PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Relation between peripheral blood inflammatory indices and severity of central retinal artery occlusion
items: Continuing challenges of elephant captivity: the captive environment, health issues, and welfare implications
items: Cholecystectomy and risk of cardiovascular disease, all-cause and cause-specific mortality: a systematic review and updated meta-analysis
items: Effects of 60Coγ-irradiation combined with sodium dehydrogenate on post-harvest preservation and physiological indices of Volvariella volvacea
items: Yield-limiting nutrient response of lowbush blueberry grown in recent and ancient alluvial soils of the Mekong Delta
items: SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs
items: A psychophysical evaluation of techniques for Mooney image generation
items: High microvessel and lymphatic vessel density predict poor prognosis in patients with esophageal squamous cell carcinoma
items: Reliability of motion phase identification for long-track speed skating using inertial measurement units
items: Impact of atmospheric particulate matter retention on physiological characters of five plant species under different pollution levels in Zhengzhou

Relation between peripheral blood inflammatory indices and severity of central retinal artery occlusion
type: item
type: AcademicArticle
description: Background Central retinal artery occlusion (CRAO) has been identified as an acute emergency resulting in vision loss, with its pathogenesis potentially involving systemic inflammation and abnormal lipid metabolism. Over recent years, it has been established that peripheral blood inflammatory indices, including the neutrophil-to-lymphocyte ratio (NLR), the systemic immunoinflammatory index (SII), and the monocyte-to-high-density lipoprotein ratio (MHR), play significant roles in assessing systemic inflammation and lipid metabolism. However, the role of these indices in assessing the severity of CRAO has rarely been explored. This study aimd to investigate the relationship between these inflammatory indices and the severity of CRAO. Methods This was a retrospective clinical study with a total of 49 CRAO patients and 50 age- and sex-matched controls involved. The patients with CRAO were divided into three groups (13 with incomplete CRAO, 16 with subtotal CRAO and 20 with total CRAO). Data were compared across these groups, and additionally, correlation analysis, restricted cubic spline plots, and receiver operating characteristic curve analysis were performed. Results The values of NLR, SII and MHR were significantly higher in the CRAO group compared to controls (NLR: 2.49(1.71,3.44) vs 1.60(1.24,1.97), P<0.001; SII: 606.46(410.25,864.35) vs 403.91(332.90,524.31), P=0.001; MHR: 0.33(0.26,0.44) vs 0.25(0.21,0.34), P<0.001). MHR was also significantly higher in total CRAO than in incomplete CRAO and subtotal CRAO (0.41(0.32,0.60) vs 0.29(0.21,0.43), P=0.036; 0.41(0.32,0.60) vs 0.29(0.23,0.38), P=0.017). Significant positive associations were found between MHR, NLR, SII and both the incidence (all P<0.001) and severity (P<0.001, P<0.001, P=0.003, respectively) of CRAO. MHR had a linear relationship with both the occurrence and severity of CRAO (P-overall=0.013, P-non-linear=0.427 and P-overall=0.013, P-non-linear=0.825). Combining MHR and NLR significantly improved diagn…
format: application/pdf
format: text/html
creator: Weiwen Hu
creator: Yikeng Huang
creator: Qiong Zhou
creator: Xionggao Huang
subject: Hematology
subject: Immunology
subject: Ophthalmology
description: doi:10.7717/peerj.18129
publisher: PeerJ Inc.
rights: © 2024 Hu et al.
abstract: Background Central retinal artery occlusion (CRAO) has been identified as an acute emergency resulting in vision loss, with its pathogenesis potentially involving systemic inflammation and abnormal lipid metabolism. Over recent years, it has been established that peripheral blood inflammatory indices, including the neutrophil-to-lymphocyte ratio (NLR), the systemic immunoinflammatory index (SII), and the monocyte-to-high-density lipoprotein ratio (MHR), play significant roles in assessing systemic inflammation and lipid metabolism. However, the role of these indices in assessing the severity of CRAO has rarely been explored. This study aimd to investigate the relationship between these inflammatory indices and the severity of CRAO. Methods This was a retrospective clinical study with a total of 49 CRAO patients and 50 age- and sex-matched controls involved. The patients with CRAO were divided into three groups (13 with incomplete CRAO, 16 with subtotal CRAO and 20 with total CRAO). Data were compared across these groups, and additionally, correlation analysis, restricted cubic spline plots, and receiver operating characteristic curve analysis were performed. Results The values of NLR, SII and MHR were significantly higher in the CRAO group compared to controls (NLR: 2.49(1.71,3.44) vs 1.60(1.24,1.97), P<0.001; SII: 606.46(410.25,864.35) vs 403.91(332.90,524.31), P=0.001; MHR: 0.33(0.26,0.44) vs 0.25(0.21,0.34), P<0.001). MHR was also significantly higher in total CRAO than in incomplete CRAO and subtotal CRAO (0.41(0.32,0.60) vs 0.29(0.21,0.43), P=0.036; 0.41(0.32,0.60) vs 0.29(0.23,0.38), P=0.017). Significant positive associations were found between MHR, NLR, SII and both the incidence (all P<0.001) and severity (P<0.001, P<0.001, P=0.003, respectively) of CRAO. MHR had a linear relationship with both the occurrence and severity of CRAO (P-overall=0.013, P-non-linear=0.427 and P-overall=0.013, P-non-linear=0.825). Combining MHR and NLR significantly improved diagn…
bibliographic citation: Hu et al. (2024) Relation between peripheral blood inflammatory indices and severity of central retinal artery occlusion. PeerJ 12:e18129 https://doi.org/10.7717/peerj.18129
date submitted: 2024-04-17
date accepted: 2024-08-28
issued: 2024-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Weiwen
author list: Agent
  family name: Huang
  given name: Yikeng
author list: Agent
  family name: Zhou
  given name: Qiong
author list: Agent
  family name: Huang
  given name: Xionggao
doi: 10.7717/peerj.18129
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-30
copyright: ©2024 Hu et al.
attribution name: Hu et al.

