title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=67 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: New approaches for capturing and estimating variation in complex animal color patterns from digital photographs: application to the Eastern Box Turtle (Terrapene carolina) link: https://peerj.com/articles/19690 last-modified: 2025-07-21 description: Color pattern plays a crucial role in various aspects of an organism’s biology, including camouflage, mating, and communication. Despite its significance, methods to quantify and study color pattern variation are often lacking, especially for complex patterns that defy simple categorization. In this study, we developed algorithms to capture and obtain data on 19 different pattern measurements from digital images of 55 individuals of the Eastern box turtle Terrapene carolina sampled in the field and in a museum. The Eastern box turtle is an ideal species to study variation of complex color patterns as this species is easily encountered in the field and in museum collections in Northeastern US, has a relatively easy to identify bright color pattern against a dark background, and has a rigid shell structure, which removes problems related to body distortion. The selected measurements capture the different aspects of the complexity of the color pattern, including the symmetry of the pattern on the turtles’ scutes, a critical component in developmental and evolutionary studies. We estimated the variation of each of these 19 measurements across our samples. We determined how much of this variation was influenced by the sensitivity of the pattern capture algorithm due to non-standardized elements of the image acquisition, lighting conditions, and animal shape on pattern variation. To our knowledge, this is the first study to use a comprehensive set of pattern measurements to capture variation in a complex color pattern while also assessing the susceptibility of each of these measurements to noise introduced during data collection. Additionally, we carried out a citizen science approach to characterize the complexity of the color pattern based on human perception and determine which of the 19 pattern measurements best describe this complexity. The most variable measurements across individuals were blue and yellow contrast between the pattern and non-pattern coloration and the average size of objects. From our estimates of the measurement noise due to image acquisition and analysis, we found that the contrast differences reflected true pattern variations between individual turtles, whereas differences in the average size of objects were influenced by both individual turtle variation and measurement inconsistencies. We found that due to the complexity of the patterns, measurements had lower variability if they did not depend on the algorithm defining a set of discrete objects. For example, total area had much less measurement variability than average object area. Our study provides a comprehensive workflow and tools to study variation in complex color patterns in organisms sampled under non-standardized conditions while also estimating the influence of noise due to biological and non-biological factors. creator: Erik Maki creator: Tilmann Glimm creator: Paramahansa Pramanik creator: Ylenia Chiari creator: Maria Kiskowski uri: https://doi.org/10.7717/peerj.19690 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Maki et al. title: Pectoral muscle area index is an independent protective factor for mortality in sepsis patients: a retrospective observational study link: https://peerj.com/articles/19689 last-modified: 2025-07-21 description: BackgroundSepsis is an infection-induced systemic inflammatory response involving multiple mediators. Identifying risk factors for mortality in patients with sepsis is important for determining treatment strategies. Sarcopenia is a systemic pathology of the skeletal muscles associated with poor outcomes in patients with sepsis. However, there exists a gap in the literature regarding the thoracic muscle area and early outcomes of sepsis. Thus, this study investigated the relationship between 28-day survival and indicators of sarcopenia (pectoral muscle area and pectoral muscle density) from chest computed tomography images of patients with sepsis.MethodsPatients (n = 134, median age = 75 years) who met the Sepsis-3 diagnosis criteria were included. Pectoral muscle area and density were measured in patients who underwent pulmonary computed tomography within ±3 days of admission. Univariate and multivariable factors associated with 28-day mortality were evaluated via Cox regression analysis. Factors with a single-factor p  <  0.05 were included in the multivariate Cox regression analysis to evaluate the factors associated with 28-day mortality in sepsis.ResultsIn this study, 88 patients survived, whereas 46 did not survive at the 28-day mark. Body mass index (BMI) (P = 0.044), pectoral muscle area (P = 0.005), pectoral muscle density (P = 0.008), and pectoral muscle area index (P = 0.003) significantly differed between patients who survived