PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19
items: A quantitative test of the “Ecomorphotype Hypothesis” for fossil true seals (Family Phocidae)
items: The role of monocyte chemoattractant protein-1 (MCP-1) as an immunological marker for patients with leprosy: a systematic literature review
items: Bioinformatic analysis and experimental validation of six cuproptosis-associated genes as a prognostic signature of breast cancer
items: Serum proteomics study on cognitive impairment after cardiac valve replacement surgery: a prospective observational study
items: Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato
items: Identification of key genes as potential diagnostic biomarkers in sepsis by bioinformatics analysis
items: Behavioral responses of a clonal fish to perceived predation risk
items: Knowledge, attitudes, and practices (KAPs) regarding tick-borne rickettsial disease among medical staff in endemic areas of China
items: Hypertrophic effects of low-load blood flow restriction training with different repetition schemes: a systematic review and meta-analysis

VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19
type: item
type: AcademicArticle
description: Background The development of serodiagnostic tests and vaccines for COVID-19 depends on the identification of epitopes from the SARS-CoV-2 genome. An epitope is the specific part of an antigen that is recognized by the immune system and can elicit an immune response. However, when the genetic variants contained in epitopes are used to develop rapid antigen tests (Ag-RDTs) and DNA or RNA vaccines, test sensitivity and vaccine efficacy can be low. Methods Here, we developed a “variant on epitope (VOE)” software, a new Python script for identifying variants located on an epitope. Variant analysis and sensitivity calculation for seven recommended epitopes were processed by VOE. Variants in 1,011 Omicron SRA reads from two variant databases (BCFtools and SARS-CoV-2-Freebayes) were processed by VOE. Results A variant with HIGH or MODERATE impact was found on all epitopes from both variant databases except the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK on the S gene and ORF7a gene. All epitope variants from the BCFtools and SARS-CoV-2 Freebayes variant databases showed about 100% sensitivity except epitopes APGQTGK and DSKVGGNYN on the S gene, which showed respective sensitivities of 28.4866% and 6.8249%, and 87.7349% and 71.1177%. Conclusions Therefore, the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK may be useful for the development of an epitope-based peptide vaccine and GGDGKMKD on the N gene may be useful for the development of serodiagnostic tests. Moreover, VOE can also be used to analyze other epitopes, and a new variant database for VOE may be further established when a new variant of SARS-CoV-2 emerges.
format: application/pdf
format: text/html
creator: Danusorn Lee
creator: Unitsa Sangket
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: COVID-19
description: doi:10.7717/peerj.17504
publisher: PeerJ Inc.
rights: © 2024 Lee and Sangket
abstract: Background The development of serodiagnostic tests and vaccines for COVID-19 depends on the identification of epitopes from the SARS-CoV-2 genome. An epitope is the specific part of an antigen that is recognized by the immune system and can elicit an immune response. However, when the genetic variants contained in epitopes are used to develop rapid antigen tests (Ag-RDTs) and DNA or RNA vaccines, test sensitivity and vaccine efficacy can be low. Methods Here, we developed a “variant on epitope (VOE)” software, a new Python script for identifying variants located on an epitope. Variant analysis and sensitivity calculation for seven recommended epitopes were processed by VOE. Variants in 1,011 Omicron SRA reads from two variant databases (BCFtools and SARS-CoV-2-Freebayes) were processed by VOE. Results A variant with HIGH or MODERATE impact was found on all epitopes from both variant databases except the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK on the S gene and ORF7a gene. All epitope variants from the BCFtools and SARS-CoV-2 Freebayes variant databases showed about 100% sensitivity except epitopes APGQTGK and DSKVGGNYN on the S gene, which showed respective sensitivities of 28.4866% and 6.8249%, and 87.7349% and 71.1177%. Conclusions Therefore, the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK may be useful for the development of an epitope-based peptide vaccine and GGDGKMKD on the N gene may be useful for the development of serodiagnostic tests. Moreover, VOE can also be used to analyze other epitopes, and a new variant database for VOE may be further established when a new variant of SARS-CoV-2 emerges.
bibliographic citation: Lee et al. (2024) VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19. PeerJ 12:e17504 https://doi.org/10.7717/peerj.17504
date submitted: 2024-01-22
date accepted: 2024-05-13
issued: 2024-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Danusorn
author list: Agent
  family name: Sangket
  given name: Unitsa
doi: 10.7717/peerj.17504
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-19
copyright: ©2024 Lee and Sangket
attribution name: Lee and Sangket

A quantitative test of the “Ecomorphotype Hypothesis” for fossil true seals (Family Phocidae)
type: item
type: AcademicArticle
description: The fossil record of true seals (Family Phocidae) is mostly made up of isolated bones, some of which are type specimens. Previous studies have sought to increase referral of non-overlapping and unrelated fossils to these taxa using the ‘Ecomorphotype Hypothesis’, which stipulates that certain differences in morphology between taxa represent adaptations to differing ecology. On this basis, bulk fossil material could be lumped to a specific ecomorphotype, and then referred to species in that ecomorphotype, even if they are different bones. This qualitative and subjective method has been used often to expand the taxonomy of fossil phocids, but has never been quantitatively tested. We test the proposed ecomorphotypes using morphometric analysis of fossil and extant northern true seal limb bones, specifically principal components analysis and discriminant function analysis. A large amount of morphological overlap between ecomorphotypes, and poor discrimination between them, suggests that the ‘Ecomorphotype Hypothesis’ is not a valid approach. Further, the analysis failed to assign fossils to ecomorphotypes designated in previous studies, with some fossils from the same taxa being designated as different ecomorphotypes. The failure of this approach suggests that all fossils referred using this method should be considered to have unknown taxonomic status. In light of this, and previous findings that phocid limb bones have limited utility as type specimens, we revise the status of named fossil phocid species. We conclude that the majority of named fossil phocid taxa should be considered nomina dubia.
