PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification of common and specific cold resistance pathways from cold tolerant and non-cold tolerant mango varieties
items: Reliability and validity of My Jump 2® app to measure the vertical jump in visually impaired five-a-side soccer athletes
items: Risk factors for recovery from oculomotor nerve palsy after aneurysm surgery: a meta-analysis
items: Clocks at a snail pace: biological rhythms in terrestrial gastropods
items: Cordyceps cateniannulata, a new potential strain for controlling Allantus luctifer from China
items: In-depth study of pyroptosis-related genes and immune infiltration in colon cancer
items: Genomic evaluation of the probiotic and pathogenic features of Enterococcus faecalis from human breast milk and comparison with the isolates from animal milk and clinical specimens
items: Forkhead box D subfamily genes in colorectal cancer: potential biomarkers and therapeutic targets
items: Using a natural capital risk register to support the funding of seagrass habitat enhancement in Plymouth Sound
items: An interpretable deep learning model for detecting BRCA pathogenic variants of breast cancer from hematoxylin and eosin-stained pathological images

Identification of common and specific cold resistance pathways from cold tolerant and non-cold tolerant mango varieties
type: item
type: AcademicArticle
description: Mango has frequently encountered severe climate and environmental challenges such as low temperatures, seriously affecting the sustainable development of the industry. In the study, physiological measurements showed that the activities of superoxide dismutase (SOD) and peroxidase (POD) were found to be higher in Jinhuang (JH) mango plants than those of Tainong (TN) mango plants under cold stress, indicating cold tolerant (JH) and non-cold tolerant (TN) mango varieties were firstly determined. Subsequently, transcriptomics showed 8,337 and 7,996 differentially expressed genes (DEGs) were respectively identified in JH and TN mango varieties treated at 4 °C for 36 h, while more DEGs (10,683 and 10,723) were screened when treated at 4 °C for 72 h. Quantitative real-time PCR (qRT-PCR) of the selected DEGs confirmed their transcriptional levels displayed agreement to the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed two primary cold resistant regulation pathways, photosynthesis-antenna proteins pathway and photosynthesis pathway, were both significant annotated in the two mango varieties, indicating share the common regulation mechanism response to cold stress. However, five specific cold resistant pathways, such as amino acid and carbohydrate metabolisms, were identified in JH mango variety with cold stress for longer duration, indicating the specific regulation pathways in the cold tolerant mango varieties. Furthermore, 43 ethylene-responsive transcription factors (ERFs) were significantly annotated in JH mango after cold-treated for 72 h comparing with the control group, and three of them ERF109-1, ERF017-1 and ERF017-2 were highly expressed, which may play important regulatory roles in plant cold resistance. These results provided insights into the primary and specific molecular mechanisms of different mango varieties resistance to chill.
format: application/pdf
format: text/html
creator: Jian-hua Wang
creator: Xiaoyan Feng
creator: Muhammad Aleem Ashraf
creator: Yufeng Li
creator: Yu Kong
creator: Qiuliang Cai
creator: Shuli Xian
creator: Huixiang Yin
creator: Nai-tong Yu
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.18431
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Mango has frequently encountered severe climate and environmental challenges such as low temperatures, seriously affecting the sustainable development of the industry. In the study, physiological measurements showed that the activities of superoxide dismutase (SOD) and peroxidase (POD) were found to be higher in Jinhuang (JH) mango plants than those of Tainong (TN) mango plants under cold stress, indicating cold tolerant (JH) and non-cold tolerant (TN) mango varieties were firstly determined. Subsequently, transcriptomics showed 8,337 and 7,996 differentially expressed genes (DEGs) were respectively identified in JH and TN mango varieties treated at 4 °C for 36 h, while more DEGs (10,683 and 10,723) were screened when treated at 4 °C for 72 h. Quantitative real-time PCR (qRT-PCR) of the selected DEGs confirmed their transcriptional levels displayed agreement to the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed two primary cold resistant regulation pathways, photosynthesis-antenna proteins pathway and photosynthesis pathway, were both significant annotated in the two mango varieties, indicating share the common regulation mechanism response to cold stress. However, five specific cold resistant pathways, such as amino acid and carbohydrate metabolisms, were identified in JH mango variety with cold stress for longer duration, indicating the specific regulation pathways in the cold tolerant mango varieties. Furthermore, 43 ethylene-responsive transcription factors (ERFs) were significantly annotated in JH mango after cold-treated for 72 h comparing with the control group, and three of them ERF109-1, ERF017-1 and ERF017-2 were highly expressed, which may play important regulatory roles in plant cold resistance. These results provided insights into the primary and specific molecular mechanisms of different mango varieties resistance to chill.
bibliographic citation: Wang et al. (2024) Identification of common and specific cold resistance pathways from cold tolerant and non-cold tolerant mango varieties. PeerJ 12:e18431 https://doi.org/10.7717/peerj.18431
date submitted: 2024-05-30
date accepted: 2024-10-09
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jian-hua
author list: Agent
  family name: Feng
  given name: Xiaoyan
author list: Agent
  family name: Ashraf
  given name: Muhammad Aleem
author list: Agent
  family name: Li
  given name: Yufeng
author list: Agent
  family name: Kong
  given name: Yu
author list: Agent
  family name: Cai
  given name: Qiuliang
author list: Agent
  family name: Xian
  given name: Shuli
author list: Agent
  family name: Yin
  given name: Huixiang
author list: Agent
  family name: Yu
  given name: Nai-tong
doi: 10.7717/peerj.18431
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: © 2024 Wang et al.
attribution name: Wang et al.

