PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Investigating molecular markers linked to acute myocardial infarction and cuproptosis: bioinformatics analysis and validation in the AMI mice model
items: Genome-wide identification and expression analysis of the WRKY gene family in Rhododendron henanense subsp. lingbaoense
items: Effects of high-intensity sprint exercise on neuromuscular function in sprinters: the countermovement jump as a fatigue assessment tool
items: Dose-response relationship between weekly physical activity level and the frequency of colds in Chinese middle-aged and elderly individuals
items: Effect of SlSAHH2 on metabolites in over-expressed and wild-type tomato fruit
items: The impact of history of depression and access to weapons on suicide risk assessment: a comparison of ChatGPT-3.5 and ChatGPT-4
items: SlZIP11 mediates zinc accumulation and sugar storage in tomato fruits
items: Neoadjuvant chemotherapy efficacy and prognosis in HER2-low and HER2-zero breast cancer patients by HR status: a retrospective study in China
items: Genome-wide identification and characterization of SPXdomain-containing genes family in eggplant
items: Single-cell transcriptome reveals the heterogeneity of malignant ductal cells and the prognostic value of REG4 and SPINK1 in primary pancreatic ductal adenocarcinoma

Investigating molecular markers linked to acute myocardial infarction and cuproptosis: bioinformatics analysis and validation in the AMI mice model
type: item
type: AcademicArticle
description: Cuproptosis-related key genes play a significant role in the pathological processes of acute myocardial infarction (AMI). However, a complete understanding of the molecular mechanisms behind this participation remains elusive. This study was designed to identify genes and immune cells critical to AMI pathogenesis. Based on the GSE48060 dataset (31 AMI patients and 21 healthy persons, GPL570-55999), we identified genes associated with dysregulated cuproptosis and the activation of immune responses between normal subjects and patients with a first myocardial attack. Two molecular clusters associated with cuproptosis were defined in patients with AMI. Immune infiltration analysis showed that there was significant immunity heterogeneity among different clusters. Multiple immune responses were closely associated with Cluster2-specific differentially expressed genes (DEGs). The generalized linear model machine model presented the best discriminative performance with relatively lower residual and root mean square error, and a higher area under the curve (AUC = 0.870). A final two-gene-based generalized linear model was constructed, exhibiting satisfactory performance in two external validation datasets (AUC = 0.719, GSE66360 and AUC = 0.856, GSE123342). Column graph, calibration curve, and decision curve analyses also proved the accuracy of AMI prediction. We also constructed a mouse C57BL/6 model of AMI (3 h, 48 h, and 1 week) and used qRT-PCR and immunofluorescence to detect the expression changes of CBLB and ZNF302. In this study, we present a systematic analysis of the complex relationship between cuproptosis and a first AMI attack, and provide new insights into the diagnosis and treatment of AMI.
format: application/pdf
format: text/html
creator: Bingyu Wang
creator: Jianqing Zhou
creator: Ning An
subject: Bioinformatics
subject: Cardiology
subject: Internal Medicine
subject: Nutrition
description: doi:10.7717/peerj.17280
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Cuproptosis-related key genes play a significant role in the pathological processes of acute myocardial infarction (AMI). However, a complete understanding of the molecular mechanisms behind this participation remains elusive. This study was designed to identify genes and immune cells critical to AMI pathogenesis. Based on the GSE48060 dataset (31 AMI patients and 21 healthy persons, GPL570-55999), we identified genes associated with dysregulated cuproptosis and the activation of immune responses between normal subjects and patients with a first myocardial attack. Two molecular clusters associated with cuproptosis were defined in patients with AMI. Immune infiltration analysis showed that there was significant immunity heterogeneity among different clusters. Multiple immune responses were closely associated with Cluster2-specific differentially expressed genes (DEGs). The generalized linear model machine model presented the best discriminative performance with relatively lower residual and root mean square error, and a higher area under the curve (AUC = 0.870). A final two-gene-based generalized linear model was constructed, exhibiting satisfactory performance in two external validation datasets (AUC = 0.719, GSE66360 and AUC = 0.856, GSE123342). Column graph, calibration curve, and decision curve analyses also proved the accuracy of AMI prediction. We also constructed a mouse C57BL/6 model of AMI (3 h, 48 h, and 1 week) and used qRT-PCR and immunofluorescence to detect the expression changes of CBLB and ZNF302. In this study, we present a systematic analysis of the complex relationship between cuproptosis and a first AMI attack, and provide new insights into the diagnosis and treatment of AMI.
bibliographic citation: Wang et al. (2024) Investigating molecular markers linked to acute myocardial infarction and cuproptosis: bioinformatics analysis and validation in the AMI mice model. PeerJ 12:e17280 https://doi.org/10.7717/peerj.17280
date submitted: 2023-10-24
date accepted: 2024-04-01
issued: 2024-05-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Bingyu
author list: Agent
  family name: Zhou
  given name: Jianqing
author list: Agent
  family name: An
  given name: Ning
doi: 10.7717/peerj.17280
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-29
copyright: © 2024 Wang et al.
attribution name: Wang et al.