format: application/pdf
format: text/html
creator: James Patrick Rule
creator: Gustavo Burin
creator: Travis Park
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.17592
publisher: PeerJ Inc.
rights: © 2024 Rule et al.
abstract: The fossil record of true seals (Family Phocidae) is mostly made up of isolated bones, some of which are type specimens. Previous studies have sought to increase referral of non-overlapping and unrelated fossils to these taxa using the ‘Ecomorphotype Hypothesis’, which stipulates that certain differences in morphology between taxa represent adaptations to differing ecology. On this basis, bulk fossil material could be lumped to a specific ecomorphotype, and then referred to species in that ecomorphotype, even if they are different bones. This qualitative and subjective method has been used often to expand the taxonomy of fossil phocids, but has never been quantitatively tested. We test the proposed ecomorphotypes using morphometric analysis of fossil and extant northern true seal limb bones, specifically principal components analysis and discriminant function analysis. A large amount of morphological overlap between ecomorphotypes, and poor discrimination between them, suggests that the ‘Ecomorphotype Hypothesis’ is not a valid approach. Further, the analysis failed to assign fossils to ecomorphotypes designated in previous studies, with some fossils from the same taxa being designated as different ecomorphotypes. The failure of this approach suggests that all fossils referred using this method should be considered to have unknown taxonomic status. In light of this, and previous findings that phocid limb bones have limited utility as type specimens, we revise the status of named fossil phocid species. We conclude that the majority of named fossil phocid taxa should be considered nomina dubia.
bibliographic citation: Rule et al. (2024) A quantitative test of the “Ecomorphotype Hypothesis” for fossil true seals (Family Phocidae). PeerJ 12:e17592 https://doi.org/10.7717/peerj.17592
date submitted: 2024-01-26
date accepted: 2024-05-28
issued: 2024-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rule
  given name: James Patrick
author list: Agent
  family name: Burin
  given name: Gustavo
author list: Agent
  family name: Park
  given name: Travis
doi: 10.7717/peerj.17592
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-19
copyright: © 2024 Rule et al.
attribution name: Rule et al.

The role of monocyte chemoattractant protein-1 (MCP-1) as an immunological marker for patients with leprosy: a systematic literature review
type: item
type: AcademicArticle
description: Leprosy, a significant global health concern affecting primarily the peripheral nerves and integumentary system, is influenced by the host immune system’s response, affecting its pathology, disease progression, and reaction occurrence. MCP-1, integral to leprosy’s immunological processes, holds promise as a diagnostic tool and predictor of reaction occurrence. This systematic review aimed to investigate MCP-1’s involvement in leprosy. Literature search, employing specified MeSH keywords, covered databases such as PubMed, Scopus, ScienceDirect, and Wiley Online Library until September 30th, 2023, yielding seventeen relevant studies. Assessing each study’s quality with the Newcastle-Ottawa Scale (NOS) and investigating bias using the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS), a narrative synthesis compiled findings. Seventeen distinct studies were included, each characterized by diverse designs, sample sizes, demographics, and outcome measures, highlighting MCP-1’s potential in diagnosing leprosy, differentiating it from control groups, and discerning leprosy types. Furthermore, MCP-1 shows promise in predicting leprosy reversal reactions. Although MCP-1 offers clinical benefits, including early diagnosis and type differentiation, further research with larger sample sizes and standardized methodologies is imperative to confirm its diagnostic utility fully.
format: application/pdf
format: text/html
creator: Flora Ramona Sigit Prakoeswa
creator: Ellen Josephine Handoko
creator: Erika Diana Risanti
creator: Nabila Haningtyas
creator: Nasrurrofiq Risvana Bayu Pambudi
creator: Muhana Fawwazy Ilyas
subject: Dermatology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.17400
publisher: PeerJ Inc.
rights: © 2024 Prakoeswa et al.
