title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=543 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: On the improvement of heart rate prediction using the combination of singular spectrum analysis and copula-based analysis approach link: https://peerj.com/articles/14601 last-modified: 2022-12-19 description: In recent years, many people have been working from home due to the exceptional circumstances concerning the coronavirus disease 2019 (COVID-19) pandemic. It has also negatively influenced general health and quality of life. Therefore, physical activity has been gaining much attention in preventing the spread of Severe Acute Respiratory Syndrome Coronavirus. For planning an effective physical activity for different clients, physical activity intensity and load degree needs to be appropriately adjusted depending on the individual’s physical/health conditions. Heart rate (HR) is one of the most critical health indicators for monitoring exercise intensity and load degree because it is closely related to the heart rate. Heart rate prediction estimates the heart rate at the next moment based on now and other influencing factors. Therefore, an accurate short-term HR prediction technique can deliver efficient early warning for human health and decrease the happening of harmful events. The work described in this article aims to introduce a novel hybrid approach to model and predict the heart rate dynamics for different exercises. The results indicate that the combination of singular spectrum analysis (SSA) and the Clayton Copula model can accurately predict HR for the short term. creator: Asieh Namazi uri: https://doi.org/10.7717/peerj.14601 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Namazi title: Transcriptome-wide identification of NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors potentially involved in salt stress response in garlic link: https://peerj.com/articles/14602 last-modified: 2022-12-19 description: Soil salinity has been an increasing problem worldwide endangering crop production and human food security. It is an ideal strategy to excavate stress resistant genes and develop salt tolerant crops. NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors have been demonstrated to be involved in salt stress response. However, relevant studies have not been observed in garlic, an important vegetable consumed in the world. In this study, a total of 46 AsNAC genes encoding NAC proteins were identified in garlic plant by transcriptome data. Phylogenetic analysis showed that the examined AsNAC proteins were clustered into 14 subgroups. Motif discovery revealed that the conserved domain region was mainly composed of five conserved subdomains. Most of the genes selected could be induced by salt stress in different tissues, indicating a potential role in salt stress response. Further studies may focus on the molecular mechanisms of the AsNAC genes in salt stress response. The results of the current work provided valuable resources for researchers aimed at developing salt tolerant crops. creator: Guang-Long Wang creator: Ya-Hong An creator: Cheng-Ling Zhou creator: Zhen-Zhu Hu creator: Xu-Qin Ren creator: Ai-Sheng Xiong uri: https://doi.org/10.7717/peerj.14602 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Using Peromyscus leucopus as a biomonitor to determine the impact of heavy metal exposure on the kidney and bone mineral density: results from the Tar Creek Superfund Site link: https://peerj.com/articles/14605 last-modified: 2022-12-19 description: BackgroundHuman population growth and industrialization contribute to increased pollution of wildlife habitats. Heavy metal exposure from industrial and environmental sources is still a threat to public health, increasing disease susceptibility. In this study, I investigated the effects of heavy metals (cadmium (Cd), lead (Pb), and zinc (Zn)) on kidney and bone density.ObjectiveThis study aims to determine the concentrations of Cd, Pb, and Zn in soil and compare them to the levels of the same metals in Peromyscus leucopus kidney tissue. Furthermore, the study seeks to investigate the impact of heavy metals on bone density and fragility using the fourth lumbar vertebra (L4) of P. leucopus.MethodsCd, Pb, and Zn concentrations in soil specimens collected from Tar Creek Superfund Site (TCSFS), Beaver Creek (BC), and two reference sites (Oologah Wildlife Management Area (OWMA) and Sequoyah National Wildlife Refuge (SNWR)). Heavy metal concentrations were analyzed using inductively coupled plasma-mass spectroscopy (ICP-MS). Micro-computed tomography (µCT) was used to assess the influence of heavy metals on bone fragility and density.ResultsOn the one hand, soil samples revealed that Pb is the most common pollutant in the sediment at all of the investigated sites (the highest contaminated site with Pb was TCSFS). Pb levels in the soil of TCSFS, BC, OWMA, and SNWR were found to be 1,132 ± 278, 6.4 ± 1.1, and 2.3 ± 0.3 mg/kg in the soil of TCSFS, BC and OWMA and SNWR, respectively. This is consistent with the fact that Pb is one of the less mobile heavy metals, causing its compounds to persist in soils and sediments and being barely influenced by microbial decomposition. On the other hand, the kidney samples revealed greater Cd levels, even higher than those found in the soil samples from the OWMA and SNWR sites. Cd concentrations in the kidney specimens were found to be 4.62 ± 0.71, 0.53 ± 0.08, and 0.53 ± 0.06 µg/kg, respectively. In addition, micro-CT analysis of L4 from TCSFS showed significant Pearson’s correlation coefficients between Cd concentrations and trabecular bone number (−0.67, P ≤ 0.05) and trabecular separation (0.72, P ≤ 0.05). The results showed no correlation between bone parameters and metal concentrations at reference sites. This study is one of the few that aims to employ bone architecture as an endpoint in the field of biomonitoring. Furthermore, this study confirmed some earlier research by demonstrating substantial levels of heavy metal contamination in soil samples, kidney samples, and P. leucopus L4 trabecular bone separations from TCSFS. Moreover, this is the first study to record information regarding bone microarchitecture parameters in P. leucopus in North America. creator: Maha Abdulftah Elturki uri: https://doi.org/10.7717/peerj.14605 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Elturki 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.