PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Spatio-temporal distribution of ostracod species in saline inland lakes (Mansfeld lake area; Central Germany)
items: Genome-wide characterization and expression analysis of bHLH gene family in physic nut (Jatropha curcas L.)
items: The use of synthetic agonists of quorum sensing N- acyl homoserine lactone pathway improves the bioleaching ability in Acidithiobacillus and Pseudomonas bacteria
items: Arbuscular mycorrhizal fungi enhanced the growth, phosphorus uptake and Pht expression of olive (Olea europaea L.) plantlets
items: Association between lung function impairment with urinary heavy metals in a community in Klang Valley, Malaysia
items: Application of plasma metabolome for monitoring the effect of rivaroxaban in patients with nonvalvular atrial fibrillation
items: https://peerj.com/articles/13758
items: Early Miocene remains of Melissiodon from Mokrá-Quarry (Moravia, Czech Republic) shed light on the evolutionary history of the rare cricetid genus
items: Development of a COVID-19 risk assessment model for participants at outdoor music festivals: evaluation of the validity and control measure effectiveness based on two actual events in Japan and Spain
items: One step further in biomechanical models in palaeontology: a nonlinear finite element analysis review

Spatio-temporal distribution of ostracod species in saline inland lakes (Mansfeld lake area; Central Germany)
type: item
type: AcademicArticle
description: Ostracods are a diverse group of microcrustaceans with a ubiquitous distribution in a wide array of aquatic habitats and are common constituents of lake sediments. Inferences on the temporal-spatial distribution of ostracod species is a prerequisite for reconstructions of palaeoenvironmental conditions. This requires a precise knowledge not only about ecological preferences and specific life histories, but also the understanding how (local) ecological parameters affect ostracod species assemblages (abundance and composition). Generally, these studies are rare and often characterized by an insufficient differentiation of living specimens from the total amount of valves of the modern population leading to uncertainties in species occurrences and diversity data. Modern ostracod populations were sampled from 12 water bodies within a relatively small study area (Mansfeld lake area, Central Germany). Physico-chemical parameters (temperature, oxygen content, conductivity, pH) were measured in situ and the uppermost 2 cm of sediment were collected in different seasons (April, June, September). Relative abundances of ostracods (living and dead), differentiated for adults and juveniles, were used for statistical analyses (Spearman‘s rank correlation, Canonical correspondence analysis, Cluster analyses, Fisher’s α), to investigate relationships between species distribution and environmental factors as well as to identify habitat similarities and ostracod species assemblages. In total, 27 ostracod species (20 living species) were identified. Majority of them are considered as very common (cosmopolitan) freshwater species. Only two species are usually known from brackish water (Cytheromorpha fuscata and Cyprideis torosa). This is the first confirmation of living C. torosa in German inland waters. The relative abundances of ostracods show strong fluctuations during the study period and differences in composition of the ostracod species assemblages between and within the water bod…
format: application/pdf
format: text/html
creator: Marlene Hoehle
creator: Claudia Wrozyna
subject: Biogeography
subject: Ecology
subject: Microbiology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.13668
publisher: PeerJ Inc.
rights: © 2022 Hoehle and Wrozyna
abstract: Ostracods are a diverse group of microcrustaceans with a ubiquitous distribution in a wide array of aquatic habitats and are common constituents of lake sediments. Inferences on the temporal-spatial distribution of ostracod species is a prerequisite for reconstructions of palaeoenvironmental conditions. This requires a precise knowledge not only about ecological preferences and specific life histories, but also the understanding how (local) ecological parameters affect ostracod species assemblages (abundance and composition). Generally, these studies are rare and often characterized by an insufficient differentiation of living specimens from the total amount of valves of the modern population leading to uncertainties in species occurrences and diversity data. Modern ostracod populations were sampled from 12 water bodies within a relatively small study area (Mansfeld lake area, Central Germany). Physico-chemical parameters (temperature, oxygen content, conductivity, pH) were measured in situ and the uppermost 2 cm of sediment were collected in different seasons (April, June, September). Relative abundances of ostracods (living and dead), differentiated for adults and juveniles, were used for statistical analyses (Spearman‘s rank correlation, Canonical correspondence analysis, Cluster analyses, Fisher’s α), to investigate relationships between species distribution and environmental factors as well as to identify habitat similarities and ostracod species assemblages. In total, 27 ostracod species (20 living species) were identified. Majority of them are considered as very common (cosmopolitan) freshwater species. Only two species are usually known from brackish water (Cytheromorpha fuscata and Cyprideis torosa). This is the first confirmation of living C. torosa in German inland waters. The relative abundances of ostracods show strong fluctuations during the study period and differences in composition of the ostracod species assemblages between and within the water bod…
bibliographic citation: Hoehle et al. (2022) Spatio-temporal distribution of ostracod species in saline inland lakes (Mansfeld lake area; Central Germany). PeerJ 10:e13668 https://doi.org/10.7717/peerj.13668
date submitted: 2022-01-31
date accepted: 2022-06-10
issued: 2022-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoehle
  given name: Marlene
author list: Agent
  family name: Wrozyna
  given name: Claudia
doi: 10.7717/peerj.13668
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-09
copyright: ©2022 Hoehle and Wrozyna
attribution name: Hoehle and Wrozyna

Genome-wide characterization and expression analysis of bHLH gene family in physic nut (Jatropha curcas L.)
