PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Environmental detection of Fasciola hepatica by loop-mediated isothermal amplification
items: HMGB1-activatied NLRP3 inflammasome induces thrombocytopenia in heatstroke rat
items: Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil
items: Research progress in toxicological effects and mechanism of aflatoxin B1 toxin
items: Radiographic assessment of endodontic mishaps in an undergraduate student clinic: a 2-year retrospective study
items: A new nurse frog of the Allobates tapajos species complex (Anura: Aromobatidae) from the upper Madeira River, Brazilian Amazonia
items: Protecting endangered megafauna through AI analysis of drone images in a low-connectivity setting: a case study from Namibia
items: Differential proteomic analysis of mouse cerebrums with high-fat diet (HFD)-induced hyperlipidemia
items: Assisted migration and the rare endemic plant species: the case of two endangered Mexican spruces
items: Criteria for assessing the adaptive changes in mixed martial arts (MMA) athletes of strike fighting style in different training load regimes

Environmental detection of Fasciola hepatica by loop-mediated isothermal amplification
type: item
type: AcademicArticle
description: Fasciola hepatica, commonly referred to as liver flukes, is a substantial zoonotic parasitic disease of humans and livestock globally. While infection is readily controlled by anthelmintics, namely triclabendazole, the heavy reliance on triclabendazole has resulted in drug resistance appearing worldwide. Due to drug resistance, it is imperative to adopt an integrated parasite management program to preserve the efficacy of currently available anthelmintics. A integrated liver fluke management plan would benefit from a simple rapid, field-deployable diagnostic for detection of F. hepatica in environment and the host. Therefore, a rapid DNA test using loop-mediated isothermal amplification was developed and optimised for the detection of F. hepatica from faecal and water samples to enable the detection of parasites both within the host and from the environment. The assay presented here is fast, with amplification in ≤20 min, and highly sensitive, with a detection limit of 5 × 10−4 ng/µL. The workflow presented here provides a time to result of ≤60 min without requiring a commercial kit for the extraction of DNA from faecal and water samples, and pending further validation from field-samples, could potentially be used to enable real-time decision making to mitigate parasite prevalence on a farming property and with no requirement for sample transportation.
format: application/pdf
format: text/html
creator: Lily Tran
creator: Hayley Toet
creator: Travis Beddoe
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.13778
publisher: PeerJ Inc.
rights: © 2022 Tran et al.
abstract: Fasciola hepatica, commonly referred to as liver flukes, is a substantial zoonotic parasitic disease of humans and livestock globally. While infection is readily controlled by anthelmintics, namely triclabendazole, the heavy reliance on triclabendazole has resulted in drug resistance appearing worldwide. Due to drug resistance, it is imperative to adopt an integrated parasite management program to preserve the efficacy of currently available anthelmintics. A integrated liver fluke management plan would benefit from a simple rapid, field-deployable diagnostic for detection of F. hepatica in environment and the host. Therefore, a rapid DNA test using loop-mediated isothermal amplification was developed and optimised for the detection of F. hepatica from faecal and water samples to enable the detection of parasites both within the host and from the environment. The assay presented here is fast, with amplification in ≤20 min, and highly sensitive, with a detection limit of 5 × 10−4 ng/µL. The workflow presented here provides a time to result of ≤60 min without requiring a commercial kit for the extraction of DNA from faecal and water samples, and pending further validation from field-samples, could potentially be used to enable real-time decision making to mitigate parasite prevalence on a farming property and with no requirement for sample transportation.
bibliographic citation: Tran et al. (2022) Environmental detection of Fasciola hepatica by loop-mediated isothermal amplification. PeerJ 10:e13778 https://doi.org/10.7717/peerj.13778
date submitted: 2022-01-31
date accepted: 2022-07-02
issued: 2022-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tran
  given name: Lily
author list: Agent
  family name: Toet
  given name: Hayley
author list: Agent
  family name: Beddoe
  given name: Travis
doi: 10.7717/peerj.13778
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-04
copyright: © 2022 Tran et al.
attribution name: Tran et al.

