PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Automated identification and segmentation of urine spots based on deep-learning
items: Intraspecific variation in the pterosaur Rhamphorhynchus muensteri—implications for flight and socio-sexual signaling
items: The prognostic role of lymphocyte-to-monocyte ratio in patients with resectable pancreatic cancer: a systematic review and meta-analysis
items: A multi-ethnic proteomic profiling analysis in Alzheimer’s disease identifies the disparities in dysregulation of proteins and pathogenesis
items: Classification of major species in the sericite–Artemisia desert grassland using hyperspectral images and spectral feature identification
items: Associations between SNPs and vegetation indices: unraveling molecular insights for enhanced cultivation of tea plant (Camellia sinensis (L.) O. Kuntze)
items: Treatment gap and barriers to access mental healthcare among women with postpartum depression symptoms in Pakistan
items: Monitoring deforestation, forest health, and environmental criticality in a protected area periphery using Geospatial Techniques
items: Flowering-associated gene expression and metabolic characteristics in adzuki bean (Vigna angularis L.) with different short-day induction periods
items: Comparing and characterizing scapular muscle activation ratios in males and females during execution of common functional movements

Automated identification and segmentation of urine spots based on deep-learning
type: item
type: AcademicArticle
description: Micturition serves an essential physiological function that allows the body to eliminate metabolic wastes and maintain water-electrolyte balance. The urine spot assay (VSA), as a simple and economical assay, has been widely used in the study of micturition behavior in rodents. However, the traditional VSA method relies on manual judgment, introduces subjective errors, faces difficulty in obtaining appearance time of each urine spot, and struggles with quantitative analysis of overlapping spots. To address these challenges, we developed a deep learning-based approach for the automatic identification and segmentation of urine spots. Our system employs a target detection network to efficiently detect each urine spot and utilizes an instance segmentation network to achieve precise segmentation of overlapping urine spots. Compared with the traditional VSA method, our system achieves automated detection of urine spot area of micturition in rodents, greatly reducing subjective errors. It accurately determines the urination time of each spot and effectively quantifies the overlapping spots. This study enables high-throughput and precise urine spot detection, providing important technical support for the analysis of urination behavior and the study of the neural mechanism underlying urination.
format: application/pdf
format: text/html
creator: Xin Fan
creator: Jun Li
creator: Junan Yan
subject: Biochemistry
subject: Computational Biology
subject: Urology
description: doi:10.7717/peerj.17398
publisher: PeerJ Inc.
rights: © 2024 Fan et al.
abstract: Micturition serves an essential physiological function that allows the body to eliminate metabolic wastes and maintain water-electrolyte balance. The urine spot assay (VSA), as a simple and economical assay, has been widely used in the study of micturition behavior in rodents. However, the traditional VSA method relies on manual judgment, introduces subjective errors, faces difficulty in obtaining appearance time of each urine spot, and struggles with quantitative analysis of overlapping spots. To address these challenges, we developed a deep learning-based approach for the automatic identification and segmentation of urine spots. Our system employs a target detection network to efficiently detect each urine spot and utilizes an instance segmentation network to achieve precise segmentation of overlapping urine spots. Compared with the traditional VSA method, our system achieves automated detection of urine spot area of micturition in rodents, greatly reducing subjective errors. It accurately determines the urination time of each spot and effectively quantifies the overlapping spots. This study enables high-throughput and precise urine spot detection, providing important technical support for the analysis of urination behavior and the study of the neural mechanism underlying urination.
bibliographic citation: Fan et al. (2024) Automated identification and segmentation of urine spots based on deep-learning. PeerJ 12:e17398 https://doi.org/10.7717/peerj.17398
date submitted: 2024-02-09
date accepted: 2024-04-25
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Xin
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Yan
  given name: Junan
doi: 10.7717/peerj.17398
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: ©2024 Fan et al.
attribution name: Fan et al.

Intraspecific variation in the pterosaur Rhamphorhynchus muensteri—implications for flight and socio-sexual signaling
type: item
type: AcademicArticle
description: Pterosaurs were the first powered flying vertebrates, with a fossil record that stretches back to about 230 million years before present. Most species are only known from one to three specimens, which are most often fragmentary. However, Rhamphorhynchus muensteri is known from numerous excellent specimens, including multiple specimens with soft tissue preservation. As such, Rhamphorhynchus muensteri is one of the only pterosaurs amenable to analysis for intraspecific variation. It has been previously predicted that elements directly involved in the flight apparatus, such as those of the forelimb, will be more highly constrained in their proportions than other parts of the skeleton. We investigated the degree of variation seen in elements and body parts of Rhamphorhynchus, which represents the best model system among pterosaurs for testing these expectations of intraspecific variation. We recover evidence for high levels of constraint throughout the appendicular and axial elements (head, neck, torso, tail, forelimbs, hindlimbs), suggesting that all were important for flight. We further find that tail variation increases among the largest specimens, suggesting reduced constraint and/or stronger sexual selection on the tail in more mature individuals.
format: application/pdf
format: text/html
creator: Michael B. Habib
creator: David WE. Hone
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.17524
publisher: PeerJ Inc.
