hearing recovery than did the long-term administration groups.ConclusionsThe administration duration of vit B12 and ATP did not influence the overall hearing prognosis in ISSNHL, but long-term administration of vit B12 and ATP helped prevent the progression of HL after ISSNHL. Our results suggest that long-term administration of vit B12 and ATP is not necessarily required to treat ISSNHL patients, except for slowly progressing HL in the affected ears. creator: Takaomi Kurioka creator: Hajime Sano creator: Shogo Furuki creator: Taku Yamashita uri: https://doi.org/10.7717/peerj.10406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kurioka et al. title: Characterization of DNA methylation in Malawian Mycobacterium tuberculosis clinical isolates link: https://peerj.com/articles/10432 last-modified: 2020-12-16 description: BackgroundAlthough Mycobacterium tuberculosis (Mtb) strains exhibit genomic homology of >99%, there is considerable variation in the phenotype. The underlying mechanisms of phenotypic heterogeneity in Mtb are not well understood but epigenetic variation is thought to contribute. At present the methylome of Mtb has not been completely characterized.MethodsWe completed methylomes of 18 Mycobacterium tuberculosis (Mtb) clinical isolates from Malawi representing the largest number of Mtb genomes to be completed in a single study using Single Molecule Real Time (SMRT) sequencing to date.ResultsWe replicate and confirm four methylation disrupting mutations in 4 lineages of Mtb. For the first time we report complete loss of methylation courtesy of C758T (S253L) mutation in the MamB gene of Indo-oceanic lineage of Mtb. Additionally, we report a novel missense mutation G454A (G152S) in the MamA gene of the Euro-American lineage which could potentially be attributed to total disruption of methylation in the CCCAG motif but partial loss in a partner motif. Through a genomic and methylome comparative analysis with a global sample of sixteen, we report previously unknown mutations affecting the pks15/1 locus in L6 isolates. We confirm that methylation in Mtb is lineage specific although some unresolved issues still remain. creator: Victor Ndhlovu creator: Anmol Kiran creator: Derek J. Sloan creator: Wilson Mandala creator: Marriott Nliwasa creator: Dean B. Everett creator: Benjamin Kumwenda creator: Mphatso Mwapasa creator: Konstantina Kontogianni creator: Mercy Kamdolozi creator: Elizabeth Corbett creator: Maxine Caws creator: Gerry Davies uri: https://doi.org/10.7717/peerj.10432 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ndhlovu et al. title: Urinary MMP-9/UCr association with albumin concentration and albumin-creatinine-ratio in Mexican patients with type 2 diabetes mellitus link: https://peerj.com/articles/10474 last-modified: 2020-12-16 description: BackgroundChronic kidney disease is one of the most common complications of type 2 diabetes mellitus (T2DM), causing an increased risk of cardiovascular morbidity and mortality. Matrix metalloproteinase (MMP) activity has been proposed as useful biomarker for diabetic renal and vascular complications.MethodsA cross-sectional study was conducted among T2DM patients who attended a public secondary hospital in Mexico. We performed clinical, biochemical, and microbiological assessments, as well chronic kidney disease diagnosis according to the KDIGO guideline. Urinary MMP-9 was quantified by ELISA and adjusted using urinary creatinine (UCr).ResultsA total of 111 patients were included. Most participants were women (66%). Mean age was 61 ± 10 years and median T2DM duration was estimated at 11 years. Through multivariate analysis, MMP-9/UCr was found to be associated with albumin concentration and albumin to creatinine ratio.DiscussionValidation of non-invasive biomarkers of chronic kidney disease among T2DM patients is necessary. Here, we demonstrate MMP-9/UCr as a potential biomarker of albumin concentration and albumin to creatinine ratio in Mexican patients with T2DM. creator: Víctor Gildardo Arcos-Sacramento creator: Clara Luz Sampieri creator: Víctor Hugo Sandoval-Lozano creator: Rubén Arturo Orozco-Ortega creator: Mariel Alejandra Acuña-Hernández creator: Jaime Morales-Romero creator: Magda Elena Hernández-Hernández creator: Arturo Rodríguez-Hernández uri: https://doi.org/10.7717/peerj.10474 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Arcos-Sacramento et al. title: Combination of circulating miR-145-5p/miR-191-5p as biomarker for breast cancer detection link: https://peerj.com/articles/10494 last-modified: 2020-12-16 description: BackgroundBreast cancer (BC) is the most common cancer among women worldwide. At present, there is a need to search for new, accurate, reliable, minimally invasive and cheap biomarkers in addition to existing methods for the diagnosis and prognosis of BC. The main goal of this study was to test the diagnostic value of six circulating miRNAs in Kazakh women.Materials and methodsTaqMan-based miRNA profiling was conducted using plasma specimens from 35 BC women patients and 33 healthy women samples (control group).ResultsThe level of all seven miRNAs (including endogenous control) normalized by synthetic cel-miR-39 were significantly elevated in the group of BC patients. Normalization using miR-222-3p as endogenous control reduced differences in level of miRNAs between groups; as a result, only three miRNAs were significantly upregulated in the group of BC patients—miR-145-5p (P = 6.5e−12), miR-191-5p (P = 3.7e−10) and miR-21-5p (P = 0.0034). Moreover, ROC analysis showed that the use of miR-145-5p and miR-191-5p, both individually (AUC = 0.931 and 0.904, respectively) or in combination (AUC = 0.984), allows to accurately differentiate BC patients from healthy individuals.ConclusionsTwo plasma miRNAs—miR-145-5p and miR-191-5p—are potential biomarkers for diagnosis of BC in the Kazakh population. The findings need to be further substantiated using a more representative sample. creator: Yeldar Ashirbekov creator: Arman Abaildayev creator: Nazgul Omarbayeva creator: Dauren Botbayev creator: Ayaz Belkozhayev creator: Anel Askandirova creator: Alena Neupokoyeva creator: Gulzhakhan Utegenova creator: Kamalidin Sharipov creator: Nagima Aitkhozhina uri: https://doi.org/10.7717/peerj.10494 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ashirbekov et al. title: Clinical features and prognostic factors of spinal fibroblastic/myofibroblastic tumors: a long-term, single-center, retrospective study link: https://peerj.com/articles/10530 last-modified: 2020-12-16 description: BackgroundSpinal fibroblastic and myofibroblastic tumors (FMTs) are extremely rare. Few studies have reported on the features and outcomes of this condition that affects the axial skeleton. We explored the clinical characteristics and factors affecting the prognosis of spinal FMTs.MethodsWe retroactively assessed the survival of 51 patients with spinal FMTs who underwent surgical and adjuvant treatments in our center between April 2006 and September 2018. Factors affecting disease-free survival (DFS) and overall survival (OS) were analyzed using the Kaplan–Meier method. Variables with p value ≤ 0.05 were subjected to multivariate analysis using the Cox proportional hazards regression model. A two-sided P value < 0.05 was considered statistically significant.ResultsThe mean follow-up period was 50.8 ± 35.6 months (Range 4.2–172.6). Kaplan–Meier survival curves showed that the 5-year DFS was 10% (95% CI [31.09-42.56]) and the 5-year OS was 53% (95% CI [61.28–97.20]). Multivariate analysis showed that en bloc excision was associated with better DFS (HR 0.214, 0.011) and OS (HR 0.273, 0.043), radiotherapy negatively affected OS (HR 0.353, 0.033), and the recurrence and Ki-67 index <5% significantly affected DFS (HR 3.008, 0.008 and 2.754, 0.029).ConclusionsSpinal FMTs are rare. Surgery is the treatment of choice and en bloc excision is strongly recommended to improve outcomes. Disease recurrence and the Ki-67 marker are correlated with the progression of these tumors. creator: Haitao Sun creator: Shaohui He creator: Yuechao Zhao creator: Chen Ye creator: Xinghai Yang creator: Wei Xu creator: Jianru Xiao uri: https://doi.org/10.7717/peerj.10530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sun et al. title: WeChat-based mHealth intention and preferences among people living with schizophrenia link: https://peerj.com/articles/10550 last-modified: 2020-12-16 description: BackgroundThe past few decades have seen a rapid expansion of mHealth programs among people with serious mental illness, yet mHealth for schizophrenia is in a much earlier stage of development. This study examined the intention of WeChat-based mHealth programs among people living with schizophrenia (PLS) and evaluated correlates of the intention.MethodsA total of 400 PLS aged 18–77 completed a cross-sectional survey by face-to-face interviews. The survey included a general question asking about participants’ willingness to attend WeChat-based mHealth programs, followed by preferences of three specific WeChat-based programs: psychoeducation, peer support, and professional support. PLS symptoms, functioning and disability were measured using the 18-item Brief Psychiatric Rating Scale (BPRS-18), the Global Assessment of Functioning (GAF), and the 12-item World Health Organization Disability Assessment Schedule 2.0 (WHODAS 2.0), respectively. A multivariate logistic regression was used to determine correlates of program participation intention.ResultsOver forty percent (43%, n = 172) of participants were willing to participate in WeChat-based mHealth programs, among whom preferences for each specific program were shown in descending order: psychoeducation (68.60%), professional support (60.47%), and peer support (52.33%). A multivariate analysis revealed that younger age (OR: 0.13–0.20, 95% CI [0.05–0.43]), higher education (OR: 3.48–6.84, 95% CI [1.69–18.21]), and lower disability (OR: 0.97, 95% CI [0.94–0.99]) were all independently associated with WeChat-based mHealth program participation intention.ConclusionThe findings provide guidance for further development of WeChat-based mHealth programs among PLS in China, and targeted at those who are younger, well-educated and with lower disability. creator: Shuiyuan Xiao creator: Tongxin Li creator: Wei Zhou creator: Minxue Shen creator: Yu Yu uri: https://doi.org/10.7717/peerj.10550 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xiao et al. title: Description of the microbiota in epidermal mucus and skin of sharks (Ginglymostoma cirratum and Negaprion brevirostris) and one stingray (Hypanus americanus) link: https://peerj.com/articles/10240 last-modified: 2020-12-15 description: Skin mucus in fish is the first barrier between the organism and the environment but the role of skin mucus in protecting fish against pathogens is not well understood. During copulation in sharks, the male bites the female generating wounds, which are then highly likely to become infected by opportunistic bacteria from the water or from the male shark’s mouth. Describing the microbial component of epithelial mucus may allow future understanding of this first line of defense in sharks. In this study, we analyzed mucus and skin samples obtained from 19 individuals of two shark species and a stingray: the nurse shark (Ginglymostoma cirratum), the lemon shark (Negaprion brevirostris) and the southern stingray (Hypanus americanus). Total DNA was extracted from all samples, and the bacterial 16S rRNA gene (region V3-V4) was amplified and sequenced on the Ion Torrent Platform. Bacterial diversity (order) was higher in skin and mucus than in water. Order composition was more similar between the two shark species. Alpha-diversities (Shannon and Simpson) for OTUs (clusters of sequences defined by a 97% identity threshold for the16S rRNA gene) were high and there were non-significant differences between elasmobranch species or types of samples. We found orders of potentially pathogenic bacteria in water samples collected from the area where the animals were found, such as Pasteurellales (i.e., genus Pasteurella spp. and Haemophilus spp.) and Oceanospirillales (i.e., genus Halomonas spp.) but these were not found in the skin or mucus samples from any species. Some bacterial orders, such as Flavobacteriales, Vibrionales (i.e., genus Pseudoalteromonas), Lactobacillales and Bacillales were found only in mucus and skin samples. However, in a co-occurrence analyses, no significant relationship was found among these orders (strength less than 0.6, p-value > 0.01) but significant relationships were found among the order Trembayales, Fusobacteriales, and some previously described marine environmental Bacteria and Archaea, including Elusimicrobiales, Thermoproteales, Deinococcales and Desulfarculales. This is the first study focusing on elasmobranch microbial communities. The functional role and the benefits of these bacteria still needs understanding as well as the potential changes to microbial communities as a result of changing environmental conditions. creator: Susana Caballero creator: Ana Maria Galeano creator: Juan Diego Lozano creator: Martha Vives uri: https://doi.org/10.7717/peerj.10240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Caballero et al. title: Fungal survival under temperature stress: a proteomic perspective link: https://peerj.com/articles/10423 last-modified: 2020-12-15 description: BackgroundIncreases in knowledge of climate change generally, and its impact on agricultural industries specifically, have led to a greater research effort aimed at improving understanding of the role of fungi in various fields. Fungi play a key role in soil ecosystems as the primary agent of decomposition, recycling of organic nutrients. Fungi also include important pathogens of plants, insects, bacteria, domestic animals and humans, thus highlighting their importance in many contexts. Temperature directly affects fungal growth and protein dynamics, which ultimately will cascade through to affect crop performance. To study changes in the global protein complement of fungi, proteomic approaches have been used to examine links between temperature stress and fungal proteomic profiles.Survey methodology and objectivesA traditional rather than a systematic review approach was taken to focus on fungal responses to temperature stress elucidated using proteomic approaches. The effects of temperature stress on fungal metabolic pathways and, in particular, heat shock proteins (HSPs) are discussed. The objective of this review is to provide an overview of the effects of temperature stress on fungal proteomes.Concluding remarksElucidating fungal proteomic response under temperature stress is useful in the context of increasing understanding of fungal sensitivity and resilience to the challenges posed by contemporary climate change processes. Although useful, a more thorough work is needed such as combining data from multiple -omics platforms in order to develop deeper understanding of the factor influencing and controlling cell physiology. This information can be beneficial to identify potential biomarkers for monitoring environmental changes in soil, including the agricultural ecosystems vital to human society and economy. creator: Nurlizah Abu Bakar creator: Saiful Anuar Karsani creator: Siti Aisyah Alias uri: https://doi.org/10.7717/peerj.10423 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abu Bakar et al. title: The performance of a modified EWMA control chart for monitoring autocorrelated PM2.5 and carbon monoxide air pollution data link: https://peerj.com/articles/10467 last-modified: 2020-12-15 description: PM2.5 (particulate matter less than or equal to 2.5 micron) is found in the air and comprises dust, dirt, soot, smoke, and liquid droplets. PM2.5 and carbon monoxide emissions can have a negative impact on humans and animals throughout the world. In this paper, we present the performance of a modified exponentially weighted moving average (modified EWMA) control chart to detect small changes when the observations are autocorrelated with exponential white noise through the average run length evaluated (ARLs) by explicit formulas. The accuracy of the solution was verified with a numerical integral equation method. The efficacy of the modified EWMA control chart to monitor PM2.5 and carbon monoxide air pollution data and compare its performance with the standard EWMA control chart. The results suggest that the modified EWMA control chart is far superior to the standard one. creator: Yadpirun Supharakonsakun creator: Yupaporn Areepong creator: Saowanit Sukparungsee uri: https://doi.org/10.7717/peerj.10467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Supharakonsakun et al. title: Identification of histone deacetylase genes in Dendrobium officinale and their expression profiles under phytohormone and abiotic stress treatments link: https://peerj.com/articles/10482 last-modified: 2020-12-15 description: The deacetylation of core histones controlled by the action of histone deacetylases (HDACs) plays an important role in the epigenetic regulation of plant gene transcription. However, no systematic analysis of HDAC genes in Dendrobium officinale, a medicinal orchid, has been performed. In the current study, a total of 14 histone deacetylases in D. officinale were identified and characterized using bioinformatics-based methods. These genes were classified into RPD3/HDA1, SIR2, and HD2 subfamilies. Most DoHDAC genes in the same subfamily shared similar structures, and their encoded proteins contained similar motifs, suggesting that the HDAC family members are highly conserved and might have similar functions. Different cis-acting elements in promoters were related to abiotic stresses and exogenous plant hormones. A transient expression assay in onion epidermal cells by Agrobacterium-mediated transformation indicated that all of the detected histone deacetylases such as DoHDA7, DoHDA9, DoHDA10, DoHDT3, DoHDT4, DoSRT1 and DoSRT2, were localized in the nucleus. A tissue-specific analysis based on RNA-seq suggested that DoHDAC genes play a role in growth and development in D. officinale. The expression profiles of selected DoHDAC genes under abiotic stresses and plant hormone treatments were analyzed by qRT-PCR. DoHDA3, DoHDA8, DoHDA10 and DoHDT4 were modulated by multiple abiotic stresses and phytohormones, indicating that these genes were involved in abiotic stress response and phytohormone signaling pathways. These results provide valuable information for molecular studies to further elucidate the function of DoHDAC genes. creator: Mingze Zhang creator: Jaime A. Teixeira da Silva creator: Zhenming Yu creator: Haobin Wang creator: Can Si creator: Conghui Zhao creator: Chunmei He creator: Jun Duan uri: https://doi.org/10.7717/peerj.10482 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors link: https://peerj.com/articles/10483 last-modified: 2020-12-15 description: The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions. creator: Lei Dong creator: Yue Lu creator: Shubing Liu uri: https://doi.org/10.7717/peerj.10483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dong et al. title: Polyester or epoxy: assessing embedding product efficacy in paleohistological methods link: https://peerj.com/articles/10495 last-modified: 2020-12-15 description: Histological examination of bone microstructure provides insight into extant and extinct vertebrate physiology. Fossil specimens sampled for histological examination are typically first embedded in an inexpensive polyester resin and then cut into thin sections, mounted on slides, and polished for viewing. Modern undecalcified bone is chemically processed prior to embedding in plastic resin, sectioning, mounting, and polishing. Conversely, small fossil material and modern undecalcified bone are typically embedded in higher priced epoxy resin because these specimen types require final sections near or below 100 µm thick. Anecdotal evidence suggests thin sections made of polyester resin embedded material polished thinner than 100 µm increases likelihood of sample peeling, material loss, and is unsuitable for modern tissue and small fossil material. To test this assertion, a sample of modern bones and fossil bones, teeth, and scales were embedded in either polyester resin or epoxy resin. Embedded specimens were sectioned and mounted following standard published protocol. Thin sections were ground on a lapidary wheel using decreasing grit sizes until tissue microstructure was completely discernible when viewed under a polarizing light microscope. Additionally, eight prepared thin sections (four from polyester resin embedded specimens and four from epoxy resin embedded specimens) were continuously ground on a lapidary wheel using 600 grit carbide paper until peeling occurred or material integrity was lost. Slide thickness