title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=878 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The Erlang distribution approximates the age distribution of incidence of childhood and young adulthood cancers link: https://peerj.com/articles/11976 last-modified: 2021-08-06 description: BackgroundIt is widely believed that cancers develop upon acquiring a particular number of (epi) mutations in driver genes, but the law governing the kinetics of this process is not known. We have previously shown that the age distribution of incidence for the 20 most prevalent cancers of old age is best approximated by the Erlang probability distribution. The Erlang distribution describes the probability of several successive random events occurring by the given time according to the Poisson process, which allows an estimate for the number of critical driver events.MethodsHere we employ a computational grid search method to find global parameter optima for five probability distributions on the CDC WONDER dataset of the age distribution of childhood and young adulthood cancer incidence.ResultsWe show that the Erlang distribution is the only classical probability distribution we found that can adequately model the age distribution of incidence for all studied childhood and young adulthood cancers, in addition to cancers of old age.ConclusionsThis suggests that the Poisson process governs driver accumulation at any age and that the Erlang distribution can be used to determine the number of driver events for any cancer type. The Poisson process implies the fundamentally random timing of driver events and their constant average rate. As waiting times for the occurrence of the required number of driver events are counted in decades, and most cells do not live this long, it suggests that driver mutations accumulate silently in the longest-living dividing cells in the body—the stem cells. creator: Aleksey V. Belikov creator: Alexey Vyatkin creator: Sergey V. Leonov uri: https://doi.org/10.7717/peerj.11976 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Belikov et al. title: Gene selection for studying frugivore-plant interactions: a review and an example using Queensland fruit fly in tomato link: https://peerj.com/articles/11762 last-modified: 2021-08-05 description: Fruit production is negatively affected by a wide range of frugivorous insects, among them tephritid fruit flies are one of the most important. As a replacement for pesticide-based controls, enhancing natural fruit resistance through biotechnology approaches is a poorly researched but promising alternative. The use of quantitative reverse transcription PCR (RT-qPCR) is an approach to studying gene expression which has been widely used in studying plant resistance to pathogens and non-frugivorous insect herbivores, and offers a starting point for fruit fly studies. In this paper, we develop a gene selection pipe-line for known induced-defense genes in tomato fruit, Solanum lycopersicum, and putative detoxification genes in Queensland fruit fly, Bactrocera tryoni, as a basis for future RT-qPCR research. The pipeline started with a literature review on plant/herbivore and plant/pathogen molecular interactions. With respect to the fly, this was then followed by the identification of gene families known to be associated with insect resistance to toxins, and then individual genes through reference to annotated B. tryoni transcriptomes and gene identity matching with related species. In contrast for tomato, a much better studied species, individual defense genes could be identified directly through literature research. For B. tryoni, gene selection was then further refined through gene expression studies. Ultimately 28 putative detoxification genes from cytochrome P450 (P450), carboxylesterase (CarE), glutathione S-transferases (GST), and ATP binding cassette transporters (ABC) gene families were identified for B. tryoni, and 15 induced defense genes from receptor-like kinase (RLK), D-mannose/L-galactose, mitogen-activated protein kinase (MAPK), lipoxygenase (LOX), gamma-aminobutyric acid (GABA) pathways and polyphenol oxidase (PPO), proteinase inhibitors (PI) and resistance (R) gene families were identified from tomato fruit. The developed gene selection process for B. tryoni can be applied to other herbivorous and frugivorous insect pests so long as the minimum necessary genomic information, an annotated transcriptome, is available. creator: Shirin Roohigohar creator: Anthony R. Clarke creator: Peter J. Prentis uri: https://doi.org/10.7717/peerj.11762 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Roohigohar et al. title: The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters link: https://peerj.com/articles/11805 last-modified: 2021-08-05 description: The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as “Ocadia” kehreri and “Ocadia” messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade. creator: Eduardo Ascarrunz creator: Julien Claude creator: Walter G. Joyce uri: https://doi.org/10.7717/peerj.11805 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ascarrunz et al. title: Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae) link: https://peerj.com/articles/11843 last-modified: 2021-08-05 description: BackgroundWith about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in wing patterns. Geographic infraspecific variation is sometimes more substantial than variation between species. In this paper we present a large DNA barcode dataset of South American Lycaenidae. We analyze how well DNA barcode BINs match