type: item
type: AcademicArticle
description: The basic helix loop helix (bHLH) transcription factor perform essential roles in plant development and abiotic stress. Here, a total of 122 bHLH family members were identified from the physic nut (Jatropha curcas L.) genomic database. Chromosomal localization results showed that 120 members were located on 11 chromosomes. The phylogenetic tree manifested that the JcbHLHs could be grouped into 28 subfamilies. Syntenic analysis showed that there were 10 bHLH collinear genes among the physic nut, Arabidopsis thaliana and Oryza sativa. These genes, except JcbHLH84, were highly expressed in various tissues of the physic nut, implying a key role in plant development. Gene expression profiles showed that ten genes (especially JcbHLH33, JcbHLH45 and JcbHLH55) correspond to both salinity and drought stresses; while eight genes only respond to salinity and another eight genes only respond to drought stress. Moreover, the protein interaction network revealed that the JcbHLHs are involved in growth, development and stress signal transduction pathways. These discoveries will help to excavate several key genes may involve in salt or drought stresses and seed development, elucidate the complex transcriptional regulation mechanism of JcbHLH genes and provide the theoretical basis for stress response and genetic improvement of physic nut.
format: application/pdf
format: text/html
creator: Lin Zhang
creator: Wei Chen
creator: Rongrong Liu
creator: Ben Shi
creator: Youju Shu
creator: Haoyu Zhang
subject: Biochemistry
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13786
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: The basic helix loop helix (bHLH) transcription factor perform essential roles in plant development and abiotic stress. Here, a total of 122 bHLH family members were identified from the physic nut (Jatropha curcas L.) genomic database. Chromosomal localization results showed that 120 members were located on 11 chromosomes. The phylogenetic tree manifested that the JcbHLHs could be grouped into 28 subfamilies. Syntenic analysis showed that there were 10 bHLH collinear genes among the physic nut, Arabidopsis thaliana and Oryza sativa. These genes, except JcbHLH84, were highly expressed in various tissues of the physic nut, implying a key role in plant development. Gene expression profiles showed that ten genes (especially JcbHLH33, JcbHLH45 and JcbHLH55) correspond to both salinity and drought stresses; while eight genes only respond to salinity and another eight genes only respond to drought stress. Moreover, the protein interaction network revealed that the JcbHLHs are involved in growth, development and stress signal transduction pathways. These discoveries will help to excavate several key genes may involve in salt or drought stresses and seed development, elucidate the complex transcriptional regulation mechanism of JcbHLH genes and provide the theoretical basis for stress response and genetic improvement of physic nut.
bibliographic citation: Zhang et al. (2022) Genome-wide characterization and expression analysis of bHLH gene family in physic nut (Jatropha curcas L.). PeerJ 10:e13786 https://doi.org/10.7717/peerj.13786
date submitted: 2022-03-11
date accepted: 2022-07-05
issued: 2022-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Lin
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: Liu
  given name: Rongrong
author list: Agent
  family name: Shi
  given name: Ben
author list: Agent
  family name: Shu
  given name: Youju
author list: Agent
  family name: Zhang
  given name: Haoyu
doi: 10.7717/peerj.13786
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-09
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

The use of synthetic agonists of quorum sensing N- acyl homoserine lactone pathway improves the bioleaching ability in Acidithiobacillus and Pseudomonas bacteria
type: item
type: AcademicArticle
description: Metal solubilization from discarded electrical material and electronic devices (e-waste) using the bioleaching capabilities of bacterial cells is highly effective. However, gaps in understanding about the microbiological processes involved in the bioleaching reaction leads to less efficient metal solubilization in large-scale e-waste processing. In this study, bacterial species belonging to the genera Acidithiobacillus and Pseudomonas were used to leach copper and gold from discarded printed circuit boards (PCB). Through modulation of the cell-to-cell communication system in these bacteria, phenotypic traits directly involved in the bioleaching reaction were regulated in order to improve the metal solubilization. Addition of the long chain synthetic autoinducer molecule N-acyl homoserine lactone (AHL) of the quorum sensing pathway to the bioleaching reaction resulted in a significant enhancement of metal extraction from PCB. Factors such as: cell attachment to PCB, biofilm formation and hydrogen cyanide (HCN) production were regulated by the quorum sensing system and could be directly related to the improvement of metal bioleaching. Bioleaching reactions using bacterial quorum sensing modulation could represent a valuable tool in overcoming limitations at the industrial level imposed by microbiological traits that lead to inefficient metal bioleaching from e-waste.