rights: © 2024 Habib and Hone
abstract: Pterosaurs were the first powered flying vertebrates, with a fossil record that stretches back to about 230 million years before present. Most species are only known from one to three specimens, which are most often fragmentary. However, Rhamphorhynchus muensteri is known from numerous excellent specimens, including multiple specimens with soft tissue preservation. As such, Rhamphorhynchus muensteri is one of the only pterosaurs amenable to analysis for intraspecific variation. It has been previously predicted that elements directly involved in the flight apparatus, such as those of the forelimb, will be more highly constrained in their proportions than other parts of the skeleton. We investigated the degree of variation seen in elements and body parts of Rhamphorhynchus, which represents the best model system among pterosaurs for testing these expectations of intraspecific variation. We recover evidence for high levels of constraint throughout the appendicular and axial elements (head, neck, torso, tail, forelimbs, hindlimbs), suggesting that all were important for flight. We further find that tail variation increases among the largest specimens, suggesting reduced constraint and/or stronger sexual selection on the tail in more mature individuals.
bibliographic citation: Habib et al. (2024) Intraspecific variation in the pterosaur Rhamphorhynchus muensteri—implications for flight and socio-sexual signaling. PeerJ 12:e17524 https://doi.org/10.7717/peerj.17524
date submitted: 2023-12-10
date accepted: 2024-05-16
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Habib
  given name: Michael B.
author list: Agent
  family name: Hone
  given name: David WE.
doi: 10.7717/peerj.17524
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: © 2024 Habib and Hone
attribution name: Habib and Hone

The prognostic role of lymphocyte-to-monocyte ratio in patients with resectable pancreatic cancer: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objectives This systematic review and meta-analysis examined whether the lymphocyte-to-monocyte ratio (LMR) can serve as an indicator for predicting the prognosis of patients with resectable pancreatic cancer. Patients and Methods This meta-analysis was registered with PROSPERO: CRD42023461260. A systematic literature search was conducted in the PubMed, Embase, Cochrane, and Web of Science databases up to September 2023 to assess whether LMR can predict the prognosis of patients with resectable pancreatic cancer. The outcomes measured included subgroup analyses of overall survival (OS) with hazard ratios (HR) and confidence intervals of geographical region, patient population, and LMR threshold. A sensitivity analysis was also performed for OS and HR and confidence intervals were calculated for recurrence-free survival (RFS). Results A total of 14 eligible articles, comprising 4,019 patients, were included in the comprehensive analysis. The results of this comprehensive analysis indicate that LMR is a robust predictor of OS, demonstrating strong prognostic significance (HR = 0.55, 95% CI [0.44–0.69], I2 = 79%, P < 0.00001). This predictive significance extended to various types of pancreatic cancer, such as pancreatic ductal adenocarcinoma (HR = 0.73, 95% CI [0.57–0.93], I2 = 46%, P = 0.01), pancreatic neuroendocrine neoplasms (HR = 0.81, 95% CI [0.66–0.99], P = 0.04) and other subtypes (HR = 0.40, 95% CI [0.22–0.72], I2 = 89%, P < 0.00001), but not to pancreatic head cancer (HR = 0.46, 95% CI [0.16–1.13], I2 = 59%, P = 0.12). LMR retained its predictive value across different regions, including Asia (HR = 0.62, 95% CI [0.47–0.76], I2 = 68%, P < 0.0001), Europe (HR = 0.78, 95% CI [0.67–0.91], I2 = 0%, P = 0.002), and the Americas (HR = 0.14, 95% CI [0.08–0.24], I2 = 0%, P < 0.00001). Notably, both LMR cut-off values greater than or equal to three (HR = 0.62, 95% CI [0.47–0.82], I2 = 67%, P = 0.0009) and less than three (HR = 0.47, 95% CI [0.32–0.69], I2 = 85%, P = 0…
format: application/pdf
format: text/html
creator: Haipeng Li
creator: Shang Peng
creator: Ran An
creator: Nana Du
creator: Huan Wu
creator: Xiangcheng Zhen
creator: Yuanzhi Gao
creator: Zhenghong Li
creator: Jingting Min
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.17585
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Objectives This systematic review and meta-analysis examined whether the lymphocyte-to-monocyte ratio (LMR) can serve as an indicator for predicting the prognosis of patients with resectable pancreatic cancer. Patients and Methods This meta-analysis was registered with PROSPERO: CRD42023461260. A systematic literature search was conducted in the PubMed, Embase, Cochrane, and Web of Science databases up to September 2023 to assess whether LMR can predict the prognosis of patients with resectable pancreatic cancer. The outcomes measured included subgroup analyses of overall survival (OS) with hazard ratios (HR) and confidence intervals of geographical region, patient population, and LMR threshold. A sensitivity analysis was also performed for OS and HR and confidence intervals were calculated for recurrence-free survival (RFS). Results A total of 14 eligible articles, comprising 4,019 patients, were included in the comprehensive analysis. The results of this comprehensive analysis indicate that LMR is a robust predictor of OS, demonstrating strong prognostic significance (HR = 0.55, 95% CI [0.44–0.69], I2 = 79%, P < 0.00001). This predictive significance extended to various types of pancreatic cancer, such as pancreatic ductal adenocarcinoma (HR = 0.73, 95% CI [0.57–0.93], I2 = 46%, P = 0.01), pancreatic neuroendocrine neoplasms (HR = 0.81, 95% CI [0.66–0.99], P = 0.04) and other subtypes (HR = 0.40, 95% CI [0.22–0.72], I2 = 89%, P < 0.00001), but not to pancreatic head cancer (HR = 0.46, 95% CI [0.16–1.13], I2 = 59%, P = 0.12). LMR retained its predictive value across different regions, including Asia (HR = 0.62, 95% CI [0.47–0.76], I2 = 68%, P < 0.0001), Europe (HR = 0.78, 95% CI [0.67–0.91], I2 = 0%, P = 0.002), and the Americas (HR = 0.14, 95% CI [0.08–0.24], I2 = 0%, P < 0.00001). Notably, both LMR cut-off values greater than or equal to three (HR = 0.62, 95% CI [0.47–0.82], I2 = 67%, P = 0.0009) and less than three (HR = 0.47, 95% CI [0.32–0.69], I2 = 85%, P = 0…
bibliographic citation: Li et al. (2024) The prognostic role of lymphocyte-to-monocyte ratio in patients with resectable pancreatic cancer: a systematic review and meta-analysis. PeerJ 12:e17585 https://doi.org/10.7717/peerj.17585
date submitted: 2023-12-19
date accepted: 2024-05-27
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Haipeng
author list: Agent
  family name: Peng
  given name: Shang
author list: Agent
  family name: An
  given name: Ran
author list: Agent
  family name: Du
  given name: Nana
author list: Agent
  family name: Wu
  given name: Huan
author list: Agent
  family name: Zhen
  given name: Xiangcheng
author list: Agent
  family name: Gao
  given name: Yuanzhi
author list: Agent
  family name: Li
  given name: Zhenghong
author list: Agent
  family name: Min
  given name: Jingting
doi: 10.7717/peerj.17585
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: © 2024 Li et al.
