title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=402 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant (Ribes nigrum), red and white currant (Ribes rubrum), and gooseberry (Ribes uva-crispa) provide new insights into the phylogeny of Grossulariaceae link: https://peerj.com/articles/16272 last-modified: 2023-10-10 description: BackgroundBlackcurrant (Ribes nigrum), red currant (R. rubrum), white currant (R. rubrum), and gooseberry (R. uva-crispa) belong to Grossulariaceae and are popular small-berry crops worldwide. The lack of genomic data has severely limited their systematic classification and molecular breeding.MethodsThe complete chloroplast (cp) genomes of these four taxa were assembled for the first time using MGI-DNBSEQ reads, and their genome structures, repeat elements and protein-coding genes were annotated. By genomic comparison of the present four and previous released five Ribes cp genomes, the genomic variations were identified. By phylogenetic analysis based on maximum-likelihood and Bayesian methods, the phylogeny of Grossulariaceae and the infrageneric relationships of the Ribes were revealed.ResultsThe four cp genomes have lengths ranging from 157,450 to 157,802 bp and 131 shared genes. A total of 3,322 SNPs and 485 Indels were identified from the nine released Ribes cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant (R. rubrum) is a fruit color variant of red currant (R. rubrum). The most polymorphic genic and intergenic region is ycf1 and trnT-psbD, respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the Grossularia subgenus is well nested within the Ribes subgenus and shows a paraphyletic relationship with the co-ancestor of Calobotrya and Coreosma sections, which challenges the dichotomous subclassification of the Ribes genus based on morphology (subgenus Ribes and subgenus Grossularia). These data, results, and insights lay a foundation for the phylogenetic research and breeding of Ribes species. creator: Xinyu Sun creator: Ying Zhan creator: Songlin Li creator: Yu Liu creator: Qiang Fu creator: Xin Quan creator: Jinyu Xiong creator: Huixin Gang creator: Lijun Zhang creator: Huijuan Qi creator: Aoxue Wang creator: Junwei Huo creator: Dong Qin creator: Chenqiao Zhu uri: https://doi.org/10.7717/peerj.16272 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Sun et al. title: Repeated response execution and inhibition alter subjective preferences but do not affect automatic approach and avoidance tendencies toward an object link: https://peerj.com/articles/16275 last-modified: 2023-10-10 description: BackgroundRepeated action or inaction toward objects changes preferences for those objects. However, it remains unclear whether such training activates approach-avoidance motivation toward the objects, which leads to actual behavior. We conducted a pre-registered online experiment to examine whether approach and avoidance tendencies were affected by the experience of having executed or withheld a button-press response to a stimulus.MethodsParticipants (N = 236) performed a Go/NoGo task in which they were asked to repeatedly execute a response to a picture of a mug (i.e., Go-primed stimulus) and suppress a response to another picture of a mug (i.e., NoGo-primed stimulus). They then received one of two manikin tasks, which were implicit association tests designed to assess approach–avoidance tendencies. One manikin task measured the reaction times of moving a manikin toward or away from the Go-primed stimulus and the other picture of a mug (i.e., unprimed stimulus). The other manikin task measured the reaction times of moving a manikin toward or away from the NoGo-primed stimulus and the unprimed stimulus. The participants then rated their preference for the Go-primed, NoGo-primed, and unprimed items.ResultsThe Go-primed item was evaluated as more highly preferable than the unprimed item in the Go condition, while the NoGo-primed item was evaluated as less preferable than the unprimed item in the NoGo condition. In contrast, the mean approach/avoidance reaction times in the manikin task showed no difference between the Go-primed and unprimed stimuli or between the NoGo-primed and unprimed stimuli.ConclusionWhen participants repeatedly responded or inhibited their responses to an object, their explicit preference for the object increased or decreased, respectively. However, the effect did not occur in approach-avoidance behaviors toward the object. creator: Izumi Matsuda creator: Hiroshi Nittono uri: https://doi.org/10.7717/peerj.16275 