PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Validity and reliability of My Jump 2® app to measure the vertical jump on elite women beach volleyball players
items: Seasonal occurrence and individual variability of bull sharks, Carcharhinus leucas, in a marine reserve of the southwestern Gulf of California
items: Balance performance, falls-efficacy and social participation in patients with type 2 diabetes mellitus with and without vestibular dysfunction
items: Environmental awareness and sustainable consumption behaviours of Turkish nursing students
items: Effects of extreme meteorological factors and high air pollutant concentrations on the incidence of hand, foot and mouth disease in Jining, China
items: https://peerj.com/articles/17377
items: The prognostic value of preoperative neoindices consisting of lymphocytes, neutrophils and albumin (LANR) in operable breast cancer: a retrospective study
items: Var3PPred: variant prediction based on 3-D structure and sequence analyses of protein-protein interactions on autoinflammatory diseases
items: Similar and divergent responses to salinity stress of jamun (Syzygium cumini L. Skeels) genotypes
items: Vocal complexity in the long calls of Bornean orangutans

Validity and reliability of My Jump 2® app to measure the vertical jump on elite women beach volleyball players
type: item
type: AcademicArticle
description: Purpose The aim of this study was to assess the reliability and validity of the My Jump 2® app in measuring jump height, flight time, and peak power among elite women beach volleyball players on sand surfaces. Methods Eleven elite female beach volleyball players (aged 23.6 ± 6.2 years; weight 66.3 ± 5.8 kg; height 174.4 ± 5.8 cm; with 8.4 ± 4.8 years of professional experience) participated in this study. Each player performed six countermovement jumps in a wooden box filled with sand on a force platform while simultaneously recording a video for subsequent analysis using the My Jump 2® app. Results We found excellent agreement for flight time, jump height and peak power between observers (ICC = 0.92, 0.91 and 0.97, respectively). No significant differences between force platform and My Jump 2® app were detected in the values obtained for the three variables (P > 0.05). For the force platform and the My Jump 2® app, we found a good agreement measuring jump height and flight time (ICC = 0.85 and 0.85, respectively). However, we only found a moderate agreement for peak power (ICC = 0.64). The difference in jump height showed a limit of agreement between −4.10 and 4.74 cm in Bland-Altman, indicating a high level of agreement between the two measurement tools. Conclusion Based on our findings, the My Jump 2® app reveals a valid tool for measuring jump height and flight time of CMJ on sand surfaces. However, more caution is needed when measuring peak power.
format: application/pdf
format: text/html
creator: Alexandre Igor Araripe Medeiros
creator: Geovani Messias da Silva
creator: Francisco Oliveira Neto
creator: Mário Simim
creator: Túlio Banja
creator: Victor S. Coswig
creator: José Afonso
creator: Ana Ramos
creator: Isabel Mesquita
subject: Kinesiology
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.17387
publisher: PeerJ Inc.
rights: © 2024 Medeiros et al.
abstract: Purpose The aim of this study was to assess the reliability and validity of the My Jump 2® app in measuring jump height, flight time, and peak power among elite women beach volleyball players on sand surfaces. Methods Eleven elite female beach volleyball players (aged 23.6 ± 6.2 years; weight 66.3 ± 5.8 kg; height 174.4 ± 5.8 cm; with 8.4 ± 4.8 years of professional experience) participated in this study. Each player performed six countermovement jumps in a wooden box filled with sand on a force platform while simultaneously recording a video for subsequent analysis using the My Jump 2® app. Results We found excellent agreement for flight time, jump height and peak power between observers (ICC = 0.92, 0.91 and 0.97, respectively). No significant differences between force platform and My Jump 2® app were detected in the values obtained for the three variables (P > 0.05). For the force platform and the My Jump 2® app, we found a good agreement measuring jump height and flight time (ICC = 0.85 and 0.85, respectively). However, we only found a moderate agreement for peak power (ICC = 0.64). The difference in jump height showed a limit of agreement between −4.10 and 4.74 cm in Bland-Altman, indicating a high level of agreement between the two measurement tools. Conclusion Based on our findings, the My Jump 2® app reveals a valid tool for measuring jump height and flight time of CMJ on sand surfaces. However, more caution is needed when measuring peak power.
bibliographic citation: Medeiros et al. (2024) Validity and reliability of My Jump 2® app to measure the vertical jump on elite women beach volleyball players. PeerJ 12:e17387 https://doi.org/10.7717/peerj.17387
date submitted: 2023-09-15
date accepted: 2024-04-23
issued: 2024-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Medeiros
  given name: Alexandre Igor Araripe
author list: Agent
  family name: Silva
  given name: Geovani Messias da
author list: Agent
  family name: Neto
  given name: Francisco Oliveira
author list: Agent
  family name: Simim
  given name: Mário
author list: Agent
  family name: Banja
  given name: Túlio
author list: Agent
  family name: Coswig
  given name: Victor S.
author list: Agent
  family name: Afonso
  given name: José
author list: Agent
  family name: Ramos
  given name: Ana
author list: Agent
  family name: Mesquita
  given name: Isabel
doi: 10.7717/peerj.17387
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-17
copyright: © 2024 Medeiros et al.
attribution name: Medeiros et al.

