title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=801 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Does long-term fire suppression impact leaf litter breakdown and aquatic invertebrate colonization in pine flatwoods wetlands? link: https://peerj.com/articles/12534 last-modified: 2021-11-29 description: Ephemeral wetlands are commonly embedded within pine uplands of the southeastern United States. These wetlands support diverse communities but have often been degraded by a lack of growing-season fires that historically maintained the vegetation structure. In the absence of fire, wetlands develop a dense mid-story of woody vegetation that increases canopy cover and decreases the amount of herbaceous vegetation. To understand how reduced fire frequency impacts wetland processes, we measured leaf litter breakdown rates and invertebrate communities using three common plant species (Longleaf Pine (Pinus palustris), Pineland Threeawn Grass (Aristida stricta), and Black Gum (Nyssa sylvatica)) that occur in pine flatwoods wetlands located on Eglin Air Force Base, Florida. We also tested whether or not the overall habitat type within a wetland (fire maintained or fire suppressed) affected these processes. We placed leaf packs containing 15.0 g of dried leaf litter from each species in both fire-maintained and fire-suppressed sections of three wetlands, removing them after 103–104 days submerged in the wetland. The amount of leaf litter remaining at the end of the study varied across species (N. sylvatica = 7.97 ± 0.17 g, A. stricta = 11.84 ± 0.06 g, and P. palustris = 11.37 ± 0.07 g (mean ± SE)) and was greater in fire-maintained habitat (leaf type: F2,45 = 437.2, P < 0.001; habitat type: F1,45 = 4.6, P = 0.037). We identified an average of 260 ± 33.5 (SE) invertebrates per leaf pack (range: 19–1,283), and the most abundant taxonomic groups were Cladocera, Isopoda, Acariformes, and Diptera. Invertebrate relative abundance varied significantly among litter species (approximately 39.9 ± 9.4 invertebrates per gram of leaf litter remaining in N. sylvatica leaf packs, 27.2 ± 5.3 invertebrates per gram of A. stricta, and 14.6 ± 3.1 invertebrates per gram of P. palustris (mean ± SE)) but not habitat type. However, both habitat (pseudo-F1,49 = 4.30, P = 0.003) and leaf litter type (pseudo-F2,49 = 3.62, P = 0.001) had a significant effect on invertebrate community composition. Finally, this work was part of ongoing projects focusing on the conservation of the critically imperiled Reticulated Flatwoods Salamander (Ambystoma bishopi), which breeds exclusively in pine flatwoods wetlands, and we examined the results as they relate to potential prey items for larval flatwoods salamanders. Overall, our results suggest that the vegetation changes associated with a lack of growing-season fires can impact both invertebrate communities and leaf litter breakdown. creator: Houston C. Chandler creator: J. Checo Colón-Gaud creator: Thomas A. Gorman creator: Khalil Carson creator: Carola A. Haas uri: https://doi.org/10.7717/peerj.12534 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chandler et al. title: Alexithymia and facial emotion recognition in patients with craniofacial pain and association of alexithymia with anxiety and depression: a systematic review with meta-analysis link: https://peerj.com/articles/12545 last-modified: 2021-11-29 description: BackgroundWe aimed to determine the presence of alexithymia in patients with craniofacial pain (CFP) compared with asymptomatic individuals. Our secondary aims were to assess the relationship of alexithymia with anxiety and depression levels, as well as to assess the presence of facial emotion recognition deficit.MethodsMedline, Scielo and Google Scholar were searched, with the last search performed in 8 September 2021. Standardized mean differences (SMDs) and 95% CIs were calculated for relevant outcomes and were pooled in a meta-analysis using the random effects model. In addition, meta-analyses of correlations and a meta-regression of alexithymia with depression and anxiety were performed.ResultsRegarding alexithymia, assessed through the Toronto Alexithymia Scale (TAS), the results showed significant differences, with higher values in patients compared with asymptomatic individuals, with a large clinical effect (SMD 0.46; 95% CI [0.22–0.71]; heterogeneity-Q 66.86; p < 0.001; inconsistency (I2) = 81%). We found statistically significant correlations with a small clinical effect of alexithymia with anxiety and depression. The meta-regression showed no significant association between the TAS and anxiety or depression. With respect to facial emotion recognition, the results showed statistically significant differences, with greater recognition difficulty in patients compared with asymptomatic individuals, with a large clinical effect (SMD −1.17; 95% CI [−2.01 to −0.33]; heterogeneity-Q 2.97; p = 0.080; I2 = 66%).ConclusionsPatients