PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Pesticide dynamics in three small agricultural creeks in Hesse, Germany
items: Basil functional and growth responses when cultivated via different aquaponic and hydroponics systems
items: Variation in Pheidole nodus (Hymenoptera: Formicidae) functional morphology across urban parks
items: Tea intake or consumption and the risk of dementia: a meta-analysis of prospective cohort studies
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

Pesticide dynamics in three small agricultural creeks in Hesse, Germany
type: item
type: AcademicArticle
description: Background Due to their high biodiversity, small water bodies play an important role for freshwater ecosystems. Nonetheless, systematic pesticide monitoring in small creeks with a catchment <30 km2 is rarely conducted. Methods In this study, event-driven water samples were taken from May until November 2017 and March until July 2018 after 20 rain events at three sampling sites with catchment areas of <27 km2 in the Wetterau, a region with intensive agriculture in Southern Hesse, Germany. Additionally, enriched extracts of the native water samples from the campaign in 2018 were used for the Microtox assay to determine baseline toxicity to invertebrates over time and sum of toxic units (STU) were calculated to compare the potential toxicity of the samples. Results Overall, 37 pesticides and 17 transformation products were found, whereby the herbicide metamitron (79 µg/L) showed the highest concentration. Regularly, pesticide concentrations peaked at the time of the highest water level within each sampling event. Within each sampling event maximum pesticide concentration was mostly reached in water samples taken during the first two hours. The sum of the time-weighted mean concentration values of all pesticides was between 2.0 µg/L and 7.2 µg/L, whereby the measured concentrations exceeded their regulatory acceptable concentration (RAC) at 55% of all sampling events for at least one pesticide. The mean EC50 values varied between 28.6 ± 13.1 to 41.3 ± 12.1 REF (relative enrichment factor). The results indicated that several samples caused baseline toxicity, whereby the highest activity was measured at the time of highest water levels and pesticides concentrations, and then steadily decreased in parallel with the water level. Median STUs of invertebrates ranged from −2.10 to −3.91, of algae/aquatic plants from −0.79 to −1.84 and of fish from −2.47 to −4.24. For one of the three sampling sites, a significant linear correlation between baseline toxicity and STUinvertebrate…
format: application/pdf
format: text/html
creator: Sarah Betz-Koch
creator: Björn Jacobs
creator: Jörg Oehlmann
creator: Dominik Ratz
creator: Christian Reutter
creator: Arne Wick
creator: Matthias Oetken
subject: Ecotoxicology
subject: Freshwater Biology
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.15650
publisher: PeerJ Inc.
rights: © 2023 Betz-Koch et al.
abstract: Background Due to their high biodiversity, small water bodies play an important role for freshwater ecosystems. Nonetheless, systematic pesticide monitoring in small creeks with a catchment <30 km2 is rarely conducted. Methods In this study, event-driven water samples were taken from May until November 2017 and March until July 2018 after 20 rain events at three sampling sites with catchment areas of <27 km2 in the Wetterau, a region with intensive agriculture in Southern Hesse, Germany. Additionally, enriched extracts of the native water samples from the campaign in 2018 were used for the Microtox assay to determine baseline toxicity to invertebrates over time and sum of toxic units (STU) were calculated to compare the potential toxicity of the samples. Results Overall, 37 pesticides and 17 transformation products were found, whereby the herbicide metamitron (79 µg/L) showed the highest concentration. Regularly, pesticide concentrations peaked at the time of the highest water level within each sampling event. Within each sampling event maximum pesticide concentration was mostly reached in water samples taken during the first two hours. The sum of the time-weighted mean concentration values of all pesticides was between 2.0 µg/L and 7.2 µg/L, whereby the measured concentrations exceeded their regulatory acceptable concentration (RAC) at 55% of all sampling events for at least one pesticide. The mean EC50 values varied between 28.6 ± 13.1 to 41.3 ± 12.1 REF (relative enrichment factor). The results indicated that several samples caused baseline toxicity, whereby the highest activity was measured at the time of highest water levels and pesticides concentrations, and then steadily decreased in parallel with the water level. Median STUs of invertebrates ranged from −2.10 to −3.91, of algae/aquatic plants from −0.79 to −1.84 and of fish from −2.47 to −4.24. For one of the three sampling sites, a significant linear correlation between baseline toxicity and STUinvertebrate…
bibliographic citation: Betz-Koch et al. (2023) Pesticide dynamics in three small agricultural creeks in Hesse, Germany. PeerJ 11:e15650 https://doi.org/10.7717/peerj.15650
date submitted: 2023-02-20
date accepted: 2023-06-06
issued: 2023-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Betz-Koch
  given name: Sarah
author list: Agent
  family name: Jacobs
  given name: Björn
author list: Agent
  family name: Oehlmann
  given name: Jörg
author list: Agent
  family name: Ratz
  given name: Dominik
author list: Agent
  family name: Reutter
  given name: Christian
author list: Agent
  family name: Wick
  given name: Arne
author list: Agent
  family name: Oetken
  given name: Matthias
doi: 10.7717/peerj.15650
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-18
copyright: ©2023 Betz-Koch et al.