HMGB1-activatied NLRP3 inflammasome induces thrombocytopenia in heatstroke rat
type: item
type: AcademicArticle
description: Background Thrombocytopenia, an early common complication in heatstroke (HS), has been widely considered as a mortality predictor of HS. The mechanism underlying thrombocytopenia in HS remains unknown. It is not known whether NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome is activated in HS platelet, which, in turn, induces platelet activation and thrombocytopenia. This study tried to clarify the activation of the NOD-like receptor signaling pathway under HS conditions and investigate its roles in mediating HS-induced thrombocytopenia. Methods Rat HS models were established in a certain ambient temperature and humidity. Platelets, isolated from blood, were counted and CD62P, an index of platelet activation, was measured by flow cytometry in all rats. The colocalization of NLRP3 inflammasome in platelet was detected by confocal fluorescence microscopy. Mitochondrial-derived reactive oxygen species (ROS) was detected using the molecular probes. Plasma HMGB1 and IL-1β levels were measured by ELISA. Results Platelet activation, showed by upregulated CD62P, and thrombocytopenia were observed in HS rats. HS activated the NLRP3 inflammasome, which was induced by elevated levels of ROS, while the upregulated CD62P and thrombocytopenia triggered by NLRP3 inflammasome were attributed to the high mobility group box protein 1 (HMGB1) inplasma. Moreover, inhibition of the NOD-like receptor signaling pathway in rats with HS suppressed platelet activation and the decline of platelet count. Similar results were obtained when the receptor toll-like receptor 4 (TLR4)/advanced glycation end product (RAGE) was blocked. Conclusions The NOD-like receptor signaling pathway induces platelet activation and thrombocytopenia in HS rats. These findings suggested that the NLRP3 inflammasome might be the potential target for HS treatment.
format: application/pdf
format: text/html
creator: Huimei Yin
creator: Ming Wu
creator: Yong Lu
creator: Xinghui Wu
creator: BaoJun Yu
creator: Ronglin Chen
creator: JieFu Lu
creator: Huasheng Tong
subject: Emergency and Critical Care
subject: Hematology
description: doi:10.7717/peerj.13799
publisher: PeerJ Inc.
rights: © 2022 Yin et al.
abstract: Background Thrombocytopenia, an early common complication in heatstroke (HS), has been widely considered as a mortality predictor of HS. The mechanism underlying thrombocytopenia in HS remains unknown. It is not known whether NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome is activated in HS platelet, which, in turn, induces platelet activation and thrombocytopenia. This study tried to clarify the activation of the NOD-like receptor signaling pathway under HS conditions and investigate its roles in mediating HS-induced thrombocytopenia. Methods Rat HS models were established in a certain ambient temperature and humidity. Platelets, isolated from blood, were counted and CD62P, an index of platelet activation, was measured by flow cytometry in all rats. The colocalization of NLRP3 inflammasome in platelet was detected by confocal fluorescence microscopy. Mitochondrial-derived reactive oxygen species (ROS) was detected using the molecular probes. Plasma HMGB1 and IL-1β levels were measured by ELISA. Results Platelet activation, showed by upregulated CD62P, and thrombocytopenia were observed in HS rats. HS activated the NLRP3 inflammasome, which was induced by elevated levels of ROS, while the upregulated CD62P and thrombocytopenia triggered by NLRP3 inflammasome were attributed to the high mobility group box protein 1 (HMGB1) inplasma. Moreover, inhibition of the NOD-like receptor signaling pathway in rats with HS suppressed platelet activation and the decline of platelet count. Similar results were obtained when the receptor toll-like receptor 4 (TLR4)/advanced glycation end product (RAGE) was blocked. Conclusions The NOD-like receptor signaling pathway induces platelet activation and thrombocytopenia in HS rats. These findings suggested that the NLRP3 inflammasome might be the potential target for HS treatment.
bibliographic citation: Yin et al. (2022) HMGB1-activatied NLRP3 inflammasome induces thrombocytopenia in heatstroke rat. PeerJ 10:e13799 https://doi.org/10.7717/peerj.13799
date submitted: 2022-01-12
date accepted: 2022-07-06
issued: 2022-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Huimei
author list: Agent
  family name: Wu
  given name: Ming
author list: Agent
  family name: Lu
  given name: Yong
author list: Agent
  family name: Wu
  given name: Xinghui
author list: Agent
  family name: Yu
  given name: BaoJun
author list: Agent
  family name: Chen
  given name: Ronglin
author list: Agent
  family name: Lu
  given name: JieFu
author list: Agent
  family name: Tong
  given name: Huasheng
doi: 10.7717/peerj.13799
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-04
copyright: ©2022 Yin et al.
attribution name: Yin et al.

Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil
type: item
type: AcademicArticle
description: Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.
format: application/pdf
format: text/html
creator: Li Bin Liao
creator: Xiao Xia Chen
creator: Jun Xiang
creator: Nan Nan Zhang
creator: En Tao Wang
creator: Fu Sun Shi
subject: Agricultural Science
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.13808
publisher: PeerJ Inc.
rights: © 2022 Liao et al.
abstract: Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.
bibliographic citation: Liao et al. (2022) Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil. PeerJ 10:e13808 https://doi.org/10.7717/peerj.13808
date submitted: 2022-04-08
date accepted: 2022-07-07
issued: 2022-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liao
  given name: Li Bin
author list: Agent
  family name: Chen
  given name: Xiao Xia
author list: Agent
  family name: Xiang
  given name: Jun
author list: Agent
  family name: Zhang
  given name: Nan Nan
author list: Agent
  family name: Wang
  given name: En Tao
author list: Agent
  family name: Shi
  given name: Fu Sun
doi: 10.7717/peerj.13808
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-04
copyright: ©2022 Liao et al.
attribution name: Liao et al.

