PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Antimicrobial and antibiofilm activity of specialized metabolites isolated from Centaurea hyalolepis
items: Similarities and differences: species and diet impact gut microbiota of captive pheasants
items: Plasticity-led and mutation-led evolutions are different modes of the same developmental gene regulatory network
items: Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review
items: Role of macrophages and their exosomes in orthopedic diseases
items: The feasibility of the posterior tibial nerve-flexor hallucis brevis pathway applied in neuromuscular monitoring: a multicentric, controlled, and prospective clinical trial
items: Variation and trade-offs in life history traits of the protist parasite Monocystis perplexa (Apicomplexa) in its earthworm host Amynthas agrestis
items: Assessing the risk of concurrent mycoplasma pneumoniae pneumonia in children with tracheobronchial tuberculosis: retrospective study
items: Plantar load distribution with centers of gravity balance and rearfoot posture in daily lives of Taiwanese college elite table tennis players: a cross-sectional study
items: The responses of CO2 emission to nitrogen application and earthworm addition in the soybean cropland

Antimicrobial and antibiofilm activity of specialized metabolites isolated from Centaurea hyalolepis
type: item
type: AcademicArticle
description: The discovery of plant-derived compounds that are able to combat antibiotic-resistant pathogens is an urgent demand. Over years, Centaurea hyalolepis attracted considerable attention because of its beneficial medical properties. Phytochemical analyses revealed that Centaurea plant species contain several metabolites, such as sesquiterpene lactones (STLs), essential oils, flavonoids, alkaloids, and lignans.The organic extract of C. hyalolepis plant, collected in Palestine, showed significant antimicrobial properties towards a panel of Gram-negative and Gram-positive bacterial strains when the Minimal Inhibitory Concentration (MIC) values were evaluated by broth microdilution assays. A bio-guided fractionation of the active extract via multiple steps of column and thin layer chromatography allowed us to obtain three main compounds. The isolated metabolites were identified as the STLs cnicin, 11β,13-dihydrosalonitenolide and salonitenolide by spectroscopic and spectrometric analyses. Cnicin conferred the strongest antimicrobial activity among the identified compounds. Moreover, the evaluation of its antibiofilm activity by biomass assays through crystal violet staining revealed almost 30% inhibition of biofilm formation in the case of A. baumannii ATCC 17878 strain. Furthermore, the quantification of carbohydrates and proteins present in the extracellular polymeric substance (EPS) revealed the ability of cnicin to significantly perturb biofilm structure. Based on these promising results, further investigations might open interesting perspectives to its applicability in biomedical field to counteract multidrug resistant infections.
format: application/pdf
format: text/html
creator: Shurooq Ismail
creator: Marco Masi
creator: Rosa Gaglione
creator: Angela Arciello
creator: Alessio Cimmino
subject: Biochemistry
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.16973
publisher: PeerJ Inc.
rights: © 2024 Ismail et al.
abstract: The discovery of plant-derived compounds that are able to combat antibiotic-resistant pathogens is an urgent demand. Over years, Centaurea hyalolepis attracted considerable attention because of its beneficial medical properties. Phytochemical analyses revealed that Centaurea plant species contain several metabolites, such as sesquiterpene lactones (STLs), essential oils, flavonoids, alkaloids, and lignans.The organic extract of C. hyalolepis plant, collected in Palestine, showed significant antimicrobial properties towards a panel of Gram-negative and Gram-positive bacterial strains when the Minimal Inhibitory Concentration (MIC) values were evaluated by broth microdilution assays. A bio-guided fractionation of the active extract via multiple steps of column and thin layer chromatography allowed us to obtain three main compounds. The isolated metabolites were identified as the STLs cnicin, 11β,13-dihydrosalonitenolide and salonitenolide by spectroscopic and spectrometric analyses. Cnicin conferred the strongest antimicrobial activity among the identified compounds. Moreover, the evaluation of its antibiofilm activity by biomass assays through crystal violet staining revealed almost 30% inhibition of biofilm formation in the case of A. baumannii ATCC 17878 strain. Furthermore, the quantification of carbohydrates and proteins present in the extracellular polymeric substance (EPS) revealed the ability of cnicin to significantly perturb biofilm structure. Based on these promising results, further investigations might open interesting perspectives to its applicability in biomedical field to counteract multidrug resistant infections.
bibliographic citation: Ismail et al. (2024) Antimicrobial and antibiofilm activity of specialized metabolites isolated from Centaurea hyalolepis. PeerJ 12:e16973 https://doi.org/10.7717/peerj.16973
date submitted: 2023-11-03
date accepted: 2024-01-29
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ismail
  given name: Shurooq
author list: Agent
  family name: Masi
  given name: Marco
author list: Agent
  family name: Gaglione
  given name: Rosa
author list: Agent
  family name: Arciello
  given name: Angela
author list: Agent
  family name: Cimmino
  given name: Alessio
doi: 10.7717/peerj.16973
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: ©2024 Ismail et al.
attribution name: Ismail et al.