Seasonal occurrence and individual variability of bull sharks, Carcharhinus leucas, in a marine reserve of the southwestern Gulf of California
type: item
type: AcademicArticle
description: Background Studying how the bull sharks aggregate and how they can be driven by life history traits such as reproduction, prey availability, predator avoidance and social interaction in a National Park such as Cabo Pulmo, is key to understand and protect the species. Methods The occurrence variability of 32 bull sharks tracked with passive acoustic telemetry were investigated via a hierarchical logistic regression model, with inference conducted in a Bayesian framework, comparing sex, and their response to temperature and chlorophyll. Results Based on the fitted model, occurrence probability varied by sex and length. Juvenile females had the highest values, whereas adult males the lowest. A strong seasonality or day of the year was recorded, where sharks were generally absent during September–November. However, some sharks did not show the common pattern, being detected just for a short period. This is one of the first studies where the Bayesian framework is used to study passive acoustic telemetry proving the potential to be used in further studies.
format: application/pdf
format: text/html
creator: Frida Lara-Lizardi
creator: Eleazar Castro
creator: Vianey Leos Barajas
creator: Juan Manuel Morales
creator: Edgar Mauricio Hoyos-Padilla
creator: James Ketchum
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.17192
publisher: PeerJ Inc.
rights: © 2024 Lara-Lizardi et al.
abstract: Background Studying how the bull sharks aggregate and how they can be driven by life history traits such as reproduction, prey availability, predator avoidance and social interaction in a National Park such as Cabo Pulmo, is key to understand and protect the species. Methods The occurrence variability of 32 bull sharks tracked with passive acoustic telemetry were investigated via a hierarchical logistic regression model, with inference conducted in a Bayesian framework, comparing sex, and their response to temperature and chlorophyll. Results Based on the fitted model, occurrence probability varied by sex and length. Juvenile females had the highest values, whereas adult males the lowest. A strong seasonality or day of the year was recorded, where sharks were generally absent during September–November. However, some sharks did not show the common pattern, being detected just for a short period. This is one of the first studies where the Bayesian framework is used to study passive acoustic telemetry proving the potential to be used in further studies.
bibliographic citation: Lara-Lizardi et al. (2024) Seasonal occurrence and individual variability of bull sharks, Carcharhinus leucas, in a marine reserve of the southwestern Gulf of California. PeerJ 12:e17192 https://doi.org/10.7717/peerj.17192
date submitted: 2023-03-24
date accepted: 2024-03-13
issued: 2024-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lara-Lizardi
  given name: Frida
author list: Agent
  family name: Castro
  given name: Eleazar
author list: Agent
  family name: Leos Barajas
  given name: Vianey
author list: Agent
  family name: Morales
  given name: Juan Manuel
author list: Agent
  family name: Hoyos-Padilla
  given name: Edgar Mauricio
author list: Agent
  family name: Ketchum
  given name: James
doi: 10.7717/peerj.17192
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-16
copyright: ©2024 Lara-Lizardi et al.
attribution name: Lara-Lizardi et al.

Balance performance, falls-efficacy and social participation in patients with type 2 diabetes mellitus with and without vestibular dysfunction
type: item
type: AcademicArticle
description: Background The performance of balance is an important factor to perform activities. The complications of type 2 diabetes mellitus (T2DM), especially vestibular dysfunction (VD), could decrease balance performance and falls-efficacy (FE) which consequently impacts social participation and quality of life (QoL). Purpose This study aimed to compare balance performance, FE, social participation and QoL between individuals with T2DM with and without VD. Methods The participants comprised 161 T2DM with VD and 161 without VD. Three clinical tests used for confirming VD included the Head Impulse Test (HIT), the Dix Hallpike Test (DHT) and the Supine Roll Test (SRT). The scores of static and dynamic balances, FE, social participation and QoL were compared between groups. Results The balance performance, FE, social participation and QoL were lower in the group with VD. The number of patients who had severe social restriction was higher in T2DM with VD than without VD (58.4% vs 48.4%). Moreover, all domains of QoL (physical, psychological, social relationships and environmental) were lower in T2DM with VD than without VD. Conclusion The presence of VD in T2DM patients was associated with decreased physical balance performances and increased social and QoL disengagement. Comprehensive management related to balance and FE, as well as the monitoring to support social participation and QoL, should be emphasized in patients with T2DM with VD.
format: application/pdf
format: text/html
creator: Dwi Rosella Komalasari
creator: Mantana Vongsirinavarat
creator: Vimonwan Hiengkaew
creator: Nantinee Nualnim
subject: Diabetes and Endocrinology
subject: Geriatrics
subject: Kinesiology
subject: Rehabilitation
description: doi:10.7717/peerj.17287
publisher: PeerJ Inc.
rights: © 2024 Komalasari et al.