format: application/pdf
format: text/html
creator: Juan Carlos Caicedo
creator: Sonia Villamizar
creator: Giampaolo Orlandoni
subject: Biochemistry
subject: Biotechnology
subject: Microbiology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.13801
publisher: PeerJ Inc.
rights: © 2022 Caicedo et al.
abstract: Metal solubilization from discarded electrical material and electronic devices (e-waste) using the bioleaching capabilities of bacterial cells is highly effective. However, gaps in understanding about the microbiological processes involved in the bioleaching reaction leads to less efficient metal solubilization in large-scale e-waste processing. In this study, bacterial species belonging to the genera Acidithiobacillus and Pseudomonas were used to leach copper and gold from discarded printed circuit boards (PCB). Through modulation of the cell-to-cell communication system in these bacteria, phenotypic traits directly involved in the bioleaching reaction were regulated in order to improve the metal solubilization. Addition of the long chain synthetic autoinducer molecule N-acyl homoserine lactone (AHL) of the quorum sensing pathway to the bioleaching reaction resulted in a significant enhancement of metal extraction from PCB. Factors such as: cell attachment to PCB, biofilm formation and hydrogen cyanide (HCN) production were regulated by the quorum sensing system and could be directly related to the improvement of metal bioleaching. Bioleaching reactions using bacterial quorum sensing modulation could represent a valuable tool in overcoming limitations at the industrial level imposed by microbiological traits that lead to inefficient metal bioleaching from e-waste.
bibliographic citation: Caicedo et al. (2022) The use of synthetic agonists of quorum sensing N- acyl homoserine lactone pathway improves the bioleaching ability in Acidithiobacillus and Pseudomonas bacteria. PeerJ 10:e13801 https://doi.org/10.7717/peerj.13801
date submitted: 2022-01-24
date accepted: 2022-07-06
issued: 2022-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caicedo
  given name: Juan Carlos
author list: Agent
  family name: Villamizar
  given name: Sonia
author list: Agent
  family name: Orlandoni
  given name: Giampaolo
doi: 10.7717/peerj.13801
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-09
copyright: ©2022 Caicedo et al.
attribution name: Caicedo et al.

Arbuscular mycorrhizal fungi enhanced the growth, phosphorus uptake and Pht expression of olive (Olea europaea L.) plantlets
type: item
type: AcademicArticle
description: Olive (Olea europaea L.) is a highly mycotrophic species that has been introduced and cultivated in China for half a century. The arbuscular mycorrhizal fungi (AMF) is extremely valuable as a kind of biofertilizer to promote the health and vigor of olive plants. However, it is still unclear how native AMF impact growth and mineral nutrients, especially phosphorus absorption in the area where olive trees were introduced in China. In the present study, through a pot experiment, the effects of native AMF on the growth, phosphorus uptake and expression levels of four phosphate transporter genes (Pht) of olive plantlets were characterized. We found that (1) typical AMF colonization was observed within the roots of inoculated olive plantlets, and the growth of plantlets was significantly promoted; (2) some indigenous consortia (AMF1 and AMF2) notably promoted the absorption of phosphorus, fertilizers significantly increased the foliar content of nitrogen, and both AMF inoculation and fertilization had no significant effect on the uptake of potassium; and (3) AMF inoculation enhanced the expression of phosphate transporter genes in inoculated olive roots. This work demonstrates the effectiveness of native AMF on the cultivation of robust olive plantlets and highlights the role of AMF in increasing phosphorus uptake. There is great potential in using native AMF consortia as inoculants for the production of healthy and robust olive plantlets.
format: application/pdf
format: text/html
creator: Tao Wu
creator: Li Pan
creator: Isaac Zipori
creator: Jihua Mao
creator: Rongbo Li
creator: Yongpeng Li
creator: Yongjie Li
creator: Yuebo Jing
creator: Haiyun Chen
subject: Agricultural Science
subject: Molecular Biology
subject: Mycology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13813
publisher: PeerJ Inc.
rights: © 2022 Wu et al.