morphologically delimited species.MethodsWe compare morphology-based species identifications with the clustering of molecular operational taxonomic units (MOTUs) delimitated by the RESL algorithm in BOLD, which assigns Barcode Index Numbers (BINs). We examine intra- and interspecific divergences for genera represented by at least four morphospecies. We discuss the existence of local barcode gaps in a genus by genus analysis. We also note differences in the percentage of species with barcode gaps in groups of lowland and high mountain genera.ResultsWe identified 2,213 specimens and obtained 1,839 sequences of 512 species in 90 genera. Overall, the mean intraspecific divergence value of CO1 sequences was 1.20%, while the mean interspecific divergence between nearest congeneric neighbors was 4.89%, demonstrating the presence of a barcode gap. However, the gap seemed to disappear from the entire set when comparing the maximum intraspecific distance (8.40%) with the minimum interspecific distance (0.40%). Clear barcode gaps are present in many genera but absent in others. From the set of specimens that yielded COI fragment lengths of at least 650 bp, 75% of the a priori morphology-based identifications were unambiguously assigned to a single Barcode Index Number (BIN). However, after a taxonomic a posteriori review, the percentage of matched identifications rose to 85%. BIN splitting was observed for 17% of the species and BIN sharing for 9%. We found that genera that contain primarily lowland species show higher percentages of local barcode gaps and congruence between BINs and morphology than genera that contain exclusively high montane species. The divergence values to the nearest neighbors were significantly lower in high Andean species while the intra-specific divergence values were significantly lower in the lowland species. These results raise questions regarding the causes of observed low inter and high intraspecific genetic variation. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the montane species concerned are relatively young and hybridization is probable. The release of our data set represents an essential baseline for a reference library for biological assessment studies of butterflies in mega diverse countries using modern high-throughput technologies an highlights the necessity of taxonomic revisions for various genera combining both molecular and morphological data. creator: Carlos Prieto creator: Christophe Faynel creator: Robert Robbins creator: Axel Hausmann uri: https://doi.org/10.7717/peerj.11843 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Prieto et al. title: An efficient sorghum transformation system using embryogenic calli derived from mature seeds link: https://peerj.com/articles/11849 last-modified: 2021-08-05 description: Significant progress has been made on sorghum transformation in the last decades; however, the transformation process has been constrained by the availability of immature embryos because most of the researchers have utilized immature embryos as favorable explants. Although immature embryos have been proven to be optimal for tissue culture and transformation, isolation of immature embryos is time-consuming, labor-intensive, and limited by warm weather. In this study, we developed an efficient genetic transformation system using mature seeds as explants. The nptII and gus gene, used as the selective marker and report gene respectively, have been co-transformed by particle bombardment. After optimization of tissue culture, the G418 concentration, and transgenic, the average transformation frequency at 13.33% was achieved routinely. The transgenic events and transgene copy numbers were determined by PCR and RT-PCR, respectively. The geneticin selection and GUS staining on T1 seedlings confirmed that the transgenic plants were heritable. Our results demonstrated that the efficient sorghum transformation system has been established using mature seeds as explants. This transformation system will promote sorghum research on genetic engineering and genome editing without seasonal weather conditions restriction and explant resources restriction. creator: Lihua Wang creator: Li Gao creator: Guoquan Liu creator: Ruirui Meng creator: Yanlong Liu creator: Jieqin Li uri: https://doi.org/10.7717/peerj.11849 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Pain and satisfaction: the case of isolated COVID-19 patients of Pakistan link: https://peerj.com/articles/11859 last-modified: 2021-08-05 description: BackgroundOver 3 million people lost their lives across the globe due to the COVID-19 related pandemic. The unprecedented restrictions on mobility have imposed in the form of isolation, quarantines, and lockdowns to curb the profound effects of the pandemic and retain physical health. This study examined the relationship between various pain levels, demographic variables and patient satisfaction with COVID-19 during isolation.MethodsThe primary data in this study were collected from isolated patients during their isolation and treatment in a public hospital. We obtained information from patients with COVID-19 (N = 100) about their demographic characteristics, varying levels of pain, and satisfaction with the services provided during the isolation period. We computed the descriptive statistics to explain the profile of participants, ANOVA was used to find out the difference between various groups on patient satisfaction, and structural equation modeling was performed to examine the link between pain levels, demographic factors, and patient satisfaction. This analysis