abstract: Background The performance of balance is an important factor to perform activities. The complications of type 2 diabetes mellitus (T2DM), especially vestibular dysfunction (VD), could decrease balance performance and falls-efficacy (FE) which consequently impacts social participation and quality of life (QoL). Purpose This study aimed to compare balance performance, FE, social participation and QoL between individuals with T2DM with and without VD. Methods The participants comprised 161 T2DM with VD and 161 without VD. Three clinical tests used for confirming VD included the Head Impulse Test (HIT), the Dix Hallpike Test (DHT) and the Supine Roll Test (SRT). The scores of static and dynamic balances, FE, social participation and QoL were compared between groups. Results The balance performance, FE, social participation and QoL were lower in the group with VD. The number of patients who had severe social restriction was higher in T2DM with VD than without VD (58.4% vs 48.4%). Moreover, all domains of QoL (physical, psychological, social relationships and environmental) were lower in T2DM with VD than without VD. Conclusion The presence of VD in T2DM patients was associated with decreased physical balance performances and increased social and QoL disengagement. Comprehensive management related to balance and FE, as well as the monitoring to support social participation and QoL, should be emphasized in patients with T2DM with VD.
bibliographic citation: Komalasari et al. (2024) Balance performance, falls-efficacy and social participation in patients with type 2 diabetes mellitus with and without vestibular dysfunction. PeerJ 12:e17287 https://doi.org/10.7717/peerj.17287
date submitted: 2023-03-02
date accepted: 2024-04-02
issued: 2024-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Komalasari
  given name: Dwi Rosella
author list: Agent
  family name: Vongsirinavarat
  given name: Mantana
author list: Agent
  family name: Hiengkaew
  given name: Vimonwan
author list: Agent
  family name: Nualnim
  given name: Nantinee
doi: 10.7717/peerj.17287
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-16
copyright: ©2024 Komalasari et al.
attribution name: Komalasari et al.

Environmental awareness and sustainable consumption behaviours of Turkish nursing students
type: item
type: AcademicArticle
description: Objectives This study aims to determine the environmental awareness and sustainable consumption behaviours of nursing students. Methods This cross-sectional study was conducted with 380 undergraduate nursing students studying at Faculty of Nursing, Ege University, Türkiye. The Personal Information Form, Environmental Awareness Scale (EAS), and Sustainable Consumption Behaviours Scale (SCBS) were used to collect the research data. Number, percentage, mean, Kolmogorov-Smirnov Z test, t-test, one-way analysis of variance, Pearson’s correlation test, and linear regression analysis were used in statistical evaluation. Results The mean total score on the EAS was 46.12 (SD = 6.60), and the mean total score of the SCBS was 61.83 (SD = 9.10). A significant, moderate, and positive correlation was found between students’ environmental awareness and sustainable consumption behaviours. Moreover, students’ gender and the people they lived with caused statistically significant differences in the EAS score. The people students lived with, the place where they lived for the longest time, and their perceived income level caused statistically significant differences in the SCBS score. Conclusions Nursing students had high environmental awareness and moderate to good sustainable consumption behaviours. It is necessary to include the contribution of sustainable practices to the environment and the effects of these practices on human health in curricula for nurses and thus provide environmental awareness to students.
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creator: Renginar Öztürk Dönmez
creator: Eda Yardımcı
subject: Nursing
subject: Natural Resource Management
subject: Environmental Health
description: doi:10.7717/peerj.17366
publisher: PeerJ Inc.
rights: © 2024 Dönmez and Yardımcı
abstract: Objectives This study aims to determine the environmental awareness and sustainable consumption behaviours of nursing students. Methods This cross-sectional study was conducted with 380 undergraduate nursing students studying at Faculty of Nursing, Ege University, Türkiye. The Personal Information Form, Environmental Awareness Scale (EAS), and Sustainable Consumption Behaviours Scale (SCBS) were used to collect the research data. Number, percentage, mean, Kolmogorov-Smirnov Z test, t-test, one-way analysis of variance, Pearson’s correlation test, and linear regression analysis were used in statistical evaluation. Results The mean total score on the EAS was 46.12 (SD = 6.60), and the mean total score of the SCBS was 61.83 (SD = 9.10). A significant, moderate, and positive correlation was found between students’ environmental awareness and sustainable consumption behaviours. Moreover, students’ gender and the people they lived with caused statistically significant differences in the EAS score. The people students lived with, the place where they lived for the longest time, and their perceived income level caused statistically significant differences in the SCBS score. Conclusions Nursing students had high environmental awareness and moderate to good sustainable consumption behaviours. It is necessary to include the contribution of sustainable practices to the environment and the effects of these practices on human health in curricula for nurses and thus provide environmental awareness to students.