Similarities and differences: species and diet impact gut microbiota of captive pheasants
type: item
type: AcademicArticle
description: The fecal microbiota plays an important role in maintaining animal health and is closely related to host life activities. In recent years, there have been an increasing number of studies on the fecal microbiota from birds. An exploration of the effects of species and living environments on the composition of gut microbiota will provide better protection for wildlife. In this study, non-injury sampling and 16S rDNA high-throughput sequencing were used to investigate the bacterial composition and diversity of the fecal microbiota in silver pheasants (Lophura nycthemera) and golden pheasants (Chrysolophus pictus) from Tianjin Zoo and Beijing Wildlife Park. The results showed that the abundance of Firmicutes was the highest in all fecal samples. At the genus level, Bacteroides was the common dominant bacteria, while there were some differences in other dominant bacteria genera. There were significant differences in fecal microbial composition between the golden pheasants from Tianjin Zoo and Beijing Wildlife Park. The metabolic analysis and functional prediction suggested that the gut microbiota composition and host metabolism were influenced by dietary interventions and living conditions. The results of this study provide the basis for further research of intestinal microbial of L. nycthemera and C. pictus, and valuable insights for conservation of related species.
format: application/pdf
format: text/html
creator: Yushuo Zhang
creator: Xin He
creator: Xiuhong Mo
creator: Hong Wu
creator: Dapeng Zhao
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.16979
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: The fecal microbiota plays an important role in maintaining animal health and is closely related to host life activities. In recent years, there have been an increasing number of studies on the fecal microbiota from birds. An exploration of the effects of species and living environments on the composition of gut microbiota will provide better protection for wildlife. In this study, non-injury sampling and 16S rDNA high-throughput sequencing were used to investigate the bacterial composition and diversity of the fecal microbiota in silver pheasants (Lophura nycthemera) and golden pheasants (Chrysolophus pictus) from Tianjin Zoo and Beijing Wildlife Park. The results showed that the abundance of Firmicutes was the highest in all fecal samples. At the genus level, Bacteroides was the common dominant bacteria, while there were some differences in other dominant bacteria genera. There were significant differences in fecal microbial composition between the golden pheasants from Tianjin Zoo and Beijing Wildlife Park. The metabolic analysis and functional prediction suggested that the gut microbiota composition and host metabolism were influenced by dietary interventions and living conditions. The results of this study provide the basis for further research of intestinal microbial of L. nycthemera and C. pictus, and valuable insights for conservation of related species.
bibliographic citation: Zhang et al. (2024) Similarities and differences: species and diet impact gut microbiota of captive pheasants. PeerJ 12:e16979 https://doi.org/10.7717/peerj.16979
date submitted: 2023-06-15
date accepted: 2024-01-29
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yushuo
author list: Agent
  family name: He
  given name: Xin
author list: Agent
  family name: Mo
  given name: Xiuhong
author list: Agent
  family name: Wu
  given name: Hong
author list: Agent
  family name: Zhao
  given name: Dapeng
doi: 10.7717/peerj.16979
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

Plasticity-led and mutation-led evolutions are different modes of the same developmental gene regulatory network
type: item
type: AcademicArticle
description: The standard theory of evolution proposes that mutations cause heritable variations, which are naturally selected, leading to evolution. However, this mutation-led evolution (MLE) is being questioned by an alternative theory called plasticity-led evolution (PLE). PLE suggests that an environmental change induces adaptive phenotypes, which are later genetically accommodated. According to PLE, developmental systems should be able to respond to environmental changes adaptively. However, developmental systems are known to be robust against environmental and mutational perturbations. Thus, we expect a transition from a robust state to a plastic one. To test this hypothesis, we constructed a gene regulatory network (GRN) model that integrates developmental processes, hierarchical regulation, and environmental cues. We then simulated its evolution over different magnitudes of environmental changes. Our findings indicate that this GRN model exhibits PLE under large environmental changes and MLE under small environmental changes. Furthermore, we observed that the GRN model is susceptible to environmental or genetic fluctuations under large environmental changes but is robust under small environmental changes. This indicates a breakdown of robustness due to large environmental changes. Before the breakdown of robustness, the distribution of phenotypes is biased and aligned to the environmental changes, which would facilitate rapid adaptation should a large environmental change occur. These observations suggest that the evolutionary transition from mutation-led to plasticity-led evolution is due to a developmental transition from robust to susceptible regimes over increasing magnitudes of environmental change. Thus, the GRN model can reconcile these conflicting theories of evolution.
format: application/pdf
format: text/html
creator: Eden T.H. Ng
creator: Akira R. Kinjo
subject: Biophysics
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.17102
publisher: PeerJ Inc.