and those who did not survive. BMI was positively correlated with pectoral muscle area (r = 0.516, P  <  0.001) and index (r = 0.560, P  <  0.001). Acute Physiology and Chronic Health Evaluation II score (hazard ratio (HR) = 1.119, P  <  0.001) constituted an independent risk factor for 28-day mortality, whereas the pectoral muscle area index (HR, 0.847; P = 0.027) was a protective factor for 28-day mortality in patients with sepsis. The pectoral muscle area index was associated with a reduced risk of early mortality in patients with sepsis. creator: Xin Li creator: Meijiao Li creator: Yongchang Sun creator: Qingtao Zhou uri: https://doi.org/10.7717/peerj.19689 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Assesment of bone healing after surgical management of odontogenic cysts utilizing fractal analysis—a retrospective cross-sectional study link: https://peerj.com/articles/19745 last-modified: 2025-07-18 description: ObjectivesOdontogenic cysts, originating from inflammatory or developmental processes of the tooth germ epithelium, represent the most common intraosseous pathology in the head and neck region. This retrospective study aimed to evaluate bone healing following the surgical removal of odontogenic cysts using fractal analysis.Materials and MethodsBone changes in 17 patients who underwent cyst enucleation were assessed using fractal dimension and lacunarity measurements on digital panoramic radiographs obtained before and six months after surgery. Statistical analyses included the Shapiro–Wilk test, paired t-test, Wilcoxon signed-rank test, repeated measures ANOVA, and the Friedman test.ResultsAt six months postoperatively, bone structure differences had largely normalized. In the cyst center, there were no statistically significant differences in fractal dimension or lacunarity (P > 0.05). At the cyst edge, fractal dimension remained statistically unchanged (P = 0.446), while lacunarity significantly decreased from 0.06 to 0.04 (P = 0.04). In unaffected control regions, no significant changes were observed (P > 0.05). Preoperative fractal dimension values significantly differed between regions (P < 0.001), but these differences were no longer significant postoperatively (P = 0.077). Lacunarity values showed no significant regional differences at either time point (P > 0.05).ConclusionsFractal analysis offers valuable insights into bone regeneration and may surpass traditional radiographic evaluations. Despite limitations such as small sample size and potential subjectivity in region of interest (ROI) selection, the results support the utility of fractal dimension and lacunarity in tracking bone healing after cyst surgery. creator: Ayse Tas creator: Elif Celebi creator: Zeynep Çukurova Yilmaz uri: https://doi.org/10.7717/peerj.19745 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Tas et al. title: Cavy lifespan: survival analysis and lifetables for the pet guinea pig (Cavia porcellus, L.) in Britain link: https://peerj.com/articles/19702 last-modified: 2025-07-18 description: In Britain, an estimated number of 700,000 guinea pigs are currently kept as pets. Despite their widespread presence, research on pet guinea pig survivability remains limited. While demographic studies exist, they primarily focus on morbidity rather than lifespan analysis. This study aims to fill this gap by investigating factors influencing pet guinea pig longevity and constructing life tables, contributing valuable insights into their survival patterns and potential improvements in care practices. The study was conducted using publicly available data from the VetCompass™ UK Program, including 675 guinea pigs receiving veterinary care in the UK in 2019. The survival analysis was conducted using Kaplan–Meier models, with lifespan differences tested via the Log-Rank test. Key predictors included sex, neutering status, and breed classification.The results of the study indicate an average lifespan of the British pet guinea pigs is 4.022 (3.875; 4,170) years; a median survival time of 4.025 95% confidence interval (3.830; 4,290) years; and an interquartile range of (2.563; 5447) years. Unlike other companion animals, no significant differences in longevity were found between sexes, neutering status, or breed (log-rank Mantel-Cox χ2 p > 0.05), suggesting that these factors may play a less critical role in guinea pigs. The findings challenge common assumptions about lifespan determinants in domesticated species. The study also highlights low neutering rates, likely influenced by concerns over surgical risks. Additionally, breed classification remains inconsistent, indicating a possible lack of standardised identification among owners and veterinarians. This study is limited by potential selection bias, lack of environmental and husbandry data, few neutered animals, unclear breeding backgrounds, unaccounted cohort effects, and no geographical analysis of care variation across different regions of Britain. creator: Fernando Mata uri: https://doi.org/10.7717/peerj.19702 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mata title: Identification of Cassiopea sp. in Lake Macquarie, Australia and revision of the taxonomic status of Cassiopea maremetens Gershwin, Zeidler & Davie, 2010 (Cnidaria: Scyphozoa: Cassiopeidae) link: https://peerj.com/articles/19669 last-modified: 2025-07-18 description: Scyphozoans of the genus Cassiopea are notable for their unusual benthic habit of lying upside-down with their exumbrella resting on the substrate and oral arms facing upwards resulting in their common name “upside-down jellyfish”. Cassiopea includes species that have been historically confused because of taxonomic ambiguity. Additionally, some species are considered to be invasive, which can have significant economic and environmental consequences by impacting fisheries, tourism, and trophic structures. In temperate southeastern Australia, Cassiopea medusae were first reported in temperate Wallis Lake and Lake Illawarra in 2016, and then Lake Macquarie in 2017, though historically these jellyfish have a more northern tropical distribution in Queensland, eastern Australia. Owing to the invasive potential of Cassiopea, correct species identification is crucial for future management. To address this knowledge gap, this study used genetic comparison through the cytochrome c oxidase subunit I (COI) barcoding gene and morphometric analysis, together with revision of type and topotype material of Cassiopea maremetens Gershwin, Zeidler & Davie, 2010, an incompletely known nominal species from Queensland, to investigate the identity of Cassiopea occurring in Lake Macquarie. The morphometric analysis was also used to identify key features that distinguish the Lake Macquarie species from a second species, designated Cassiopea sp.3, that is also expanding its range southwards in eastern Australia, and which may be sympatric in some areas. The results of this study show the species occurring in Lake Macquarie is Cassiopea xamachana Bigelow, 1892, originally described from Jamaica and subsequently widely reported from the Western Atlantic and the Indo-West Pacific. Additionally, we demonstrate that Cassiopea maremetens, is a junior synonym of C. xamachana. Morphological characters that can be most readily used to distinguish mature specimens of C. xamachana from C. sp.3, which has an overlapping distribution on the Australian east coast, are: (1) the number of large appendages on the oral disc, which is much higher in Cassiopea sp.3 (at least 1 but up to 14) vs. a maximum of two in C. xamachana; (2) the oral arm branching pattern, which is usually alternating for C. xamachana, but a combination of alternating, bifurcating and pinnate for Cassiopea sp.3; (3) the length of the large appendage on the oral arm, which is proportionally longer relative to the bell diameter in C. xamachana. creator: Claire E. Rowe creator: Shane T. Ahyong creator: Will F. Figueira creator: Ingo Burghardt creator: Stephen J. Keable uri: https://doi.org/10.7717/peerj.19669 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Rowe et al. title: Electrical characteristics of the extracellular fluid in the body segments of Apis mellifera bees link: https://peerj.com/articles/19691 last-modified: 2025-07-17 description: This study investigates the electrical properties of the extracellular fluid in honeybees (Apis mellifera) and its relationship with different body segments. By characterizing resistance, capacitance, and electrical impedance, aspects such as ionic composition, molecular polarization, and the differential response of live bees to electrical stimuli were evaluated. The results show that electrical characteristics vary significantly depending on the body segment, with the head exhibiting high resistance values and the abdomen displaying high capacitance, reflecting differences in molecular composition and functionality. Additionally, experiments with live bees demonstrated the feasibility of measuring electrical parameters non-invasively, opening new possibilities for monitoring the health of these pollinators under controlled conditions and in natural environments. This work lays the foundation for developing innovative tools in ecological monitoring, the assessment of environmental stressors, and the sustainable management of bee colonies. creator: Juan Hernandez creator: Fredy Mesa creator: Anderson Dussan creator: Andre Riveros uri: https://doi.org/10.7717/peerj.19691 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hernandez et al. title: Core body temperature correlates of transition from aerobic to anaerobic metabolism in running link: https://peerj.com/articles/19686 last-modified: 2025-07-17 description: PurposeWe investigated core body temperature (CBT) during a graded exercise test (GXT) in comparison with gas exchange dynamics.MethodsThirty-two active males performed a treadmill GXT (0.5 km/h increments every 30 seconds, 1.5% incline) until exhaustion. Gas exchange data and rectal temperature (Tre) were continuously registered. Ten participants repeated the test for reliability assessment. The first and second gas exchange thresholds (VT1 and VT2) were determined by the simplified