title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=490 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Immune responses in carp strains with different susceptibility to carp edema virus disease link: https://peerj.com/articles/15614 last-modified: 2023-07-14 description: Carp edema virus disease (CEVD), also known as koi sleepy disease (KSD), represents a serious threat to the carp industry. The expression of immune-related genes to CEV infections could lead to the selection of crucial biomarkers of the development of the disease. The expression of a total of eleven immune-related genes encoding cytokines (IL-1β, IL-10, IL-6a, and TNF-α2), antiviral response (Mx2), cellular receptors (CD4, CD8b1, and GzmA), immunoglobulin (IgM), and genes encoding-mucins was monitored in gills of four differently KSD-susceptible strains of carp (Amur wild carp, Amur Sasan, AS; Ropsha scaly carp, Rop; Prerov scaly carp, PS; and koi) on days 6 and 11 post-infection. Carp strains were infected through two cohabitation infection trials with CEV genogroups I or IIa. The results showed that during the infection with both CEV genogroups, KSD-susceptible koi induced an innate immune response with significant up-regulation (p < 0.05) of IL-1β, IL-10, IL-6a, and TNF-α2 genes on both 6 and 11 days post-infection (dpi) compared to the fish sampled on day 0. Compared to koi, AS and Rop strains showed up-regulation of IL-6a and TNF-α2 but no other cytokine genes. During the infection with CEV genogroup IIa, Mx2 was significantly up-regulated in all strains and peaked on 6 dpi in AS, PS, and Rop. In koi, it remained high until 11 dpi. With genogroup I infection, Mx2 was up-expressed in koi on 6 dpi and in PS on both 6 and 11 dpi. No significant differences were noticed in selected mucin genes expression measured in gills of any carp strains exposed to both CEV genogroups. During both CEV genogroups infections, the expression levels of most of the genes for T cell response, including CD4, CD8b1, and GzmA were down-regulated in AS and koi at all time points compared to day 0 control. The expression data for the above experimental trials suggest that both CEV genogroups infections in common carp strains lead to activation of the same expression pattern regardless of the fish’s susceptibility towards the virus. The expression of the same genes in AS and koi responding to CEV genogroup IIa infection in mucosal tissues such as gill, gut, and skin showed the significant up-regulation of all the cytokine genes in gill and gut tissues from koi carp at 5 dpi. Significant down-regulation of CD4 and GzmA levels were only detected in koi gill on 5 dpi but not in other tissues. AS carp displayed significant up-expression of Mx2 gene in all mucosal tissues on 5 dpi, whereas in koi, it was up-regulated in gill and gut only. In both carp strains, gill harbored a higher virus load on 5 dpi compared to the other tissues. The results showed that resistance to CEV could not be linked with the selected immune responses measured. The up-regulation of mRNA expression of most of the selected immune-related genes in koi gill and gut suggests that CEV induces a more systemic mucosal immune response not restricted to the target tissue of gills. creator: Ali Asghar Baloch creator: Dieter Steinhagen creator: David Gela creator: Martin Kocour creator: Veronika Piačková creator: Mikolaj Adamek uri: https://doi.org/10.7717/peerj.15614 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Baloch et al. title: Spatio-temporal dengue risk modelling in the south of Thailand: a Bayesian approach to dengue vulnerability link: https://peerj.com/articles/15619 last-modified: 2023-07-14 description: BackgroundMore than half of the global population is predicted to be living in areas susceptible to dengue transmission with the vast majority in Asia. Dengue fever is of public health concern, particularly in the southern region of Thailand due to favourable environmental factors for its spread. The risk of dengue infection at the population level varies in time and space among sub-populations thus, it is important to study the risk of infection considering spatio-temporal variation.MethodsThis study presents a joint spatio-temporal epidemiological model in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation with the CARBayesST package of R software. For this purpose, monthly dengue records by district from 2002 to 2018 from the southern region of Thailand provided by the Ministry of Public Health of Thailand and eight environmental variables were used.ResultsResults show that an increasing level of temperature, number of rainy days and sea level pressure are associated with a higher occurrence of dengue fever and consequently higher incidence risk, while an increasing level of wind speed seems to suggest a protective factor. Likewise, we found that the elevated risks of dengue in the immediate future are in the districts of Phipun, Phrom Kili, Lan Saka, Phra Phrom and Chaloem Phakiat. The resulting estimates provide insights into the effects of covariate risk factors, spatio-temporal trends and dengue-related health inequalities at the district level in southern Thailand.ConclusionPossible implications are discussed considering some anthropogenic factors that could inhibit or enhance dengue occurrence. Risk maps indicated which districts are above and below baseline risk, allowing for the identification of local anomalies and high-risk boundaries. In the event of near future, the threat of elevated disease risk needs to be prevented and controlled considering the factors underlying the spread of mosquitoes in the Southeast Asian region. creator: Fatima Ibrahim Abdulsalam creator: Pablo Antúnez creator: Warit Jawjit uri: https://doi.org/10.7717/peerj.15619 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Abdulsalam et al. title: First report of the ectomycorrhizal fungal community associated with two herbaceous plants in Inner Mongolia, China link: https://peerj.com/articles/15626 last-modified: 2023-07-14 description: Ectomycorrhizal (EM) fungi play a vital role in ensuring plant health, plant diversity, and ecosystem function. However, the study on fungal diversity and community assembly of EM fungi associated with herbaceous plants remains poorly understood. Thus, in our study, Carex pediformis and Polygonum divaricatum in the subalpine meadow of central Inner Mongolia, China were selected for exploring EM fungal diversity and community assembly mechanisms by using llumina MiSeq sequencing of the fungal internal transcribed spacer 2 region (ITS2). We evaluated the impact of soil, climatic, and spatial variables on EM fungal diversity and community turnover. Deterministic vs. stochastic processes for EM fungal community assembly were quantified using β-Nearest taxon index scores. The results showed that a total of 70 EM fungal OTUs belonging to 21 lineages were identified, of which Tomentella-Thelephora, Helotiales1, Tricholoma, Inocybe, Wilcoxina were the most dominant EM fungal lineages. EM fungal communities were significantly different between the two herbaceous plants and among the two sampling sites, and this difference was mainly influenced by soil organic matter (OM) content and mean annual precipitation (MAP). The neutral community model (NCM) explained 45.7% of the variations in EM fungi community assembly. A total of 99.27% of the β-Nearest Taxa Index (βNTI) value was between −2 and 2. These results suggest that the dominant role of stochastic processes in shaping EM fungal community assembly. In addition, RCbray values showed that ecological drift in stochastic processes dominantly determined community assembly of EM fungi. Overall, our study shed light on the EM fungal diversity and community assembly associated with herbaceous plants in the subalpine region of central Inner Mongolia for the first time, which provided a better understanding of the role of herbaceous EM fungi. creator: Yongjun Fan creator: Simin Xiang creator: Jing Wang creator: Xuan Zhang creator: Zhimin Yu creator: Shupeng Zhu creator: Meng Lv creator: Lijun Bai creator: Luyu Han creator: Jianjun Ma creator: Yonglong Wang uri: https://doi.org/10.7717/peerj.15626 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Fan et al.