bibliographic citation: Dönmez et al. (2024) Environmental awareness and sustainable consumption behaviours of Turkish nursing students. PeerJ 12:e17366 https://doi.org/10.7717/peerj.17366
date submitted: 2023-09-28
date accepted: 2024-04-18
issued: 2024-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dönmez
  given name: Renginar Öztürk
author list: Agent
  family name: Yardımcı
  given name: Eda
doi: 10.7717/peerj.17366
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-16
copyright: © 2024 Dönmez and Yardımcı
attribution name: Dönmez and Yardımcı

Effects of extreme meteorological factors and high air pollutant concentrations on the incidence of hand, foot and mouth disease in Jining, China
type: item
type: AcademicArticle
description: Background The evidence on the effects of extreme meteorological conditions and high air pollution levels on incidence of hand, foot and mouth disease (HFMD) is limited. Moreover, results of the available studies are inconsistent. Further investigations are imperative to elucidate the specific issue. Methods Data on the daily cases of HFMD, meteorological factors and air pollution were obtained from 2017 to 2022 in Jining City. We employed distributed lag nonlinear model (DLNM) incorporated with Poisson regression to explore the impacts of extreme meteorological conditions and air pollution on HFMD incidence. Results We found that there were nonlinear relationships between temperature, wind speed, PM2.5, SO2, O3 and HFMD. The cumulative risk of extreme high temperature was higher at the 95th percentile (P95th) than at the 90th percentile(P90th), and the RR values for both reached their maximum at 10-day lag (P95th RR = 1.880 (1.261–2.804), P90th RR = 1.787 (1.244–2.569)), the hazardous effect of extreme low temperatures on HFMD is faster than that of extreme high temperatures. The cumulative effect of extreme low wind speeds reached its maximum at 14-day lag (P95th RR = 1.702 (1.389-2.085), P90th RR = 1.498(1.283–1.750)). The cumulative effect of PM2.5 concentration at the P90th was largest at 14-day lag (RR = 1.637 (1.069–2.506)), and the cumulative effect at the P95th was largest at 10-day lag (RR = 1.569 (1.021–2.411)). High SO2 concentration at the P95th at 14-day lag was associated with higher risk for HFMD (RR: 1.425 (1.001–2.030)). Conclusion Our findings suggest that high temperature, low wind speed, and high concentrations of PM2.5 and SO2 are associated with an increased risk of HFMD. This study not only adds insights to the understanding of the impact of extreme meteorological conditions and high levels of air pollutants on HFMD incidence but also holds practical significance for the development and enhancement of an early warning system for HFMD.
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creator: Haoyue Cao
creator: Rongrong Xu
creator: Yongmei Liang
creator: Qinglin Li
creator: Wenguo Jiang
creator: Yudi Jin
creator: Wenjun Wang
creator: Juxiang Yuan
subject: Epidemiology
subject: Pediatrics
subject: Public Health
subject: Environmental Health
description: doi:10.7717/peerj.17163
publisher: PeerJ Inc.
rights: © 2024 Cao et al.
abstract: Background The evidence on the effects of extreme meteorological conditions and high air pollution levels on incidence of hand, foot and mouth disease (HFMD) is limited. Moreover, results of the available studies are inconsistent. Further investigations are imperative to elucidate the specific issue. Methods Data on the daily cases of HFMD, meteorological factors and air pollution were obtained from 2017 to 2022 in Jining City. We employed distributed lag nonlinear model (DLNM) incorporated with Poisson regression to explore the impacts of extreme meteorological conditions and air pollution on HFMD incidence. Results We found that there were nonlinear relationships between temperature, wind speed, PM2.5, SO2, O3 and HFMD. The cumulative risk of extreme high temperature was higher at the 95th percentile (P95th) than at the 90th percentile(P90th), and the RR values for both reached their maximum at 10-day lag (P95th RR = 1.880 (1.261–2.804), P90th RR = 1.787 (1.244–2.569)), the hazardous effect of extreme low temperatures on HFMD is faster than that of extreme high temperatures. The cumulative effect of extreme low wind speeds reached its maximum at 14-day lag (P95th RR = 1.702 (1.389-2.085), P90th RR = 1.498(1.283–1.750)). The cumulative effect of PM2.5 concentration at the P90th was largest at 14-day lag (RR = 1.637 (1.069–2.506)), and the cumulative effect at the P95th was largest at 10-day lag (RR = 1.569 (1.021–2.411)). High SO2 concentration at the P95th at 14-day lag was associated with higher risk for HFMD (RR: 1.425 (1.001–2.030)). Conclusion Our findings suggest that high temperature, low wind speed, and high concentrations of PM2.5 and SO2 are associated with an increased risk of HFMD. This study not only adds insights to the understanding of the impact of extreme meteorological conditions and high levels of air pollutants on HFMD incidence but also holds practical significance for the development and enhancement of an early warning system for HFMD.
bibliographic citation: Cao et al. (2024) Effects of extreme meteorological factors and high air pollutant concentrations on the incidence of hand, foot and mouth disease in Jining, China. PeerJ 12:e17163 https://doi.org/10.7717/peerj.17163
date submitted: 2023-11-09
date accepted: 2024-03-06
issued: 2024-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Haoyue
author list: Agent
  family name: Xu
  given name: Rongrong
author list: Agent
  family name: Liang
  given name: Yongmei
author list: Agent
  family name: Li
  given name: Qinglin
author list: Agent
  family name: Jiang
  given name: Wenguo
author list: Agent
  family name: Jin
  given name: Yudi
author list: Agent
  family name: Wang
  given name: Wenjun
author list: Agent
  family name: Yuan
  given name: Juxiang
doi: 10.7717/peerj.17163
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-15
copyright: © 2024 Cao et al.
attribution name: Cao et al.

