title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=467 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Data-specific substitution models improve protein-based phylogenetics link: https://peerj.com/articles/15716 last-modified: 2023-08-08 description: Calculating amino-acid substitution models that are specific for individual protein data sets is often difficult due to the computational burden of estimating large numbers of rate parameters. In this study, we tested the computational efficiency and accuracy of five methods used to estimate substitution models, namely Codeml, FastMG, IQ-TREE, P4 (maximum likelihood), and P4 (Bayesian inference). Data-specific substitution models were estimated from simulated alignments (with different lengths) that were generated from a known simulation model and simulation tree. Each of the resulting data-specific substitution models was used to calculate the maximum likelihood score of the simulation tree and simulated data that was used to calculate the model, and compared with the maximum likelihood scores of the known simulation model and simulation tree on the same simulated data. Additionally, the commonly-used empirical models, cpREV and WAG, were assessed similarly. Data-specific models performed better than the empirical models, which under-fitted the simulated alignments, had the highest difference to the simulation model maximum-likelihood score, clustered further from the simulation model in principal component analysis ordination, and inferred less accurate trees. Data-specific models and the simulation model shared statistically indistinguishable maximum-likelihood scores, indicating that the five methods were reasonably accurate at estimating substitution models by this measure. Nevertheless, tree statistics showed differences between optimal maximum likelihood trees. Unlike other model estimating methods, trees inferred using data-specific models generated with IQ-TREE and P4 (maximum likelihood) were not significantly different from the trees derived from the simulation model in each analysis, indicating that these two methods alone were the most accurate at estimating data-specific models. To show the benefits of using data-specific protein models several published data sets were reanalysed using IQ-TREE-estimated models. These newly estimated models were a better fit to the data than the empirical models that were used by the original authors, often inferred longer trees, and resulted in different tree topologies in more than half of the re-analysed data sets. The results of this study show that software availability and high computation burden are not limitations to generating better-fitting data-specific amino-acid substitution models for phylogenetic analyses. creator: João M. Brazão creator: Peter G. Foster creator: Cymon J. Cox uri: https://doi.org/10.7717/peerj.15716 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Brazão et al. title: Impact of ocean warming on a coral reef fish learning and memory link: https://peerj.com/articles/15729 last-modified: 2023-08-08 description: Tropical ectotherms are highly sensitive to environmental warming, especially coral reef fishes, which are negatively impacted by an increase of a few degrees in ocean temperature. However, much of our understanding on the thermal sensitivity of reef fish is focused on a few traits (e.g., metabolism, reproduction) and we currently lack knowledge on warming effects on cognition, which may endanger decision-making and survival. Here, we investigated the effects of warming on learning and memory in a damselfish species, Acanthochromis polyacanthus. Fish were held at 28–28.5 °C (control group), 30–30.5 °C (moderate warming group) or 31.5–32 °C (high warming group) for 2 weeks, and then trained to associate a blue tag (cue) to the presence of a conspecific (reward). Following 20 training trials (5 days), fish were tested for associative learning (on the following day) and memory storage (after a 5-days interval). The control group A. polyacanthus showed learning of the task and memory retention after five days, but increasing water temperature impaired learning and memory. A thorough understanding of the effects of heat stress, cognition, and fitness is urgently required because cognition may be a key factor determining animals’ performance in the predicted scenario of climate changes. Knowing how different species respond to warming can lead to better predictions of future community dynamics, and because it is species specific, it could pinpoint vulnerable/resilience species. creator: Mayara M. Silveira creator: Jennifer M. Donelson creator: Mark I. McCormick creator: Heloysa Araujo-Silva creator: Ana C. Luchiari uri: https://doi.org/10.7717/peerj.15729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Silveira et al. title: Implementation of artificial intelligence for the detection of cutaneous melanoma within a primary care setting: prevalence and types of skin cancer in outdoor enthusiasts link: https://peerj.com/articles/15737 last-modified: 2023-08-08 description: BackgroundThere is enthusiasm for implementing artificial intelligence (AI) to assist clinicians detect skin cancer. Performance metrics of AI from dermoscopic images have been promising, with studies documenting sensitivity and specificity values equal to or superior to specialists for the detection of malignant melanomas (MM). Early detection rates would particularly benefit Australia, which has the worlds highest incidence of MM per capita. The detection of skin cancer may be delayed due to late screening or the inherent difficulty in diagnosing early skin cancers