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Matsuda and Nittono title: Distribution of multidrug-resistant bacterial infections in diabetic foot ulcers and risk factors for drug resistance: a retrospective analysis link: https://peerj.com/articles/16162 last-modified: 2023-10-09 description: ObjectiveTo investigate the distribution, drug resistance and risk factors of multi-drug resistant bacterias (MDROs) in patients with Type 2 diabetic foot ulcers (DFU).MethodThe clinical data, foot secretions, pathogenic microorganisms and drug sensitivity tests of 147 patients with type 2 diabetes admitted to our department from January 2018 to December 2021 were analyzed. Patients were divided into two groups according to whether they had been infected with MDROs or not. Seventy-one cases were infected with MDROs as the case group, and the remaining 76 cases were the control group. Chi-square test and t-test were used to analyze the results of MDROs infection and DFU, and logistic multivariate regression was used to evaluate the risk factors of MDROs infection.ResultsA total of 71 strains were isolated from the MDROs-positive group, with the top three being Staphylococcus aureus (46.48%), Escherichia coli (22.53%), and Pseudomonas aeruginosa (18.31%), respectively. Logistic multifactorial regression analysis showed that history of previous antimicrobial exposure, neuroischemic wound, Wagner grade 3–5, and combined osteomyelitis were associated with Type 2 diabetic foot infection MDROs (P < 0.05).ConclusionPrevious history of antimicrobial exposure, neuroischemic wounds, Wagner grade 3–5, and combined osteomyelitis are independent risk factors for MDROs, which can identify the risk factors for MDROs at an early stage and help to identify people at high risk of MDROs infection and take relevant comprehensive treatment in time to slow down the development of the disease. creator: Huihui Guo creator: Qiwei Song creator: Siwei Mei creator: Zhenqiang Xue creator: Junjie Li creator: Tao Ning uri: https://doi.org/10.7717/peerj.16162 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guo et al. title: Replacing mechanical protection with colorful faces–twice: parallel evolution of the non-operculate marine worm-snail genera Thylacodes (Guettard, 1770) and Cayo n. gen. (Gastropoda: Vermetidae) link: https://peerj.com/articles/15854 last-modified: 2023-10-09 description: Vermetid worm-snails are sessile and irregularly coiled marine mollusks common in warmer nearshore and coral reef environments that are subject to high predation pressures by fish. Often cryptic, some have evolved sturdy shells or long columellar muscles allowing quick withdrawal into better protected parts of the shell tube, and most have variously developed opercula that protect and seal the shell aperture trapdoor-like. Members of Thylacodes (previously: Serpulorbis) lack such opercular protection. Its species often show polychromatic head-foot coloration, and some have aposematic coloration likely directed at fish predators. A new polychromatic species, Thylacodes bermudensis n. sp., is described from Bermuda and compared morphologically and by DNA barcode markers to the likewise polychromatic western Atlantic species T. decussatus (Gmelin, 1791). Operculum loss, previously assumed to be an autapomorphy of Thylacodes, is shown to have occurred convergently in a second clade of the family, for which a new genus Cayo n. gen. and four new western Atlantic species are introduced: C. margarita n. sp. (type species; with type locality in the Florida Keys), C. galbinus n. sp., C. refulgens n. sp., and C. brunneimaculatus n. sp. (the last three with type locality in the Belizean reef) (all new taxa authored by Bieler, Collins, Golding & Rawlings). Cayo n. gen. differs from Thylacodes in morphology (e.g., a protoconch that is wider than tall), behavior (including deep shell entrenchment into the substratum), reproductive biology (fewer egg capsules and eggs per female; an obliquely attached egg capsule stalk), and in some species, a luminous, “neon-like”, head-foot coloration. Comparative investigation of the eusperm and parasperm ultrastructure also revealed differences, with a laterally flattened eusperm acrosome observed in two species of Cayo n. gen. and a spiral keel on the eusperm nucleus in one, the latter feature currently unique within the family. A molecular phylogenetic analysis based on mitochondrial and nuclear rRNA gene sequences (12SrRNA, trnV, 16SrRNA, 28SrRNA) strongly supports the independent evolution of the two non-operculate