Continuing challenges of elephant captivity: the captive environment, health issues, and welfare implications
type: item
type: AcademicArticle
description: Although the well-being of elephants in captivity is of paramount importance, the confinement of these long-lived, highly intelligent, and socially complex animals continues to present significant challenges. Here, we provide an overview of the current state of elephant confinement (primarily in the West) by examining captive facilities, improvements, and continuing problems, and the clinical/behavioral/neural issues that remain. Specifically, we examine quantitative and qualitative aspects of the enclosed space, sociocognitive factors, dietary differences, and health/welfare concerns (e.g., stereotypies, physical health, nutrition, reproduction, life expectancy). The challenges of the captive environment become especially salient when juxtaposed next to the complex, multifaceted characteristics of the elephant’s natural environment. Despite the best efforts of some facilities to improve the captive environment, serious welfare challenges remain. Such confinement issues thus raise important welfare and ethical concerns with regards to captive elephant well-being.
format: application/pdf
format: text/html
creator: Catherine Doyle
creator: Heather Rally
creator: Lester O’Brien
creator: Mackenzie Tennison
creator: Lori Marino
creator: Bob Jacobs
subject: Animal Behavior
subject: Ethical Issues
description: doi:10.7717/peerj.18161
publisher: PeerJ Inc.
rights: © 2024 Doyle et al.
abstract: Although the well-being of elephants in captivity is of paramount importance, the confinement of these long-lived, highly intelligent, and socially complex animals continues to present significant challenges. Here, we provide an overview of the current state of elephant confinement (primarily in the West) by examining captive facilities, improvements, and continuing problems, and the clinical/behavioral/neural issues that remain. Specifically, we examine quantitative and qualitative aspects of the enclosed space, sociocognitive factors, dietary differences, and health/welfare concerns (e.g., stereotypies, physical health, nutrition, reproduction, life expectancy). The challenges of the captive environment become especially salient when juxtaposed next to the complex, multifaceted characteristics of the elephant’s natural environment. Despite the best efforts of some facilities to improve the captive environment, serious welfare challenges remain. Such confinement issues thus raise important welfare and ethical concerns with regards to captive elephant well-being.
bibliographic citation: Doyle et al. (2024) Continuing challenges of elephant captivity: the captive environment, health issues, and welfare implications. PeerJ 12:e18161 https://doi.org/10.7717/peerj.18161
date submitted: 2024-06-18
date accepted: 2024-09-02
issued: 2024-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doyle
  given name: Catherine
author list: Agent
  family name: Rally
  given name: Heather
author list: Agent
  family name: O’Brien
  given name: Lester
author list: Agent
  family name: Tennison
  given name: Mackenzie
author list: Agent
  family name: Marino
  given name: Lori
author list: Agent
  family name: Jacobs
  given name: Bob
doi: 10.7717/peerj.18161
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-30
copyright: © 2024 Doyle et al.
attribution name: Doyle et al.

Cholecystectomy and risk of cardiovascular disease, all-cause and cause-specific mortality: a systematic review and updated meta-analysis
type: item
type: AcademicArticle
description: Objective Questions remain about the association among cholecystectomy, cardiovascular disease, all-cause and cause-specific mortality. We performed a systematic review and meta-analysis to clarify these associations. Methods PubMed, Web of Science, Embase, and Cochrane Library databases were searched up to February 2024. Summary relative risks (RRs) and 95% confidence intervals (CIs) were calculated using a DerSimonian–Laird random effects model. Results We screened 16,595 articles and included 14 studies. No significant association was found between cholecystectomy and cardiovascular disease (CVD), with RR being 1.03 (95% CI [0.77–1.37], p = 0.848, I2 = 99.6%), even in results with high heterogenous studies excluded (RR 1.20, 95% CI [0.97–1.49], p = 0.095, I2 = 77.7%). Same result was proved in its subtype, coronary heart disease (RR 1.06, 95% CI [0.84–1.33], p = 0.633, I2 = 96.6%). Cholecystectomy increased CVD risk compared with healthy controls without gallstones (RR 1.19, 95% CI [1.05–1.35], p = 0.007, I2 = 83.3%) and lowered CVD risk compared with gallstone carriers (RR 0.62, 95% CI [0.57–0.67], p < 0.001, I2 = 82.1%). As for mortality, increase in the risk for all-cause (RR 1.17, 95% CI [1.03–1.34], p = 0.020, I2 = 51.6%) and cardiovascular (RR 1.24, 95% CI [1.06–1.47], p = 0.009, I2 = 20.7%) mortality, but not for cancer mortality (RR 1.18, 95% CI [0.95–1.47], p = 0.131, I2 = 0.0%), were observed after cholecystectomy. Conclusion Cholecystectomy may not be associated with the overall development of CVD, as well as CHD. Cholecystectomized patients showed increased CVD risk compared with healthy controls without gallstones, but decreased CVD risk compared with gallstone patients. Increased risk for all-cause and cardiovascular, but not cancer mortality was observed following cholecystectomy.
