PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: https://peerj.com/articles/15709
items: Sex difference in the discordance between Abbott Architect and EuroImmun serological assays
items: Immunostimulation of Parasteatoda tepidariorum (Araneae: Theridiidae) in juvenile and adult stages. Immunity reactions to injury with foreign body and Bacillus subtilis infection
items: Integrative species delimitation in the common ophiuroid Ophiothrix angulata (Echinodermata: Ophiuroidea): insights from COI, ITS2, arm coloration, and geometric morphometrics
items: Review of feature selection approaches based on grouping of features
items: Presence of an ultra-small microbiome in fermented cabbages
items: Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers
items: Identification of PIMREG as a novel prognostic signature in breast cancer via integrated bioinformatics analysis and experimental validation
items: The effect of perceived stress for work engagement in volunteers during the COVID-19 pandemic: the mediating role of psychological resilience and age differences
items: 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

https://peerj.com/articles/15709
type: item
type: AcademicArticle
title: Elevated estradiol levels on hCG trigger day adversely effects on the clinical pregnancy rates of blastocyst embryo transfer but not cleavage-stage embryo transfer in fresh cycles: a retrospective cohort study
description: Background Elevated estradiol (E2) levels are an inevitable outcome of the controlled ovulation hyperstimulation. However, the effect of this change on pregnancy is still uncertain. Our study aimed to analyze the impact of increased serum E2 at the day of human chorionic gonadotropin (hCG) administration on the clinical outcomes of women with fresh embryo transfer (ET) cycles. Methods This study included 3,009 fresh ET cycles from October 2015 to September 2021. Based on the stage of embryos transferred, these cycles were categorized into the cleavage group and blastocyst group. Both groups were then divided into four sets according to E2 levels when hCG was administered: set 1 (E2 ≤ 2,000 pg/ml), set 2 (E2 = 2,001–3,000 pg/ml), set 3 (E2 = 3,001–4,000 pg/ml), and set 4 (E2 > 4,000 pg/ml). The primary outcome was the clinical pregnancy rate (CPR). Binary logistics regression analysis was established to explore the association between CPR and E2 levels. Specifically, the threshold effect of serum E2 on CPR was revealed using the two-piecewise linear regression analyses. Results The multivariate regression model in the cleavage group showed that patients’ CPR in set 4 was 1.59 times higher than those in reference set 1, but the statistical difference was insignificant (P = 0.294). As for the blastocyst group, patients in set 4 had a lower CPR with adjusted ORs of 0.43 (P = 0.039) compared to patients in set 1. The inflection point for the blastocyst group was 39.7 pg/dl according to the results of the two-piecewise linear regression model. When E2 levels were over the point, the CPR decreased by 17% with every 1 pg/dl increases in serum E2 (adjusted OR = 0.83, 95% CI [0.72–0.96], P = 0.012). Conclusions Elevated E2 levels (>39.7 pg/dl) on hCG trigger day were associated with decreased CPR in patients with fresh blastocyst ET. However, it had no similar effect on the CPR of patients with fresh cleavage-stage ET.
format: application/pdf
format: text/html
creator: Yue Meng
creator: Linlin Tao
creator: Tingting Xia
creator: Jieru Zhu
creator: Xiaoqi Lin
creator: Wen Zhou
creator: Yuxia Liu
creator: Jianping Ou
creator: Weijie Xing
subject: Evidence Based Medicine
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.15709
publisher: PeerJ Inc.
rights: © 2023 Meng et al.
abstract: Background Elevated estradiol (E2) levels are an inevitable outcome of the controlled ovulation hyperstimulation. However, the effect of this change on pregnancy is still uncertain. Our study aimed to analyze the impact of increased serum E2 at the day of human chorionic gonadotropin (hCG) administration on the clinical outcomes of women with fresh embryo transfer (ET) cycles. Methods This study included 3,009 fresh ET cycles from October 2015 to September 2021. Based on the stage of embryos transferred, these cycles were categorized into the cleavage group and blastocyst group. Both groups were then divided into four sets according to E2 levels when hCG was administered: set 1 (E2 ≤ 2,000 pg/ml), set 2 (E2 = 2,001–3,000 pg/ml), set 3 (E2 = 3,001–4,000 pg/ml), and set 4 (E2 > 4,000 pg/ml). The primary outcome was the clinical pregnancy rate (CPR). Binary logistics regression analysis was established to explore the association between CPR and E2 levels. Specifically, the threshold effect of serum E2 on CPR was revealed using the two-piecewise linear regression analyses. Results The multivariate regression model in the cleavage group showed that patients’ CPR in set 4 was 1.59 times higher than those in reference set 1, but the statistical difference was insignificant (P = 0.294). As for the blastocyst group, patients in set 4 had a lower CPR with adjusted ORs of 0.43 (P = 0.039) compared to patients in set 1. The inflection point for the blastocyst group was 39.7 pg/dl according to the results of the two-piecewise linear regression model. When E2 levels were over the point, the CPR decreased by 17% with every 1 pg/dl increases in serum E2 (adjusted OR = 0.83, 95% CI [0.72–0.96], P = 0.012). Conclusions Elevated E2 levels (>39.7 pg/dl) on hCG trigger day were associated with decreased CPR in patients with fresh blastocyst ET. However, it had no similar effect on the CPR of patients with fresh cleavage-stage ET.
bibliographic citation: Meng et al. (2023) Elevated estradiol levels on hCG trigger day adversely effects on the clinical pregnancy rates of blastocyst embryo transfer but not cleavage-stage embryo transfer in fresh cycles: a retrospective cohort study. PeerJ 11:e15709 https://doi.org/10.7717/peerj.15709
date submitted: 2023-02-20
date accepted: 2023-06-15
issued: 2023-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Yue
author list: Agent
  family name: Tao
  given name: Linlin
author list: Agent
  family name: Xia
  given name: Tingting
author list: Agent
  family name: Zhu
  given name: Jieru
author list: Agent
  family name: Lin
  given name: Xiaoqi
author list: Agent
  family name: Zhou
  given name: Wen
author list: Agent
  family name: Liu
  given name: Yuxia
author list: Agent
  family name: Ou
  given name: Jianping
author list: Agent
  family name: Xing
  given name: Weijie
doi: 10.7717/peerj.15709
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-18
copyright: ©2023 Meng et al.
attribution name: Meng et al.

