PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Body mass index and attention bias of food cues in women: a mediation model of body weight dissatisfaction
items: Probability-based preservational variations within the early Cambrian Chengjiang biota (China)
items: Long non-coding RNA BZRAP1-AS1 functions in malignancy and prognosis for non-small-cell lung cancer
items: Predictability and transferability of local biodiversity environment relationships
items: Pediatrics HIV-positive status disclosure and its predictors in Ethiopia: a systematic review and meta-analysis
items: Chemistry, taxonomy and ecology of the potentially chimpanzee-dispersed Vepris teva sp.nov. (Rutaceae) endangered in coastal thicket in the Congo Republic
items: An assessment of heavy metals in green sea turtle (Chelonia mydas) hatchlings from Saudi Arabia’s largest rookery, Ras Baridi
items: Synchrotron µ-XRF mapping analysis of trace elements in in-situ cultured Japanese red coral, Corallium japonicum
items: Fish habitat restoration on the basis of water morphology simulation
items: Estimating uncertainty in density surface models

Body mass index and attention bias of food cues in women: a mediation model of body weight dissatisfaction
type: item
type: AcademicArticle
description: Food attention bias could be used to indicate diet-related diseases in individuals with obesity. The purpose of this study is to explore the relationship between body mass index (BMI) and food attention bias, and the mediating role of body weight dissatisfaction (BWD) on this relationship in women. Seventy-five participants were recruited to complete a visual dot task with eye tracking. The results showed that BMI would positively predict response latency and duration bias on high-calorie foods; the relationship between BMI and response latency of high-calorie food was a complete mediation of BWD; the relationship between BMI and duration bias of high-calorie food was a complete mediation of BWD; and BWD positively predicts response latency and duration bias on high-calorie foods. These findings suggest a positive relationship between BMI and food attention bias, and the effect of a complete mediation of BWD in women.
format: application/pdf
format: text/html
creator: Aibao Zhou
creator: Pei Xie
creator: Md Zahir Ahmed
creator: Mary C. Jobe
creator: Oli Ahmed
subject: Nutrition
subject: Psychiatry and Psychology
subject: Women’s Health
subject: Obesity
description: doi:10.7717/peerj.13863
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Food attention bias could be used to indicate diet-related diseases in individuals with obesity. The purpose of this study is to explore the relationship between body mass index (BMI) and food attention bias, and the mediating role of body weight dissatisfaction (BWD) on this relationship in women. Seventy-five participants were recruited to complete a visual dot task with eye tracking. The results showed that BMI would positively predict response latency and duration bias on high-calorie foods; the relationship between BMI and response latency of high-calorie food was a complete mediation of BWD; the relationship between BMI and duration bias of high-calorie food was a complete mediation of BWD; and BWD positively predicts response latency and duration bias on high-calorie foods. These findings suggest a positive relationship between BMI and food attention bias, and the effect of a complete mediation of BWD in women.
bibliographic citation: Zhou et al. (2022) Body mass index and attention bias of food cues in women: a mediation model of body weight dissatisfaction. PeerJ 10:e13863 https://doi.org/10.7717/peerj.13863
date submitted: 2022-05-10
date accepted: 2022-07-18
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Aibao
author list: Agent
  family name: Xie
  given name: Pei
author list: Agent
  family name: Ahmed
  given name: Md Zahir
author list: Agent
  family name: Jobe
  given name: Mary C.
author list: Agent
  family name: Ahmed
  given name: Oli
doi: 10.7717/peerj.13863
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: ©2022 Zhou et al.
attribution name: Zhou et al.

Probability-based preservational variations within the early Cambrian Chengjiang biota (China)
type: item
type: AcademicArticle
description: The Chengjiang biota (Yunnan Province, China) is a treasure trove of soft-bodied animal fossils from the earliest stages of the Cambrian explosion. The mechanisms contributing to its unique preservation, known as the Burgess Shale-type preservation, are well understood. However, little is known about the preservation differences between various animal groups within this biota. This study compares tissue-occurrence data of 11 major animal groups in the Chengjiang biota using a probabilistic methodology. The fossil-based data from this study is compared to previous decay experiments. This shows that all groups are not equally preserved with some higher taxa more likely to preserve soft tissues than others. These differences in fossil preservation between taxa can be explained by the interaction of biological and environmental characteristics. A bias also results from differential taxonomic recognition, as some taxa are easily recognized from even poorly preserved fragments while other specimens are difficult to assign to higher taxa even with exquisite preservation.
format: application/pdf
format: text/html
creator: Farid Saleh
creator: Xiaoya Ma
creator: Pauline Guenser
creator: M. Gabriela Mángano
creator: Luis A. Buatois
creator: Jonathan B. Antcliffe
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.13869
publisher: PeerJ Inc.
rights: © 2022 Saleh et al.