format: application/pdf
format: text/html
creator: Yang Song
creator: Haishu Wang
creator: Yaowen Xu
subject: Cardiology
subject: Epidemiology
subject: Evidence Based Medicine
subject: Internal Medicine
description: doi:10.7717/peerj.18174
publisher: PeerJ Inc.
rights: © 2024 Song et al.
abstract: Objective Questions remain about the association among cholecystectomy, cardiovascular disease, all-cause and cause-specific mortality. We performed a systematic review and meta-analysis to clarify these associations. Methods PubMed, Web of Science, Embase, and Cochrane Library databases were searched up to February 2024. Summary relative risks (RRs) and 95% confidence intervals (CIs) were calculated using a DerSimonian–Laird random effects model. Results We screened 16,595 articles and included 14 studies. No significant association was found between cholecystectomy and cardiovascular disease (CVD), with RR being 1.03 (95% CI [0.77–1.37], p = 0.848, I2 = 99.6%), even in results with high heterogenous studies excluded (RR 1.20, 95% CI [0.97–1.49], p = 0.095, I2 = 77.7%). Same result was proved in its subtype, coronary heart disease (RR 1.06, 95% CI [0.84–1.33], p = 0.633, I2 = 96.6%). Cholecystectomy increased CVD risk compared with healthy controls without gallstones (RR 1.19, 95% CI [1.05–1.35], p = 0.007, I2 = 83.3%) and lowered CVD risk compared with gallstone carriers (RR 0.62, 95% CI [0.57–0.67], p < 0.001, I2 = 82.1%). As for mortality, increase in the risk for all-cause (RR 1.17, 95% CI [1.03–1.34], p = 0.020, I2 = 51.6%) and cardiovascular (RR 1.24, 95% CI [1.06–1.47], p = 0.009, I2 = 20.7%) mortality, but not for cancer mortality (RR 1.18, 95% CI [0.95–1.47], p = 0.131, I2 = 0.0%), were observed after cholecystectomy. Conclusion Cholecystectomy may not be associated with the overall development of CVD, as well as CHD. Cholecystectomized patients showed increased CVD risk compared with healthy controls without gallstones, but decreased CVD risk compared with gallstone patients. Increased risk for all-cause and cardiovascular, but not cancer mortality was observed following cholecystectomy.
bibliographic citation: Song et al. (2024) Cholecystectomy and risk of cardiovascular disease, all-cause and cause-specific mortality: a systematic review and updated meta-analysis. PeerJ 12:e18174 https://doi.org/10.7717/peerj.18174
date submitted: 2024-05-24
date accepted: 2024-09-04
issued: 2024-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Song
  given name: Yang
author list: Agent
  family name: Wang
  given name: Haishu
author list: Agent
  family name: Xu
  given name: Yaowen
doi: 10.7717/peerj.18174
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-30
copyright: © 2024 Song et al.
attribution name: Song et al.

Effects of 60Coγ-irradiation combined with sodium dehydrogenate on post-harvest preservation and physiological indices of Volvariella volvacea
type: item
type: AcademicArticle
description: Volvariella volvacea is a mushroom known for its high palatability and nutritional value. However, it is susceptible to spoilage thus making it challenging to preserve and keep fresh after harvest, resulting in constraints in long-distance transportation and long-term storage. This study aimed to investigate the feasibility of using irradiation and sodium dehydrogenate (SD) as a preservative in the preservation process of V. volvacea. The effects of three treatments of 0.8 kGy 60Coγ irradiation (B), 0.04% SD (C), combined with 0.04% SD and 0.8 kGy 60Coγ irradiation (A) on the postharvest freshness of V. volvacea were investigated. The assessment indices for V. volvacea, including appearance, browning rate, weight loss, respiration rate, MDA content, antioxidant enzyme activities, vitamin C (Vc), and soluble protein content, were measured and compared. The three treatments were compared to determine the changes in storage time over 7 days post-harvest. The results demonstrated that the hardness of the fruiting body exhibited a significant increase of 81.19%, 97.96% and 168.81% in comparison to the control, B and C, respectively, following the application of the treatment A. Compared to the control group, the soluble protein content was significantly increased by 20.28%. Respiration intensity and browning rate were significantly lower in the control treatment, decreasing by 35.07% and 45.49% respectively. On the 6th day of storage, the activities of SOD and POD increased by 81.06% and 73.71%, respectively, compared to the control, which significantly delayed the senescence of the fruiting bodies. The Vc content was significantly increased by 50.27%, 133.90%, and 101.39% in treatment B, which received 0.8 kGy 60Coγ irradiation alone, compared to the control, treatment A, and treatment C, respectively. The treatment C alone significantly reduced respiratory intensity and MDA variables by 39.55% and 31.01%, respectively, compared to the control. The findings can provide …
format: application/pdf
format: text/html
creator: Mingjuan Mao
creator: Lin Ma
creator: Ning Jiang
creator: Jinsheng Lin
creator: Shaoxuan Qu
creator: Huiping Li
creator: Ping Xu
creator: Di Liu
creator: Lijuan Hou
subject: Agricultural Science
subject: Biochemistry
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.18177
publisher: PeerJ Inc.
rights: © 2024 Mao et al.