rights: © 2024 Ng and Kinjo
abstract: The standard theory of evolution proposes that mutations cause heritable variations, which are naturally selected, leading to evolution. However, this mutation-led evolution (MLE) is being questioned by an alternative theory called plasticity-led evolution (PLE). PLE suggests that an environmental change induces adaptive phenotypes, which are later genetically accommodated. According to PLE, developmental systems should be able to respond to environmental changes adaptively. However, developmental systems are known to be robust against environmental and mutational perturbations. Thus, we expect a transition from a robust state to a plastic one. To test this hypothesis, we constructed a gene regulatory network (GRN) model that integrates developmental processes, hierarchical regulation, and environmental cues. We then simulated its evolution over different magnitudes of environmental changes. Our findings indicate that this GRN model exhibits PLE under large environmental changes and MLE under small environmental changes. Furthermore, we observed that the GRN model is susceptible to environmental or genetic fluctuations under large environmental changes but is robust under small environmental changes. This indicates a breakdown of robustness due to large environmental changes. Before the breakdown of robustness, the distribution of phenotypes is biased and aligned to the environmental changes, which would facilitate rapid adaptation should a large environmental change occur. These observations suggest that the evolutionary transition from mutation-led to plasticity-led evolution is due to a developmental transition from robust to susceptible regimes over increasing magnitudes of environmental change. Thus, the GRN model can reconcile these conflicting theories of evolution.
bibliographic citation: Ng et al. (2024) Plasticity-led and mutation-led evolutions are different modes of the same developmental gene regulatory network. PeerJ 12:e17102 https://doi.org/10.7717/peerj.17102
date submitted: 2023-12-06
date accepted: 2024-02-21
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ng
  given name: Eden T.H.
author list: Agent
  family name: Kinjo
  given name: Akira R.
doi: 10.7717/peerj.17102
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: ©2024 Ng and Kinjo
attribution name: Ng and Kinjo

Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review
type: item
type: AcademicArticle
description: Environmental stresses diversely affect multiple processes related to the growth, development, and yield of many crops worldwide. In response, plants have developed numerous sophisticated defense mechanisms at the cellular and subcellular levels to react and adapt to biotic and abiotic stressors. RNA silencing, which is an innate immune mechanism, mediates sequence-specific gene expression regulation in higher eukaryotes. ARGONAUTE (AGO) proteins are essential components of the RNA-induced silencing complex (RISC). They bind to small noncoding RNAs (sRNAs) and target complementary RNAs, causing translational repression or triggering endonucleolytic cleavage pathways. In this review, we aim to illustrate the recently published molecular functions, regulatory mechanisms, and biological roles of AGO family proteins in model plants and cash crops, especially in the defense against diverse biotic and abiotic stresses, which could be helpful in crop improvement and stress tolerance in various plants.
format: application/pdf
format: text/html
creator: Uroosa Zaheer
creator: Faisal Munir
creator: Yussuf Mohamed Salum
creator: Weiyi He
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.17115
publisher: PeerJ Inc.
rights: © 2024 Zaheer et al.
abstract: Environmental stresses diversely affect multiple processes related to the growth, development, and yield of many crops worldwide. In response, plants have developed numerous sophisticated defense mechanisms at the cellular and subcellular levels to react and adapt to biotic and abiotic stressors. RNA silencing, which is an innate immune mechanism, mediates sequence-specific gene expression regulation in higher eukaryotes. ARGONAUTE (AGO) proteins are essential components of the RNA-induced silencing complex (RISC). They bind to small noncoding RNAs (sRNAs) and target complementary RNAs, causing translational repression or triggering endonucleolytic cleavage pathways. In this review, we aim to illustrate the recently published molecular functions, regulatory mechanisms, and biological roles of AGO family proteins in model plants and cash crops, especially in the defense against diverse biotic and abiotic stresses, which could be helpful in crop improvement and stress tolerance in various plants.
bibliographic citation: Zaheer et al. (2024) Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review. PeerJ 12:e17115 https://doi.org/10.7717/peerj.17115
date submitted: 2023-09-20
date accepted: 2024-02-26
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zaheer
  given name: Uroosa
author list: Agent
  family name: Munir
  given name: Faisal
author list: Agent
  family name: Salum
  given name: Yussuf Mohamed
author list: Agent
  family name: He
  given name: Weiyi
doi: 10.7717/peerj.17115
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: ©2024 Zaheer et al.
attribution name: Zaheer et al.