Reliability and validity of My Jump 2® app to measure the vertical jump in visually impaired five-a-side soccer athletes
type: item
type: AcademicArticle
description: Background Although My Jump 2® consistently presented excellent values of reliability and validity when compared to force platforms (FPs) and contact mats, to date no scientific investigation assessed the validity and reliability of My Jump 2® to measure jump height in visually impaired five-a-side soccer athletes. Thus, the study aimed at analyzing the validity and reliability of the My Jump 2® to measure the vertical jump of five-a-side soccer athletes. Methods Twelve visually impaired five-a-side soccer athletes, volunteered for this study. Each player performed five countermovement jumps (CMJs) and squat jumps (SJs) on a contact platform (CP) while they were simultaneously recorded using My Jump 2®. Results There was almost perfect agreement between the My Jump 2® and the contact platform measurements of CMJ (intraclass correlation coefficient = 0.99; p < 0.001) and SJ (intraclass correlation coefficient = 0.99; p < 0.001), heights for athletes during the first and second measurement days. Bland-Altman analysis showed a bias of 0.25 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.88 for CMJ, while that Bland-Altman analysis showed bias 0.18 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.96, for SJ. Conclusion We can conclude that the My Jump 2® is a valid and reliable method to measure CMJ and SJ in visually impaired five-a-side soccer athletes.
format: application/pdf
format: text/html
creator: Julio Cesar Silva
creator: Kalinne Fernandes Silva
creator: Vitor Bruno Torres
creator: Maria Socorro Cirilo-Sousa
creator: Alexandre Igor Araripe Medeiros
creator: Jacques Eanes Esmeraldo Melo
creator: Gilmário Ricarte Batista
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.18170
publisher: PeerJ Inc.
rights: © 2024 Silva et al.
abstract: Background Although My Jump 2® consistently presented excellent values of reliability and validity when compared to force platforms (FPs) and contact mats, to date no scientific investigation assessed the validity and reliability of My Jump 2® to measure jump height in visually impaired five-a-side soccer athletes. Thus, the study aimed at analyzing the validity and reliability of the My Jump 2® to measure the vertical jump of five-a-side soccer athletes. Methods Twelve visually impaired five-a-side soccer athletes, volunteered for this study. Each player performed five countermovement jumps (CMJs) and squat jumps (SJs) on a contact platform (CP) while they were simultaneously recorded using My Jump 2®. Results There was almost perfect agreement between the My Jump 2® and the contact platform measurements of CMJ (intraclass correlation coefficient = 0.99; p < 0.001) and SJ (intraclass correlation coefficient = 0.99; p < 0.001), heights for athletes during the first and second measurement days. Bland-Altman analysis showed a bias of 0.25 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.88 for CMJ, while that Bland-Altman analysis showed bias 0.18 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.96, for SJ. Conclusion We can conclude that the My Jump 2® is a valid and reliable method to measure CMJ and SJ in visually impaired five-a-side soccer athletes.
bibliographic citation: Silva et al. (2024) Reliability and validity of My Jump 2® app to measure the vertical jump in visually impaired five-a-side soccer athletes. PeerJ 12:e18170 https://doi.org/10.7717/peerj.18170
date submitted: 2024-05-01
date accepted: 2024-09-03
issued: 2024-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Julio Cesar
author list: Agent
  family name: Silva
  given name: Kalinne Fernandes
author list: Agent
  family name: Torres
  given name: Vitor Bruno
author list: Agent
  family name: Cirilo-Sousa
  given name: Maria Socorro
author list: Agent
  family name: Medeiros
  given name: Alexandre Igor Araripe
author list: Agent
  family name: Esmeraldo Melo
  given name: Jacques Eanes
author list: Agent
  family name: Batista
  given name: Gilmário Ricarte
doi: 10.7717/peerj.18170
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-29
copyright: © 2024 Silva et al.
attribution name: Silva et al.

Risk factors for recovery from oculomotor nerve palsy after aneurysm surgery: a meta-analysis
type: item
type: AcademicArticle
description: Background Risk factors for recovery from oculomotor nerve palsy (ONP) after aneurysm surgery explored by meta-analysis. Methods The PubMed, Embase, web of science, Cochrane library, China Knowledge, Wan fang, and VIP databases were searched for case-control or cohort studies on risk factors of oculomotor nerve palsy recovery after aneurysm surgery, with a cut-off date of 14 February 2024, and data were analyzed using Stata 15. Result A total of 12 articles involving 866 individuals were included, meta-analysis results suggesting that gender (OR = 0.75, 95% CI [0.51–1.10]), age (OR = 1.00, 95% CI [0.93–1.07]), aneurysm size (OR = 0.85, 95% CI [−0.71 to 1.01]), treatment time (OR = 1.01, 95% CI [0.91–1.13]) is not a risk factor for recovery of motor nerve palsy after aneurysm surgery. Preoperative complete ONP (OR = 2.27, 95% CI [1.07–4.81]), surgery (OR = 9.88, 95% CI [2.53–38.57]), subarachnoid hemorrhage (OR = 1.29, 95% CI [1.06–1.56]) is a risk factor for recovery of motor nerve palsy after aneurysm surgery. Conclusion Based on the results of the studies we included, we found that complete ONP before surgery led to poorer recovery, but patients with post-operative and subarachnoid hemorrhage had better recovery.