abstract: Volvariella volvacea is a mushroom known for its high palatability and nutritional value. However, it is susceptible to spoilage thus making it challenging to preserve and keep fresh after harvest, resulting in constraints in long-distance transportation and long-term storage. This study aimed to investigate the feasibility of using irradiation and sodium dehydrogenate (SD) as a preservative in the preservation process of V. volvacea. The effects of three treatments of 0.8 kGy 60Coγ irradiation (B), 0.04% SD (C), combined with 0.04% SD and 0.8 kGy 60Coγ irradiation (A) on the postharvest freshness of V. volvacea were investigated. The assessment indices for V. volvacea, including appearance, browning rate, weight loss, respiration rate, MDA content, antioxidant enzyme activities, vitamin C (Vc), and soluble protein content, were measured and compared. The three treatments were compared to determine the changes in storage time over 7 days post-harvest. The results demonstrated that the hardness of the fruiting body exhibited a significant increase of 81.19%, 97.96% and 168.81% in comparison to the control, B and C, respectively, following the application of the treatment A. Compared to the control group, the soluble protein content was significantly increased by 20.28%. Respiration intensity and browning rate were significantly lower in the control treatment, decreasing by 35.07% and 45.49% respectively. On the 6th day of storage, the activities of SOD and POD increased by 81.06% and 73.71%, respectively, compared to the control, which significantly delayed the senescence of the fruiting bodies. The Vc content was significantly increased by 50.27%, 133.90%, and 101.39% in treatment B, which received 0.8 kGy 60Coγ irradiation alone, compared to the control, treatment A, and treatment C, respectively. The treatment C alone significantly reduced respiratory intensity and MDA variables by 39.55% and 31.01%, respectively, compared to the control. The findings can provide …
bibliographic citation: Mao et al. (2024) Effects of 60Coγ-irradiation combined with sodium dehydrogenate on post-harvest preservation and physiological indices of Volvariella volvacea. PeerJ 12:e18177 https://doi.org/10.7717/peerj.18177
date submitted: 2024-05-10
date accepted: 2024-09-04
issued: 2024-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Mingjuan
author list: Agent
  family name: Ma
  given name: Lin
author list: Agent
  family name: Jiang
  given name: Ning
author list: Agent
  family name: Lin
  given name: Jinsheng
author list: Agent
  family name: Qu
  given name: Shaoxuan
author list: Agent
  family name: Li
  given name: Huiping
author list: Agent
  family name: Xu
  given name: Ping
author list: Agent
  family name: Liu
  given name: Di
author list: Agent
  family name: Hou
  given name: Lijuan
doi: 10.7717/peerj.18177
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-30
copyright: © 2024 Mao et al.
attribution name: Mao et al.

Yield-limiting nutrient response of lowbush blueberry grown in recent and ancient alluvial soils of the Mekong Delta
type: item
type: AcademicArticle
description: Background Blueberries are ornamental plants grown in pots in many yards in the Mekong Delta (MD) region. In this region, the recent alluvial (RA) soil is fertile and ancient alluvial (AA) soil is considered degraded because it only has around a quarter of the nutrient content of the RA soil. Both soils have a high clay content, so organic matter is needed to improve their physical condition. This study aimed to identify the nutrients that limit the yield of blueberries in RA and AA soils of the MD. Methods The pot experiment was performed using a factorial randomized block design (RBD) with two factors: (a) two soil types (RA and AA) and (b) four omission or treatment conditions (NPK, PK, NK, and NP). The same fertilizer formula was used for all treatments, including 45N–20P2O5–20K2O and mixing CHC (10 tha-1) into the potting soil. Results The blueberry yield in AA soil was only 81% of that in RA soil. In both RA and AA soils, N omission caused foliar N content deficiency (10.42 g kg−1), resulting in the content of foliar P (0.84 g kg−1) and K (3.78 g kg−1) to fall below the Trevett threshold. In both RA and AA, N omission resulted in reduced fruit yield (47% and 39%, respectively) as well as reduced weight of the stem (70% and 42%, respectively) and leaf (59% and 46%, respectively). Increased crop yields in soils were mainly related to nitrogen fertilizer. The indigenous nutrient supply (INS) of RA, which is fertile, was high but its apparent nutrient recovery efficiency (ARE) index was low, whereas the INS of AA, or the level of degraded soil, was low but its ARE index was high. In alluvial soils, the higher the INS level, the less positive the impact on the ARE index. In AA soil, the indigenous N and K supplies can be improved through fertilizer investment; however, a balance must be achieved considering economic efficiency.
format: application/pdf
format: text/html
creator: Ngo Phuong Ngoc
creator: Le Minh Ly
creator: Pham Thi Phuong Thao
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.17992
publisher: PeerJ Inc.
rights: © 2024 Ngoc et al.