attribution name: Betz-Koch et al.

Basil functional and growth responses when cultivated via different aquaponic and hydroponics systems
type: item
type: AcademicArticle
description: Background Aquaponics is an innovative farming system that combines hydroponics and aquaculture, resulting in the production of both crops and fish. Decoupled aquaponics is a new approach introduced in aquaponics research for the elimination of certain system bottlenecks, specifically targeting the optimization of crops and fish production conditions. The aquaponics-related literature predominantly examines the system’s effects on crop productivity, largely overlooking the plant functional responses which underlie growth and yield performance. The aim of the study was the integrated evaluation of basil performance cultivated under coupled and decoupled aquaponic systems compared with a hydroponic one, in terms of growth and functional parameters in a pilot-scale aquaponics greenhouse. Methods We focused on the efficiency of the photosynthetic process and the state of the photosynthetic machinery, assessed by instantaneous gas exchange measurements as well as photosynthetic light response curves, and in vivo chlorophyll a fluorescence. Light use efficiency was estimated through leaf reflectance determination. Photosynthetic pigments content and leaf nutritional state assessments completed the picture of basil functional responses to the three different treatments/systems. The plant’s functional parameters were assessed at 15-day intervals. The experiment lasted for two months and included an intermediate and a final harvest during which several basil growth parameters were determined. Results Coupled aquaponics resulted in reduced growth, which was mainly ascribed to sub-sufficient leaf nutrient levels, a fact that triggered a series of negative feedbacks on all aspects of their photosynthetic performance. These plants experienced a down-regulation of PSII activity as reflected in the significant decreases of quantum yield and efficiency of electron transport, along with decreased photosynthetic pigments content. On the contrary, decoupled aquaponics favored both gro…
format: application/pdf
format: text/html
creator: Anastasia Mourantian
creator: Maria Aslanidou
creator: Eleni Mente
creator: Nikolaos Katsoulas
creator: Efi Levizou
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Plant Science
description: doi:10.7717/peerj.15664
publisher: PeerJ Inc.
rights: © 2023 Mourantian et al.
abstract: Background Aquaponics is an innovative farming system that combines hydroponics and aquaculture, resulting in the production of both crops and fish. Decoupled aquaponics is a new approach introduced in aquaponics research for the elimination of certain system bottlenecks, specifically targeting the optimization of crops and fish production conditions. The aquaponics-related literature predominantly examines the system’s effects on crop productivity, largely overlooking the plant functional responses which underlie growth and yield performance. The aim of the study was the integrated evaluation of basil performance cultivated under coupled and decoupled aquaponic systems compared with a hydroponic one, in terms of growth and functional parameters in a pilot-scale aquaponics greenhouse. Methods We focused on the efficiency of the photosynthetic process and the state of the photosynthetic machinery, assessed by instantaneous gas exchange measurements as well as photosynthetic light response curves, and in vivo chlorophyll a fluorescence. Light use efficiency was estimated through leaf reflectance determination. Photosynthetic pigments content and leaf nutritional state assessments completed the picture of basil functional responses to the three different treatments/systems. The plant’s functional parameters were assessed at 15-day intervals. The experiment lasted for two months and included an intermediate and a final harvest during which several basil growth parameters were determined. Results Coupled aquaponics resulted in reduced growth, which was mainly ascribed to sub-sufficient leaf nutrient levels, a fact that triggered a series of negative feedbacks on all aspects of their photosynthetic performance. These plants experienced a down-regulation of PSII activity as reflected in the significant decreases of quantum yield and efficiency of electron transport, along with decreased photosynthetic pigments content. On the contrary, decoupled aquaponics favored both gro…
bibliographic citation: Mourantian et al. (2023) Basil functional and growth responses when cultivated via different aquaponic and hydroponics systems. PeerJ 11:e15664 https://doi.org/10.7717/peerj.15664
date submitted: 2022-12-30
date accepted: 2023-06-08
issued: 2023-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mourantian
  given name: Anastasia
author list: Agent
  family name: Aslanidou
  given name: Maria
author list: Agent
  family name: Mente
  given name: Eleni
author list: Agent
  family name: Katsoulas
  given name: Nikolaos
author list: Agent
  family name: Levizou
  given name: Efi
doi: 10.7717/peerj.15664
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-18
copyright: ©2023 Mourantian et al.
attribution name: Mourantian et al.