format: application/pdf
format: text/html
creator: Yuan Li
creator: Ming Zhao
creator: Xuemei Li
creator: Tiejuan Liu
creator: Lin Zheng
creator: Deyu Hu
creator: Tongyan Liu
creator: Lingyun Zhou
subject: Cardiology
subject: Neurology
subject: Ophthalmology
description: doi:10.7717/peerj.18207
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background Risk factors for recovery from oculomotor nerve palsy (ONP) after aneurysm surgery explored by meta-analysis. Methods The PubMed, Embase, web of science, Cochrane library, China Knowledge, Wan fang, and VIP databases were searched for case-control or cohort studies on risk factors of oculomotor nerve palsy recovery after aneurysm surgery, with a cut-off date of 14 February 2024, and data were analyzed using Stata 15. Result A total of 12 articles involving 866 individuals were included, meta-analysis results suggesting that gender (OR = 0.75, 95% CI [0.51–1.10]), age (OR = 1.00, 95% CI [0.93–1.07]), aneurysm size (OR = 0.85, 95% CI [−0.71 to 1.01]), treatment time (OR = 1.01, 95% CI [0.91–1.13]) is not a risk factor for recovery of motor nerve palsy after aneurysm surgery. Preoperative complete ONP (OR = 2.27, 95% CI [1.07–4.81]), surgery (OR = 9.88, 95% CI [2.53–38.57]), subarachnoid hemorrhage (OR = 1.29, 95% CI [1.06–1.56]) is a risk factor for recovery of motor nerve palsy after aneurysm surgery. Conclusion Based on the results of the studies we included, we found that complete ONP before surgery led to poorer recovery, but patients with post-operative and subarachnoid hemorrhage had better recovery.
bibliographic citation: Li et al. (2024) Risk factors for recovery from oculomotor nerve palsy after aneurysm surgery: a meta-analysis. PeerJ 12:e18207 https://doi.org/10.7717/peerj.18207
date submitted: 2024-03-08
date accepted: 2024-09-10
issued: 2024-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yuan
author list: Agent
  family name: Zhao
  given name: Ming
author list: Agent
  family name: Li
  given name: Xuemei
author list: Agent
  family name: Liu
  given name: Tiejuan
author list: Agent
  family name: Zheng
  given name: Lin
author list: Agent
  family name: Hu
  given name: Deyu
author list: Agent
  family name: Liu
  given name: Tongyan
author list: Agent
  family name: Zhou
  given name: Lingyun
doi: 10.7717/peerj.18207
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-29
copyright: © 2024 Li et al.
attribution name: Li et al.

Clocks at a snail pace: biological rhythms in terrestrial gastropods
type: item
type: AcademicArticle
description: Biological rhythms are ubiquitous across the tree of life. Organisms must allocate their activities into moments of the day and of the season that will increase their probability of surviving and reproducing, which is done in the form of daily and annual rhythms. So far, the vast majority of studies on biological rhythms have focused on classical laboratory model species. Still, the use of non-model species is gaining traction, as part of an effort to achieve a more holistic understanding of clock/calendar mechanisms in the “real world” but this requires species that can be studied in both the lab and in nature. Terrestrial gastropods, i.e., land snails and slugs, have the potential to be exciting models for the study of biological rhythms in nature. Therefore, we provide a review of the research on biological rhythms in terrestrial gastropods, with a focus on ecology and evolution. We present the state of the art in the field while giving a historical perspective of the studies, exploring each of the main lineages of terrestrial gastropods. We also point out some interesting directions that future studies could take to fill some of the more urgent gaps in current knowledge. We hope that our contribution will renew interest in this area and spark novel projects.
format: application/pdf
format: text/html
creator: Rodrigo Brincalepe Salvador
creator: Barbara Mizumo Tomotani
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.18318
publisher: PeerJ Inc.
rights: © 2024 Salvador and Tomotani
abstract: Biological rhythms are ubiquitous across the tree of life. Organisms must allocate their activities into moments of the day and of the season that will increase their probability of surviving and reproducing, which is done in the form of daily and annual rhythms. So far, the vast majority of studies on biological rhythms have focused on classical laboratory model species. Still, the use of non-model species is gaining traction, as part of an effort to achieve a more holistic understanding of clock/calendar mechanisms in the “real world” but this requires species that can be studied in both the lab and in nature. Terrestrial gastropods, i.e., land snails and slugs, have the potential to be exciting models for the study of biological rhythms in nature. Therefore, we provide a review of the research on biological rhythms in terrestrial gastropods, with a focus on ecology and evolution. We present the state of the art in the field while giving a historical perspective of the studies, exploring each of the main lineages of terrestrial gastropods. We also point out some interesting directions that future studies could take to fill some of the more urgent gaps in current knowledge. We hope that our contribution will renew interest in this area and spark novel projects.