Research progress in toxicological effects and mechanism of aflatoxin B1 toxin
type: item
type: AcademicArticle
description: Fungal contamination of animal feed can severely affect the health of farm animals, and result in considerable economic losses. Certain filamentous fungi or molds produce toxic secondary metabolites known as mycotoxins, of which aflatoxins (AFTs) are considered the most critical dietary risk factor for both humans and animals. AFTs are ubiquitous in the environment, soil, and food crops, and aflatoxin B1(AFB1) has been identified by the World Health Organization (WHO) as one of the most potent natural group 1A carcinogen. We reviewed the literature on the toxic effects of AFB1 in humans and animals along with its toxicokinetic properties. The damage induced by AFB1 in cells and tissues is mainly achieved through cell cycle arrest and inhibition of cell proliferation, and the induction of apoptosis, oxidative stress, endoplasmic reticulum (ER) stress and autophagy. In addition, numerous coding genes and non-coding RNAs have been identified that regulate AFB1 toxicity. This review is a summary of the current research on the complexity of AFB1 toxicity, and provides insights into the molecular mechanisms as well as the phenotypic characteristics.
format: application/pdf
format: text/html
creator: Congcong Li
creator: Xiangdong Liu
creator: Jiao Wu
creator: Xiangbo Ji
creator: Qiuliang Xu
subject: Agricultural Science
subject: Biochemistry
subject: Mycology
subject: Toxicology
description: doi:10.7717/peerj.13850
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Fungal contamination of animal feed can severely affect the health of farm animals, and result in considerable economic losses. Certain filamentous fungi or molds produce toxic secondary metabolites known as mycotoxins, of which aflatoxins (AFTs) are considered the most critical dietary risk factor for both humans and animals. AFTs are ubiquitous in the environment, soil, and food crops, and aflatoxin B1(AFB1) has been identified by the World Health Organization (WHO) as one of the most potent natural group 1A carcinogen. We reviewed the literature on the toxic effects of AFB1 in humans and animals along with its toxicokinetic properties. The damage induced by AFB1 in cells and tissues is mainly achieved through cell cycle arrest and inhibition of cell proliferation, and the induction of apoptosis, oxidative stress, endoplasmic reticulum (ER) stress and autophagy. In addition, numerous coding genes and non-coding RNAs have been identified that regulate AFB1 toxicity. This review is a summary of the current research on the complexity of AFB1 toxicity, and provides insights into the molecular mechanisms as well as the phenotypic characteristics.
bibliographic citation: Li et al. (2022) Research progress in toxicological effects and mechanism of aflatoxin B1 toxin. PeerJ 10:e13850 https://doi.org/10.7717/peerj.13850
date submitted: 2022-04-04
date accepted: 2022-07-16
issued: 2022-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Congcong
author list: Agent
  family name: Liu
  given name: Xiangdong
author list: Agent
  family name: Wu
  given name: Jiao
author list: Agent
  family name: Ji
  given name: Xiangbo
author list: Agent
  family name: Xu
  given name: Qiuliang
doi: 10.7717/peerj.13850
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-04
copyright: ©2022 Li et al.
attribution name: Li et al.

Radiographic assessment of endodontic mishaps in an undergraduate student clinic: a 2-year retrospective study
type: item
type: AcademicArticle
description: Objectives The aim of this study was to compare the occurrence of instrumentation and obturation related endodontic procedural mishaps following the use of either, stainless steel hand or engine-driven rotary instrumentation techniques. Methods From a computerized hospital database, a total of 730 dental patient records who had received endodontic treatment by undergraduate dental students between August 2018 to September 2020 were retrieved. The inclusion criteria were primary (non-surgical) endodontic treatment on permanent teeth with complete radiographic records. Following record screening, a final sample of n = 475 dental records were included. Radiographic records were evaluated for both instrumentation and obturation related mishaps. The data was analysed using multiple logistic regression analysis (α = 0.05). Results Engine-driven rotary instrumentation resulted in a significant decrease in the overall occurrence of instrumentation related endodontic mishaps by 40% compared to hand instrumentation (Odds Ratio = 0.59 [0.36–0.97], p = 0.04). In particular, rotary instrumentation decreased ledge formation, perforation and obturation related mishaps, with minimal effect on the limitation of zipping. Conclusion The use of rotary instrumentation techniques may reduce the incidence of instrumentation and obturation endodontic mishaps in the undergraduate dental clinic.