abstract: Olive (Olea europaea L.) is a highly mycotrophic species that has been introduced and cultivated in China for half a century. The arbuscular mycorrhizal fungi (AMF) is extremely valuable as a kind of biofertilizer to promote the health and vigor of olive plants. However, it is still unclear how native AMF impact growth and mineral nutrients, especially phosphorus absorption in the area where olive trees were introduced in China. In the present study, through a pot experiment, the effects of native AMF on the growth, phosphorus uptake and expression levels of four phosphate transporter genes (Pht) of olive plantlets were characterized. We found that (1) typical AMF colonization was observed within the roots of inoculated olive plantlets, and the growth of plantlets was significantly promoted; (2) some indigenous consortia (AMF1 and AMF2) notably promoted the absorption of phosphorus, fertilizers significantly increased the foliar content of nitrogen, and both AMF inoculation and fertilization had no significant effect on the uptake of potassium; and (3) AMF inoculation enhanced the expression of phosphate transporter genes in inoculated olive roots. This work demonstrates the effectiveness of native AMF on the cultivation of robust olive plantlets and highlights the role of AMF in increasing phosphorus uptake. There is great potential in using native AMF consortia as inoculants for the production of healthy and robust olive plantlets.
bibliographic citation: Wu et al. (2022) Arbuscular mycorrhizal fungi enhanced the growth, phosphorus uptake and Pht expression of olive (Olea europaea L.) plantlets. PeerJ 10:e13813 https://doi.org/10.7717/peerj.13813
date submitted: 2022-02-21
date accepted: 2022-07-08
issued: 2022-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Tao
author list: Agent
  family name: Pan
  given name: Li
author list: Agent
  family name: Zipori
  given name: Isaac
author list: Agent
  family name: Mao
  given name: Jihua
author list: Agent
  family name: Li
  given name: Rongbo
author list: Agent
  family name: Li
  given name: Yongpeng
author list: Agent
  family name: Li
  given name: Yongjie
author list: Agent
  family name: Jing
  given name: Yuebo
author list: Agent
  family name: Chen
  given name: Haiyun
doi: 10.7717/peerj.13813
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-09
copyright: ©2022 Wu et al.
attribution name: Wu et al.

Association between lung function impairment with urinary heavy metals in a community in Klang Valley, Malaysia
type: item
type: AcademicArticle
description: Lung function status can be directly or indirectly affected by exposure to pollutants in the environment. Urinary heavy metals may be an indirect indicator of lung function impairment that leads to various diseases such as chronic obstructive pulmonary disease (COPD). This study aimed to explore the prevalence of lung function impairment as well as its association with urinary heavy metal levels and other influencing factors among the community in Klang Valley, Malaysia. Urinary sampling was done during various community events in the housing areas of Klang Valley between March and October 2019. Only respondents who consented would undergo a lung function test. Urine samples were obtained and sent for Inductively Coupled Plasma Mass Spectrometry (ICP-MS) analysis for heavy metal cadmium (Cd) and lead (Pb) concentration. Of the 200 recruited respondents, 52% were male and their ages ranged from 18 years old to 74 years old with a mean age of 38.4 ± 14.05 years. Urinary samples show high urinary Cd level in 12% of the respondents (n = 24) whereas none recorded a high urinary Pb level. There was a positive correlation between the levels of urinary Cd and urinary Pb (r = 0.303; p = 0.001). Furthermore, a negative correlation was detected between urinary Cd level and forced vital capacity (FVC) (r = − 0.202, p = 0.004), force expiratory volume at the first second (FEV1) (r = − 0.225, p = 0.001), and also force expiratory flow between 25–75% of FVC (FEF 25–75%) (r = − 0.187, p = 0.008). However, urinary Pb did not show any correlation with lung function parameters. Multiple linear regression analysis showed that urinary Cd had a significant negative effect on FVC (p = 0.025) and FEV1 (p = 0.004) based on the predicted value. Additionally, other factors such as education level (p = 0.013) also influenced lung function. However, no interaction was detected between heavy metals or other factors. In short, there was a significant negative linear relationship between urinary C…
format: application/pdf
format: text/html
creator: Ammar Amsyar Abdul Haddi
creator: Mohd Hasni Ja’afar
creator: Halim Ismail
subject: Public Health
subject: Respiratory Medicine
subject: Environmental Health
description: doi:10.7717/peerj.13845
publisher: PeerJ Inc.
rights: © 2022 Abdul Haddi et al.