when peeling occurred was measured for comparing slide thickness when specimen integrity was lost between the two resin types. Final slide thickness ranged from 38 µm to 247 µm when tissue was identifiable using a polarizing microscope. Finished slide thickness varied between resin types despite similar tissue visibility. However, finished slide thickness appears more dependent on hard tissue composition than resin type. Additionally, we did not find a difference of slide thickness when material was lost between resin types. The results of this preliminary study suggest that polyester resins can be used for embedding undecalcified modern hard tissues and fossilized hard tissues without loss of tissue visibility or material integrity, at least in the short term. creator: Christian T. Heck creator: Gwyneth Volkmann creator: Holly N. Woodward uri: https://doi.org/10.7717/peerj.10495 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Heck et al. title: Changes in sprint performance and sagittal plane kinematics after heavy resisted sprint training in professional soccer players link: https://peerj.com/articles/10507 last-modified: 2020-12-15 description: BackgroundSprint performance is an essential skill to target within soccer, which can be likely achieved with a variety of methods, including different on-field training options. One such method could be heavy resisted sprint training. However, the effects of such overload on sprint performance and the related kinetic changes are unknown in a professional setting. Another unknown factor is whether violating kinematic specificity via heavy resistance will lead to changes in unloaded sprinting kinematics. We investigated whether heavy resisted sled training (HS) affects sprint performance, kinetics, sagittal plane kinematics, and spatiotemporal parameters in professional male soccer players.MethodsAfter familiarization, a nine-week training protocol and a two-week taper was completed with sprint performance and force-velocity (FV) profiles compared before and after. Out of the two recruited homogenous soccer teams (N = 32, age: 24.1 ± 5.1 years: height: 180 ± 10 cm; body-mass: 76.7 ± 7.7 kg, 30-m split-time: 4.63 ± 0.13 s), one was used as a control group continuing training as normal with no systematic acceleration training (CON, N = 13), while the intervention team was matched into two HS subgroups based on their sprint performance. Subgroup one trained with a resistance that induced a 60% velocity decrement from maximal velocity (N = 10, HS60%) and subgroup two used a 50% velocity decrement resistance (N = 9, HS50%) based on individual load-velocity profiles.ResultsBoth heavy resistance subgroups improved significantly all 10–30-m split times (p < 0.05, d =  − 1.25; −0.62). Post-hoc analysis showed that HS50% improved significantly more compared to CON in 0–10-m split-time (d = 1.03) and peak power (d = 1.16). Initial maximal theoretical horizontal force capacity (F0) and sprint FV-sprint profile properties showed a significant moderate relationship with F0 adaptation potential (p < 0.05). No significant differences in sprinting kinematics or spatiotemporal variables were observed that remained under the between-session minimal detectable change.ConclusionWith appropriate coaching, heavy resisted sprint training could be one pragmatic option to assist improvements in sprint performance without adverse changes in sprinting kinematics in professional soccer players. Assessing each player’s initial individual sprint FV-profile may assist in predicting adaptation potential. More studies are needed that compare heavy resisted sprinting in randomized conditions. creator: Johan Lahti creator: Toni Huuhka creator: Valentin Romero creator: Ian Bezodis creator: Jean-Benoit Morin creator: Keijo Häkkinen uri: https://doi.org/10.7717/peerj.10507 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lahti et al. title: Climatic niche comparison between closely related trans-Palearctic species of the genus Orthocephalus (Insecta: Heteroptera: Miridae: Orthotylinae) link: https://peerj.com/articles/10517 last-modified: 2020-12-15 description: Previously climatic niche modelling had been studied for only a few trans-Palearctic species. It is unclear whether and to what extent those niches are different, and which climatic variables influence such a wide distribution. Here, environmental niche modelling is performed based on the Worldclim variables using Maxent for eight species of the genus Orthocephalus (Insecta: Heteroptera: Miridae: Orthotylinae). This group belongs to one of the largest insect families and it is distributed across Palearctic. Orthocephalus bivittatus, O. brevis, O. saltator and O. vittipennis are distributed across Europe and Asia; O. coriaceus, O. fulvipes, O. funestus, O. proserpinae have more limited distribution. Niche comparison using ENMTools was also undertaken to compare the niches of these species, and to test whether the niches of closely related species with trans-Palearctic distributions are more similar to each other, than to other congeners. It has been found that climatic niche models of all trans-Palearctic species under study are similar but are not identical to each other. This has been supported by niche geographic projections, climatic variables contributing to the models and variable ranges. Climatic niche models of all the trans-Palearctic Orthocephalus species are also very similar to two species having more restricted distribution (O. coriaceus, O. funestus). Results of this study suggest that trans-Palearctic distributions can have different geographic ranges and be shaped by different climatic factors. creator: Anna A. Namyatova uri: https://doi.org/10.7717/peerj.10517 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Namyatova title: Canines and carnassials as indicators of sociality in durophagous hyaenids: analyzing the past to understand the present link: https://peerj.com/articles/10541 last-modified: 2020-12-15 description: We analyzed the lower and upper dentition of the family Hyaenidae along its evolutionary history from a multivariate point of view. A total of 13,103 individual measurements of the lengths and widths of canines and the main post-canine teeth (lower third and fourth premolar, lower first molar, and upper second, third, and fourth premolars) were collected for 39 extinct and extant species of this family. We analyzed these measurements using principal component analyses. The multivariate structure characterized the main groups of previously defined hyaenid ecomorphs. Strikingly, our analyses also detected differences between social hunting durophages (such as Crocuta crocuta) and solitary scavengers (such as Hyaena hyaena or Parahyaena brunnea). Concerning the hyaenid bauplan, social hunters have large carnassials and smaller canines, whereas solitary scavengers show the exact opposite morphological adaptations. Additionally, scavengers exhibited upper canines larger than lower ones, whereas hunters have upper and lower canines of similar size. It is hypothesized that sociality has led to an increase in carnassial length for hunting durophages via scramble competition at feeding. Such competition also penalizes adults from bringing food to cubs, which are consequently breastfed. On the other hand, it is also hypothesized that natural selection has led to solitary scavengers having large canines to transport carcasses to cubs. Our results indicate that these functional aspects are also better reflected by lower teeth than the upper dentition, which leads to a mosaic evolution. creator: Juan Antonio Pérez-Claros creator: Carlos Coca-Ortega uri: https://doi.org/10.7717/peerj.10541 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pérez-Claros et al. title: Registered report: investigating a preference for certainty in conversation among autistic adults compared to dyslexic adults and the general population link: https://peerj.com/articles/10398 last-modified: 2020-12-14 description: Social communication difficulties are a diagnostic feature in autism. These difficulties are sometimes attributed, at least in part, to impaired ability in making inferences about what other people mean. In this registered report, we test a competing hypothesis that the communication profile of adults on the autism spectrum can be more strongly characterised by reduced confidence in making inferences in the face of uncertain information. We will test this hypothesis by comparing the performance of 100 autistic and 100 non-autistic adults on a test of implied meaning, using a test of grammaticality judgements as a control task. We hypothesise that autistic adults will report substantially lower confidence, allowing for differences in accuracy, than non-autistic adults on the test of implied meaning compared to the grammaticality test. In addition, we hypothesise that reduced confidence in drawing inferences will relate to the cognitive trait Intolerance of Uncertainty and self-reported social communication challenges. Finally, we will conduct exploratory analysis to assess the specificity of the communication profile of the autistic adults by comparing their performance to that of dyslexic adults, who might also be expected to experience challenges with language and communication. creator: Alexander C. Wilson creator: Dorothy V.M. Bishop uri: https://doi.org/10.7717/peerj.10398 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wilson and Bishop title: Experiences of family caregivers of patients with terminal disease and the quality of end-of-life care received: a mixed methods study link: https://peerj.com/articles/10516 last-modified: 2020-12-14 description: The aim of this study was to analyze the perceptions and experiences of relatives of patients dying from a terminal disease with regard to the care they received during the dying process, considering the oncological or non-oncological nature of the terminal disease, and the place where care was provided (at home, emergency department, hospital room, or palliative care unit). For this purpose, we conducted a mixed-methods observational study in which two studies were triangulated, one qualitative using semi-structured interviews (n = 30) and the other quantitative, using questionnaires (n = 129). The results showed that the perception of relatives on the quality of care was highly positive in the quantitative evaluation but more critical and negative in the qualitative interview. Experience of the support received and palliative measures was more positive for patients attended in hospital in the case of oncological patients but more positive for those attended at home in the case of non-oncological patients. creator: Celia Martí-García creator: Manuel Fernández-Alcántara creator: Patricia Suárez López creator: Carolina Romero Ruiz creator: Rocío Muñoz Martín creator: Mᵃ Paz Garcia-Caro uri: https://doi.org/10.7717/peerj.10516 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Martí-García et al. title: Convict cichlid parents that stay with the same mate develop unique and consistent divisions of roles link: https://peerj.com/articles/10534 last-modified: 2020-12-14 description: Previous studies, largely on avian species, have suggested that pairs that are permanently monogamous and have biparental care develop a coordination over time that enhances offspring survival. If this is the case, we predicted that a parent involved in biparental care would develop a pattern of biparental care specific to a particular mate and remain consistent in that pattern over time but would lose this pattern if it were to change mates. We tested this prediction with the convict cichlid fish (Amatitlania nigrofasciata) which has biparental care that is both complex and flexible. In this species, each parent can perform all parental roles but typically shows a division of labor in which males typically defend against offspring predators while the female typically provides direct care to the offspring. At various times, the parents briefly switch roles. Our experiments revealed that pairs that remained together for two consecutive broods were more consistent in their parental behaviors, including time they spent near the intruder and in the nest compared to pairs that were comprised of individuals that had previously mated with other partners. Also individuals that remained with the same partner were also more consistent as a parental unit, maintaining their sex-specific roles of males defending aggressively against an intruder and females spending more time directly caring for young. While our experiment clearly support our prediction that individuals do develop unique coordination with specific individuals, convict cichlids in nature appear to be largely serially monogamous in which they mate only once before changing partners. Thus, it is likely this coordination may be available in many species that have biparental care but become adaptive when repeated matings become common. creator: Jennifer L. Snekser creator: Murray Itzkowitz uri: https://doi.org/10.7717/peerj.10534 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Snekser and Itzkowitz title: Trends in summer presence of fin whales in the Western Mediterranean Sea Region: new insights from a long-term monitoring program link: https://peerj.com/articles/10544 last-modified: 2020-12-14 description: BackgroundThe Mediterranean subpopulation of fin whale Balaenoptera physalus (Linnaeus, 1758) has recently been listed as Vulnerable by the IUCN Red List of threatened species. The species is also listed as species in need of strict protection under the Habitat Directive and is one of the indicators for the assessment of Good Environmental Status under the MSFD. Reference values on population abundance and trends are needed in order to set the threshold values and to assess the conservation status of the population.MethodsYearly summer monitoring using ferries as platform of opportunity was performed since 2008 within the framework of the FLT Med Network. Data were collected along several fixed transects crossing the Western Mediterranean basin and the Adriatic and Ionian region. Species presence, expressed by density recorded along the sampled transects, was inspected for assessing interannual variability together with group size. Generalized Additive Models were used to describe density trends over a 11 years’ period (2008–2018). A spatial multi-scale approach was used to highlight intra-basin differences in species presence and distribution during the years.ResultsSummer presence of fin whales in the western Mediterranean area showed a strong interannual variability, characterized by the alternance of rich and poor years. Small and large groups of fin whales were sighted only during rich years, confirming the favorable feeding condition influencing species presence. Trends highlighted by the GAM can be summarized as positive from 2008 to 2013, and slightly negative from 2014 to 2018. The sub-areas analysis showed a similar pattern, but with a more stable trend during the second period in the Pelagos Sanctuary sub-area, and a negative one in the other two sub-areas. Our findings further confirm the need for an integrated approach foreseeing both, large scale surveys and yearly monitoring at different spatial scales to correct and interpret the basin wide abundance estimates, and to correlate spatial and temporal trends with the ecological and anthropogenic drivers. creator: Paola Tepsich creator: Ilaria Schettino creator: Fabrizio Atzori creator: Marta Azzolin creator: Ilaria Campana creator: Lara Carosso creator: Simone Cominelli creator: Roberto Crosti creator: Léa David creator: Nathalie Di-Méglio creator: Francesca Frau creator: Martina Gregorietti creator: Veronica Mazzucato creator: Clara Monaco creator: Aurelie Moulins creator: Miriam Paraboschi creator: Giuliana Pellegrino creator: Massimiliano Rosso creator: Marine Roul creator: Sébastien Saintignan creator: Antonella Arcangeli uri: https://doi.org/10.7717/peerj.10544 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tepsich et al. title: Portanini (Insecta: Hemiptera: Cicadellidae) from Peru: checklist with new records and descriptions of two new species link: https://peerj.com/articles/10222 last-modified: 2020-12-11 description: Portanini Linnavuori, 1959 is a small tribe of neotropical leafhoppers that includes two genera: Portanus Ball, 1932 and MetacephalusDeLong & Martinson, 1973. Herein, a checklist of portanines from Peru is given, including several new species records for the country, elevating the known diversity from nine to 22 species. In addition, four species have their department ranges expanded in Peru. Two new portanine species are also described: Metacephalus mamaquillasp. nov. and Portanus tambopatasp. nov. both from Tambopata National Reserve, Madre de Dios, Peru and we make available habitus photos of other Portanini species from this reserve. creator: Jádila Santos Prando creator: Clayton Corrêa Gonçalves creator: Daniela Maeda Takiya uri: https://doi.org/10.7717/peerj.10222 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Santos Prando et al. title: Driver versus navigator causation in biology: the case of insulin and fasting glucose link: https://peerj.com/articles/10396 last-modified: 2020-12-11 description: BackgroundIn biomedicine, inferring causal relation from experimental intervention or perturbation is believed to be a more reliable approach than inferring causation from cross-sectional correlation. However, we point out here that even in interventional inference there are logical traps. In homeostatic systems, causality in a steady state can be qualitatively different from that in a perturbed state. On a broader scale there is a need to differentiate driver causality from navigator causality. A driver is essential for reaching a destination but may not have any role in deciding the destination. A navigator on the other hand has a role in deciding the destination and the path but may not be able to drive the system to the destination. The failure to differentiate between types of causalities is likely to have resulted into many misinterpretations in physiology and biomedicine.MethodsWe illustrate this by critically re-examining a specific case of the causal role of insulin in glucose homeostasis using five different approaches (1) Systematic review of tissue specific insulin receptor knock-outs, (2) Systematic review of insulin suppression and insulin enhancement experiments, (3) Differentiating steady state and post-meal state glucose levels in streptozotocin treated rats in primary experiments, (4) Mathematical and theoretical considerations and (5) Glucose-insulin relationship in human epidemiological data.ResultsAll the approaches converge on the inference that although insulin action hastens the return to a steady state after a glucose load, there is no evidence that insulin action determines the steady state level of glucose. Insulin, unlike the popular belief in medicine, appears to be a driver but not a navigator for steady state glucose level. It is quite likely therefore that the current line of clinical action in the field of type 2 diabetes has limited success largely because it is based on a misinterpretation of glucose-insulin relationship. The insulin-glucose example suggests that we may have to carefully re-examine causal inferences from perturbation experiments and set up revised norms for experimental design for causal inference. creator: Manawa Diwekar-Joshi creator: Milind Watve uri: https://doi.org/10.7717/peerj.10396 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Diwekar-Joshi and Watve title: Exogenous melatonin improves salt stress adaptation of cotton seedlings by regulating active oxygen metabolism link: https://peerj.com/articles/10486 last-modified: 2020-12-11 description: Melatonin is a small-molecule indole hormone that plays an important role in participating in biotic and abiotic stress resistance. Melatonin has been confirmed to promote the normal development of plants under adversity stress by mediating physiological regulation mechanisms. However, the mechanisms by which exogenous melatonin mediates salt tolerance via regulation of antioxidant activity and osmosis in cotton seedlings remain largely unknown. In this study, the regulatory effects of melatonin on reactive oxygen species (ROS), the antioxidant system, and osmotic modulators of cotton seedlings were determined under 0–500 µM melatonin treatments with salt stress induced by 150 mM NaCl treatment. Cotton seedlings under salt stress exhibited an inhibition of growth, excessive hydrogen peroxide (H2O2), superoxide anion (O2−), and malondialdehyde (MDA) accumulations in leaves, increased activity levels of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), and elevated ascorbic acid (AsA) and glutathione (GSH) content in