https://peerj.com/articles/17377
type: item
type: AcademicArticle
title: Retrospective analysis of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER2), Ki67 changes and their clinical significance between primary breast cancer and metastatic tumors
description: Objective To explore the relationship between receptor heterogeneity and clinicopathological characteristics in 166 patients with invasive breast cancer during metastasis. Methods We conducted a retrospective analysis of 166 patients diagnosed with metastatic breast cancer through biopsy, who were admitted to our hospital from January 2018 to December 2022. Statistical analysis was employed to assess the heterogeneity of receptors in both primary and metastatic lesions, including estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER2), Ki67, as well as their association with clinicopathological features such as tumor size, lymph node metastasis, treatment regimen, and disease-free survival. Results The discordant expression rates of ER, PR, HER2, Ki-67 and Luminal classification between primary and metastatic lesions were 21.7%, 41.6%, 8.9%, 34.4% and 36.8%, respectively. There is a significant difference in disease-free survival between patients with consistent and inconsistent receptor status of primary and metastatic lesions, which is statistically significant. The median DFS for primary HER2(-) to metastatic HER2(+) was 84 months, which was relatively high. The Cox multivariate regression analysis revealed that the expression differences of ER, PR, HER2, and Ki67 were not influenced by endocrine therapy and chemotherapy. However, a statistically significant difference in HER2 expression was observed with targeted therapy. Tumor size was correlated with ER and Ki67 receptor status (P = 0.019, 0.016). Tumor size was not correlated with PR, and HER2 (P = 0.679, 0.440). Lymph node metastasis was not associated with changes in ER, PR, HER2, and Ki67. The discordant rates of ER, PR, HER2, and Ki-67 in patients with local recurrence were 22%, 23.7%, 5.1%, and 28.8% respectively, whereas those in patients with distant metastasis were 21.5%, 36.4%, 10.3%, and 31.8% respectively. Conclusions The expression levels of ER, PR, HER2…
format: application/pdf
format: text/html
creator: Gaoxiu Qi
creator: Xin Zhang
creator: Xiaoying Gai
creator: Xiong Yan
subject: Molecular Biology
subject: Oncology
subject: Pathology
subject: Women’s Health
description: doi:10.7717/peerj.17377
publisher: PeerJ Inc.
rights: © 2024 Qi et al.
abstract: Objective To explore the relationship between receptor heterogeneity and clinicopathological characteristics in 166 patients with invasive breast cancer during metastasis. Methods We conducted a retrospective analysis of 166 patients diagnosed with metastatic breast cancer through biopsy, who were admitted to our hospital from January 2018 to December 2022. Statistical analysis was employed to assess the heterogeneity of receptors in both primary and metastatic lesions, including estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER2), Ki67, as well as their association with clinicopathological features such as tumor size, lymph node metastasis, treatment regimen, and disease-free survival. Results The discordant expression rates of ER, PR, HER2, Ki-67 and Luminal classification between primary and metastatic lesions were 21.7%, 41.6%, 8.9%, 34.4% and 36.8%, respectively. There is a significant difference in disease-free survival between patients with consistent and inconsistent receptor status of primary and metastatic lesions, which is statistically significant. The median DFS for primary HER2(-) to metastatic HER2(+) was 84 months, which was relatively high. The Cox multivariate regression analysis revealed that the expression differences of ER, PR, HER2, and Ki67 were not influenced by endocrine therapy and chemotherapy. However, a statistically significant difference in HER2 expression was observed with targeted therapy. Tumor size was correlated with ER and Ki67 receptor status (P = 0.019, 0.016). Tumor size was not correlated with PR, and HER2 (P = 0.679, 0.440). Lymph node metastasis was not associated with changes in ER, PR, HER2, and Ki67. The discordant rates of ER, PR, HER2, and Ki-67 in patients with local recurrence were 22%, 23.7%, 5.1%, and 28.8% respectively, whereas those in patients with distant metastasis were 21.5%, 36.4%, 10.3%, and 31.8% respectively. Conclusions The expression levels of ER, PR, HER2…
bibliographic citation: Qi et al. (2024) Retrospective analysis of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER2), Ki67 changes and their clinical significance between primary breast cancer and metastatic tumors. PeerJ 12:e17377 https://doi.org/10.7717/peerj.17377
date submitted: 2024-01-05
date accepted: 2024-04-19
issued: 2024-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Gaoxiu
author list: Agent
  family name: Zhang
  given name: Xin
author list: Agent
  family name: Gai
  given name: Xiaoying
author list: Agent
  family name: Yan
  given name: Xiong
doi: 10.7717/peerj.17377
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-15
copyright: ©2024 Qi et al.
attribution name: Qi et al.

The prognostic value of preoperative neoindices consisting of lymphocytes, neutrophils and albumin (LANR) in operable breast cancer: a retrospective study
type: item
type: AcademicArticle
description: Background Preoperative inflammatory factors and nutritional status are strongly associated with the prognosis of a variety of cancers. We explored the relationship between preoperative lymphocytes, neutrophils and albumin (LANR) and progression-free survival in breast cancer patients. Methods The clinical and follow-up data of 200 breast cancer patients were retrospectively analyzed in this study, and the value of LANR was determined as follows: LANR, lymphocytes × albumin/neutrophils. ROC curves, COX proportional risk regression analysis and subgroup analysis were used to assess the prognostic value of LANR in progression-free survival of breast cancer patients. Results The median age of the patients was 55.5 years (range 50–62 years). The median follow-up time was 46 months (range 33–55 months). In progression-free survival, the area under the LANR curve was 0.748 and the HR (95% CI) was 0.035 (0.679–0.817). LANR was associated with age (p = 0.02), positive axillary lymph nodes (p < 0.001), TNM stage (p < 0.001) and human epidermal growth factor receptor 2(p = 0.004). The results indicated that preoperative LANR may be a reliable predictor of progression-free survival in patients with operable breast cancer. Conclusion LANR may be an essential predictor for breast cancer patients and provides a therapeutic basis for clinicians and patients.
