title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=557 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Forty new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds link: https://peerj.com/articles/13919 last-modified: 2022-12-16 description: Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur–bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most complete morphological assessment of the postcranial skeleton of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis, the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal phalanges are preserved, revealing a remarkably enlarged pes presumably related to foot-propelled swimming. Although diagnosable as Ichthyornis, the new specimens exhibit a substantial degree of morphological variation, some of which may relate to ontogenetic changes. Phylogenetic analyses incorporating our new data and employing alternative morphological datasets recover Ichthyornis stemward of Hesperornithes and Iaceornis, in line with some recent hypotheses regarding the topology of the crownward-most portion of the avian stem group, and we establish phylogenetically-defined clade names for relevant avialan subclades to help facilitate consistent discourse in future work. The new information provided by these specimens improves our understanding of morphological evolution among the crownward-most non-neornithine avialans immediately preceding the origin of crown group birds. creator: Juan Benito creator: Albert Chen creator: Laura E. Wilson creator: Bhart-Anjan S. Bhullar creator: David Burnham creator: Daniel J. Field uri: https://doi.org/10.7717/peerj.13919 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Benito et al. title: Guttigomphus avilionis gen. et sp. nov., a trirachodontid cynodont from the upper Cynognathus Assemblage Zone, Burgersdorp Formation of South Africa link: https://peerj.com/articles/14355 last-modified: 2022-12-16 description: The Burgersdorp Formation of South Africa is a richly fossiliferous rock sequence at the top of the Permian–Triassic Beaufort Group and is known for its abundance of Early–Middle Triassic vertebrate remains, particularly cynodonts. Fossils from the Burgersdorp Formation are referred biostratigraphically to the Cynognathus Assemblage Zone (CAZ), which is further divided into three subzones: Langbergia-Garjainia, Trirachodon-Kannemeyeria, and Cricodon-Ufudocyclops. Each subzone is characterised by the presence of a distinct species of trirachodontid, a group of gomphodont cynodonts found relatively abundantly throughout the CAZ, with the lower two subzones characterised by the medium-sized trirachodontids Langbergia and Trirachodon. The uppermost part of the formation, the Cricodon-Ufudocyclops subzone, yields trirachodontids of larger size. The majority of these trirachodontid specimens have previously been referred to Cricodon metabolus, a taxon also known from the Manda Beds of Tanzania and the Ntawere Formation of Zambia. Here we identify one of the specimens (BP/1/5538) previously referred to Cricodon as a new taxon, Guttigomphus avilionis. Guttigomphus can be distinguished from other gomphodont cynodonts by features of the upper postcanine teeth, such as an asymmetric crown in occlusal view (crown narrower along the lingual margin than the labial). Our phylogenetic analysis recovers Guttigomphus as a basal member of Trirachodontidae, outside of the clade including Cricodon, Langbergia and Trirachodon. creator: Romy R. Rayner creator: Richard J. Butler creator: Christian F. Kammerer creator: Jonah N. Choiniere uri: https://doi.org/10.7717/peerj.14355 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rayner et al. title: Physical fitness changes in adolescents due to social distancing during the coronavirus disease pandemic in Korea link: https://peerj.com/articles/14494 last-modified: 2022-12-16 description: BackgroundAt least 60 min of moderate-intensity physical activity per day is recommended for physical and mental health of adolescents. Schools are one of the most suitable places for promoting students’ health as it is a place where vigorous physical activity occurs. However, the physical activity of students is threatened because schools are closed worldwide owing to the coronavirus disease (COVID-19) outbreak in 2019. Therefore, this study aimed to analyze the physical fitness changes in 27,782 Korean adolescents during the pandemic and present alternative education and health policies to the school.MethodsWe included 29,882 middle school students (age: 13–15 years; males: 14,941, females: 12,841) in Korea from 2019 to 2021 . Participants’ physical fitness at school was measured using the physical activity promotion system (PAPS) manual