abstract: The Chengjiang biota (Yunnan Province, China) is a treasure trove of soft-bodied animal fossils from the earliest stages of the Cambrian explosion. The mechanisms contributing to its unique preservation, known as the Burgess Shale-type preservation, are well understood. However, little is known about the preservation differences between various animal groups within this biota. This study compares tissue-occurrence data of 11 major animal groups in the Chengjiang biota using a probabilistic methodology. The fossil-based data from this study is compared to previous decay experiments. This shows that all groups are not equally preserved with some higher taxa more likely to preserve soft tissues than others. These differences in fossil preservation between taxa can be explained by the interaction of biological and environmental characteristics. A bias also results from differential taxonomic recognition, as some taxa are easily recognized from even poorly preserved fragments while other specimens are difficult to assign to higher taxa even with exquisite preservation.
bibliographic citation: Saleh et al. (2022) Probability-based preservational variations within the early Cambrian Chengjiang biota (China). PeerJ 10:e13869 https://doi.org/10.7717/peerj.13869
date submitted: 2022-04-07
date accepted: 2022-07-19
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saleh
  given name: Farid
author list: Agent
  family name: Ma
  given name: Xiaoya
author list: Agent
  family name: Guenser
  given name: Pauline
author list: Agent
  family name: Mángano
  given name: M. Gabriela
author list: Agent
  family name: Buatois
  given name: Luis A.
author list: Agent
  family name: Antcliffe
  given name: Jonathan B.
doi: 10.7717/peerj.13869
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: ©2022 Saleh et al.
attribution name: Saleh et al.

Long non-coding RNA BZRAP1-AS1 functions in malignancy and prognosis for non-small-cell lung cancer
type: item
type: AcademicArticle
description: Purpose The function of BZRAP1-AS1 is unknown in lung cancer. We evaluated the clinicopathologic significance of BZRAP1-AS1, and its role in non-small-cell lung cancer (NSCLC) progression. Patient and methods Sixty-three NSCLC patients from Beijing Chest Hospital were included. The expression of BZRAP1-AS1 was detected by real-time quantitative polymerase chain reaction (RT-qPCR) in tumor tissues and adjacent normal tissues. Then, the clinicopathological significance and prognostic value of BZRAP1-AS1 were analyzed by using our cohort and TCGA cohort. Finally, the effect of BZRAP1-AS1 on proliferation and motility of NSCLC cell lines were evaluated by cell growth assay, colony formation assay, xenograft tumorigenesis experiment in nude mice and transwell assays respectively. Results Compared with adjacent normal tissues, BZRAP1-AS1 showed lower expression in NSCLC tumor tissues. As for the relationship between BZRAP1-AS1 and clinical characteristics, our results were consistent with those of TCGA data. BZRAP1-AS1 was lower in T1 than T2–T4 patients, N1-N3 than N0 patients. Low level BZRAP1-AS1 was related to shorter overall survival time (OS) in lung adenocarcinoma (LUAD), and poor first progression time (FP) in LUAD and lung squamous cell carcinoma (LUSC) patients. BZRAP1-AS1 was significantly associated with the prognosis of NSCLC patients. Overexpression of BZRAP1-AS1 inhibited proliferation and migration of H1299 and HCC827 cells. Conclusion BZRAP1-AS1 expression decreases in tumor tissues with the increase of malignancy grades in NSCLC. BZRAP1-AS1 plays an anticancer role by inhibiting cell proliferation, invasion, and metastasis, and has a potential prognostic value in NSCLC. BZRAP1-AS1 may serve as a diagnostic marker and therapeutic target for NSCLC.
format: application/pdf
format: text/html
creator: Xuefeng Hao
creator: Minghang Zhang
creator: Meng Gu
creator: Ziyu Wang
creator: Shijie Zhou
creator: Weiying Li
creator: Shaofa Xu
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.13871
publisher: PeerJ Inc.
rights: © 2022 Hao et al.