was performed with STATA and SmartPLS-3.ResultsThe findings of this study ascertained that respondent’s education (Beta, β = 2.961, p = 0.003), assets such as possession of a house (β = 4.563, p = 0.000), perception of income adequacy during the lockdown (=2.299, p = 0.022), and negligence in prevention (β = 1.975, p = 0.049) significantly affects patient satisfaction during the isolation period. Moreover, satisfaction with life, physicians and medicine, income adequacy, and fear of the participants was significantly linked to the pain level (Model F-stat = 86.323, p = 0.0001). Patients who were satisfied with their treatment had significantly lower odds of having pain (OR 0.023, 95% CI [0.001–0.0452]). Patients who had enough income to meet their basic necessities were found to have significantly lower odds of having pain (OR 0.155, 95% CI [0.032–0.740].Discussion and ConclusionWe conclude that a higher level of education, low income, and living in a rented house contributes significantly to the feeling of more satisfaction with the provided services. This implies that people with more affluent backgrounds are less likely to be satisfied with the provided services as low-income and living in rented house groups are more satisfied during isolation than others. The pain level is also affected by subjective factors such as fear and satisfaction which need to be considered while doing patient management. This study can be helpful in improving the delivery of public services of isolation centers by considering various characteristics and demographic factors of patients. creator: Wajiha Haq creator: Siddrah Irfan creator: Syed Hassan Raza creator: Waqar Ahmed creator: Mian Alam creator: Samia Wasif creator: Muhammad Wasif Malik creator: Saeed Ahmad uri: https://doi.org/10.7717/peerj.11859 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Haq et al. title: Evaluation of structural and ultrastructural changes in thyroid and parathyroid glands after near infrared irradiation: study on an animal model link: https://peerj.com/articles/11891 last-modified: 2021-08-05 description: Intraoperative identification of parathyroid glands is a tough task for surgeons performing thyroid or parathyroid surgery, because the small size, color and shape of these glands hinder their discrimination from other cervical tissues. In 2011, Paras described the autofluorescence of parathyroid glands, a property that could facilitate their intraoperative identification. Parathyroid glands submitted to a 785 nm laser beam emit fluorescence in the near infrared range, with a peak at 822 nm. As the intrinsic properties of secretory tissues may be affected by the exposure to the near infrared light, a situation that could preclude their intraoperative utilization, the authors compared the structural and ultra-structural patterns of rat’s thyroid and parathyroid glands submitted to irradiation replicating the conditions that allow their intraoperative identification, with those of non irradiated animals. Twenty-four Wistar rats were divided into six groups: animals of Groups 1, 3 and 5 were submitted under general anesthesia to direct irradiation of the cervical area with a 780 nm LED light for 3 minutes through a cervical incision, and animals of Groups 2, 4 and 6 were submitted to cervical dissection without irradiation. Animals of were euthanized immediately (Groups 1 and 2), at Day 30 (Groups 3 and 4) at and at Day 60 (Groups 5 and 6) and thyroid and parathyroid glands were removed: one lobe was prepared for conventional pathological examination and the other lobe for electron microscopy observed by three experienced pathological experts. Twenty-four samples were prepared for conventional histology and there were no alterations reported in any group. Due to technical problems, only 21 samples were observed by electron microscopy and there were no differences in the ultrastructure of parathyroid and thyroid glands, namely the nuclear pattern, mitochondria, endoplasmic reticulum or secretory granules, in any of the groups. These results confirm the innocuity of near infrared irradiation’, allowing its intraoperative utilization. creator: Carlos Serra creator: Luis Silveira uri: https://doi.org/10.7717/peerj.11891 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Serra and Silveira title: Eating for numbing: a community-based study of trauma exposure, emotion dysregulation, dissociation, body dissatisfaction and eating disorder symptoms link: https://peerj.com/articles/11899 last-modified: 2021-08-05 description: ObjectiveThe current study tests the relationship between eating disorder (ED) symptoms and trauma exposure. The mechanisms via which trauma is related to ED symptoms have not been sufficiently examined. This study examines the complex role of dissociation and emotional dysregulation in the context of trauma, BMI, ED symptoms and body dissatisfaction (BD). We hypothesized that dissociation and emotional dysregulation would mediate the relationship between trauma exposure and ED symptoms/BD. We further hypothesized that BMI would play a moderating role in this association.MethodA community sample of 229 (16.2% male) participants, with a mean age of 29.08 ± 10.68 reported online on traumatic events (Life Events Checklist), dissociation (Dissociative Experiences Scale-II), emotional dysregulation (Difficulties in Emotional Regulation Scale), ED symptoms (Eating Disorders Examination-Questionnaire) and BD (Figure Rating Scale).ResultsParticipants reported experiencing a mean of 2.87 ± 2.27 traumatic events, with a relatively