abstract: Leprosy, a significant global health concern affecting primarily the peripheral nerves and integumentary system, is influenced by the host immune system’s response, affecting its pathology, disease progression, and reaction occurrence. MCP-1, integral to leprosy’s immunological processes, holds promise as a diagnostic tool and predictor of reaction occurrence. This systematic review aimed to investigate MCP-1’s involvement in leprosy. Literature search, employing specified MeSH keywords, covered databases such as PubMed, Scopus, ScienceDirect, and Wiley Online Library until September 30th, 2023, yielding seventeen relevant studies. Assessing each study’s quality with the Newcastle-Ottawa Scale (NOS) and investigating bias using the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS), a narrative synthesis compiled findings. Seventeen distinct studies were included, each characterized by diverse designs, sample sizes, demographics, and outcome measures, highlighting MCP-1’s potential in diagnosing leprosy, differentiating it from control groups, and discerning leprosy types. Furthermore, MCP-1 shows promise in predicting leprosy reversal reactions. Although MCP-1 offers clinical benefits, including early diagnosis and type differentiation, further research with larger sample sizes and standardized methodologies is imperative to confirm its diagnostic utility fully.
bibliographic citation: Prakoeswa et al. (2024) The role of monocyte chemoattractant protein-1 (MCP-1) as an immunological marker for patients with leprosy: a systematic literature review. PeerJ 12:e17400 https://doi.org/10.7717/peerj.17400
date submitted: 2023-12-13
date accepted: 2024-04-25
issued: 2024-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prakoeswa
  given name: Flora Ramona Sigit
author list: Agent
  family name: Handoko
  given name: Ellen Josephine
author list: Agent
  family name: Risanti
  given name: Erika Diana
author list: Agent
  family name: Haningtyas
  given name: Nabila
author list: Agent
  family name: Pambudi
  given name: Nasrurrofiq Risvana Bayu
author list: Agent
  family name: Ilyas
  given name: Muhana Fawwazy
doi: 10.7717/peerj.17400
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-18
copyright: ©2024 Prakoeswa et al.
attribution name: Prakoeswa et al.

Bioinformatic analysis and experimental validation of six cuproptosis-associated genes as a prognostic signature of breast cancer
type: item
type: AcademicArticle
description: Background Breast carcinoma (BRCA) is a life-threatening malignancy in women and shows a poor prognosis. Cuproptosis is a novel mode of cell death but its relationship with BRCA is unclear. This study attempted to develop a cuproptosis-relevant prognostic gene signature for BRCA. Methods Cuproptosis-relevant subtypes of BRCA were obtained by consensus clustering. Differential expression analysis was implemented using the ‘limma’ package. Univariate Cox and multivariate Cox analyses were performed to determine a cuproptosis-relevant prognostic gene signature. The signature was constructed and validated in distinct datasets. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were also conducted using the prognostic signature to uncover the underlying molecular mechanisms. ESTIMATE and CIBERSORT algorithms were applied to probe the linkage between the gene signature and tumor microenvironment (TME). Immunotherapy responsiveness was assessed using the Tumor Immune Dysfunction and Exclusion (TIDE) web tool. Real-time quantitative PCR (RT-qPCR) was performed to detect the expressions of cuproptosis-relevant prognostic genes in breast cancer cell lines. Results Thirty-eight cuproptosis-associated differentially expressed genes (DEGs) in BRCA were mined by consensus clustering and differential expression analysis. Based on univariate Cox and multivariate Cox analyses, six cuproptosis-relevant prognostic genes, namely SAA1, KRT17, VAV3, IGHG1, TFF1, and CLEC3A, were mined to establish a corresponding signature. The signature was validated using external validation sets. GSVA and GSEA showed that multiple cell cycle-linked and immune-related pathways along with biological processes were associated with the signature. The results ESTIMATE and CIBERSORT analyses revealed significantly different TMEs between the two Cusig score subgroups. Finally, RT-qPCR analysis of cell lines further confirmed the expressional trends of SAA1, KRT17, IGHG1, and CLEC3A. C…
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format: text/html
creator: Xiang Chen
creator: Hening Sun
creator: Changcheng Yang
creator: Wei Wang
creator: Wenzhi Lyu
creator: Kejian Zou
creator: Fan Zhang
creator: Zhijun Dai
creator: Xionghui He
creator: Huaying Dong
subject: Bioinformatics
subject: Genetics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.17419
publisher: PeerJ Inc.
rights: © 2024 Chen et al.