abstract: Background Blueberries are ornamental plants grown in pots in many yards in the Mekong Delta (MD) region. In this region, the recent alluvial (RA) soil is fertile and ancient alluvial (AA) soil is considered degraded because it only has around a quarter of the nutrient content of the RA soil. Both soils have a high clay content, so organic matter is needed to improve their physical condition. This study aimed to identify the nutrients that limit the yield of blueberries in RA and AA soils of the MD. Methods The pot experiment was performed using a factorial randomized block design (RBD) with two factors: (a) two soil types (RA and AA) and (b) four omission or treatment conditions (NPK, PK, NK, and NP). The same fertilizer formula was used for all treatments, including 45N–20P2O5–20K2O and mixing CHC (10 tha-1) into the potting soil. Results The blueberry yield in AA soil was only 81% of that in RA soil. In both RA and AA soils, N omission caused foliar N content deficiency (10.42 g kg−1), resulting in the content of foliar P (0.84 g kg−1) and K (3.78 g kg−1) to fall below the Trevett threshold. In both RA and AA, N omission resulted in reduced fruit yield (47% and 39%, respectively) as well as reduced weight of the stem (70% and 42%, respectively) and leaf (59% and 46%, respectively). Increased crop yields in soils were mainly related to nitrogen fertilizer. The indigenous nutrient supply (INS) of RA, which is fertile, was high but its apparent nutrient recovery efficiency (ARE) index was low, whereas the INS of AA, or the level of degraded soil, was low but its ARE index was high. In alluvial soils, the higher the INS level, the less positive the impact on the ARE index. In AA soil, the indigenous N and K supplies can be improved through fertilizer investment; however, a balance must be achieved considering economic efficiency.
bibliographic citation: Ngoc et al. (2024) Yield-limiting nutrient response of lowbush blueberry grown in recent and ancient alluvial soils of the Mekong Delta. PeerJ 12:e17992 https://doi.org/10.7717/peerj.17992
date submitted: 2023-10-08
date accepted: 2024-08-07
issued: 2024-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ngoc
  given name: Ngo Phuong
author list: Agent
  family name: Ly
  given name: Le Minh
author list: Agent
  family name: Thao
  given name: Pham Thi Phuong
doi: 10.7717/peerj.17992
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-27
copyright: ©2024 Ngoc et al.
attribution name: Ngoc et al.

SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs
type: item
type: AcademicArticle
description: Background Recent advances in long-read sequencing technologies enabled accurate and contiguous de novo assemblies of large genomes and metagenomes. However, even long and accurate high-fidelity (HiFi) reads do not resolve repeats that are longer than the read lengths. This limitation negatively affects the contiguity of diploid genome assemblies since two haplomes share many long identical regions. To generate the telomere-to-telomere assemblies of diploid genomes, biologists now construct their HiFi-based phased assemblies and use additional experimental technologies to transform them into more contiguous diploid assemblies. The barcoded linked-reads, generated using an inexpensive TELL-Seq technology, provide an attractive way to bridge unresolved repeats in phased assemblies of diploid genomes. Results We developed the SpLitteR tool for diploid genome assembly using linked-reads and assembly graphs and benchmarked it against state-of-the-art linked-read scaffolders ARKS and SLR-superscaffolder using human HG002 genome and sheep gut microbiome datasets. The benchmark showed that SpLitteR scaffolding results in 1.5-fold increase in NGA50 compared to the baseline LJA assembly and other scaffolders while introducing no additional misassemblies on the human dataset. Conclusion We developed the SpLitteR tool for assembly graph phasing and scaffolding using barcoded linked-reads. We benchmarked SpLitteR on assembly graphs produced by various long-read assemblers and have demonstrated that TELL-Seq reads facilitate phasing and scaffolding in these graphs. This benchmarking demonstrates that SpLitteR improves upon the state-of-the-art linked-read scaffolders in the accuracy and contiguity metrics. SpLitteR is implemented in C++ as a part of the freely available SPAdes package and is available at https://github.com/ablab/spades/releases/tag/splitter-preprint.
format: application/pdf
format: text/html
creator: Ivan Tolstoganov
creator: Zhoutao Chen
creator: Pavel Pevzner
creator: Anton Korobeynikov
subject: Bioinformatics
subject: Computational Biology
subject: Computational Science
description: doi:10.7717/peerj.18050
publisher: PeerJ Inc.
rights: © 2024 Tolstoganov et al.
abstract: Background Recent advances in long-read sequencing technologies enabled accurate and contiguous de novo assemblies of large genomes and metagenomes. However, even long and accurate high-fidelity (HiFi) reads do not resolve repeats that are longer than the read lengths. This limitation negatively affects the contiguity of diploid genome assemblies since two haplomes share many long identical regions. To generate the telomere-to-telomere assemblies of diploid genomes, biologists now construct their HiFi-based phased assemblies and use additional experimental technologies to transform them into more contiguous diploid assemblies. The barcoded linked-reads, generated using an inexpensive TELL-Seq technology, provide an attractive way to bridge unresolved repeats in phased assemblies of diploid genomes. Results We developed the SpLitteR tool for diploid genome assembly using linked-reads and assembly graphs and benchmarked it against state-of-the-art linked-read scaffolders ARKS and SLR-superscaffolder using human HG002 genome and sheep gut microbiome datasets. The benchmark showed that SpLitteR scaffolding results in 1.5-fold increase in NGA50 compared to the baseline LJA assembly and other scaffolders while introducing no additional misassemblies on the human dataset. Conclusion We developed the SpLitteR tool for assembly graph phasing and scaffolding using barcoded linked-reads. We benchmarked SpLitteR on assembly graphs produced by various long-read assemblers and have demonstrated that TELL-Seq reads facilitate phasing and scaffolding in these graphs. This benchmarking demonstrates that SpLitteR improves upon the state-of-the-art linked-read scaffolders in the accuracy and contiguity metrics. SpLitteR is implemented in C++ as a part of the freely available SPAdes package and is available at https://github.com/ablab/spades/releases/tag/splitter-preprint.
bibliographic citation: Tolstoganov et al. (2024) SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs. PeerJ 12:e18050 https://doi.org/10.7717/peerj.18050
date submitted: 2023-11-17
date accepted: 2024-08-15
issued: 2024-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tolstoganov
  given name: Ivan
author list: Agent
  family name: Chen
  given name: Zhoutao
author list: Agent
  family name: Pevzner
  given name: Pavel
author list: Agent
  family name: Korobeynikov
  given name: Anton
doi: 10.7717/peerj.18050
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-27
copyright: © 2024 Tolstoganov et al.
attribution name: Tolstoganov et al.