Sex difference in the discordance between Abbott Architect and EuroImmun serological assays
type: item
type: AcademicArticle
description: Background This study evaluated the discordance between Abbott Architect SARS-CoV-2 IgG and EUROIMMUN SARS-COV-2 ELISA in a seroprevalence study. Methods From 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. Results EI 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.
format: application/pdf
format: text/html
creator: Joel D. Hartsell
creator: Daniel T. Leung
creator: Yue Zhang
creator: Julio C. Delgado
creator: Stephen C. Alder
creator: Matthew H. Samore
subject: Biochemistry
subject: Epidemiology
subject: Hematology
subject: Infectious Diseases
subject: COVID-19
description: doi:10.7717/peerj.15247
publisher: PeerJ Inc.
rights: © 2023 Hartsell et al.
abstract: Background This study evaluated the discordance between Abbott Architect SARS-CoV-2 IgG and EUROIMMUN SARS-COV-2 ELISA in a seroprevalence study. Methods From 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. Results EI 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.
bibliographic citation: Hartsell et al. (2023) Sex difference in the discordance between Abbott Architect and EuroImmun serological assays. PeerJ 11:e15247 https://doi.org/10.7717/peerj.15247
date submitted: 2022-10-17
date accepted: 2023-03-28
issued: 2023-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hartsell
  given name: Joel D.
author list: Agent
  family name: Leung
  given name: Daniel T.
author list: Agent
  family name: Zhang
  given name: Yue
author list: Agent
  family name: Delgado
  given name: Julio C.
author list: Agent
  family name: Alder
  given name: Stephen C.
author list: Agent
  family name: Samore
  given name: Matthew H.
doi: 10.7717/peerj.15247
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-17
copyright: ©2023 Hartsell et al.
attribution name: Hartsell et al.

Immunostimulation of Parasteatoda tepidariorum (Araneae: Theridiidae) in juvenile and adult stages. Immunity reactions to injury with foreign body and Bacillus subtilis infection
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Agnieszka Ewa Czerwonka
creator: Marta Katarzyna Sawadro
creator: Jolanta Brożek
creator: Agnieszka Izabela Babczyńska
subject: Developmental Biology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.15337
publisher: PeerJ Inc.
rights: © 2023 Czerwonka et al.
abstract: 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.
bibliographic citation: Czerwonka et al. (2023) Immunostimulation of Parasteatoda tepidariorum (Araneae: Theridiidae) in juvenile and adult stages. Immunity reactions to injury with foreign body and Bacillus subtilis infection. PeerJ 11:e15337 https://doi.org/10.7717/peerj.15337
date submitted: 2022-11-23
date accepted: 2023-04-11
issued: 2023-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Czerwonka
  given name: Agnieszka Ewa
author list: Agent
  family name: Sawadro
  given name: Marta Katarzyna
author list: Agent
  family name: Brożek
  given name: Jolanta
author list: Agent
  family name: Babczyńska
  given name: Agnieszka Izabela
doi: 10.7717/peerj.15337
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-17
copyright: © 2023 Czerwonka et al.
attribution name: Czerwonka et al.