abstract: Purpose The function of BZRAP1-AS1 is unknown in lung cancer. We evaluated the clinicopathologic significance of BZRAP1-AS1, and its role in non-small-cell lung cancer (NSCLC) progression. Patient and methods Sixty-three NSCLC patients from Beijing Chest Hospital were included. The expression of BZRAP1-AS1 was detected by real-time quantitative polymerase chain reaction (RT-qPCR) in tumor tissues and adjacent normal tissues. Then, the clinicopathological significance and prognostic value of BZRAP1-AS1 were analyzed by using our cohort and TCGA cohort. Finally, the effect of BZRAP1-AS1 on proliferation and motility of NSCLC cell lines were evaluated by cell growth assay, colony formation assay, xenograft tumorigenesis experiment in nude mice and transwell assays respectively. Results Compared with adjacent normal tissues, BZRAP1-AS1 showed lower expression in NSCLC tumor tissues. As for the relationship between BZRAP1-AS1 and clinical characteristics, our results were consistent with those of TCGA data. BZRAP1-AS1 was lower in T1 than T2–T4 patients, N1-N3 than N0 patients. Low level BZRAP1-AS1 was related to shorter overall survival time (OS) in lung adenocarcinoma (LUAD), and poor first progression time (FP) in LUAD and lung squamous cell carcinoma (LUSC) patients. BZRAP1-AS1 was significantly associated with the prognosis of NSCLC patients. Overexpression of BZRAP1-AS1 inhibited proliferation and migration of H1299 and HCC827 cells. Conclusion BZRAP1-AS1 expression decreases in tumor tissues with the increase of malignancy grades in NSCLC. BZRAP1-AS1 plays an anticancer role by inhibiting cell proliferation, invasion, and metastasis, and has a potential prognostic value in NSCLC. BZRAP1-AS1 may serve as a diagnostic marker and therapeutic target for NSCLC.
bibliographic citation: Hao et al. (2022) Long non-coding RNA BZRAP1-AS1 functions in malignancy and prognosis for non-small-cell lung cancer. PeerJ 10:e13871 https://doi.org/10.7717/peerj.13871
date submitted: 2022-02-08
date accepted: 2022-07-19
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Xuefeng
author list: Agent
  family name: Zhang
  given name: Minghang
author list: Agent
  family name: Gu
  given name: Meng
author list: Agent
  family name: Wang
  given name: Ziyu
author list: Agent
  family name: Zhou
  given name: Shijie
author list: Agent
  family name: Li
  given name: Weiying
author list: Agent
  family name: Xu
  given name: Shaofa
doi: 10.7717/peerj.13871
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: ©2022 Hao et al.
attribution name: Hao et al.

Predictability and transferability of local biodiversity environment relationships
type: item
type: AcademicArticle
description: Background Biodiversity varies in space and time, and often in response to environmental heterogeneity. Indicators in the form of local biodiversity measures–such as species richness or abundance–are common tools to capture this variation. The rise of readily available remote sensing data has enabled the characterization of environmental heterogeneity in a globally robust and replicable manner. Based on the assumption that differences in biodiversity measures are generally related to differences in environmental heterogeneity, these data have enabled projections and extrapolations of biodiversity in space and time. However so far little work has been done on quantitatively evaluating if and how accurately local biodiversity measures can be predicted. Methods Here I combine estimates of biodiversity measures from terrestrial local biodiversity surveys with remotely-sensed data on environmental heterogeneity globally. I then determine through a cross-validation framework how accurately local biodiversity measures can be predicted within (“predictability”) and across similar (“transferability”) biodiversity surveys. Results I found that prediction errors can be substantial, with error magnitudes varying between different biodiversity measures, taxonomic groups, sampling techniques and types of environmental heterogeneity characterizations. And although errors associated with model predictability were in many cases relatively low, these results question–particular for transferability–our capability to accurately predict and project local biodiversity measures based on environmental heterogeneity. I make the case that future predictions should be evaluated based on their accuracy and inherent uncertainty, and ecological theories be tested against whether we are able to make accurate predictions from local biodiversity data.
format: application/pdf
format: text/html
creator: Martin Jung
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Data Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13872
publisher: PeerJ Inc.
rights: © 2022 Jung
abstract: Background Biodiversity varies in space and time, and often in response to environmental heterogeneity. Indicators in the form of local biodiversity measures–such as species richness or abundance–are common tools to capture this variation. The rise of readily available remote sensing data has enabled the characterization of environmental heterogeneity in a globally robust and replicable manner. Based on the assumption that differences in biodiversity measures are generally related to differences in environmental heterogeneity, these data have enabled projections and extrapolations of biodiversity in space and time. However so far little work has been done on quantitatively evaluating if and how accurately local biodiversity measures can be predicted. Methods Here I combine estimates of biodiversity measures from terrestrial local biodiversity surveys with remotely-sensed data on environmental heterogeneity globally. I then determine through a cross-validation framework how accurately local biodiversity measures can be predicted within (“predictability”) and across similar (“transferability”) biodiversity surveys. Results I found that prediction errors can be substantial, with error magnitudes varying between different biodiversity measures, taxonomic groups, sampling techniques and types of environmental heterogeneity characterizations. And although errors associated with model predictability were in many cases relatively low, these results question–particular for transferability–our capability to accurately predict and project local biodiversity measures based on environmental heterogeneity. I make the case that future predictions should be evaluated based on their accuracy and inherent uncertainty, and ecological theories be tested against whether we are able to make accurate predictions from local biodiversity data.