bibliographic citation: Salvador et al. (2024) Clocks at a snail pace: biological rhythms in terrestrial gastropods. PeerJ 12:e18318 https://doi.org/10.7717/peerj.18318
date submitted: 2024-03-20
date accepted: 2024-09-24
issued: 2024-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salvador
  given name: Rodrigo Brincalepe
author list: Agent
  family name: Tomotani
  given name: Barbara Mizumo
doi: 10.7717/peerj.18318
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-29
copyright: ©2024 Salvador and Tomotani
attribution name: Salvador and Tomotani

Cordyceps cateniannulata, a new potential strain for controlling Allantus luctifer from China
type: item
type: AcademicArticle
description: Allantus luctifer is one of the most serious pests of buckwheat, with its larvae mainly damaging leaves during the seedling and flowering stages. Entomogenous fungi play a crucial role as biological regulators of arthropod populations in nature. In this paper, a newly isolated strain 19GZAl-1, was identified as Cordyceps. cateniannulata through the observetions of macroscopic and microscopic morphological features, and the results of rDNA- ITS sequence alignment and phylogenetic analysis. By comparing the efficacy of ten entomopathogenic fungal strains, including six strains of C. cateniannulata and four other Cordyceps species, against A. luctifer larvae, the new strain 19GZAl-1 exhibited the highest mortality rate. Mortality rates of A. luctifer larvae treated by spraying with the strain 19GZAl-1 increased as larval stage decreased, with first instar larvae showing the highest mortality rate of 85%. The appressorium from conidia invaded the larval body through areas with thin cuticle, such as larva pod base and internode folds, after which the hyphae grew rapidly, filling the haemocoel, and finally protruding from the integument upon melanization and decomposition of the intestinal wall cells. The results suggest that the strain 19GZAL-1 of C. cateniannulata has potential against A. luctifer larvae, which is significant for further study on the infection mechanism of C. cateniannulata on insects.
format: application/pdf
format: text/html
creator: Xiaona Zhang
creator: Yu Wu
creator: Xue Peng
creator: Can Liu
creator: Guimin Yang
creator: Qingfu Chen
creator: Daochao Jin
subject: Agricultural Science
subject: Entomology
subject: Mycology
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.18345
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Allantus luctifer is one of the most serious pests of buckwheat, with its larvae mainly damaging leaves during the seedling and flowering stages. Entomogenous fungi play a crucial role as biological regulators of arthropod populations in nature. In this paper, a newly isolated strain 19GZAl-1, was identified as Cordyceps. cateniannulata through the observetions of macroscopic and microscopic morphological features, and the results of rDNA- ITS sequence alignment and phylogenetic analysis. By comparing the efficacy of ten entomopathogenic fungal strains, including six strains of C. cateniannulata and four other Cordyceps species, against A. luctifer larvae, the new strain 19GZAl-1 exhibited the highest mortality rate. Mortality rates of A. luctifer larvae treated by spraying with the strain 19GZAl-1 increased as larval stage decreased, with first instar larvae showing the highest mortality rate of 85%. The appressorium from conidia invaded the larval body through areas with thin cuticle, such as larva pod base and internode folds, after which the hyphae grew rapidly, filling the haemocoel, and finally protruding from the integument upon melanization and decomposition of the intestinal wall cells. The results suggest that the strain 19GZAL-1 of C. cateniannulata has potential against A. luctifer larvae, which is significant for further study on the infection mechanism of C. cateniannulata on insects.
bibliographic citation: Zhang et al. (2024) Cordyceps cateniannulata, a new potential strain for controlling Allantus luctifer from China. PeerJ 12:e18345 https://doi.org/10.7717/peerj.18345
date submitted: 2024-05-15
date accepted: 2024-09-26
issued: 2024-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhang
  given name: Xiaona
author list: Agent
  family name: Wu
  given name: Yu
author list: Agent
  family name: Peng
  given name: Xue
author list: Agent
  family name: Liu
  given name: Can
author list: Agent
  family name: Yang
  given name: Guimin
author list: Agent
  family name: Chen
  given name: Qingfu
author list: Agent
  family name: Jin
  given name: Daochao
doi: 10.7717/peerj.18345
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-29
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

In-depth study of pyroptosis-related genes and immune infiltration in colon cancer
type: item
type: AcademicArticle
description: Background Pyroptosis is a form of regulated necrosis that occurs in many cell and tissue types and plays a critical role in tumor progression. The diagnostic value of pyroptosis-related genes (PRGs) in colon cancer has been widely investigated. In the present study, we explored the relationship between PRG expression and colon cancer. Methods We retrieved genomic and clinical data pertaining to The Cancer Genome Atlas-Colon Adenocarcinoma from the UCSC Xena database, along with the corresponding genome annotation information from the GENCODE data portal. Utilising these data and a list of 33 pyrogenic genes, we performed principal component analysis and unsupervised clustering analysis to assess the pyroptosis subtypes. We analysed the differential expression between these subtypes to obtain PRGs, ultimately selecting 10 PRGs. We conducted Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set variation analysis, protein–protein interaction, and immune infiltration analyses of these PRGs. We validated the expression of TNNC1 via immunohistochemistry (IHC) and real-time quantitative PCR. Results After rigorous screening, excluding patients with incomplete survival data and unmatched transcriptomes, we refined our study cohort to 431 patients. We performed differential mRNA analysis and identified 445 PRGs, 10 of which were selected as hub genes. These genes were associated with various immune cell types. Specifically, TNNC1 expression was positively associated with immature dendritic cells and NK CD56+ cells. IHC staining indicated higher TNNC1 expression levels in tumor samples. Notably, TNNC1 expression levels were high in all the colon cancer cell lines, particularly in SW480 cells. Conclusion In this study, we explored the characteristics of PRGs in colon cancer and identified novel biological targets for early individualised treatment and accurate diagnosis of colon cancer, thus contributing to the advancement of clinical oncology.