format: application/pdf
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creator: Yuan Wang
creator: Jiaru Zhuang
creator: Shan Wang
creator: Yibo Wu
creator: Ling Chen
subject: Global Health
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.17382
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Background Preoperative inflammatory factors and nutritional status are strongly associated with the prognosis of a variety of cancers. We explored the relationship between preoperative lymphocytes, neutrophils and albumin (LANR) and progression-free survival in breast cancer patients. Methods The clinical and follow-up data of 200 breast cancer patients were retrospectively analyzed in this study, and the value of LANR was determined as follows: LANR, lymphocytes × albumin/neutrophils. ROC curves, COX proportional risk regression analysis and subgroup analysis were used to assess the prognostic value of LANR in progression-free survival of breast cancer patients. Results The median age of the patients was 55.5 years (range 50–62 years). The median follow-up time was 46 months (range 33–55 months). In progression-free survival, the area under the LANR curve was 0.748 and the HR (95% CI) was 0.035 (0.679–0.817). LANR was associated with age (p = 0.02), positive axillary lymph nodes (p < 0.001), TNM stage (p < 0.001) and human epidermal growth factor receptor 2(p = 0.004). The results indicated that preoperative LANR may be a reliable predictor of progression-free survival in patients with operable breast cancer. Conclusion LANR may be an essential predictor for breast cancer patients and provides a therapeutic basis for clinicians and patients.
bibliographic citation: Wang et al. (2024) The prognostic value of preoperative neoindices consisting of lymphocytes, neutrophils and albumin (LANR) in operable breast cancer: a retrospective study. PeerJ 12:e17382 https://doi.org/10.7717/peerj.17382
date submitted: 2024-01-30
date accepted: 2024-04-21
issued: 2024-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yuan
author list: Agent
  family name: Zhuang
  given name: Jiaru
author list: Agent
  family name: Wang
  given name: Shan
author list: Agent
  family name: Wu
  given name: Yibo
author list: Agent
  family name: Chen
  given name: Ling
doi: 10.7717/peerj.17382
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-15
copyright: ©2024 Wang et al.
attribution name: Wang et al.

Var3PPred: variant prediction based on 3-D structure and sequence analyses of protein-protein interactions on autoinflammatory diseases
type: item
type: AcademicArticle
description: We developed a pathogenicity classifier, named Var3PPred, for identifying pathogenic variants in genes associated with autoinflammatory disorders. Our comprehensive approach integrates protein-protein interaction analysis and 3D structural information. Initially, we collected a dataset of 702 missense disease-associated variants from 35 genes linked to systemic autoinflammatory diseases (SAIDs). This dataset, sourced from the Infevers database, served as the training and test sets. We used the SMOTE algorithm to balance the dataset comprising 130 benign and 572 pathogenic variations. Our approach included 3D docking analysis of protein-protein interactions, utilizing data from the STRING and Intact databases. We weighted ZDOCK and SPRINT values in accordance with HGPEC gene rank scores for robustness. Additionally, we integrated sequential and structural features, such as changes in folding free energies (ΔΔ G), accessible surface area, volume, per residue local distance difference test (pLDDT) scores, and position specific independent count (PSIC) scores. These features, calculated using PyRosetta and AF2 computed structures, provided insights into amino acid conservation at variant positions and the impact of variants on protein structure and stability. Through extensive hyperparameter tuning of six machine learning algorithms, we found the random forest classifier to be the most effective, yielding an AUROC of 99% on the test set. Var3PPred outperformed three other classifiers, SIFT, PolyPhen, and CADD, on an unseen test set of a SAID-related gene. This demonstrates its capacity for pathogenicity classification of SAID variations. The source code for Var3PPred and the predictions for all 420 missense variants of uncertain significance from the Infevers database are available on GitHub: (https://github.com/alperbulbul1/Var3PPred).
format: application/pdf
format: text/html
creator: Alper Bülbül
creator: Emel Timucin
creator: Ahmet Can Timuçin
creator: Osman Uğur Sezerman
creator: Eda Tahir Turanli
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
subject: Immunology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17297
publisher: PeerJ Inc.
rights: © 2024 Bülbül et al.
abstract: We developed a pathogenicity classifier, named Var3PPred, for identifying pathogenic variants in genes associated with autoinflammatory disorders. Our comprehensive approach integrates protein-protein interaction analysis and 3D structural information. Initially, we collected a dataset of 702 missense disease-associated variants from 35 genes linked to systemic autoinflammatory diseases (SAIDs). This dataset, sourced from the Infevers database, served as the training and test sets. We used the SMOTE algorithm to balance the dataset comprising 130 benign and 572 pathogenic variations. Our approach included 3D docking analysis of protein-protein interactions, utilizing data from the STRING and Intact databases. We weighted ZDOCK and SPRINT values in accordance with HGPEC gene rank scores for robustness. Additionally, we integrated sequential and structural features, such as changes in folding free energies (ΔΔ G), accessible surface area, volume, per residue local distance difference test (pLDDT) scores, and position specific independent count (PSIC) scores. These features, calculated using PyRosetta and AF2 computed structures, provided insights into amino acid conservation at variant positions and the impact of variants on protein structure and stability. Through extensive hyperparameter tuning of six machine learning algorithms, we found the random forest classifier to be the most effective, yielding an AUROC of 99% on the test set. Var3PPred outperformed three other classifiers, SIFT, PolyPhen, and CADD, on an unseen test set of a SAID-related gene. This demonstrates its capacity for pathogenicity classification of SAID variations. The source code for Var3PPred and the predictions for all 420 missense variants of uncertain significance from the Infevers database are available on GitHub: (https://github.com/alperbulbul1/Var3PPred).