bibliographic citation: Jung (2022) Predictability and transferability of local biodiversity environment relationships. PeerJ 10:e13872 https://doi.org/10.7717/peerj.13872
date submitted: 2022-05-04
date accepted: 2022-07-19
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jung
  given name: Martin
doi: 10.7717/peerj.13872
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Jung
attribution name: Jung

Pediatrics HIV-positive status disclosure and its predictors in Ethiopia: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Introduction HIV-positive status disclosure for children is challenging for family members, guardians, and healthcare professionals. Disclosure is very challenging, particularly for children, yet no systematic synthesis of evidence accurately measures HIV-positive status disclosure in children. This systematic review and meta-analysis study aimed to quantify the national prevalence of pediatric HIV-positive status disclosure in Ethiopia and identify factors associated with HIV-positive status disclosure. Method We systematically searched PubMed, EMBASE, Web of Science databases, and google scholar for relevant published studies. Studies published in the English language and conducted with cohort, case-control, and cross-sectional designs were eligible for the review. The primary and secondary outcomes of the study were HIV-positive status disclosure and factors associated with HIV-positive status disclosure, respectively. The quality of the included studies was assessed using the Joanna Briggs Institute critical appraisal tools. A random effect- model was used to estimate the pooled prevalence of HIV-positive status disclosure. Heterogeneity and publication bias of included studies was determined using I2 and Egger’s test, respectively. Result From 601 records screened, nine relevant studies consisting of 2,442 HIV-positive children were included in the analysis. The overall pooled prevalence of HIV-positive status disclosure among children living with HIV/AIDS in Ethiopia was 31.2% (95% CI [23.9–38.5]). HIV-negative status of caregivers (AOR: 2.01; 95% CI [1.28–3.18]), long duration on ART (greater than 5 years) (AOR: 3.2; 95% CI [1.77–5.78]) and older age of the child (>10 years) (AOR: 7.2; 95% CI [4.37–11.88]) were significantly associated with HIV-positive status disclosure. Conclusion Low prevalence of pediatric HIV-positive status disclosure was observed in Ethiopia. The longer duration of ART, the HIV-negative status of the caregiver, and older age greater th…
format: application/pdf
format: text/html
creator: Getaneh Mulualem Belay
creator: Fikadu Ambaw Yehualashet
creator: Amare Wondim Ewunetie
creator: Kendalem Asmare Atalell
subject: Global Health
subject: HIV
subject: Infectious Diseases
subject: Pediatrics
description: doi:10.7717/peerj.13896
publisher: PeerJ Inc.
rights: © 2022 Belay et al.
abstract: Introduction HIV-positive status disclosure for children is challenging for family members, guardians, and healthcare professionals. Disclosure is very challenging, particularly for children, yet no systematic synthesis of evidence accurately measures HIV-positive status disclosure in children. This systematic review and meta-analysis study aimed to quantify the national prevalence of pediatric HIV-positive status disclosure in Ethiopia and identify factors associated with HIV-positive status disclosure. Method We systematically searched PubMed, EMBASE, Web of Science databases, and google scholar for relevant published studies. Studies published in the English language and conducted with cohort, case-control, and cross-sectional designs were eligible for the review. The primary and secondary outcomes of the study were HIV-positive status disclosure and factors associated with HIV-positive status disclosure, respectively. The quality of the included studies was assessed using the Joanna Briggs Institute critical appraisal tools. A random effect- model was used to estimate the pooled prevalence of HIV-positive status disclosure. Heterogeneity and publication bias of included studies was determined using I2 and Egger’s test, respectively. Result From 601 records screened, nine relevant studies consisting of 2,442 HIV-positive children were included in the analysis. The overall pooled prevalence of HIV-positive status disclosure among children living with HIV/AIDS in Ethiopia was 31.2% (95% CI [23.9–38.5]). HIV-negative status of caregivers (AOR: 2.01; 95% CI [1.28–3.18]), long duration on ART (greater than 5 years) (AOR: 3.2; 95% CI [1.77–5.78]) and older age of the child (>10 years) (AOR: 7.2; 95% CI [4.37–11.88]) were significantly associated with HIV-positive status disclosure. Conclusion Low prevalence of pediatric HIV-positive status disclosure was observed in Ethiopia. The longer duration of ART, the HIV-negative status of the caregiver, and older age greater th…
bibliographic citation: Belay et al. (2022) Pediatrics HIV-positive status disclosure and its predictors in Ethiopia: a systematic review and meta-analysis. PeerJ 10:e13896 https://doi.org/10.7717/peerj.13896
date submitted: 2022-05-24
date accepted: 2022-07-22
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Belay
  given name: Getaneh Mulualem
author list: Agent
  family name: Yehualashet
  given name: Fikadu Ambaw
author list: Agent
  family name: Ewunetie
  given name: Amare Wondim
author list: Agent
  family name: Atalell
  given name: Kendalem Asmare
doi: 10.7717/peerj.13896
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: ©2022 Belay et al.
attribution name: Belay et al.

