title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=485 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers link: https://peerj.com/articles/15683 last-modified: 2023-07-17 description: Tomato is one of the most prominent crops in global horticulture and an important vegetable crop in Kazakhstan. The lack of data on the genetic background of local varieties limits the development of tomato breeding in the country. This study aimed to perform an initial evaluation of the breeding collection of tomato varieties from the point of view of their genetic structure and pathogen resistance using a set of PCR based molecular markers, including 13 SSR markers for genetic structure analysis, and 14 SCAR and CAPS markers associated with resistance to five pathogens: three viruses, fungus Fusarium oxysporum, and oomycete P hytophthora infestans. Nine SSR markers were with a PIC value varying from 0.0562 (low information content) to 0.629 (high information content). A weak genetic structure was revealed in the samples of varieties including local cultivars and, predominantly, varieties from Russia and other ex-USSR countries. The local varieties were closely related to several groups of cultivars of Russian origin. Screening for a set of resistance markers revealed the common occurrence of the resistance locus I against Fusarium oxysporum and only the occasional presence of resistance alleles of other markers. No markers of resistance to the three considered viruses were revealed in local tomato varieties. Only two local cultivars had markers of resistance to P. infestans, and only the ‘Meruert’ cultivar had a combination of resistance markers against P. infestans and F. oxysporum. The obtained results have demonstrated the need for further studies of local tomato varieties with a wider range of molecular markers and source germplasm to lay a foundation for the development of tomato breeding in Kazakhstan. creator: Alexandr Pozharskiy creator: Valeriya Kostyukova creator: Marina Khusnitdinova creator: Kamila Adilbayeva creator: Gulnaz Nizamdinova creator: Anastasiya Kapytina creator: Nazym Kerimbek creator: Aisha Taskuzhina creator: Mariya Kolchenko creator: Aisha Abdrakhmanova creator: Nina Kisselyova creator: Ruslan Kalendar creator: Dilyara Gritsenko uri: https://doi.org/10.7717/peerj.15683 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Pozharskiy et al. title: Identification of PIMREG as a novel prognostic signature in breast cancer via integrated bioinformatics analysis and experimental validation link: https://peerj.com/articles/15703 last-modified: 2023-07-17 description: BackgroundPhosphatidylinositol binding clathrin assembly protein interacting mitotic regulator (PIMREG) expression is upregulated in a variety of cancers. However, its potential role in breast cancer (BC) remains uncertain.MethodsThe Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to gather relevant information. The expression of PIMREG and its clinical implication in BC were assessed by using Wilcoxon rank-sum test. The prognostic value of PIMREG in BC was evaluated through the Cox regression model and nomogram, and visualized by Kaplan-Meier survival curves. Genes/proteins that interact with PIMREG in BC were also identified through GeneMANIA and MaxLink. Gene set enrichment analysis (GSEA) was then performed. The correlations of the immune cell infiltration and immune checkpoints with the expression of PIMREG in BC were explored via TIMER, TISIDB, and GEPIA. Potential drugs that interact with PIMREG in BC were explored via Q-omic. The siRNA transfection, CCK-8, and transwell migration assay were conducted to explore the function of PIMREG in cell proliferation and migration.ResultsPIMREG expression was significantly higher in infiltrating ductal carcinoma, estrogen receptor negative BC, and progestin receptor negative BC. High expression of PIMREG was associated with poor overall survival, disease-specific survival, and progression-free interval. A nomogram based on PIMREG was developed with a satisfactory prognostic value. PIMREG also had a high diagnostic ability, with an area under the curve of 0.940. Its correlations with several immunomodulators were also observed. Immune checkpoint CTLA-4 was significantly positively associated with PIMREG. HDAC2 was found as a potentially critical link between PIMREG and BRCA1/2. In addition, PIMREG knockdown could inhibit cell proliferation and migration in BC.ConclusionsThe high expression of PIMREG is associated with poor prognosis and immune checkpoints in BC. HDAC2 may be a critical link between PIMREG and BRCA1/2, potentially a therapeutic target. creator: Wenjing Zhao creator: Yuanjin Chang creator: Zhaoye Wu creator: Xiaofan Jiang creator: Yong Li creator: Ruijin Xie creator: Deyuan Fu creator: Chenyu Sun creator: Ju Gao uri: https://doi.org/10.7717/peerj.15703 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhao et al. title: The effect of perceived stress for work engagement in volunteers during the COVID-19 pandemic: the mediating role of psychological resilience and age differences link: https://peerj.com/articles/15704 last-modified: 2023-07-17 description: Volunteers played an important role throughout the COVID-19 pandemic. This study investigated the characteristics of perceived stress, psychological resilience and work engagement among 910 Chinese volunteers of different ages in the first month of pandemic in Gansu