leaves. However, the content of osmotic regulators (i.e., soluble sugars and proteins) in leaves was reduced under salt stress. This indicates high levels of ROS were produced, and the cell membrane was damaged. Additionally, osmotic regulatory substance content was reduced, resulting in osmotic stress, which seriously affected cotton seedling growth under salt stress. However, exogenous melatonin at different concentrations reduced the contents of H2O2, O2−, and MDA in cotton leaves, increased the activity of antioxidant enzymes and the content of reductive substances (i.e., AsA and GSH), and promoted the accumulation of osmotic regulatory substances in leaves under salt stress. These results suggest that melatonin can inhibit ROS production in cotton seedlings, improve the activity of the antioxidant enzyme system, raise the content of osmotic regulation substances, reduce the level of membrane lipid peroxidation, and protect the integrity of the lipid membrane under salt stress, which reduces damage caused by salt stress to seedlings and effectively enhances inhibition of salt stress on cotton seedling growth. These results indicate that 200 µM melatonin treatment has the best effect on the growth and salt tolerance of cotton seedlings. creator: Dan Jiang creator: Bin Lu creator: Liantao Liu creator: Wenjing Duan creator: Li Chen creator: Jin Li creator: Ke Zhang creator: Hongchun Sun creator: Yongjiang Zhang creator: Hezhong Dong creator: Cundong Li creator: Zhiying Bai uri: https://doi.org/10.7717/peerj.10486 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jiang et al. title: Association analysis of Suboptimal health Status: a cross-sectional study in China link: https://peerj.com/articles/10508 last-modified: 2020-12-11 description: BackgroundSuboptimal health status (SHS) among urban residents is commonplace in China. However, factors influencing SHS have not been thoroughly explored, especially with regard to the effects of internal factors (e.g., personality and health awareness) on SHS.MethodsA cross-sectional study was conducted with a nationally representative sample of 5460 Chinese urban residents..SHS was measured using the Suboptimal Health Mesurement Scale Version 1.0. Demographic information, and information pertaining to lifestyle behaviors, environmental factors, and internal factors were abtained through a questionnaire. The associations between demographic information, lifestyle behaviors, environmental factors, internal factors and SHS were assessed using logistic regression.ResultsOf the 5460 participants (with a mean age of 41.56 ±  16.14 years), 2640 (48.4 %) were men. Out of 36 variables, 23 were significantly associated with SHS: age (odds ratio [OR]: 1.014), an education level of high school/junior college (OR: 1.443) , marital status (OR: 1.899), area of registered permanent residence (OR: 0.767), monthly household income (p < 0.001) , exposure to second-hand smoke (p = 0.001), alcohol drinking (OR: 1.284), bad eating habits (OR: 1.717), not sleeping before 11 p.m. every day (p = 0.002), spending time online more than five hours a day (OR: 1.526), having a good relationship with parents during one’s growth period (OR: 0.602), living with good quality air (OR:0.817), living in not crowded conditions (OR:0.636), having a harmonious neighborhood (OR:0.775), having adequate fitness facilities (OR:0.783), one’s health being affected by two-child policy (OR: 1.468) and medical policies (OR: 1.265) , high adverse quotient (OR: 0.488), many (≥3 kinds) interests and hobbies (OR: 0.617), mature and steady personality traits (OR: 0.469) , a high attention to one’s health (OR: 0.833), and effective health promotion induced by leading a leisurely lifestyle (OR: 0.466) were significantly associated with SHS.ConclusionsAll these variables were included demographic information, lifestyle behaviors, environmental factors and internal factors. Our study supports the benefits of controlling both internal and external factors in preventing suboptimal health. creator: Yunlian Xue creator: Zhuomin Huang creator: Guihao Liu creator: Yefang Feng creator: Mengyao Xu creator: Lijie Jiang creator: Jun Xu uri: https://doi.org/10.7717/peerj.10508 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xue et al. title: Detection and estimating the blood accumulation volume of brain hemorrhage in a human anatomical skull using a RF single coil link: https://peerj.com/articles/10416 last-modified: 2020-12-10 description: ObjectiveAn experimental study for testing a simple robust algorithm on data derived from an electromagnetic radiation device that can detect small changes in the tissue/fluid ratio in a realistic head configuration.MethodsChanges in the scattering parameters (S21) of an inductive coil resulting from injections of chicken blood in the 0–18 ml range into calf brain tissue in a human anatomical skull were measured over a 100–1,000 MHz frequency range.ResultsAn algorithm that combines amplitude and phase results was found to detect changes in the tissue/fluid ratio with 90% accuracy. An algorithm that estimated the injected blood volume was found to have a 1–4 ml average error. This demonstrates the possibility of the inductive coil-based device to possess a practical ability to detect a change in the tissue/fluid ratio in the head.SignificanceThis study is an important step towards the goal of building an inexpensive and safe device that can detect an early brain hemorrhagic stroke. creator: Moshe Oziel creator: Boris Rubinsky creator: Rafi Korenstein uri: https://doi.org/10.7717/peerj.10416 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Oziel et al. title: Multi-year pair-bonding in Murray cod (Maccullochella peelii) link: https://peerj.com/articles/10460 last-modified: 2020-12-10 description: Mating strategies in fishes are known to include polygyny, polyandry and monogamy and provide valuable insights regarding powerful evolutionary forces such as sexual selection. Monogamy is a complex of mating systems that has been relatively neglected. Previous work on mating strategies in fishes has often been based on observation and focused on marine species rather than freshwater fishes. SNPs are increasingly being used as a molecular ecology tool in non-model organisms, and methods of probabilistic genetic analysis of such datasets are becoming available for use in the absence of parental genotypes. This approach can be used to infer mating strategies. The long-term pair bonding seen in mammals, reptiles and birds has not been recorded in freshwater fishes—in every other respect an extremely diverse group. This study shows that multi-year pair bonding occurs in an Australian Percichthyid fish that exhibits paternal care of eggs and larvae. Using SNPs, full sibling pairs of larvae were found over multiple years in a three-year study. Stable isotope signatures of the larvae support the genetic inference that full sibling pairs shared a common mother, the ultimate source of that isotopic signature during oogenesis. Spatial and temporal clustering also suggests that the full sibling larvae are unlikely to be false positive identifications of the probabilistic identification of siblings. For the first time, we show multi-year pair bonding in a wild freshwater fish. This will have important conservation and management implications for the species. This approach could provide insights into many behavioural, ecological and evolutionary questions, particularly if this is not a unique case. Our findings are likely to initiate interest in seeking more examples of monogamy and alternative mating strategies in freshwater fishes, particularly if others improve methods of analysis of SNP data for identification of siblings in the absence of parental genotypes. creator: Alan J. Couch creator: Fiona Dyer creator: Mark Lintermans uri: https://doi.org/10.7717/peerj.10460 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Couch et al. title: Determinants of behavioural and biological risk factors for cardiovascular diseases from state level STEPS survey (2017–19) in Madhya Pradesh link: https://peerj.com/articles/10476 last-modified: 2020-12-10 description: BackgroundNational and statewide assessment of cardiovascular risk factors needs to be conducted periodically in order to inform public health policy and prioritise allocation of funds, especially in LMICs. Although there have been studies from India which have explored the determinants of cardiovascular risk factors, they have mostly been from high epidemiological transition states. The present study assessed the determinants of cardiovascular (CVD) risk factors in a low epidemiological transition state (Madhya Pradesh) using the WHO STEPwise approach to surveillance (STEPS).MethodsA total of 5,680 persons aged 18–69 years were selected from the state of Madhya Pradesh through multi-stage cluster random sampling. Key CVD risk factors we sought to evaluate were from behavioural (tobacco, alcohol, physical activity, diet) and biological domains (overweight or obese, Hypertension, Diabetes, and Raised serum cholesterol). Key socio-demographic factors of interest were the caste and tribe groups, and rural vs urban location, in addition to known influencers of CVD risk such as age, gender and education levelResultsThose belonging to the scheduled tribes were more at risk of consuming tobacco (OR 2.13 (95% CI [1.52–2.98]), and a diet with less than five servings of fruits and vegetables (OR 2.78 (95% CI [1.06–7.24]), but had had the least risk of physical inactivity (OR 0.31 (95% CI [0.02–0.54]). Residence in a rural area also reduced the odds of physical inactivity (OR 0.65 (95% CI [0.46–0.92])). Lack of formal education was a risk factor for both tobacco consumption and alcohol intake (OR 1.40 (95% CI [1.08–1.82]) for tobacco use; 1.68 (95% CI [1.14–2.49]) for alcohol intake). Those belonging to schedules tribes had much lower risk of being obese (OR 0.25; 95% CI [0.17–0.37]), but were at similar risk of all other clinical CVD risk factors as compared to other caste groups.ConclusionIn the current study we explored socio-demographic determinants of behavioural and biological CVD risks, and found that in Madhya Pradesh, belonging to a scheduled tribe or living in a rural location, protects against being physically inactive or being overweight or obese. Increasing age confers a greater CVD-risk in all domains. Being a male, and lack of formal education confers a greater risk for behavioural domains, but not for most clinical risk domains. Future efforts at curbing CVDs should be therefore two pronged –a population-based strategy targeting biological risk factors, and a more focussed approach directed at those displaying risky behaviour. creator: Arun M. Kokane creator: Rajnish Joshi creator: Ashwin Kotnis creator: Anirban Chatterjee creator: Kriti Yadav creator: G Revadi creator: Ankur Joshi creator: Abhijit P. Pakhare uri: https://doi.org/10.7717/peerj.10476 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kokane et al. title: miR-21 is upregulated, promoting fibrosis and blocking G2/M in irradiated rat cardiac fibroblasts link: https://peerj.com/articles/10502 last-modified: 2020-12-10 description: BackgroundRadiation exposure of the thorax is associated with a greatly increased risk of cardiac morbidity and mortality even after several decades of advancement in the field. Although many studies have demonstrated the damaging influence of ionizing radiation on cardiac fibroblast (CF) structure and function, myocardial fibrosis, the molecular mechanism behind this damage is not well understood. miR-21, a small microRNA, promotes the activation of CFs, leading to cardiac fibrosis. miR-21 is overexpressed after irradiation; however, the relationship between increased miR-21 and myocardial fibrosis after irradiation is unclear. This study was conducted to investigate gene expression after radiation-induced CF damage and the role of miR-21 in this process in rats.MethodsWe sequenced irradiated rat CFs and performed weighted correlation network analysis (WGCNA) combined with differentially expressed gene (DEG) analysis to observe the effect on the expression profile of CF genes after radiation.ResultsDEG analysis showed that the degree of gene changes increased with the radiation dose. WGCNA revealed three module eigengenes (MEs) associated with 8.5-Gy-radiation—the Yellow, Brown, Blue modules. The three module eigengenes were related to apoptosis, G2/M phase, and cell death and S phase, respectively. By blocking with the cardiac fibrosis miRNA miR-21, we found that miR-21 was associated with G2/M blockade in the cell cycle and was mainly involved in regulating extracellular matrix-related genes, including Grem1, Clu, Gdf15, Ccl7, and Cxcl1. Stem-loop quantitative real-time PCR was performed to verify the expression of these genes. Five genes showed higher expression after 8.5 Gy-radiation in CFs. The target genes of miR-21 predicted online were Gdf15 and Rsad2, which showed much higher expression after treatment with antagomir-miR-21 in 8.5-Gy-irradiated CFs. Thus, miR-21 may play the role of fibrosis and G2/M blockade in regulating Grem1, Clu, Gdf15, Ccl7, Cxcl1, and Rsad2 post-irradiation. creator: Huan Guo creator: Xinke Zhao creator: Haixiang Su creator: Chengxu Ma creator: Kai Liu creator: Shanshan Kong creator: Kedan Liu creator: Haining Li creator: Juan Chang creator: Tao Wang creator: Hongyun Guo creator: Huiping Wei creator: Zhaoyuan Fu creator: Xinfang Lv creator: Yingdong Li uri: https://doi.org/10.7717/peerj.10502 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guo et al. title: Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease link: https://peerj.com/articles/10513 last-modified: 2020-12-10 description: We sought to identify the biomarkers related to the clinical severity of stage I to stage IV chronic obstructive pulmonary disease (COPD). Gene expression profiles from the blood samples of COPD patients at each of the four stages were acquired from the Gene Expression Omnibus Database (GEO, accession number: GSE54837). Genes showing expression changes among the different stages were sorted by soft clustering. We performed functional enrichment, protein–protein interaction (PPI), and miRNA regulatory network analyses for the differentially expressed genes. The biomarkers associated with the clinical classification of COPD were selected from logistic regression models and the relationships between TLR2 and inflammatory factors were verified in clinical blood samples by qPCR and ELISA. Gene clusters demonstrating continuously rising or falling changes in expression (clusters 1, 2, and 7 and clusters 5, 6, and 8, respectively) from stage I to IV were defined as upregulated and downregulated genes, respectively, and further analyzed. The upregulated genes were enriched in functions associated with defense, inflammatory, or immune responses. The downregulated genes were associated with lymphocyte activation and cell activation. TLR2, HMOX1, and CD79A were hub proteins in the integrated network of PPI and miRNA regulatory networks. TLR2 and CD79A were significantly correlated with clinical classifications. TLR2 was closely associated with inflammatory responses during COPD progression. Functions associated with inflammatory and immune responses as well as lymphocyte activation may play important roles in the progression of COPD from stage I to IV. TLR2 and CD79A may serve as potential biomarkers for the clinical severity of COPD. TLR2 and CD79A may also serve as independent biomarkers in the clinical classification in COPD. TLR2 may play an important role in the inflammatory responses of COPD. creator: Jie Zhang creator: Changli Zhu creator: Hong Gao creator: Xun Liang creator: Xiaoqian Fan creator: Yulong Zheng creator: Song Chen creator: Yufeng Wan uri: https://doi.org/10.7717/peerj.10513 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Deep-sea water displacement from a turbidity current induced by the Super Typhoon Hagibis link: https://peerj.com/articles/10429 last-modified: 2020-12-09 description: Turbidity currents are the main drivers behind the transportation of terrestrial sediments to the deep sea, and turbidite deposits from such currents have been widely used in geological studies. Nevertheless, the contribution of turbidity currents to vertical displacement of seawater has rarely been discussed. This is partly because until recently, deep-sea turbidity currents have rarely been observed due to their unpredictable nature, being usually triggered by meteorological or geological events such as typhoons and earthquakes. Here, we report a direct observation of a deep-sea turbidity current using the recently developed Edokko Mark 1 monitoring system deployed in 2019 at a depth of 1,370 m in Suruga Bay, central Japan. A turbidity current occurred two days after its probable cause, the Super Typhoon Hagibis (2019), passed through Suruga Bay causing devastating damage. Over aperiod of 40 hours, we observed increased turbidity with turbulent conditions confirmed by a video camera. The turbidity exhibited two sharp peaks around 3:00 and 11:00 on October 14 (Japan Standard Time). The temperature and salinity characteristics during these high turbidity events agreed with independent measurements for shallow water layers in Suruga Bay at the same time, strongly suggesting that the turbidity current caused vertical displacement in the bay’s water column by transporting warmer and shallower waters downslope of the canyon. Our results add to the previous few examples that show meteorological and geological events may have significant contributions in the transportation of shallower seawater to the deep sea. Recent technological developments pertaining to the Edokko Mark 1 and similar devices enable straightforward, long-term monitoring of the deep-seafloor and will contribute to the understanding of similar spontaneous events in the deep ocean. creator: Shinsuke Kawagucci creator: Tetsuya Miwa creator: Dhugal J. Lindsay creator: Eri Ogura creator: Hiroyuki Yamamoto creator: Kenichiro Nishibayashi creator: Hiroyuki Yokooka creator: Shotaro Nishi creator: Ayu Takahashi creator: Sangkyun Lee uri: https://doi.org/10.7717/peerj.10429 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kawagucci et al. title: Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream (Sparus aurata) link: https://peerj.com/articles/10430 last-modified: 2020-12-09 description: BackgroundIn the last two decades, research has focused on testing cheaper and sustainable alternatives to fish oil (FO), such as vegetable oils (VO), in aquafeeds. However, FO cannot be entirely replaced by VOs due to their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), particularly eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3) acids. The oilseed plant, Camelina sativa, may have a higher potential to replace FO since it can contains up to 40% of the omega-3 precursors α-linolenic acid (ALA; 18:3n-3) and linoleic acid (LA; 18:2n-6).MethodsA 90-day feeding trial was conducted with 600 gilthead sea bream (Sparus aurata) of 32.92 ±  0.31 g mean initial weight fed three diets that replaced 20%, 40% and 60% of FO with CO and a control diet of FO. Fish were distributed into triplicate tanks per diet and with 50 fish each in a flow-through open marine system. Growth performance and fatty acid profiles of the fillet were analysed. The Illumina MiSeq platform for sequencing of 16S rRNA gene and Mothur pipeline were used to identify bacteria in the faeces, gut mucosa and diets in addition to metagenomic analysis by PICRUSt.Results and ConclusionsThe feed conversion rate and specific growth rate were not affected by diet, although final weight was significantly lower for fish fed the 60% CO diet. Reduced final weight was attributed to lower levels of EPA and DHA in the CO ingredient. The lipid profile of fillets were similar between the dietary groups in regards to total saturated, monounsaturated, PUFA (n-3 and n-6), and the ratio of n-3/n-6. Levels of EPA and DHA in the fillet reflected the progressive replacement of FO by CO in the diet and the EPA was significantly lower in fish fed the 60% CO diet, while ALA was increased. Alpha and beta-diversities of gut bacteria in both the faeces and mucosa were not affected by any dietary treatment, although a few indicator bacteria, such as Corynebacterium and Rhodospirillales, were associated with the 60% CO diet. However, lower abundance of lactic acid bacteria, specifically Lactobacillus, in the gut of fish fed the 60% CO diet may indicate a potential negative effect on gut microbiota. PICRUSt analysis revealed similar predictive functions of bacteria in the faeces and mucosa, although a higher abundance of Corynebacterium in the mucosa of fish fed 60% CO diet increased the KEGG pathway of fatty acid synthesis and may act to compensate for the