attribution name: Li et al.

A multi-ethnic proteomic profiling analysis in Alzheimer’s disease identifies the disparities in dysregulation of proteins and pathogenesis
type: item
type: AcademicArticle
description: Background Alzheimer’s disease (AD) is the most common type of dementia that affects the elderly population. Lately, blood-based proteomics have been intensively sought in the discovery of AD biomarkers studies due to the capability to link external environmental factors with the development of AD. Demographic differences have been shown to affect the expression of the proteins in different populations which play a vital role in the degeneration of cognitive function. Method In this study, a proteomic study focused on Malaysian Chinese and Malay prospects was conducted. Differentially expressed proteins (DEPs) in AD patients and normal controls for Chinese and Malays were identified. Functional enrichment analysis was conducted to further interpret the biological functions and pathways of the DEPs. In addition, a survey investigating behavioural practices among Chinese and Malay participants was conducted to support the results from the proteomic analysis. Result The variation of dysregulated proteins identified in Chinese and Malay samples suggested the disparities of pathways involved in this pathological condition for each respective ethnicity. Functional enrichment analysis supported this assumption in understanding the protein-protein interactions of the identified protein signatures and indicate that differentially expressed proteins identified from the Chinese group were significantly enriched with the functional terms related to Aβ/tau protein-related processes, oxidative stress and inflammation whereas neuroinflammation was associated with the Malay group. Besides that, a significant difference in sweet drinks/food intake habits between these two groups implies a relationship between sugar levels and the dysregulation of protein APOA4 in the Malay group. Additional meta-analysis further supported the dysregulation of proteins TF, AHSG, A1BG, APOA4 and C4A among AD groups. Conclusion These findings serve as a preliminary understanding in the molecular and de…
format: application/pdf
format: text/html
creator: Mei Sze Tan
creator: Phaik-Leng Cheah
creator: Ai-Vyrn Chin
creator: Lai-Meng Looi
creator: Siow-Wee Chang
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Epidemiology
subject: Neurology
description: doi:10.7717/peerj.17643
publisher: PeerJ Inc.
rights: © 2024 Tan et al.
abstract: Background Alzheimer’s disease (AD) is the most common type of dementia that affects the elderly population. Lately, blood-based proteomics have been intensively sought in the discovery of AD biomarkers studies due to the capability to link external environmental factors with the development of AD. Demographic differences have been shown to affect the expression of the proteins in different populations which play a vital role in the degeneration of cognitive function. Method In this study, a proteomic study focused on Malaysian Chinese and Malay prospects was conducted. Differentially expressed proteins (DEPs) in AD patients and normal controls for Chinese and Malays were identified. Functional enrichment analysis was conducted to further interpret the biological functions and pathways of the DEPs. In addition, a survey investigating behavioural practices among Chinese and Malay participants was conducted to support the results from the proteomic analysis. Result The variation of dysregulated proteins identified in Chinese and Malay samples suggested the disparities of pathways involved in this pathological condition for each respective ethnicity. Functional enrichment analysis supported this assumption in understanding the protein-protein interactions of the identified protein signatures and indicate that differentially expressed proteins identified from the Chinese group were significantly enriched with the functional terms related to Aβ/tau protein-related processes, oxidative stress and inflammation whereas neuroinflammation was associated with the Malay group. Besides that, a significant difference in sweet drinks/food intake habits between these two groups implies a relationship between sugar levels and the dysregulation of protein APOA4 in the Malay group. Additional meta-analysis further supported the dysregulation of proteins TF, AHSG, A1BG, APOA4 and C4A among AD groups. Conclusion These findings serve as a preliminary understanding in the molecular and de…
bibliographic citation: Tan et al. (2024) A multi-ethnic proteomic profiling analysis in Alzheimer’s disease identifies the disparities in dysregulation of proteins and pathogenesis. PeerJ 12:e17643 https://doi.org/10.7717/peerj.17643
date submitted: 2023-12-04
date accepted: 2024-06-06
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Mei Sze
author list: Agent
  family name: Cheah
  given name: Phaik-Leng
author list: Agent
  family name: Chin
  given name: Ai-Vyrn
author list: Agent
  family name: Looi
  given name: Lai-Meng
author list: Agent
  family name: Chang
  given name: Siow-Wee
doi: 10.7717/peerj.17643
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: © 2024 Tan et al.
attribution name: Tan et al.