format: application/pdf
format: text/html
creator: Bingbing Shang
creator: Haiyan Qiao
creator: Liang Wang
creator: Jingyu Wang
subject: Bioinformatics
subject: Oncology
description: doi:10.7717/peerj.18374
publisher: PeerJ Inc.
rights: © 2024 Shang et al.
abstract: Background Pyroptosis is a form of regulated necrosis that occurs in many cell and tissue types and plays a critical role in tumor progression. The diagnostic value of pyroptosis-related genes (PRGs) in colon cancer has been widely investigated. In the present study, we explored the relationship between PRG expression and colon cancer. Methods We retrieved genomic and clinical data pertaining to The Cancer Genome Atlas-Colon Adenocarcinoma from the UCSC Xena database, along with the corresponding genome annotation information from the GENCODE data portal. Utilising these data and a list of 33 pyrogenic genes, we performed principal component analysis and unsupervised clustering analysis to assess the pyroptosis subtypes. We analysed the differential expression between these subtypes to obtain PRGs, ultimately selecting 10 PRGs. We conducted Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set variation analysis, protein–protein interaction, and immune infiltration analyses of these PRGs. We validated the expression of TNNC1 via immunohistochemistry (IHC) and real-time quantitative PCR. Results After rigorous screening, excluding patients with incomplete survival data and unmatched transcriptomes, we refined our study cohort to 431 patients. We performed differential mRNA analysis and identified 445 PRGs, 10 of which were selected as hub genes. These genes were associated with various immune cell types. Specifically, TNNC1 expression was positively associated with immature dendritic cells and NK CD56+ cells. IHC staining indicated higher TNNC1 expression levels in tumor samples. Notably, TNNC1 expression levels were high in all the colon cancer cell lines, particularly in SW480 cells. Conclusion In this study, we explored the characteristics of PRGs in colon cancer and identified novel biological targets for early individualised treatment and accurate diagnosis of colon cancer, thus contributing to the advancement of clinical oncology.
bibliographic citation: Shang et al. (2024) In-depth study of pyroptosis-related genes and immune infiltration in colon cancer. PeerJ 12:e18374 https://doi.org/10.7717/peerj.18374
date submitted: 2024-04-24
date accepted: 2024-09-30
issued: 2024-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shang
  given name: Bingbing
author list: Agent
  family name: Qiao
  given name: Haiyan
author list: Agent
  family name: Wang
  given name: Liang
author list: Agent
  family name: Wang
  given name: Jingyu
doi: 10.7717/peerj.18374
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-29
copyright: ©2024 Shang et al.
attribution name: Shang et al.

Genomic evaluation of the probiotic and pathogenic features of Enterococcus faecalis from human breast milk and comparison with the isolates from animal milk and clinical specimens
type: item
type: AcademicArticle
description: Enterococcus faecalis is considered a probiotic, commensal lactic acid bacterium in human breast milk (HBM), but there are circulating antibiotic resistant and virulence determinants that could pose a risk in some strains. The study aimed to conduct genomic analysis of E. faecalis isolates recovered from HBM and animal milk and to evaluate their probiotic and pathogenic features through comparative genomics with isolates from clinical specimens (e.g., urine, wound, and blood). Genomic analysis of 61 isolates was performed, including E. faecalis isolates recovered from HBM in Saudi Arabia. Genome sequencing was conducted using the MiSeq system. The fewest antibiotic resistance genes (lsaA, tetM, ermB) were identified in isolates from HBM and animal milk compared to clinical isolates. Several known and unknown mutations in the gyrA and parC genes were observed in clinical isolates. However, 11 virulence genes were commonly found in more than 95% of isolates, and 13 virulence genes were consistently present in the HBM isolates. Phylogenetically, the HBM isolates from China clustered with the probiotic reference strain Symbioflor 1, but all isolates from HBM and animal milk clustered separately from the clinical reference strain V583. Subsystem functions 188 of 263 were common in all analyzed genome assemblies. Regardless of the source of isolation, genes associated with carbohydrate metabolism, fatty acid, and vitamin biosynthesis were commonly found in E. faecalis isolates. In conclusion, comparative genomic analysis can help distinguish the probiotic or pathogenic potential of E. faecalis based on genomic features.