Role of macrophages and their exosomes in orthopedic diseases
type: item
type: AcademicArticle
description: Exosomes are vesicles with a lipid bilayer structure that carry various active substances, such as proteins, DNA, non-coding RNA, and nucleic acids; these participate in the immune response, tissue formation, and cell communication. Owing to their low immunogenicity, exosomes play a key role in regulating the skeletal immune environment. Macrophages are important immune cells that swallow various cellular and tissue fragments. M1-like and M2-like macrophages differentiate to play pro-inflammatory, anti-inflammatory, and repair roles following stimulation. In recent years, the increase in the population base and the aging of the population have led to a gradual rise in orthopedic diseases, placing a heavy burden on the social medical system and making it urgent to find effective solutions. Macrophages and their exosomes have been demonstrated to be closely associated with the pathogenesis and prognosis of orthopedic diseases. An in-depth understanding of their mechanisms of action and the interaction between them will be helpful for the future clinical treatment of orthopedic diseases. This review focuses on the mechanisms of action, diagnosis, and treatment of orthopedic diseases involving macrophages and their exosomes, including fracture healing, diabetic bone damage, osteosarcoma, and rheumatoid arthritis. In addition, we discuss the prospects and major challenges faced by macrophages and their exosomes in clinical practice.
format: application/pdf
format: text/html
creator: Riming Yuan
creator: Jianjun Li
subject: Cell Biology
subject: Allergy and Clinical Immunology
subject: Immunology
subject: Public Health
subject: Rheumatology
description: doi:10.7717/peerj.17146
publisher: PeerJ Inc.
rights: © 2024 Yuan and Li
abstract: Exosomes are vesicles with a lipid bilayer structure that carry various active substances, such as proteins, DNA, non-coding RNA, and nucleic acids; these participate in the immune response, tissue formation, and cell communication. Owing to their low immunogenicity, exosomes play a key role in regulating the skeletal immune environment. Macrophages are important immune cells that swallow various cellular and tissue fragments. M1-like and M2-like macrophages differentiate to play pro-inflammatory, anti-inflammatory, and repair roles following stimulation. In recent years, the increase in the population base and the aging of the population have led to a gradual rise in orthopedic diseases, placing a heavy burden on the social medical system and making it urgent to find effective solutions. Macrophages and their exosomes have been demonstrated to be closely associated with the pathogenesis and prognosis of orthopedic diseases. An in-depth understanding of their mechanisms of action and the interaction between them will be helpful for the future clinical treatment of orthopedic diseases. This review focuses on the mechanisms of action, diagnosis, and treatment of orthopedic diseases involving macrophages and their exosomes, including fracture healing, diabetic bone damage, osteosarcoma, and rheumatoid arthritis. In addition, we discuss the prospects and major challenges faced by macrophages and their exosomes in clinical practice.
bibliographic citation: Yuan et al. (2024) Role of macrophages and their exosomes in orthopedic diseases. PeerJ 12:e17146 https://doi.org/10.7717/peerj.17146
date submitted: 2023-09-18
date accepted: 2024-03-01
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Riming
author list: Agent
  family name: Li
  given name: Jianjun
doi: 10.7717/peerj.17146
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: © 2024 Yuan and Li
attribution name: Yuan and Li

The feasibility of the posterior tibial nerve-flexor hallucis brevis pathway applied in neuromuscular monitoring: a multicentric, controlled, and prospective clinical trial
type: item
type: AcademicArticle
description: This study aimed to investigate the clinical viability of utilizing the flexor hallucis brevis as an alternative site for neuromuscular monitoring compared to the conventional adductor pollicis. Patients were recruited from three medical centers. Cis-atracurium was administered, and two monitors were employed independently to assess neuromuscular blockade of the adductor pollicis and the ipsilateral flexor hallucis brevis, following a train of four (TOF) pattern until TOF ratios exceeded 0.9 or until the conclusion of surgery. Statistical analysis revealed significant differences in onset time, duration of no-twitch response, spontaneous recovery time, and total monitoring time between the two sites, with mean differences of −53.54 s, −2.49, 3.22, and 5.89 min, respectively (P < 0.001).The posterior tibial nerve-flexor hallucis brevis pathway presents a promising alternative for neuromuscular monitoring during anesthesia maintenance. Further investigation is warranted to explore its utility in anesthesia induction and recovery. Trial registration: The trial was registered at www.chictr.org.cn (20/11/2018, ChiCTR1800019651).