Variation in Pheidole nodus (Hymenoptera: Formicidae) functional morphology across urban parks
type: item
type: AcademicArticle
description: Background Habitat fragmentation and consequent population isolation in urban areas can impose significant selection pressures on individuals and species confined to urban islands, such as parks. Despite many comparative studies on the diversity and structure of ant community living in urban areas, studies on ants’ responses to these highly variable ecosystems are often based on assemblage composition and interspecific mean trait values, which ignore the potential for high intraspecific functional trait variation among individuals. Methods Here, we examined differences in functional traits among populations of the generalist ant Pheidole nodus fragmented between urban parks. We used pitfall trapping, which is more random and objective than sampling colonies directly, despite a trade-off against sample size. We then tested whether trait-filtering could explain phenotypic differences among urban park ant populations, and whether ant populations in different parks exhibited different phenotypic optima, leading to positional shifts in anatomical morphospace through the regional ant meta-population. Results Intraspecific morphological differentiation was evident across this urban region. Populations had different convex hull volumes, positioned differently over the morphospace. Conclusions Fragmentation and habitat degradation reduced phenotypic diversity and, ultimately, changed the morphological optima of populations in this urban landscape. Considering ants’ broad taxonomic and functional diversity and their important role in ecosystems, further work over a variety of ant taxa is necessary to ascertain those varied morphological response pathways operating in response to population segregation in urban environments.
format: application/pdf
format: text/html
creator: Yi Luo
creator: Qing-Ming Wei
creator: Chris Newman
creator: Xiang-Qin Huang
creator: Xin-Yu Luo
creator: Zhao-Min Zhou
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.15679
publisher: PeerJ Inc.
rights: © 2023 Luo et al.
abstract: Background Habitat fragmentation and consequent population isolation in urban areas can impose significant selection pressures on individuals and species confined to urban islands, such as parks. Despite many comparative studies on the diversity and structure of ant community living in urban areas, studies on ants’ responses to these highly variable ecosystems are often based on assemblage composition and interspecific mean trait values, which ignore the potential for high intraspecific functional trait variation among individuals. Methods Here, we examined differences in functional traits among populations of the generalist ant Pheidole nodus fragmented between urban parks. We used pitfall trapping, which is more random and objective than sampling colonies directly, despite a trade-off against sample size. We then tested whether trait-filtering could explain phenotypic differences among urban park ant populations, and whether ant populations in different parks exhibited different phenotypic optima, leading to positional shifts in anatomical morphospace through the regional ant meta-population. Results Intraspecific morphological differentiation was evident across this urban region. Populations had different convex hull volumes, positioned differently over the morphospace. Conclusions Fragmentation and habitat degradation reduced phenotypic diversity and, ultimately, changed the morphological optima of populations in this urban landscape. Considering ants’ broad taxonomic and functional diversity and their important role in ecosystems, further work over a variety of ant taxa is necessary to ascertain those varied morphological response pathways operating in response to population segregation in urban environments.
bibliographic citation: Luo et al. (2023) Variation in Pheidole nodus (Hymenoptera: Formicidae) functional morphology across urban parks. PeerJ 11:e15679 https://doi.org/10.7717/peerj.15679
date submitted: 2023-03-20
date accepted: 2023-06-13
issued: 2023-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Yi
author list: Agent
  family name: Wei
  given name: Qing-Ming
author list: Agent
  family name: Newman
  given name: Chris
author list: Agent
  family name: Huang
  given name: Xiang-Qin
author list: Agent
  family name: Luo
  given name: Xin-Yu
author list: Agent
  family name: Zhou
  given name: Zhao-Min
doi: 10.7717/peerj.15679
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-18
copyright: ©2023 Luo et al.
attribution name: Luo et al.