format: application/pdf
format: text/html
creator: Lobna Badr
creator: Muhammad Yasir
creator: Areej A. Alkhaldy
creator: Samah A. Soliman
creator: Magdah Ganash
creator: Safaa A. Turkistani
creator: Asif A. Jiman-Fatani
creator: Ibrahim A. Al-Zahrani
creator: Esam I. Azhar
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.18392
publisher: PeerJ Inc.
rights: © 2024 Badr et al.
abstract: Enterococcus faecalis is considered a probiotic, commensal lactic acid bacterium in human breast milk (HBM), but there are circulating antibiotic resistant and virulence determinants that could pose a risk in some strains. The study aimed to conduct genomic analysis of E. faecalis isolates recovered from HBM and animal milk and to evaluate their probiotic and pathogenic features through comparative genomics with isolates from clinical specimens (e.g., urine, wound, and blood). Genomic analysis of 61 isolates was performed, including E. faecalis isolates recovered from HBM in Saudi Arabia. Genome sequencing was conducted using the MiSeq system. The fewest antibiotic resistance genes (lsaA, tetM, ermB) were identified in isolates from HBM and animal milk compared to clinical isolates. Several known and unknown mutations in the gyrA and parC genes were observed in clinical isolates. However, 11 virulence genes were commonly found in more than 95% of isolates, and 13 virulence genes were consistently present in the HBM isolates. Phylogenetically, the HBM isolates from China clustered with the probiotic reference strain Symbioflor 1, but all isolates from HBM and animal milk clustered separately from the clinical reference strain V583. Subsystem functions 188 of 263 were common in all analyzed genome assemblies. Regardless of the source of isolation, genes associated with carbohydrate metabolism, fatty acid, and vitamin biosynthesis were commonly found in E. faecalis isolates. In conclusion, comparative genomic analysis can help distinguish the probiotic or pathogenic potential of E. faecalis based on genomic features.
bibliographic citation: Badr et al. (2024) Genomic evaluation of the probiotic and pathogenic features of Enterococcus faecalis from human breast milk and comparison with the isolates from animal milk and clinical specimens. PeerJ 12:e18392 https://doi.org/10.7717/peerj.18392
date submitted: 2024-02-20
date accepted: 2024-10-02
issued: 2024-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Badr
  given name: Lobna
author list: Agent
  family name: Yasir
  given name: Muhammad
author list: Agent
  family name: Alkhaldy
  given name: Areej A.
author list: Agent
  family name: Soliman
  given name: Samah A.
author list: Agent
  family name: Ganash
  given name: Magdah
author list: Agent
  family name: Turkistani
  given name: Safaa A.
author list: Agent
  family name: Jiman-Fatani
  given name: Asif A.
author list: Agent
  family name: Al-Zahrani
  given name: Ibrahim A.
author list: Agent
  family name: Azhar
  given name: Esam I.
doi: 10.7717/peerj.18392
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-29
copyright: ©2024 Badr et al.
attribution name: Badr et al.

Forkhead box D subfamily genes in colorectal cancer: potential biomarkers and therapeutic targets
type: item
type: AcademicArticle
description: Background The forkhead box (FOX) family members regulate gene transcription and expression. FOX family members regulate various biological processes, such as cell proliferation and tumorigenesis. FOXD, a FOX protein subfamily, is associated with poor prognosis for various cancers. However, the potential clinical value of FOXD subfamily members in colorectal cancer (CRC) has not yet been elucidated. Therefore, in this study, we aimed to determine the role of the FOXD subfamily members in CRC development. Methods Using HTSeq-count data, clinical data, and single-nucleotide polymorphisms (obtained from The Cancer Genome Atlas Project), and bioinformatics analyses (using DESEQ2 software), we identified differentially expressed genes (DEGs) in CRC. Next, each DEG expression was validated in vitro using reverse transcription-quantitative polymerase chain reaction, western blotting, and immunohistochemistry (IHC). Results Among the FOXD subfamily members, the area under the receiver operating characteristic curve of FOXD3 was 0.949, indicating that FOXD3 has a high overall diagnostic accuracy for CRC. Gene Set Enrichment Analysis revealed that FOXD-DEGs were mainly related to pathways such as cytokine, cytokine, and extracellular matrix receptor interactions. Kaplan–Meier curves and nomograms showed that FOXD1, FOXD3, and FOXD4 were prognostically significant. In conclusion, FOXD subfamily members (especially FOXD3) could serve as diagnostic and prognostic biomarkers for CRC and an immunotherapy target in patients with CRC.
format: application/pdf
format: text/html
creator: Ying Chen
creator: Haiyan Qiao
creator: Ruiqi Zhong
creator: Lei Sun
creator: Bingbing Shang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.18406
publisher: PeerJ Inc.
rights: © 2024 Chen et al.