A psychophysical evaluation of techniques for Mooney image generation
type: item
type: AcademicArticle
description: Mooney images can contribute to our understanding of the processes involved in visual perception, because they allow a dissociation between image content and image understanding. Mooney images are generated by first smoothing and subsequently thresholding an image. In most previous studies this was performed manually, using subjective criteria for generation. This manual process could eventually be avoided by using automatic generation techniques. The field of computer image processing offers numerous techniques for image thresholding, but these are only rarely used to create Mooney images. Furthermore, there is little research on the perceptual effects of smoothing and thresholding. Therefore, in this study we investigated how the choice of different thresholding techniques and amount of smoothing affects the interpretability of Mooney images for human participants. We generated Mooney images using four different thresholding techniques, selected to represent various global thresholding methods, and, in a second experiment, parametrically varied the level of smoothing. Participants identified the concepts shown in Mooney images and rated their interpretability. Although the techniques generate physically-different Mooney images, identification performance and subjective ratings were similar across the different techniques. This indicates that finding the perfect threshold in the process of generating Mooney images is not critical for Mooney image interpretability, at least for globally-applied thresholds. The degree of smoothing applied before thresholding, on the other hand, requires more tuning depending on the noise of the original image and the desired interpretability of the resulting Mooney image. Future work in automatic Mooney image generation should pursue local thresholding techniques, where different thresholds are applied to image regions depending on the local image content.
format: application/pdf
format: text/html
creator: Lars C. Reining
creator: Thomas S. A. Wallis
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Human-Computer Interaction
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.18059
publisher: PeerJ Inc.
rights: © 2024 Reining and Wallis
abstract: Mooney images can contribute to our understanding of the processes involved in visual perception, because they allow a dissociation between image content and image understanding. Mooney images are generated by first smoothing and subsequently thresholding an image. In most previous studies this was performed manually, using subjective criteria for generation. This manual process could eventually be avoided by using automatic generation techniques. The field of computer image processing offers numerous techniques for image thresholding, but these are only rarely used to create Mooney images. Furthermore, there is little research on the perceptual effects of smoothing and thresholding. Therefore, in this study we investigated how the choice of different thresholding techniques and amount of smoothing affects the interpretability of Mooney images for human participants. We generated Mooney images using four different thresholding techniques, selected to represent various global thresholding methods, and, in a second experiment, parametrically varied the level of smoothing. Participants identified the concepts shown in Mooney images and rated their interpretability. Although the techniques generate physically-different Mooney images, identification performance and subjective ratings were similar across the different techniques. This indicates that finding the perfect threshold in the process of generating Mooney images is not critical for Mooney image interpretability, at least for globally-applied thresholds. The degree of smoothing applied before thresholding, on the other hand, requires more tuning depending on the noise of the original image and the desired interpretability of the resulting Mooney image. Future work in automatic Mooney image generation should pursue local thresholding techniques, where different thresholds are applied to image regions depending on the local image content.
bibliographic citation: Reining et al. (2024) A psychophysical evaluation of techniques for Mooney image generation. PeerJ 12:e18059 https://doi.org/10.7717/peerj.18059
date submitted: 2024-05-01
date accepted: 2024-08-17
issued: 2024-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reining
  given name: Lars C.
author list: Agent
  family name: Wallis
  given name: Thomas S. A.
doi: 10.7717/peerj.18059
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-27
copyright: © 2024 Reining and Wallis
attribution name: Reining and Wallis

High microvessel and lymphatic vessel density predict poor prognosis in patients with esophageal squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Microangiogenesis and lymphangiogenesis are essential for tumor growth in the tumor microenvironment, contributing to tumor invasion and metastasis. Limited literature exists on these processes in esophageal squamous cell carcinoma (ESCC). Therefore, the purpose of this study is to explore the impacts of microangiogenesis and lymphangiogenesis on the occurrence, progression, and prognosis assessment of ESCC. Methods Surgical specimens and paraffin-embedded human tissues were procured from ESCC patients, encompassing 100 ESCC tissues and 100 cancer-adjacent normal (CAN) tissues. CD34 and D2-40 were utilized as markers for microvessel endothelial cells and lymphatic vessel endothelial cells, respectively. Microvascular density (MVD) and lymphatic vessel density (LVD) were evaluated through immunohistochemical quantification. Results We found that tumor tissues in ESCC patients had significantly higher MVD and LVD than cancer-adjacent normal (CAN) tissues. High MVD and LVD were associated with lymph node metastasis and advanced tumor clinical stages. Additionally, both high MVD and high LVD were strongly linked to poorer prognosis among cancer patients. Furthermore, a positive correlation was found between high MVD and high LVD (p < 0.05). The presence of these markers individually indicated a worse prognosis, with their combined assessment showcasing enhanced prognostic value. Conclusions Overall, the increased MVD and LVD indicates higher invasion and metastasis of ESCC, closely correlating with unfavorablefor poor prognosis of ESCC patients.