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format: text/html
creator: Weiqiang Chen
creator: Zhijian Chen
creator: Fang Cheng
creator: Zhuodan Wang
creator: Juan Li
creator: Shangrong Li
creator: Hanbin Xie
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Surgery and Surgical Specialties
subject: Translational Medicine
description: doi:10.7717/peerj.17154
publisher: PeerJ Inc.
rights: © 2024 Chen et al.
abstract: This study aimed to investigate the clinical viability of utilizing the flexor hallucis brevis as an alternative site for neuromuscular monitoring compared to the conventional adductor pollicis. Patients were recruited from three medical centers. Cis-atracurium was administered, and two monitors were employed independently to assess neuromuscular blockade of the adductor pollicis and the ipsilateral flexor hallucis brevis, following a train of four (TOF) pattern until TOF ratios exceeded 0.9 or until the conclusion of surgery. Statistical analysis revealed significant differences in onset time, duration of no-twitch response, spontaneous recovery time, and total monitoring time between the two sites, with mean differences of −53.54 s, −2.49, 3.22, and 5.89 min, respectively (P < 0.001).The posterior tibial nerve-flexor hallucis brevis pathway presents a promising alternative for neuromuscular monitoring during anesthesia maintenance. Further investigation is warranted to explore its utility in anesthesia induction and recovery. Trial registration: The trial was registered at www.chictr.org.cn (20/11/2018, ChiCTR1800019651).
bibliographic citation: Chen et al. (2024) The feasibility of the posterior tibial nerve-flexor hallucis brevis pathway applied in neuromuscular monitoring: a multicentric, controlled, and prospective clinical trial. PeerJ 12:e17154 https://doi.org/10.7717/peerj.17154
date submitted: 2024-01-02
date accepted: 2024-03-04
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Weiqiang
author list: Agent
  family name: Chen
  given name: Zhijian
author list: Agent
  family name: Cheng
  given name: Fang
author list: Agent
  family name: Wang
  given name: Zhuodan
author list: Agent
  family name: Li
  given name: Juan
author list: Agent
  family name: Li
  given name: Shangrong
author list: Agent
  family name: Xie
  given name: Hanbin
doi: 10.7717/peerj.17154
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: © 2024 Chen et al.
attribution name: Chen et al.

Variation and trade-offs in life history traits of the protist parasite Monocystis perplexa (Apicomplexa) in its earthworm host Amynthas agrestis
type: item
type: AcademicArticle
description: The life history of a parasite describes its partitioning of assimilated resources into growth, reproduction, and transmission effort, and its precise timing of developmental events. The life cycle, in contrast, charts the sequence of morphological stages from feeding to the transmission forms. Phenotypic plasticity in life history traits can reveal how parasites confront variable environments within hosts. Within the protist phylum Apicomplexa major clades include the malaria parasites, coccidians, and most diverse, the gregarines (with likely millions of species). Studies on life history variation of gregarines are rare. Therefore, life history traits were examined for the gregarine Monocystis perplexa in its host, the invasive earthworm Amynthas agrestis at three sites in northern Vermont, United States of America. An important value of this system is the short life-span of the hosts, with only seven months from hatching to mass mortality; we were thus able to examine life history variation during the entire life cycle of both host and parasite. Earthworms were collected (N = 968 over 33 sample periods during one host season), then parasites of all life stages were counted, and sexual and transmission stages measured, for each earthworm. All traits varied substantially among individual earthworm hosts and across the sites. Across sites, timing of first appearance of infected earthworms, date when transmission stage (oocysts packed within gametocysts) appeared, date when number of both feeding (trophic) cells and gametocysts were at maximum, and date when 100% of earthworms were infected differed from 2–8 weeks, surprising variation for a short season available for parasite development. The maximal size of mating cells varied among hosts and across sites and this is reflected in the number of oocysts produced by the gametocyst. A negative trade-off was observed for the number of oocysts and their size. Several patterns were striking: (1) Prevalence reached 100% at…
format: application/pdf
format: text/html
creator: Erin L. Keller
creator: Jos. J. Schall
subject: Ecology
subject: Parasitology
description: doi:10.7717/peerj.17161
publisher: PeerJ Inc.
rights: © 2024 Keller and Schall
abstract: The life history of a parasite describes its partitioning of assimilated resources into growth, reproduction, and transmission effort, and its precise timing of developmental events. The life cycle, in contrast, charts the sequence of morphological stages from feeding to the transmission forms. Phenotypic plasticity in life history traits can reveal how parasites confront variable environments within hosts. Within the protist phylum Apicomplexa major clades include the malaria parasites, coccidians, and most diverse, the gregarines (with likely millions of species). Studies on life history variation of gregarines are rare. Therefore, life history traits were examined for the gregarine Monocystis perplexa in its host, the invasive earthworm Amynthas agrestis at three sites in northern Vermont, United States of America. An important value of this system is the short life-span of the hosts, with only seven months from hatching to mass mortality; we were thus able to examine life history variation during the entire life cycle of both host and parasite. Earthworms were collected (N = 968 over 33 sample periods during one host season), then parasites of all life stages were counted, and sexual and transmission stages measured, for each earthworm. All traits varied substantially among individual earthworm hosts and across the sites. Across sites, timing of first appearance of infected earthworms, date when transmission stage (oocysts packed within gametocysts) appeared, date when number of both feeding (trophic) cells and gametocysts were at maximum, and date when 100% of earthworms were infected differed from 2–8 weeks, surprising variation for a short season available for parasite development. The maximal size of mating cells varied among hosts and across sites and this is reflected in the number of oocysts produced by the gametocyst. A negative trade-off was observed for the number of oocysts and their size. Several patterns were striking: (1) Prevalence reached 100% at…
bibliographic citation: Keller et al. (2024) Variation and trade-offs in life history traits of the protist parasite Monocystis perplexa (Apicomplexa) in its earthworm host Amynthas agrestis. PeerJ 12:e17161 https://doi.org/10.7717/peerj.17161
date submitted: 2023-10-08
date accepted: 2024-03-05
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Keller
  given name: Erin L.