Genome-wide identification and expression analysis of the WRKY gene family in Rhododendron henanense subsp. lingbaoense
type: item
type: AcademicArticle
description: Background This work explored the characteristics of the WRKY transcription factor family in Rhododendron henanense subsp. lingbaoense (Rhl) and the expression patterns of these genes under abiotic stress by conducting bioinformatics and expression analyses. Methods RhlWRKY genes were identified from a gene library of Rhl. Various aspects of these genes were analyzed, including genetic structures, conserved sequences, physicochemical properties, cis-acting elements, and chromosomal location. RNA-seq was employed to analyze gene expression in five different tissues of Rhl: roots, stems, leaves, flowers, and hypocotyls. Additionally, qRT-PCR was used to detect changes in the expression of five RhlWRKY genes under abiotic stress. Result A total of 65 RhlWRKY genes were identified and categorized into three subfamilies based on their structural characteristics: Groups I, II, and III. Group II was further divided into five subtribes, with shared similar genetic structures and conserved motifs among members of the same subtribe. The physicochemical properties of these proteins varied, but the proteins are generally predicted to be hydrophilic. Most proteins are predicted to be in the cell nucleus, and distributed across 12 chromosomes. A total of 84 cis-acting elements were discovered, with many related to responses to biotic stress. Among the identified RhlWRKY genes, there were eight tandem duplicates and 97 segmental duplicates. The majority of duplicate gene pairs exhibited Ka/Ks values <1, indicating purification under environmental pressure. GO annotation analysis indicated that WRKY genes regulate biological processes and participate in a variety of molecular functions. Transcriptome data revealed varying expression levels of 66.15% of WRKY family genes in all five tissue types (roots, stems, leaves, flowers, and hypocotyls). Five RhlWRKY genes were selected for further characterization and there were changes in expression levels for these genes in response to vari…
format: application/pdf
format: text/html
creator: Xiangmeng Guo
creator: Xinyu Yan
creator: Yonghui Li
subject: Agricultural Science
subject: Bioinformatics
subject: Conservation Biology
subject: Plant Science
description: doi:10.7717/peerj.17435
publisher: PeerJ Inc.
rights: © 2024 Guo et al.
abstract: Background This work explored the characteristics of the WRKY transcription factor family in Rhododendron henanense subsp. lingbaoense (Rhl) and the expression patterns of these genes under abiotic stress by conducting bioinformatics and expression analyses. Methods RhlWRKY genes were identified from a gene library of Rhl. Various aspects of these genes were analyzed, including genetic structures, conserved sequences, physicochemical properties, cis-acting elements, and chromosomal location. RNA-seq was employed to analyze gene expression in five different tissues of Rhl: roots, stems, leaves, flowers, and hypocotyls. Additionally, qRT-PCR was used to detect changes in the expression of five RhlWRKY genes under abiotic stress. Result A total of 65 RhlWRKY genes were identified and categorized into three subfamilies based on their structural characteristics: Groups I, II, and III. Group II was further divided into five subtribes, with shared similar genetic structures and conserved motifs among members of the same subtribe. The physicochemical properties of these proteins varied, but the proteins are generally predicted to be hydrophilic. Most proteins are predicted to be in the cell nucleus, and distributed across 12 chromosomes. A total of 84 cis-acting elements were discovered, with many related to responses to biotic stress. Among the identified RhlWRKY genes, there were eight tandem duplicates and 97 segmental duplicates. The majority of duplicate gene pairs exhibited Ka/Ks values <1, indicating purification under environmental pressure. GO annotation analysis indicated that WRKY genes regulate biological processes and participate in a variety of molecular functions. Transcriptome data revealed varying expression levels of 66.15% of WRKY family genes in all five tissue types (roots, stems, leaves, flowers, and hypocotyls). Five RhlWRKY genes were selected for further characterization and there were changes in expression levels for these genes in response to vari…
bibliographic citation: Guo et al. (2024) Genome-wide identification and expression analysis of the WRKY gene family in Rhododendron henanense subsp. lingbaoense. PeerJ 12:e17435 https://doi.org/10.7717/peerj.17435
date submitted: 2024-01-24
date accepted: 2024-04-30
issued: 2024-05-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Xiangmeng
author list: Agent
  family name: Yan
  given name: Xinyu
author list: Agent
  family name: Li
  given name: Yonghui
doi: 10.7717/peerj.17435
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-29
copyright: © 2024 Guo et al.
attribution name: Guo et al.

Effects of high-intensity sprint exercise on neuromuscular function in sprinters: the countermovement jump as a fatigue assessment tool
type: item
type: AcademicArticle
description: Background High-intensity sprint exercises (HIS) are central to sprinter training and require careful monitoring of athlete muscle fatigue to improve performance and prevent injury. While the countermovement jump (CMJ) may be used to monitor neuromuscular fatigue (NMF), little is known about the specific effects from HIS. The purpose of this study is to investigate the effects of HIS on the CMJ to assess its utility for assessing NMF following HIS. Methods Ten male collegiate 400 m sprinters completed a 400 m sprint fatigue protocol and underwent five CMJ-testing sessions (baseline, 3 minutes, 10 minutes, 1 hour and 24 hours) over two days. Three CMJ trials, performed on a force plate, were completed each trial, with rating of perceived exertion (RPE) recorded as a subjective fatigue measure. Changes in RPE, CMJ variables, force-time and power-time curves at baseline and post fatigue were assessed. Results Significant changes were observed in most variables following the fatigue protocol. In particular, concentric mean power remained significantly lower after 24 hours compared to baseline. In addition, the force-time curves exhibited a significant reduction in all conditions following the fatigue protocol. This decline was most pronounced within 50–75%of the concentric phase relative to baseline measurements. Conclusion. Results indicate that the CMJ may be a useful tool for monitoring fatigue in at least 400 m sprinters. These data also indicate that HIS may disproportionately reduce force output in during concentric movement. These insights may improve training prescriptions and injury prevention strategies for sprint athletes.