lack of fatty acids in the diet. In summary, this study demonstrated that up to 40% of FO can be replaced with CO without negative effects on growth performance, fillet composition and gut microbiota of gilthead sea bream. creator: David Huyben creator: Simona Rimoldi creator: Chiara Ceccotti creator: Daniel Montero creator: Monica Betancor creator: Federica Iannini creator: Genciana Terova uri: https://doi.org/10.7717/peerj.10430 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huyben et al. title: Measuring stress in podiatric students in Spain: psychometric validation and adaptation of the KEZKAK questionnaire link: https://peerj.com/articles/10439 last-modified: 2020-12-09 description: ObjectiveThe study aim was to develop a linguistic-cultural adaptation of the KEZKAK questionnaire to be completed during the practicum of podiatric medical students in Spain, to validate the questionnaire and to evaluate its psychometric properties.MethodsThe cross-sectional study was carried out in two stages: 1. Cross-cultural adaptation; 2. Clinimetric validation based on assessments of interobserver reliability, test-retest reliability and internal consistency. The participants were podiatric medical students at the universities of Malaga and Miguel Hernandez, Alicante (Spain) and were recruited during the period February–October 2019. The following inclusion criteria were applied: aged at least 18 years, studying the third or fourth year of a university degree in Podiatry. All gave signed informed consent and completed the State-Trait Anxiety Inventory and the Podiatry version of the KEZKAK questionnaire. No sampling was performed and thus the entire eligible population was included in the study.ResultsThe analysis was based on 205 participants (33.5% male, 66.5% female), with a mean age of 23.05 (SD 5.37) years. Internal consistency was excellent, with a Cronbach’s alpha of 0.95. This version of the questionnaire had five factorial structures (61.18%). No floor/ceiling effect was observed in any item. The KEZKAK presented high test-retest reliability after 21 days, with an overall ICC of 0.95 (95% CI [0.93–0.98]).ConclusionFor university students of podiatry in Spain, the KEZKAK Podiatry version questionnaire is a valid, reliable instrument for measuring stressors during the practicum. creator: Ana Belen Ortega-Avila creator: Pablo Cervera-Garvi creator: Ana Maria Jimenez-Cebrian creator: Esther Chicharro-Luna creator: Irene Garcia-Paya creator: Gabriel Gijon-Nogueron uri: https://doi.org/10.7717/peerj.10439 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ortega-Avila et al. title: Experimental lung injury induces cerebral cytokine mRNA production in pigs link: https://peerj.com/articles/10471 last-modified: 2020-12-09 description: BackgroundAcute respiratory distress syndrome (ARDS) is an important disease with a high incidence among patients admitted to intensive care units. Over the last decades, the survival of critically ill patients has improved; however, cognitive deficits are among the long-term sequelae. We hypothesize that acute lung injury leads to upregulation of cerebral cytokine synthesis.MethodsAfter approval of the institutional and animal care committee, 20 male pigs were randomized to one of three groups: (1) Lung injury by oleic acid injection (OAI), (2) ventilation only (CTR) or (3) untreated. We compared neuronal numbers, proportion of neurons with markers for apoptosis, activation state of Iba-1 stained microglia cells and cerebral mRNA levels of different cytokines between the groups 18 hours after onset of lung injury.ResultsWe found an increase in hippocampal TNFalpha (p < 0.05) and IL-6 (p < 0.05) messenger RNA (mRNA) in the OAI compared to untreated group as well as higher hippocampal IL-6 mRNA compared to control (p < 0.05). IL-8 and IL-1beta mRNA showed no differences between the groups. We found histologic markers for beginning apoptosis in OAI compared to untreated (p < 0.05) and more active microglia cells in OAI and CTR compared to untreated (p < 0.001 each).ConclusionHippocampal cytokine transcription increases within 18 hours after the induction of acute lung injury with histological evidence of neuronal damage. It remains to be elucidated if increased cytokine mRNA synthesis plays a role in the cognitive decline observed in survivors of ARDS. creator: Jens Kamuf creator: Andreas Garcia Bardon creator: Alexander Ziebart creator: Katrin Frauenknecht creator: Konstantin Folkert creator: Johannes Schwab creator: Robert Ruemmler creator: Miriam Renz creator: Denis Cana creator: Serge C. Thal creator: Erik K. Hartmann uri: https://doi.org/10.7717/peerj.10471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kamuf et al. title: Assessment of the effects of ischaemia/ hypoxia on angiogenesis in rat myofascial trigger points using colour Doppler flow imaging link: https://peerj.com/articles/10481 last-modified: 2020-12-09 description: Background & AimsMyofascial pain syndrome (MPS) is a common non-articular disorder of the musculoskeletal system that is characterized by the presence of myofascial trigger points (MTrPs). Despite the high prevalence of MPS, its pathogenesis, which induces the onset and maintenance of MTrPs, is still not completely understood. To date, no studies have investigated the changes in the biochemical milieu caused by ischaemia/hypoxia in the MTrP regions of muscle that are proposed in the integrated hypothesis. Therefore, this study investigated whether ischaemic/hypoxic conditions participate in the formation of active MTrPs and affect angiogenesis using colour Doppler flow imaging (CDFI).MethodsTwenty-five Sprague-Dawley rats were randomly divided into a model group and a normal control group. A model of active MTrPs was established by a blunt strike combined with eccentric exercise. Enzyme-linked immunosorbent assays (ELISAs) were employed to detect the levels of HIF-1α and VEGF. Microvessel density (MVD) was evaluated using immunohistochemistry. CDFI was applied to observe the blood flow signals in the MTrPs, which were classified into four grades based on their strengths.ResultsCompared with the control group, the active MTrP group exhibited significantly higher HIF-1α and VEGF levels and MVD values. These differences were accompanied by increased blood flow signals. In the active MTrP group, the blood flow signal grade was positively correlated with the MVD (P < 0.05) and independently correlated with the VEGF level (P < 0.05) but was not correlated with the expression of HIF-1α (P > 0.05).ConclusionIschaemic/hypoxic conditions may be involved in the formation of MTrPs. CDFI is useful for detection of the features of angiogenesis in or surrounding MTrPs via assessment of blood flow signals. creator: Fangyan Jiang creator: Shuangcheng Yu creator: Haiqing Su creator: Shangyong Zhu uri: https://doi.org/10.7717/peerj.10481 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jiang et al. title: Oncolytic effects of the recombinant Newcastle disease virus, rAF-IL12, against colon cancer cells in vitro and in tumor-challenged NCr-Foxn1nu nude mice link: https://peerj.com/articles/9761 last-modified: 2020-12-08 description: Colon cancer remains one of the main cancers causing death in men and women worldwide as certain colon cancer subtypes are resistant to conventional treatments and the development of new cancer therapies remains elusive. Alternative modalities such as the use of viral-based therapeutic cancer vaccine is still limited, with only the herpes simplex virus (HSV) expressing granulocyte-macrophage colony- stimulating factor (GM-CSF) or talimogene laherparepvec (T-Vec) being approved in the USA and Europe so far. Therefore, it is imperative to continue the search for a new treatment modality. This current study evaluates a combinatorial therapy between the oncolytic Newcastle disease virus (NDV) and interleukin-12 (IL-12) cytokine as a potential therapeutic vaccine to the current anti-cancer drugs. Several in vitro analyses such as MTT assay, Annexin V/FITC flow cytometry, and cell cycle assay were performed to evaluate the cytotoxicity effect of recombinant NDV, rAF-IL12. Meanwhile, serum cytokine, serum biochemical, histopathology of organs and TUNEL assay were carried out to assess the anti-tumoral effects of rAF-IL12 in HT29 tumor-challenged nude mice. The apoptosis mechanism underlying the effect of rAF-IL12 treatment was also investigated using NanoString Gene expression analysis. The recombinant NDV, rAF-IL12 replicated in HT29 colon cancer cells as did its parental virus, AF2240-i. The rAF-IL12 treatment had slightly better cytotoxicity effects towards HT29 cancer cells when compared to the AF2240-i as revealed by the MTT, Annexin V FITC and cell cycle assay. Meanwhile, the 28-day treatment with rAF-IL12 had significantly (p < 0.05) perturbed the growth and progression of HT29 tumor in NCr-Foxn1nu nude mice when compared to the untreated and parental wild-type NDV strain AF2240-i. The rAF-IL12 also modulated the immune system in nude mice by significantly (p < 0.05) increased the level of IL-2, IL-12, and IFN-γ cytokines. Treatment with rAF-IL12 had also significantly (p < 0.05) increased the expression level of apoptosis-related genes such as Fas, caspase-8, BID, BAX, Smad3 and granzyme B in vitro and in vivo. Besides, rAF-IL12 intra-tumoral delivery was considered safe and was not hazardous to the host as evidenced in pathophysiology of the normal tissues and organs of the mice as well as from the serum biochemistry profile of liver and kidney. Therefore, this study proves that rAF-IL12 had better cytotoxicity effects than its parental AF2240-i and could potentially be an ideal treatment for colon cancer in the near future. creator: Syed Umar Faruq Syed Najmuddin creator: Zahiah Mohamed Amin creator: Sheau Wei Tan creator: Swee Keong Yeap creator: Jeevanathan Kalyanasundram creator: Abhimanyu Veerakumarasivam creator: Soon Choy Chan creator: Suet Lin Chia creator: Khatijah Yusoff creator: Noorjahan Banu Alitheen uri: https://doi.org/10.7717/peerj.9761 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Syed Najmuddin et al. title: Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico link: https://peerj.com/articles/10339 last-modified: 2020-12-08 description: BackgroundCoastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites.MethodsThe potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation.ResultsWe found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution. creator: Pablo Suárez-Moo creator: Araceli Lamelas creator: Itza Garcia-Bautista creator: Luis Felipe Barahona-Pérez creator: Gloria Sandoval-Flores creator: David Valdes-Lozano creator: Tanit Toledano-Thompson creator: Erik Polanco-Lugo creator: Ruby Valdez-Ojeda uri: https://doi.org/10.7717/peerj.10339 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Suárez-Moo et al. title: Insights into dog owner perspectives on risks, benefits, and nutritional value of raw diets compared to commercial cooked diets link: https://peerj.com/articles/10383 last-modified: 2020-12-08 description: BackgroundThe practice of feeding a raw meat-based diet (RMBD) to dogs is a topic of increasing interest to owners and veterinary professionals alike. Despite the research around the practice, particularly about the risk of nutritional imbalances and microbial contamination, an increasing number of dog owners are adopting a raw diet for their dogs. This study expands the research into owner motivations for feeding RMBDs and cooked diets and asks them their opinions about risk and nutritional value.MethodsAn anonymized, online, internationally accessible questionnaire was developed to ascertain owner perspectives on the risks, benefits, and nutritional value of commercially prepared and homemade RMBDs as compared with commercially prepared cooked diets (CCDs).ResultsThe questionnaire was completed by 419 dog owners of diverse backgrounds across the world. Of the participants, 25.3% fed RMBDs. Just over 70.0% of all participants had spoken to their veterinarian about their dog’s nutrition. Owners who fed RMBDs ranked their veterinarian’s knowledge lower and their own knowledge of canine nutrition higher than owners who fed CCDs. They rated commercial and homemade RMBDs as highly nutritious 83.5% and 73.6% of the time, respectively, while only 12.5% rated CCDs as highly nutritious. Owners who fed CCDs ranked RMBDs as highly nutritious less often, but also only ranked CCDs as highly nutritious 52.7% of the time. All participants agreed that CCDs were low risk to human health. Owners who fed RMBDs ranked raw diets as highly risky to human or dog health under 20.0% of the time but deemed CCDs risky to animal health over 65.0% of the time. When asked about benefits of raw diets, the most repeated words offered by owners were “health”, “better”, “coat” and “teeth”. The most repeated risks presented were “bacteria”, “nutrition”, “risk” and “Salmonella”. Owners who fed RMBDs tended to use vague terminology like “health” and “better” when asked why they fed a raw diet. Owners who did not feed RMBDs used more specific terminology like “expensive”, “time” and “risk” when asked why they did not feed a raw diet. Overall, the two groups differed in their perceptions around RMBD and CCD feeding, which highlights the need for a better line of communication and education between veterinarians and owners. creator: Alysia Empert-Gallegos creator: Sally Hill creator: Philippa S. Yam uri: https://doi.org/10.7717/peerj.10383 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Empert-Gallegos et al. title: Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods link: https://peerj.com/articles/10458 last-modified: 2020-12-08 description: BackgroundExisting studies of PLK1 in cervical cancer had several flaws. The methods adopted by those studies of detecting PLK1 expression in cervical cancer were single and there lacks comprehensive evaluation of the clinico-pathological significance of PLK1 in cervical cancer.MethodsA total of 303 cervical tissue samples were collected for in-house tissue microarrays. Immunohistochemistry was performed for evaluating PLK1 expression between cervical cancer (including cervical squamous cell carcinoma (CESC) and cervical adenocarcinoma) and non-cancer samples. The Expression Atlas database was searched for querying PLK1 expression in different cervical cancer cell lines and different tissues in the context of pan-cancer. Standard mean difference (SMD) was calculated and the summarized receiver’s operating characteristics (SROC) curves were plotted for integrated tissue microarrays, exterior high-throughput microarrays and RNA sequencing data as further verification. The effect of PLK1 expression on the overall survival, disease-free survival and event-free survival of cervical cancer patients was analyzed through Kaplan Meier survival curves for cervical cancer patients from RNA-seq and GSE44001 datasets. The gene mutation and alteration status of PLK1 in cervical cancer was inspected in COSMIC and cBioPortal databases. Functional enrichment analysis was performed for genes correlated with PLK1 from aggregated RNA-seq and microarrays.ResultsA total of 963 cervical cancer samples and 178 non-cancer samples were collected from in-house tissue microarrays and exterior microarrays and RNA-seq datasets. The combined expression analysis supported overexpression of PLK1 in CESC, cervical adenocarcinoma and all types of cervical cancer (SMD = 1.59, 95%CI [0.56–2.63]; SMD = 2.99, 95%CI [0.75–5.24]; SMD = 1.57, 95% CI [0.85–2.29]) and the significant power of PLK1 expression in distinguishing CESC or all types of cervical cancer samples from non-cancer samples (AUC = 0.94, AUC = 0.92). Kaplan-Meier survival curves showed that the event-free survival rate of cervical cancer patients with higher expression of PLK1 was shorter than that of patients with lower PLK1 (HR = 2.020, P = 0.0197). Genetic alteration of PLK1 including missense mutation and mRNA low occurred in 6% of cervical cancer samples profiled in mRNA expression. Genes positively or negatively correlated with PLK1 were mainly assembled in pathways such as DNA replication, cell cycle, mismatch repair, Ras signaling pathway, melanoma, EGFR tyrosine kinase inhibitor resistance and homologous recombination (P < 0.05).ConclusionsHere, we provided sufficient evidence of PLK1 overexpression in cervical cancer. The overexpression of PLK1 in cervical cancer and the contributory effect of it on clinical progression indicated the hopeful prospect of PLK1 as a biomarker for cervical cancer. creator: Li Gao creator: Yu-Yan Pang creator: Xian-Yu Guo creator: Jing-Jing Zeng creator: Zhong-Qing Tang creator: Dan-Dan Xiong creator: Xia Yang creator: Ying Li creator: Fu-Chao Ma creator: Lin-Jiang Pan creator: Zhen-Bo Feng creator: Gang Chen uri: https://doi.org/10.7717/peerj.10458 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gao et al. title: Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers link: https://peerj.com/articles/10485 last-modified: 2020-12-08 description: Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro. creator: Zhixin Wang creator: Yalin Sun creator: Xinfang Huang creator: Feng Li creator: Yuping Liu creator: Honglian Zhu creator: Zhengwei Liu creator: Weidong Ke uri: https://doi.org/10.7717/peerj.10485 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot link: https://peerj.com/articles/10492 last-modified: 2020-12-08 description: Carrot is an important root vegetable crop abundant in bioactive compounds including carotenoids, vitamins, and dietary fibers. Carrot intake and its products are gradually growing owing to its high antioxidant activity. Auxins are a class of plant hormones that control many processes of plant growth and development. Yet, the effects of exogenous application of auxin on lignin biosynthesis and gene expression profiles of lignin-related genes in carrot taproot are still unclear. In order to investigate the effect of exogenous indole-3-butyric acid (IBA) on lignin-related gene profiles, lignin accumulation, anatomical structures and morphological characteristics in carrot taproots, carrots were treated with different concentrations of IBA (0, 50, 100, and 150 µM). The results showed that IBA application significantly improved the growth parameters of carrot. The 100 or 150 µM IBA treatment increased the number and area of xylem vessels, whereas transcript levels of lignin-related genes were restricted, resulting in a decline in lignin content in carrot taproots. The results indicate that taproot development and lignin accumulation may be influenced by the auxin levels within carrot plants. creator: Ahmed Khadr creator: Guang-Long Wang creator: Ya-Hui Wang creator: Rong-Rong Zhang creator: Xin-Rui Wang creator: Zhi-Sheng Xu creator: Yong-Sheng Tian creator: Ai-Sheng Xiong uri: https://doi.org/10.7717/peerj.10492 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Khadr et al. title: Density-dependent condition of juvenile penaeid shrimps in seagrass-dominated aquatic vegetation beds located at different distance from a tidal inlet link: https://peerj.com/articles/10496 last-modified: 2020-12-08 description: Seagrasses are critical habitats for the recruitment and growth of juvenile penaeid shrimps within estuaries and coastal lagoons. The location of a seagrass bed within the lagoon can determine the value of a particular bed for shrimp populations. Consequently, differences in the abundance of shrimp can be found in seagrasses depending on their location. As shrimp density increases, density-dependent effects on biological parameters are more likely to occur. However, knowledge about density-dependent processes on shrimp populations in nursery habitats remains limited. The present investigation was undertaken to examine the effects of population density on shrimp condition in two selected seagrass beds, located at different distance from a tidal inlet, one 25 km away (distant) and the other 1 km away (nearby), in a subtropical coastal lagoon. The study was based on monthly samplings during one year in Laguna Madre (Mexico), performing a total of 36 shrimp trawls (100 m2 each one) within each seagrass bed (n = 3 trawls per bed per month for 12 months). Shrimp density was related to the proximity to the tidal inlet (higher density was consistently observed in the nearby seagrass bed), which in turn adversely affected the condition of both species studied (Penaeus aztecus and P. duorarum). In this regard, the present study provides the first evidence of density-dependent effects on shrimp condition inhabiting a nursery habitat. Both shrimp species exhibited a negative relationship between condition and shrimp density. However, this pattern differed depending on the proximity to the tidal inlet, suggesting that shrimp populations inhabiting the nearby seagrass bed are