format: application/pdf
format: text/html
creator: Manal Matoug-Elwerfelli
creator: Ahmed Abdou
creator: Wejdan Almutairi
creator: Malak Alhuthayli
creator: Shaikhah Aloyaynaa
creator: Rahaf Almohareb
subject: Dentistry
subject: Drugs and Devices
subject: Science and Medical Education
description: doi:10.7717/peerj.13858
publisher: PeerJ Inc.
rights: © 2022 Matoug-Elwerfelli et al.
abstract: Objectives The aim of this study was to compare the occurrence of instrumentation and obturation related endodontic procedural mishaps following the use of either, stainless steel hand or engine-driven rotary instrumentation techniques. Methods From a computerized hospital database, a total of 730 dental patient records who had received endodontic treatment by undergraduate dental students between August 2018 to September 2020 were retrieved. The inclusion criteria were primary (non-surgical) endodontic treatment on permanent teeth with complete radiographic records. Following record screening, a final sample of n = 475 dental records were included. Radiographic records were evaluated for both instrumentation and obturation related mishaps. The data was analysed using multiple logistic regression analysis (α = 0.05). Results Engine-driven rotary instrumentation resulted in a significant decrease in the overall occurrence of instrumentation related endodontic mishaps by 40% compared to hand instrumentation (Odds Ratio = 0.59 [0.36–0.97], p = 0.04). In particular, rotary instrumentation decreased ledge formation, perforation and obturation related mishaps, with minimal effect on the limitation of zipping. Conclusion The use of rotary instrumentation techniques may reduce the incidence of instrumentation and obturation endodontic mishaps in the undergraduate dental clinic.
bibliographic citation: Matoug-Elwerfelli et al. (2022) Radiographic assessment of endodontic mishaps in an undergraduate student clinic: a 2-year retrospective study. PeerJ 10:e13858 https://doi.org/10.7717/peerj.13858
date submitted: 2022-04-25
date accepted: 2022-07-17
issued: 2022-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matoug-Elwerfelli
  given name: Manal
author list: Agent
  family name: Abdou
  given name: Ahmed
author list: Agent
  family name: Almutairi
  given name: Wejdan
author list: Agent
  family name: Alhuthayli
  given name: Malak
author list: Agent
  family name: Aloyaynaa
  given name: Shaikhah
author list: Agent
  family name: Almohareb
  given name: Rahaf
doi: 10.7717/peerj.13858
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-04
copyright: ©2022 Matoug-Elwerfelli et al.
attribution name: Matoug-Elwerfelli et al.

A new nurse frog of the Allobates tapajos species complex (Anura: Aromobatidae) from the upper Madeira River, Brazilian Amazonia
type: item
type: AcademicArticle
description: Cryptic diversity is extremely common in widespread Amazonian anurans, but especially in nurse frogs of the genus Allobates. There is an urgent need to formally describe the many distinct but unnamed species, both to enable studies of their basic biology but especially to facilitate conservation of threatened environments in which many are found. Here, we describe through integrative taxonomy a new species of the Allobates tapajos species complex from the upper Madeira River, southwestern Amazonia. Species delimitation analyses based on molecular data are congruent and delimit five candidate species in addition to A. tapajos sensu stricto. The new species is recovered as sister to A. tapajos clade F, a candidate species from Teles-Pires River, southeastern Amazonia. The new species differs from nominal congeners in adult and larval morphology and in male advertisement call. Egg deposition sites differ between east and west banks of the upper Madeira River, but there is no evidence of corresponding morphologic or bioacoustic differentiation. The new species appears to be restricted to riparian forests; its known geographic range falls entirely within the influence zone of reservoirs of two large dams, which underscores the urgent need of a conservation assessment through long-term monitoring. This region harbors the richest assemblage of Allobates reported for Brazilian Amazonia, with six nominal species and four additional candidate species awaiting formal description.
format: application/pdf
format: text/html
creator: Miquéias Ferrão
creator: James Hanken
creator: Albertina P. Lima
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13751
publisher: PeerJ Inc.
rights: © 2022 Ferrão et al.
abstract: Cryptic diversity is extremely common in widespread Amazonian anurans, but especially in nurse frogs of the genus Allobates. There is an urgent need to formally describe the many distinct but unnamed species, both to enable studies of their basic biology but especially to facilitate conservation of threatened environments in which many are found. Here, we describe through integrative taxonomy a new species of the Allobates tapajos species complex from the upper Madeira River, southwestern Amazonia. Species delimitation analyses based on molecular data are congruent and delimit five candidate species in addition to A. tapajos sensu stricto. The new species is recovered as sister to A. tapajos clade F, a candidate species from Teles-Pires River, southeastern Amazonia. The new species differs from nominal congeners in adult and larval morphology and in male advertisement call. Egg deposition sites differ between east and west banks of the upper Madeira River, but there is no evidence of corresponding morphologic or bioacoustic differentiation. The new species appears to be restricted to riparian forests; its known geographic range falls entirely within the influence zone of reservoirs of two large dams, which underscores the urgent need of a conservation assessment through long-term monitoring. This region harbors the richest assemblage of Allobates reported for Brazilian Amazonia, with six nominal species and four additional candidate species awaiting formal description.