format: application/pdf
format: text/html
creator: Takahiro Hasegawa
creator: Kotaro Muratomi
creator: Yuki Furuhashi
creator: Jun Mizushima
creator: Hirohiko Maemura
subject: Kinesiology
subject: Biomechanics
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.17443
publisher: PeerJ Inc.
rights: © 2024 Hasegawa et al.
abstract: Background High-intensity sprint exercises (HIS) are central to sprinter training and require careful monitoring of athlete muscle fatigue to improve performance and prevent injury. While the countermovement jump (CMJ) may be used to monitor neuromuscular fatigue (NMF), little is known about the specific effects from HIS. The purpose of this study is to investigate the effects of HIS on the CMJ to assess its utility for assessing NMF following HIS. Methods Ten male collegiate 400 m sprinters completed a 400 m sprint fatigue protocol and underwent five CMJ-testing sessions (baseline, 3 minutes, 10 minutes, 1 hour and 24 hours) over two days. Three CMJ trials, performed on a force plate, were completed each trial, with rating of perceived exertion (RPE) recorded as a subjective fatigue measure. Changes in RPE, CMJ variables, force-time and power-time curves at baseline and post fatigue were assessed. Results Significant changes were observed in most variables following the fatigue protocol. In particular, concentric mean power remained significantly lower after 24 hours compared to baseline. In addition, the force-time curves exhibited a significant reduction in all conditions following the fatigue protocol. This decline was most pronounced within 50–75%of the concentric phase relative to baseline measurements. Conclusion. Results indicate that the CMJ may be a useful tool for monitoring fatigue in at least 400 m sprinters. These data also indicate that HIS may disproportionately reduce force output in during concentric movement. These insights may improve training prescriptions and injury prevention strategies for sprint athletes.
bibliographic citation: Hasegawa et al. (2024) Effects of high-intensity sprint exercise on neuromuscular function in sprinters: the countermovement jump as a fatigue assessment tool. PeerJ 12:e17443 https://doi.org/10.7717/peerj.17443
date submitted: 2024-01-09
date accepted: 2024-04-30
issued: 2024-05-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hasegawa
  given name: Takahiro
author list: Agent
  family name: Muratomi
  given name: Kotaro
author list: Agent
  family name: Furuhashi
  given name: Yuki
author list: Agent
  family name: Mizushima
  given name: Jun
author list: Agent
  family name: Maemura
  given name: Hirohiko
doi: 10.7717/peerj.17443
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-29
copyright: ©2024 Hasegawa et al.
attribution name: Hasegawa et al.

Dose-response relationship between weekly physical activity level and the frequency of colds in Chinese middle-aged and elderly individuals
type: item
type: AcademicArticle
description: Background Engaging in appropriate physical activity can significantly lower the risk of various diseases among middle-aged and older adults. Investigating optimal levels of physical activity (PA) is crucial for enhancing the health of this demographic. This study aims to explore the dose–response relationship between weekly PA levels and the frequency of colds among Chinese middle-aged and elderly individuals, identifying the necessary PA level to effectively diminish the risk of colds. Methods We conducted a cross-sectional study using a web-based survey targeting individuals aged 40 and older (n = 1, 683) in China. The survey collected information on PA and the frequency of colds. Data was analyzed using Kruskal–Wallis test and the χ2 test. We explored the dose–response relationship between weekly PA and cold frequency over the past year through an ordered multivariate logistic regression model and a restricted cubic spline model. Results (1) Brisk walking emerged as the preferred physical exercise for those over 40. The findings suggest that engaging in moderate (odds ratio (OR) = 0.64, P < 0.001, 95% confidence interval (CI) [0.50–0.81]) and high (OR = 0.64, P < 0.001, 95% CI [0.51–0.79]) levels of PA weekly significantly reduces the risk of catching a cold. Individuals with one (OR = 1.47, P < 0.001, 95% CI [1.20–1.80]) or multiple chronic diseases (OR = 1.56, P < 0.001, 95% CI [1.21–2.00]) were at increased risk. Those residing in central (OR = 1.64, P < 0.001, 95% CI [1.33–02.01]) and western China (OR = 1.49, P = 0.008, 95% CI [1.11–02.00]) faced a higher risk compared to their counterparts in eastern China. (2) According to the restricted cubic spline model, adults who experienced one cold in the past year had a weekly PA level of 537.29 metabolic equivalent-minutes per week (MET-min/wk) with an OR value of 1. For those reporting two or more colds, the PA level was 537.76 MET-min/wk with an OR of 1. Conclusions (1) Brisk walking is the most favored exercis…
format: application/pdf
format: text/html
creator: Xiaona Tang
creator: Yichao Yu
creator: Xiaoxue Wu
creator: Chengru Xu
creator: Zhao Zhang
creator: Yifan Lu
subject: Geriatrics
subject: Global Health
subject: Public Health
subject: Sports Medicine
description: doi:10.7717/peerj.17459
publisher: PeerJ Inc.
rights: © 2024 Tang et al.
