title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=568 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Evaluation of a dill (Anethum graveolens L.) gene bank germplasm collection using multivariate analysis of morphological traits, molecular genotyping and chemical composition to identify novel genotypes for plant breeding link: https://peerj.com/articles/15043 last-modified: 2023-03-29 description: Dill (Anethum graveolens L.) is an aromatic herb widely used in the food industry, with several commercial cultivars available with different qualitative characteristics. Commercial cultivars are usually preferred over landraces due to their higher yield and also the lack of improved landraces than can be commercialized. In Greece, however, traditional dill landraces are cultivated by local communities. Many are conserved in the Greek Gene Bank and the aim here was to investigate and compare the morphological, genetic, and chemical biodiversity of twenty-two Greek landraces and nine modern/commercial cultivars. Multivariate analysis of the morphological descriptors, molecular markers, and essential oil and polyphenol composition revealed that the Greek landraces were clearly distinguished compared with modern cultivars at the level of phenological, molecular and chemical traits. Landraces were typically taller, with larger umbels, denser foliage, and larger leaves. Plant height, density of foliage, density of feathering as well as aroma characteristics were desirable traits observed for some landraces, such as T538/06 and GRC-1348/04, which were similar or superior to those of some commercial cultivars. Polymorphic loci for inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) molecular markers were 76.47% and 72.41% for landraces, and 68.24% and 43.10% for the modern cultivars, respectively. Genetic divergence was shown, but not complete isolation, indicating that some gene flow may have occurred between landraces and cultivars. The major constituent in all dill leaf essential oils was α-phellandrene (54.42–70.25%). Landraces had a higher α-phellandrene and dill ether content than cultivars. Two dill landraces were rich in chlorogenic acid, the main polyphenolic compound determined. The study highlighted for the first-time Greek landraces with desirable characteristics regarding quality, yield, and harvest time suitable for breeding programs to develop new dill cultivars with superior features. creator: Kalliopi Kadoglidou creator: Catherine Cook creator: Anastasia Boutsika creator: Eirini Sarrou creator: Ifigeneia Mellidou creator: Christina Aidonidou creator: Ioannis Grigoriadis creator: Andrea Angeli creator: Stefan Martens creator: Vasiliki Georgiadou creator: Theodoros Moysiadis creator: Parthenopi Ralli creator: Ioannis Mylonas creator: Nikolaos Tourvas creator: Michail Michailidis creator: Apostolos Kalivas creator: Eleni Maloupa creator: Ioannis Ganopoulos creator: Aliki Xanthopoulou uri: https://doi.org/10.7717/peerj.15043 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kadoglidou et al. title: Atypical ‘long-tailed’ cockroaches arose during Cretaceous in response to angiosperm terrestrial revolution link: https://peerj.com/articles/15067 last-modified: 2023-03-29 description: Typical cockroaches are flat, broad, with large pronotum and wings covering the body. This conserved morphotype dates back to the Carboniferous, during which the ancestral cockroaches, or roachoids, originated. On the other hand, the ovipositor of cockroaches gradually reduced during the Mesozoic, coupled with a major shift of reproductive strategy. By the Cretaceous, long external ovipositors became rare, most cockroaches used very short or even hidden internal ovipositors to fabricate egg cases (oothecae), which is an innovation for egg protection. Here, we describe two cockroaches from mid-Cretaceous Myanmar amber: Ensiferoblatta oecanthoides gen. et sp. nov. (Ensiferoblattidae fam. nov.) and Proceroblatta colossea gen. et sp. nov. They are slim, elongate, fusiform, with longitudinal pronotum, and have long external ovipositors. The combination of these traits represents a unique morphotype, which resembles crickets and katydids (Ensifera) more than general cockroaches. Ensiferoblatta and Proceroblatta may be arboreal, feeding on and/or laying eggs into certain angiosperms that newly emerged. Their open habit causes latent impairment to viability, and may contribute to their extinction. These new taxa are the youngest members of the ancient, extinct group of cockroaches, namely Eoblattodea, which are characterized