abstract: Lung function status can be directly or indirectly affected by exposure to pollutants in the environment. Urinary heavy metals may be an indirect indicator of lung function impairment that leads to various diseases such as chronic obstructive pulmonary disease (COPD). This study aimed to explore the prevalence of lung function impairment as well as its association with urinary heavy metal levels and other influencing factors among the community in Klang Valley, Malaysia. Urinary sampling was done during various community events in the housing areas of Klang Valley between March and October 2019. Only respondents who consented would undergo a lung function test. Urine samples were obtained and sent for Inductively Coupled Plasma Mass Spectrometry (ICP-MS) analysis for heavy metal cadmium (Cd) and lead (Pb) concentration. Of the 200 recruited respondents, 52% were male and their ages ranged from 18 years old to 74 years old with a mean age of 38.4 ± 14.05 years. Urinary samples show high urinary Cd level in 12% of the respondents (n = 24) whereas none recorded a high urinary Pb level. There was a positive correlation between the levels of urinary Cd and urinary Pb (r = 0.303; p = 0.001). Furthermore, a negative correlation was detected between urinary Cd level and forced vital capacity (FVC) (r = − 0.202, p = 0.004), force expiratory volume at the first second (FEV1) (r = − 0.225, p = 0.001), and also force expiratory flow between 25–75% of FVC (FEF 25–75%) (r = − 0.187, p = 0.008). However, urinary Pb did not show any correlation with lung function parameters. Multiple linear regression analysis showed that urinary Cd had a significant negative effect on FVC (p = 0.025) and FEV1 (p = 0.004) based on the predicted value. Additionally, other factors such as education level (p = 0.013) also influenced lung function. However, no interaction was detected between heavy metals or other factors. In short, there was a significant negative linear relationship between urinary C…
bibliographic citation: Abdul Haddi et al. (2022) Association between lung function impairment with urinary heavy metals in a community in Klang Valley, Malaysia. PeerJ 10:e13845 https://doi.org/10.7717/peerj.13845
date submitted: 2022-03-25
date accepted: 2022-07-14
issued: 2022-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdul Haddi
  given name: Ammar Amsyar
author list: Agent
  family name: Ja’afar
  given name: Mohd Hasni
author list: Agent
  family name: Ismail
  given name: Halim
doi: 10.7717/peerj.13845
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-09
copyright: ©2022 Abdul Haddi et al.
attribution name: Abdul Haddi et al.

Application of plasma metabolome for monitoring the effect of rivaroxaban in patients with nonvalvular atrial fibrillation
type: item
type: AcademicArticle
description: Rivaroxaban, an oral factor Xa inhibitor, has been used to treating a series of thromboembolic disorders in clinical practice. Measurement of the anticoagulant effect of rivaroxaban is important to avoid serious bleeding events, thus ensuring the safety and efficacy of drug administration. Metabolomics could help to predict differences in the responses among patients by profiling metabolites in biosamples. In this study, plasma metabolomes before and 3 hours after rivaroxaban intake in 150 nonvalvular atrial fibrillation (NVAF) patients and 100 age/gender-matched controls were analyzed by liquid chromatography coupled with mass spectrometry (LC–MS/MS). When compared with controls, a total of thirteen plasma metabolites were differentially expressed in the NVAF patients. Pathway analysis revealed that purine and lipid metabolism were dysregulated. A panel of three metabolites (17a-ethynylestradiol, tryptophyl-glutamate and adenosine) showed good predictive ability to distinguish nonvalvular atrial fibrillation with an area under the receiver operating characteristic curve (AUC) of 1 for the discovery phase and 1 for validation. Under rivaroxaban treatment, a total of seven metabolites changed, the lipid and glycosylphosphatidylinositol biosynthesis pathways were altered and the panel consisting of avocadene, prenyl glucoside and phosphatidylethanolamine showed predictive ability with an AUC of 0.86 for the discovery dataset and 0.82 for the validation. The study showed that plasma metabolomic analyses hold the potential to differentiate nonvalvular atrial fibrillation and can help to monitor the effect of rivaroxaban anticoagulation.
format: application/pdf
format: text/html
creator: Mindi Zhao
creator: Xiaoyan Liu
creator: Xiaoxiao Bu
creator: Yao Li
creator: Meng Wang
creator: Bo Zhang
creator: Wei Sun
creator: Chuanbao Li
subject: Molecular Biology
subject: Cardiology
subject: Hematology
subject: Metabolic Sciences
description: doi:10.7717/peerj.13853
publisher: PeerJ Inc.
rights: © 2022 Zhao et al.