Classification of major species in the sericite–Artemisia desert grassland using hyperspectral images and spectral feature identification
type: item
type: AcademicArticle
description: Background The species composition of and changes in grassland communities are important indices for inferring the number, quality and community succession of grasslands, and accurate monitoring is the foundation for evaluating, protecting, and utilizing grassland resources. Remote sensing technology provides a reliable and powerful approach for measuring regional terrain information, and the identification of grassland species by remote sensing will improve the quality and effectiveness of grassland monitoring. Methods Ground hyperspectral images of a sericite–Artemisia desert grassland in different seasons were obtained with a Soc710 VP imaging spectrometer. First-order differential processing was used to calculate the characteristic parameters. Analysis of variance was used to extract the main species, namely, Seriphidium transiliense (Poljak), Ceratocarpus arenarius L., Petrosimonia sibirica (Pall), bare land and the spectral characteristic parameters and vegetation indices in different seasons. On this basis, Fisher discriminant analysis was used to divide the samples into a training set and a test set at a ratio of 7:3. The spectral characteristic parameters and vegetation indices were used to identify the three main plants and bare land. Results The selection of parameters with significant differences (P < 0.05) between the recognition objects effectively distinguished different land features, and the identification parameters also differed due to differences in growth period and species. The overall accuracy of the recognition model established by the vegetation index decreased in the following order: June (98.87%) > September (91.53%) > April (90.37%). The overall accuracy of the recognition model established by the feature parameters decreased in the following order: September (89.77%) > June (88.48%) > April (85.98%). Conclusions The recognition models based on vegetation indices in different months are superior to those based on feature parameters, with …
format: application/pdf
format: text/html
creator: Wenhao Liu
creator: Wanqiang Han
creator: Guili Jin
creator: Ke Gong
creator: Jian Ma
subject: Agricultural Science
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.17663
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Background The species composition of and changes in grassland communities are important indices for inferring the number, quality and community succession of grasslands, and accurate monitoring is the foundation for evaluating, protecting, and utilizing grassland resources. Remote sensing technology provides a reliable and powerful approach for measuring regional terrain information, and the identification of grassland species by remote sensing will improve the quality and effectiveness of grassland monitoring. Methods Ground hyperspectral images of a sericite–Artemisia desert grassland in different seasons were obtained with a Soc710 VP imaging spectrometer. First-order differential processing was used to calculate the characteristic parameters. Analysis of variance was used to extract the main species, namely, Seriphidium transiliense (Poljak), Ceratocarpus arenarius L., Petrosimonia sibirica (Pall), bare land and the spectral characteristic parameters and vegetation indices in different seasons. On this basis, Fisher discriminant analysis was used to divide the samples into a training set and a test set at a ratio of 7:3. The spectral characteristic parameters and vegetation indices were used to identify the three main plants and bare land. Results The selection of parameters with significant differences (P < 0.05) between the recognition objects effectively distinguished different land features, and the identification parameters also differed due to differences in growth period and species. The overall accuracy of the recognition model established by the vegetation index decreased in the following order: June (98.87%) > September (91.53%) > April (90.37%). The overall accuracy of the recognition model established by the feature parameters decreased in the following order: September (89.77%) > June (88.48%) > April (85.98%). Conclusions The recognition models based on vegetation indices in different months are superior to those based on feature parameters, with …
bibliographic citation: Liu et al. (2024) Classification of major species in the sericite–Artemisia desert grassland using hyperspectral images and spectral feature identification. PeerJ 12:e17663 https://doi.org/10.7717/peerj.17663
date submitted: 2023-10-23
date accepted: 2024-06-10
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Liu
  given name: Wenhao
author list: Agent
  family name: Han
  given name: Wanqiang
author list: Agent
  family name: Jin
  given name: Guili
author list: Agent
  family name: Gong
  given name: Ke
author list: Agent
  family name: Ma
  given name: Jian
doi: 10.7717/peerj.17663
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: ©2024 Liu et al.
attribution name: Liu et al.