abstract: Background Engaging in appropriate physical activity can significantly lower the risk of various diseases among middle-aged and older adults. Investigating optimal levels of physical activity (PA) is crucial for enhancing the health of this demographic. This study aims to explore the dose–response relationship between weekly PA levels and the frequency of colds among Chinese middle-aged and elderly individuals, identifying the necessary PA level to effectively diminish the risk of colds. Methods We conducted a cross-sectional study using a web-based survey targeting individuals aged 40 and older (n = 1, 683) in China. The survey collected information on PA and the frequency of colds. Data was analyzed using Kruskal–Wallis test and the χ2 test. We explored the dose–response relationship between weekly PA and cold frequency over the past year through an ordered multivariate logistic regression model and a restricted cubic spline model. Results (1) Brisk walking emerged as the preferred physical exercise for those over 40. The findings suggest that engaging in moderate (odds ratio (OR) = 0.64, P < 0.001, 95% confidence interval (CI) [0.50–0.81]) and high (OR = 0.64, P < 0.001, 95% CI [0.51–0.79]) levels of PA weekly significantly reduces the risk of catching a cold. Individuals with one (OR = 1.47, P < 0.001, 95% CI [1.20–1.80]) or multiple chronic diseases (OR = 1.56, P < 0.001, 95% CI [1.21–2.00]) were at increased risk. Those residing in central (OR = 1.64, P < 0.001, 95% CI [1.33–02.01]) and western China (OR = 1.49, P = 0.008, 95% CI [1.11–02.00]) faced a higher risk compared to their counterparts in eastern China. (2) According to the restricted cubic spline model, adults who experienced one cold in the past year had a weekly PA level of 537.29 metabolic equivalent-minutes per week (MET-min/wk) with an OR value of 1. For those reporting two or more colds, the PA level was 537.76 MET-min/wk with an OR of 1. Conclusions (1) Brisk walking is the most favored exercis…
bibliographic citation: Tang et al. (2024) Dose-response relationship between weekly physical activity level and the frequency of colds in Chinese middle-aged and elderly individuals. PeerJ 12:e17459 https://doi.org/10.7717/peerj.17459
date submitted: 2024-01-25
date accepted: 2024-05-03
issued: 2024-05-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Xiaona
author list: Agent
  family name: Yu
  given name: Yichao
author list: Agent
  family name: Wu
  given name: Xiaoxue
author list: Agent
  family name: Xu
  given name: Chengru
author list: Agent
  family name: Zhang
  given name: Zhao
author list: Agent
  family name: Lu
  given name: Yifan
doi: 10.7717/peerj.17459
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-29
copyright: ©2024 Tang et al.
attribution name: Tang et al.

Effect of SlSAHH2 on metabolites in over-expressed and wild-type tomato fruit
type: item
type: AcademicArticle
description: Background Tomato (Solanum lycopersicum) is an annual or perennial herb that occupies an important position in daily agricultural production. It is an essential food crop for humans and its ripening process is regulated by a number of genes. S-adenosyl-l-homocysteine hydrolase (AdoHcyase, EC 3.3.1.1) is widespread in organisms and plays an important role in regulating biological methylation reactions. Previous studies have revealed that transgenic tomato that over-express SlSAHH2 ripen earlier than the wild-type (WT). However, the differences in metabolites and the mechanisms driving how these differences affect the ripening cycle are unclear. Objective To investigate the effects of SlSAHH2 on metabolites in over-expressed tomato and WT tomato. Methods SlSAHH2 over-expressed tomato fruit (OE-5# and OE-6#) and WT tomato fruit at the breaker stage (Br) were selected for non-targeted metabolome analysis. Results A total of 733 metabolites were identified by mass spectrometry using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the Human Metabolome database (HMDB). The metabolites were divided into 12 categories based on the superclass results and a comparison with the HMDB. The differences between the two databases were analyzed by PLS-DA. Based on a variable important in projection value >1 and P < 0.05, 103 differential metabolites were found between tomato variety OE-5# and WT and 63 differential metabolites were found between OE-6# and WT. These included dehydrotomatine, L-serine, and gallic acid amongst others. Many metabolites are associated with fruit ripening and eight common metabolites were found between the OE-5# vs. WT and OE-6# vs. WT comparison groups. The low L-tryptophan expression in OE-5# and OE-6# is consistent with previous reports that its content decreases with fruit ripening. A KEGG pathway enrichment analysis of the significantly different metabolites revealed that in the OE-5# and WT groups, up-regulated metabolites were enrich…
format: application/pdf
format: text/html
creator: Lu Yang
creator: Yue Teng
creator: Sijia Bu
creator: Ben Ma
creator: Shijia Guo
creator: Mengxiao Liang
creator: Lifen Huang
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.17466
publisher: PeerJ Inc.
rights: © 2024 Yang et al.