province, China. The present study tested the correlations between perceived stress and work engagement, the mediating role of psychological resilience in the relationship and the differences among age groups. The results of this study showed that work engagement and psychological resilience increased with the age of the volunteers. Work engagement and resilience levels were higher in middle adulthood than in early adulthood. As predicted, perceived stress negatively predicted work engagement. A mediation analysis showed that psychological resilience partially explained the correlations between perceived stress and work engagement. Specifically, the mediating effect of psychological resilience in early adulthood was significant, but not in middle adulthood. Overall, this study demonstrates that work engagement increased with age and was negatively predicted by perceived stress, showing these factors were important for volunteers’ work during COVID-19. Further, for those in early adulthood, psychological resilience mediated this relationship—highlighting another age difference among volunteers during COVID-19. creator: Yatong Li creator: Pei Xie creator: Liang He creator: Xiaolong Fu creator: Xiaobing Ding creator: Mary C. Jobe creator: Md Zahir Ahmed uri: https://doi.org/10.7717/peerj.15704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Comparative analysis of automatic segmentation of esophageal cancer using 3D Res-UNet on conventional and 40-keV virtual mono-energetic CT Images: a retrospective study link: https://peerj.com/articles/15707 last-modified: 2023-07-17 description: ObjectivesTo assess the performance of 3D Res-UNet for fully automated segmentation of esophageal cancer (EC) and compare the segmentation accuracy between conventional images (CI) and 40-keV virtual mono-energetic images (VMI40 kev).MethodsPatients underwent spectral CT scanning and diagnosed of EC by operation or gastroscope biopsy in our hospital from 2019 to 2020 were analyzed retrospectively. All artery spectral base images were transferred to the dedicated workstation to generate VMI40 kev and CI. The segmentation model of EC was constructed by 3D Res-UNet neural network in VMI40 kev and CI, respectively. After optimization training, the Dice similarity coefficient (DSC), overlap (IOU), average symmetrical surface distance (ASSD) and 95% Hausdorff distance (HD_95) of EC at pixel level were tested and calculated in the test set. The paired rank sum test was used to compare the results of VMI40 kev and CI.ResultsA total of 160 patients were included in the analysis and randomly divided into the training dataset (104 patients), validation dataset (26 patients) and test dataset (30 patients). VMI40 kevas input data in the training dataset resulted in higher model performance in the test dataset in comparison with using CI as input data (DSC:0.875 vs 0.859, IOU: 0.777 vs 0.755, ASSD:0.911 vs 0.981, HD_95: 4.41 vs 6.23, all p-value <0.05).ConclusionFully automated segmentation of EC with 3D Res-UNet has high accuracy and clinically feasibility for both CI and VMI40 kev. Compared with CI, VMI40 kev indicated slightly higher accuracy in this test dataset. creator: Hua Zhong creator: Anqi Li creator: Yingdong Chen creator: Qianwen Huang creator: Xingbiao Chen creator: Jianghe Kang creator: Youkuang You uri: https://doi.org/10.7717/peerj.15707 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhong et al. title: Unexpected lower level of oral periodontal pathogens in patients with high numbers of systemic diseases link: https://peerj.com/articles/15502 last-modified: 2023-07-14 description: BackgroundPeriodontal disease is associated with systemic conditions such as diabetes, arthritis, and cardiovascular disease, all diseases with large inflammatory components. Some, but not all, reports show periopathogens Porphyromonas gingivialis and Tannerella forsythia at higher levels orally in people with one of these chronic diseases and in people with more severe cases. These oral pathogens are thought to be positively associated with systemic inflammatory diseases through induction of oral inflammation that works to distort systemic inflammation or by directly inducing inflammation at distal sites in the body. This study aimed to determine if, among patients with severe periodontal disease, those with multi-morbidity (or many chronic diseases) showed higher levels of periodontal pathogens.MethodsA total of 201 adult subjects, including 84 with severe periodontal disease were recruited between 1/2017 and 6/2019 at a city dental clinic. Electronic charts supplied self-reported diseases and conditions which informed a morbidity index based on the number of chronic diseases and conditions present. Salivary composition was determined by 16S rRNA gene sequencing.ResultsAs expected, patients with severe periodontal disease showed higher levels of periodontal pathogens in their saliva. Also, those with severe periodontal disease showed higher levels of multiple chronic diseases (multimorbidity). An examination of the 84 patients with severe periodontal disease revealed some subjects despite being of advanced age were free or nearly free of systemic disease. Surprisingly, the salivary microbiota of the least healthy of these 84 subjects, defined here as those with maximal multimorbidity, showed significantly lower relative numbers of periodontal pathogens, including Porphyromonas gingivalis and Tannerella