author list: Agent
  family name: Schall
  given name: Jos. J.
doi: 10.7717/peerj.17161
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: ©2024 Keller and Schall
attribution name: Keller and Schall

Assessing the risk of concurrent mycoplasma pneumoniae pneumonia in children with tracheobronchial tuberculosis: retrospective study
type: item
type: AcademicArticle
description: Objective This study aimed to create a predictive model based on machine learning to identify the risk for tracheobronchial tuberculosis (TBTB) occurring alongside Mycoplasma pneumoniae pneumonia in pediatric patients. Methods Clinical data from 212 pediatric patients were examined in this retrospective analysis. This cohort included 42 individuals diagnosed with TBTB and Mycoplasma pneumoniae pneumonia (combined group) and 170 patients diagnosed with lobar pneumonia alone (pneumonia group). Three predictive models, namely XGBoost, decision tree, and logistic regression, were constructed, and their performances were assessed using the receiver’s operating characteristic (ROC) curve, precision-recall curve (PR), and decision curve analysis (DCA). The dataset was divided into a 7:3 ratio to test the first and second groups, utilizing them to validate the XGBoost model and to construct the nomogram model. Results The XGBoost highlighted eight significant signatures, while the decision tree and logistic regression models identified six and five signatures, respectively. The ROC analysis revealed an area under the curve (AUC) of 0.996 for XGBoost, significantly outperforming the other models (p < 0.05). Similarly, the PR curve demonstrated the superior predictive capability of XGBoost. DCA further confirmed that XGBoost offered the highest AIC (43.226), the highest average net benefit (0.764), and the best model fit. Validation efforts confirmed the robustness of the findings, with the validation groups 1 and 2 showing ROC and PR curves with AUC of 0.997, indicating a high net benefit. The nomogram model was shown to possess significant clinical value. Conclusion Compared to machine learning approaches, the XGBoost model demonstrated superior predictive efficacy in identifying pediatric patients at risk of concurrent TBTB and Mycoplasma pneumoniae pneumonia. The model’s identification of critical signatures provides valuable insights into the pathogenesis of these condit…
format: application/pdf
format: text/html
creator: Lin Liu
creator: Jie Jiang
creator: Lei Wu
creator: De miao Zeng
creator: Can Yan
creator: Linlong Liang
creator: Jiayun Shi
creator: Qifang Xie
subject: Bioinformatics
subject: Immunology
subject: Internal Medicine
subject: Respiratory Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17164
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Objective This study aimed to create a predictive model based on machine learning to identify the risk for tracheobronchial tuberculosis (TBTB) occurring alongside Mycoplasma pneumoniae pneumonia in pediatric patients. Methods Clinical data from 212 pediatric patients were examined in this retrospective analysis. This cohort included 42 individuals diagnosed with TBTB and Mycoplasma pneumoniae pneumonia (combined group) and 170 patients diagnosed with lobar pneumonia alone (pneumonia group). Three predictive models, namely XGBoost, decision tree, and logistic regression, were constructed, and their performances were assessed using the receiver’s operating characteristic (ROC) curve, precision-recall curve (PR), and decision curve analysis (DCA). The dataset was divided into a 7:3 ratio to test the first and second groups, utilizing them to validate the XGBoost model and to construct the nomogram model. Results The XGBoost highlighted eight significant signatures, while the decision tree and logistic regression models identified six and five signatures, respectively. The ROC analysis revealed an area under the curve (AUC) of 0.996 for XGBoost, significantly outperforming the other models (p < 0.05). Similarly, the PR curve demonstrated the superior predictive capability of XGBoost. DCA further confirmed that XGBoost offered the highest AIC (43.226), the highest average net benefit (0.764), and the best model fit. Validation efforts confirmed the robustness of the findings, with the validation groups 1 and 2 showing ROC and PR curves with AUC of 0.997, indicating a high net benefit. The nomogram model was shown to possess significant clinical value. Conclusion Compared to machine learning approaches, the XGBoost model demonstrated superior predictive efficacy in identifying pediatric patients at risk of concurrent TBTB and Mycoplasma pneumoniae pneumonia. The model’s identification of critical signatures provides valuable insights into the pathogenesis of these condit…
bibliographic citation: Liu et al. (2024) Assessing the risk of concurrent mycoplasma pneumoniae pneumonia in children with tracheobronchial tuberculosis: retrospective study. PeerJ 12:e17164 https://doi.org/10.7717/peerj.17164
date submitted: 2023-12-29
date accepted: 2024-03-06
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Lin
author list: Agent
  family name: Jiang
  given name: Jie
author list: Agent
  family name: Wu
  given name: Lei
author list: Agent
  family name: Zeng
  given name: De miao
author list: Agent
  family name: Yan
  given name: Can
author list: Agent
  family name: Liang
  given name: Linlong
author list: Agent
  family name: Shi
  given name: Jiayun
author list: Agent
  family name: Xie
  given name: Qifang
doi: 10.7717/peerj.17164
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: © 2024 Liu et al.