high percentage (~86%) reporting at least one. The most commonly reported traumatic events were transportation accidents and physical assault. Although frequency of traumatic events did not directly predict ED symptoms, BMI, dissociation, emotional dysregulation and BD did. An SEM model showed that traumatic events predicted ED symptoms indirectly through dissociation, emotional dysregulation and BMI. Dissociation and emotional dysregulation predicted ED symptoms directly. BMI also moderated the association between traumatic events and both ED symptoms and BD.ConclusionsTherapists treating patients with high BMI or obesity should be aware of these relationships and investigate the possibility that trauma and/or PTSD may underlie the presenting disordered eating or eating disorder. creator: Lilac Lev-ari creator: Ada H. Zohar creator: Rachel Bachner-Melman uri: https://doi.org/10.7717/peerj.11899 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Lev-ari et al. title: Signature identification of relapse-related overall survival of early lung adenocarcinoma after radical surgery link: https://peerj.com/articles/11923 last-modified: 2021-08-05 description: BackgroundThe widespread use of low-dose chest CT screening has improved the detection of early lung adenocarcinoma. Radical surgery is the best treatment strategy for patients with early lung adenocarcinoma; however, some patients present with postoperative recurrence and poor prognosis. Through this study, we hope to establish a model that can identify patients that are prone to recurrence and have poor prognosis after surgery for early lung adenocarcinoma.Materials and MethodsWe screened prognostic and relapse-related genes using The Cancer Genome Atlas (TCGA) database and the GSE50081 dataset from the Gene Expression Omnibus (GEO) database. The GSE30219 dataset was used to further screen target genes and construct a risk prognosis signature. Time-dependent ROC analysis, calibration degree analysis, and DCA were used to evaluate the reliability of the model. We validated the TCGA dataset, GSE50081, and GSE30219 internally. External validation was conducted in the GSE31210 dataset.ResultsA novel four-gene signature (INPP5B, FOSL2, CDCA3, RASAL2) was established to predict relapse-related survival outcomes in patients with early lung adenocarcinoma after surgery. The discovery of these genes may reveal the molecular mechanism of recurrence and poor prognosis of early lung adenocarcinoma. In addition, ROC analysis, calibration analysis and DCA were used to verify the genetic signature internally and externally. Our results showed that our gene signature had a good predictive ability for recurrence and prognosis.ConclusionsWe established a four-gene signature and predictive model to predict the recurrence and corresponding survival rates in patients with early lung adenocarcinoma after surgery. These may be helpful for reforumulating post-operative consolidation treatment strategies. creator: Peng Han creator: Jiaqi Yue creator: Kangle Kong creator: Shan Hu creator: Peng Cao creator: Yu Deng creator: Fan Li creator: Bo Zhao uri: https://doi.org/10.7717/peerj.11923 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Han et al. title: Global warming and neurological practice: systematic review link: https://peerj.com/articles/11941 last-modified: 2021-08-04 description: BackgroundClimate change, including global warming, will cause poorer global health and rising numbers of environmental refugees. As neurological disorders account for a major share of morbidity and mortality worldwide, global warming is also destined to alter neurological practice; however, to what extent and by which mechanisms is unknown. We aimed to collect information about the effects of ambient temperatures and human migration on the epidemiology and clinical manifestations of neurological disorders.MethodsWe searched PubMed and Scopus from 01/2000 to 12/2020 for human studies addressing the influence of ambient temperatures and human migration on Alzheimer’s and non-Alzheimer’s dementia, epilepsy, headache/migraine, multiple sclerosis, Parkinson’s disease, stroke, and tick-borne encephalitis (a model disease for neuroinfections). The protocol was pre-registered with PROSPERO (2020 CRD42020147543).ResultsNinety-three studies met inclusion criteria, 84 of which reported on ambient temperatures and nine on migration. Overall, most temperature studies suggested a relationship between increasing temperatures and higher mortality and/or morbidity, whereas results were more ambiguous for migration studies. However, we were unable to identify a single adequately designed study addressing how global warming and human migration will change neurological practice. Still, extracted data indicated multiple ways by which these aspects might alter neurological morbidity and mortality soon.ConclusionSignificant heterogeneity exists across studies with respect to methodology, outcome measures, confounders and study design, including lack of data from low-income countries, but the evidence so far suggests that climate change will affect the practice of all major neurological disorders in the near future. Adequately designed studies to address this issue are urgently needed, requiring concerted efforts from the entire neurological community. creator: Moshgan Amiri creator: Costanza Peinkhofer creator: Marwan H. Othman creator: Teodoro De Vecchi creator: Vardan Nersesjan creator: Daniel Kondziella uri: https://doi.org/10.7717/peerj.11941 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Amiri et al.