lineages of vermetids. Thylacodes forms a sister grouping to a clade comprising Petaloconchus, Eualetes, and Cupolaconcha, whereas Cayo n. gen is strongly allied with the small-operculate species Vermetus triquetrus and V. bieleri. COI barcode markers provide support for the species-level status of the new taxa. Aspects of predator avoidance/deterrence are discussed for these non-operculate vermetids, which appear to involve warning coloration, aggressive behavior when approached by fish, and deployment of mucous feeding nets that have been shown, for one vermetid in a prior study, to contain bioactive metabolites avoided by fish. As such, non-operculate vermetids show characteristics similar to nudibranch slugs for which the evolution of warning coloration and chemical defenses has been explored previously. creator: Rüdiger Bieler creator: Timothy M. Collins creator: Rosemary Golding creator: Camila Granados-Cifuentes creator: John M. Healy creator: Timothy A. Rawlings creator: Petra Sierwald uri: https://doi.org/10.7717/peerj.15854 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Bieler et al. title: Relationship between swimming speed, intra-cycle variation of horizontal speed, and Froude efficiency during consecutive stroke cycles in adolescent swimmers link: https://peerj.com/articles/16019 last-modified: 2023-10-09 description: The purpose of this study was to investigate the relationship between swimming speed, intra-cycle variation of horizontal speed of displacement (dv), and Froude efficiency (ηF) in front-crawl during three consecutive stroke cycles. The sample consisted of 15 boys aged 16.07 ± 0.77 years and 15 girls aged 15.05 ± 1.07 years. Swimming speed, dv and ηF were measured during a 25 m front-crawl trial. Three consecutive stroke cycles were measured. Swimming speed showed a non-significant stroke-by-stroke effect (F = 2.55, p = 0.087, η2 = 0.08), but a significant sex effect (F = 90.46, p < 0.001, η2 = 0.76). The dv and ηF had the same trend as the swimming speed for the stroke-by-stroke effect, but a non-significant sex effect (p > 0.05). The Spearman correlation matrix between swimming speed and dv, and swimming speed and ηF showed non-significant correlations for the three stroke cycles in both sexes. However, the tendency of the former was not always inverse, and the latter was not always direct. Coaches and swimmers need to be aware that lower dvs are not always associated with faster swimming speeds and vice-versa, and that ηF is a predictor of swimming speed, not dv. creator: Mafalda P. Pinto creator: Daniel A. Marinho creator: Henrique P. Neiva creator: Jorge E. Morais uri: https://doi.org/10.7717/peerj.16019 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Pinto et al. title: The Early Childhood Oral Health Impact Scale (ECOHIS): psychometric properties and application on preschoolers link: https://peerj.com/articles/16035 last-modified: 2023-10-09 description: BackgroundThe concept of oral health related to quality of life involves the impact that oral health has on an individual’s well-being. The Early Childhood Oral Health Impact Scale (ECOHIS) was developed to measure the impact of oral health problems on the lives of children and their families.ObjectiveTo evaluate the psychometric properties of ECOHIS applied to mothers of preschool children and estimate the influence of demographic characteristics, caries experience, and plaque index on the ECOHIS score.MethodsThe fit of ECOHIS to the data was assessed by confirmatory analysis. Chi-square for degrees of freedom ratio (χ2/df), Comparative Fit Index (CFI), Tucker-Lewis Index (TLI), and Root Mean Square Error of Approximation (RMSEA) were used. Reliability was estimated by the ordinal coefficients alpha (α) and omega (ω). The factorial invariance was estimated by the difference in CFI (ΔCFI). Comparisons of the ECOHIS mean scores according to the demographic characteristics, caries experience, and plaque index was performed using analysis of variance (ANOVA).ResultsA total of 371 children participated in the study. Mothers’ mean age was 33.0 (SD = 7.04) years. The ECOHIS presented a good fit to the data (χ2/df = 4.31; CFI = 0.95; TLI = 0.94; RMSEA = 0.09) and a strict model invariance. Children without caries and from higher income class had lower oral health impact.ConclusionThe data obtained with the ECOHIS were valid, reliable, and invariant. Children with caries experience and from lower income families had a greater impact of oral problems. creator: Bianca Núbia Souza Silva creator: Lucas A. Campos creator: João Marôco creator: Juliana A.D.B Campos uri: https://doi.org/10.7717/peerj.16035 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Silva et al. title: Assessing the effect of heavy metals on maize (Zea mays L.) growth and soil characteristics: plants-implications for phytoremediation link: https://peerj.com/articles/16067 last-modified: 2023-10-09 description: BackgroundHeavy metal pollution has become a global environmental issue. Heavy metals are contaminating the agro-soils, growing crops, and vegetables through different agricultural practices. In this study, besides the phytoremediation potential of maize, the role of chromium (Cr) and lead (Pb) on crop and soil health has been investigated.MethodsTwo maize varieties, Pak-Afgoi and Neelem, were grown under varying concentrations of Cr (50–300 ppm) and Pb (30–300 ppm) and different growth parameters i.e., seed germination, leaf size/number, stem girth, plant height, biomass, chlorophyll content, relative growth rate (RGR), and net assimilation rate (NAR) were studied under Cr and Pb stress. Likewise, the effect of metals was also assessed on different soil characteristics including soil texture, pH, EC, soil organic matter, urease activity and nutrients.ResultsStudied plant attributes were adversely affected by heavy metals toxicity. Affected values of RGR and NAR showed a linear correlation with affected growth and dry matter yield of maize. Heavy metals impacted different soil parameters including soil microbial performance and revealed a declining trend as compared to control soil. Maize varieties showed a significant phytoremediation potential i.e., uptake of Cr and Pb was 33% and 22% in Pak-Afgoi, while Neelem showed 38% and 24% at 300 ppm, respectively. Data regarding metal translocation factor (TF), bioaccumulation factor (ACF), and biomagnification ratio (BMR) significantly revealed the potential of maize varieties in the removal of Cr and Pb metals from affected soils. However, Cr-accumulation was higher in shoots, and Pb accumulated in plant roots showed a differential behavior of metal translocation and affinity with the varieties. These maize varieties may be recommended for general cultivation in the Cr and Pb-contaminated areas. creator: Muhammad Imran Atta creator: Syeda Sadaf Zehra creator: Habib Ali creator: Basharat Ali creator: Syed Naveed Abbas creator: Sara Aimen creator: Sadia Sarwar creator: Ijaz Ahmad creator: Mumtaz Hussain creator: Ibrahim Al-Ashkar creator: Dinakaran Elango creator: Ayman El Sabagh uri: https://doi.org/10.7717/peerj.16067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Atta et al. title: Effects of food-based enrichment on enclosure use and behavioral patterns in captive mammalian predators: a case study from an Austrian wildlife park link: https://peerj.com/articles/16091 last-modified: 2023-10-09 description: BackgroundCombining naturalistic enclosure design and animal welfare with visitor interests and education can be challenging for zoos and wildlife parks. To accomplish both purposes, different types of enrichment (food-based or non-food-based items, such as environmental, sensory, cognitive, social) can be used. The aim of the present study is to investigate the effect of food-based and olfactory enrichments on enclosure use, behavior, and visibility of captive brown bears (Ursus arctos), pine martens (Martes martes), domestic ferrets (Mustela putorius furo), and golden jackals (Canis aureus).MethodsWe used observational approaches to measure enclosure use, behavior, and visibility during three different experimental phases: (1) pre-enrichment (baseline, no experience with the enrichment yet), (2) during enrichment (enrichment was provided at low frequented locations in the enclosures that are easily visible to visitors), and (3) post-enrichment (enrichment was removed from the enclosures).ResultsWe found that enrichment led to a uniform use of the enclosure and enhanced visibility in brown bears, increased activity budgets in pine martens, and observed high object interaction in both species. No effects of enrichment were detected in domestic ferrets. Golden jackals did not leave their burrows during daytime during the entire observation period; thus, observations were not possible at all. Our results suggest different effects of food-based enrichment, e.g., enclosure use, temporal activity patterns, and animal visibility. However, further studies should control for the specific role of the factors involved. Our study represents one of the first