V-slope method, while CBT dynamics and eventual temperature thresholds (TT1 and TT2) were assessed according to the criteria defined in this study. Three independent evaluators determined gas exchange and temperature thresholds.ResultsIn 29 subjects, Tre increase was best fitted with a 3-phase segmented model of successively steeper slopes, with a linear relationship in all three segments (17 subjects), or in two segments, with a quadratic relationship for the remaining segment (12 subjects). The between-segment intersection points were considered as TT1 and TT2. In three participants, Tre was best fitted with a two-segment, single-breakpoint (TT1 or TT2) model. The evaluators’ objectivity was satisfactory for VT1 (α = 0.786), very high for TT2 (α = 0.941) and VT2 (α = 0.948). TT1 and VT1 were moderately correlated (ρ = 0.41, p = 0.021) while VT2 and TT2 were highly correlated (r = 0.78, p < 0.001) showing a small, yet statistically significant difference (12.95 ± 1.9 vs 13.43 ± 1.7 km/h, p = 0.039). However, test-retest reliability was low.ConclusionThe breakpoints in CBT increase observed during graded running may represent transitions between the three intensity domains of physical activity. creator: Marija Rakovac creator: Davor Šentija creator: Tošo Maršić creator: Vesna Babić uri: https://doi.org/10.7717/peerj.19686 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Rakovac et al. title: Analysis of epidemic trend of respiratory pathogens in children after long-term pathogen isolation link: https://peerj.com/articles/19710 last-modified: 2025-07-16 description: BackgroundChina implemented strict prevention and control measures during the COVID-19 pandemic, leading to prolonged home confinement of children and significantly reduced exposure to respiratory pathogens. The ability of children under these conditions to resist respiratory pathogens post-lifting of containment measures remained unknown. The children’s ability to face respiratory pathogens post-isolation was assessed through collecting respiratory pathogens detection data, statistical analysis and comparing with pre-epidemic data. In this way, we addressed data gaps in related fields and provided empirical support for research and public health sectors.MethodsThe pathogen detection method was real-time polymerase chain reaction (PCR). Data analysis software: SPSS Statistics 23.ResultsFour environmental factors—temperature, humidity, wind speed and sunshine time—exerted interactive effects ton respiratory pathogens prevalence. Influenza A and B viruses, Mycoplasma pneumoniae and adenovirus exhibited seasonally prevalent patterns in winter, while respiratory syncytial virus showed lower prevalence in summer, and rhinovirus had no significant seasonal variation. The infection rate of respiratory syncytial virus and the number of expected infections decreased with the increase of age, whereas adenovirus, influenza virus, Mycoplasma pneumoniae and bacterial pathogens showed age-related increases in both metrics. Gender-related differences were observed in higher infection rates of Klebsiella pneumoniae, Haemophilus influenzae and Pseudomonas aeruginosa in men compared to women. Co-infection analysis revealed that respiratory syncytial virus exhibited the highest co-infection diversity, followed by influenza B virus, Mycoplasma pneumoniae, and Staphylococcus aureus. Pseudomonas aeruginosa showed inhibition of co-infection with Klebsiella pneumoniae. Streptococcus pneumoniae had been shown to inhibit co-infection with Haemophilus influenzae, Staphylococcus aureus, and Klebsiella pneumoniae. The lower respiratory tract infection rate of Mycoplasma pneumoniae and bacterial pathogens exceeded the overall infection rate. Infection rates of influenza B virus and adenovirus were lower than the overall rate, while those of influenza A and rhinovirus paralleled the overall rate. Analysis of statistical data from China and Gansu Provincial Centers for Disease Control and Prevention revealed that most respiratory pathogens showed an increase in the infection rates post-COVID-19, particularly respiratory syncytial virus, indicating altered prevalence patterns in children due to prolonged exposure to isolated pathogens. creator: Ping Chen creator: Yahong Li creator: Shiwei Li creator: Xin Hua creator: Yu Liu uri: https://doi.org/10.7717/peerj.19710 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Influence of phragmites density, algal concentration and water velocity on cyanobacterial bloom dynamics link: https://peerj.com/articles/19704 last-modified: 2025-07-16 description: BackgroundCyanobacterial blooms present a significant global water challenge, often accumulating in lakeside wetlands and impacting water quality. Despite this, wetland characteristics influencing bacterial diversity during cyanobacterial bloom degradation remain unclear.MethodsTo address this gap, we conducted a 30-day simulation experiment near Lake Taihu, China, to investigate the effects of Phragmites density, algae concentration and water velocity on bacterial diversity and water quality. An