by long ovipositors. We speculate that the extinction of certain gymnosperm hosts almost ended the 200-My triumph of Eoblattodea. Despite an attempt to adapt to angiosperm hosts, Ensiferoblatta, Proceroblatta and suchlike cockroaches as an evolutionary dead end failed to save Eoblattodea from extinction. The lack of protection for eggs (maternal care in particular) might accelerate the extinction of Eoblattodea as a whole. creator: Xin-Ran Li creator: Di-Ying Huang uri: https://doi.org/10.7717/peerj.15067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li and Huang title: Seasonal and longitudinal water quality dynamics in three effluent-dependent rivers in Arizona link: https://peerj.com/articles/15069 last-modified: 2023-03-29 description: Effluent-fed streams, which receive inputs from wastewater treatment plants, are becoming increasingly common across the globe as urbanization intensifies. In semi-arid and arid regions, where many natural streams have dried up due to over extraction of water, many streams rely completely on treated effluent to sustain baseflow during dry seasons. These systems are often thought of as ‘second-class’ or highly disturbed stream ecosystems, but they have the potential to serve as refuges for native aquatic biota if water quality is high, especially in areas where few natural habitats remain. In this study, we investigated seasonal and longitudinal water quality dynamics at multiple sites across six reaches of three effluent-dependent rivers in Arizona (USA) with the objective (1) to quantify changes in effluent water quality due to distance traveled and season/climate and (2) to qualify whether water quality conditions in these systems are sufficient to support native aquatic species. Study reaches ranged in length from 3 to 31 km and in geographic setting from low desert to montane conifer forest. We observed the lowest water quality conditions (e.g., elevated temperature and low dissolved oxygen) during the summer in low desert reaches, and significantly greater natural remediation of water quality in longer vs. shorter reaches for several factors, including temperature, dissolved oxygen and ammonia. Nearly all sites met or exceeded water quality conditions needed to support robust assemblages of native species across multiple seasons. However, our results also indicated that temperature (max 34.2 °C), oxygen levels (min 2.7 mg/L) and ammonia concentrations (max 5.36 mg/L N) may occasionally be stressful for sensitive taxa at sites closest to effluent outfalls. Water quality conditions may be a concern during the summer. Overall, effluent-dependent streams have the capacity to serve as refuges for native biota in Arizona, and they may become the only aquatic habitat available in many urbanizing arid and semi-arid regions. creator: Hamdhani Hamdhani creator: Drew E. Eppehimer creator: David M. Quanrud creator: Michael T. Bogan uri: https://doi.org/10.7717/peerj.15069 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hamdhani et al. title: A 3D-printed passive exoskeleton for upper limb assistance in children with motor disorders: proof of concept through an electromyography-based assessment link: https://peerj.com/articles/15095 last-modified: 2023-03-29 description: The rehabilitation of children with motor disorders is mainly focused on physical interventions. Numerous studies have demonstrated the benefits of upper function using robotic exoskeletons. However, there is still a gap between research and clinical practice, owing to the cost and complexity of these devices. This study presents a proof of concept of a 3D-printed exoskeleton for the upper limb, following a design that replicates the main characteristics of other effective exoskeletons described in the literature. 3D printing enables rapid prototyping, low cost, and easy adjustment to the patient anthropometry. The 3D-printed exoskeleton, called POWERUP, assists the user’s movement by reducing the effect of gravity, thereby allowing them to perform upper limb exercises. To validate the design, this study performed an electromyography-based assessment of the assistive performance of POWERUP, focusing on the muscular response of both the biceps and triceps during elbow flexion–extension movements in 11 healthy children. The Muscle Activity Distribution (MAD) is the proposed metric for the assessment. The results show that (1) the exoskeleton correctly assists elbow flexion, and (2) the proposed metric easily identifies the exoskeleton configuration: statistically significant differences (p-value = 2.26 ⋅ 10−7 < 