abstract: Background Breast carcinoma (BRCA) is a life-threatening malignancy in women and shows a poor prognosis. Cuproptosis is a novel mode of cell death but its relationship with BRCA is unclear. This study attempted to develop a cuproptosis-relevant prognostic gene signature for BRCA. Methods Cuproptosis-relevant subtypes of BRCA were obtained by consensus clustering. Differential expression analysis was implemented using the ‘limma’ package. Univariate Cox and multivariate Cox analyses were performed to determine a cuproptosis-relevant prognostic gene signature. The signature was constructed and validated in distinct datasets. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were also conducted using the prognostic signature to uncover the underlying molecular mechanisms. ESTIMATE and CIBERSORT algorithms were applied to probe the linkage between the gene signature and tumor microenvironment (TME). Immunotherapy responsiveness was assessed using the Tumor Immune Dysfunction and Exclusion (TIDE) web tool. Real-time quantitative PCR (RT-qPCR) was performed to detect the expressions of cuproptosis-relevant prognostic genes in breast cancer cell lines. Results Thirty-eight cuproptosis-associated differentially expressed genes (DEGs) in BRCA were mined by consensus clustering and differential expression analysis. Based on univariate Cox and multivariate Cox analyses, six cuproptosis-relevant prognostic genes, namely SAA1, KRT17, VAV3, IGHG1, TFF1, and CLEC3A, were mined to establish a corresponding signature. The signature was validated using external validation sets. GSVA and GSEA showed that multiple cell cycle-linked and immune-related pathways along with biological processes were associated with the signature. The results ESTIMATE and CIBERSORT analyses revealed significantly different TMEs between the two Cusig score subgroups. Finally, RT-qPCR analysis of cell lines further confirmed the expressional trends of SAA1, KRT17, IGHG1, and CLEC3A. C…
bibliographic citation: Chen et al. (2024) Bioinformatic analysis and experimental validation of six cuproptosis-associated genes as a prognostic signature of breast cancer. PeerJ 12:e17419 https://doi.org/10.7717/peerj.17419
date submitted: 2023-10-10
date accepted: 2024-04-28
issued: 2024-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Chen
  given name: Xiang
author list: Agent
  family name: Sun
  given name: Hening
author list: Agent
  family name: Yang
  given name: Changcheng
author list: Agent
  family name: Wang
  given name: Wei
author list: Agent
  family name: Lyu
  given name: Wenzhi
author list: Agent
  family name: Zou
  given name: Kejian
author list: Agent
  family name: Zhang
  given name: Fan
author list: Agent
  family name: Dai
  given name: Zhijun
author list: Agent
  family name: He
  given name: Xionghui
author list: Agent
  family name: Dong
  given name: Huaying
doi: 10.7717/peerj.17419
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-18
copyright: © 2024 Chen et al.
attribution name: Chen et al.

Serum proteomics study on cognitive impairment after cardiac valve replacement surgery: a prospective observational study
type: item
type: AcademicArticle
description: Objective The incidence of perioperative neurocognitive disorders (PND) is high, especially after cardiac surgeries, and the underlying mechanisms remain elusive. Here, we conducted a prospective observational study to observe serum proteomics differences in PND patients after cardiac valve replacement surgery. Methods Two hundred and twenty-six patients who underwent cardiac valve surgery were included. They were categorized based on scoring into non-PND group (group non-P) and PND group (group P’). The risk factors associated with PND were analyzed. These patients were further divided into group C and group P by propensity score matching (PSM) to investigate the serum proteome related to the PND by serum proteomics. Results The postoperative 6-week incidence of PND was 16.8%. Risk factors for PND include age, chronic illness, sufentanil dosage, and time of cardiopulmonary bypass (CPB). Proteomics identified 31 down-regulated proteins and six up-regulated proteins. Finally, GSTO1, IDH1, CAT, and PFN1 were found to be associated with PND. Conclusion The occurrence of PND can impact some oxidative stress proteins. This study provided data for future studies about PND to general anaesthesia and surgeries.
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creator: Huanhuan Ma
creator: Yiyong Wei
creator: Wei Chen
creator: Song Chen
creator: Yan Wang
creator: Song Cao
creator: Haiying Wang
subject: Anesthesiology and Pain Management
subject: Cardiology
subject: Cognitive Disorders
subject: Neurology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.17536
publisher: PeerJ Inc.
rights: © 2024 Ma et al.
abstract: Objective The incidence of perioperative neurocognitive disorders (PND) is high, especially after cardiac surgeries, and the underlying mechanisms remain elusive. Here, we conducted a prospective observational study to observe serum proteomics differences in PND patients after cardiac valve replacement surgery. Methods Two hundred and twenty-six patients who underwent cardiac valve surgery were included. They were categorized based on scoring into non-PND group (group non-P) and PND group (group P’). The risk factors associated with PND were analyzed. These patients were further divided into group C and group P by propensity score matching (PSM) to investigate the serum proteome related to the PND by serum proteomics. Results The postoperative 6-week incidence of PND was 16.8%. Risk factors for PND include age, chronic illness, sufentanil dosage, and time of cardiopulmonary bypass (CPB). Proteomics identified 31 down-regulated proteins and six up-regulated proteins. Finally, GSTO1, IDH1, CAT, and PFN1 were found to be associated with PND. Conclusion The occurrence of PND can impact some oxidative stress proteins. This study provided data for future studies about PND to general anaesthesia and surgeries.
bibliographic citation: Ma et al. (2024) Serum proteomics study on cognitive impairment after cardiac valve replacement surgery: a prospective observational study. PeerJ 12:e17536 https://doi.org/10.7717/peerj.17536
date submitted: 2024-02-02
date accepted: 2024-05-18
issued: 2024-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Huanhuan
author list: Agent
  family name: Wei
  given name: Yiyong
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: Chen
  given name: Song
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Cao
  given name: Song
author list: Agent
  family name: Wang
  given name: Haiying
doi: 10.7717/peerj.17536
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-18
copyright: ©2024 Ma et al.
attribution name: Ma et al.

Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato
type: item
type: AcademicArticle
description: The domain of unknown function 668 (DUF668) is a gene family that may play a key role in plant growth and development as well as in responding to adversity coercion stresses. However, the DUF668 gene family has not yet been well identified and characterized in tomato. In this study, a total of nine putative SlDUF668 genes were identified in tomato, distributed on six chromosomes. Phylogenetic analyses revealed that SlDUF668 proteins were classified into two major groups. Members within the same group largely displayed analogous gene structure and conserved motif compositions. Several cis-elements were exhibited in the upstream sequences of the SlDUF668 genes, including elements implicated in plant growth and development processes, abiotic stress and hormone responses. Further, the study assessed the expression patterns of the SlDUF668 gene family in various tomato tissues, five plant hormones treatments, three abiotic stresses using qRT-PCR. The SlDUF668 genes expressed ubiquitously in various tissues, and five genes (SlDUF668-04, SlDUF668-06, SlDUF668-07, SlDUF668-08 and SlDUF668-09) showed tissue specificity. And SlDUF668 genes responded to abiotic stresses such as salt, drought and cold to varying degrees. Overall, our study provided a base for the tomato DUF668 gene family and laid a foundation for further understanding the functional characteristics of DUF668 genes in tomato plants.
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creator: Hui Li
creator: Tingrui Zou
creator: Shuisen Chen
creator: Ming Zhong
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.17537
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: The domain of unknown function 668 (DUF668) is a gene family that may play a key role in plant growth and development as well as in responding to adversity coercion stresses. However, the DUF668 gene family has not yet been well identified and characterized in tomato. In this study, a total of nine putative SlDUF668 genes were identified in tomato, distributed on six chromosomes. Phylogenetic analyses revealed that SlDUF668 proteins were classified into two major groups. Members within the same group largely displayed analogous gene structure and conserved motif compositions. Several cis-elements were exhibited in the upstream sequences of the SlDUF668 genes, including elements implicated in plant growth and development processes, abiotic stress and hormone responses. Further, the study assessed the expression patterns of the SlDUF668 gene family in various tomato tissues, five plant hormones treatments, three abiotic stresses using qRT-PCR. The SlDUF668 genes expressed ubiquitously in various tissues, and five genes (SlDUF668-04, SlDUF668-06, SlDUF668-07, SlDUF668-08 and SlDUF668-09) showed tissue specificity. And SlDUF668 genes responded to abiotic stresses such as salt, drought and cold to varying degrees. Overall, our study provided a base for the tomato DUF668 gene family and laid a foundation for further understanding the functional characteristics of DUF668 genes in tomato plants.
bibliographic citation: Li et al. (2024) Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato. PeerJ 12:e17537 https://doi.org/10.7717/peerj.17537
date submitted: 2023-12-29
date accepted: 2024-05-19
issued: 2024-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Hui
author list: Agent
  family name: Zou
  given name: Tingrui
author list: Agent
  family name: Chen
  given name: Shuisen
author list: Agent
  family name: Zhong
  given name: Ming
doi: 10.7717/peerj.17537
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-18
copyright: ©2024 Li et al.
attribution name: Li et al.

Identification of key genes as potential diagnostic biomarkers in sepsis by bioinformatics analysis
type: item
type: AcademicArticle
description: Background Sepsis, an infection-triggered inflammatory syndrome, poses a global clinical challenge with limited therapeutic options. Our study is designed to identify potential diagnostic biomarkers of sepsis onset in critically ill patients by bioinformatics analysis. Methods Gene expression profiles of GSE28750 and GSE74224 were obtained from the Gene Expression Omnibus (GEO) database. These datasets were merged, normalized and de-batched. Weighted gene co-expression network analysis (WGCNA) was performed and the gene modules most associated with sepsis were identified as key modules. Functional enrichment analysis of the key module genes was then conducted. Moreover, differentially expressed gene (DEG) analysis was conducted by the “limma” R package. Protein-protein interaction (PPI) network was created using STRING and Cytoscape, and PPI hub genes were identified with the cytoHubba plugin. The PPI hub genes overlapping with the genes in key modules of WGCNA were determined to be the sepsis-related key genes. Subsequently, the key overlapping genes were validated in an external independent dataset and sepsis patients recruited in our hospital. In addition, CIBERSORT analysis evaluated immune cell infiltration and its correlation with key genes. Results By WGCNA, the greenyellow module showed the highest positive correlation with sepsis (0.7, p = 2e − 19). 293 DEGs were identified in the merged datasets. The PPI network was created, and the CytoHubba was used to calculate the top 20 genes based on four algorithms (Degree, EPC, MCC, and MNC). Ultimately, LTF, LCN2, ELANE, MPO and CEACAM8 were identified as key overlapping genes as they appeared in the PPI hub genes and the key module genes of WGCNA. These sepsis-related key genes were validated in an independent external dataset (GSE131761) and sepsis patients recruited in our hospital. Additionally, the immune infiltration profiles differed significantly between sepsis and non-sepsis critical illness groups. Corre…
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creator: Guoxin Lin
creator: Nannan Li
creator: Jishi Liu
creator: Jian Sun
creator: Hao Zhang
creator: Ming Gui
creator: Youjie Zeng
creator: Juan Tang
subject: Bioinformatics
subject: Molecular Biology
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17542
publisher: PeerJ Inc.