Integrative species delimitation in the common ophiuroid Ophiothrix angulata (Echinodermata: Ophiuroidea): insights from COI, ITS2, arm coloration, and geometric morphometrics
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Yoalli Quetzalli Hernández-Díaz
creator: Francisco Solis
creator: Rosa G. Beltrán-López
creator: Hugo A. Benítez
creator: Píndaro Díaz-Jaimes
creator: Gustav Paulay
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15655
publisher: PeerJ Inc.
rights: © 2023 Hernández-Díaz et al.
abstract: 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.
bibliographic citation: Hernández-Díaz et al. (2023) Integrative species delimitation in the common ophiuroid Ophiothrix angulata (Echinodermata: Ophiuroidea): insights from COI, ITS2, arm coloration, and geometric morphometrics. PeerJ 11:e15655 https://doi.org/10.7717/peerj.15655
date submitted: 2023-02-02
date accepted: 2023-06-07
issued: 2023-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Díaz
  given name: Yoalli Quetzalli
author list: Agent
  family name: Solis
  given name: Francisco
author list: Agent
  family name: Beltrán-López
  given name: Rosa G.
author list: Agent
  family name: Benítez
  given name: Hugo A.
author list: Agent
  family name: Díaz-Jaimes
  given name: Píndaro
author list: Agent
  family name: Paulay
  given name: Gustav
doi: 10.7717/peerj.15655
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-17
copyright: ©2023 Hernández-Díaz et al.
attribution name: Hernández-Díaz et al.

Review of feature selection approaches based on grouping of features
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Cihan Kuzudisli
creator: Burcu Bakir-Gungor
creator: Nurten Bulut
creator: Bahjat Qaqish
creator: Malik Yousef
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.15666
publisher: PeerJ Inc.
rights: © 2023 Kuzudisli et al.
abstract: 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.
bibliographic citation: Kuzudisli et al. (2023) Review of feature selection approaches based on grouping of features. PeerJ 11:e15666 https://doi.org/10.7717/peerj.15666
date submitted: 2022-11-14
date accepted: 2023-06-08
issued: 2023-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuzudisli
  given name: Cihan
author list: Agent
  family name: Bakir-Gungor
  given name: Burcu
author list: Agent
  family name: Bulut
  given name: Nurten
author list: Agent
  family name: Qaqish
  given name: Bahjat
author list: Agent
  family name: Yousef
  given name: Malik
doi: 10.7717/peerj.15666
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-17
copyright: ©2023 Kuzudisli et al.
attribution name: Kuzudisli et al.

Presence of an ultra-small microbiome in fermented cabbages
type: item
type: AcademicArticle
description: Background Ultramicrobacteria (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. Methods The 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. Results To 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), dive…
format: application/pdf
format: text/html
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
subject: Food Science and Technology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15680
publisher: PeerJ Inc.
rights: © 2023 Lee et al.
abstract: Background Ultramicrobacteria (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. Methods The 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. Results To 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), dive…
bibliographic citation: Lee et al. (2023) Presence of an ultra-small microbiome in fermented cabbages. PeerJ 11:e15680 https://doi.org/10.7717/peerj.15680
date submitted: 2023-02-14
date accepted: 2023-06-13
issued: 2023-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Hae-Won
author list: Agent
  family name: Yoon
  given name: So-Ra
author list: Agent
  family name: Dang
  given name: Yun-Mi
author list: Agent
  family name: Kang
  given name: Miran
author list: Agent
  family name: Lee
  given name: Kwangho
author list: Agent
  family name: Ha
  given name: Ji-Hyung
author list: Agent
  family name: Bae
  given name: Jin-Woo
doi: 10.7717/peerj.15680
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-17
copyright: ©2023 Lee et al.
attribution name: Lee et al.

Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
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
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.15683
publisher: PeerJ Inc.
rights: © 2023 Pozharskiy et al.
abstract: 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.
bibliographic citation: Pozharskiy et al. (2023) Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers. PeerJ 11:e15683 https://doi.org/10.7717/peerj.15683
date submitted: 2023-03-17
date accepted: 2023-06-14
issued: 2023-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pozharskiy
  given name: Alexandr
author list: Agent
  family name: Kostyukova
  given name: Valeriya
author list: Agent
  family name: Khusnitdinova
  given name: Marina
author list: Agent
  family name: Adilbayeva
  given name: Kamila
author list: Agent
  family name: Nizamdinova
  given name: Gulnaz
author list: Agent
  family name: Kapytina
  given name: Anastasiya
author list: Agent
  family name: Kerimbek
  given name: Nazym
author list: Agent
  family name: Taskuzhina
  given name: Aisha
author list: Agent
  family name: Kolchenko
  given name: Mariya
author list: Agent
  family name: Abdrakhmanova
  given name: Aisha
author list: Agent
  family name: Kisselyova
  given name: Nina
author list: Agent
  family name: Kalendar
  given name: Ruslan
author list: Agent
  family name: Gritsenko
  given name: Dilyara
doi: 10.7717/peerj.15683
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-17
copyright: ©2023 Pozharskiy et al.
attribution name: Pozharskiy et al.