0.001) and a large effect size (Cohen’s d = 3.78 > 0.8) in the mean MAD value were identified for both the biceps and triceps when comparing the transparent mode (no assistance provided) with the assistive mode (anti-gravity effect). Therefore, this metric was proposed as a method for assessing the assistive performance of exoskeletons. Further research is required to determine its usefulness for both the evaluation of selective motor control (SMC) and the impact of robot-assisted therapies. creator: Cristina Sanchez creator: Laura Blanco creator: Carmina del Río creator: Eloy Urendes creator: Vanina Costa creator: Rafael Raya uri: https://doi.org/10.7717/peerj.15095 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sanchez et al. title: “Integrative learning” promotes learning but not memory in older rats link: https://peerj.com/articles/15101 last-modified: 2023-03-29 description: BackgroundWe had previously advanced the concept of “Integrative Learning”, that is, “under the role of ‘meta-learning self’, learners actively integrate learning materials to achieve rapid and in-depth understanding of knowledge”, and designed an animal behavioral model to compare the effects of “Integrative Learning” (IL) vs. “Progressive Learning” (PL) in young rats. It was found that IL is more advantageous than PL. Here, we aim to examine whether the same phenomenon persist in older rats.MethodsFifteen 12-month-old male Sprague-Dawley (SD) rats were selected as subjects and randomly divided into the IL group and the PL group, and a 14-unit integrative T-maze was constructed for the study. Training and testing procedures contained three stages: the learning stage, the memory retention test stage and the Gestalt transfer learning stage. Data on young rats (1-month-old) from the previous study were also drawn here for comparisons on learning performance.Results(1) The 12-session learning stage can be divided into three sub-stages as each sub-stage represented the new opening of one third of the whole path in the PL group. There were significant interactions in total errors made between groups and sessions: the PL group had significantly fewer errors during Sub-stage One due to a much shorter path to be learned, however, the IL group’s errors made sharply dropped as learning progressed into Sub-stage Two and Three, and were maintained at a significantly lower level than the PL group during Sub-stage Three. (2) When compared with young rats, age had a main effect on the number of errors made—the 1-month-old groups learned overall better and faster than the older groups, whereas the pattern of group differences between the IL and PL learning modes remained consistent across young and older groups. (3) Unlike young rats, during the memory retention test stage and the Gestalt transfer learning stage, the IL group did not perform better than the PL group in older rats.Conclusions(1) “Integrative Learning” promotes learning but not memory in older rats. (2) Higher-order cognitive abilities that support meta-cognition, long-term retention and knowledge transfer might be deteriorating in older rats. creator: Bin Yin creator: Xiao-Rui Wu creator: Rong Lian uri: https://doi.org/10.7717/peerj.15101 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yin et al. title: Volcanic-associated ecosystems of the Mediterranean Sea: a systematic map and an interactive tool to support their conservation link: https://peerj.com/articles/15162 last-modified: 2023-03-29 description: BackgroundHydrothermal vents, cold seeps, pockmarks and seamounts are widely distributed on the ocean floor. Over the last fifty years, the knowledge about these volcanic-associated marine ecosystems has notably increased, yet available information is still limited, scattered, and unsuitable to support decision-making processes for the conservation and management of the marine environment.MethodsHere we searched the Scopus database and the platform Web of Science to collect the scientific information available for these ecosystems in the Mediterranean Sea. The collected literature and the bio-geographic and population variables extracted are provided into a systematic map as an online tool that includes an updated database searchable through a user-friendly R-shiny app.ResultsThe 433 literature items with almost one thousand observations provided evidence of more than 100 different volcanic-associated marine ecosystem sites, mostly distributed in the shallow waters of the Mediterranean Sea. Less than 30% of these sites are currently included in protected or regulated areas. The