Chemistry, taxonomy and ecology of the potentially chimpanzee-dispersed Vepris teva sp.nov. (Rutaceae) endangered in coastal thicket in the Congo Republic
type: item
type: AcademicArticle
description: Continuing a survey of the chemistry of species of the largely continental African genus Vepris, we investigate a species previously referred to as Vepris sp. 1 of Congo. From the leaves of Vepris sp. 1 we report six compounds. The compounds were three furoquinoline alkaloids, kokusaginine (1), maculine (2), and flindersiamine (3), two acridone alkaloids, arborinine (4) and 1-hydroxy-3-methoxy-10-methylacridone (5), and the triterpenoid, ß-amyrin (6). Compounds 1–4 are commonly isolated from other Vepris species, compound 5 has been reported before once, from Malagasy Vepris pilosa, while this is the first report of ß-amyrin from Vepris. This combination of compounds has never before been reported from any species of Vepris. We test the hypothesis that Vepris sp. 1 is new to science and formally describe it as Vepris teva, unique in the genus in that the trifoliolate leaves are subsessile, with the median petiolule far exceeding the petiole in length. Similar fleshy-leathery four-locular syncarpous fruits are otherwise only known in the genus in Vepris glaberrima (formerly the monotypic genus Oriciopsis Engl.), a potential sister species, but requiring further investigation to confirm this phylogenetic position. We briefly characterise the unusual and poorly documented Atlantic coast equatorial ecosystem, where Vepris teva is restricted to evergreen thicket on white sand, unusual in a genus usually confined to evergreen forest. This endemic-rich ecosystem with a unique amphibian as well as plants, extends along the coastline from the mouth of the Congo River to southern Rio Muni, a distance of about 1,000 km, traversing five countries. We map and illustrate Vepris teva and assess its extinction risk as Endangered (EN B1ab(iii)+B2ab(iii)) using the IUCN, 2012 standard. Only three locations are known, and threats include port and oil refinery construction and associated activities, with only one protected location, the Jane Goodall Institute’s Tchimpounga Reserve. Ini…
format: application/pdf
format: text/html
creator: Moses K. Langat
creator: Teva Kami
creator: Martin Cheek
subject: Biochemistry
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.13926
publisher: PeerJ Inc.
rights: © 2022 Langat et al.
abstract: Continuing a survey of the chemistry of species of the largely continental African genus Vepris, we investigate a species previously referred to as Vepris sp. 1 of Congo. From the leaves of Vepris sp. 1 we report six compounds. The compounds were three furoquinoline alkaloids, kokusaginine (1), maculine (2), and flindersiamine (3), two acridone alkaloids, arborinine (4) and 1-hydroxy-3-methoxy-10-methylacridone (5), and the triterpenoid, ß-amyrin (6). Compounds 1–4 are commonly isolated from other Vepris species, compound 5 has been reported before once, from Malagasy Vepris pilosa, while this is the first report of ß-amyrin from Vepris. This combination of compounds has never before been reported from any species of Vepris. We test the hypothesis that Vepris sp. 1 is new to science and formally describe it as Vepris teva, unique in the genus in that the trifoliolate leaves are subsessile, with the median petiolule far exceeding the petiole in length. Similar fleshy-leathery four-locular syncarpous fruits are otherwise only known in the genus in Vepris glaberrima (formerly the monotypic genus Oriciopsis Engl.), a potential sister species, but requiring further investigation to confirm this phylogenetic position. We briefly characterise the unusual and poorly documented Atlantic coast equatorial ecosystem, where Vepris teva is restricted to evergreen thicket on white sand, unusual in a genus usually confined to evergreen forest. This endemic-rich ecosystem with a unique amphibian as well as plants, extends along the coastline from the mouth of the Congo River to southern Rio Muni, a distance of about 1,000 km, traversing five countries. We map and illustrate Vepris teva and assess its extinction risk as Endangered (EN B1ab(iii)+B2ab(iii)) using the IUCN, 2012 standard. Only three locations are known, and threats include port and oil refinery construction and associated activities, with only one protected location, the Jane Goodall Institute’s Tchimpounga Reserve. Ini…
bibliographic citation: Langat et al. (2022) Chemistry, taxonomy and ecology of the potentially chimpanzee-dispersed Vepris teva sp.nov. (Rutaceae) endangered in coastal thicket in the Congo Republic. PeerJ 10:e13926 https://doi.org/10.7717/peerj.13926
date submitted: 2021-09-22
date accepted: 2022-07-30
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Langat
  given name: Moses K.
author list: Agent
  family name: Kami
  given name: Teva
author list: Agent
  family name: Cheek
  given name: Martin
doi: 10.7717/peerj.13926
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Langat et al.
attribution name: Langat et al.