abstract: Background Tomato (Solanum lycopersicum) is an annual or perennial herb that occupies an important position in daily agricultural production. It is an essential food crop for humans and its ripening process is regulated by a number of genes. S-adenosyl-l-homocysteine hydrolase (AdoHcyase, EC 3.3.1.1) is widespread in organisms and plays an important role in regulating biological methylation reactions. Previous studies have revealed that transgenic tomato that over-express SlSAHH2 ripen earlier than the wild-type (WT). However, the differences in metabolites and the mechanisms driving how these differences affect the ripening cycle are unclear. Objective To investigate the effects of SlSAHH2 on metabolites in over-expressed tomato and WT tomato. Methods SlSAHH2 over-expressed tomato fruit (OE-5# and OE-6#) and WT tomato fruit at the breaker stage (Br) were selected for non-targeted metabolome analysis. Results A total of 733 metabolites were identified by mass spectrometry using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the Human Metabolome database (HMDB). The metabolites were divided into 12 categories based on the superclass results and a comparison with the HMDB. The differences between the two databases were analyzed by PLS-DA. Based on a variable important in projection value >1 and P < 0.05, 103 differential metabolites were found between tomato variety OE-5# and WT and 63 differential metabolites were found between OE-6# and WT. These included dehydrotomatine, L-serine, and gallic acid amongst others. Many metabolites are associated with fruit ripening and eight common metabolites were found between the OE-5# vs. WT and OE-6# vs. WT comparison groups. The low L-tryptophan expression in OE-5# and OE-6# is consistent with previous reports that its content decreases with fruit ripening. A KEGG pathway enrichment analysis of the significantly different metabolites revealed that in the OE-5# and WT groups, up-regulated metabolites were enrich…
bibliographic citation: Yang et al. (2024) Effect of SlSAHH2 on metabolites in over-expressed and wild-type tomato fruit. PeerJ 12:e17466 https://doi.org/10.7717/peerj.17466
date submitted: 2023-11-16
date accepted: 2024-05-05
issued: 2024-05-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Lu
author list: Agent
  family name: Teng
  given name: Yue
author list: Agent
  family name: Bu
  given name: Sijia
author list: Agent
  family name: Ma
  given name: Ben
author list: Agent
  family name: Guo
  given name: Shijia
author list: Agent
  family name: Liang
  given name: Mengxiao
author list: Agent
  family name: Huang
  given name: Lifen
doi: 10.7717/peerj.17466
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-29
copyright: © 2024 Yang et al.
attribution name: Yang et al.

The impact of history of depression and access to weapons on suicide risk assessment: a comparison of ChatGPT-3.5 and ChatGPT-4
type: item
type: AcademicArticle
description: The aim of this study was to evaluate the effectiveness of ChatGPT-3.5 and ChatGPT-4 in incorporating critical risk factors, namely history of depression and access to weapons, into suicide risk assessments. Both models assessed suicide risk using scenarios that featured individuals with and without a history of depression and access to weapons. The models estimated the likelihood of suicidal thoughts, suicide attempts, serious suicide attempts, and suicide-related mortality on a Likert scale. A multivariate three-way ANOVA analysis with Bonferroni post hoc tests was conducted to examine the impact of the forementioned independent factors (history of depression and access to weapons) on these outcome variables. Both models identified history of depression as a significant suicide risk factor. ChatGPT-4 demonstrated a more nuanced understanding of the relationship between depression, access to weapons, and suicide risk. In contrast, ChatGPT-3.5 displayed limited insight into this complex relationship. ChatGPT-4 consistently assigned higher severity ratings to suicide-related variables than did ChatGPT-3.5. The study highlights the potential of these two models, particularly ChatGPT-4, to enhance suicide risk assessment by considering complex risk factors.
format: application/pdf
format: text/html
creator: Shiri Shinan-Altman
creator: Zohar Elyoseph
creator: Inbar Levkovich
subject: Psychiatry and Psychology
subject: Public Health
subject: Ethical Issues
subject: Mental Health
description: doi:10.7717/peerj.17468
publisher: PeerJ Inc.
rights: © 2024 Shinan-Altman et al.
abstract: The aim of this study was to evaluate the effectiveness of ChatGPT-3.5 and ChatGPT-4 in incorporating critical risk factors, namely history of depression and access to weapons, into suicide risk assessments. Both models assessed suicide risk using scenarios that featured individuals with and without a history of depression and access to weapons. The models estimated the likelihood of suicidal thoughts, suicide attempts, serious suicide attempts, and suicide-related mortality on a Likert scale. A multivariate three-way ANOVA analysis with Bonferroni post hoc tests was conducted to examine the impact of the forementioned independent factors (history of depression and access to weapons) on these outcome variables. Both models identified history of depression as a significant suicide risk factor. ChatGPT-4 demonstrated a more nuanced understanding of the relationship between depression, access to weapons, and suicide risk. In contrast, ChatGPT-3.5 displayed limited insight into this complex relationship. ChatGPT-4 consistently assigned higher severity ratings to suicide-related variables than did ChatGPT-3.5. The study highlights the potential of these two models, particularly ChatGPT-4, to enhance suicide risk assessment by considering complex risk factors.
bibliographic citation: Shinan-Altman et al. (2024) The impact of history of depression and access to weapons on suicide risk assessment: a comparison of ChatGPT-3.5 and ChatGPT-4. PeerJ 12:e17468 https://doi.org/10.7717/peerj.17468
date submitted: 2023-11-07
date accepted: 2024-05-05
issued: 2024-05-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shinan-Altman
  given name: Shiri
author list: Agent
  family name: Elyoseph
  given name: Zohar
author list: Agent
  family name: Levkovich
  given name: Inbar
doi: 10.7717/peerj.17468
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-29
copyright: © 2024 Shinan-Altman et al.
attribution name: Shinan-Altman et al.