rights: © 2024 Lin et al.
abstract: Background Sepsis, an infection-triggered inflammatory syndrome, poses a global clinical challenge with limited therapeutic options. Our study is designed to identify potential diagnostic biomarkers of sepsis onset in critically ill patients by bioinformatics analysis. Methods Gene expression profiles of GSE28750 and GSE74224 were obtained from the Gene Expression Omnibus (GEO) database. These datasets were merged, normalized and de-batched. Weighted gene co-expression network analysis (WGCNA) was performed and the gene modules most associated with sepsis were identified as key modules. Functional enrichment analysis of the key module genes was then conducted. Moreover, differentially expressed gene (DEG) analysis was conducted by the “limma” R package. Protein-protein interaction (PPI) network was created using STRING and Cytoscape, and PPI hub genes were identified with the cytoHubba plugin. The PPI hub genes overlapping with the genes in key modules of WGCNA were determined to be the sepsis-related key genes. Subsequently, the key overlapping genes were validated in an external independent dataset and sepsis patients recruited in our hospital. In addition, CIBERSORT analysis evaluated immune cell infiltration and its correlation with key genes. Results By WGCNA, the greenyellow module showed the highest positive correlation with sepsis (0.7, p = 2e − 19). 293 DEGs were identified in the merged datasets. The PPI network was created, and the CytoHubba was used to calculate the top 20 genes based on four algorithms (Degree, EPC, MCC, and MNC). Ultimately, LTF, LCN2, ELANE, MPO and CEACAM8 were identified as key overlapping genes as they appeared in the PPI hub genes and the key module genes of WGCNA. These sepsis-related key genes were validated in an independent external dataset (GSE131761) and sepsis patients recruited in our hospital. Additionally, the immune infiltration profiles differed significantly between sepsis and non-sepsis critical illness groups. Corre…
bibliographic citation: Lin et al. (2024) Identification of key genes as potential diagnostic biomarkers in sepsis by bioinformatics analysis. PeerJ 12:e17542 https://doi.org/10.7717/peerj.17542
date submitted: 2023-07-27
date accepted: 2024-05-19
issued: 2024-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Guoxin
author list: Agent
  family name: Li
  given name: Nannan
author list: Agent
  family name: Liu
  given name: Jishi
author list: Agent
  family name: Sun
  given name: Jian
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Gui
  given name: Ming
author list: Agent
  family name: Zeng
  given name: Youjie
author list: Agent
  family name: Tang
  given name: Juan
doi: 10.7717/peerj.17542
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-18
copyright: ©2024 Lin et al.
attribution name: Lin et al.

Behavioral responses of a clonal fish to perceived predation risk
type: item
type: AcademicArticle
description: Predation threat is a major driver of behavior in many prey species. Animals can recognize their relative risk of predation based on cues in the environment, including visual and/or chemical cues released by a predator or from its prey. When threat of predation is high, prey often respond by altering their behavior to reduce their probability of detection and/or capture. Here, we test how a clonal fish, the Amazon molly (Poecilia formosa), behaviorally responds to predation cues. We measured aggressive and social behaviors both under ‘risk’, where chemical cues from predatory fish and injured conspecifics were present, and control contexts (no risk cues present). We predicted that mollies would exhibit reduced aggression towards a simulated intruder and increased sociability under risk contexts as aggression might increase their visibility to a predator and shoaling should decrease their chance of capture through the dilution effect. As predicted, we found that Amazon mollies spent more time with a conspecific when risk cues were present, however they did not reduce their aggression. This highlights the general result of the ‘safety in numbers’ behavioral response that many small shoaling species exhibit, including these clonal fish, which suggests that mollies may view this response as a more effective anti-predator response compared to limiting their detectability by reducing aggressive conspecific interactions.
format: application/pdf
format: text/html
creator: Jonathan Aguiñaga
creator: Sophia Jin
creator: Ishita Pesati
creator: Kate L. Laskowski
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.17547
publisher: PeerJ Inc.
rights: © 2024 Aguiñaga et al.
abstract: Predation threat is a major driver of behavior in many prey species. Animals can recognize their relative risk of predation based on cues in the environment, including visual and/or chemical cues released by a predator or from its prey. When threat of predation is high, prey often respond by altering their behavior to reduce their probability of detection and/or capture. Here, we test how a clonal fish, the Amazon molly (Poecilia formosa), behaviorally responds to predation cues. We measured aggressive and social behaviors both under ‘risk’, where chemical cues from predatory fish and injured conspecifics were present, and control contexts (no risk cues present). We predicted that mollies would exhibit reduced aggression towards a simulated intruder and increased sociability under risk contexts as aggression might increase their visibility to a predator and shoaling should decrease their chance of capture through the dilution effect. As predicted, we found that Amazon mollies spent more time with a conspecific when risk cues were present, however they did not reduce their aggression. This highlights the general result of the ‘safety in numbers’ behavioral response that many small shoaling species exhibit, including these clonal fish, which suggests that mollies may view this response as a more effective anti-predator response compared to limiting their detectability by reducing aggressive conspecific interactions.