exposed to density-dependent effects on condition; whereas, such effects were not detected in the distant seagrass bed. Shrimp density within the distant seagrass bed was probably below carrying capacity, which is suggested by the better shrimp condition observed in that area of the lagoon. Intra and interspecific competition for food items is surmised to occur, predominantly within seagrass beds near the tidal inlet. However, this hypothesis needs to be tested in future studies. creator: Zeferino Blanco-Martínez creator: Roberto Pérez-Castañeda creator: Jesús Genaro Sánchez-Martínez creator: Flaviano Benavides-González creator: Jaime Luis Rábago-Castro creator: María de la Luz Vázquez-Sauceda creator: Lorena Garrido-Olvera uri: https://doi.org/10.7717/peerj.10496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Blanco-Martínez et al. title: Pro-inflammatory effect of obesity on rats with burn wounds link: https://peerj.com/articles/10499 last-modified: 2020-12-08 description: ObjectiveA burn is an inflammatory injury to the skin or other tissue due to contact with thermal, radioactive, electric, or chemical agents. Burn injury is an important cause of disability and death worldwide. Obesity is a significant public health problem, often causing underlying systemic inflammation. Studying the combined impact of burn injuries on obese patients has become critical to the successful treatment of these patients. The aim of this paper is to highlight the effect of inflammation associated with burn injuries on several body weight group in a rat study.Materials and methodsDifferent degrees of obesity and burns were established in rats and divided into a normal weight group, overweight group, obese group, second-degree burn group, third-degree burn group, over-weight second-degree burn group, over-weight third-degree burn group, obese second-degree burn group, and obese third-degree burn group (20 rats per group). Changes in inflammatory factors and growth factor were measured on the 1st, 3rd, 7th and 14th days after burns were inflicted.ResultsThe ELISA test showed that in the unburned control group, MCP-1, IL-1β and TNF-α protein expressions in the obese and over-weight groups were higher than the normal-weight group (P < 0.05). RT-PCR test showed that the expressions of MCP-1, IL-1β and TNF-α genes in the obese group were higher compared to the overweight and normal weight groups (P < 0.05). Three and 7 days after burns were inflicted, the level of VEGF in the normal weight group was higher than the obese group (P < 0.05), however increased VEGF was not observed on days 1 and 14.ConclusionBurn injury and obesity have a mutually synergistic effect on the body’s inflammatory response. creator: Chan Nie creator: Huiting Yu creator: Xue Wang creator: Xiahong Li creator: Zairong Wei creator: Xiuquan Shi uri: https://doi.org/10.7717/peerj.10499 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nie et al. title: Self-reports vs. physical measures of spinal stiffness link: https://peerj.com/articles/9598 last-modified: 2020-12-07 description: BackgroundObjectively measured reduction in lumbar posterior-to-anterior (PA) stiffness is associated with pain relief in some, but not all persons with low back pain. Unfortunately, these measurements can be time consuming to perform. In comparison, the Lumbar Spine Instability Questionnaire (LSIQ) is intended to measure spinal instability and the Lumbar Spine Disability Index (LSDI) is created for self-reporting functional disability due to increased spinal stiffness. Given the above, the aim of this study is to compare measures of the LSIQ and LSDI with objective measures of lumbar PA stiffness as measured by a mechanical device, Vertetrack (VT), in patients with persistent non-specific low back pain (nsLBP).MethodsTwenty-nine patients with nsLBP completed the LSIQ and LSDI at baseline and after two weeks. On these same occasions, PA spinal stiffness was measured using the VT. Between measurements, patients received four sessions of spinal manipulation. The resulting data was analyzed to determine the correlation between the self-report and objective measures of stiffness at both time points. Further, the patients were categorized into responders and non-responders based on pre-established cut points depending on values from the VT and compared those to self-report measures in order to determine whether the LSIQ and the LSDI were sensitive to change.ResultsTwenty-nine participants completed the study. Measures from the LSIQ and LSDI correlated poorly with objectively measured lumbar PA stiffness at baseline and also with the change scores. The change in objectively measured lumbar PA stiffness following spinal manipulation did not differ between those who improved, and those who did not improve according to the pre-specified cut-points. Finally, a reduction in lumbar PA stiffness following intervention was not associated with improvement in LSIQ and LSDI outcomes.ConclusionsThe current data indicate that the LSIQ and LSDI questionnaires do not correlate with measures obtained objectively by VT. Our results suggest that these objective and self- reported measures represent different domains and as such, cannot stand in place of one another. creator: Jonas Nielsen creator: Casper Glissmann Nim creator: Søren O’Neill creator: Eleanor Boyle creator: Jan Hartvigsen creator: Gregory N. Kawchuk uri: https://doi.org/10.7717/peerj.9598 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nielsen et al. title: Identification of key genes and pathways in endometriosis by integrated expression profiles analysis link: https://peerj.com/articles/10171 last-modified: 2020-12-07 description: The purpose of this study was to integrate the existing expression profile data on endometriosis (EM)-related tissues in order to identify the differentially expressed genes. In this study, three series of raw expression data were downloaded from GEO database. Differentially expressed genes (DEGs) in three tissue types were screened. GO, KEGG pathway enrichment analysis, core differential genes (CDGs) protein–protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA) were performed, finally, the dysregulation of Hippo pathway in ectopic endometrium (EC) was detected by Western blotting. A total of 1,811 DEGs between eutopic (EU) and normal endometrium (NE), 5,947 DEGs between EC and EU, and 3,192 DEGs between EC and NE datasets were identified. After screening, 394 CDGs were obtained, and 5 hub genes identified in the PPI network. CDGs enrichment and WGCNA network analysis revealed cell proliferation, differentiation, migration and other biological processes, Hippo and Wnt signaling pathways, and a variety of tumor-related pathways. Western blotting results showed that YAP/TAZ was upregulated, and MOB1, pMOB1, SAV1, LATS1 and LATS2 were downregulated in EC. Moreover, CDGs, especially the hub genes, are potential biomarkers and therapeutic targets. Finally, the Hippo pathway might play a key role in the development of endometriosis. creator: Ding Cui creator: Yang Liu creator: Junyan Ma creator: Kaiqing Lin creator: Kaihong Xu creator: Jun Lin uri: https://doi.org/10.7717/peerj.10171 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cui et al. title: Influence of montane altitudinal ranges on species distribution models; evidence in Andean blow flies link: https://peerj.com/articles/10370 last-modified: 2020-12-07 description: BackgroundBlow flies are a family of dipterans of medical, veterinary and sanitary importance. We aim to predict the current geographical distribution of six neotropical blowfly species with different altitudinal ranges of distribution (high, medium, and lowlands) and degree of synanthropy (eusynanthropic, hemisynanthropic and asynanthropic) based on their existing fundamental niche (EA) in Northwestern South America.MethodsGeographical records were compiled based on data from museum specimens and literature. The accessible area hypothesis (M) was calculated based on three criteria: (1) Altitudinal range, (2) Synanthropy values deducted based on the Human Influence Index (HII) raster dataset, and (3). The mean dispersal capability of flies. The modeling was performed using the Maxent entropy modeling software. The selection of parameters was made with the R Program ENMeval package.ResultsThe models were assessed using the area under the operator-partial receiver curve (ROCp). The high statistical performance was evidenced in every modeling prediction. The modeling allowed identifying possible taxonomic inaccuracies and the lack of exhaustive collection in the field, especially for lowlands species. Geographical distribution predicted by the modeling and empirical data was remarkably coherent in montane species.DiscussionThe data obtained evidence that montane elevational ranges affect the performance of the distribution models. These models will allow a more precise predicting of medium and high elevation blow flies than lowlands species. Montane species modeling will accurately predict the fly occurrence to use such biological information for medical, legal, veterinary, and conservation purposes. creator: Mariano Altamiranda-Saavedra creator: Eduardo Amat creator: Luz Miryam Gómez-P uri: https://doi.org/10.7717/peerj.10370 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Altamiranda-Saavedra et al. title: Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery link: https://peerj.com/articles/10381 last-modified: 2020-12-07 description: Throughout the history of drug discovery, an enzymatic-based approach for identifying new drug molecules has been primarily utilized. Recently, protein–protein interfaces that can be disrupted to identify small molecules that could be viable targets for certain diseases, such as cancer and the human immunodeficiency virus, have been identified. Existing studies computationally identify hotspots on these interfaces, with most models attaining accuracies of ~70%. Many studies do not effectively integrate information relating to amino acid chains and other structural information relating to the complex. Herein, (1) a machine learning model has been created and (2) its ability to integrate multiple features, such as those associated with amino-acid chains, has been evaluated to enhance the ability to predict protein–protein interface hotspots. Virtual drug screening analysis of a set of hotspots determined on the EphB2-ephrinB2 complex has also been performed. The predictive capabilities of this model offer an AUROC of 0.842, sensitivity/recall of 0.833, and specificity of 0.850. Virtual screening of a set of hotspots identified by the machine learning model developed in this study has identified potential medications to treat diseases caused by the overexpression of the EphB2-ephrinB2 complex, including prostate, gastric, colorectal and melanoma cancers which are linked to EphB2 mutations. The efficacy of this model has been demonstrated through its successful ability to predict drug-disease associations previously identified in literature, including cimetidine, idarubicin, pralatrexate for these conditions. In addition, nadolol, a beta blocker, has also been identified in this study to bind to the EphB2-ephrinB2 complex, and the possibility of this drug treating multiple cancers is still relatively unexplored. creator: Rohit Nandakumar creator: Valentin Dinu uri: https://doi.org/10.7717/peerj.10381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nandakumar and Dinu title: Trials in developing a nanoscale material for extravascular contrast-enhanced ultrasound targeting hepatocellular carcinoma link: https://peerj.com/articles/10403 last-modified: 2020-12-07 description: BackgroundMedical imaging is an important approach for the diagnosis of hepatocellular carcinoma (HCC), a common life threaten disease, however, the diagnostic efficiency is still not optimal. Developing a novel method to improve diagnosis is necessary. The aim of this project was to formulate a material that can combine with GPC3 of HCC for targeted enhanced ultrasound.MethodsA material of sulfur hexafluoride (SF6) filled liposome microbubbles and conjugated with synthesized peptide (LSPMbs) was prepared and assessed in vitro and vivo. Liposome microbubbles were made of DPPC, DPPG, DSPE-PEG2000,and SF6, using thin film method to form shell, followed filling SF6, and conjugating peptide. A carbodiimide method was used for covalent conjugation of peptide to LSMbs.ResultsThe prepared LSPMbs appeared round shaped, with size of 380.9 ±  176.5 nm, and Zeta potential of −51.4 ±  10.4mV. LSPMbs showed high affinity to Huh-7 cells in vitro, presented good enhanced ultrasound effects, did not show cytotoxicity, and did not exhibit targeted fluorescence and enhanced ultrasound in animal xenograft tumors.ConclusionExtravascular contrast-enhanced ultrasound targeted GPC3 on HCC may not be realized, and the reason may be that targeted contrast agents of microbubbles are hard to access and accumulate in the tumor stroma and matrix. creator: Size Wu creator: Xiyuan Lin uri: https://doi.org/10.7717/peerj.10403 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu and Lin title: Neither ant dominance nor abundance explain ant-plant network structure in Mexican temperate forests link: https://peerj.com/articles/10435 last-modified: 2020-12-07 description: BackgroundAnt-plant mutualistic networks tend to have a nested structure that contributes to their stability, but the ecological factors that give rise to this structure are not fully understood. Here, we evaluate whether ant abundance and dominance hierarchy determine the structure of the ant-plant networks in two types of vegetation: oak and grassland, in two temperate environments of Mexico: Flor del Bosque State Park (FBSP) and La Malinche National Park (MNP). We predicted that dominant and abundant ant species make up the core, and submissives, the periphery of the network. We also expected a higher specialization level in the ant trophic level than in plant trophic level due to competition among the ant species for the plant-derived resources.MethodsThe ant-plant interaction network was obtained from the frequency of ant-plant interactions. We calculated a dominance hierarchy index for the ants using sampling with baits and evaluated their abundance using pitfall traps.ResultsIn MNP, the Formica spp. species complex formed the core of the network (in both the oak forest and the grassland), while in FBSP, the core species were Prenolepis imparis (oak forest) and Camponotus rubrithorax (grassland). Although these core species were dominant in their respective sites, they were not necessarily the most dominant ant species. Three of the four networks (oak forest and grassland in FBSP, and oak forest in MNP) were nested and had a higher number of plant species than ant species. Although greater specialization was observed in the ant trophic level in the two sites and vegetations, possibly due to competition with the more dominant ant species, this was not statistically significant. In three of these networks (grassland and oak forest of MNP and oak forest of FBSP), we found no correlation between the dominance hierarchy and abundance of the ant species and their position within the network. However, a positive correlation was found between the nestedness contribution value and ant dominance hierarchy in the grassland of the site FBSP, which could be due to the richer ant-plant network and higher dominance index of this community.ConclusionsOur evidence suggests that ant abundance and dominance hierarchy have little influence on network structure in temperate ecosystems, probably due to the species-poor ant-plant network and a dominance hierarchy formed only by the presence of dominant and submissive species with no intermediate dominant species between them (absence of gradient in hierarchy) in these ecosystems. creator: Brenda Juárez-Juárez creator: Mariana Cuautle creator: Citlalli Castillo-Guevara creator: Karla López-Vázquez creator: María Gómez-Ortigoza creator: María Gómez-Lazaga creator: Cecilia Díaz-Castelazo creator: Carlos Lara creator: Gibrán R. Pérez-Toledo creator: Miguel Reyes uri: https://doi.org/10.7717/peerj.10435 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Juárez-Juárez et al. title: Association between parenting and non-suicidal self-injury among adolescents in Yunnan, China: a cross-sectional survey link: https://peerj.com/articles/10493 last-modified: 2020-12-07 description: BackgroundNon-suicidal self-injury (NSSI) among adolescents is prevalent and its rate has increased in recent years worldwide. Previous studies had investigated the association between parenting and childhood NSSI, but little is known about the relationship between parental rearing and repetition and severity of NSSI. The aim of this study was to investigate associations of parenting with NSSI and its repetition and severity in a representative adolescent sample from southwestern China.MethodsIn this cross-sectional study, a sample of 2,705 adolescents (F/M: 1,245/1,460; mean age: 13.4 ± 2.2 years) was recruited from 14 randomly selected schools in Lincang municipality, Yunnan province, China. A self-report questionnaire was used to collect data. The Adolescent Non-Suicidal Self-Injury Function Assessment Scale and the short Chinese Egna Minnen av Barndoms Uppfostran (s-EMBU-C) were used to evaluate NSSI behaviors and parenting style, respectively. Univariate and multivariate logistic regression models were adopted to examine association between parenting and NSSI.ResultsOverall lifetime prevalence of NSSI was 47.1% (95% CI [36.2–58.0]), with self-cutting being the most common form (23.5% (95% CI [19.3–27.7])), followed by hitting hard objects (23.4% (95% CI [20.2–26.7])) and pulling hairs (20.9% (95% CI [18.8–22.6])). In multiple logistic regression analyses, NSSI was positively associated with high level of father’s rejection (OR: 1.32 (95% CI [1.01–1.72])), high level of mother’s rejection (OR: 1.76 (95% CI [1.46–2.13])), low level of mother’s emotional warmth (OR: 1.42 (95% CI [1.15–1.75])), and high level of mother’s overprotection (OR: 1.74 (95% CI [1.49–2.03])), repeated NSSI was positively associated with low level of father’s emotional warmth (OR: 1.39 (95% CI [1.10–1.75])) and high level of mother’s overprotection (OR: 1.79 (95% CI [1.33–2.41])), and severe NSSI was positively associated with low level of father’s emotional warmth (OR: 1.64 (95% CI [1.11–2.43])) and high level of mother’s rejection (OR: 2.16 (95% CI [1.71–2.71])).ConclusionNSSI is common among adolescents in southwestern China. Negative parenting styles are associated with NSSI, repeated NSSI, and severe NSSI. The development of intervention measures for preventing or reducing NSSI among Chinese adolescents in school settings should consider parenting styles. creator: Yi Liu creator: Yuanyuan Xiao creator: Hailiang Ran creator: Xingting He creator: Linling Jiang creator: TianLan Wang creator: Run-xu Yang creator: Xiufeng Xu creator: Guangya Yang creator: Jin Lu uri: https://doi.org/10.7717/peerj.10493 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Liu et al. title: Recalibration of mapping quality scores in Illumina short-read alignments improves SNP detection results in low-coverage sequencing data link: https://peerj.com/articles/10501 last-modified: 2020-12-07 description: BackgroundLow-coverage sequencing is a cost-effective way to obtain reads spanning an entire genome. However, read depth at each locus is low, making sequencing error difficult to separate from actual variation. Prior to variant calling, sequencer reads are aligned to a reference genome, with alignments stored in Sequence Alignment/Map (SAM) files. Each alignment has a mapping quality (MAPQ) score indicating the probability a read is incorrectly aligned. This study investigated the recalibration of probability estimates used to compute MAPQ scores for improving variant calling performance in single-sample, low-coverage settings.Materials and MethodsSimulated tomato, hot pepper and rice genomes were implanted with known variants. From these, simulated paired-end reads were generated at low coverage and aligned to the original reference genomes. Features extracted from the SAM formatted alignment files for tomato were used to train machine learning models to detect incorrectly aligned reads and output estimates of the probability of misalignment for each read in all three data sets. MAPQ scores were then re-computed from these estimates. Next, the SAM files were updated with new MAPQ scores. Finally, Variant calling was performed on the original and recalibrated alignments and the results compared.ResultsIncorrectly aligned reads comprised only 0.16% of the reads in the training set. This severe class imbalance required special consideration for model training. The F1 score for detecting