An assessment of heavy metals in green sea turtle (Chelonia mydas) hatchlings from Saudi Arabia’s largest rookery, Ras Baridi
type: item
type: AcademicArticle
description: Background Anthropogenic sources can lead to the accumulation of heavy metals in marine organisms through ingestion, absorption, or inhalation. For sea turtle embryos, heavy metals can be absorbed into the egg from the incubation environment or be maternally transferred to the offspring causing neurological, reproductive, and developmental problems. Here, we report heavy metal concentrations in green turtle hatchlings from the largest rookery on the Red Sea, Ras Baridi. Methods Deceased hatchlings were collected from two beaches near a cement factory at Ras Baridi, from which heavy metal concentrations (chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), selenium (Se), cadmium (Cd), and lead (Pb)) were measured from the liver, muscle, and residual yolk of the hatchlings. Results Although based on a small sample of hatchlings, the data presented here provides the first measurements of heavy metals from sea turtles in the Red Sea and highlights the link between human activity and its impact on the ecology of sea turtles. In general, the heavy metal concentrations of heavy metals were not significantly different between the beach next to the cement factory and the beach downwind from the factory. However, the concentrations of heavy metals were significantly different between sampled tissues (liver, muscle, and residual yolk). Discussion This study provides insight into current heavy metal levels in green turtle hatchlings, which can be used as bio-indicators for environmental contaminants as coastal development increases in the Red Sea. Moreover, we found a lack of standardized methodology to evaluate heavy metals in hatchling sea turtles. Future efforts should work toward creating comparable techniques for long-term heavy metal monitoring, as this is a useful determinant of anthropogenic pollution.
format: application/pdf
format: text/html
creator: Lyndsey K. Tanabe
creator: Kirsty Scott
creator: Vijayalaxmi Dasari
creator: Michael L. Berumen
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.13928
publisher: PeerJ Inc.
rights: © 2022 Tanabe et al.
abstract: Background Anthropogenic sources can lead to the accumulation of heavy metals in marine organisms through ingestion, absorption, or inhalation. For sea turtle embryos, heavy metals can be absorbed into the egg from the incubation environment or be maternally transferred to the offspring causing neurological, reproductive, and developmental problems. Here, we report heavy metal concentrations in green turtle hatchlings from the largest rookery on the Red Sea, Ras Baridi. Methods Deceased hatchlings were collected from two beaches near a cement factory at Ras Baridi, from which heavy metal concentrations (chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), selenium (Se), cadmium (Cd), and lead (Pb)) were measured from the liver, muscle, and residual yolk of the hatchlings. Results Although based on a small sample of hatchlings, the data presented here provides the first measurements of heavy metals from sea turtles in the Red Sea and highlights the link between human activity and its impact on the ecology of sea turtles. In general, the heavy metal concentrations of heavy metals were not significantly different between the beach next to the cement factory and the beach downwind from the factory. However, the concentrations of heavy metals were significantly different between sampled tissues (liver, muscle, and residual yolk). Discussion This study provides insight into current heavy metal levels in green turtle hatchlings, which can be used as bio-indicators for environmental contaminants as coastal development increases in the Red Sea. Moreover, we found a lack of standardized methodology to evaluate heavy metals in hatchling sea turtles. Future efforts should work toward creating comparable techniques for long-term heavy metal monitoring, as this is a useful determinant of anthropogenic pollution.
bibliographic citation: Tanabe et al. (2022) An assessment of heavy metals in green sea turtle (Chelonia mydas) hatchlings from Saudi Arabia’s largest rookery, Ras Baridi. PeerJ 10:e13928 https://doi.org/10.7717/peerj.13928
date submitted: 2022-05-02
date accepted: 2022-07-31
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tanabe
  given name: Lyndsey K.
author list: Agent
  family name: Scott
  given name: Kirsty
author list: Agent
  family name: Dasari
  given name: Vijayalaxmi
author list: Agent
  family name: Berumen
  given name: Michael L.
doi: 10.7717/peerj.13928
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Tanabe et al.
attribution name: Tanabe et al.

Synchrotron µ-XRF mapping analysis of trace elements in in-situ cultured Japanese red coral, Corallium japonicum
type: item
type: AcademicArticle
description: Precious corals belong to the family Coralliidae (Cnidaria, Octocorallia), and their axis, which consists of high magnesian calcium carbonate, has long been used in jewelry. With its low growth rate and long lifespan, precious coral is a representative taxon of the vulnerable marine ecosystem. Due to years of overfishing, coral fishery has become a controversial issue. To estimate the growth rate and clarify the uptake process of trace elements in relation to the growth of the carbonate axis, Japanese red coral (Corallium japonicum) was cultured at a depth of 135 m off Takeshima Island, Kagoshima, Japan for 98 months and analyzed by microscopic X-ray fluorescence/soft X-ray photoabsorption (µ-XRF/XAS) speciation mapping. The growth rate was estimated to be 0.37 mm/year in diameter, and 10–11 growth rings were observed in a cross section of the axis. This estimated growth-rate value is the first ever to be obtained from the in-situ culture of Japanese precious coral. The fluctuation in water temperature near the in-situ-culture site was recorded for part of the culture period and then compared with the changes in the growth ring and the distribution of trace elements in a cross section of the coral axis during the same period. When the water temperature was increasing, the growth ring was light in color, sulfur and phosphorus concentrations were low, and magnesium was high. Conversely, a dark band in the growth ring, high sulfur and phosphorus, and low magnesium concentrations were observed when the water temperature was decreasing. In a cross section of the coral axis, the distribution of sulfur and magnesium from the center to the surface corresponded, respectively, to dark and light bands in the annual growth ring. Sulfur concentration was high in the dark band and low in the light band, while magnesium was negatively correlated with sulfur.