format: application/pdf
format: text/html
creator: Li Wen Qi
creator: Yu Fang Xie
creator: Wei Nan Wang
creator: Jia Liu
creator: Kai Ge Yang
creator: Kai Chen
creator: Cheng Hua Luo
creator: Jing Fei
creator: Jian Ming Hu
subject: Cell Biology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.18080
publisher: PeerJ Inc.
rights: © 2024 Qi et al.
abstract: Background Microangiogenesis and lymphangiogenesis are essential for tumor growth in the tumor microenvironment, contributing to tumor invasion and metastasis. Limited literature exists on these processes in esophageal squamous cell carcinoma (ESCC). Therefore, the purpose of this study is to explore the impacts of microangiogenesis and lymphangiogenesis on the occurrence, progression, and prognosis assessment of ESCC. Methods Surgical specimens and paraffin-embedded human tissues were procured from ESCC patients, encompassing 100 ESCC tissues and 100 cancer-adjacent normal (CAN) tissues. CD34 and D2-40 were utilized as markers for microvessel endothelial cells and lymphatic vessel endothelial cells, respectively. Microvascular density (MVD) and lymphatic vessel density (LVD) were evaluated through immunohistochemical quantification. Results We found that tumor tissues in ESCC patients had significantly higher MVD and LVD than cancer-adjacent normal (CAN) tissues. High MVD and LVD were associated with lymph node metastasis and advanced tumor clinical stages. Additionally, both high MVD and high LVD were strongly linked to poorer prognosis among cancer patients. Furthermore, a positive correlation was found between high MVD and high LVD (p < 0.05). The presence of these markers individually indicated a worse prognosis, with their combined assessment showcasing enhanced prognostic value. Conclusions Overall, the increased MVD and LVD indicates higher invasion and metastasis of ESCC, closely correlating with unfavorablefor poor prognosis of ESCC patients.
bibliographic citation: Qi et al. (2024) High microvessel and lymphatic vessel density predict poor prognosis in patients with esophageal squamous cell carcinoma. PeerJ 12:e18080 https://doi.org/10.7717/peerj.18080
date submitted: 2024-05-03
date accepted: 2024-08-20
issued: 2024-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Li Wen
author list: Agent
  family name: Xie
  given name: Yu Fang
author list: Agent
  family name: Wang
  given name: Wei Nan
author list: Agent
  family name: Liu
  given name: Jia
author list: Agent
  family name: Yang
  given name: Kai Ge
author list: Agent
  family name: Chen
  given name: Kai
author list: Agent
  family name: Luo
  given name: Cheng Hua
author list: Agent
  family name: Fei
  given name: Jing
author list: Agent
  family name: Hu
  given name: Jian Ming
doi: 10.7717/peerj.18080
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-27
copyright: © 2024 Qi et al.
attribution name: Qi et al.

Reliability of motion phase identification for long-track speed skating using inertial measurement units
type: item
type: AcademicArticle
description: Background Precise identification of motion phases in long-track speed skating is critical to characterize and optimize performance. This study aimed to estimate the intra- and inter-rater reliability of movement phase identification using inertial measurement units (IMUs) in long-track speed skating. Methods We analyzed 15 skaters using IMUs attached to specific body locations during a 500m skate, focusing on the stance phase, and identifying three movement events: Onset, Edge-flip, and Push-off. Reliability was assessed using intraclass correlation coefficients (ICC) and Bland-Altman analysis. Results Results showed high intra- and inter-rater reliability (ICC [1,1]: 0.86 to 0.99; ICC [2,1]: 0.81 to 0.99) across all events. Absolute error ranged from 0.56 to 6.15 ms and from 0.92 to 26.29 ms for intra- and inter-rater reliability, respectively. Minimally detectable change (MDC) ranged from 17.56 to 62.22 ms and from 33.23 to 131.25 ms for intra- and inter-rater reliability, respectively. Discussion Despite some additive and proportional errors, the overall error range was within acceptable limits, indicating negligible systematic errors. The measurement error range was small, demonstrating the accuracy of IMUs. IMUs demonstrate high reliability in movement phase identification during speed skating, endorsing their application in sports science for enhanced kinematic studies and training.
format: application/pdf
format: text/html
creator: Tomoki Iizuka
creator: Yosuke Tomita
subject: Kinesiology
subject: Biomechanics
description: doi:10.7717/peerj.18102
publisher: PeerJ Inc.
rights: © 2024 Iizuka et al.
abstract: Background Precise identification of motion phases in long-track speed skating is critical to characterize and optimize performance. This study aimed to estimate the intra- and inter-rater reliability of movement phase identification using inertial measurement units (IMUs) in long-track speed skating. Methods We analyzed 15 skaters using IMUs attached to specific body locations during a 500m skate, focusing on the stance phase, and identifying three movement events: Onset, Edge-flip, and Push-off. Reliability was assessed using intraclass correlation coefficients (ICC) and Bland-Altman analysis. Results Results showed high intra- and inter-rater reliability (ICC [1,1]: 0.86 to 0.99; ICC [2,1]: 0.81 to 0.99) across all events. Absolute error ranged from 0.56 to 6.15 ms and from 0.92 to 26.29 ms for intra- and inter-rater reliability, respectively. Minimally detectable change (MDC) ranged from 17.56 to 62.22 ms and from 33.23 to 131.25 ms for intra- and inter-rater reliability, respectively. Discussion Despite some additive and proportional errors, the overall error range was within acceptable limits, indicating negligible systematic errors. The measurement error range was small, demonstrating the accuracy of IMUs. IMUs demonstrate high reliability in movement phase identification during speed skating, endorsing their application in sports science for enhanced kinematic studies and training.
bibliographic citation: Iizuka et al. (2024) Reliability of motion phase identification for long-track speed skating using inertial measurement units. PeerJ 12:e18102 https://doi.org/10.7717/peerj.18102
date submitted: 2024-05-15
date accepted: 2024-08-26
issued: 2024-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Iizuka
  given name: Tomoki
author list: Agent
  family name: Tomita
  given name: Yosuke
doi: 10.7717/peerj.18102
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-27
copyright: ©2024 Iizuka et al.
attribution name: Iizuka et al.