SlZIP11 mediates zinc accumulation and sugar storage in tomato fruits
type: item
type: AcademicArticle
description: Background Zinc (Zn) is a vital micronutrient essential for plant growth and development. Transporter proteins of the ZRT/IRT-like protein (ZIP) family play crucial roles in maintaining Zn homeostasis. Although the acquisition, translocation, and intracellular transport of Zn are well understood in plant roots and leaves, the genes that regulate these pathways in fruits remain largely unexplored. In this study, we aimed to investigate the function of SlZIP11 in regulating tomato fruit development. Methods We used Solanum lycopersicum L. ‘Micro-Tom’ SlZIP11 (Solanum lycopersicum) is highly expressed in tomato fruit, particularly in mature green (MG) stages. For obtaining results, we employed reverse transcription-quantitative polymerase chain reaction (RT-qPCR), yeast two-hybrid assay, bimolecular fluorescent complementation, subcellular localization assay, virus-induced gene silencing (VIGS), SlZIP11 overexpression, determination of Zn content, sugar extraction and content determination, and statistical analysis. Results RT-qPCR analysis showed elevated SlZIP11 expression in MG tomato fruits. SlZIP11 expression was inhibited and induced by Zn deficiency and toxicity treatments, respectively. Silencing SlZIP11 via the VIGS technology resulted in a significant increase in the Zn content of tomato fruits. In contrast, overexpression of SlZIP11 led to reduced Zn content in MG fruits. Moreover, both silencing and overexpression of SlZIP11 caused alterations in the fructose and glucose contents of tomato fruits. Additionally, SlSWEEET7a interacted with SlZIP11. The heterodimerization between SlSWEET7a and SlZIP11 affected subcellular targeting, thereby increasing the amount of intracellularly localized oligomeric complexes. Overall, this study elucidates the role of SlZIP11 in mediating Zn accumulation and sugar transport during tomato fruit ripening. These findings underscore the significance of SlZIP11 in regulating Zn levels and sugar content, providing insights into i…
format: application/pdf
format: text/html
creator: Jiaqi Sun
creator: Manning Wang
creator: Xinsheng Zhang
creator: Xin Liu
creator: Jing Jiang
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.17473
publisher: PeerJ Inc.
rights: © 2024 Sun et al.
abstract: Background Zinc (Zn) is a vital micronutrient essential for plant growth and development. Transporter proteins of the ZRT/IRT-like protein (ZIP) family play crucial roles in maintaining Zn homeostasis. Although the acquisition, translocation, and intracellular transport of Zn are well understood in plant roots and leaves, the genes that regulate these pathways in fruits remain largely unexplored. In this study, we aimed to investigate the function of SlZIP11 in regulating tomato fruit development. Methods We used Solanum lycopersicum L. ‘Micro-Tom’ SlZIP11 (Solanum lycopersicum) is highly expressed in tomato fruit, particularly in mature green (MG) stages. For obtaining results, we employed reverse transcription-quantitative polymerase chain reaction (RT-qPCR), yeast two-hybrid assay, bimolecular fluorescent complementation, subcellular localization assay, virus-induced gene silencing (VIGS), SlZIP11 overexpression, determination of Zn content, sugar extraction and content determination, and statistical analysis. Results RT-qPCR analysis showed elevated SlZIP11 expression in MG tomato fruits. SlZIP11 expression was inhibited and induced by Zn deficiency and toxicity treatments, respectively. Silencing SlZIP11 via the VIGS technology resulted in a significant increase in the Zn content of tomato fruits. In contrast, overexpression of SlZIP11 led to reduced Zn content in MG fruits. Moreover, both silencing and overexpression of SlZIP11 caused alterations in the fructose and glucose contents of tomato fruits. Additionally, SlSWEEET7a interacted with SlZIP11. The heterodimerization between SlSWEET7a and SlZIP11 affected subcellular targeting, thereby increasing the amount of intracellularly localized oligomeric complexes. Overall, this study elucidates the role of SlZIP11 in mediating Zn accumulation and sugar transport during tomato fruit ripening. These findings underscore the significance of SlZIP11 in regulating Zn levels and sugar content, providing insights into i…
bibliographic citation: Sun et al. (2024) SlZIP11 mediates zinc accumulation and sugar storage in tomato fruits. PeerJ 12:e17473 https://doi.org/10.7717/peerj.17473
date submitted: 2024-02-08
date accepted: 2024-05-06
issued: 2024-05-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Jiaqi
author list: Agent
  family name: Wang
  given name: Manning
author list: Agent
  family name: Zhang
  given name: Xinsheng
author list: Agent
  family name: Liu
  given name: Xin
author list: Agent
  family name: Jiang
  given name: Jing
doi: 10.7717/peerj.17473
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-29
copyright: © 2024 Sun et al.
attribution name: Sun et al.

Neoadjuvant chemotherapy efficacy and prognosis in HER2-low and HER2-zero breast cancer patients by HR status: a retrospective study in China
type: item
type: AcademicArticle
description: Background The promising efficacy of novel anti-HER2 antibody-drug conjugates (ADC) in HER2-low breast cancer has made HER2-low a research hotspot. However, controversy remains regarding the neoadjuvant chemotherapy (NAC) efficacy, prognosis, and the relationship with hormone receptor (HR) status of HER2-low. Methods A retrospective analysis was conducted on 975 patients with HER2-negative breast cancer undergoing NAC at Tianjin Medical University Cancer Institute and Hospital, evaluating pathological complete response (pCR) rate and prognosis between HER2-low and HER2-zero in the overall cohort and subgroups. Results Overall, 579 (59.4%) and 396 (40.6%) patients were HER2-low and HER2-zero disease, respectively. Compared with HER2-zero, the HER2-low cohort consists of more postmenopausal patients, with lower histological grade and higher HR positivity. In the HR-positive subgroup, HER2-low cases remain to exhibit lower histological grade, while in the HR-negative subgroup, they show higher grade. The HER2-low group had lower pCR rates than the HER2-zero group (16.4% vs. 24.0%). In the HR-positive subgroup, HER2-low consistently showed lower pCR rate (8.1% vs. 15.5%), and served as an independent suppressive factor for the pCR rate. However, no significant difference was observed in the pCR rates between HER2-low and HER2-zero in the HR-negative breast cancer. In the entire cohort and in stratified subgroups based on HR and pCR statuses, no difference in disease-free survival were observed between HER2-low and HER2-zero. Conclusions In the Chinese population, HER2-low breast cancer exhibits distinct characteristics and efficacy of NAC in different HR subgroups. Its reduced pCR rate in HR-positive subgroup is particularly important for clinical decisions. However, HER2-low is not a reliable factor for assessing long-term survival outcomes.