explorations of food-based enrichment in rather understudied species. creator: Verena Puehringer-Sturmayr creator: Monika Fiby creator: Stephanie Bachmann creator: Stefanie Filz creator: Isabella Grassmann creator: Theresa Hoi creator: Claudia Janiczek creator: Didone Frigerio uri: https://doi.org/10.7717/peerj.16091 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Puehringer-Sturmayr et al. title: Bird diversity along an urban to rural gradient in large tropical cities peaks in mid-level urbanization link: https://peerj.com/articles/16098 last-modified: 2023-10-09 description: The gradient from natural to urban areas strongly associates with the structure of avian communities over that gradient. Most research on urban birds is from temperate areas and knowledge from tropical Southeast Asia is lacking. We examined bird species diversity, relative abundance, and species composition along an urban to rural gradient in three Myanmar cities, and assessed potential environmental factors responsible for the changes. We counted birds within 40 point-count sites with 50-m fixed-radius in three large cities of Myanmar, namely Mandalay, Mawlamyine, and Myeik. We distinguished four urban habitat types (Downtown–urban, University Campus–suburban, Paddy Field–agriculture, Hill–forest). We classified all species into migrant or resident and into major feeding groups and related with several environmental parameters such as ‘impervious surface’. We counted 5,423 individuals of 103 species with roughly equal species diversity between the three cities. Rock Pigeon (Columba livia) was the most frequent species. The species composition differed significantly between the four major habitat types. Omnivores were more abundant in the city center than all other functional groups. Interestingly, insectivores were also predominant in the city center. In addition, more generalist’ species occurred towards the city center compared to the periphery, indicating that the periphery has increased relevance for specialized birds. We found some marked differences in species composition between the three cities of Mandalay, Mawlamyine, and Myeik. Additionally to species composition, species diversity and relative abundance differed significantly between each of the four major habitat types in all three cities. creator: Marcela Suarez-Rubio creator: Paul J.J. Bates creator: Thein Aung creator: Nay Myo Hlaing creator: Sai Sein Lin Oo creator: Yu Kay Zin Htun creator: Saw Myat Ohn Mar creator: Aye Myint creator: Thin Lae Lae Wai creator: Pann Mo Mo creator: Lutz Fehrmann creator: Nils Nölke creator: Christoph Kleinn creator: Swen C. Renner uri: https://doi.org/10.7717/peerj.16098 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Suarez-Rubio et al. title: Identification of genetic loci for early maturity in spring bread wheat using the association analysis and gene dissection link: https://peerj.com/articles/16109 last-modified: 2023-10-09 description: BackgroundEarly maturity in spring bread wheat is highly desirable in the regions where it enables the plants to evade high temperatures and plant pathogens at the end of the growing season.MethodsTo reveal the genetic loci responsible for the maturity time association analysis was carried out based on phenotyping for an 11-year period and high-throughput SNP genotyping of a panel of the varieties contrasting for this trait. The expression of candidate genes was verified using qPCR. The association between the SNP markers and the trait was validated using the biparental F2:3 population.ResultsOur data showed that under long-day conditions, the period from seedling to maturity is mostly influenced by the time from heading to maturity, rather than the heading time. The QTLs associated with the trait were located on 2A, 3B, 4A, 5B, 7A and 7B chromosomes with the 7BL locus being the most significant and promising for its SNPs accelerated the maturity time by about 9 days. Gene dissection in this locus detected a number of candidates, the best being TraesCS7B02G391800 (bZIP9) and TraesCS7B02G412200 (photosystem II reaction center). The two genes are predominantly expressed in the flag leaf while flowering. The effect of the SNPs was verified in F2:3 population and confirmed the association of the 4A, 5B and 7BL loci with the maturity time. creator: Antonina A. Kiseleva creator: Irina N. Leonova creator: Elena V. Ageeva creator: Ivan E. Likhenko creator: Elena A. Salina uri: https://doi.org/10.7717/peerj.16109 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kiseleva et al.