bibliographic citation: Aguiñaga et al. (2024) Behavioral responses of a clonal fish to perceived predation risk. PeerJ 12:e17547 https://doi.org/10.7717/peerj.17547
date submitted: 2024-03-28
date accepted: 2024-05-19
issued: 2024-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aguiñaga
  given name: Jonathan
author list: Agent
  family name: Jin
  given name: Sophia
author list: Agent
  family name: Pesati
  given name: Ishita
author list: Agent
  family name: Laskowski
  given name: Kate L.
doi: 10.7717/peerj.17547
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-18
copyright: ©2024 Aguiñaga et al.
attribution name: Aguiñaga et al.

Knowledge, attitudes, and practices (KAPs) regarding tick-borne rickettsial disease among medical staff in endemic areas of China
type: item
type: AcademicArticle
description: Tick-borne rickettsial disease (TBRD) is a perilous acute infection that often eludes diagnosis in its early stages. The triad of knowledge, attitudes, and practices (KAPs) among medical professionals is key to reducing missed diagnosis rates. Therefore, a meticulous evaluation of KAPs is imperative. This study aimed to delve into the understanding of TBRD and explore the beliefs and practices related to personal prevention methods among individuals in Lu’an, a hotspot for TBRD. During the summer months of 2023, convenience sampling was employed by circulating a confidential questionnaire to 1,206 participants in the endemic regions of China. This questionnaire painted a comprehensive picture of the participants’ sociodemographic profiles and their KAPs levels vis-à-vis TBRD. The findings revealed that participants scored a mere 55.78% in knowledge, while their attitudes and practices garnered impressive scores of 90.09% and 90.83%, respectively. Upon further analysis using multiple linear regression, several intriguing patterns emerged. Male participants, employed in the Infectious Disease Department, held vice-senior or higher titles, or had prior medical training demonstrated superior knowledge scores. On the other hand, medical personnel who were younger than 30, possessed graduate degrees or higher qualifications, and had training excelled in attitudes and practices. Notably, when employing the Boston Consulting Group (BCG) matrix, a significant distribution of medical personnel was observed across the four quadrants. Specifically, 37.43%, 13.19%, 19.61%, and 29.77% fell into the first, second, third, and fourth quadrants. This survey underscores the commendable attitudes and practices of medical staff towards TBRD in endemic regions of China. However, their knowledge level remains wanting and demands urgent improvement.
format: application/pdf
format: text/html
creator: Miaohui Shao
creator: Peiyuan Hu
creator: Pengpeng Xu
creator: Jie Sun
creator: Xiaqing Zhang
creator: Dan Zhang
creator: Yong Shen
creator: Dawei Gao
creator: Weigang Zhang
creator: Wei Qin
creator: Yong Lyu
subject: Epidemiology
subject: Mental Health
subject: Environmental Health
subject: Healthcare Services
description: doi:10.7717/peerj.17562
publisher: PeerJ Inc.
rights: © 2024 Shao et al.
abstract: Tick-borne rickettsial disease (TBRD) is a perilous acute infection that often eludes diagnosis in its early stages. The triad of knowledge, attitudes, and practices (KAPs) among medical professionals is key to reducing missed diagnosis rates. Therefore, a meticulous evaluation of KAPs is imperative. This study aimed to delve into the understanding of TBRD and explore the beliefs and practices related to personal prevention methods among individuals in Lu’an, a hotspot for TBRD. During the summer months of 2023, convenience sampling was employed by circulating a confidential questionnaire to 1,206 participants in the endemic regions of China. This questionnaire painted a comprehensive picture of the participants’ sociodemographic profiles and their KAPs levels vis-à-vis TBRD. The findings revealed that participants scored a mere 55.78% in knowledge, while their attitudes and practices garnered impressive scores of 90.09% and 90.83%, respectively. Upon further analysis using multiple linear regression, several intriguing patterns emerged. Male participants, employed in the Infectious Disease Department, held vice-senior or higher titles, or had prior medical training demonstrated superior knowledge scores. On the other hand, medical personnel who were younger than 30, possessed graduate degrees or higher qualifications, and had training excelled in attitudes and practices. Notably, when employing the Boston Consulting Group (BCG) matrix, a significant distribution of medical personnel was observed across the four quadrants. Specifically, 37.43%, 13.19%, 19.61%, and 29.77% fell into the first, second, third, and fourth quadrants. This survey underscores the commendable attitudes and practices of medical staff towards TBRD in endemic regions of China. However, their knowledge level remains wanting and demands urgent improvement.
bibliographic citation: Shao et al. (2024) Knowledge, attitudes, and practices (KAPs) regarding tick-borne rickettsial disease among medical staff in endemic areas of China. PeerJ 12:e17562 https://doi.org/10.7717/peerj.17562
date submitted: 2024-01-12
date accepted: 2024-05-21
issued: 2024-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shao
  given name: Miaohui
author list: Agent
  family name: Hu
  given name: Peiyuan
author list: Agent
  family name: Xu
  given name: Pengpeng
author list: Agent
  family name: Sun
  given name: Jie
author list: Agent
  family name: Zhang
  given name: Xiaqing
author list: Agent
  family name: Zhang
  given name: Dan
author list: Agent
  family name: Shen
  given name: Yong
author list: Agent
  family name: Gao
  given name: Dawei
author list: Agent
  family name: Zhang
  given name: Weigang
author list: Agent
  family name: Qin
  given name: Wei
author list: Agent
  family name: Lyu
  given name: Yong
doi: 10.7717/peerj.17562
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-18
copyright: © 2024 Shao et al.
attribution name: Shao et al.