abstract: Background The forkhead box (FOX) family members regulate gene transcription and expression. FOX family members regulate various biological processes, such as cell proliferation and tumorigenesis. FOXD, a FOX protein subfamily, is associated with poor prognosis for various cancers. However, the potential clinical value of FOXD subfamily members in colorectal cancer (CRC) has not yet been elucidated. Therefore, in this study, we aimed to determine the role of the FOXD subfamily members in CRC development. Methods Using HTSeq-count data, clinical data, and single-nucleotide polymorphisms (obtained from The Cancer Genome Atlas Project), and bioinformatics analyses (using DESEQ2 software), we identified differentially expressed genes (DEGs) in CRC. Next, each DEG expression was validated in vitro using reverse transcription-quantitative polymerase chain reaction, western blotting, and immunohistochemistry (IHC). Results Among the FOXD subfamily members, the area under the receiver operating characteristic curve of FOXD3 was 0.949, indicating that FOXD3 has a high overall diagnostic accuracy for CRC. Gene Set Enrichment Analysis revealed that FOXD-DEGs were mainly related to pathways such as cytokine, cytokine, and extracellular matrix receptor interactions. Kaplan–Meier curves and nomograms showed that FOXD1, FOXD3, and FOXD4 were prognostically significant. In conclusion, FOXD subfamily members (especially FOXD3) could serve as diagnostic and prognostic biomarkers for CRC and an immunotherapy target in patients with CRC.
bibliographic citation: Chen et al. (2024) Forkhead box D subfamily genes in colorectal cancer: potential biomarkers and therapeutic targets. PeerJ 12:e18406 https://doi.org/10.7717/peerj.18406
date submitted: 2024-05-10
date accepted: 2024-10-05
issued: 2024-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Ying
author list: Agent
  family name: Qiao
  given name: Haiyan
author list: Agent
  family name: Zhong
  given name: Ruiqi
author list: Agent
  family name: Sun
  given name: Lei
author list: Agent
  family name: Shang
  given name: Bingbing
doi: 10.7717/peerj.18406
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-29
copyright: © 2024 Chen et al.
attribution name: Chen et al.

Using a natural capital risk register to support the funding of seagrass habitat enhancement in Plymouth Sound
type: item
type: AcademicArticle
description: Seagrass is an important marine habitat that provides benefits to society in the form of ecosystem services. Services include the provision of food via fisheries, the regulation of water quality and the ability to sequester and store carbon. In the UK, seagrass beds are in decline, increasing the risk of ecosystem service loss. Current efforts to protect, restore and create seagrass habitat, beyond spatial management measures, rely on grant funding and donations. Emerging carbon, biodiversity and wider ecosystem service markets offering potential revenue sources could facilitate the enhancement of seagrass habitat at scale. Participation in ecosystem service markets, requires that projects deliver on the ecosystem service benefits defined. As the benefits will have been paid for, there are risks associated with not delivering on ecosystem service benefits. It is important that the risk is clearly defined. In this study we further the marine natural capital and risk register approach and apply the method to a case study area to support the development of sustainable funding options for seagrass habitat enhancement in Plymouth Sound, UK. Habitat Suitability modelling is also used to map potential areas for seagrass habitat enhancement. We find that, in the Plymouth Sound area, the risk of loss of ecosystem services for subtidal seagrass habitats is, at present, high. This is primarily linked to the declining extent and condition of subtidal seagrass assets. Under current governance, all of Plymouth Sound’s subtidal seagrass are within a Marine Protected Area, though this conservation designation does not guarantee that the seagrass bed is protected from damaging activity. Under current environmental conditions there is opportunity for widespread seagrass restoration and creation. Risk to seagrass beds and any future private funding could be reduced by governance actions that enable effective direct protection of the seagrass assets and mitigate harmful pressures (e.g.…
format: application/pdf
format: text/html
creator: Guy Hooper
creator: Matthew Ashley
creator: Tom Mullier
creator: Martin Attrill
creator: Amelia Sturgeon
creator: Zoe Sydenham
creator: Mark Parry
creator: Katey Valentine
creator: Sian Rees
subject: Ecosystem Science
subject: Science Policy
subject: Coupled Natural and Human Systems
subject: Environmental Impacts
description: doi:10.7717/peerj.17969
publisher: PeerJ Inc.
rights: © 2024 Hooper et al.
abstract: Seagrass is an important marine habitat that provides benefits to society in the form of ecosystem services. Services include the provision of food via fisheries, the regulation of water quality and the ability to sequester and store carbon. In the UK, seagrass beds are in decline, increasing the risk of ecosystem service loss. Current efforts to protect, restore and create seagrass habitat, beyond spatial management measures, rely on grant funding and donations. Emerging carbon, biodiversity and wider ecosystem service markets offering potential revenue sources could facilitate the enhancement of seagrass habitat at scale. Participation in ecosystem service markets, requires that projects deliver on the ecosystem service benefits defined. As the benefits will have been paid for, there are risks associated with not delivering on ecosystem service benefits. It is important that the risk is clearly defined. In this study we further the marine natural capital and risk register approach and apply the method to a case study area to support the development of sustainable funding options for seagrass habitat enhancement in Plymouth Sound, UK. Habitat Suitability modelling is also used to map potential areas for seagrass habitat enhancement. We find that, in the Plymouth Sound area, the risk of loss of ecosystem services for subtidal seagrass habitats is, at present, high. This is primarily linked to the declining extent and condition of subtidal seagrass assets. Under current governance, all of Plymouth Sound’s subtidal seagrass are within a Marine Protected Area, though this conservation designation does not guarantee that the seagrass bed is protected from damaging activity. Under current environmental conditions there is opportunity for widespread seagrass restoration and creation. Risk to seagrass beds and any future private funding could be reduced by governance actions that enable effective direct protection of the seagrass assets and mitigate harmful pressures (e.g.…
bibliographic citation: Hooper et al. (2024) Using a natural capital risk register to support the funding of seagrass habitat enhancement in Plymouth Sound. PeerJ 12:e17969 https://doi.org/10.7717/peerj.17969
date submitted: 2023-09-22
date accepted: 2024-08-02
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hooper
  given name: Guy
author list: Agent
  family name: Ashley
  given name: Matthew
author list: Agent
  family name: Mullier
  given name: Tom
author list: Agent
  family name: Attrill
  given name: Martin
author list: Agent
  family name: Sturgeon
  given name: Amelia
author list: Agent
  family name: Sydenham
  given name: Zoe
author list: Agent
  family name: Parry
  given name: Mark
author list: Agent
  family name: Valentine
  given name: Katey
author list: Agent
  family name: Rees
  given name: Sian
doi: 10.7717/peerj.17969
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: ©2024 Hooper et al.