format: application/pdf
format: text/html
creator: Nozomu Iwasaki
creator: Hiroshi Hasegawa
creator: Yusuke Tamenori
creator: Mutsuro Kikunaga
creator: Toshihiro Yoshimura
creator: Hikaru Sawai
subject: Marine Biology
subject: Zoology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.13931
publisher: PeerJ Inc.
rights: © 2022 Iwasaki et al.
abstract: Precious corals belong to the family Coralliidae (Cnidaria, Octocorallia), and their axis, which consists of high magnesian calcium carbonate, has long been used in jewelry. With its low growth rate and long lifespan, precious coral is a representative taxon of the vulnerable marine ecosystem. Due to years of overfishing, coral fishery has become a controversial issue. To estimate the growth rate and clarify the uptake process of trace elements in relation to the growth of the carbonate axis, Japanese red coral (Corallium japonicum) was cultured at a depth of 135 m off Takeshima Island, Kagoshima, Japan for 98 months and analyzed by microscopic X-ray fluorescence/soft X-ray photoabsorption (µ-XRF/XAS) speciation mapping. The growth rate was estimated to be 0.37 mm/year in diameter, and 10–11 growth rings were observed in a cross section of the axis. This estimated growth-rate value is the first ever to be obtained from the in-situ culture of Japanese precious coral. The fluctuation in water temperature near the in-situ-culture site was recorded for part of the culture period and then compared with the changes in the growth ring and the distribution of trace elements in a cross section of the coral axis during the same period. When the water temperature was increasing, the growth ring was light in color, sulfur and phosphorus concentrations were low, and magnesium was high. Conversely, a dark band in the growth ring, high sulfur and phosphorus, and low magnesium concentrations were observed when the water temperature was decreasing. In a cross section of the coral axis, the distribution of sulfur and magnesium from the center to the surface corresponded, respectively, to dark and light bands in the annual growth ring. Sulfur concentration was high in the dark band and low in the light band, while magnesium was negatively correlated with sulfur.
bibliographic citation: Iwasaki et al. (2022) Synchrotron µ-XRF mapping analysis of trace elements in in-situ cultured Japanese red coral, Corallium japonicum. PeerJ 10:e13931 https://doi.org/10.7717/peerj.13931
date submitted: 2022-03-10
date accepted: 2022-07-31
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Iwasaki
  given name: Nozomu
author list: Agent
  family name: Hasegawa
  given name: Hiroshi
author list: Agent
  family name: Tamenori
  given name: Yusuke
author list: Agent
  family name: Kikunaga
  given name: Mutsuro
author list: Agent
  family name: Yoshimura
  given name: Toshihiro
author list: Agent
  family name: Sawai
  given name: Hikaru
doi: 10.7717/peerj.13931
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Iwasaki et al.
attribution name: Iwasaki et al.

Fish habitat restoration on the basis of water morphology simulation
type: item
type: AcademicArticle
description: The hydrodynamic conditions of rivers affect fish habitats by influencing parameters such as river bottom topography. Ecological restoration projects change the water morphological characteristics of rivers. Here, water flow characteristics of the upper Yangtze River before and after the construction of a restoration project were analyzed using the computational fluid dynamics simulation method. The longitudinal diversion dam could divide the river into two flow velocity zones, and the outer flow is similar to the original river with a flow velocity of 0.75 m/s. However, flow velocity on the inner side of the river was about 0.25 m/s, forming a larger buffer area. The eddy became more diversified and stable, with a high eddy viscosity coefficient and less fluctuations, at 9 Pa·s; this was conducive to fish aggregation and spawning. At different depths, large gradient differences were observed between the inner and outer sides of the longitudinal diversion dam, and the turbulent current and upward flow of the inner side were obvious; this was more favorable to the aggregation of different fish species. The longitudinal dam body was under a pressure of about 200.2 Pa at the same flow rate; this was significantly lower than the pressure on the transverse dam body. The field flow test and fish survey data showed that the error rate of the simulation using the RNG turbulent model was less than 10% compared with actual mapping. After the restoration of fish habitats by the longitudinal diversion dam, the number of fish species in the area increased from 40 to 49; The density of fish in the water increased from 71.40 fish per 1,000 m2 before the project to 315.70 fish per 1,000 m2 after the project. These results can provide a reference for the rapid assessment of water morphology and fish habitat restoration in the future.