Associations between SNPs and vegetation indices: unraveling molecular insights for enhanced cultivation of tea plant (Camellia sinensis (L.) O. Kuntze)
type: item
type: AcademicArticle
description: Background Breeding programs for nutrient-efficient tea plant varieties could be advanced by the combination of genotyping and phenotyping technologies. This study was aimed to search functional SNPs in key genes related to the nitrogen-assimilation in the collection of tea plant Camellia sinensis (L.) Kuntze. In addition, the objective of this study was to reveal efficient vegetation indices for phenotyping of nitrogen deficiency response in tea collection. Methods The study was conducted on the tea plant collection of Camellia sinensis (L.) Kuntze of Western Caucasus grown without nitrogen fertilizers. Phenotypic data was collected by measuring the spectral reflectance of leaves in the 350–1100 nm range calculated as vegetation indices by the portable hyperspectral spectrometer Ci710s. Single nucleotide polymorphisms were identified in 30 key genes related to nitrogen assimilation and tea quality. For this, pooled amplicon sequencing, SNPs annotation and effect prediction with SnpEFF tool were used. Further, a linear regression model was applied to reveal associations between the functional SNPs and the efficient vegetation indices. Results PCA and regression analysis revealed significant vegetation indices with high R2 values (more than 0.5) and the most reliable indices to select ND-tolerant genotypes were established: ZMI, CNDVI, RENDVI, VREI1, GM2, GM1, PRI, and Ctr2, VREI3, VREI2. The largest SNPs frequency was observed in several genes, namely F3’5’Hb, UFGTa, UFGTb, 4Cl, and AMT1.2. SNPs in NRT2.4, PIP, AlaDC, DFRa, and GS1.2 were inherent in ND-susceptible genotypes. Additionally, SNPs in AlaAT1, MYB4, and WRKY57, were led to alterations in protein structure and were observed in ND-susceptible tea genotypes. Associations were revealed between flavanol reflectance index (FRI) and SNPs in ASNb and PIP, that change the amino acids. In addition, two SNPs in 4Cl were associated with water band index (WBI). Conclusions The results will be useful to identify toler…
format: application/pdf
format: text/html
creator: Daria Kuzmina
creator: Lyudmila S. Malyukova
creator: Karina Manakhova
creator: Tatyana Kovalenko
creator: Jaroslava Fedorina
creator: Aleksandra O. Matskiv
creator: Alexey V. Ryndin
creator: Maya V. Gvasaliya
creator: Yuriy L. Orlov
creator: Lidiia S. Samarina
subject: Agricultural Science
subject: Biochemistry
subject: Bioinformatics
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.17689
publisher: PeerJ Inc.
rights: © 2024 Kuzmina et al.
abstract: Background Breeding programs for nutrient-efficient tea plant varieties could be advanced by the combination of genotyping and phenotyping technologies. This study was aimed to search functional SNPs in key genes related to the nitrogen-assimilation in the collection of tea plant Camellia sinensis (L.) Kuntze. In addition, the objective of this study was to reveal efficient vegetation indices for phenotyping of nitrogen deficiency response in tea collection. Methods The study was conducted on the tea plant collection of Camellia sinensis (L.) Kuntze of Western Caucasus grown without nitrogen fertilizers. Phenotypic data was collected by measuring the spectral reflectance of leaves in the 350–1100 nm range calculated as vegetation indices by the portable hyperspectral spectrometer Ci710s. Single nucleotide polymorphisms were identified in 30 key genes related to nitrogen assimilation and tea quality. For this, pooled amplicon sequencing, SNPs annotation and effect prediction with SnpEFF tool were used. Further, a linear regression model was applied to reveal associations between the functional SNPs and the efficient vegetation indices. Results PCA and regression analysis revealed significant vegetation indices with high R2 values (more than 0.5) and the most reliable indices to select ND-tolerant genotypes were established: ZMI, CNDVI, RENDVI, VREI1, GM2, GM1, PRI, and Ctr2, VREI3, VREI2. The largest SNPs frequency was observed in several genes, namely F3’5’Hb, UFGTa, UFGTb, 4Cl, and AMT1.2. SNPs in NRT2.4, PIP, AlaDC, DFRa, and GS1.2 were inherent in ND-susceptible genotypes. Additionally, SNPs in AlaAT1, MYB4, and WRKY57, were led to alterations in protein structure and were observed in ND-susceptible tea genotypes. Associations were revealed between flavanol reflectance index (FRI) and SNPs in ASNb and PIP, that change the amino acids. In addition, two SNPs in 4Cl were associated with water band index (WBI). Conclusions The results will be useful to identify toler…
bibliographic citation: Kuzmina et al. (2024) Associations between SNPs and vegetation indices: unraveling molecular insights for enhanced cultivation of tea plant (Camellia sinensis (L.) O. Kuntze). PeerJ 12:e17689 https://doi.org/10.7717/peerj.17689
date submitted: 2024-03-15
date accepted: 2024-06-14
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuzmina
  given name: Daria
author list: Agent
  family name: Malyukova
  given name: Lyudmila S.
author list: Agent
  family name: Manakhova
  given name: Karina
author list: Agent
  family name: Kovalenko
  given name: Tatyana
author list: Agent
  family name: Fedorina
  given name: Jaroslava
author list: Agent
  family name: Matskiv
  given name: Aleksandra O.
author list: Agent
  family name: Ryndin
  given name: Alexey V.
author list: Agent
  family name: Gvasaliya
  given name: Maya V.
author list: Agent
  family name: Orlov
  given name: Yuriy L.
author list: Agent
  family name: Samarina
  given name: Lidiia S.
doi: 10.7717/peerj.17689
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: ©2024 Kuzmina et al.
attribution name: Kuzmina et al.