misaligned reads ranged from 0.76 to 0.82. The best performing model was used to compute new MAPQ scores. Single Nucleotide Polymorphism (SNP) detection was improved after mapping score recalibration. In rice, recall for called SNPs increased by 5.2%, while for tomato and pepper it increased by 3.1% and 1.5%, respectively. For all three data sets the precision of SNP calls ranged from 0.91 to 0.95, and was largely unchanged both before and after mapping score recalibration.ConclusionRecalibrating MAPQ scores delivers modest improvements in single-sample variant calling results. Some variant callers operate on multiple samples simultaneously. They exploit every sample’s reads to compensate for the low read-depth of individual samples. This improves polymorphism detection and genotype inference. It may be that small improvements in single-sample settings translate to larger gains in a multi-sample experiment. A study to investigate this is ongoing. creator: Eliot Cline creator: Nuttachat Wisittipanit creator: Tossapon Boongoen creator: Ekachai Chukeatirote creator: Darush Struss creator: Anant Eungwanichayapant uri: https://doi.org/10.7717/peerj.10501 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cline et al. title: Characterization of a profilin-like protein from Fasciola hepatica link: https://peerj.com/articles/10503 last-modified: 2020-12-07 description: Fasciola hepatica is the causative agent of fasciolosis, an important disease of humans and livestock around the world. There is an urgent requirement for novel treatments for F. hepatica due to increasing reports of drug resistance appearing around the world. The outer body covering of F. hepatica is referred to as the tegument membrane which is of crucial importance for the modulation of the host response and parasite survival; therefore, tegument proteins may represent novel drug or vaccine targets. Previous studies have identified a profilin-like protein in the tegument of F. hepatica. Profilin is a regulatory component of the actin cytoskeleton in all eukaryotic cells, and in some protozoan parasites, profilin has been shown to drive a potent IL-12 response. This study characterized the identified profilin form F. hepatica (termed FhProfilin) for the first time. Recombinant expression of FhProfilin resulted in a protein approximately 14 kDa in size which was determined to be dimeric like other profilins isolated from a range of eukaryotic organisms. FhProfilin was shown to bind poly-L-proline (pLp) and sequester actin monomers which is characteristic of the profilin family; however, there was no binding of FhProfilin to phosphatidylinositol lipids. Despite FhProfilin being a component of the tegument, it was shown not to generate an immune response in experimentally infected sheep or cattle. creator: Jessica Wilkie creator: Timothy C. Cameron creator: Travis Beddoe uri: https://doi.org/10.7717/peerj.10503 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wilkie et al. title: Description of a new genus and species for a common and widespread Amazonian satyrine butterfly (Lepidoptera: Nymphalidae: Satyrinae: Satyrini) link: https://peerj.com/articles/10324 last-modified: 2020-12-04 description: We here propose a new monotypic butterfly genus Scriptor Nakahara & Espeland, n. gen. to accommodate a new species, S. sphenophorus Lamas & Nakahara, n. sp., described and named herein. Scriptor sphenophorusn. gen. and n. sp.is a relatively common and widespread butterfly species which is recovered as a member of the so-called “Splendeuptychia clade” in the nymphalid subtribe Euptychiina, based on our molecular phylogenetic analysis using a maximum likelihood approach. Nevertheless, its sister group is not confidently resolved in any analysis, supporting a relatively distant relationship to any described genus as well as our decision to establish a new monotypic genus. We further discuss the proposed taxonomy in the light of frequent criticism of the description of monotypic taxa, as well as emphasize the importance of incorporating multiple evidence when describing new genera, illustrated by reference to several recent generic descriptions in this subtribe. creator: Shinichi Nakahara creator: Gerardo Lamas creator: Keith Willmott creator: Marianne Espeland uri: https://doi.org/10.7717/peerj.10324 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nakahara et al. title: Comparing multiple comparisons: practical guidance for choosing the best multiple comparisons test link: https://peerj.com/articles/10387 last-modified: 2020-12-04 description: Multiple comparisons tests (MCTs) include the statistical tests used to compare groups (treatments) often following a significant effect reported in one of many types of linear models. Due to a variety of data and statistical considerations, several dozen MCTs have been developed over the decades, with tests ranging from very similar to each other to very different from each other. Many scientific disciplines use MCTs, including >40,000 reports of their use in ecological journals in the last 60 years. Despite the ubiquity and utility of MCTs, several issues remain in terms of their correct use and reporting. In this study, we evaluated 17 different MCTs. We first reviewed the published literature for recommendations on their correct use. Second, we created a simulation that evaluated the performance of nine common MCTs. The tests examined in the simulation were those that often overlapped in usage, meaning the selection of the test based on fit to the data is not unique and that the simulations could inform the selection of one or more tests when a researcher has choices. Based on the literature review and recommendations: planned comparisons are overwhelmingly recommended over unplanned comparisons, for planned non-parametric comparisons the Mann-Whitney-Wilcoxon U test is recommended, Scheffé’s S test is recommended for any linear combination of (unplanned) means, Tukey’s HSD and the Bonferroni or the Dunn-Sidak tests are recommended for pairwise comparisons of groups, and that many other tests exist for particular types of data. All code and data used to generate this paper are available at: https://github.com/stevemidway/MultipleComparisons. creator: Stephen Midway creator: Matthew Robertson creator: Shane Flinn creator: Michael Kaller uri: https://doi.org/10.7717/peerj.10387 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Midway et al. title: The phylogeny and systematics of Xiphosura link: https://peerj.com/articles/10431 last-modified: 2020-12-04 description: Xiphosurans are aquatic chelicerates with a fossil record extending into the Early Ordovician and known from a total of 88 described species, four of which are extant. Known for their apparent morphological conservatism, for which they have gained notoriety as supposed ‘living fossils’, recent analyses have demonstrated xiphosurans to have an ecologically diverse evolutionary history, with several groups moving into non-marine environments and developing morphologies markedly different from those of the modern species. The combination of their long evolutionary and complex ecological history along with their paradoxical patterns of morphological stasis in some clades and experimentation among others has resulted in Xiphosura being of particular interest for macroevolutionary study. Phylogenetic analyses have shown the current taxonomic framework for Xiphosura—set out in the Treatise of Invertebrate Paleontology in 1955—to be outdated and in need of revision, with several common genera such as PaleolimulusDunbar, 1923 and LimulitellaStørmer, 1952 acting as wastebasket taxa. Here, an expanded xiphosuran phylogeny is presented, comprising 58 xiphosuran species as part of a 158 taxon chelicerate matrix coded for 259 characters. Analysing the matrix under both Bayesian inference and parsimony optimisation criteria retrieves a concordant tree topology that forms the basis of a genus-level systematic revision of xiphosuran taxonomy. The genera EuproopsMeek, 1867, BelinurusKönig, 1820, Paleolimulus, Limulitella, and Limulus are demonstrated to be non-monophyletic and the previously synonymized genera KoenigiellaRaymond, 1944 and PrestwichianellaCockerell, 1905 are shown to be valid. In addition, nine new genera (Andersoniella gen. nov., Macrobelinurus gen. nov., and Parabelinurus gen. nov. in Belinurina; Norilimulus gen. nov. in Paleolimulidae; Batracholimulus gen. nov. and Boeotiaspis gen. nov. in Austrolimulidae; and Allolimulus gen. nov., Keuperlimulus gen. nov., and Volanalimulus gen. nov. in Limulidae) are erected to accommodate xiphosuran species not encompassed by existing genera. One new species, Volanalimulus madagascarensis gen. et sp. nov., is also described. Three putative xiphosuran genera—ElleriaRaymond, 1944, ArcheolimulusChlupáč, 1963, and DrabovaspisChlupáč, 1963—are determined to be non-xiphosuran arthropods and as such are removed from Xiphosura. The priority of BelinurusKönig, 1820 over BellinurusPictet, 1846 is also confirmed. This work is critical for facilitating the study of the xiphosuran fossil record and is the first step in resolving longstanding questions regarding the geographic distribution of the modern horseshoe crab species and whether they truly represent ‘living fossils’. Understanding the long evolutionary history of Xiphosura is vital for interpreting how the modern species may respond to environmental change and in guiding conservation efforts. creator: James C. Lamsdell uri: https://doi.org/10.7717/peerj.10431 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lamsdell title: Identification and characterization of critical genes associated with tamoxifen resistance in breast cancer link: https://peerj.com/articles/10468 last-modified: 2020-12-04 description: BackgroundTamoxifen resistance in breast cancer is an unsolved problem in clinical practice. The aim of this study was to determine the potential mechanisms of tamoxifen resistance through bioinformatics analysis.MethodsGene expression profiles of tamoxifen-resistant MCF-7/TR and MCF-7 cells were acquired from the Gene Expression Omnibus dataset GSE26459, and differentially expressed genes (DEGs) were detected with R software. We conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses using Database for Annotation, Visualization and Integrated Discovery. A protein–protein interaction (PPI) network was generated, and we analyzed hub genes in the network with the Search Tool for the Retrieval of Interacting Genes database. Finally, we used siRNAs to silence the target genes and conducted the MTS assay.ResultsWe identified 865 DEGs, 399 of which were upregulated. GO analysis indicated that most genes are related to telomere organization, extracellular exosomes, and binding-related items for protein heterodimerization. PPI network construction revealed that the top 10 hub genes—ACLY, HSPD1, PFAS, GART, TXN, HSPH1, HSPE1, IRAS, TRAP1, and ATIC—might be associated with tamoxifen resistance. Consistently, RT-qPCR analysis indicated that the expression of these 10 genes was increased in MCF-7/TR cells comparing with MCF-7 cells. Four hub genes (TXN, HSPD1, HSPH1 and ATIC) were related to overall survival in patients who accepted tamoxifen. In addition, knockdown of HSPH1 by siRNA may lead to reduced growth of MCF-7/TR cell with a trend close to significance (P = 0.07), indicating that upregulation of HSPH1 may play a role in tamoxifen resistance.ConclusionThis study revealed a number of critical hub genes that might serve as therapeutic targets in breast cancer resistant to tamoxifen and provided potential directions for uncovering the mechanisms of tamoxifen resistance. creator: Kai Zhang creator: Kuikui Jiang creator: Ruoxi Hong creator: Fei Xu creator: Wen Xia creator: Ge Qin creator: Kaping Lee creator: Qiufan Zheng creator: Qianyi Lu creator: Qinglian Zhai creator: Shusen Wang uri: https://doi.org/10.7717/peerj.10468 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Zhang et al. title: Patterns of telomere length with age in African mole-rats: New insights from quantitative fluorescence in situ hybridisation (qFISH) link: https://peerj.com/articles/10498 last-modified: 2020-12-04 description: Naked mole-rats Heterocephalus glaber (NMRs) are the longest-lived rodent and also resist the normal signs of senescence. In a number of species, cellular ageing has been correlated with a reduction in telomere length, yet relatively little is known about telomeres and their age-related dynamics in NMRs and other African mole-rats. Here, we apply fluorescence in situ hybridisation (FISH) to quantify telomeric repeat sequences in the NMR, the Damaraland mole-rat, Fukomys damarensis (DMR) and the Mahali mole-rat, Cryptomys hottentotus mahali (MMR). Both terminal and non-terminal telomeric sequences were identified in chromosomes of the NMR and DMR, whilst the MMR displayed only terminal telomeric repeats. Measurements of tooth wear and eruption patterns in wild caught DMRs and MMRs, and known ages in captive bred NMRs, were used to place individuals into relative age classes and compared with a quantitative measure of telomeric fluorescence (as a proxy for telomere size). While NMRs and MMRs failed to show an age-related decline in telomeric fluorescence, the DMR had a significant decrease in fluorescence with age, suggesting a decrease in telomere size in older animals. Our results suggest that among African mole-rats there is variation between species with respect to the role of telomere shortening in ageing, and the replicative theory of cellular senescence. creator: Stephanie R.L. Leonida creator: Nigel C. Bennett creator: Andrew R. Leitch creator: Chris G. Faulkes uri: https://doi.org/10.7717/peerj.10498 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Leonida et al. title: Comprehensive analysis of circRNA expression profiles and circRNA-associated competing endogenous RNA networks in IgA nephropathy link: https://peerj.com/articles/10395 last-modified: 2020-12-03 description: BackgroundImmunoglobulin A nephropathy (IgAN) is immune-mediated primary glomerulonephritis, which is the most common reason leading to renal failure worldwide. The exact pathogenesis of IgAN is not well defined. Accumulating evidence indicates that circular RNAs (circRNAs) play crucial roles in the immune disease by involving in the competing endogenous RNA (ceRNA) network mechanism. At present, the studies of the circRNA profiles and circRNA-associated ceRNA networks in the IgAN are still scarce. This study aimed to elucidate the potential roles of circRNA-associated ceRNA networks of peripheral blood mononuclear cells (PBMCs) in IgAN patientsMethodCircRNA sequencing was used to identify the differential expressed circRNAs (DEcircRNAs) of PBMCs in IgAN and healthy controls; limma packages from data sets GSE25590 and GSE73953 in the Gene Expression Omnibus (GEO) database, were used to identify differentially expressed micro RNAs (miRNAs) and message RNAs (mRNAs). A circRNA-miRNA-mRNA ceRNA network was constructed to further investigate the mechanisms of IgAN. Then, GO analysis and KEGG enrichment analyses were used to annotate the genes involved in the circRNA-associated ceRNA network. Further, Protein-protein interaction (PPI) networks were established to screen potential hub genes, by using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). Last, a quantitative real-time polymerase chain reaction (qRT-PCR) was applied to verify the hub genes in the ceRNA network.ResultA total of 145 circRNAs, 22 miRNAs, and 1,117 mRNAs were differentially expressed in IgAN compared with controls (P < 0.05). A ceRNA network was constructed which contained 16 DEcircRNAs, 72 differential expressed mRNAs (DEmRNAs) and 11 differential expressed miRNAs (DEmiRNAs). KEGG pathway enrichment analysis illustrated the underlying biological functions of the ceRNA-associated genes, such as Nitrogen compound metabolic process, COPII-coated ER to Golgi transport vesicle, CAMP response element protein binding process (P < 0.01); meanwhile, Hepatitis B, GnRH signaling, and Prion disease were the most significant enrichment GO terms (P < 0.01). PPI network based on STRING analysis identified 4 potentially hub genes. Finally, Ankyrin repeat and SOCS box containing 16 (ASB16), SEC24 homolog C, COPII coat complex component (SEC24C) were confirmed by qRT-PCR (P < 0.05) and were identified as the hub genes of the ceRNA network in our study.ConclusionOur study identified a novel circRNA-mediated ceRNA regulatory network mechanisms in the pathogenesis of IgAN. creator: Haiyang Liu creator: Di Liu creator: Yexin Liu creator: Ming Xia creator: Yan Li creator: Mei Li creator: Hong Liu uri: https://doi.org/10.7717/peerj.10395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Effects of monofilament nylon versus braided multifilament nylon gangions on catch rates of Greenland shark (Somniosus microcephalus) in bottom set longlines link: https://peerj.com/articles/10407 last-modified: 2020-12-03 description: The Greenland shark (Somniosus microcephalus) is the main bycatch species in established and exploratory inshore longline fisheries for Greenland halibut (Reinhardtius hippoglossoides) on the east coast of Baffin Island, Canada. Bycatch and entanglement in longline gear has at times been substantial and post-release survival is questionable when Greenland sharks are released with trailing fishing gear. This study investigated the effect of the type of fishing line used in the gangion and gangion breaking strength on catch rates of Greenland shark and Greenland halibut in bottom set longlines. Circle (size 14/0, 0° offset) hooks were used throughout the study. Behavior of captured sharks, mode of capture (i.e., jaw hook and/or entanglement), level of entanglement in longline gear, time required to disentangle sharks and biological information (sex, body length and health status) were recorded. Catch rates of Greenland shark were independent of monofilament nylon gangion breaking strength and monofilament gangions captured significantly fewer Greenland sharks than the traditional braided multifilament nylon gangion. Catch rates and body size of Greenland halibut did not differ significantly between gangion treatments. Although most (84%) of the Greenland sharks were hooked by the jaw, a high percentage (76%) were entangled in the mainline. The mean length of mainline entangled around the body and/or caudal peduncle and caudal fin was 28.7 m. Greenland sharks exhibited cannibalistic behavior with 15% of captured sharks cannibalized. All remaining sharks were alive and survived the disentanglement process which can be attributed to their lethargic behavior and lack of resistance when hauled to the surface. Thus, as a conservation measure fishers should be encouraged to remove trailing fishing gear prior to release. Our results are used to demonstrate benefits to the fishing industry with regard to an overall reduction in the period of time to disentangle sharks and damage to fishing gear by switching from braided multifilament to monofilament gangions in Greenland halibut longline fisheries. creator: Scott M. Grant creator: Jenna G. Munden creator: Kevin J. Hedges uri: https://doi.org/10.7717/peerj.10407 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Grant et al. title: Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species link: https://peerj.com/articles/10412 last-modified: 2020-12-03 description: Social insects have co-existed with microbial species for millions of years and have evolved a diversity of collective defenses, including the use of antimicrobials. While many studies have revealed strategies that ants use against microbial entomopathogens, and several have shown ant-produced compounds inhibit environmental bacterial growth, few studies have tested whether exposure to environmental bacteria represents a health threat to ants. We compare four ant species’ responses to exposure to Escherichia coli and Staphylococcus epidermidis bacteria in order to broaden our understanding of microbial health-threats to ants and their ability to defend against them. In a first experiment, we measure worker mortality of Solenopsis invicta, Brachymyrmex chinensis, Aphaenogaster rudis, and Dorymyrmex bureni in response to exposure to E. coli and S. epidermidis. We found that exposure to E. coli was lethal for S. invicta and D. bureni, while all other effects of exposure were not different from experimental controls. In a second experiment, we compared the antimicrobial ability of surface extracts from bacteria-exposed and non-exposed S. invicta and B. chinensis worker ants, to see if exposure to E. coli or S. epidermidis led to an increase in antimicrobial compounds. We found no difference in the inhibitory effects from either treatment group in either species. Our results demonstrate the susceptibility to bacteria