orthogonal design with three factors and levels was used with 18 tanks, each with a soil layer. Phragmites density, algae concentration and water velocity were adjusted to simulate lake conditions. Physicochemical parameters were measured within a month, and water samples were collected for bacterial biomass and DNA extraction. Bacterial 16S rRNA gene sequencing was performed to assess diversity, and statistical analyses including α-diversity, β-diversity, and analysis of similarities (ANOSIM) were conducted to evaluate the impact of the experimental factors on water quality and bacterial community structures.ResultsAlgal concentration and water velocity had a greater impact on water quality than Phragmites density. Employing 16S rRNA gene sequencing technology, we discovered that bacterial α-diversity was significantly affected by phragmites density, water velocity, and time (P < 0.01), whereas bacterial β-diversity was significantly influenced by algal concentration and time (P < 0.001). The bacterial community structure was significantly impacted by phragmites density, water velocity, algal concentration, and time (P < 0.001). During the degradation of cyanobacterial blooms, the most abundant bacteria were Proteobacteria (36.8%), Bacteroidetes (20.4%), Cyanobacteria (19.1%), and Actinobacteria (10.3%). Algal density had a stronger influence on bacterial community structure than Phragmites density or water velocity. Orthogonal test results indicated that high algal concentration, coupled with reduced Phragmites density and increased water velocity, rapidly decreased nitrogen, phosphorus concentrations, and bacterial diversity. These findings deepen our understanding of Phragmites wetland effects on cyanobacterial blooms, offering insights for water ecological conservation and resource management in cyanobacteria-affected lakes. creator: Jiaming Lv creator: Guijun Yang creator: Yuqing Zhang creator: Keqiang Shao creator: Xiangming Tang uri: https://doi.org/10.7717/peerj.19704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lv et al. title: Association between vitamin D receptor gene polymorphisms and athletic performance in Chinese male youth soccer players link: https://peerj.com/articles/19696 last-modified: 2025-07-16 description: BackgroundThe relationship between the vitamin D receptor (VDR) gene and muscle strength has been extensively investigated; however, the findings of this research remain inconclusive. The aim of this study was to evaluate the association between VDR variants (ApaIrs797523, BsmI rs1544410, and FokIrs2228570 genotypes) and athletic performance in youth soccer players in China.Materials and MethodsA total of 142 male soccer players (73 from an elite group and 69 from a sub-lite group) aged 13–15 years, and 107 controls (13- to 14-year-old students) were recruited for this study. We measured height, weight, speed, explosive power, anaerobic endurance, and aerobic endurance in both the elite and sub-elite athletes. ApaI, BsmI and FokI genotypes were detected in controls, elite, and sub-elite soccer players with the single-nucleotide polymorphism (SNP) technique. The χ2 test was applied to analyze the correlation between genotype distribution and allelic frequency in elite and sub-elite athletes and controls. One-way analysis of variance and Bonferroni’s post hoc test were implemented to analyze the differences in parameters among groups, and statistical significance was set at p ≤ 0.05.Results(1) The genotype distributions of the ApaI, BsmI, and FokI in controls, elite, and sub-elite soccer players were consistent with the Hardy–Weinberg equilibrium (HWE) results, except for the BsmI genotype distribution in control s (χ2 = 7.396, df = 1, p = 0.025). (2) The BsmI AG frequency in the controls and sub-elite players was significantly higher than in the elite players (χ2 = 6.4, df = 1, p = 0.011; χ2 = 4.50, df = 1, p = 0.034, respectively). The frequency of the FokI TT genotype in the controls was significantly higher than in the elite and sub-elite players (χ2 = 12.737, df = 1, p < 0.001, χ2 = 8.805, df = 1, p = 0.003, respectively). The frequency of the ApaI A in the elite players was significantly lower than that in the controls and sub-elite players (χ2 = 3.765, df = 1, p = 0.05; χ2 = 12.19, df = 1, p < 0.001 respectively). (3) ApaI CC players had longer distances in the standing long jump (SLJ) (p = 0.026) and shorter times in the 30-m run (p = 0.003) than ApaI AC players. Additionally, ApaI AA players had significantly longer Yo-Yo Intermittent Recovery Test Level 1 (YYIR1) running distances compared to ApaI AC players (p = 0.002).ConclusionChinese elite youth soccer players are more likely to possess the ApaI CC genotype and are less likely than sub-elite players to have the BsmI A alleles. Additionally, the ApaI CC genotype is associated with better speed and explosive power among Chinese elite youth soccer players. creator: Shidong Yang creator: Wei Zhang creator: Meng Jia creator: Haichun Chen uri: https://doi.org/10.7717/peerj.19696 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al.