updated database available in the R-shiny app is a tool that could guide the implementation of more effective protection measures for volcanic-associated marine ecosystems in the Mediterranean Sea within existing management instruments under the EU Habitats Directive. Moreover, the information provided in this study could aid policymakers in defining the priorities for the future protection measures needed to achieve the targets of the UN Agenda 2030. creator: Valentina Costa creator: Valentina Sciutteri creator: Pierpaolo Consoli creator: Elisabetta Manea creator: Elisabetta Menini creator: Franco Andaloro creator: Teresa Romeo creator: Roberto Danovaro uri: https://doi.org/10.7717/peerj.15162 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Costa et al. title: Micro-shear bond strength of different calcium silicate materials to bulk-fill composite link: https://peerj.com/articles/15183 last-modified: 2023-03-29 description: IntroductionThis study aimed to compare the micro-shear bond strength (µSBS) performances of two resin-based calcium silicate-based cement (CSC) (TheraCal PT and TheraCal LC), Biodentine, and two modified-MTA CSC materials (NeoMTA 2 and BioMTA+) to bulk-fill restorative material.Materials and MethodsFifty 3D printed cylindrical resin blocks with a central hole were used (2 mm in depth and 4 mm in diameter). CSCs were placed in the holes (per each group n = 10) and incubated for 24 h. Cylindrical polyethylene molds (2 mm in height and diameter) were used to place the bulk-fill restorative materials on the CSCs and polymerize for 20 s. Then, all specimens were incubated for 24 h at 37 °C at a humidity of 100%. Specimen’s µSBSs were determined with a universal testing machine. Data were analyzed with one-way ANOVA (Welch) and Tamhane test.ResultsStatistically higher µSBS was found for TheraCal PT (29.91 ± 6.13 MPa) (p < 0.05) respect to all the other materials tested. TheraCal LC (20.23 ± 6.32 MPa) (p > 0.05) reported higher µSBS than NeoMTA 2 (11.49 ± 5.78 MPa) and BioMTA+ (6.45 ± 1.89 MPa) (p < 0.05). There was no statistical difference among TheraCal LC, NeoMTA 2 and Biodentine (15.23 ± 7.37 MPa) and between NeoMTA 2 and BioMTA+ (p > 0.05).ConclusionChoosing TheraCal PT as the pulp capping material may increase the adhesion and µSBS to the bulk-fill composite superstructure and sealing ability. creator: Seda Falakaloğlu creator: Merve Yeniçeri Özata creator: Gianluca Plotino uri: https://doi.org/10.7717/peerj.15183 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Falakaloğlu et al. title: The assessment of internal adaptation and fracture resistance of glass ionomer and resin-based restorative materials applied after different caries removal techniques in primary teeth: an in-vitro study link: https://peerj.com/articles/14825 last-modified: 2023-03-28 description: BackgroundThe aim of this study was to evaluate the 3-dimensional (3D) internal adaptation (IA) and fracture resistance (FR) of compomer and glass ionomers applied after conventional caries removal to sound dentin (CCRSD) and selective caries removal to firm dentin (SCRFD) in in-vitro.MethodsThirty extracted primary molars were randomly assigned to three main groups (n = 10) as glass hybrid restorative (GHR) (Equia Forte® HT), conventional glass ionomer (CGIR) (Voco Ionofil Molar) and compomer (Dyract XP). Each group was randomly divided into two subgroups according to caries removal technique as CCRSD (n = 5) and SCRFD (n = 5). The restoration procedures were completed after caries removal (CCRSD or SCRFD) in all samples. Then, specimens were subjected to IA and FR tests. Data were analyzed with Student’s t, one-way ANOVA, and Kruskal Wallis-H tests. The correlation between IA and FR results was analyzed with a Pearson test. The statistical significance level was considered as 5%.ResultsWhile CCRSD showed superior IA results than SCRFD for all restorative materials (p < 0.05), no statistical difference was found between CCRSD and SCRFD in FR assessment (p > 0.05). In CCRSD, compomer showed superior results for IA and FR than glass ionomers (p < 0.05). In SCRFD, it was found no significant difference between the restoratives for IA (p > 0.05). However, compomer showed superior FR results than glass ionomers (p < 0.05). There was moderate negative correlation between internal voids and FR without statistically significant difference (r = −0.333, p = 0.072).ConclusionsDespite the advantages of SCRFD, it was found to be less superior than CCRSD in IA assessment. Therefore, when SCRFD is preferred, a peripheral seal should be provided