with CFP showed alexithymia with moderate evidence. There was also moderate evidence indicating that these patients had significant deficits in facial emotion recognition compared with asymptomatic individuals. Furthermore, alexithymia showed statistically significant correlations with anxiety and depression levels. creator: Roy La Touche creator: Alberto García-Salgado creator: Ferran Cuenca-Martínez creator: Santiago Angulo-Díaz-Parreño creator: Alba Paris-Alemany creator: Luis Suso-Martí creator: Aida Herranz-Gómez uri: https://doi.org/10.7717/peerj.12545 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 La Touche et al. title: Innate and learnt color preferences in the common green-eyed white butterfly (Leptophobia aripa): experimental evidence link: https://peerj.com/articles/12567 last-modified: 2021-11-29 description: BackgroundLearning abilities help animals modify their behaviors based on experience and innate sensory biases to confront environmental unpredictability. In a food acquisition context, the ability to detect, learn, and switch is fundamental in a wide range of insect species facing the ever-changing availability of their floral rewards. Here, we used an experimental approach to address the innate color preferences and learning abilities of the common green-eyed white butterfly (Leptophobia aripa).MethodsIn Experiment 1, we conducted innate preference choice-tests to determine whether butterflies had a strong innate color preference and to evaluate whether color preferences differed depending on the array of colors offered. We faced naïve butterflies to artificial flowers of four colors (quadruple choice-test): yellow, pink, white, and red; their choices were assessed. In Experiment 2, we examined the ability of this butterfly species to associate colors with rewards while exploring if the spectral reflectance value of a flower color can slow or accelerate this behavioral response. Butterflies were first trained to be fed from artificial yellow flowers inserted in a feeder. These were later replaced by artificial flowers with a similar (blue) or very different (white) spectral reflectance range. Each preference test comprised a dual-choice test (yellow vs blue, yellow vs white).ResultsButterflies showed an innate strong preference for red flowers. Both the number of visits and the time spent probing these flowers were much greater than the pink, white, and yellow color flowers. Butterflies learn to associate colors with sugar rewards. They then learned the newly rewarded colors as quickly and proficiently as if the previously rewarded color was similar in spectral reflectance value; the opposite occurs if the newly rewarded color is very different than the previously rewarded color.ConclusionsOur findings suggest that common green-eyed white butterflies have good learning abilities. These capabilities may allow them to respond rapidly to different color stimulus. creator: Deysi Muñoz-Galicia creator: Citlalli Castillo-Guevara creator: Carlos Lara uri: https://doi.org/10.7717/peerj.12567 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Muñoz-Galicia et al. title: Whole-limb scaling of muscle mass and force-generating capacity in amniotes link: https://peerj.com/articles/12574 last-modified: 2021-11-29 description: Skeletal muscle mass, architecture and force-generating capacity are well known to scale with body size in animals, both throughout ontogeny and across species. Investigations of limb muscle scaling in terrestrial amniotes typically focus on individual muscles within select clades, but here this question was examined at the level of the whole limb across amniotes generally. In particular, the present study explored how muscle mass, force-generating capacity (measured by physiological cross-sectional area) and internal architecture (fascicle length) scales in the fore- and hindlimbs of extant mammals, non-avian saurians (‘reptiles’) and bipeds (birds and humans). Sixty species spanning almost five orders of magnitude in body mass were investigated, comprising previously published architectural data and new data obtained via dissections of the opossum Didelphis virginiana and the tegu lizard Salvator merianae. Phylogenetic generalized least squares was used to determine allometric scaling slopes (exponents) and intercepts, to assess whether patterns previously reported for individual muscles or functional groups were retained at the level of the whole limb, and to test whether mammals, reptiles and bipeds followed different allometric trajectories. In general, patterns of scaling observed in individual muscles were also observed in the whole limb. Reptiles generally have proportionately lower muscle mass and force-generating capacity compared to mammals, especially at larger body size, and bipeds exhibit strong to extreme positive allometry in the distal hindlimb. Remarkably, when muscle mass was accounted for in analyses