which often have a paucity of clinical features and may blend into sun damaged skin. Individuals who participate in outdoor sports and recreation experience high levels of intermittent ultraviolet radiation (UVR), which is associated with the development of skin cancer, including MM. This research aimed to assess the prevalence of skin cancer in individuals who regularly participate in activities outdoors and to report the performance parameters of a commercially available AI-powered software to assess the predictive risk of MM development.MethodsCross-sectional study design incorporating a survey, total body skin cancer screening and AI-embedded software capable of predictive scoring of queried MM.ResultsA total of 423 participants consisting of surfers (n = 108), swimmers (n = 60) and walkers/runners (n = 255) participated. Point prevalence for MM was highest for surfers (6.48%), followed by walkers/runners (4.3%) and swimmers (3.33%) respectively. When compared to the general Australian population, surfers had the highest odds ratio (OR) for MM (OR 119.8), followed by walkers/runners (OR 79.74), and swimmers (OR 61.61) rounded out the populations. Surfers and swimmers reported comparatively lower lifetime hours of sun exposure (5,594 and 5,686, respectively) but more significant amounts of activity within peak ultraviolet index compared with walkers/runners (9,554 h). A total of 48 suspicious pigmented lesions made up of histopathology-confirmed MM (n = 15) and benign lesions (n = 33) were identified. The performance of the AI from this clinical population was found to have a sensitivity of 53.33%, specificity of 54.44% and accuracy of 54.17%.ConclusionsRates of both keratinocyte carcinomas and MM were notably higher in aquatic and land-based enthusiasts compared to the general Australian population. These findings further highlight the clinical importance of sun-safe protection measures and regular skin screening in individuals who spend significant time outdoors. The use of AI in the early identification of MM is promising. However, the lower-than-expected performance metrics of the AI software used in this study indicated reservations should be held before recommending this particular version of this AI software as a reliable adjunct for clinicians in skin imaging diagnostics in patients with potentially sun damaged skin. creator: Ian J. Miller creator: Michael Stapelberg creator: Nedeljka Rosic creator: Jeremy Hudson creator: Paul Coxon creator: James Furness creator: Joe Walsh creator: Mike Climstein uri: https://doi.org/10.7717/peerj.15737 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Miller et al. title: Recognition of emotion and pain by owners benefits the welfare of donkeys in a challenging working environment link: https://peerj.com/articles/15747 last-modified: 2023-08-08 description: Working donkeys (Equus asinus) support human living standards globally. However, there is little information on the effect of human perceptions of emotion and pain on the welfare of working donkeys. We interviewed donkey owners (n = 332) in Pakistan to determine the relationship between human perspectives on donkey sentience: emotions and the ability to feel pain, and the routine working practices that could impact donkey welfare. The majority of donkey owners used padding under the saddle (n = 211; 63.6%; 95% CI (58.3%–68.9%)) and provided access to food (n = 213; 64.2%; 95% CI (58.9%–69.3%)) and water (n = 195; 58.7%; 95% CI (53.4%–64.1%)) during the working day. Owners reported that at some point in their donkey’s life, 65.3% (95% CI (60.2%–70.5%)) had load-associated injuries, of which 27.7% (n = 92; 95% CI (22.8%–32.5%)) were wounds, 20.5% (n = 68; 95% CI (16.1%–24.8%)) were lameness and 7.2% (n = 24; 95% CI 4.4%–10.0%) were back pain. In total, 81.3% (95% CI 77.1%–85.5%; n = 270) of owners believed that their donkeys felt pain, and 70.2% (95% CI (65.2%–75.1%; n = 233) of owners believed that their donkeys had emotions. Multiple correspondence analysis (MCA) was used to understand the relationship between owners’ recognition of emotions and pain in donkeys and their working practices. The MCA factor map revealed two clusters, named positive and negative clusters. The positive cluster included owner’s recognition of donkey pain and emotions, the availability of food and water, use of padding under the saddle, absence of injuries along with the willingness to follow loading guidelines. The negative cluster represented practices that did not benefit donkey welfare, such as using saddles without padding and a lack of food and water during work. The presence of injuries, owners not recognizing that donkeys feel pain and emotion along with an unwillingness to follow loading guidelines were also found in the negative cluster. We show that the owners who recognized sentience in their donkeys were more likely to use practices that are good for donkey welfare. The ability of owners to identify sentience in donkeys, along with their willingness to follow welfare guidelines, are important factors in improving the lives of working donkeys. creator: Syed S.U.H. Bukhari creator: Alan G. McElligott creator: Sarah M. Rosanowski creator: Rebecca S.V. Parkes uri: https://doi.org/10.7717/peerj.15747 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Bukhari et al. title: Genetic and morphological diversity in populations of Annona senegalensis Pers. occurring in Western (Benin) and Southern (Mozambique) Africa link: https://peerj.com/articles/15767 last-modified: 2023-08-08 description: BackgroundUnderstanding morpho-genetic diversity and differentiation of species with relatively large