for ideal restorative treatment. On the other hand, compomer mostly showed superior results compared to others. creator: Akif Demirel creator: Ayşe Işıl Orhan creator: Arda Büyüksungur uri: https://doi.org/10.7717/peerj.14825 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Demirel et al. title: Pandemic-driven changes in the nearshore non-commercial fishery in Hawai’i: catch photos posted to social media capture changes in fisher behavior link: https://peerj.com/articles/14994 last-modified: 2023-03-28 description: Using social media, we collect evidence for how nearshore fisheries are impacted by the global COVID-19 pandemic in Hawai’i. We later confirm our social media findings and obtain a more complete understanding of the changes in nearshore non-commercial fisheries in Hawai’i through a more conventional approach—speaking directly with fishers. Resource users posted photographs to social media nearly three times as often during the pandemic with nearly double the number of fishes pictured per post. Individuals who fished for subsistence were more likely to increase the amount of time spent fishing and relied more on their catch for food security. Furthermore, individuals fishing exclusively for subsistence were more likely to fish for different species during the pandemic than individuals fishing recreationally. Traditional data collection methods are resource-intensive and this study shows that during times of rapid changes, be it ecological or societal, social media can more quickly identify how near shore marine resource use adapts. As climate change threatens additional economic and societal disturbances, it will be necessary for resource managers to collect reliable data efficiently to better target monitoring and management efforts. creator: Timothy Grabowski creator: Michelle E. Benedum creator: Andrew Curley creator: Cole Dill-De Sa creator: Michelle Shuey uri: https://doi.org/10.7717/peerj.14994 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Grabowski et al. title: Identification and biodiversity patterns of Aspergillus species isolated from some soil invertebrates at high altitude using morphological characteristics and phylogenetic analyses link: https://peerj.com/articles/15035 last-modified: 2023-03-28 description: BackgroundThe carcinogenic, mutagenic, and teratogenic chemicals such as aflatoxin are a worldwide health problem. Aspergillus spp., responsible for most cases of aflatoxin contamination, are common in the environment and spread easily to many different types of food. The objectives of this study were to conduct a survey of fungi associated with three soil invertebrates in Taif, Saudi Arabia, identify these isolates and explore mycotoxins formation.MethodsIn total, 114 fungal isolates were collected from various soil invertebrates (millipedes, Armadillidium vulgare and Porcellio laevis) in Taif, Saudi Arabia, among them, 22 isolates were identified as Aspergillus spp. based on morphological and molecular characteristics followed by both Fusarium and Penicillium.ResultsThe sequences of ITS 1 and ITS 4 were utilized. Using bootstrap analysis, phylogenetic tree was split into two distinct clusters. Five sub clusters were included inside the first major cluster, and their bootstrap value was 99%. While, there were two small clusters in the second major cluster. All the tested Aspergillus strains were able to have a single PCR fragment amplified using the primer AspTef. TEF-1 DNA sequence bootstrap analysis with 1,000 replicates revealed two distinct groups. Additionally, the Aspergillus isolates were grouped into two different clusters with about 65% genetic similarity using ISSR-PCR analysis. The standard polymerase chain reaction was used to effectively amplify the Aopks, afl-A and omt-A genes in aflatoxigenic Aspergillus strains. Four Aspergillus strains used in this investigation were shown to generate aflatoxin B1. While, three Aspergillus stains showed ochratoxin genes.ConclusionsIn conclusion, the results indicate significant differences in the fungal community between ecoregions and soil invertebrates. Moreover, mycotoxin detection and identification among Aspergillus isolates were elucidated. This study could shed light on the risk of mycotoxin contamination along the supply chain. creator: Mohamed Fadl Awad creator: Bander Albogami creator: Tarombera Mwabvu creator: Montaser M. Hassan creator: Alaa Baazeem creator: Mohamed M. Hassan creator: Mohsen Mohamed Elsharkawy uri: https://doi.org/10.7717/peerj.15035 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Awad et al.