Treatment gap and barriers to access mental healthcare among women with postpartum depression symptoms in Pakistan
type: item
type: AcademicArticle
description: Background and Objectives Postpartum depression (PPD) is prevalent among women after childbirth, but accessing mental healthcare for PPD is challenging. This study aimed to assess the treatment gap and barriers to mental healthcare access for women with PPD symptoms living in Punjab, Pakistan. Methods A multicenter cross-sectional study was conducted in five populous cities of Punjab from January to June 2023 by administering the questionnaire to the women using stratified random sampling. A total of 3,220 women in first 6 months postpartum were screened using the Edinburgh Postnatal Depression Scale. Of them, 1,503 women scored thirteen or above, indicating potential depressive disorder. Interviews were conducted to explore help-seeking behavior and barriers to accessing mental healthcare. Descriptive statistics along with nonparametric tests (e.g., Kruskal–Wallis, Mann–Whitney U) were used and group differences were examined. Scatter plot matrices with fitted lines were used to explore associations between variables. Classification and regression tree methods were used to classify the importance and contribution of different variables for the intensity of PPD. Results Only 2% of women (n = 33) with high PPD symptoms sought mental healthcare, and merely 5% of women (n = 75) had been in contact with a health service since the onset of their symptoms. 92.80% of women with PPD symptoms did not seek any medical attention. The majority of women, 1,215 (81%), perceived the need for mental health treatment; however, 91.23% of them did not seek treatment from healthcare services. Women who recently gave birth to a female child had higher mean depression scores compared to those who gave birth to a male child. Age, education, and birth location of newborn were significantly associated (p < 0.005) with mean barrier scores, mean social support scores, mean depression scores and treatment gap. The results of classification and regression decision tree model showed that instrum…
format: application/pdf
format: text/html
creator: Aqsa Sajjad
creator: Shahid Shah
creator: Ghulam Abbas
creator: Ayesha Aslam
creator: Fawad Randhawa
creator: Haris Khurram
creator: Abdullah Assiri
subject: Gynecology and Obstetrics
subject: Psychiatry and Psychology
subject: Women’s Health
subject: Mental Health
description: doi:10.7717/peerj.17711
publisher: PeerJ Inc.
rights: © 2024 Sajjad et al.
abstract: Background and Objectives Postpartum depression (PPD) is prevalent among women after childbirth, but accessing mental healthcare for PPD is challenging. This study aimed to assess the treatment gap and barriers to mental healthcare access for women with PPD symptoms living in Punjab, Pakistan. Methods A multicenter cross-sectional study was conducted in five populous cities of Punjab from January to June 2023 by administering the questionnaire to the women using stratified random sampling. A total of 3,220 women in first 6 months postpartum were screened using the Edinburgh Postnatal Depression Scale. Of them, 1,503 women scored thirteen or above, indicating potential depressive disorder. Interviews were conducted to explore help-seeking behavior and barriers to accessing mental healthcare. Descriptive statistics along with nonparametric tests (e.g., Kruskal–Wallis, Mann–Whitney U) were used and group differences were examined. Scatter plot matrices with fitted lines were used to explore associations between variables. Classification and regression tree methods were used to classify the importance and contribution of different variables for the intensity of PPD. Results Only 2% of women (n = 33) with high PPD symptoms sought mental healthcare, and merely 5% of women (n = 75) had been in contact with a health service since the onset of their symptoms. 92.80% of women with PPD symptoms did not seek any medical attention. The majority of women, 1,215 (81%), perceived the need for mental health treatment; however, 91.23% of them did not seek treatment from healthcare services. Women who recently gave birth to a female child had higher mean depression scores compared to those who gave birth to a male child. Age, education, and birth location of newborn were significantly associated (p < 0.005) with mean barrier scores, mean social support scores, mean depression scores and treatment gap. The results of classification and regression decision tree model showed that instrum…
bibliographic citation: Sajjad et al. (2024) Treatment gap and barriers to access mental healthcare among women with postpartum depression symptoms in Pakistan. PeerJ 12:e17711 https://doi.org/10.7717/peerj.17711
date submitted: 2024-02-15
date accepted: 2024-06-18
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sajjad
  given name: Aqsa
author list: Agent
  family name: Shah
  given name: Shahid
author list: Agent
  family name: Abbas
  given name: Ghulam
author list: Agent
  family name: Aslam
  given name: Ayesha
author list: Agent
  family name: Randhawa
  given name: Fawad
author list: Agent
  family name: Khurram
  given name: Haris
author list: Agent
  family name: Assiri
  given name: Abdullah
doi: 10.7717/peerj.17711
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: ©2024 Sajjad et al.
attribution name: Sajjad et al.

Monitoring deforestation, forest health, and environmental criticality in a protected area periphery using Geospatial Techniques
type: item
type: AcademicArticle
description: Protected areas in South Asia face significant challenges due to human disturbance and deforestation. The ongoing debate surrounds the recent surge in illegal encroachment of forest buffer zones in the Musali divisional secretariat division (DSD), which has led to a significant loss of forest cover over the past three decades. In this context, detecting changes in forest cover, assessing forest health, and evaluating environmental quality are crucial for sustainable forest management. As such, our efforts focused on assessing forest cover dynamics, forest health, and environmental conditions in the DSD from 1988 to 2022. We employed standardized image processing techniques, utilizing Landsat-5 (TM) and Landsat-8 (OLI) images. However, the forest area in the DSD has shown minimal changes, and environmental conditions and forest health have illustrated considerable spatial-temporal variations over the 34 years. The results indicated that 8.5 km2 (1.9%) of forest cover in the DSD has been converted to other land use classes. Overall, the Normalized Difference Vegetation Index (NDVI) has declined over time, while Land Surface Temperature (LST) exhibits an increasing trend. The regression results demonstrated a robust inverse relationship between LST and NDVI. The declining vegetation conditions and the increasing LST contribute to an increase in environmental criticality. The derived maps and indices will be beneficial for forest authorities in identifying highly sensitive locations. Additionally, they could enable land use planners to develop sustainable land management strategies.