Identification of PIMREG as a novel prognostic signature in breast cancer via integrated bioinformatics analysis and experimental validation
type: item
type: AcademicArticle
description: Background Phosphatidylinositol 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. Methods The 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. Results PIMREG 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. Conclusions The high expression of PIMREG is associated with poor prognosis and immune checkpoints in BC. HDAC2 may be a crit…
format: application/pdf
format: text/html
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
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.15703
publisher: PeerJ Inc.
rights: © 2023 Zhao et al.
abstract: Background Phosphatidylinositol 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. Methods The 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. Results PIMREG 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. Conclusions The high expression of PIMREG is associated with poor prognosis and immune checkpoints in BC. HDAC2 may be a crit…
bibliographic citation: Zhao et al. (2023) Identification of PIMREG as a novel prognostic signature in breast cancer via integrated bioinformatics analysis and experimental validation. PeerJ 11:e15703 https://doi.org/10.7717/peerj.15703
date submitted: 2023-03-19
date accepted: 2023-06-14
issued: 2023-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Wenjing
author list: Agent
  family name: Chang
  given name: Yuanjin
author list: Agent
  family name: Wu
  given name: Zhaoye
author list: Agent
  family name: Jiang
  given name: Xiaofan
author list: Agent
  family name: Li
  given name: Yong
author list: Agent
  family name: Xie
  given name: Ruijin
author list: Agent
  family name: Fu
  given name: Deyuan
author list: Agent
  family name: Sun
  given name: Chenyu
author list: Agent
  family name: Gao
  given name: Ju
doi: 10.7717/peerj.15703
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-17
copyright: ©2023 Zhao et al.
attribution name: Zhao et al.

The effect of perceived stress for work engagement in volunteers during the COVID-19 pandemic: the mediating role of psychological resilience and age differences
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Yatong Li
creator: Pei Xie
creator: Liang He
creator: Xiaolong Fu
creator: Xiaobing Ding
creator: Mary C. Jobe
creator: Md Zahir Ahmed
subject: Psychiatry and Psychology
subject: Mental Health
subject: COVID-19
description: doi:10.7717/peerj.15704
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: 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.
bibliographic citation: Li et al. (2023) The effect of perceived stress for work engagement in volunteers during the COVID-19 pandemic: the mediating role of psychological resilience and age differences. PeerJ 11:e15704 https://doi.org/10.7717/peerj.15704
date submitted: 2023-03-09
date accepted: 2023-06-14
issued: 2023-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yatong
author list: Agent
  family name: Xie
  given name: Pei
author list: Agent
  family name: He
  given name: Liang
author list: Agent
  family name: Fu
  given name: Xiaolong
author list: Agent
  family name: Ding
  given name: Xiaobing
author list: Agent
  family name: Jobe
  given name: Mary C.
author list: Agent
  family name: Ahmed
  given name: Md Zahir
doi: 10.7717/peerj.15704
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-17
copyright: ©2023 Li et al.
attribution name: Li et al.

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
type: item
type: AcademicArticle
description: Objectives To 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). Methods Patients 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. Results A 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). Conclusion Fully 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.
format: application/pdf
format: text/html
creator: Hua Zhong
creator: Anqi Li
creator: Yingdong Chen
creator: Qianwen Huang
creator: Xingbiao Chen
creator: Jianghe Kang
creator: Youkuang You
subject: Computational Biology
subject: Gastroenterology and Hepatology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15707
publisher: PeerJ Inc.
rights: © 2023 Zhong et al.
abstract: Objectives To 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). Methods Patients 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. Results A 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). Conclusion Fully 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.
bibliographic citation: Zhong et al. (2023) 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. PeerJ 11:e15707 https://doi.org/10.7717/peerj.15707
date submitted: 2023-03-07
date accepted: 2023-06-15
issued: 2023-07-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Hua
author list: Agent
  family name: Li
  given name: Anqi
author list: Agent
  family name: Chen
  given name: Yingdong
author list: Agent
  family name: Huang
  given name: Qianwen
author list: Agent
  family name: Chen
  given name: Xingbiao
author list: Agent
  family name: Kang
  given name: Jianghe
author list: Agent
  family name: You
  given name: Youkuang
doi: 10.7717/peerj.15707
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-17
copyright: ©2023 Zhong et al.
attribution name: Zhong et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359