Hypertrophic effects of low-load blood flow restriction training with different repetition schemes: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective This systematic review and meta-analysis analyzed the effect of low-load resistance training (LL-RT) with blood flow restriction (BFR) versus high-load resistance training (HL-RT) on muscle hypertrophy focusing on the repetition scheme adopted. Methods Four databases were searched to identify randomized controlled trials that compared the effect of LL-RT with BFR versus HL-RT on muscle hypertrophy. Standardized mean differences (SMD) were pooled in a random effects meta-analysis. Results The overall analysis did not demonstrate significant differences between conditions (SMD = 0.046; p = 0.14). A similar result was observed when we separately analyzed studies that used sets to momentary muscle failure (SMD = 0.033; p = 0.520), sets of 15 repetitions (SMD = 0.005; p = 0.937) and a fixed repetition scheme composed of 75 repetitions (SMD = 0.088; p = 0.177). The analysis considering body region indicates no difference in lower limb exercise between HL-RT and LL-RT with BFR (SMD = 0.00066; p = 0.795) while upper limb exercise favors HL-RT (SMD = 0.231; p = 0.005). Conclusion LL-RT with BFR elicits muscle hypertrophy similar to HL-RT regardless of the employed repetition scheme, although there appears to be a small beneficial effect in favor of HL-RT in upper limb exercise.
format: application/pdf
format: text/html
creator: Victor S. de Queiros
creator: Nicholas Rolnick
creator: Brad J. Schoenfeld
creator: Ingrid Martins de França
creator: João Guilherme Vieira
creator: Amanda Veiga Sardeli
creator: Okan Kamis
creator: Gabriel Rodrigues Neto
creator: Breno Guilherme de Araújo Tinôco Cabral
creator: Paulo Moreira Silva Dantas
subject: Kinesiology
subject: Sports Injury
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.17195
publisher: PeerJ Inc.
rights: © 2024 de Queiros et al.
abstract: Objective This systematic review and meta-analysis analyzed the effect of low-load resistance training (LL-RT) with blood flow restriction (BFR) versus high-load resistance training (HL-RT) on muscle hypertrophy focusing on the repetition scheme adopted. Methods Four databases were searched to identify randomized controlled trials that compared the effect of LL-RT with BFR versus HL-RT on muscle hypertrophy. Standardized mean differences (SMD) were pooled in a random effects meta-analysis. Results The overall analysis did not demonstrate significant differences between conditions (SMD = 0.046; p = 0.14). A similar result was observed when we separately analyzed studies that used sets to momentary muscle failure (SMD = 0.033; p = 0.520), sets of 15 repetitions (SMD = 0.005; p = 0.937) and a fixed repetition scheme composed of 75 repetitions (SMD = 0.088; p = 0.177). The analysis considering body region indicates no difference in lower limb exercise between HL-RT and LL-RT with BFR (SMD = 0.00066; p = 0.795) while upper limb exercise favors HL-RT (SMD = 0.231; p = 0.005). Conclusion LL-RT with BFR elicits muscle hypertrophy similar to HL-RT regardless of the employed repetition scheme, although there appears to be a small beneficial effect in favor of HL-RT in upper limb exercise.
bibliographic citation: de Queiros et al. (2024) Hypertrophic effects of low-load blood flow restriction training with different repetition schemes: a systematic review and meta-analysis. PeerJ 12:e17195 https://doi.org/10.7717/peerj.17195
date submitted: 2023-11-24
date accepted: 2024-03-13
issued: 2024-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Queiros
  given name: Victor S.
author list: Agent
  family name: Rolnick
  given name: Nicholas
author list: Agent
  family name: Schoenfeld
  given name: Brad J.
author list: Agent
  family name: Martins de França
  given name: Ingrid
author list: Agent
  family name: Vieira
  given name: João Guilherme
author list: Agent
  family name: Sardeli
  given name: Amanda Veiga
author list: Agent
  family name: Kamis
  given name: Okan
author list: Agent
  family name: Neto
  given name: Gabriel Rodrigues
author list: Agent
  family name: Cabral
  given name: Breno Guilherme de Araújo Tinôco
author list: Agent
  family name: Dantas
  given name: Paulo Moreira Silva
doi: 10.7717/peerj.17195
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-17
copyright: ©2024 de Queiros et al.
attribution name: de Queiros et al.

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