of muscle force-generating capacity, reptiles, mammals and bipeds almost ubiquitously followed a single common scaling pattern, implying that differences in whole-limb force-generating capacity are principally driven by differences in muscle mass, not internal architecture. In addition to providing a novel perspective on skeletal muscle allometry in animals, the new dataset assembled was used to generate pan-amniote statistical relationships that can be used to predict muscle mass or force-generating capacity in extinct amniotes, helping to inform future reconstructions of musculoskeletal function in the fossil record. creator: Peter J. Bishop creator: Mark A. Wright creator: Stephanie E. Pierce uri: https://doi.org/10.7717/peerj.12574 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bishop et al. title: Helicobacter pylori virulence factors: relationship between genetic variability and phylogeographic origin link: https://peerj.com/articles/12272 last-modified: 2021-11-26 description: BackgroundHelicobacter pylori is a pathogenic bacteria that colonize the gastrointestinal tract from human stomachs and causes diseases including gastritis, peptic ulcers, gastric lymphoma (MALT), and gastric cancer, with a higher prevalence in developing countries. Its high genetic diversity among strains is caused by a high mutation rate, observing virulence factors (VFs) variations in different geographic lineages. This study aimed to postulate the genetic variability associated with virulence factors present in the Helicobacter pylori strains, to identify the relationship of these genes with their phylogeographic origin.MethodsThe complete genomes of 135 strains available in NCBI, from different population origins, were analyzed using bioinformatics tools, identifying a high rate; as well as reorganization events in 87 virulence factor genes, divided into seven functional groups, to determine changes in position, number of copies, nucleotide identity and size, contrasting them with their geographical lineage and pathogenic phenotype.ResultsBioinformatics analyses show a high rate of gene annotation errors in VF. Analysis of genetic variability of VFs shown that there is not a direct relationship between the reorganization and geographic lineage. However, regarding the pathogenic phenotype demonstrated in the analysis of many copies, size, and similarity when dividing the strains that possess and not the cag pathogenicity island (cagPAI), having a higher risk of developing gastritis and peptic ulcer was evidenced. Our data has shown that the analysis of the overall genetic variability of all VFs present in each strain of H. pylori is key information in understanding its pathogenic behavior. creator: Aura M. Rodriguez creator: Daniel A. Urrea creator: Carlos F. Prada uri: https://doi.org/10.7717/peerj.12272 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Rodriguez et al. title: Systematic review and meta-analysis on the effect of continuous subjective tinnitus on attention and habituation link: https://peerj.com/articles/12340 last-modified: 2021-11-26 description: BackgroundAttention and habituation are two domains known to play key roles in the perception and maintenance of tinnitus. The heterogeneous nature of tinnitus and the methodologies adopted by various studies make it difficult to generalize findings. The current review aims at assessing and synthesizing evidence on the possible roles of attention and habituation in continuous subjective tinnitus.MethodologyThe literature search included five databases (PubMed, Scopus, Web of Sciences, CINAHL and ProQuest) that resulted in 1,293 articles, published by July 2019. Studies on attention and/or habituation in individuals with tinnitus using either behavioural or electrophysiological tests were included in the review after a quality assessment.ResultsSeventeen studies on attention in tinnitus were included in the narrative synthesis. Two meta-analyses were performed to assess the role of attention in tinnitus using a behavioural methodology (z = 4.06; p < 0.0001) and P300 amplitude (z = 2.70; p = 0.007) with 531 participants. With respect to habituation, the review indicates the lack of quality articles for habituation inclusion in the narrative synthesis.ConclusionsThe review highlights that selective domains of attention were consistently impaired in individuals with tinnitus. Habituation, on the other hand, needs further exploration. creator: Harini Vasudevan creator: Kanaka Ganapathy creator: Hari Prakash Palaniswamy creator: Grant Searchfield creator: Bellur Rajashekhar uri: https://doi.org/10.7717/peerj.12340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vasudevan et al. title: Monitoring newt communities in urban area using eDNA metabarcoding link: https://peerj.com/articles/12357 last-modified: 2021-11-26 description: Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales. creator: Léo Charvoz creator: Laure Apothéloz-Perret-Gentil creator: Emanuela Reo creator: Jacques Thiébaud creator: Jan Pawlowski uri: https://doi.org/10.7717/peerj.12357 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Charvoz et al. title: Quadriceps femoris cross-sectional area and specific leg strength: relationship between different muscles and squat variations link: https://peerj.com/articles/12435 last-modified: 2021-11-26 description: BackgroundThe aim was to determine the relationship between the cross-sectional area of the quadriceps femoris and strength performance in the deep and parallel barbell squat.MethodsThe sample included 16 university students (seven female, 24.1 ± 1.7 years). Muscle strength was expressed as external load, including the one-repetition maximum and the body mass segments involved (calculated according to Dempster’s method). The cross-sectional area of the quadriceps femoris muscles was determined using ultrasound, while leg muscle mass was measured using the Bioelectrical Impedance method.ResultsThe cross-sectional areas of the three vastii muscles and leg muscle mass showed moderate to strong correlation with external load in both squat types (r = 0.509–0.873). However, partial correlation (cross-sectional area of quadriceps femoris muscles were controlled) showed significant association only between leg muscle mass and deep squat (r = 0.64, p < 0.05). The cross-sectional area of the vastus lateralis showed a slightly higher correlation with external load in the parallel than in the deep squat (r = 0.67, p < 0.01 vs. r = 0.59, p < 0.05). The regression analysis extracted the vastus medialis cross-sectional area as the most important factor in manifesting strength (parallel squat: R2 = 0.569; deep squat: R2 = 0.499, both p < 0.01). The obtained results suggest that parallel squat strength depends mainly on the cross-sectional area of the vastii muscles, while it seems that the performance in the deep squat requires an additional engagement of the hip and back extensor muscle groups. creator: Filip Kojic creator: Saša Ðurić creator: Igor Ranisavljev creator: Stanimir Stojiljkovic creator: Vladimir Ilic uri: https://doi.org/10.7717/peerj.12435 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kojic et al. title: treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data link: https://peerj.com/articles/12450 last-modified: 2021-11-26 description: The number of terminals in phylogenetic trees has significantly increased over the last decade. This trend reflects recent advances in next-generation sequencing, accessibility of public data repositories, and the increased use of phylogenies in many fields. Despite R being central to the analysis of phylogenetic data, manipulation of phylogenetic comparative datasets remains slow, complex, and poorly reproducible. Here, we describe the first R package extending the functionality and syntax of data.table to explicitly deal with phylogenetic comparative datasets. treedata.table significantly increases speed and reproducibility during the data manipulation steps involved in the phylogenetic comparative workflow in R. The latest release of treedata.table is currently available through CRAN (https://cran.r-project.org/web/packages/treedata.table/). Additional documentation can be accessed through rOpenSci (https://ropensci.github.io/treedata.table/). creator: Cristian Román Palacios creator: April Wright creator: Josef Uyeda uri: https://doi.org/10.7717/peerj.12450 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Román Palacios et al. title: The influence of storage time on ponazuril concentrations in feline plasma link: https://peerj.com/articles/12516 last-modified: 2021-11-26 description: BackgroundThe pharmacokinetics of ponazuril have been determined in several species; however, there is very little information on the stability of the drug after storage for long periods of time. This study was undertaken to determine the stability of ponazuril in plasma samples stored at −80 °C, which is the temperature most commonly used in the author’s laboratory.MethodSpiked plasma samples (0.3, 7.5, and 15 µg/mL) were stored at −80 °C for three months. Analysis occurred on the first day and then once a week for the following twelve weeks. The drug was extracted using a chloroform extraction and separated by high performance liquid chromatography using ultraviolet detection.ResultsThere was no loss of drug for any concentration for the first four weeks of storage. There was an average loss of less than 5% from day 35 through day 70 and an average loss of 6% on day 77 and 84. The data suggest that ponazuril is stable for 4 weeks when stored at −80 °C and undergoes minimal loss in the remaining 8 weeks. creator: Sherry Cox creator: Lainey Harvill creator: Sarah Singleton creator: Joan B. Bergman creator: Becky DeBolt uri: https://doi.org/10.7717/peerj.12516 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cox et al.