Tea intake or consumption and the risk of dementia: a meta-analysis of prospective cohort studies
type: item
type: AcademicArticle
description: Purpose Dementia affects as many as 130 million people, which presents a significant and growing medical burden globally. This meta-analysis aims to assess whether tea intake, tea consumption can reduce the risk of dementia, Alzheimer’s disease (AD) and Vascular dementia (VD). Patients and methods Cochrane Library, PubMed and Embase were searched for cohort studies from inception to November 1, 2022. The Newcastle Ottawa Quality Assessment Scale (NOS) was applied to evaluate the risk of bias of the included studies. We extracted the data as the relative risks (RRs) for the outcome of the interest, and conducted the meta-analysis utilizing the random effect model due to the certain heterogeneity. Sensitivity analysis were performed by moving one study at a time, Subgroup-analysis was carried out according to different ages and dementia types. And the funnel plots based on Egger’s and Begger’s regression tests were used to evaluate publication bias. All statistical analyses were performed using Stata statistical software version 14.0 and R studio version 4.2.0. Results Seven prospective cohort studies covering 410,951 individuals, which were published from 2009 and 2022 were included in this meta-analysis. The methodological quality of these studies was relatively with five out of seven being of high quality and the remaining being of moderate. The pooling analysis shows that the relationship between tea intake or consumption is associated with a reduced risk of all-cause dementia (RR = 0.71, 95% CI [0.57–0.88], I2 = 79.0%, p < 0.01). Further, the subgroup-analysis revealed that tea intake or consumption is associated with a reduced risk of AD (RR = 0.88, 95% CI [0.79–0.99], I2 = 52.6%, p = 0.024) and VD (RR = 0.75, 95% CI [0.66–0.85], I = 0.00%, p < 0.001). Lastly, tea intake or consumption could reduce the risk of all-cause dementia to a greater degree among populations with less physical activity, older age, APOE carriers, and smokers. Conclusion Our meta-analysis …
format: application/pdf
format: text/html
creator: Ning Jiang
creator: Jinlong Ma
creator: Qian Wang
creator: Yuzhen Xu
creator: Baojian Wei
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Immunology
subject: Internal Medicine
description: doi:10.7717/peerj.15688
publisher: PeerJ Inc.
rights: © 2023 Jiang et al.
abstract: Purpose Dementia affects as many as 130 million people, which presents a significant and growing medical burden globally. This meta-analysis aims to assess whether tea intake, tea consumption can reduce the risk of dementia, Alzheimer’s disease (AD) and Vascular dementia (VD). Patients and methods Cochrane Library, PubMed and Embase were searched for cohort studies from inception to November 1, 2022. The Newcastle Ottawa Quality Assessment Scale (NOS) was applied to evaluate the risk of bias of the included studies. We extracted the data as the relative risks (RRs) for the outcome of the interest, and conducted the meta-analysis utilizing the random effect model due to the certain heterogeneity. Sensitivity analysis were performed by moving one study at a time, Subgroup-analysis was carried out according to different ages and dementia types. And the funnel plots based on Egger’s and Begger’s regression tests were used to evaluate publication bias. All statistical analyses were performed using Stata statistical software version 14.0 and R studio version 4.2.0. Results Seven prospective cohort studies covering 410,951 individuals, which were published from 2009 and 2022 were included in this meta-analysis. The methodological quality of these studies was relatively with five out of seven being of high quality and the remaining being of moderate. The pooling analysis shows that the relationship between tea intake or consumption is associated with a reduced risk of all-cause dementia (RR = 0.71, 95% CI [0.57–0.88], I2 = 79.0%, p < 0.01). Further, the subgroup-analysis revealed that tea intake or consumption is associated with a reduced risk of AD (RR = 0.88, 95% CI [0.79–0.99], I2 = 52.6%, p = 0.024) and VD (RR = 0.75, 95% CI [0.66–0.85], I = 0.00%, p < 0.001). Lastly, tea intake or consumption could reduce the risk of all-cause dementia to a greater degree among populations with less physical activity, older age, APOE carriers, and smokers. Conclusion Our meta-analysis …
bibliographic citation: Jiang et al. (2023) Tea intake or consumption and the risk of dementia: a meta-analysis of prospective cohort studies. PeerJ 11:e15688 https://doi.org/10.7717/peerj.15688
date submitted: 2023-04-03
date accepted: 2023-06-14
issued: 2023-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Ning
author list: Agent
  family name: Ma
  given name: Jinlong
author list: Agent
  family name: Wang
  given name: Qian
author list: Agent
  family name: Xu
  given name: Yuzhen
author list: Agent
  family name: Wei
  given name: Baojian
doi: 10.7717/peerj.15688
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-18
copyright: © 2023 Jiang et al.
attribution name: Jiang et al.

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.

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