bibliographic citation: Bülbül et al. (2024) Var3PPred: variant prediction based on 3-D structure and sequence analyses of protein-protein interactions on autoinflammatory diseases. PeerJ 12:e17297 https://doi.org/10.7717/peerj.17297
date submitted: 2023-12-13
date accepted: 2024-04-03
issued: 2024-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bülbül
  given name: Alper
author list: Agent
  family name: Timucin
  given name: Emel
author list: Agent
  family name: Timuçin
  given name: Ahmet Can
author list: Agent
  family name: Sezerman
  given name: Osman Uğur
author list: Agent
  family name: Tahir Turanli
  given name: Eda
doi: 10.7717/peerj.17297
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-14
copyright: ©2024 Bülbül et al.
attribution name: Bülbül et al.

Similar and divergent responses to salinity stress of jamun (Syzygium cumini L. Skeels) genotypes
type: item
type: AcademicArticle
description: Background Genetic variation for salt tolerance remains elusive in jamun (Syzygium cumini). Methods Effects of gradually increased salinity (2.0–12.0 dS/m) were examined in 20 monoembryonic and 28 polyembryonic genotypes of jamun. Six genotypes were additionally assessed for understanding salt-induced changes in gas exchange attributes and antioxidant enzymes. Results Salt-induced reductions in leaf, stem, root and plant dry mass (PDM) were relatively greater in mono- than in poly-embryonic types. Reductions in PDM relative to control implied more adverse impacts of salinity on genotypes CSJ-28, CSJ-31, CSJ-43 and CSJ-47 (mono) and CSJ-1, CSJ-24, CSJ-26 and CSJ-27 (poly). Comparably, some mono- (CSJ-5, CSJ-18) and poly-embryonic (CSJ-7, CSJ-8, CSJ-14, CSJ-19) genotypes exhibited least reductions in PDM following salt treatment. Most polyembryonic genotypes showed lower reductions in root than in shoot mass, indicating that they may be more adept at absorbing water and nutrients when exposed to salt. The majority of genotypes did not exhibit leaf tip burn and marginal scorch despite significant increases in Na+ and Cl−, suggesting that tissue tolerance existed for storing excess Na+ and Cl− in vacuoles. Jamun genotypes were likely more efficient in Cl− exclusion because leaf, stem and root Cl− levels were consistently lower than those of Na+ under salt treatment. Leaf K+ was particularly little affected in genotypes with high leaf Na+. Lack of discernible differences in leaf, stem and root Ca2+ and Mg2+ contents between control and salt treatments was likely due to their preferential uptake. Correlation analysis suggested that Na+ probably had a greater inhibitory effect on biomass in both mono- and poly-embryonic types. Discriminant analysis revealed that while stem and root Cl− probably accounted for shared responses, root Na+, leaf K+ and leaf Cl− explained divergent responses to salt stress of mono- and poly-embryonic types. Genotypes CSJ-18 and CSJ-19 seemed eff…
format: application/pdf
format: text/html
creator: Anshuman Singh
creator: Ashwani Kumar
creator: Jai Prakash
creator: Arvind Kumar Verma
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.17311
publisher: PeerJ Inc.
rights: © 2024 Singh et al.
abstract: Background Genetic variation for salt tolerance remains elusive in jamun (Syzygium cumini). Methods Effects of gradually increased salinity (2.0–12.0 dS/m) were examined in 20 monoembryonic and 28 polyembryonic genotypes of jamun. Six genotypes were additionally assessed for understanding salt-induced changes in gas exchange attributes and antioxidant enzymes. Results Salt-induced reductions in leaf, stem, root and plant dry mass (PDM) were relatively greater in mono- than in poly-embryonic types. Reductions in PDM relative to control implied more adverse impacts of salinity on genotypes CSJ-28, CSJ-31, CSJ-43 and CSJ-47 (mono) and CSJ-1, CSJ-24, CSJ-26 and CSJ-27 (poly). Comparably, some mono- (CSJ-5, CSJ-18) and poly-embryonic (CSJ-7, CSJ-8, CSJ-14, CSJ-19) genotypes exhibited least reductions in PDM following salt treatment. Most polyembryonic genotypes showed lower reductions in root than in shoot mass, indicating that they may be more adept at absorbing water and nutrients when exposed to salt. The majority of genotypes did not exhibit leaf tip burn and marginal scorch despite significant increases in Na+ and Cl−, suggesting that tissue tolerance existed for storing excess Na+ and Cl− in vacuoles. Jamun genotypes were likely more efficient in Cl− exclusion because leaf, stem and root Cl− levels were consistently lower than those of Na+ under salt treatment. Leaf K+ was particularly little affected in genotypes with high leaf Na+. Lack of discernible differences in leaf, stem and root Ca2+ and Mg2+ contents between control and salt treatments was likely due to their preferential uptake. Correlation analysis suggested that Na+ probably had a greater inhibitory effect on biomass in both mono- and poly-embryonic types. Discriminant analysis revealed that while stem and root Cl− probably accounted for shared responses, root Na+, leaf K+ and leaf Cl− explained divergent responses to salt stress of mono- and poly-embryonic types. Genotypes CSJ-18 and CSJ-19 seemed eff…
bibliographic citation: Singh et al. (2024) Similar and divergent responses to salinity stress of jamun (Syzygium cumini L. Skeels) genotypes. PeerJ 12:e17311 https://doi.org/10.7717/peerj.17311
date submitted: 2024-02-22
date accepted: 2024-04-08
issued: 2024-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Singh
  given name: Anshuman
author list: Agent
  family name: Kumar
  given name: Ashwani
author list: Agent
  family name: Prakash
  given name: Jai
author list: Agent
  family name: Verma
  given name: Arvind Kumar
doi: 10.7717/peerj.17311
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-14
copyright: © 2024 Singh et al.