bibliographic citation: Ferrão et al. (2022) A new nurse frog of the Allobates tapajos species complex (Anura: Aromobatidae) from the upper Madeira River, Brazilian Amazonia. PeerJ 10:e13751 https://doi.org/10.7717/peerj.13751
date submitted: 2021-10-18
date accepted: 2022-06-28
issued: 2022-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferrão
  given name: Miquéias
author list: Agent
  family name: Hanken
  given name: James
author list: Agent
  family name: Lima
  given name: Albertina P.
doi: 10.7717/peerj.13751
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-03
copyright: ©2022 Ferrão et al.
attribution name: Ferrão et al.

Protecting endangered megafauna through AI analysis of drone images in a low-connectivity setting: a case study from Namibia
type: item
type: AcademicArticle
description: Assessing the numbers and distribution of at-risk megafauna such as the black rhino (Diceros bicornis) is key to effective conservation, yet such data are difficult to obtain. Many current monitoring technologies are invasive to the target animals and expensive. Satellite monitoring is emerging as a potential tool for very large animals (e.g., elephant) but detecting smaller species requires higher resolution imaging. Drones can deliver the required resolution and speed of monitoring, but challenges remain in delivering automated monitoring systems where internet connectivity is unreliable or absent. This study describes a model built to run on a drone to identify in situ images of megafauna. Compared with previously reported studies, this automated detection framework has a lower hardware cost and can function with a reduced internet bandwidth requirement for local network communication. It proposes the use of a Jetson Xavier NX, onboard a Parrot Anafi drone, connected to the internet throughout the flight to deliver a lightweight web-based notification system upon detection of the target species. The GPS location with the detected target species images is sent using MQ Telemetry Transport (MQTT), a lightweight messaging protocol using a publisher/subscriber architecture for IoT devices. It provides reliable message delivery when internet connection is sporadic. We used a YOLOv5l6 object detection architecture trained to identify a bounding box for one of five objects of interest in a frame of video. At an intersection over union (IoU) threshold of 0.5, our model achieved an average precision (AP) of 0.81 for black rhino (our primary target) and 0.83 for giraffe (Giraffa giraffa). The model was less successful at identifying the other smaller objects which were not our primary targets: 0.34, 0.25, and 0.42 for ostrich (Struthio camelus australis), springbok (Antidorcas marsupialis) and human respectively. We used several techniques to optimize performance and overc…
format: application/pdf
format: text/html
creator: Alice Hua
creator: Kevin Martin
creator: Yuzeng Shen
creator: Nicole Chen
creator: Catherine Mou
creator: Maximilian Sterk
creator: Berend Reinhard
creator: Friedrich F. Reinhard
creator: Stephen Lee
creator: Sky Alibhai
creator: Zoe C. Jewell
subject: Conservation Biology
subject: Zoology
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.13779
publisher: PeerJ Inc.
rights: © 2022 Hua et al.
abstract: Assessing the numbers and distribution of at-risk megafauna such as the black rhino (Diceros bicornis) is key to effective conservation, yet such data are difficult to obtain. Many current monitoring technologies are invasive to the target animals and expensive. Satellite monitoring is emerging as a potential tool for very large animals (e.g., elephant) but detecting smaller species requires higher resolution imaging. Drones can deliver the required resolution and speed of monitoring, but challenges remain in delivering automated monitoring systems where internet connectivity is unreliable or absent. This study describes a model built to run on a drone to identify in situ images of megafauna. Compared with previously reported studies, this automated detection framework has a lower hardware cost and can function with a reduced internet bandwidth requirement for local network communication. It proposes the use of a Jetson Xavier NX, onboard a Parrot Anafi drone, connected to the internet throughout the flight to deliver a lightweight web-based notification system upon detection of the target species. The GPS location with the detected target species images is sent using MQ Telemetry Transport (MQTT), a lightweight messaging protocol using a publisher/subscriber architecture for IoT devices. It provides reliable message delivery when internet connection is sporadic. We used a YOLOv5l6 object detection architecture trained to identify a bounding box for one of five objects of interest in a frame of video. At an intersection over union (IoU) threshold of 0.5, our model achieved an average precision (AP) of 0.81 for black rhino (our primary target) and 0.83 for giraffe (Giraffa giraffa). The model was less successful at identifying the other smaller objects which were not our primary targets: 0.34, 0.25, and 0.42 for ostrich (Struthio camelus australis), springbok (Antidorcas marsupialis) and human respectively. We used several techniques to optimize performance and overc…
bibliographic citation: Hua et al. (2022) Protecting endangered megafauna through AI analysis of drone images in a low-connectivity setting: a case study from Namibia. PeerJ 10:e13779 https://doi.org/10.7717/peerj.13779
date submitted: 2021-11-22
date accepted: 2022-07-03
issued: 2022-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hua
  given name: Alice
author list: Agent
  family name: Martin
  given name: Kevin
author list: Agent
  family name: Shen
  given name: Yuzeng
author list: Agent
  family name: Chen
  given name: Nicole
author list: Agent
  family name: Mou
  given name: Catherine
author list: Agent
  family name: Sterk
  given name: Maximilian
author list: Agent
  family name: Reinhard
  given name: Berend
author list: Agent
  family name: Reinhard
  given name: Friedrich F.