attribution name: Liu et al.

Plantar load distribution with centers of gravity balance and rearfoot posture in daily lives of Taiwanese college elite table tennis players: a cross-sectional study
type: item
type: AcademicArticle
description: Background Table tennis is an asymmetric sport involving the powerful forward swing of the upper limbs depends on the solid support of the lower limbs. The foot drive really affects the weight balance and stroke accuracy even though the distance and momentum of the lower limb displacement are limited within a limited range. Given that previous research on table tennis has typically focused on the footwork and stroke performance of professional players, the study aimed to investigate the daily static and dynamic plantar load distribution as well as the centers of gravity balance and rearfoot posture among Taiwanese college elite table tennis players. Methods This is a cross-sectional study of 70 elite male table tennis players (age: 20.0 ± 0.9 years; height: 173.4 ± 5.1 cm, weight: 67.6 ± 5.3 kg, experience: 10.0 ± 1.6 years) and 77 amateur table tennis players of the same gender (age: 20.1 ± 0.8 years, height: 167.4 ± 4.4 cm, weight: 64.3 ± 4.0 kg, experience: 4.4 ± 1.2 years) from Taiwanese universities. The JC Mat optical plantar pressure analyzer was applied to determine the plantar load distribution along with arch index (AI) and centers of gravity balance. Assessment of rearfoot postural alignment was mainly used to contrast the performance of the centers of gravity balance. Results The static arch indices of both feet in the elite group were symmetrical and considered normal arches (AI: 0.22 ± 0.07) during their non-training and non-competition daily lives. Their static plantar loads were symmetrically concentrated on the bipedal lateral metatarsals (P < 0.05) as well as shifted to the medial and lateral heels (P < 0.05) and the lateral metatarsals (P < 0.05) during the walking midstance phase. Additionally, the plantar loads were mainly applied to the bipedal medial (P < 0.01) and lateral heels (P < 0.05) during the transitional changes between both states. Elite athletes had symmetrical and evenly distributed centers of gravity on both feet (left: 50.03 ± 4.…
format: application/pdf
format: text/html
creator: Tong-Hsien Chow
creator: Yu-Ling Lee
subject: Bioengineering
subject: Kinesiology
subject: Biomechanics
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.17173
publisher: PeerJ Inc.
rights: © 2024 Chow and Lee
abstract: Background Table tennis is an asymmetric sport involving the powerful forward swing of the upper limbs depends on the solid support of the lower limbs. The foot drive really affects the weight balance and stroke accuracy even though the distance and momentum of the lower limb displacement are limited within a limited range. Given that previous research on table tennis has typically focused on the footwork and stroke performance of professional players, the study aimed to investigate the daily static and dynamic plantar load distribution as well as the centers of gravity balance and rearfoot posture among Taiwanese college elite table tennis players. Methods This is a cross-sectional study of 70 elite male table tennis players (age: 20.0 ± 0.9 years; height: 173.4 ± 5.1 cm, weight: 67.6 ± 5.3 kg, experience: 10.0 ± 1.6 years) and 77 amateur table tennis players of the same gender (age: 20.1 ± 0.8 years, height: 167.4 ± 4.4 cm, weight: 64.3 ± 4.0 kg, experience: 4.4 ± 1.2 years) from Taiwanese universities. The JC Mat optical plantar pressure analyzer was applied to determine the plantar load distribution along with arch index (AI) and centers of gravity balance. Assessment of rearfoot postural alignment was mainly used to contrast the performance of the centers of gravity balance. Results The static arch indices of both feet in the elite group were symmetrical and considered normal arches (AI: 0.22 ± 0.07) during their non-training and non-competition daily lives. Their static plantar loads were symmetrically concentrated on the bipedal lateral metatarsals (P < 0.05) as well as shifted to the medial and lateral heels (P < 0.05) and the lateral metatarsals (P < 0.05) during the walking midstance phase. Additionally, the plantar loads were mainly applied to the bipedal medial (P < 0.01) and lateral heels (P < 0.05) during the transitional changes between both states. Elite athletes had symmetrical and evenly distributed centers of gravity on both feet (left: 50.03 ± 4.…
bibliographic citation: Chow et al. (2024) Plantar load distribution with centers of gravity balance and rearfoot posture in daily lives of Taiwanese college elite table tennis players: a cross-sectional study. PeerJ 12:e17173 https://doi.org/10.7717/peerj.17173