Forsythia, after controlling for active caries, tobacco usage, age, and gender. Analysis of a control group with none to moderate periodontal disease revealed no association of multimorbidity or numbers of medications used and specific oral bacteria, indicating the importance of severe periodontal disease as a variable of interest.ConclusionThe hypothesis that periodontal disease patients with higher levels of multimorbidity would have higher levels of oral periodontal pathogens is false. Multimorbidity is associated with a reduced relative number of periodontal pathogens Porphyromonas gingivalis and Tannerella forsythia. creator: Michael T. Shen creator: Betti Shahin creator: Zhengjia Chen creator: Guy R. Adami uri: https://doi.org/10.7717/peerj.15502 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Shen et al. title: Micro-CT imaging in species description: exploring beyond sclerotized structures in lichen moths (Lepidoptera: Erebidae, Arctiinae, Lithosiini) link: https://peerj.com/articles/15505 last-modified: 2023-07-14 description: X-ray micro-computed tomography imaging (micro-CT) is valuable for systematic research since it permits the non-destructive scanning and imaging of internal structures of very rare species and/or type specimens. Additionally, micro-CT allows to view the morphology and the functional anatomy of structures in their natural anatomical position, without deformations that typically occur using classical dissection protocols. In this study we provide the description of two new species of lichen moths (Lepidoptera: Erebidae, Lithosiini) from the Atlantic Forest in eastern Brazil: Nodozana heliae Moraes sp. nov. from Rio de Janeiro state and Epeiromulona pataxo Moraes & Aguiar sp. nov. from Bahia state. The male and female genitalia as well as the wing morphology were examined by means of non-destructive micro-CT, subsequent 3D model reconstruction, 360 degree spinning animations, 2D images from different angles, and those were compared against classical genitalia dissections from the same specimens. We conclude that techniques complement each other, micro-CT being particularly useful to study wing venation, sclerotized internal structures and muscles, while classical dissection is useful to study membranous structures, particularly in the female genitalia, abdominal skin and specialised scales on the male 8th sternite. creator: Simeão S. Moraes creator: Max S. Söderholm creator: Tamara M.C. Aguiar creator: André V.L. Freitas creator: Pasi Sihvonen uri: https://doi.org/10.7717/peerj.15505 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Moraes et al. title: Coral affected by stony coral tissue loss disease can produce viable offspring link: https://peerj.com/articles/15519 last-modified: 2023-07-14 description: Stony coral tissue loss disease (SCTLD) has caused high mortality of at least 25 coral species across the Caribbean, with Pseudodiploria strigosa being the second most affected species in the Mexican Caribbean. The resulting decreased abundance and colony density reduces the fertilization potential of SCTLD-susceptible species. Therefore, larval-based restoration could be of great benefit, though precautionary concerns about disease transmission may foster reluctance to implement this approach with SCTLD-susceptible species. We evaluated the performance of offspring obtained by crossing gametes of a healthy P. strigosa colony (100% apparently healthy tissue) with that of a colony affected by SCTLD (>50% tissue loss) and compared these with prior crosses between healthy parents. Fertilization and settlement were as high as prior crosses among healthy parents, and post-settlement survivorship over a year in outdoor tanks was 7.8%. After thirteen months, the diseased-parent recruits were outplanted to a degraded reef. Their survivorship was ∼44% and their growth rate was 0.365 mm ± 1.29 SD per month. This study shows that even diseased parent colonies can be effective in assisted sexual reproduction for the restoration of species affected by SCTLD. creator: Sandra Mendoza Quiroz creator: Raúl Tecalco Renteria creator: Gandhi Germán Ramírez Tapia creator: Margaret W. Miller creator: Maria Victoria Grosso-Becerra creator: Anastazia T. Banaszak uri: https://doi.org/10.7717/peerj.15519 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mendoza Quiroz et al. title: The role of the Sunda shelf biogeographic barrier in the cryptic differentiation of Conus litteratus (Gastropoda: Conidae) across the Indo-Pacific region link: https://peerj.com/articles/15534 last-modified: 2023-07-14 description: Geographical and oceanographic processes have influenced the speciation of marine organisms. Cone snails are marine mollusks that show high levels of endemism and a wide distributional range across the Indian and Pacific Oceans. Discontinuities in distributions caused by biogeographic barriers can affect genetic connectivity. Here we analysed the connectivity within Conus litteratus using samples from the Lakshadweep archipelago (Arabian Sea, Indian Ocean) and from the Pacific Ocean. Maximum likelihood analyses based on the mitochondrial cytochrome C oxidase subunit I (COI) and on the non-coding 16S ribosomal RNA (16S rRNA) genes revealed cryptic diversity within C. literatus occupying distinct oceanographic regions. The intraspecific genetic distances between the two distinct clades of C. literatus from the Arabian Sea and the Pacific Ocean ranged