format: application/pdf
format: text/html
creator: Neel Chaminda Withanage
creator: Prabuddh Kumar Mishra
creator: Kamal Abdelrahman
creator: Rajender Singh
subject: Ecology
subject: Environmental Impacts
subject: Forestry
subject: Spatial and Geographic Information Science
subject: Environmental Health
description: doi:10.7717/peerj.17714
publisher: PeerJ Inc.
rights: © 2024 Withanage et al.
abstract: Protected areas in South Asia face significant challenges due to human disturbance and deforestation. The ongoing debate surrounds the recent surge in illegal encroachment of forest buffer zones in the Musali divisional secretariat division (DSD), which has led to a significant loss of forest cover over the past three decades. In this context, detecting changes in forest cover, assessing forest health, and evaluating environmental quality are crucial for sustainable forest management. As such, our efforts focused on assessing forest cover dynamics, forest health, and environmental conditions in the DSD from 1988 to 2022. We employed standardized image processing techniques, utilizing Landsat-5 (TM) and Landsat-8 (OLI) images. However, the forest area in the DSD has shown minimal changes, and environmental conditions and forest health have illustrated considerable spatial-temporal variations over the 34 years. The results indicated that 8.5 km2 (1.9%) of forest cover in the DSD has been converted to other land use classes. Overall, the Normalized Difference Vegetation Index (NDVI) has declined over time, while Land Surface Temperature (LST) exhibits an increasing trend. The regression results demonstrated a robust inverse relationship between LST and NDVI. The declining vegetation conditions and the increasing LST contribute to an increase in environmental criticality. The derived maps and indices will be beneficial for forest authorities in identifying highly sensitive locations. Additionally, they could enable land use planners to develop sustainable land management strategies.
bibliographic citation: Withanage et al. (2024) Monitoring deforestation, forest health, and environmental criticality in a protected area periphery using Geospatial Techniques. PeerJ 12:e17714 https://doi.org/10.7717/peerj.17714
date submitted: 2024-03-03
date accepted: 2024-06-18
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Withanage
  given name: Neel Chaminda
author list: Agent
  family name: Mishra
  given name: Prabuddh Kumar
author list: Agent
  family name: Abdelrahman
  given name: Kamal
author list: Agent
  family name: Singh
  given name: Rajender
doi: 10.7717/peerj.17714
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: ©2024 Withanage et al.
attribution name: Withanage et al.

Flowering-associated gene expression and metabolic characteristics in adzuki bean (Vigna angularis L.) with different short-day induction periods
type: item
type: AcademicArticle
description: Background The adzuki bean is a typical short-day plant and an important grain crop that is widely used due to its high nutritional and medicinal value. The adzuki bean flowering time is affected by multiple environmental factors, particularly the photoperiod. Adjusting the day length can induce flower synchronization in adzuki bean and accelerate the breeding process. In this study, we used RNA sequencing analysis to determine the effects of different day lengths on gene expression and metabolic characteristics related to adzuki bean flowering time. Methods ‘Tangshan hong xiao dou’ was used as the experimental material in this study and field experiments were conducted in 2022 using a randomized block design with three treatments: short-day induction periods of 5 d (SD-5d), 10 d (SD-10d), and 15 d (SD-15d). Results A total of 5,939 differentially expressed genes (DEGs) were identified, of which 38.09% were up-regulated and 23.81% were down-regulated. Gene ontology enrichment analysis was performed on the target genes to identify common functions related to photosystems I and II. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified two pathways involved in the antenna protein and circadian rhythm. Furthermore, florescence was promoted by down-regulating genes in the circadian rhythm pathway through the blue light metabolic pathway; whereas, antenna proteins promoted flowering by enhancing the reception of light signals and accelerating electron transport. In these two metabolic pathways, the number of DEGs was the greatest between the SD-5d VS SD-15d groups. Real-time reverse transcription‒quantitative polymerase chain reaction analysis results of eight DEGs were consistent with the sequencing results. Thus, the sequencing results were accurate and reliable and eight genes were identified as candidates for the regulation of short-day induction at the adzuki bean seedling stage. Conclusions Short-day induction was able to down-regulate the expressio…
format: application/pdf
format: text/html
creator: Weixin Dong
creator: Dongxiao Li
creator: Lei Zhang
creator: Peijun Tao
creator: Yuechen Zhang
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.17716
publisher: PeerJ Inc.
rights: © 2024 Dong et al.