developed to measure students’ physical fitness. Physical fitness variables included body mass index (BMI), 20 m shuttle run, handgrip strength, sit-and-reach, and 50 m run.ResultsThe COVID-19 pandemic has had a negative impact on the BMI and cardiorespiratory endurance of Korean middle school students. Specifically, male students’ BMI increased, while body composition, cardiorespiratory endurance, and grip strength decreased significantly. Female students showed significant decreases in BMI and sit-and-reach test scores. It is clear that the physical fitness level of adolescents decreased by a greater degree after the COVID-19 pandemic than before, and the decrease in the physical fitness level of male students was noticeable. Therefore, a lesson strategy should be prepared that considers the contents and methods of physical education classes to improve the physical fitness level of male and female adolescents.ConclusionsFitness-based classes suitable for online methods should be urgently added as alternative physical education classes to prepare for the second COVID-19 outbreak. In addition, it is necessary to create an environment in which physical activity is a possibility in physical education classes, in any situation using artificial intelligence and virtual reality. creator: Kwang-Jin Lee creator: Se-Young Seon creator: Byungjoo Noh creator: Keun-Ok An uri: https://doi.org/10.7717/peerj.14494 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lee et al. title: Genetic diversity of Venturia inaequalis isolates from the scabs in apple trees in Gansu Province, China, using AFLP markers link: https://peerj.com/articles/14512 last-modified: 2022-12-16 description: Apple scab is a serious disease that restricts the growth of cultivated apples. The objective of this study is to investigate the genetic variations and genetic structure of Venturia inaequalis in Gansu Province, China. 108 isolates of the pathogen V. inaequalis from the Jingning, Lingtai, Jingchuan, Xifeng, Ning and Maiji regions were collected, and their genetic diversity was analyzed using AFLP molecular marker technique. The results showed that genetic diversity was present among the isolates but was not statistically significant. Genetic distance values ranged from 0.0095 to 0.0762. Cluster analysis results showed that the 108 isolates could be divided into two clusters using a similarity coefficient of 0.69. A total of 104 isolates were contained in cluster I while four isolates were contained in Cluster II. From the AMOVA analysis, 98% of variations were observed within the same region, while 2% were observed across different regions. The analysis of population structure showed that 108 isolates had two common ancestors, with the Jingning isolates mainly being derived from the red ancestor. PCoA analysis showed that the Jingning isolates were independent to a certain extent. The different geographical location caused the genetic difference of the isolates. The genetic diversity of apple scab in Gansu Province is greatly aided by this work, which also offers a theoretical foundation for the use of molecular markers in assisted breeding to create novel resistant types. creator: Zhaolong Lü creator: Nana Hui creator: Li Wang creator: Guo Zheng creator: Senshan Wang creator: Jiping Li uri: https://doi.org/10.7717/peerj.14512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lü et al. title: Metal tolerance capacity and antioxidant responses of new Salix spp. clones in a combined Cd-Pb polluted system link: https://peerj.com/articles/14521 last-modified: 2022-12-16 description: To investigate the physiochemical characteristics of two new clones, Salix matsudana ‘J172’ (A7) and Salix matsudana ‘Yankang1’ (A64) in combined Cd-Pb contaminated systems, a hydroponic experiment was designed. The plant biomass, photosynthesis, antioxidant responses and the accumulation of metals in different plant parts (leaf, stem, and root) were measured after 35-day treatments with Cd (15, 30 µM) and Pb (250, 500 µM). The results showed that exposure to Cd-Pb decreased the biomass but increased the net photosynthetic rate for both A7 and A64, demonstrating that photosynthesis may be one of the metabolic processes used to resist Cd-Pb stress. Compared with control, roots exposed to Cd-Pb had higher activity of superoxide dismutase and more malondialdehyde concentrations, which indicated the roots of both clones were apt to be damaged. The concentrations of soluble protein were obviously higher in the roots of A64 than A7, indicating the roles of the antioxidative substance were different between two willow clones. Soluble protein also had significant relationship with translocation