is varied across ant species. This variation may correlate with an ant species’ use of surface antimicrobials, as we found significant mortality effects in species which also were producing antimicrobials. Further exploration of a wide range of both bacteria and ant species is likely to reveal unique and nuanced antimicrobial strategies and deepen our understanding of how ant societies respond to microbial health threats. creator: Omar Halawani creator: Robert R. Dunn creator: Amy M. Grunden creator: Adrian A. Smith uri: https://doi.org/10.7717/peerj.10412 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Halawani et al. title: Moderately low nitrogen application mitigate the negative effects of salt stress on annual ryegrass seedlings link: https://peerj.com/articles/10427 last-modified: 2020-12-03 description: Appropriate application of nitrogen (N) can alleviate the salt stress-induced damage on plants. This study explores the changes of nitrogen requirement in feeding annual ryegrass seedlings under mild salt concentrations (50 mM, 100 mM) plus its underlying mitigation mechanism. Results showed that low salt concentration decreased N requirement as observed from the increment in plant height and biomass at a relative low N level (2.0 mM not 5.0 mM). Under salt treatment, especially at 50 mM NaCl, the OJIP (Chl a fluorescence induction transient) curve and a series of performance indexes (PIABS, RC/CS0, ET0/CS0, ϕE0, ϕ0) peaked whereas DI0/RC, Vj and M0 were the lowest under moderately low N level (2.0 mM). In addition, under salt stress, moderately low N application could maintain the expression of NR (nitrate reductase) and GS (glutamine synthetase) encoding genes at a relatively stable level but had no effect on the expression of detected NRT (nitrate transporter) gene. The seedlings cultured at 2.0 mM N also exhibited the highest activity of CAT and POD antioxidant enzymes and the lowest MDA content and EL under relative low level of salt treatment. These results indicated that mild salt treatment of annual ryegrass seedlings might reduce N requirement while moderately low N application could promote their growth via regulating photosynthesis, alleviating ROS-induced (reactive oxygen species) damage and maintenance of N metabolism. These results also can provide useful reference for nitrogen application in moderation rather than in excess on annual ryegrass in mild or medium salinity areas through understanding the underlying response mechanisms. creator: An Shao creator: Zhichao Sun creator: Shugao Fan creator: Xiao Xu creator: Wei Wang creator: Erick Amombo creator: Yanling Yin creator: Xiaoning Li creator: Guangyang Wang creator: Hongli Wang creator: Jinmin Fu uri: https://doi.org/10.7717/peerj.10427 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shao et al. title: Analysis of 44 Vibrio anguillarum genomes reveals high genetic diversity link: https://peerj.com/articles/10451 last-modified: 2020-12-03 description: Vibriosis, a hemorrhagic septicemic disease caused by the bacterium Vibrio anguillarum, is an important bacterial infection in Danish sea-reared rainbow trout. Despite of vaccination, outbreaks still occur, likely because the vaccine is based on V. anguillarum strains from abroad/other hosts than rainbow trout. Information about the genetic diversity of V. anguillarum specifically in Danish rainbow trout, is required to investigate this claim. Consequently, the aim of the present investigation was to sequence and to characterize a collection of 44 V. anguillarum strains obtained primarily from vibriosis outbreaks in Danish rainbow trout. The strains were sequenced, de novo assembled, and the genomes examined for the presence of plasmids, virulence, and acquired antibiotic resistance genes. To investigate the phylogeny, single nucleotide polymorphisms were identified, and the pan-genome was calculated. All strains carried tet(34) encoding tetracycline resistance, and 36 strains also contained qnrVC6 for increased fluoroquinolone/quinolone resistance. But interestingly, all strains were phenotypic sensitive to both oxytetracycline and oxolinic acid. Almost all serotype O1 strains contained a pJM1-like plasmid and nine serotype O2A strains carried the plasmid p15. The distribution of virulence genes was rather similar across the strains, although evident variance among serotypes was observed. Most significant, almost all serotype O2 and O3 strains, as well as the serotype O1 strain without a pJM1-like plasmid, carried genes encoding piscibactin biosynthesis. Hence supporting the hypothesis, that piscibactin plays a crucial role in virulence for pathogenic strains lacking the anguibactin system. The phylogenetic analysis and pan-genome calculations revealed great diversity within V. anguillarum. Serotype O1 strains were in general very similar, whereas considerable variation was found among serotype O2A strains. The great diversity within the V. anguillarum serotype O2A genomes is most likely the reason why vaccines provide good protection from some strains, but not from others. Hopefully, the new genomic data and knowledge provided in this study might help develop an optimized vaccine against V. anguillarum in the future to reduce the use of antibiotics, minimize economic losses and improve the welfare of the fish. creator: Mie Johanne Hansen creator: Egle Kudirkiene creator: Inger Dalsgaard uri: https://doi.org/10.7717/peerj.10451 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hansen et al. title: ARID1A alterations and their clinical significance in cholangiocarcinoma link: https://peerj.com/articles/10464 last-modified: 2020-12-03 description: BackgroundARID1A is a member of the SWI/SNF chromatin remodeling complex. It functions as a tumor suppressor and several therapeutic targets in ARID1A-mutated cancers are currently under development, including EZH2. A synthetic lethal relationship between ARID1A and EZH2 has been revealed in several tumor entities. Although genomic alterations of ARID1A have been described in various cancers, no study has examined correlations between ARID1A gene mutation and protein expression with clinicopathologic parameters and prognosis, particularly in liver fluke-related cholangiocarcinoma (Ov-CCA). Here, we investigated the clinical significance of ARID1A mutations and protein expression in CCA tissues and determined whether there is a correlation with EZH2 protein expression.MethodsWe evaluated ARID1A and EZH2 immunoreactivity using immunohistochemistry in 98 Ov-CCA with a wide range of clinicopathological features. Somatic mutations of ARID1A were analyzed using the ICGC sequencing data in 489 of Ov and non Ov-CCA and assessed prognostic values.ResultsWhile detecting a loss or reduction of ARID1A expression in 54 cases (55%) in Ov-CCA, ARID1A expression was associated with ARID1A mutations (p < 0.001, adjusted p-value < 0.001). We observed that 12 of 13 tumors (92%) with loss of ARID1A expression had truncating mutations. There were nine of 13 tumors (69%) with loss of ARID1A expression and 25 of 41 tumors (61%) with low ARID1A expression exhibited distant metastasis (p = 0.028, adjusted p-value = 0.168). ARID1A was predominantly mutated in Ov-CCA compared to non Ov-CCA (24% and 14% in Ov-CCA and non Ov-CCA, respectively, p = 0.027). There were 36 of 72 (50%) and 52 of 79 (66%) tumors with ARID1A mutation showed tumor stage IV and T3/T4, respectively. The significant mutual exclusivity and co-occurrence between ARID1A and TP53/KRAS mutations were not found in ICGC cohort. In addition, high EZH2 expression, a potential synthetic lethal target in ARID1A-mutated tumors, was detected in 49 of 98 Ov-CCA (50%). Importantly, neither ARID1A expression nor ARID1A mutations correlated with EZH2 expression in this cohort.ConclusionWe found that ARID1A inactivation, by somatic mutation or by loss of expression, frequently occurs in Ov-CCA. Reduction of ARID1A expression and/or somatic mutation was shown to be associated with CCA progression. These findings suggest that ARID1A may serve as a prognostic biomarker, and thus may be a promising therapeutic target for CCA. creator: Achira Namjan creator: Anchalee Techasen creator: Watcharin Loilome creator: Prakasit Sa-ngaimwibool creator: Apinya Jusakul uri: https://doi.org/10.7717/peerj.10464 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Namjan et al. title: Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs link: https://peerj.com/articles/10487 last-modified: 2020-12-03 description: The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress. creator: Aline Bruna M. Vaz creator: Paula Luize C. Fonseca creator: Felipe F. Silva creator: Gabriel Quintanilha-Peixoto creator: Inmaculada Sampedro creator: Jose A. Siles creator: Anderson Carmo creator: Rodrigo B. Kato creator: Vasco Azevedo creator: Fernanda Badotti creator: Juan A. Ocampo creator: Carlos A. Rosa creator: Aristóteles Góes-Neto uri: https://doi.org/10.7717/peerj.10487 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Vaz et al. title: Identification of a six-gene metabolic signature predicting overall survival for patients with lung adenocarcinoma link: https://peerj.com/articles/10320 last-modified: 2020-12-02 description: BackgroundLung cancer is the leading cause of cancer-related deaths worldwide. Lung adenocarcinoma (LUAD) is one of the main subtypes of lung cancer. Hundreds of metabolic genes are altered consistently in LUAD; however, their prognostic role remains to be explored. This study aimed to establish a molecular signature that can predict the prognosis in patients with LUAD based on metabolic gene expression.MethodsThe transcriptome expression profiles and corresponding clinical information of LUAD were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The differentially expressed genes (DEGs) between LUAD and paired non-tumor samples were identified by the Wilcoxon rank sum test. Univariate Cox regression analysis and the lasso Cox regression model were used to construct the best-prognosis molecular signature. A nomogram was established comprising the prognostic model for predicting overall survival. To validate the prognostic ability of the molecular signature and the nomogram, the Kaplan–Meier survival analysis, Cox proportional hazards model, and receiver operating characteristic analysis were used.ResultsThe six-gene molecular signature (PFKP, PKM, TPI1, LDHA, PTGES, and TYMS) from the DEGs was constructed to predict the prognosis. The molecular signature demonstrated a robust independent prognostic ability in the training and validation sets. The nomogram including the prognostic model had a greater predictive accuracy than previous systems. Furthermore, a gene set enrichment analysis revealed several significantly enriched metabolic pathways, which suggests a correlation of the molecular signature with metabolic systems and may help explain the underlying mechanisms.ConclusionsOur study identified a novel six-gene metabolic signature for LUAD prognosis prediction. The molecular signature could reflect the dysregulated metabolic microenvironment, provide potential biomarkers for predicting prognosis, and indicate potential novel metabolic molecular-targeted therapies. creator: Yubo Cao creator: Xiaomei Lu creator: Yue Li creator: Jia Fu creator: Hongyuan Li creator: Xiulin Li creator: Ziyou Chang creator: Sa Liu uri: https://doi.org/10.7717/peerj.10320 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cao et al. title: Risk factors for new-onset atrial fibrillation in patients with chronic obstructive pulmonary disease: a systematic review and meta-analysis link: https://peerj.com/articles/10376 last-modified: 2020-12-02 description: BackgroundNew-onset atrial fibrillation (AF) in patients with chronic obstructive pulmonary disease (COPD) is associated with an accelerated decline in lung function, and a significant increase in mortality rate. A deeper understanding of the risk factors for new-onset AF during COPD will provide insights into the relationship between COPD and AF and guide clinical practice. This systematic review and meta-analysis is designed to identify risk factors for new-onset AF in patients with COPD, and to formulate recommendations for preventing AF in COPD patients that will assist clinical decision making.MethodsPubMed, Embase, Web of Science and Cochrane Library databases were searched for studies, which reported the results of potential risk factors for new-onset AF in COPD patients.ResultsTwenty studies involving 8,072,043 participants were included. Fifty factors were examined as potential risk factors for new-onset AF during COPD. Risk factors were grouped according to demographics, comorbid conditions, and COPD- and cardiovascular-related factors. In quantitative analysis, cardiovascular- and demographic-related factors with a greater than 50% increase in the odds of new-onset AF included age (over 65 years and over 75 years), acute care encounter, coronary artery disease, heart failure and congestive heart failure. Only one factor is related to the reduction of odds by more than 33.3%, which is black race (vs white). In qualitative analysis, the comparison of the risk factors was conducted between COPD-associated AF and non-COPD-associated AF. Cardiovascular-related factors for non-COPD-associated AF were also considered as risk factors for new-onset AF during COPD; however, the influence tended to be stronger during COPD. In addition, comorbid factors identified in non-COPD-associated AF were not associated with an increased risk of AF during COPD.ConclusionsNew-onset AF in COPD has significant demographic characteristics. Older age (over 65 years), males and white race are at higher risk of developing AF. COPD patients with a history of cardiovascular disease should be carefully monitored for new-onset of AF, and appropriate preventive measures should be implemented. Even patients with mild COPD are at high risk of new-onset AF. This study shows that risk factors for new-onset AF during COPD are mainly those associated with the cardiovascular-related event and are not synonymous with comorbid factors for non-COPD-associated AF. The pathogenesis of COPD-associated AF may be predominantly related to the cardiac dysfunction caused by the chronic duration of COPD, which increases the risk of cardiovascular-related factors and further increases the risk of AF during COPD.PROSPERO registration numberCRD42019137758. creator: Qiangru Huang creator: Huaiyu Xiong creator: Tiankui Shuai creator: Meng Zhang creator: Chuchu Zhang creator: Yalei Wang creator: Lei Zhu creator: Jiaju Lu creator: Jian Liu uri: https://doi.org/10.7717/peerj.10376 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Identification of significant genes signatures and prognostic biomarkers in cervical squamous carcinoma via bioinformatic data link: https://peerj.com/articles/10386 last-modified: 2020-12-02 description: BackgroundCervical squamous cancer (CESC) is an intractable gynecological malignancy because of its high mortality rate and difficulty in early diagnosis. Several biomarkers have been found to predict the prognose of CESC using bioinformatics methods, but they still lack clinical effectiveness. Most of the existing bioinformatic studies only focus on the changes of oncogenes but neglect the differences on the protein level and molecular biology validation are rarely conducted.MethodsGene set data from the NCBI-GEO database were used in this study to compare the differences of gene and protein levels between normal and cancer tissues through significant pathway selection and core gene signature analysis to screen potential clinical biomarkers of CESC. Subsequently, the molecular and protein levels of clinical samples were verified by quantitative transcription PCR, western blot and immunohistochemistry.ResultsThree differentially expressed genes (RFC4, MCM2, TOP2A) were found to have a significant survival (P < 0.05) and highly expressed in CESC tissues. Molecular biological verification using quantitative reverse transcribed PCR, western blotting and immunohistochemistry assays exhibited significant differences in the expression of RFC4 between CESC and para-cancerous tissues (P < 0.05).ConclusionThis study identified three potential biomarkers (RFC4, MCM2, TOP2A) of CESC which may be useful to clarify the underlying mechanisms of CESC and predict the prognosis of CESC patients. creator: Yunan He creator: Shunjie Hu creator: Jiaojiao Zhong creator: Anran Cheng creator: Nianchun Shan uri: https://doi.org/10.7717/peerj.10386 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 He et al. title: Ixodes scapularis microbiome correlates with life stage, not the presence of human pathogens, in ticks submitted for diagnostic testing link: https://peerj.com/articles/10424 last-modified: 2020-12-02 description: Ticks are globally distributed arthropods and a public health concern due to the many human pathogens they carry and transmit, including the causative agent of Lyme disease, Borrelia burgdorferi. As tick species’ ranges increase, so do the number of reported tick related illnesses. The microbiome is a critical part of understanding arthropod biology, and the microbiome of pathogen vectors may provide critical insight into disease transmission and management. Yet we lack a comprehensive understanding of the microbiome of wild ticks, including what effect the presence of multiple tick-borne pathogens (TBPs) has on the microbiome. In this study we chose samples based on life stage (adult or nymph) and which TBPs were present. We used DNA from previously extracted Ixodes scapularis ticks that tested positive for zero, one, two or three common TBPs (B. burgdorferi, B. miyamotoi, Anaplasma phagocytophilum, Babesia microti). We produced 16S rRNA amplicon data for the whole tick microbiome and compared samples across TBPs status, single vs multiple coinfections, and life stages. Focusing on samples with a single TBP, we found no significant differences in microbiome diversity in ticks that were infected with B. burgdorferi and ticks with no TBPs. When comparing multiple TBPs, we found no significant difference in both alpha and beta diversity between ticks with a single TBP and ticks with multiple TBPs. Removal of TBPs from the microbiome did not alter alpha or beta diversity results. Life stage significantly correlated to variation in beta diversity and nymphs had higher alpha diversity than adult ticks. Rickettsia, a common tick endosymbiont, was the most abundant genus. This study confirms that the wild tick microbiome is highly influenced by life stage and much less by the presence of human pathogenic bacteria. creator: Joshua C. Gil creator: Zeinab H. Helal creator: Guillermo Risatti creator: Sarah M. Hird uri: https://doi.org/10.7717/peerj.10424 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gil et al. title: Phospho-islands and the evolution of phosphorylated amino acids in mammals link: https://peerj.com/articles/10436 last-modified: 2020-12-02 description: BackgroundProtein phosphorylation is the best studied post-translational modification strongly influencing protein function. Phosphorylated amino acids not only differ in physico-chemical properties from non-phosphorylated counterparts, but also exhibit different evolutionary patterns, tending to mutate to and originate from negatively charged amino acids (NCAs). The distribution of phosphosites along protein sequences is non-uniform, as phosphosites tend to cluster, forming so-called phospho-islands.MethodsHere, we have developed a hidden Markov model-based procedure for the identification of phospho-islands and studied the properties of the obtained phosphorylation clusters. To check robustness of evolutionary analysis, we consider different models for the reconstructions of ancestral phosphorylation states.ResultsClustered phosphosites differ from individual phosphosites in several functional and evolutionary aspects including underrepresentation of phosphotyrosines, higher conservation, more frequent mutations to NCAs. The spectrum of tissues, frequencies of specific phosphorylation contexts, and mutational patterns observed near clustered sites also are different. creator: Mikhail Moldovan creator: Mikhail S. Gelfand uri: https://doi.org/10.7717/peerj.10436 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Moldovan and Gelfand title: Distribution of phylogenetic groups, adhesin genes, biofilm formation, and antimicrobial resistance of uropathogenic Escherichia coli isolated from hospitalized patients in Thailand link: https://peerj.com/articles/10453 last-modified: 2020-12-02 description: BackgroundUrinary tract infections (UTIs) are the most common bacterial infections and are often caused by uropathogenic Escherichia coli (UPEC). We investigated the distribution of phylogenetic groups, adhesin genes, antimicrobial resistance, and