abstract: Background The adzuki bean is a typical short-day plant and an important grain crop that is widely used due to its high nutritional and medicinal value. The adzuki bean flowering time is affected by multiple environmental factors, particularly the photoperiod. Adjusting the day length can induce flower synchronization in adzuki bean and accelerate the breeding process. In this study, we used RNA sequencing analysis to determine the effects of different day lengths on gene expression and metabolic characteristics related to adzuki bean flowering time. Methods ‘Tangshan hong xiao dou’ was used as the experimental material in this study and field experiments were conducted in 2022 using a randomized block design with three treatments: short-day induction periods of 5 d (SD-5d), 10 d (SD-10d), and 15 d (SD-15d). Results A total of 5,939 differentially expressed genes (DEGs) were identified, of which 38.09% were up-regulated and 23.81% were down-regulated. Gene ontology enrichment analysis was performed on the target genes to identify common functions related to photosystems I and II. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified two pathways involved in the antenna protein and circadian rhythm. Furthermore, florescence was promoted by down-regulating genes in the circadian rhythm pathway through the blue light metabolic pathway; whereas, antenna proteins promoted flowering by enhancing the reception of light signals and accelerating electron transport. In these two metabolic pathways, the number of DEGs was the greatest between the SD-5d VS SD-15d groups. Real-time reverse transcription‒quantitative polymerase chain reaction analysis results of eight DEGs were consistent with the sequencing results. Thus, the sequencing results were accurate and reliable and eight genes were identified as candidates for the regulation of short-day induction at the adzuki bean seedling stage. Conclusions Short-day induction was able to down-regulate the expressio…
bibliographic citation: Dong et al. (2024) Flowering-associated gene expression and metabolic characteristics in adzuki bean (Vigna angularis L.) with different short-day induction periods. PeerJ 12:e17716 https://doi.org/10.7717/peerj.17716
date submitted: 2023-11-29
date accepted: 2024-06-18
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Weixin
author list: Agent
  family name: Li
  given name: Dongxiao
author list: Agent
  family name: Zhang
  given name: Lei
author list: Agent
  family name: Tao
  given name: Peijun
author list: Agent
  family name: Zhang
  given name: Yuechen
doi: 10.7717/peerj.17716
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: © 2024 Dong et al.
attribution name: Dong et al.

Comparing and characterizing scapular muscle activation ratios in males and females during execution of common functional movements
type: item
type: AcademicArticle
description: Background The shoulder complex relies on scapular movement controlled by periscapular muscles for optimal arm function. However, minimal research has explored scapular muscle activation ratios during functional tasks, nor how they might be influenced by biological sex. This investigation aims to characterize how sex impacts scapular muscle activation ratios during functional tasks. Methods Twenty participants (ten females, ten males) were assessed with surface electromyography (EMG) and motion tracking during seven functional tasks. Activation ratios were calculated from normalized EMG for the three trapezius muscles and serratus anterior. Scapular angles were calculated using a YXZ Euler sequence. Two-way mixed methods ANOVAs (p < .05) were used to assess the effects of sex and humeral elevation level on ratios and angles. Results Sex-based differences were present in the Tie Apron task, with males exhibiting higher upper trapezius/lower trapezius and upper trapezius/middle trapezius ratios than females. Males also demonstrated decreased internal rotation in this task. Other tasks showcased significant sex-based differences in scapular upward rotation but not in activation ratios. Humeral elevation generally demonstrated an inverse relationship with scapular muscle activation ratios. Conclusions This study highlights sex-based differences in scapular muscle activation ratios during specific functional tasks, emphasizing the need to consider sex in analyses of shoulder movements. Normative activation ratios for functional tasks were provided, offering a foundation for future comparisons with non-normative groups. Further research is warranted to confirm and explore additional influencing factors, advancing our understanding of shoulder activation and movement in diverse populations.
format: application/pdf
format: text/html
creator: Angelica E. Lang
creator: Annaka Chorneyko
creator: Vivian Heinrichs
subject: Anatomy and Physiology
subject: Kinesiology
subject: Biomechanics
description: doi:10.7717/peerj.17728
publisher: PeerJ Inc.
rights: © 2024 Lang et al.
abstract: Background The shoulder complex relies on scapular movement controlled by periscapular muscles for optimal arm function. However, minimal research has explored scapular muscle activation ratios during functional tasks, nor how they might be influenced by biological sex. This investigation aims to characterize how sex impacts scapular muscle activation ratios during functional tasks. Methods Twenty participants (ten females, ten males) were assessed with surface electromyography (EMG) and motion tracking during seven functional tasks. Activation ratios were calculated from normalized EMG for the three trapezius muscles and serratus anterior. Scapular angles were calculated using a YXZ Euler sequence. Two-way mixed methods ANOVAs (p < .05) were used to assess the effects of sex and humeral elevation level on ratios and angles. Results Sex-based differences were present in the Tie Apron task, with males exhibiting higher upper trapezius/lower trapezius and upper trapezius/middle trapezius ratios than females. Males also demonstrated decreased internal rotation in this task. Other tasks showcased significant sex-based differences in scapular upward rotation but not in activation ratios. Humeral elevation generally demonstrated an inverse relationship with scapular muscle activation ratios. Conclusions This study highlights sex-based differences in scapular muscle activation ratios during specific functional tasks, emphasizing the need to consider sex in analyses of shoulder movements. Normative activation ratios for functional tasks were provided, offering a foundation for future comparisons with non-normative groups. Further research is warranted to confirm and explore additional influencing factors, advancing our understanding of shoulder activation and movement in diverse populations.
bibliographic citation: Lang et al. (2024) Comparing and characterizing scapular muscle activation ratios in males and females during execution of common functional movements. PeerJ 12:e17728 https://doi.org/10.7717/peerj.17728
date submitted: 2024-02-09
date accepted: 2024-06-20
issued: 2024-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Lang
  given name: Angelica E.
author list: Agent
  family name: Chorneyko
  given name: Annaka
author list: Agent
  family name: Heinrichs
  given name: Vivian
doi: 10.7717/peerj.17728
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-18
copyright: ©2024 Lang et al.
attribution name: Lang et al.

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