factors from accumulation in roots of A64, which illustrated it played important roles in the tolerance of A64 roots to heavy metals. The roots could accumulate more Pb rather than transport to the shoots compared with Cd. The tolerance index was more than 85% on average for both clones under all the treatments, indicating their tolerance capacities to the combined stress of Cd and Pb are strong under the tested metal levels. Both clones are the good candidates for phytoremediation of Cd and Pb by the root filtration in the combined contamination environment. creator: Chuanfeng Zhang creator: Baoshan Yang creator: Hui Wang creator: Xiaohan Xu creator: Jiaxing Shi creator: Guanghua Qin uri: https://doi.org/10.7717/peerj.14521 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Effect of hyperglycemia on the immune function of COVID-19 patients with type 2 diabetes mellitus: a retrospective study link: https://peerj.com/articles/14570 last-modified: 2022-12-16 description: PurposeTo analyze the clinical characteristics and immune function parameters and to explore the effect of hyperglycemia on the immune function in patients with Corona Virus Disease 2019 (COVID-19) with type 2 diabetes mellitus (T2DM).MethodsThis retrospective study included patients with COVID-19 with T2DM hospitalized in Renmin Hospital of Wuhan University between January 31, 2020, and February 10, 2020. The clinical data were collected and patients were divided into a well-controlled group (blood glucose 3.9–10.0 mmol/L) and a poorly-controlled group (blood glucose >10.0 mmol/L). The differences in routine blood tests, peripheral lymphocyte subsets, humoral immune components, C-reactive protein (CRP) level, and cytokines were compared, and the correlation between blood glucose and immune parameters as well as the severity of the disease was analyzed.ResultsA total of 65 patients with COVID-19 and T2DM were included in the final analysis. Compared with the well-controlled group, patients in the poorly-controlled group had decreased lymphocytes, CD16+ 56+ NK cells, CD3+ T cells, CD8+ T cells and increased neutrophil percentage, IL-6 levels, CRP levels and serum concentration of IgA. Blood glucose was inversely correlated with CD16+ 56+ NK cells, CD3+ T cells, CD4+ T cells, and CD8+ T cells and positively correlated with IL-6 and CRP levels. There was a positive correlation between blood glucose and the severity of the COVID-19.ConclusionHyperglycemia will aggravate the immune dysfunction of COVID-19 patients with T2DM and affect the severity of COVID-19. creator: Ye Wang creator: Bo Yi creator: Shujun Wang creator: Xiaolin Chen creator: Zhongyuan Wen uri: https://doi.org/10.7717/peerj.14570 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Mitochondria and chloroplasts function in microalgae energy production link: https://peerj.com/articles/14576 last-modified: 2022-12-16 description: Microalgae are organisms that have the ability to perform photosynthesis, capturing CO2 from the atmosphere to produce different metabolites such as vitamins, sugars, lipids, among others, many of them with different biotechnological applications. Recently, these microorganisms have been widely studied due to their possible use to obtain clean energy. It has been postulated that the growth of microalgae and the production of high-energy metabolites depend on the correct function of cellular organelles such as mitochondria and chloroplasts. Thus, the development of different genetic tools to improve the function of these organelles is of high scientific and technological interest. In this paper we review the recent advances in microalgae engineering and the role of cellular organelles in order to increase cell productivity and biomass. creator: Diego F. Gomez-Casati creator: Julieta Barchiesi creator: Maria V. Busi uri: https://doi.org/10.7717/peerj.14576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gomez-Casati et al. title: Functional groups of Afrotropical EPT (Ephemeroptera, Plecoptera and Trichoptera) as bioindicators of semi-urban pollution in the Tsitsa River Catchment, Eastern Cape, South Africa link: https://peerj.com/articles/13970 last-modified: 2022-12-15 description: We examined the distribution patterns of Ephemeroptera, Plecoptera, and Trichoptera functional feeding groups (EPT FFGs) in five streams that drain semi-urban landscapes in the Tsitsa River catchment, Eastern Cape Province of South Africa. We undertook macroinvertebrate and physicochemical analysis over four seasons between 2016 and 2017 at eight sites in three land-use categories (Sites 1, 2 and 3), representing an increasing gradient of semi-urban pollution. Five EPT FFGs (shredders, grazers/scrapers, predators, collector-gatherers