abstract: Rivaroxaban, an oral factor Xa inhibitor, has been used to treating a series of thromboembolic disorders in clinical practice. Measurement of the anticoagulant effect of rivaroxaban is important to avoid serious bleeding events, thus ensuring the safety and efficacy of drug administration. Metabolomics could help to predict differences in the responses among patients by profiling metabolites in biosamples. In this study, plasma metabolomes before and 3 hours after rivaroxaban intake in 150 nonvalvular atrial fibrillation (NVAF) patients and 100 age/gender-matched controls were analyzed by liquid chromatography coupled with mass spectrometry (LC–MS/MS). When compared with controls, a total of thirteen plasma metabolites were differentially expressed in the NVAF patients. Pathway analysis revealed that purine and lipid metabolism were dysregulated. A panel of three metabolites (17a-ethynylestradiol, tryptophyl-glutamate and adenosine) showed good predictive ability to distinguish nonvalvular atrial fibrillation with an area under the receiver operating characteristic curve (AUC) of 1 for the discovery phase and 1 for validation. Under rivaroxaban treatment, a total of seven metabolites changed, the lipid and glycosylphosphatidylinositol biosynthesis pathways were altered and the panel consisting of avocadene, prenyl glucoside and phosphatidylethanolamine showed predictive ability with an AUC of 0.86 for the discovery dataset and 0.82 for the validation. The study showed that plasma metabolomic analyses hold the potential to differentiate nonvalvular atrial fibrillation and can help to monitor the effect of rivaroxaban anticoagulation.
bibliographic citation: Zhao et al. (2022) Application of plasma metabolome for monitoring the effect of rivaroxaban in patients with nonvalvular atrial fibrillation. PeerJ 10:e13853 https://doi.org/10.7717/peerj.13853
date submitted: 2022-03-29
date accepted: 2022-07-16
issued: 2022-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Mindi
author list: Agent
  family name: Liu
  given name: Xiaoyan
author list: Agent
  family name: Bu
  given name: Xiaoxiao
author list: Agent
  family name: Li
  given name: Yao
author list: Agent
  family name: Wang
  given name: Meng
author list: Agent
  family name: Zhang
  given name: Bo
author list: Agent
  family name: Sun
  given name: Wei
author list: Agent
  family name: Li
  given name: Chuanbao
doi: 10.7717/peerj.13853
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-09
copyright: ©2022 Zhao et al.
attribution name: Zhao et al.

https://peerj.com/articles/13758
type: item
type: AcademicArticle
title: Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts
description: Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in …
format: application/pdf
format: text/html
creator: Min Hui
creator: Aiyang Wang
creator: Jiao Cheng
creator: Zhongli Sha
subject: Biodiversity
subject: Marine Biology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.13758
publisher: PeerJ Inc.
rights: © 2022 Hui et al.
abstract: Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in …
bibliographic citation: Hui et al. (2022) Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts. PeerJ 10:e13758 https://doi.org/10.7717/peerj.13758
date submitted: 2021-12-28
date accepted: 2022-06-29
issued: 2022-08-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hui
  given name: Min
author list: Agent
  family name: Wang
  given name: Aiyang
author list: Agent
  family name: Cheng
  given name: Jiao
author list: Agent
  family name: Sha
  given name: Zhongli
doi: 10.7717/peerj.13758
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-08
copyright: ©2022 Hui et al.
attribution name: Hui et al.

Early Miocene remains of Melissiodon from Mokrá-Quarry (Moravia, Czech Republic) shed light on the evolutionary history of the rare cricetid genus
type: item
type: AcademicArticle
description: Background Melissiodon is a rare cricetid genus endemic to Europe, known from the Early Oligoceneto the Early Miocene. It is usually a very rare find, and even in the few localities where Melissiodon remains are found, those are scarce and fragmentary. Only a few Central European localities have yielded rich remains of the genus. Currently, two species are known from the Early Miocene: Melissiodon schlosseri, which is based on two teeth from the MN2 German locality of Haslach and only found in two other sites of similar age (Ulm-Uniklinik and La Chaux, from Germany and Switzerland respectively); and Melissiodon dominans, found in MN3 and MN4 localities across Europe, even though the scarce and fragmentary remains make some of these attributions dubious. For that reason, Melissiodon dominans has become a catch-all species. However, Mokrá-Quarry represents one of the best documented findings of Melissiodon remains from MN4 localities of Europe. Methods The Melissiodon assemblage from Mokrá-Quarry has been studied thoroughly, providing metrics and detailed descriptions of all teeth positions, as well as complete comparisons with other MN3 and MN4 localities bearing Melissiodon remains. Results In this work, new remains of Melissiodon have been identified as a new morphotype that clearly differs from Melissiodon dominans by its unique m1 morphology but still shows some resemblance with Melissiodon schlosseri. Based on that, we here propose the hypothesis of an evolutionary lineage starting from Melissiodon schlosseri, diverging from the lineage leading towards Melissiodon dominans. With this finding, there are at least two different taxa of Melissiodon known during the Early Miocene, prior to the genus extinction. This study arises the certainty that the evolution history of the genus is more complex than previously thought and that more studies are necessary to elucidate it, including a complete revision of the type material of Melissiodon dominans and Melissiodon schl…
format: application/pdf
format: text/html
creator: Isaac Bonilla-Salomón
creator: Stanislav Čermák
creator: Àngel H. Luján
creator: Sílvia Jovells-Vaqué
creator: Martin Ivanov
creator: Martin Sabol
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13820
publisher: PeerJ Inc.