from 7.4% to 7.6% for COI and from 2.4% to 2.8% for 16S rRNA genes, which is larger than the threshold limit for interspecific differentiation. The haplotype network analysis also corroborated the existence of two different lineages within C. litteratus. The detected genetic discontinuities reflect the effect of the Sunda shelf biogeographic barrier on the allopatric divergence of C. litteratus. creator: Shijin Ameri creator: Laxmilatha Pappurajam creator: K. A. Labeeb creator: Ranjith Lakshmanan creator: Kathirvelpandian P. V. Ayyathurai uri: https://doi.org/10.7717/peerj.15534 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ameri et al. title: Investigation of high flow nasal cannule efficiency with electric impedance tomography based parameters in COVID-19 adults patients: a retrospective study link: https://peerj.com/articles/15555 last-modified: 2023-07-14 description: Background/AimThis study aimed to investigate the effects of oxygen therapy using a high flow nasal cannula (HFNC) on patients diagnosed with COVID-19 Acute Respiratory Distress Syndrome (C-ARDS) by utilizing electrical impedance tomography (EIT)-based parameters.Materials and MethodsOxygen therapy was administered to the patients at two different flow rates and two different positions: T0—baseline measurements were taken in the supine position before any therapy was initiated. T1—HFNC was administered in the supine position with a flow rate of 30 L/min. T2—HFNC was administered in the supine position with a flow rate of 50 L/min. T3—HFNC was administered in the prone position with a flow rate of 30 L/min. T4—HFNC was administered in the prone position with a flow rate of 50 L/min. EIT-based parameters (global inhomogeneity index (GI index), center of ventilation (CoV), regional ventilation delay index (RVD index), region of interest ratio (ROI ratio)), as well as respiratory and hemodynamic parameters of the patients, were recorded from the database.ResultsA total of twenty patients were included in this retrospective observational study. The mean age of the included patients was 64.3 ± 10.6 years. Statistically significant differences were observed in the measurements of GI index, CoV, RVD index, ROI ratio, PaO2/FiO2 ratio, respiratory rate, and mean arterial pressure parameters across different time intervals (p < 0.005). Pairwise comparisons of EIT parameters and measurements of respiratory and hemodynamic parameters at five different time points revealed statistically significant differences. For the GI index, significant differences were observed between the mean measurements taken at T0–T1, T0–T2, T0–T3, T0–T4, T1–T3, T1–T4, T2–T3, T2–T4, and T3–T4 time intervals (p < 0.05). Regarding CoV, significant differences were found between the mean measurements taken at T0–T3, T1–T3, T2–T3, and T3–T4 time intervals (p < 0.05). Additionally, for the ROI ratio, significant differences were observed between the measurement averages taken at each time interval (p < 0.05).ConclusionOur findings suggest that prone positioning during the management of C-ARDS patients leads to improved lung homogeneity, as indicated by EIT parameters. However, further research is required to enhance the visualization of ventilation using EIT. creator: Özlem Öner creator: Begum Ergan creator: Ayse Sezin Kizil creator: Mehmet Cagatay Gurkok creator: Esra Dugral creator: Necati Gökmen uri: https://doi.org/10.7717/peerj.15555 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Öner et al. title: Skin bacterial community differences among three species of co-occurring Ranid frogs link: https://peerj.com/articles/15556 last-modified: 2023-07-14 description: Skin microbial communities are an essential part of host health and can play a role in mitigating disease. Host and environmental factors can shape and alter these microbial communities and, therefore, we need to understand to what extent these factors influence microbial communities and how this can impact disease dynamics. Microbial communities have been studied in amphibian systems due to skin microbial communities providing some resistance to the amphibian chytrid fungus, Batrachochytrium dendrobatidis. However, we are only starting to understand how host and environmental factors shape these communities for amphibians. In this study, we examined whether amphibian skin bacterial communities differ among host species, host infection status, host developmental stage, and host habitat. We collected skin swabs from tadpoles and adults of three Ranid frog species (Lithobates spp.) at the Mianus River Gorge Preserve in Bedford, New York, USA, and used 16S rRNA gene amplicon sequencing to determine bacterial community composition. Our analysis suggests amphibian skin bacterial communities change across host developmental stages, as has been documented previously. Additionally, we found that skin bacterial communities differed among Ranid species, with skin communities on the host species captured in streams or bogs differing from the communities of the species captured on land. Thus, habitat use of different species may drive differences in host-associated microbial communities for closely-related host species. creator: Zachary Gajewski creator: Leah R. Johnson creator: Daniel Medina creator: William W. Crainer creator: Christopher M. Nagy creator: Lisa K. Belden uri: https://doi.org/10.7717/peerj.15556 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gajewski et al.