and collector-filterers) were fuzzy coded and analyzed using RLQ-R (environmental characteristics of samples), L (taxa distribution across samples) and Q (species traits) and fourth-corner analyses. Physicochemical variables, including phosphate-phosphorus, total inorganic nitrogen and temperature, were the most influential variables that significantly influenced the distribution patterns of EPT FFGs in the Tsitsa River. RLQ and the fourth-corner model revealed varying responses of FFGs to semi-urban pollution. Of the five FFGs, collectors were the most abundant EPT FFGs in the study area, exhibiting disparate responses to disturbances, with collector-gatherers associated with impacted sites and significantly associated with phosphate-phosphorus. On the other hand, collector-filterers decreased with increasing semi-urban disturbance and exhibited a significant negative association with phosphate-phosphorus, total inorganic nitrogen and temperature. Overall, this study provides further insights into the environmental factors that influence the distribution patterns of FFGs in Afrotropical streams and the potential use of FFGs as indicators of anthropogenic pollution in tropical streams and rivers. creator: Frank Chukwuzuoke Akamagwuna creator: Augustine Ovie Edegbene creator: Phindiwe Ntloko creator: Francis Ofurum Arimoro creator: Chika Felicitas Nnadozie creator: Dennis Junior Choruma creator: Oghenekaro Nelson Odume uri: https://doi.org/10.7717/peerj.13970 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Akamagwuna et al. title: Impacts of river fragmentation on limiting individual dietary specialization of Amazonian predatory fish link: https://peerj.com/articles/14266 last-modified: 2022-12-15 description: Individual dietary specialization is one of the factors that promotes variation in resource use at the individual level. Here we used stable isotope analysis of multiple tissues with different turnover rates to examine the degree of individual specialization in two sub-populations of the predator Cichla temensis inhabiting both fragmented and undammed rivers within the Uatumã River basin of the Amazon. Our results showed that the undammed river provides better conditions to promote individual dietary specialization than the fragmented river. This study contributes to the understanding of how specific life history characteristics of populations of generalist predators are impacted by fragmentation within megadiverse environments such as the Amazon basin. creator: Jamerson Aguiar-Santos creator: Pieter deHart creator: Bruce Forsberg creator: Carlos Freitas uri: https://doi.org/10.7717/peerj.14266 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Aguiar-Santos et al. title: Neospongodes atlantica, a potential case of an early biological introduction in the Southwestern Atlantic link: https://peerj.com/articles/14347 last-modified: 2022-12-15 description: Soft corals (Anthozoa: Octocorallia) are discreet components in the Southwestern Atlantic reef communities. In Brazil, the native octocoral shallow-reef fauna is mostly represented by gorgonians. Consequently, except for the nephtheid Neospongodes atlantica, most of the known soft corals from this region are considered non-indigenous. Hitherto, the monotypic genus Neospongodes, which was proposed in the early 1900s, has been considered to be endemic to the Northeastern Brazilian coast. Herein, based on in situ records, we show that N. atlantica is a substrate generalist that has been probably expanding its distribution by dominating extensive shallow and mesophotic sandy and reef bottoms, generally outcompeting other reef benthic organisms, including Brazilian endemic species. Based on previously unidentified museum specimens, new records, and a broad literature review, we provide the most comprehensive modelling of the potential distribution of this species in the Southwestern Atlantic. Based on molecular inference supported by in-depth morphological analysis, the probable non-indigenous and, therefore, ancient introduction of N. atlantica in Brazilian waters is discussed. Finally, these results support that Neospongodes and the Indo-Pacific Stereonephthya are synonyms, which led us to propose the latter as taxonomically invalid. creator: Ralf T.S. Cordeiro creator: Ágatha Nascimento Carpinelli creator: Ronaldo B. Francini-Filho creator: Barbara de Moura Neves creator: Carlos D. Pérez creator: Umberto de Oliveira creator: Paulo Sumida creator: Henrique Maranhão creator: Leonardo H.U. Monteiro creator: Pedro Carneiro creator: Marcelo V. Kitahara uri: https://doi.org/10.7717/peerj.14347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cordeiro et al.