format: application/pdf
format: text/html
creator: Shaorong Zhao
creator: Yuyun Wang
creator: Angxiao Zhou
creator: Xu Liu
creator: Yi Zhang
creator: Jin Zhang
subject: Genetics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.17492
publisher: PeerJ Inc.
rights: © 2024 Zhao et al.
abstract: Background The promising efficacy of novel anti-HER2 antibody-drug conjugates (ADC) in HER2-low breast cancer has made HER2-low a research hotspot. However, controversy remains regarding the neoadjuvant chemotherapy (NAC) efficacy, prognosis, and the relationship with hormone receptor (HR) status of HER2-low. Methods A retrospective analysis was conducted on 975 patients with HER2-negative breast cancer undergoing NAC at Tianjin Medical University Cancer Institute and Hospital, evaluating pathological complete response (pCR) rate and prognosis between HER2-low and HER2-zero in the overall cohort and subgroups. Results Overall, 579 (59.4%) and 396 (40.6%) patients were HER2-low and HER2-zero disease, respectively. Compared with HER2-zero, the HER2-low cohort consists of more postmenopausal patients, with lower histological grade and higher HR positivity. In the HR-positive subgroup, HER2-low cases remain to exhibit lower histological grade, while in the HR-negative subgroup, they show higher grade. The HER2-low group had lower pCR rates than the HER2-zero group (16.4% vs. 24.0%). In the HR-positive subgroup, HER2-low consistently showed lower pCR rate (8.1% vs. 15.5%), and served as an independent suppressive factor for the pCR rate. However, no significant difference was observed in the pCR rates between HER2-low and HER2-zero in the HR-negative breast cancer. In the entire cohort and in stratified subgroups based on HR and pCR statuses, no difference in disease-free survival were observed between HER2-low and HER2-zero. Conclusions In the Chinese population, HER2-low breast cancer exhibits distinct characteristics and efficacy of NAC in different HR subgroups. Its reduced pCR rate in HR-positive subgroup is particularly important for clinical decisions. However, HER2-low is not a reliable factor for assessing long-term survival outcomes.
bibliographic citation: Zhao et al. (2024) Neoadjuvant chemotherapy efficacy and prognosis in HER2-low and HER2-zero breast cancer patients by HR status: a retrospective study in China. PeerJ 12:e17492 https://doi.org/10.7717/peerj.17492
date submitted: 2024-02-28
date accepted: 2024-05-09
issued: 2024-05-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Shaorong
author list: Agent
  family name: Wang
  given name: Yuyun
author list: Agent
  family name: Zhou
  given name: Angxiao
author list: Agent
  family name: Liu
  given name: Xu
author list: Agent
  family name: Zhang
  given name: Yi
author list: Agent
  family name: Zhang
  given name: Jin
doi: 10.7717/peerj.17492
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-29
copyright: © 2024 Zhao et al.
attribution name: Zhao et al.

Genome-wide identification and characterization of SPXdomain-containing genes family in eggplant
type: item
type: AcademicArticle
description: Phosphorus is one of the lowest elements absorbed and utilized by plants in the soil. SPX domain-containing genes family play an important role in plant response to phosphate deficiency signaling pathway, and related to seed development, disease resistance, absorption and transport of other nutrients. However, there are no reports on the mechanism of SPX domain-containing genes in response to phosphorus deficiency in eggplant. In this study, the whole genome identification and functional analysis of SPX domain-containing genes family in eggplant were carried out. Sixteen eggplant SPX domain-containing genes were identified and divided into four categories. Subcellular localization showed that these proteins were located in different cell compartments, including nucleus and membrane system. The expression patterns of these genes in different tissues as well as under phosphate deficiency with auxin were explored. The results showed that SmSPX1, SmSPX5 and SmSPX12 were highest expressed in roots. SmSPX1, SmSPX4, SmSPX5 and SmSPX14 were significantly induced by phosphate deficiency and may be the key candidate genes in response to phosphate starvation in eggplant. Among them, SmSPX1 and SmSPX5 can be induced by auxin under phosphate deficiency. In conclusion, our study preliminary identified the SPX domain genes in eggplant, and the relationship between SPX domain-containing genes and auxin was first analyzed in response to phosphate deficiency, which will provide theoretical basis for improving the absorption of phosphorus in eggplants through molecular breeding technology.
format: application/pdf
format: text/html
creator: Li Zhuomeng
creator: Tuo Ji
creator: Qi Chen
creator: Chenxiao Xu
creator: Yuqing Liu
creator: Xiaodong Yang
creator: Jing Li
creator: Fengjuan Yang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.17341
publisher: PeerJ Inc.
rights: © 2024 Zhuomeng et al.