format: application/pdf
format: text/html
creator: Xiaolong Chen
creator: Xuan Che
creator: Xingguo Liu
creator: Lin Zhu
creator: Changfeng Tian
creator: Xinfeng Li
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Ecosystem Science
subject: Freshwater Biology
description: doi:10.7717/peerj.13943
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: The hydrodynamic conditions of rivers affect fish habitats by influencing parameters such as river bottom topography. Ecological restoration projects change the water morphological characteristics of rivers. Here, water flow characteristics of the upper Yangtze River before and after the construction of a restoration project were analyzed using the computational fluid dynamics simulation method. The longitudinal diversion dam could divide the river into two flow velocity zones, and the outer flow is similar to the original river with a flow velocity of 0.75 m/s. However, flow velocity on the inner side of the river was about 0.25 m/s, forming a larger buffer area. The eddy became more diversified and stable, with a high eddy viscosity coefficient and less fluctuations, at 9 Pa·s; this was conducive to fish aggregation and spawning. At different depths, large gradient differences were observed between the inner and outer sides of the longitudinal diversion dam, and the turbulent current and upward flow of the inner side were obvious; this was more favorable to the aggregation of different fish species. The longitudinal dam body was under a pressure of about 200.2 Pa at the same flow rate; this was significantly lower than the pressure on the transverse dam body. The field flow test and fish survey data showed that the error rate of the simulation using the RNG turbulent model was less than 10% compared with actual mapping. After the restoration of fish habitats by the longitudinal diversion dam, the number of fish species in the area increased from 40 to 49; The density of fish in the water increased from 71.40 fish per 1,000 m2 before the project to 315.70 fish per 1,000 m2 after the project. These results can provide a reference for the rapid assessment of water morphology and fish habitat restoration in the future.
bibliographic citation: Chen et al. (2022) Fish habitat restoration on the basis of water morphology simulation. PeerJ 10:e13943 https://doi.org/10.7717/peerj.13943
date submitted: 2022-03-28
date accepted: 2022-08-03
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xiaolong
author list: Agent
  family name: Che
  given name: Xuan
author list: Agent
  family name: Liu
  given name: Xingguo
author list: Agent
  family name: Zhu
  given name: Lin
author list: Agent
  family name: Tian
  given name: Changfeng
author list: Agent
  family name: Li
  given name: Xinfeng
doi: 10.7717/peerj.13943
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Chen et al.
attribution name: Chen et al.

Estimating uncertainty in density surface models
type: item
type: AcademicArticle
description: Providing uncertainty estimates for predictions derived from species distribution models is essential for management but there is little guidance on potential sources of uncertainty in predictions and how best to combine these. Here we show where uncertainty can arise in density surface models (a multi-stage spatial modelling approach for distance sampling data), focussing on cetacean density modelling. We propose an extensible, modular, hybrid analytical-simulation approach to encapsulate these sources. We provide example analyses of fin whales Balaenoptera physalus in the California Current Ecosystem.
format: application/pdf
format: text/html
creator: David L. Miller
creator: Elizabeth A. Becker
creator: Karin A. Forney
creator: Jason J. Roberts
creator: Ana Cañadas
creator: Robert S. Schick
subject: Conservation Biology
subject: Marine Biology
subject: Statistics
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13950
publisher: PeerJ Inc.
rights: © 2022 Miller et al.
abstract: Providing uncertainty estimates for predictions derived from species distribution models is essential for management but there is little guidance on potential sources of uncertainty in predictions and how best to combine these. Here we show where uncertainty can arise in density surface models (a multi-stage spatial modelling approach for distance sampling data), focussing on cetacean density modelling. We propose an extensible, modular, hybrid analytical-simulation approach to encapsulate these sources. We provide example analyses of fin whales Balaenoptera physalus in the California Current Ecosystem.
bibliographic citation: Miller et al. (2022) Estimating uncertainty in density surface models. PeerJ 10:e13950 https://doi.org/10.7717/peerj.13950
date submitted: 2022-06-30
date accepted: 2022-08-05
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Miller
  given name: David L.
author list: Agent
  family name: Becker
  given name: Elizabeth A.
author list: Agent
  family name: Forney
  given name: Karin A.
author list: Agent
  family name: Roberts
  given name: Jason J.
author list: Agent
  family name: Cañadas
  given name: Ana
author list: Agent
  family name: Schick
  given name: Robert S.
doi: 10.7717/peerj.13950
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
attribution name: Miller et al.

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