Impact of atmospheric particulate matter retention on physiological characters of five plant species under different pollution levels in Zhengzhou
type: item
type: AcademicArticle
description: Atmospheric particulate matter (PM) pollution has become a major environmental risk, and green plants can mitigate air pollution by regulating their enzymatic activity, osmoregulatory substances, photosynthetic pigments, and other biochemical characteristics. The present investigation aims to evaluate the mitigation potential of five common evergreen tree species (Photinia serrulata, Ligustrum lucidum, Eriobotrya japonica, Euonymus japonicus, Pittosporum tobira) against air pollution and to assess the effect of dust retention on plant physiological functions exposed to three different pollution levels (road, campus, and park). The results found that the amount of dust retained per unit leaf area of the plants was proportional to the mass concentration of atmospheric particulate matter in the environment, and that dust accumulation was higher on the road and campus than in the park. There were significant differences in dust retention among the five tree species, with the highest leaf dust accumulation observed for E. japonica (5.45 g·m−2), and the lowest for P. tobira (1.53 g·m−2). In addition, the increase in PM adsorption by different plants was uneven with increasing pollution levels, with significant decreases in chlorophyll content, photosynthetic and transpiration rate. From a physiological perspective, P. tobira exhibited greater potential to respond to PM pollution. Biochemical indicators suggested that PM pollution caused changes in plant protective enzyme activities, with a decrease in superoxide dismutase (SOD) and peroxidase (POD) activities, as well as promoting membrane lipid peroxidation, and appropriate stress also enables plants to counteract oxidative damage. In particular, PM exposure also induced stomatal constriction. Overall, PM retention was significantly associated with physiological and photosynthetic traits. In conclusion, our study contributes to the understanding of the effects of PM on plant physiology. Furthermore, it also provides insi…
format: application/pdf
format: text/html
creator: Dan He
creator: Jiangqin Yuan
creator: Runze Lin
creator: Dongbo Xie
creator: Yifei Wang
creator: Gunwoo Kim
creator: Yakai Lei
creator: Yonghua Li
subject: Plant Science
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.18119
publisher: PeerJ Inc.
rights: © 2024 He et al.
abstract: Atmospheric particulate matter (PM) pollution has become a major environmental risk, and green plants can mitigate air pollution by regulating their enzymatic activity, osmoregulatory substances, photosynthetic pigments, and other biochemical characteristics. The present investigation aims to evaluate the mitigation potential of five common evergreen tree species (Photinia serrulata, Ligustrum lucidum, Eriobotrya japonica, Euonymus japonicus, Pittosporum tobira) against air pollution and to assess the effect of dust retention on plant physiological functions exposed to three different pollution levels (road, campus, and park). The results found that the amount of dust retained per unit leaf area of the plants was proportional to the mass concentration of atmospheric particulate matter in the environment, and that dust accumulation was higher on the road and campus than in the park. There were significant differences in dust retention among the five tree species, with the highest leaf dust accumulation observed for E. japonica (5.45 g·m−2), and the lowest for P. tobira (1.53 g·m−2). In addition, the increase in PM adsorption by different plants was uneven with increasing pollution levels, with significant decreases in chlorophyll content, photosynthetic and transpiration rate. From a physiological perspective, P. tobira exhibited greater potential to respond to PM pollution. Biochemical indicators suggested that PM pollution caused changes in plant protective enzyme activities, with a decrease in superoxide dismutase (SOD) and peroxidase (POD) activities, as well as promoting membrane lipid peroxidation, and appropriate stress also enables plants to counteract oxidative damage. In particular, PM exposure also induced stomatal constriction. Overall, PM retention was significantly associated with physiological and photosynthetic traits. In conclusion, our study contributes to the understanding of the effects of PM on plant physiology. Furthermore, it also provides insi…
bibliographic citation: He et al. (2024) Impact of atmospheric particulate matter retention on physiological characters of five plant species under different pollution levels in Zhengzhou. PeerJ 12:e18119 https://doi.org/10.7717/peerj.18119
date submitted: 2024-05-16
date accepted: 2024-08-28
issued: 2024-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Dan
author list: Agent
  family name: Yuan
  given name: Jiangqin
author list: Agent
  family name: Lin
  given name: Runze
author list: Agent
  family name: Xie
  given name: Dongbo
author list: Agent
  family name: Wang
  given name: Yifei
author list: Agent
  family name: Kim
  given name: Gunwoo
author list: Agent
  family name: Lei
  given name: Yakai
author list: Agent
  family name: Li
  given name: Yonghua
doi: 10.7717/peerj.18119
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-27
copyright: © 2024 He et al.
attribution name: He et al.

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