rights: © 2022 Bonilla-Salomón et al.
abstract: Background Melissiodon is a rare cricetid genus endemic to Europe, known from the Early Oligoceneto the Early Miocene. It is usually a very rare find, and even in the few localities where Melissiodon remains are found, those are scarce and fragmentary. Only a few Central European localities have yielded rich remains of the genus. Currently, two species are known from the Early Miocene: Melissiodon schlosseri, which is based on two teeth from the MN2 German locality of Haslach and only found in two other sites of similar age (Ulm-Uniklinik and La Chaux, from Germany and Switzerland respectively); and Melissiodon dominans, found in MN3 and MN4 localities across Europe, even though the scarce and fragmentary remains make some of these attributions dubious. For that reason, Melissiodon dominans has become a catch-all species. However, Mokrá-Quarry represents one of the best documented findings of Melissiodon remains from MN4 localities of Europe. Methods The Melissiodon assemblage from Mokrá-Quarry has been studied thoroughly, providing metrics and detailed descriptions of all teeth positions, as well as complete comparisons with other MN3 and MN4 localities bearing Melissiodon remains. Results In this work, new remains of Melissiodon have been identified as a new morphotype that clearly differs from Melissiodon dominans by its unique m1 morphology but still shows some resemblance with Melissiodon schlosseri. Based on that, we here propose the hypothesis of an evolutionary lineage starting from Melissiodon schlosseri, diverging from the lineage leading towards Melissiodon dominans. With this finding, there are at least two different taxa of Melissiodon known during the Early Miocene, prior to the genus extinction. This study arises the certainty that the evolution history of the genus is more complex than previously thought and that more studies are necessary to elucidate it, including a complete revision of the type material of Melissiodon dominans and Melissiodon schl…
bibliographic citation: Bonilla-Salomón et al. (2022) Early Miocene remains of Melissiodon from Mokrá-Quarry (Moravia, Czech Republic) shed light on the evolutionary history of the rare cricetid genus. PeerJ 10:e13820 https://doi.org/10.7717/peerj.13820
date submitted: 2022-02-16
date accepted: 2022-07-08
issued: 2022-08-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bonilla-Salomón
  given name: Isaac
author list: Agent
  family name: Čermák
  given name: Stanislav
author list: Agent
  family name: Luján
  given name: Àngel H.
author list: Agent
  family name: Jovells-Vaqué
  given name: Sílvia
author list: Agent
  family name: Ivanov
  given name: Martin
author list: Agent
  family name: Sabol
  given name: Martin
doi: 10.7717/peerj.13820
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-08
copyright: ©2022 Bonilla-Salomón et al.
attribution name: Bonilla-Salomón et al.

Development of a COVID-19 risk assessment model for participants at outdoor music festivals: evaluation of the validity and control measure effectiveness based on two actual events in Japan and Spain
type: item
type: AcademicArticle
description: We developed an environmental exposure model to estimate the coronavirus disease 2019 (COVID-19) risk among participants at outdoor music festivals and validated the model using two real events—one in Japan (Event 1) and one in Spain (Event 2). Furthermore, we considered a hypothetical situation in which Event 1 was held but enhanced measures were implemented to evaluate the extent to which the risk could be reduced by additional infection control measures, such as negative antigen tests on the day of the event, wearing of masks, disinfection of environmental surfaces, and vaccination. Among 7,392 participants, the total number of already- and newly-infected individuals who participated in Event 1 according to the new model was 47.0 (95% uncertainty interval: 12.5–185.5), which is in good agreement with the reported value (45). The risk of infection at Event 2 (1.98 × 10−2; 95% uncertainty interval: 0.55 × 10−2–6.39 × 10−2), calculated by the model in this study, was also similar to the estimated value in the previous epidemiological study (1.25 × 10−2). These results for the two events in different countries highlighted the validity of the model. Among the additional control measures in the hypothetical Event 1, vaccination, mask-wearing, and disinfection of surfaces were determined to be effective. Based on the combination of all measures, a 94% risk reduction could be achieved. In addition to setting a benchmark for an acceptable number of newly-infected individuals at the time of an event, the application of this model will enable us to determine whether it is necessary to implement additional measures, limit the number of participants, or refrain from holding an event.
format: application/pdf
format: text/html
creator: Michio Murakami
creator: Tsukasa Fujita
creator: Pinqi Li
creator: Seiya Imoto
creator: Tetsuo Yasutaka
subject: Epidemiology
subject: Infectious Diseases
subject: COVID-19
description: doi:10.7717/peerj.13846
publisher: PeerJ Inc.