biofilm formation in E. coli isolated from patients with UTIs.MethodsIn the present study, 208 UPEC isolated from Thai patients were classified into phylogenetic groups and adhesin genes were detected using multiplex PCR. Antimicrobial susceptibility testing was performed using agar disk diffusion. The Congo red agar method was used to determine the ability of the UPEC to form biofilm.ResultsThe most prevalent UPEC strains in this study belonged to phylogenetic group B2 (58.7%), followed by group C (12.5%), group E (12.0%), and the other groups (16.8%). Among adhesin genes, the prevalence of fimH (91.8%) was highest, followed by pap (79.3%), sfa (12.0%), and afa (7.7%). The rates of resistance to fluoroquinolones, trimethoprim-sulfamethoxazole, and amoxicillin-clavulanate were  65%, 54.3%, and 36.5%, respectively. The presence of adhesin genes and antibiotic resistance were more frequent in groups B2 and C compared to the other groups. Of the 129 multidrug-resistant UPEC strains, 54% were biofilm producers. Our findings further indicated that biofilm production was significantly correlated with the pap adhesin gene (p ≤ 0.05).ConclusionThese findings provide molecular epidemiologic data, antibiotic resistance profiles, and the potential for biofilm formation among UPEC strains that can inform further development of the appropriate prevention and control strategies for UTIs in this region. creator: Nipaporn Tewawong creator: Siriporn Kowaboot creator: Yaowaluk Pimainog creator: Naiyana Watanagul creator: Thanunrat Thongmee creator: Yong Poovorawan uri: https://doi.org/10.7717/peerj.10453 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tewawong et al. title: Genome-wide identification and evolution of HECT genes in wheat link: https://peerj.com/articles/10457 last-modified: 2020-12-02 description: BackgroundAs an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops.MethodsUsing a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana.ResultsThe predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat. creator: Xianwen Meng creator: Ting Yang creator: Jing Liu creator: Mingde Zhao creator: Jiuli Wang uri: https://doi.org/10.7717/peerj.10457 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Meng et al. title: Comparative genomic analysis of the principal Cryptosporidium species that infect humans link: https://peerj.com/articles/10478 last-modified: 2020-12-02 description: Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins. creator: Laura M. Arias-Agudelo creator: Gisela Garcia-Montoya creator: Felipe Cabarcas creator: Ana L. Galvan-Diaz creator: Juan F. Alzate uri: https://doi.org/10.7717/peerj.10478 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Arias-Agudelo et al. title: The gut microbiota in the common kestrel (Falco tinnunculus): a report from the Beijing Raptor Rescue Center link: https://peerj.com/articles/9970 last-modified: 2020-12-01 description: As a complex microecological system, the gut microbiota plays crucial roles in many aspects, including immunology, physiology and development. The specific function and mechanism of the gut microbiota in birds are distinct due to their body structure, physiological attributes and life history. Data on the gut microbiota of the common kestrel, a second-class protected animal species in China, are currently scarce. With high-throughput sequencing technology, we characterized the bacterial community of the gut from nine fecal samples from a wounded common kestrel by sequencing the V3-V4 region of the 16S ribosomal RNA gene. Our results showed that Proteobacteria (41.078%), Firmicutes (40.923%) and Actinobacteria (11.191%) were the most predominant phyla. Lactobacillus (20.563%) was the most dominant genus, followed by Escherichia-Shigella (17.588%) and Acinetobacter (5.956%). Our results would offer fundamental data and direction for the wildlife rescue. creator: Yu Guan creator: Hongfang Wang creator: Yinan Gong creator: Jianping Ge creator: Lei Bao uri: https://doi.org/10.7717/peerj.9970 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guan et al. title: Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration link: https://peerj.com/articles/10260 last-modified: 2020-12-01 description: Sea cucumbers possess the remarkable capacity to regenerate their body parts or organs. Regeneration of host organs and/or body parts involves reconstruction of the host associated microbiota, however, the dynamics and contribution of microbiota to the regeneration process are largely unknown due to a lack of experimental models. To track the dynamics of individual gut microbiomes during gut regeneration, both caged mariculture and laboratory isolator systems of sea cucumbers (Apostichopus japonicus) were developed and longitudinal meta16S analyses were performed. Under natural environmental conditions in the caged mariculture system, both bacterial and eukaryotic communities in sea cucumbers’ guts appeared to be reconstructed within 4 months after evisceration. Using the laboratory isolator, which can trace daily dynamics, we found that fecal microbiota collected before evisceration were clearly different from those collected after evisceration. We also identified eight key bacteria, belonging to Alteromonadaceae, Rhodobacteraceae, Oceanospirillaceae and family-unassigned Gammaproteobacteria, suggesting that these bacteria might interact with the host during the gut regeneration process. Six of the eight key bacteria were isolated for further bioassay using the isolator developed in this study to test whether these isolates affect gut regeneration. creator: Yohei Yamazaki creator: Yuichi Sakai creator: Juanwen Yu creator: Sayaka Mino creator: Tomoo Sawabe uri: https://doi.org/10.7717/peerj.10260 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yamazaki et al. title: In vitro and in vivo hypolipidemic properties of the aqueous extract of Spirulina platensis, cultivated in colored flasks under artificial illumination link: https://peerj.com/articles/10366 last-modified: 2020-12-01 description: BackgroundSpirulina is blue-green algae that grows mainly in tropical and subtropical lakes and is commonly used due to its nutritional features including high concentrations of protein, vitamins, mineral salts, carotenoids and antioxidants. This study aimed to investigate the anti-hypercholesterolemic potential of aqueous extract of Spirulina platensis cultivated in different colored flasks under artificial illumination; in vitro and in the diet induced hypercholesterolemic Swiss albino mice.MethodsSpirulina platensis was cultivated in red, blue, green and colorless Erlenmeyer flasks containing Zarrouk’s medium under aerobic conditions, with incessant illumination by artificial cool white fluorescent with light intensity of 2500 lux (35 µmol photon m−2 s−1). Chlorophyll a and total carotenoid contents were estimated using colorimetric methods, fatty acids composition was determined by GC-Mass, in vitro and in vivo anti-cholesterol assays were used in assessing the anti-hypercholesterolemia potential of obtained Spirulina cells.ResultsThe results showed that the highest cell dry weight, chlorophyl a, and carotenoid of S. platensis were observed in colorless flasks and that the lowest values were recorded with the green colored flasks. Also, the hot water extract of S. platensis obtained from colorless flasks at a concentration of 15 mg/mL after 60 min of incubation exhibited the greatest reduction of cholesterol level. Gas chromatography-mass spectrometry analysis of S. platensis methanolic extract showed 15 bioactive compounds were identified and grouped according to their chemical structures. An experimental model of hypercholesterolemic mice had been examined for impact of S. platensis individually and combined with atorvastatin drug. All S. platensis groups resulted in a remarkable decrease in plasma total cholesterol, triglycerides and low density lipoprotein; and increase in high density lipoprotein.ConclusionThe present study concluded that the hot aqueous extract of S. platensis developed in colorless flasks is recommended as a natural source for bioactive compounds, with anti-cholesterol and antioxidant potentialities. creator: Mahmoud A. Al-Saman creator: Nada M. Doleib creator: Mohamed R. Ibrahim creator: Mohamed Y. Nasr creator: Ahmed A. Tayel creator: Ragaa A. Hamouda uri: https://doi.org/10.7717/peerj.10366 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Al-Saman et al. title: Effects of plastic mulching on the accumulation and distribution of macro and micro plastics in soils of two farming systems in Northwest China link: https://peerj.com/articles/10375 last-modified: 2020-12-01 description: BackgroundInappropriate disposal of the plastic mulching debris could create macroplastics (MaPs) and microplastics (MiPs) pollution in agricultural soil.MethodsTo study the effects of farming systems on accumulation and distribution of agricultural plastic debris, research was carried out on two farming systems in Northwest China. Farming in Wutong Village (S1) is characterized by small plots and low-intensity machine tillage while farming in Shihezi (S2) is characterized by large plots and high-intensity machine tillage. In September 2017, we selected six fields in S1, three fields with 6–8 years of continuous plastic mulching (CM) as well as three fields with over 30 years of intermittent mulching (IM). In S2, we selected five cotton fields with 6, 7, 8, 15 and 18 years of continuous mulching. In both regions, MaPs and MiPs from soil surface to 30 cm depth (0–30 cm) were sampled.ResultsThe results showed that in S1, MaPs mass in fields with 6–8 years CM (i.e., 97.4kg·ha−1) were significantly higher than in fields with 30 years IM (i.e., 53.7 kg·ha−1). MaPs in size category of 10–50 cm2 accounted for 46.9% in fields of CM and 44.5% in fields of IM of total collected MaPs number. In S2, MaPs mass ranged from 43.5 kg·ha−1 to 148 kg·ha−1. MaPs in size category of 2–10 cm2 account for 41.1% of total collected MaPs number while 0.25–2 cm2 accounted for 40.6%. MiPs in S1 were mainly detected in fields with over 30 years of intermittent mulching (up to 2,200 particles·kg−1 soil), whereas in S2 were detected in all fields (up to 900 particles·kg−1 soil). The results indicated farming systems could substantially affect the accumulation and distribution of agricultural plastic debris. Continuous plastic mulching could accumulate higher amount of MaPs than intermittent plastic mulching. High-intensity machine tillage could lead to higher fragmentation of MaPs and more severe MiPs pollution. These results suggest that agricultural plastic regulations are needed. creator: Fanrong Meng creator: Tinglu Fan creator: Xiaomei Yang creator: Michel Riksen creator: Minggang Xu creator: Violette Geissen uri: https://doi.org/10.7717/peerj.10375 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Meng et al. title: Expression and phylogeny of multidrug resistance protein 2 and 4 in African white backed vulture (Gyps africanus) link: https://peerj.com/articles/10422 last-modified: 2020-12-01 description: Diclofenac toxicity in old world vultures is well described in the literature by both the severity of the toxicity induced and the speed of death. While the mechanism of toxicity remains unknown at present, the necropsy signs of gout suggests primary renal involvement at the level of the uric acid excretory pathways. From information in the chicken and man, uric acid excretion is known to be a complex process that involves a combination of glomerular filtration and active tubular excretion. For the proximal convoluted tubules excretion occurs as a two-step process with the basolateral cell membrane using the organic anion transporters and the apical membrane using the multidrug resistant protein to transport uric acid from the blood into the tubular fluid. With uric acid excretion seemingly inhibited by diclofenac, it becomes important to characterize these transporter mechanism at the species level. With no information being available on the molecular characterization/expression of MRPs of Gyps africanus, for this study we used next generation sequencing, and Sanger sequencing on the renal tissue of African white backed vulture (AWB), as the first step to establish if the MRPs gene are expressed in AWB. In silico analysis was conducted using different software to ascertain the function of the latter genes. The sequencing results revealed that the MRP2 and MRP4 are expressed in AWB vultures. Phylogeny of avian MRPs genes confirms that vultures and eagles are closely related, which could be attributed to having the same ancestral genes and foraging behavior. In silico analysis confirmed the transcribed proteins would transports anionic compounds and glucose. creator: Bono Nethathe creator: Aron Abera creator: Vinny Naidoo uri: https://doi.org/10.7717/peerj.10422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nethathe et al. title: Comprehensive pathway-related genes signature for prognosis and recurrence of ovarian cancer link: https://peerj.com/articles/10437 last-modified: 2020-12-01 description: BackgroundOvarian cancer (OC) is a highly malignant disease with a poor prognosis and high recurrence rate. At present, there is no accurate strategy to predict the prognosis and recurrence of OC. The aim of this study was to identify gene-based signatures to predict OC prognosis and recurrence.MethodsmRNA expression profiles and corresponding clinical information regarding OC were collected from The Cancer Genome Atlas (TCGA) database. Gene set enrichment analysis (GSEA) and LASSO analysis were performed, and Kaplan–Meier curves, time-dependent ROC curves, and nomograms were constructed using R software and GraphPad Prism7.ResultsWe first identified several key signalling pathways that affected ovarian tumorigenesis by GSEA. We then established a nine-gene-based signature for overall survival (OS) and a five-gene-based-signature for relapse-free survival (RFS) using LASSO Cox regression analysis of the TCGA dataset and validated the prognostic value of these signatures in independent GEO datasets. We also confirmed that these signatures were independent risk factors for OS and RFS by multivariate Cox analysis. Time-dependent ROC analysis showed that the AUC values for OS and RFS were 0.640, 0.663, 0.758, and 0.891, and 0.638, 0.722, 0.813, and 0.972 at 1, 3, 5, and 10 years, respectively. The results of the nomogram analysis demonstrated that combining two signatures with the TNM staging system and tumour status yielded better predictive ability.ConclusionIn conclusion, the two-gene-based signatures established in this study may serve as novel and independent prognostic indicators for OS and RFS. creator: Xinnan Zhao creator: Miao He uri: https://doi.org/10.7717/peerj.10437 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao and He title: Salivary microbial changes during the first 6 months of orthodontic treatment link: https://peerj.com/articles/10446 last-modified: 2020-12-01 description: BackgroundOrthodontic treatment is widely used to treat malocclusion. However, the influence of treatment on the oral microbiome remains unclear. In this study, we investigated salivary microbial changes in patients undergoing orthodontic treatment.MethodsIn total, 19 orthodontic patients participated in this study. Saliva samples were collected at the following three timepoints: before (T0) and 3 months (T1) and 6 months (T2) after the placement of orthodontic appliances. High-throughput sequencing was performed based on the 16S rRNA gene V4 region.ResultsThe phyla of Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Fusobacteria were predominant. Observed Species, Chao1 and ACE, which represent α diversity, were significantly decreased at T1 and subsequently increased at T2. In addition, the β diversity at T1 based on the Bray-Curtis distances differed from T0 and T2. The relative abundances of Prevotella, Porphyromonas and Peptostreptococcus were decreased with treatment, whereas those of Capnocytophaga and Neisseria exhibited the opposite results. In total, 385 of 410 operational taxonomic units were shared at T0, T1 and T2. The co-occurrence networks with hub nodes at T1 were the most complex.ConclusionOrthodontic treatment temporarily affected the saliva microbial community. This dynamic alteration in species did not induce deterioration in oral health. Oral hygiene instructions were necessary and should be emphasized during each visit. Further studies with longer observation periods and more participants are required. creator: Mei Zhao creator: Min Liu creator: Wei Chen creator: Haiping Zhang creator: Yuxing Bai creator: Wen Ren uri: https://doi.org/10.7717/peerj.10446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al. title: Assessing anxiety, depression and quality of life in patients with peripheral facial palsy: a systematic review link: https://peerj.com/articles/10449 last-modified: 2020-12-01 description: ObjectivePeripheral facial palsy (PFP) is predominantly a unilateral disorder of the facial nerve, which can lead to psychological disorders that can result in decreased quality of life. The aim of this systematic review was to assess anxiety, depression and quality of life symptoms associated with PFP.Data sourcesWe searched the Medline, PEDro, CINAHL and Google Scholar databases to conduct this systematic review while following Preferred Reporting Items for Systematic Reviews and Meta-Analyses standards. The search was performed by two independent reviewers, and differences between the two reviewers were resolved by consensus.Study SelectionThe search terms used were derived from the combination of the following MeSH terms: “facial paralysis”, “bell palsy”, “anxiety”, “anxiety disorders”, “depression”, “depressive disorders”, “quality of life” and not MeSH: “facial palsy”, “hemifacial paralysis”, “facial paresis”, “Peripheral Facial Paralysis”, using the combination of different Boolean operators (AND/OR).Data ExtractionOn November 1st (2019).Data SynthesisIn total, 18 cross-sectional articles and two case-control studies were selected.ConclusionsThe cross-sectional articles showed low methodological quality, while the case-control studies showed acceptable methodological quality. Limited evidence suggests that patients with PFP might have increased levels of anxiety and depressive symptoms. A qualitative analysis also showed limited evidence that quality of life might be diminished in patients with PFP.PROSPEROCRD42020159843. creator: Ferran Cuenca-Martínez creator: Eva Zapardiel-Sánchez creator: Enrique Carrasco-González creator: Roy La Touche creator: Luis Suso-Martí uri: https://doi.org/10.7717/peerj.10449 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cuenca-Martínez et al. title: Clinical significance of pretreatment prognostic nutritional index and lymphocyte-to-monocyte ratio in patients with advanced p16-negative oropharyngeal cancer—a retrospective study link: https://peerj.com/articles/10465 last-modified: 2020-12-01 description: BackgroundSystemic inflammation and nutritional status both play roles in the survival of cancer patients. Therefore, it is important to understand the effects of prognostic nutritional index (PNI) and lymphocyte-to-monocyte ratio (LMR) on the survival of patients with advanced p16-negative oropharyngeal cancer.MethodsA total of 142 patients diagnosed with advanced p16-negative oropharyngeal cancer between 2008 and 2015 were enrolled in this study. All patients received primary treatment with definite concurrent chemoradiotherapy (CCRT). Optimal cutoff values for PNI and LMR were determined using receiver operating characteristic curves for survival prediction. Survival rates for different level of PNI and LMR were estimated and compared using Kaplan–Meier method and log-rank test to see if there were significant effects on these end points, including 5-year overall survival (OS), disease-specific survival (DSS) and disease-free survival (DFS) rates. The effects of PNI and LMR on survival were assessed using Cox regression model adjusted for other prognostic factors.ResultsThe results showed the optimal cutoff values for PNI and LMR were 50.5 and 4.45, respectively. A high PNI (≧50.5) was significantly improved the 5-year OS. A low LMR (<4.45) was significantly associated with a poor 5-year DFS, DSS, and OS. In multivariate analysis, both PNI and LMR were independent prognosticators for 5-year OS.ConclusionsElevated pretreatment PNI and LMR are both favorable prognosticators in advanced p16-negative oropharyngeal cancer patients undergoing CCRT. creator: Ming-Hsien Tsai creator: Tai-Lin Huang creator: Hui-Ching Chuang creator: Yu-Tsai Lin creator: Fu-Min Fang creator: Hui Lu creator: Chih-Yen Chien uri: https://doi.org/10.7717/peerj.10465 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tsai et al.