abstract: Phosphorus is one of the lowest elements absorbed and utilized by plants in the soil. SPX domain-containing genes family play an important role in plant response to phosphate deficiency signaling pathway, and related to seed development, disease resistance, absorption and transport of other nutrients. However, there are no reports on the mechanism of SPX domain-containing genes in response to phosphorus deficiency in eggplant. In this study, the whole genome identification and functional analysis of SPX domain-containing genes family in eggplant were carried out. Sixteen eggplant SPX domain-containing genes were identified and divided into four categories. Subcellular localization showed that these proteins were located in different cell compartments, including nucleus and membrane system. The expression patterns of these genes in different tissues as well as under phosphate deficiency with auxin were explored. The results showed that SmSPX1, SmSPX5 and SmSPX12 were highest expressed in roots. SmSPX1, SmSPX4, SmSPX5 and SmSPX14 were significantly induced by phosphate deficiency and may be the key candidate genes in response to phosphate starvation in eggplant. Among them, SmSPX1 and SmSPX5 can be induced by auxin under phosphate deficiency. In conclusion, our study preliminary identified the SPX domain genes in eggplant, and the relationship between SPX domain-containing genes and auxin was first analyzed in response to phosphate deficiency, which will provide theoretical basis for improving the absorption of phosphorus in eggplants through molecular breeding technology.
bibliographic citation: Zhuomeng et al. (2024) Genome-wide identification and characterization of SPXdomain-containing genes family in eggplant. PeerJ 12:e17341 https://doi.org/10.7717/peerj.17341
date submitted: 2023-12-29
date accepted: 2024-04-15
issued: 2024-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhuomeng
  given name: Li
author list: Agent
  family name: Ji
  given name: Tuo
author list: Agent
  family name: Chen
  given name: Qi
author list: Agent
  family name: Xu
  given name: Chenxiao
author list: Agent
  family name: Liu
  given name: Yuqing
author list: Agent
  family name: Yang
  given name: Xiaodong
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Yang
  given name: Fengjuan
doi: 10.7717/peerj.17341
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-28
copyright: ©2024 Zhuomeng et al.
attribution name: Zhuomeng et al.

Single-cell transcriptome reveals the heterogeneity of malignant ductal cells and the prognostic value of REG4 and SPINK1 in primary pancreatic ductal adenocarcinoma
type: item
type: AcademicArticle
description: Background Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related deaths, with very limited therapeutic options available. This study aims to comprehensively depict the heterogeneity and identify prognostic targets for PDAC with single-cell RNA sequencing (scRNA-seq) analysis. Methods ScRNA-seq analysis was performed on 16 primary PDAC and three adjacent lesions. A series of analytical methods were applied for analysis in cell clustering, gene profiling, lineage trajectory analysis and cell-to-cell interactions. In vitro experiments including colony formation, wound healing and sphere formation assay were performed to assess the role of makers. Results A total of 32,480 cells were clustered into six major populations, among which the ductal cell cluster expressing high copy number variants (CNVs) was defined as malignant cells. Malignant cells were further subtyped into five subgroups which exhibited specific features in immunologic and metabolic activities. Pseudotime trajectory analysis indicated that components of various oncogenic pathways were differentially expressed along tumor progression. Furthermore, intensive substantial crosstalk between ductal cells and stromal cells was identified. Finally, genes (REG4 and SPINK1) screened out of differentially expressed genes (DEGs) were upregulated in PDAC cell lines. Silencing either of them significantly impaired proliferation, invasion, migration and stemness of PDAC cells. Conclusions Our findings offer a valuable resource for deciphering the heterogeneity of malignant ductal cells in PDAC. REG4 and SPINK1 are expected to be promising targets for PDAC therapy.
format: application/pdf
format: text/html
creator: Yutian Ji
creator: Qianhui Xu
creator: Weilin Wang
subject: Bioinformatics
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.17350
publisher: PeerJ Inc.
rights: © 2024 Ji et al.
abstract: Background Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related deaths, with very limited therapeutic options available. This study aims to comprehensively depict the heterogeneity and identify prognostic targets for PDAC with single-cell RNA sequencing (scRNA-seq) analysis. Methods ScRNA-seq analysis was performed on 16 primary PDAC and three adjacent lesions. A series of analytical methods were applied for analysis in cell clustering, gene profiling, lineage trajectory analysis and cell-to-cell interactions. In vitro experiments including colony formation, wound healing and sphere formation assay were performed to assess the role of makers. Results A total of 32,480 cells were clustered into six major populations, among which the ductal cell cluster expressing high copy number variants (CNVs) was defined as malignant cells. Malignant cells were further subtyped into five subgroups which exhibited specific features in immunologic and metabolic activities. Pseudotime trajectory analysis indicated that components of various oncogenic pathways were differentially expressed along tumor progression. Furthermore, intensive substantial crosstalk between ductal cells and stromal cells was identified. Finally, genes (REG4 and SPINK1) screened out of differentially expressed genes (DEGs) were upregulated in PDAC cell lines. Silencing either of them significantly impaired proliferation, invasion, migration and stemness of PDAC cells. Conclusions Our findings offer a valuable resource for deciphering the heterogeneity of malignant ductal cells in PDAC. REG4 and SPINK1 are expected to be promising targets for PDAC therapy.
bibliographic citation: Ji et al. (2024) Single-cell transcriptome reveals the heterogeneity of malignant ductal cells and the prognostic value of REG4 and SPINK1 in primary pancreatic ductal adenocarcinoma. PeerJ 12:e17350 https://doi.org/10.7717/peerj.17350
date submitted: 2023-12-12
date accepted: 2024-04-17
issued: 2024-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Yutian
author list: Agent
  family name: Xu
  given name: Qianhui
author list: Agent
  family name: Wang
  given name: Weilin
doi: 10.7717/peerj.17350
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-28
copyright: ©2024 Ji et al.
attribution name: Ji et al.

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