title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=488 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Sex difference in the discordance between Abbott Architect and EuroImmun serological assays link: https://peerj.com/articles/15247 last-modified: 2023-07-17 description: BackgroundThis study evaluated the discordance between Abbott Architect SARS-CoV-2 IgG and EUROIMMUN SARS-COV-2 ELISA in a seroprevalence study.MethodsFrom June 10 to August 15, 2020, 8,246 specimens were dually evaluated by the Abbott Architect SARS-CoV-2 IgG (Abbott) and the EUROIMMUN SARS-CoV-2 ELISA (EI) assays. Sex-stratified phi correlation coefficients were calculated to evaluate the concordance between Abbott and EI assay’s quantitative results. Multivariable mixed-effect logistic models were implemented to evaluate the association between assay positivity and sex on a low prevalence sample while controlling for age, race, ethnicity, diabetes, cardiovascular disease, hypertension, immunosuppressive therapy, and autoimmune disease.ResultsEI positivity among males was 2.1-fold that of females; however, no significant differences in Abbott positivity were observed between sexes. At the manufacturer-recommended threshold, the phi correlation coefficient for the Abbott and EI qualitative results among females (Φ = 0.47) was 34% greater than males (Φ = 0.35). The unadjusted and fully adjusted models yielded a strong association between sex and positive EI result for the low prevalence subgroup (unadjusted OR: 2.24, CI: 1.63, 3.11, adjusted OR: 3.40, CI: 2.15, 5.39). A similar analysis of Abbott positivity in the low prevalence subgroup did not find an association with any of the covariates examined. Significant quantitative and qualitative discordance was observed between Abbott and EI throughout the seroprevalence study. Our results suggest the presence of sex-associated specificity limitations with the EI assay. As these findings may extend to other anti-S assays utilized for SARS-CoV-2 seroprevalence investigations, further investigation is needed to evaluate the generalizability of these findings. creator: Joel D. Hartsell creator: Daniel T. Leung creator: Yue Zhang creator: Julio C. Delgado creator: Stephen C. Alder creator: Matthew H. Samore uri: https://doi.org/10.7717/peerj.15247 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hartsell et al. title: Immunostimulation of Parasteatoda tepidariorum (Araneae: Theridiidae) in juvenile and adult stages. Immunity reactions to injury with foreign body and Bacillus subtilis infection link: https://peerj.com/articles/15337 last-modified: 2023-07-17 description: To assess the immune potential of spiders, in the present study juvenile and adult females of Parasteatoda tepidariorum were exposed to Bacillus subtilis infection, injury by a nylon monofilament and a combination of both. The expression level of selected immune-related genes: defensin 1 (PtDEF1), lysozyme 1 (PtLYS1), lysozyme C (PtLYSC), lysozyme M1 (PtLYSM1), autophagy-related protein 101 (PtATG101), dynamin (PtDYN) and heat shock proteins (HSP70) (PtHSPB, PtHSPB2A, PtHSPB2B), production of lysozyme and HSP70 proteins, and hemocytes viability were measured. The obtained results indicated expression of the lysozyme, autophagy-related protein and HSP70 genes in both ontogenetic stages of P. tepidariorum. It has been also shown that the simultaneous action of mechanical and biological factors causes higher level of lysozyme and HSP70, cell apoptosis intensity and lower level of hemocytes viability than in the case of exposure to a single immunostimulant. Moreover, mature females showed stronger early immune responses compared to juveniles. creator: Agnieszka Ewa Czerwonka creator: Marta Katarzyna Sawadro creator: Jolanta Brożek creator: Agnieszka Izabela Babczyńska uri: https://doi.org/10.7717/peerj.15337 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Czerwonka et al. title: Integrative species delimitation in the common ophiuroid Ophiothrix angulata (Echinodermata: Ophiuroidea): insights from COI, ITS2, arm coloration, and geometric morphometrics link: https://peerj.com/articles/15655 last-modified: 2023-07-17 description: Ophiothrix angulata (Say, 1825) is one of the most common and well-known ophiuroids in the Western Atlantic, with a wide geographic and bathymetric range. The taxonomy of this species has been controversial for a century because of its high morphological variability. Here we integrate information from DNA sequence data, color patterns, and geometric morphometrics to assess species delimitation and geographic differentiation in O. angulata. We found three deeply divergent mtDNA-COI clades (K2P 17.0–27.9%). ITS2 nuclear gene and geometric morphometrics of dorsal and ventral arm plates differentiate one of these lineages, as do integrative species delineation analyses, making this a confirmed candidate species. creator: Yoalli Quetzalli Hernández-Díaz creator: Francisco Solis creator: Rosa G. Beltrán-López creator: Hugo A. Benítez creator: Píndaro Díaz-Jaimes creator: Gustav Paulay uri: https://doi.org/10.7717/peerj.15655 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hernández-Díaz et al. title: Review of feature selection approaches based on grouping of features link: https://peerj.com/articles/15666 last-modified: 2023-07-17 description: With the rapid development in technology, large amounts of high-dimensional data have been generated. This high dimensionality including redundancy and irrelevancy poses a great challenge in data analysis and decision making. Feature selection (FS) is an effective way to reduce dimensionality by eliminating redundant and irrelevant data. Most traditional FS approaches score and rank each feature individually; and then perform FS either by eliminating lower ranked features or by retaining highly-ranked features. In this review, we discuss an emerging approach to FS that is based on initially grouping features, then scoring groups of features rather than scoring individual features. Despite the presence of reviews on clustering and FS algorithms, to the best of our knowledge, this is the first review focusing on FS techniques based on grouping. The typical idea behind FS through grouping is to generate groups of similar features with dissimilarity between groups, then select representative features from each cluster. Approaches under supervised, unsupervised, semi supervised and integrative frameworks are explored. The comparison of experimental results indicates the effectiveness of sequential, optimization-based (i.e., fuzzy or evolutionary), hybrid and multi-method approaches. When it comes to biological data, the involvement of external biological sources can improve analysis results. We hope this work’s findings can guide effective design of new FS approaches using feature grouping. creator: Cihan Kuzudisli creator: Burcu Bakir-Gungor creator: Nurten Bulut creator: Bahjat Qaqish creator: Malik Yousef uri: https://doi.org/10.7717/peerj.15666 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kuzudisli et al. title: Presence of an ultra-small microbiome in fermented cabbages link: https://peerj.com/articles/15680 last-modified: 2023-07-17 description: BackgroundUltramicrobacteria (UMB), also known as ultra-small bacteria, are tiny bacteria with a size less than 0.1 µm3. They have a high surface-to-volume ratio and are found in various ecosystems, including the human body. UMB can be classified into two types: one formed through cell contraction and the other that maintains a small size. The ultra-small microbiome (USM), which may contain UMB, includes all bacteria less than 0.2 µm in size and is difficult to detect with current methods. However, it poses a potential threat to food hygiene, as it can pass through sterilization filters and exist in a viable but non-culturable (VBNC) state. The data on the USM of foods is limited. Some bacteria, including pathogenic species, are capable of forming UMB under harsh conditions, making it difficult to detect them through conventional culture techniques.MethodsThe study described above focused on exploring the diversity of USM in fermented cabbage samples from three different countries (South Korea, China, and Germany). The samples of fermented cabbage (kimchi, suancai, and sauerkraut) were purchased and stored in chilled conditions at approximately 4 °C until filtration. The filtration process involved two steps of tangential flow filtration (TFF) using TFF cartridges with different pore sizes (0.2 µm and 100 kDa) to separate normal size bacteria (NM) and USM. The USM and NM isolated via TFF were stored in a refrigerator at 4 °C until DNA extraction. The extracted DNA was then amplified using PCR and the full-length 16S rRNA gene was sequenced using single-molecule-real-time (SMRT) sequencing. The transmission electron microscope (TEM) was used to confirm the presence of microorganisms in the USM of fermented cabbage samples.ResultsTo the best of our knowledge, this is the first study to identify the differences between USM and NM in fermented cabbages. Although the size of the USM (average 2,171,621 bp) was smaller than that of the NM (average 15,727,282 bp), diversity in USM (average H′ = 1.32) was not lower than that in NM (average H′ = 1.22). In addition, some members in USM probably underwent cell shrinkage due to unfavorable environments, while others maintained their size. Major pathogens were not detected in the USM in fermented cabbages. Nevertheless, several potentially suspicious strains (genera Cellulomonas and Ralstonia) were detected. Our method can be used to screen food materials for the presence of USM undetectable via conventional methods. USM and NM were efficiently separated using tangential flow filtration and analyzed via single-molecule real-time sequencing. The USM of fermented vegetables exhibited differences in size, diversity, and composition compared with the conventional microbiome. This study could provide new insights into the ultra-small ecosystem in fermented foods, including fermented cabbages. creator: Hae-Won Lee creator: So-Ra Yoon creator: Yun-Mi Dang creator: Miran Kang creator: Kwangho Lee creator: Ji-Hyung Ha creator: Jin-Woo Bae uri: https://doi.org/10.7717/peerj.15680 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lee et al. 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.