author list: Agent
  family name: Lee
  given name: Stephen
author list: Agent
  family name: Alibhai
  given name: Sky
author list: Agent
  family name: Jewell
  given name: Zoe C.
doi: 10.7717/peerj.13779
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-03
copyright: © 2022 Hua et al.
attribution name: Hua et al.

Differential proteomic analysis of mouse cerebrums with high-fat diet (HFD)-induced hyperlipidemia
type: item
type: AcademicArticle
description: Hyperlipidemia is a chronic disease characterized by elevated blood cholesterol and triglycerides and there is accumulated evidence that the disease might affect brain functions. Here we report on a proteomic analysis of the brain proteins in hyperlipidemic mice. Hyperlipidemia was successfully induced in mice by a 20 week high-fat diet (HFD) feeding (model group). A control group with a normal diet and a treatment group with HFD-fed mice treated with a lipid-lowering drug simvastatin (SIM) were established accordingly. The proteins were extracted from the left and right cerebrum hemispheres of the mice in the three groups and subjected to shotgun proteomic analysis. A total of 4,422 proteins were detected in at least half of the samples, among which 324 proteins showed significant difference (fold change >1.5 or <0.67, p < 0.05) in at least one of the four types of comparisons (left cerebrum hemispheres of the model group versus the control group, right cerebrums of model versus control, left cerebrums of SIM versus model, right cerebrums of SIM versus model). Biological process analysis revealed many of these proteins were enriched in the processes correlated with lipid metabolism, neurological disorders, synaptic events and nervous system development. For the first time, it has been reported that some of the proteins have been altered in the brain under the conditions of HFD feeding, obesity or hyperlipidemia. Further, 22 brain processes-related proteins showed different expression in the two cerebrum hemispheres, suggesting changes of the brain proteins caused by hyperlipidemia might also be asymmetric. We hope this work will provide useful information to understand the effects of HFD and hyperlipidemia on brain proteins.
format: application/pdf
format: text/html
creator: Changming Chen
creator: Meiling Wen
creator: Caixia Wang
creator: Zhongwen Yuan
creator: Ya Jin
subject: Biochemistry
subject: Molecular Biology
subject: Neuroscience
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.13806
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Hyperlipidemia is a chronic disease characterized by elevated blood cholesterol and triglycerides and there is accumulated evidence that the disease might affect brain functions. Here we report on a proteomic analysis of the brain proteins in hyperlipidemic mice. Hyperlipidemia was successfully induced in mice by a 20 week high-fat diet (HFD) feeding (model group). A control group with a normal diet and a treatment group with HFD-fed mice treated with a lipid-lowering drug simvastatin (SIM) were established accordingly. The proteins were extracted from the left and right cerebrum hemispheres of the mice in the three groups and subjected to shotgun proteomic analysis. A total of 4,422 proteins were detected in at least half of the samples, among which 324 proteins showed significant difference (fold change >1.5 or <0.67, p < 0.05) in at least one of the four types of comparisons (left cerebrum hemispheres of the model group versus the control group, right cerebrums of model versus control, left cerebrums of SIM versus model, right cerebrums of SIM versus model). Biological process analysis revealed many of these proteins were enriched in the processes correlated with lipid metabolism, neurological disorders, synaptic events and nervous system development. For the first time, it has been reported that some of the proteins have been altered in the brain under the conditions of HFD feeding, obesity or hyperlipidemia. Further, 22 brain processes-related proteins showed different expression in the two cerebrum hemispheres, suggesting changes of the brain proteins caused by hyperlipidemia might also be asymmetric. We hope this work will provide useful information to understand the effects of HFD and hyperlipidemia on brain proteins.
bibliographic citation: Chen et al. (2022) Differential proteomic analysis of mouse cerebrums with high-fat diet (HFD)-induced hyperlipidemia. PeerJ 10:e13806 https://doi.org/10.7717/peerj.13806
date submitted: 2022-04-15
date accepted: 2022-07-07
issued: 2022-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Changming
author list: Agent
  family name: Wen
  given name: Meiling
author list: Agent
  family name: Wang
  given name: Caixia
author list: Agent
  family name: Yuan
  given name: Zhongwen
author list: Agent
  family name: Jin
  given name: Ya
doi: 10.7717/peerj.13806
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-03
copyright: ©2022 Chen et al.
attribution name: Chen et al.