attribution name: Hooper et al.

An interpretable deep learning model for detecting BRCA pathogenic variants of breast cancer from hematoxylin and eosin-stained pathological images
type: item
type: AcademicArticle
description: Background Determining the status of breast cancer susceptibility genes (BRCA) is crucial for guiding breast cancer treatment. Nevertheless, the need for BRCA genetic testing among breast cancer patients remains unmet due to high costs and limited resources. This study aimed to develop a Bi-directional Self-Attention Multiple Instance Learning (BiAMIL) algorithm to detect BRCA status from hematoxylin and eosin (H&E) pathological images. Methods A total of 319 histopathological slides from 254 breast cancer patients were included, comprising two dependent cohorts. Following image pre-processing, 633,484 tumor tiles from the training dataset were employed to train the self-developed deep-learning model. The performance of the network was evaluated in the internal and external test sets. Results BiAMIL achieved AUC values of 0.819 (95% CI [0.673–0.965]) in the internal test set, and 0.817 (95% CI [0.712–0.923]) in the external test set. To explore the relationship between BRCA status and interpretable morphological features in pathological images, we utilized Class Activation Mapping (CAM) technique and cluster analysis to investigate the connections between BRCA gene mutation status and tissue and cell features. Significantly, we observed that tumor-infiltrating lymphocytes and the morphological characteristics of tumor cells appeared to be potential features associated with BRCA status. Conclusions An interpretable deep neural network model based on the attention mechanism was developed to predict the BRCA status in breast cancer. Keywords: Breast cancer, BRCA, deep learning, self-attention, interpretability.
format: application/pdf
format: text/html
creator: Yi Li
creator: Xiaomin Xiong
creator: Xiaohua Liu
creator: Yihan Wu
creator: Xiaoju Li
creator: Bo Liu
creator: Bo Lin
creator: Yu Li
creator: Bo Xu
subject: Computational Biology
subject: Oncology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.18098
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background Determining the status of breast cancer susceptibility genes (BRCA) is crucial for guiding breast cancer treatment. Nevertheless, the need for BRCA genetic testing among breast cancer patients remains unmet due to high costs and limited resources. This study aimed to develop a Bi-directional Self-Attention Multiple Instance Learning (BiAMIL) algorithm to detect BRCA status from hematoxylin and eosin (H&E) pathological images. Methods A total of 319 histopathological slides from 254 breast cancer patients were included, comprising two dependent cohorts. Following image pre-processing, 633,484 tumor tiles from the training dataset were employed to train the self-developed deep-learning model. The performance of the network was evaluated in the internal and external test sets. Results BiAMIL achieved AUC values of 0.819 (95% CI [0.673–0.965]) in the internal test set, and 0.817 (95% CI [0.712–0.923]) in the external test set. To explore the relationship between BRCA status and interpretable morphological features in pathological images, we utilized Class Activation Mapping (CAM) technique and cluster analysis to investigate the connections between BRCA gene mutation status and tissue and cell features. Significantly, we observed that tumor-infiltrating lymphocytes and the morphological characteristics of tumor cells appeared to be potential features associated with BRCA status. Conclusions An interpretable deep neural network model based on the attention mechanism was developed to predict the BRCA status in breast cancer. Keywords: Breast cancer, BRCA, deep learning, self-attention, interpretability.
bibliographic citation: Li et al. (2024) An interpretable deep learning model for detecting BRCA pathogenic variants of breast cancer from hematoxylin and eosin-stained pathological images. PeerJ 12:e18098 https://doi.org/10.7717/peerj.18098
date submitted: 2024-04-17
date accepted: 2024-08-26
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yi
author list: Agent
  family name: Xiong
  given name: Xiaomin
author list: Agent
  family name: Liu
  given name: Xiaohua
author list: Agent
  family name: Wu
  given name: Yihan
author list: Agent
  family name: Li
  given name: Xiaoju
author list: Agent
  family name: Liu
  given name: Bo
author list: Agent
  family name: Lin
  given name: Bo
author list: Agent
  family name: Li
  given name: Yu
author list: Agent
  family name: Xu
  given name: Bo
doi: 10.7717/peerj.18098
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: © 2024 Li et al.
attribution name: Li et al.

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