distributions is crucial for the conservation and sustainable management of their genetic resources. The present study focused on Annona senegalensis Pers., an important multipurpose wild plant, distributed exclusively in natural ecosystems but facing several threats. The study assessed the genetic and morphological diversity, structure, and differentiation of the species in populations from Western (Benin) and Southern (Mozambique) Africa. The material was evaluated to ascertain the environmental (climatic) determinants of the variation within this species.MethodsFour sub-populations comprised of 154 individuals were phenotyped based on nineteen plant, fruit, and leaf morphological traits and further genotyped using ten polymorphic nuclear microsatellite (nSSR) markers.ResultsThe results indicated strong differences in plant, fruit, and leaf morphological traits between Western and Southern populations. Furthermore, the studied populations were characterized by high genetic diversity, with an average genetic diversity index of 1.02. Western populations showed higher heterozygosity values (0.61–0.71) than Southern populations (0.41–0.49). Western and Southern populations were clearly differentiated into two different genetic groups, with further genetic subdivisions reflecting four sub-populations. Genetic variation between regions (populations) was higher (69.1%) than among (21.3%) and within (9.6%) sub-populations. Four distinct morphological clusters were obtained, which were strongly associated with the four genetic groups representing each sub-population. Climate, mainly precipitation and temperature indexes, explained the relatively higher variation found in morphological traits from Western (40.47%) in relation to Southern (27.98%) populations. Our study suggests that both environmental and genetic dynamics play an important role in the development of morphological variation in A. senegalensis. creator: Janine Conforte Fifonssi Donhouedé creator: Isabel Marques creator: Kolawolé Valère Salako creator: Achille Ephrem Assogbadjo creator: Natasha Ribeiro creator: Ana IF Ribeiro-Barros uri: https://doi.org/10.7717/peerj.15767 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Donhouedé et al. title: I feel addicted to watching TV series: association between binge-watching and mental health link: https://peerj.com/articles/15796 last-modified: 2023-08-08 description: BackgroundBinge-watching (BW) is the consecutive viewing of three or more episodes of the same series in one sitting. Although some negative effects on mental health were evidenced, the continuum of BW from leisure activity to problematic behavior is still unclear. This study aimed to analyze mental health (depression, trait anxiety, social anxiety, impulsivity, alexithymia) of people involved in different expressions of BW.MethodsA cross-sectional survey collected data from 482 respondents. According to a validated BW questionnaire, participants were divided into Problematic BW, Moderate BW, Non-BW, and No-viewer, and differences between groups were tested on psychological dimensions assessed via standardized questionnaires evaluating: trait and social anxiety, depression, impulsivity, and emotional dysregulation.ResultsAn association between problematic BW and worse mental health conditions was evidenced, and a positive effect of non-problematic BW was supported. A negative linear trend from the BW as a leisure activity to problematic BW was marked, indicating how a possible maladaptive behavior orientation of BW in specific mental health conditions could be figured out as a behavioral addiction. creator: Francesca Favieri creator: Giuseppe Forte creator: Renata Tambelli creator: Manuela Tomai creator: Maria Casagrande uri: https://doi.org/10.7717/peerj.15796 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Favieri et al. title: Potential factors promoting the natural regeneration of Larix principis-rupprechtii in North China link: https://peerj.com/articles/15809 last-modified: 2023-08-08 description: Natural regeneration plays an important role in species diversity and evolution. Exploring the causes of variation in regeneration dynamics can provide key insights into the factors affecting regeneration. However, the relationship between the regeneration of Larix principis-rupprechtii and environmental factors in North China has remained unexplored. In this study, 14 plots were established based on the three extents of regenerated plant numbers in Shanxi Province. Redundancy analysis determined that environmental factors (topography, stand structure, soil property, and litter) affected natural regeneration. Structural equation modeling identified the most important direct and indirect factors that affected L. principis-rupprechtii natural regeneration. Litter thickness, canopy density, and adult tree diameter at breast height were positively correlated with natural regeneration. Aspect and total nitrogen volume were negatively associated with natural regeneration. Additionally, there was no significant correlation between natural regeneration and other environmental factors (altitude, slope, adult tree height, stand density, soil water content, SOC, total P, available N, available P, or soil enzyme). Further artificial intervention measures should be considered to promote plantation regeneration. These findings provide an effective basis for future forest restorations and sustainable management. creator: Weiwen Zhao creator: Yanjun Sun creator: Yufeng Gao uri: https://doi.org/10.7717/peerj.15809 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhao et al. title: Impact of cooling on shaping ability of thermally