rights: © 2022 Murakami et al.
abstract: We developed an environmental exposure model to estimate the coronavirus disease 2019 (COVID-19) risk among participants at outdoor music festivals and validated the model using two real events—one in Japan (Event 1) and one in Spain (Event 2). Furthermore, we considered a hypothetical situation in which Event 1 was held but enhanced measures were implemented to evaluate the extent to which the risk could be reduced by additional infection control measures, such as negative antigen tests on the day of the event, wearing of masks, disinfection of environmental surfaces, and vaccination. Among 7,392 participants, the total number of already- and newly-infected individuals who participated in Event 1 according to the new model was 47.0 (95% uncertainty interval: 12.5–185.5), which is in good agreement with the reported value (45). The risk of infection at Event 2 (1.98 × 10−2; 95% uncertainty interval: 0.55 × 10−2–6.39 × 10−2), calculated by the model in this study, was also similar to the estimated value in the previous epidemiological study (1.25 × 10−2). These results for the two events in different countries highlighted the validity of the model. Among the additional control measures in the hypothetical Event 1, vaccination, mask-wearing, and disinfection of surfaces were determined to be effective. Based on the combination of all measures, a 94% risk reduction could be achieved. In addition to setting a benchmark for an acceptable number of newly-infected individuals at the time of an event, the application of this model will enable us to determine whether it is necessary to implement additional measures, limit the number of participants, or refrain from holding an event.
bibliographic citation: Murakami et al. (2022) Development of a COVID-19 risk assessment model for participants at outdoor music festivals: evaluation of the validity and control measure effectiveness based on two actual events in Japan and Spain. PeerJ 10:e13846 https://doi.org/10.7717/peerj.13846
date submitted: 2022-03-30
date accepted: 2022-07-14
issued: 2022-08-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murakami
  given name: Michio
author list: Agent
  family name: Fujita
  given name: Tsukasa
author list: Agent
  family name: Li
  given name: Pinqi
author list: Agent
  family name: Imoto
  given name: Seiya
author list: Agent
  family name: Yasutaka
  given name: Tetsuo
doi: 10.7717/peerj.13846
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-08
copyright: ©2022 Murakami et al.
attribution name: Murakami et al.

One step further in biomechanical models in palaeontology: a nonlinear finite element analysis review
type: item
type: AcademicArticle
description: Finite element analysis (FEA) is no longer a new technique in the fields of palaeontology, anthropology, and evolutionary biology. It is nowadays a well-established technique within the virtual functional-morphology toolkit. However, almost all the works published in these fields have only applied the most basic FEA tools i.e., linear materials in static structural problems. Linear and static approximations are commonly used because they are computationally less expensive, and the error associated with these assumptions can be accepted. Nonetheless, nonlinearities are natural to be used in biomechanical models especially when modelling soft tissues, establish contacts between separated bones or the inclusion of buckling results. The aim of this review is to, firstly, highlight the usefulness of non-linearities and secondly, showcase these FEA tool to researchers that work in functional morphology and biomechanics, as non-linearities can improve their FEA models by widening the possible applications and topics that currently are not used in palaeontology and anthropology.
format: application/pdf
format: text/html
creator: Jordi Marcé-Nogué
subject: Anthropology
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
subject: Biomechanics
description: doi:10.7717/peerj.13890
publisher: PeerJ Inc.
rights: © 2022 Marcé-Nogué
abstract: Finite element analysis (FEA) is no longer a new technique in the fields of palaeontology, anthropology, and evolutionary biology. It is nowadays a well-established technique within the virtual functional-morphology toolkit. However, almost all the works published in these fields have only applied the most basic FEA tools i.e., linear materials in static structural problems. Linear and static approximations are commonly used because they are computationally less expensive, and the error associated with these assumptions can be accepted. Nonetheless, nonlinearities are natural to be used in biomechanical models especially when modelling soft tissues, establish contacts between separated bones or the inclusion of buckling results. The aim of this review is to, firstly, highlight the usefulness of non-linearities and secondly, showcase these FEA tool to researchers that work in functional morphology and biomechanics, as non-linearities can improve their FEA models by widening the possible applications and topics that currently are not used in palaeontology and anthropology.
bibliographic citation: Marcé-Nogué (2022) One step further in biomechanical models in palaeontology: a nonlinear finite element analysis review. PeerJ 10:e13890 https://doi.org/10.7717/peerj.13890
date submitted: 2022-05-13
date accepted: 2022-07-21
issued: 2022-08-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marcé-Nogué
  given name: Jordi
doi: 10.7717/peerj.13890
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-08
copyright: © 2022 Marcé-Nogué
attribution name: Marcé-Nogué

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