attribution name: Singh et al.

Vocal complexity in the long calls of Bornean orangutans
type: item
type: AcademicArticle
description: Vocal complexity is central to many evolutionary hypotheses about animal communication. Yet, quantifying and comparing complexity remains a challenge, particularly when vocal types are highly graded. Male Bornean orangutans (Pongo pygmaeus wurmbii) produce complex and variable “long call” vocalizations comprising multiple sound types that vary within and among individuals. Previous studies described six distinct call (or pulse) types within these complex vocalizations, but none quantified their discreteness or the ability of human observers to reliably classify them. We studied the long calls of 13 individuals to: (1) evaluate and quantify the reliability of audio-visual classification by three well-trained observers, (2) distinguish among call types using supervised classification and unsupervised clustering, and (3) compare the performance of different feature sets. Using 46 acoustic features, we used machine learning (i.e., support vector machines, affinity propagation, and fuzzy c-means) to identify call types and assess their discreteness. We additionally used Uniform Manifold Approximation and Projection (UMAP) to visualize the separation of pulses using both extracted features and spectrogram representations. Supervised approaches showed low inter-observer reliability and poor classification accuracy, indicating that pulse types were not discrete. We propose an updated pulse classification approach that is highly reproducible across observers and exhibits strong classification accuracy using support vector machines. Although the low number of call types suggests long calls are fairly simple, the continuous gradation of sounds seems to greatly boost the complexity of this system. This work responds to calls for more quantitative research to define call types and quantify gradedness in animal vocal systems and highlights the need for a more comprehensive framework for studying vocal complexity vis-à-vis graded repertoires.
format: application/pdf
format: text/html
creator: Wendy M. Erb
creator: Whitney Ross
creator: Haley Kazanecki
creator: Tatang Mitra Setia
creator: Shyam Madhusudhana
creator: Dena J. Clink
subject: Animal Behavior
subject: Anthropology
description: doi:10.7717/peerj.17320
publisher: PeerJ Inc.
rights: © 2024 Erb et al.
abstract: Vocal complexity is central to many evolutionary hypotheses about animal communication. Yet, quantifying and comparing complexity remains a challenge, particularly when vocal types are highly graded. Male Bornean orangutans (Pongo pygmaeus wurmbii) produce complex and variable “long call” vocalizations comprising multiple sound types that vary within and among individuals. Previous studies described six distinct call (or pulse) types within these complex vocalizations, but none quantified their discreteness or the ability of human observers to reliably classify them. We studied the long calls of 13 individuals to: (1) evaluate and quantify the reliability of audio-visual classification by three well-trained observers, (2) distinguish among call types using supervised classification and unsupervised clustering, and (3) compare the performance of different feature sets. Using 46 acoustic features, we used machine learning (i.e., support vector machines, affinity propagation, and fuzzy c-means) to identify call types and assess their discreteness. We additionally used Uniform Manifold Approximation and Projection (UMAP) to visualize the separation of pulses using both extracted features and spectrogram representations. Supervised approaches showed low inter-observer reliability and poor classification accuracy, indicating that pulse types were not discrete. We propose an updated pulse classification approach that is highly reproducible across observers and exhibits strong classification accuracy using support vector machines. Although the low number of call types suggests long calls are fairly simple, the continuous gradation of sounds seems to greatly boost the complexity of this system. This work responds to calls for more quantitative research to define call types and quantify gradedness in animal vocal systems and highlights the need for a more comprehensive framework for studying vocal complexity vis-à-vis graded repertoires.
bibliographic citation: Erb et al. (2024) Vocal complexity in the long calls of Bornean orangutans. PeerJ 12:e17320 https://doi.org/10.7717/peerj.17320
date submitted: 2023-04-11
date accepted: 2024-04-09
issued: 2024-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Erb
  given name: Wendy M.
author list: Agent
  family name: Ross
  given name: Whitney
author list: Agent
  family name: Kazanecki
  given name: Haley
author list: Agent
  family name: Mitra Setia
  given name: Tatang
author list: Agent
  family name: Madhusudhana
  given name: Shyam
author list: Agent
  family name: Clink
  given name: Dena J.
doi: 10.7717/peerj.17320
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-14
copyright: ©2024 Erb et al.
attribution name: Erb et al.

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