treated files in canal models with double curvature link: https://peerj.com/articles/15830 last-modified: 2023-08-08 description: BackgroundThis study compared the ability of thermally treated files in shaping simulated canals with double curvature. Fifty-six canals were enlarged to a final size of 25 with ProTaper Next (PTN) or ZenFlex (ZF).MaterialsHalf of the samples were shaped with cooled files (n = 14 each). The amount of removed resin was measured and canal deviation was determined at eight levels. Shaping time and maximum shaping torque values were also recorded. Data were statistically analyzed using analysis of variance and LSD, Kruskal–Wallis, and chi-square tests at a 0.05 significance level.ResultsCompared to PTN and cooled PTN, ZF and cooled ZF required lesser time to shape the canals. The maximum torques were found comparable between the groups. All the groups generated negligible deviations at every canal level evaluated and maintained the canal geometry. Although not significant, the cooled PTN and ZF files exhibited lesser canal deviations than their counterparts.ConclusionAll groups demonstrated similar shaping ability whilst maintaining the original curvature of the canal in simulated canals with double curvature. However, ZF groups were able to shape the canals faster than PTN groups. There was a trend that cooled files made lesser canal deviations compared to their counterparts. creator: Ahmed Jamleh creator: Hajar Albanyan creator: Ali Alaqla creator: Hamad Alissa creator: Nawaf Alshetan creator: Sulaiman Alraffa creator: Abdulmohsen Alfadley uri: https://doi.org/10.7717/peerj.15830 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jamleh et al. title: The hypoxia-associated genes in immune infiltration and treatment options of lung adenocarcinoma link: https://peerj.com/articles/15621 last-modified: 2023-08-07 description: BackgroundLung adenocarcinoma (LUAD) is a common lung cancer with a poor prognosis under standard chemotherapy. Hypoxia is a crucial factor in the development of solid tumors, and hypoxia-related genes (HRGs) are closely associated with the proliferation of LUAD cells.MethodsIn this study, LUAD HRGs were screened, and bioinformatics analysis and experimental validation were conducted. The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases were used to gather LUAD RNA-seq data and accompanying clinical information. LUAD subtypes were identified by unsupervised cluster analysis, and immune infiltration analysis of subtypes was conducted by GSVA and ssGSEA. Cox regression and LASSO regression analyses were used to obtain prognosis-related HRGs. Prognostic analysis was used to evaluate HRGs. Differences in enrichment pathways and immunotherapy were observed between risk groups based on GSEA and the TIDE method. Finally, RT-PCR and in vitro experiments were used to confirm prognosis-related HRG expression in LUAD cells.ResultsTwo hypoxia-associated subtypes of LUAD were distinguished, demonstrating significant differences in prognostic analysis and immunological characteristics between subtypes. A prognostic model based on six HRGs (HK1, PDK3, PFKL, SLC2A1, STC1, and XPNPEP1) was developed for LUAD. HK1, SLC2A1, STC1, and XPNPEP1 were found to be risk factors for LUAD. PDK3 and PFKL were protective factors in LUAD patients.ConclusionThis study demonstrates the effect of hypoxia-associated genes on immune infiltration in LUAD and provides options for immunotherapy and therapeutic strategies in LUAD. creator: Liu Liu creator: Lina Han creator: Lei Dong creator: Zihao He creator: Kai Gao creator: Xu Chen creator: Jin-Cheng Guo creator: Yi Zhao uri: https://doi.org/10.7717/peerj.15621 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Health status of the red-billed tropicbird (Phaethon aethereus) determined by hematology, biochemistry, blood gases, and physical examination link: https://peerj.com/articles/15713 last-modified: 2023-08-07 description: The red-billed tropicbird, Phaethon aethereus, is a species of seabird native to the Galápagos archipelago, and widely distributed across the neotropics. General health, blood chemistry, and haematology parameters have not been published for this species. Blood analyses were performed on samples drawn from 51 clinically healthy red-billed tropicbirds captured from their burrows at Islote Pitt on San Cristóbal Island in July, 2016 (21) and Daphne Major Island in June, 2017 (30). In the field, a point of care blood analyser (iSTAT) was used to obtain results for HCO3-, pH, pCO2, pO2, TCO2, iCa, Na, K, Cl, Hb, HCT, anion gap, creatinine, glucose and urea nitrogen. Additionally, a portable Lactate PlusTM analyser was used to measure blood lactate, and blood smears were also created in situ. The blood slides were used to estimate leukocyte counts and 100-cell differentials. Alongside these biochemistry and haematology parameters, average heart rate, respiratory rate, body temperature and scaled mass index (calculated from weight and a body measurement) were compared to determine the standard measurements for a healthy individual. The baseline data, and reference intervals reported in this paper are essential to detecting changes in the health of red-billed tropicbirds in the future. creator: Alice Skehel creator: Catalina Ulloa creator: Diane Deresienski creator: Cristina Regalado creator: Juan Pablo Muñoz-Pérez creator: Juan Augusto Garcia creator: Britta Denise Hardesty creator: Ronald K. Passingham creator: Jason Steve Castañeda creator: Gregory A. Lewbart creator: Carlos A. Valle uri: https://doi.org/10.7717/peerj.15713 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Skehel et al.