date submitted: 2023-10-09
date accepted: 2024-03-08
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chow
  given name: Tong-Hsien
author list: Agent
  family name: Lee
  given name: Yu-Ling
doi: 10.7717/peerj.17173
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: © 2024 Chow and Lee
attribution name: Chow and Lee

The responses of CO2 emission to nitrogen application and earthworm addition in the soybean cropland
type: item
type: AcademicArticle
description: The effects of nitrogen application or earthworms on soil respiration in the Huang-Huai-Hai Plain of China have received increasing attention. However, the response of soil carbon dioxide (CO2) emission to nitrogen application and earthworm addition is still unclear. A field experiment with nitrogen application frequency and earthworm addition was conducted in the Huang-Huai-Hai Plain. Results showed nitrogen application frequency had a significant effect on soil respiration, but neither earthworms nor their interaction with nitrogen application frequency were significant. Low-frequency nitrogen application (NL) significantly increased soil respiration by 25%, while high-frequency nitrogen application (NH), earthworm addition (E), earthworm and high-frequency nitrogen application (E*NH), and earthworm and low-frequency nitrogen application (E*NL) also increased soil respiration by 21%, 21%, 12%, and 11%, respectively. The main reason for the rise in soil respiration was alterations in the bacterial richness and keystone taxa (Myxococcales). The NH resulted in higher soil nitrogen levels compared to NL, but NL had the highest bacterial richness. The abundance of Corynebacteriales and Gammaproteobacteria were positively connected with the CO2 emissions, while Myxococcales, Thermoleophilia, and Verrucomicrobia were negatively correlated. Our findings indicate the ecological importance of bacterial communities in regulating the carbon cycle in the Huang-Huai-Hai Plain.
format: application/pdf
format: text/html
creator: Mei Guang Jiang
creator: Jingyuan Yang
creator: Qi Xu
creator: Linyu Qi
creator: Yue Gao
creator: Cancan Zhao
creator: Huijie Lu
creator: Yuan Miao
creator: Shijie Han
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.17176
publisher: PeerJ Inc.
rights: © 2024 Jiang et al.
abstract: The effects of nitrogen application or earthworms on soil respiration in the Huang-Huai-Hai Plain of China have received increasing attention. However, the response of soil carbon dioxide (CO2) emission to nitrogen application and earthworm addition is still unclear. A field experiment with nitrogen application frequency and earthworm addition was conducted in the Huang-Huai-Hai Plain. Results showed nitrogen application frequency had a significant effect on soil respiration, but neither earthworms nor their interaction with nitrogen application frequency were significant. Low-frequency nitrogen application (NL) significantly increased soil respiration by 25%, while high-frequency nitrogen application (NH), earthworm addition (E), earthworm and high-frequency nitrogen application (E*NH), and earthworm and low-frequency nitrogen application (E*NL) also increased soil respiration by 21%, 21%, 12%, and 11%, respectively. The main reason for the rise in soil respiration was alterations in the bacterial richness and keystone taxa (Myxococcales). The NH resulted in higher soil nitrogen levels compared to NL, but NL had the highest bacterial richness. The abundance of Corynebacteriales and Gammaproteobacteria were positively connected with the CO2 emissions, while Myxococcales, Thermoleophilia, and Verrucomicrobia were negatively correlated. Our findings indicate the ecological importance of bacterial communities in regulating the carbon cycle in the Huang-Huai-Hai Plain.
bibliographic citation: Jiang et al. (2024) The responses of CO2 emission to nitrogen application and earthworm addition in the soybean cropland. PeerJ 12:e17176 https://doi.org/10.7717/peerj.17176
date submitted: 2023-09-01
date accepted: 2024-03-08
issued: 2024-03-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Mei Guang
author list: Agent
  family name: Yang
  given name: Jingyuan
author list: Agent
  family name: Xu
  given name: Qi
author list: Agent
  family name: Qi
  given name: Linyu
author list: Agent
  family name: Gao
  given name: Yue
author list: Agent
  family name: Zhao
  given name: Cancan
author list: Agent
  family name: Lu
  given name: Huijie
author list: Agent
  family name: Miao
  given name: Yuan
author list: Agent
  family name: Han
  given name: Shijie
doi: 10.7717/peerj.17176
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-26
copyright: © 2024 Jiang et al.
attribution name: Jiang et al.

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