Assisted migration and the rare endemic plant species: the case of two endangered Mexican spruces
type: item
type: AcademicArticle
description: Background In the projected climate change scenarios, assisted migration might play an important role in the ex situ conservation of the threatened plant species, by translocate them to similar suitable habitats outside their native distributions. However, it is unclear if such habitats will be available for the Rare Endemic Plant Species (REPS), because of their very restricted habitats. The aims of this study were to perform a population size assessment for the REPS Picea martinezii Patterson and Picea mexicana Martínez, and to evaluate the potential species distributions and their possibilities for assisted migration inside México and worldwide. Methods We performed demographic censuses, field surveys in search for new stands, and developed distribution models for Last Glacial Maximum (22,000 years ago), Middle Holocene (6,000 years ago), current (1961–1990) and future (2050 and 2070) periods, for the whole Mexican territory (considering climatic, soil, geologic and topographic variables) and for all global land areas (based only on climate). Results Our censuses showed populations of 89,266 and 39,059 individuals for P. martinezii and P. mexicana, respectively, including known populations and new stands. Projections for México indicated somewhat larger suitable areas in the past, now restricted to the known populations and new stands, where they will disappear by 2050 in a pessimistic climatic scenario, and scarce marginal areas (p = 0.5–0.79) remaining only for P. martinezii by 2070. Worldwide projections (based only on climate variables) revealed few marginal areas in 2050 only in México for P. martinezii, and several large areas (p ≥ 0.5) for P. mexicana around the world (all outside México), especially on the Himalayas in India and the Chungyang mountains in Taiwan with highly suitable (p ≥ 0.8) climate habitats in current and future (2050) conditions. However, those suitable areas are currently inhabited by other endemic spruces: Picea smithiana (Wall.) Boi…
format: application/pdf
format: text/html
creator: Eduardo Mendoza-Maya
creator: Erika Gómez-Pineda
creator: Cuauhtémoc Sáenz-Romero
creator: José Ciro Hernández-Díaz
creator: Carlos A. López-Sánchez
creator: J. Jesús Vargas-Hernández
creator: José Ángel Prieto-Ruíz
creator: Christian Wehenkel
subject: Biogeography
subject: Conservation Biology
subject: Climate Change Biology
subject: Forestry
description: doi:10.7717/peerj.13812
publisher: PeerJ Inc.
rights: © 2022 Mendoza-Maya et al.
abstract: Background In the projected climate change scenarios, assisted migration might play an important role in the ex situ conservation of the threatened plant species, by translocate them to similar suitable habitats outside their native distributions. However, it is unclear if such habitats will be available for the Rare Endemic Plant Species (REPS), because of their very restricted habitats. The aims of this study were to perform a population size assessment for the REPS Picea martinezii Patterson and Picea mexicana Martínez, and to evaluate the potential species distributions and their possibilities for assisted migration inside México and worldwide. Methods We performed demographic censuses, field surveys in search for new stands, and developed distribution models for Last Glacial Maximum (22,000 years ago), Middle Holocene (6,000 years ago), current (1961–1990) and future (2050 and 2070) periods, for the whole Mexican territory (considering climatic, soil, geologic and topographic variables) and for all global land areas (based only on climate). Results Our censuses showed populations of 89,266 and 39,059 individuals for P. martinezii and P. mexicana, respectively, including known populations and new stands. Projections for México indicated somewhat larger suitable areas in the past, now restricted to the known populations and new stands, where they will disappear by 2050 in a pessimistic climatic scenario, and scarce marginal areas (p = 0.5–0.79) remaining only for P. martinezii by 2070. Worldwide projections (based only on climate variables) revealed few marginal areas in 2050 only in México for P. martinezii, and several large areas (p ≥ 0.5) for P. mexicana around the world (all outside México), especially on the Himalayas in India and the Chungyang mountains in Taiwan with highly suitable (p ≥ 0.8) climate habitats in current and future (2050) conditions. However, those suitable areas are currently inhabited by other endemic spruces: Picea smithiana (Wall.) Boi…
bibliographic citation: Mendoza-Maya et al. (2022) Assisted migration and the rare endemic plant species: the case of two endangered Mexican spruces. PeerJ 10:e13812 https://doi.org/10.7717/peerj.13812
date submitted: 2022-03-09
date accepted: 2022-07-07
issued: 2022-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mendoza-Maya
  given name: Eduardo
author list: Agent
  family name: Gómez-Pineda
  given name: Erika
author list: Agent
  family name: Sáenz-Romero
  given name: Cuauhtémoc
author list: Agent
  family name: Hernández-Díaz
  given name: José Ciro
author list: Agent
  family name: López-Sánchez
  given name: Carlos A.
author list: Agent
  family name: Vargas-Hernández
  given name: J. Jesús
author list: Agent
  family name: Prieto-Ruíz
  given name: José Ángel
author list: Agent
  family name: Wehenkel
  given name: Christian
doi: 10.7717/peerj.13812
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-03
copyright: © 2022 Mendoza-Maya et al.
attribution name: Mendoza-Maya et al.

Criteria for assessing the adaptive changes in mixed martial arts (MMA) athletes of strike fighting style in different training load regimes
type: item
type: AcademicArticle
description: Background To study the peculiarities of changes in functional indicators and body composition parameters of mixed martial arts (MMA) athletes of strike fighting style and a number of biochemical blood indicators during two months of using different intensity training load regimes, and to determine the most informative criteria for assessing adaptive body changes in these training conditions. Methods We examined 40 MMA athletes (men) aged 20–22, who used mainly strike fighting style in their competitive activity, and divided them into 2 research groups (A and B), 20 athletes in each group. Group A athletes used medium intensity (Ra = 0.64), and group B—high intensity (Ra = 0.72) training load regime. To assess the adaptive body changes we applied methods of control testing of maximum muscle strength growth (1 RM), special training (the number of accurate kicks on the mannequin for 30 s), and bioimpedansometry. By monitoring biochemical parameters (testosterone, cortisol, creatinine, phosphorus, calcium, cholesterol, LDH) in the blood serum of athletes, we determined the peculiarities of adaptive-compensatory body reactions in response to training loads. Results The obtained results of special training increased during the study period by an average of 10.5% in group B athletes, but group A participants’ results had no significant changes compared to basal data. The largest increase in the development of maximum muscle strength growth by an average of 44.4% was recorded after 2 months of research in group B. Group B athletes also had positive changes in body fat and fat-free mass indicators during the study which were two times higher than the results of group A. The laboratory studies and correlation analysis showed informative biochemical markers (cortisol, testosterone and creatinine) for assessing the condition of athletes in both groups before using high and medium training load regimes. The biochemical markers for assessing the adaptive-compensatory reactions o…
format: application/pdf
format: text/html
creator: Andrii Chernozub
creator: Veaceslav Manolachi
creator: Georgiy Korobeynikov
creator: Vladimir Potop
creator: Liudmyla Sherstiuk
creator: Victor Manolachi
creator: Ion Mihaila
subject: Biochemistry
subject: Anatomy and Physiology
subject: Hematology
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.13827
publisher: PeerJ Inc.
rights: © 2022 Chernozub et al.
abstract: Background To study the peculiarities of changes in functional indicators and body composition parameters of mixed martial arts (MMA) athletes of strike fighting style and a number of biochemical blood indicators during two months of using different intensity training load regimes, and to determine the most informative criteria for assessing adaptive body changes in these training conditions. Methods We examined 40 MMA athletes (men) aged 20–22, who used mainly strike fighting style in their competitive activity, and divided them into 2 research groups (A and B), 20 athletes in each group. Group A athletes used medium intensity (Ra = 0.64), and group B—high intensity (Ra = 0.72) training load regime. To assess the adaptive body changes we applied methods of control testing of maximum muscle strength growth (1 RM), special training (the number of accurate kicks on the mannequin for 30 s), and bioimpedansometry. By monitoring biochemical parameters (testosterone, cortisol, creatinine, phosphorus, calcium, cholesterol, LDH) in the blood serum of athletes, we determined the peculiarities of adaptive-compensatory body reactions in response to training loads. Results The obtained results of special training increased during the study period by an average of 10.5% in group B athletes, but group A participants’ results had no significant changes compared to basal data. The largest increase in the development of maximum muscle strength growth by an average of 44.4% was recorded after 2 months of research in group B. Group B athletes also had positive changes in body fat and fat-free mass indicators during the study which were two times higher than the results of group A. The laboratory studies and correlation analysis showed informative biochemical markers (cortisol, testosterone and creatinine) for assessing the condition of athletes in both groups before using high and medium training load regimes. The biochemical markers for assessing the adaptive-compensatory reactions o…
bibliographic citation: Chernozub et al. (2022) Criteria for assessing the adaptive changes in mixed martial arts (MMA) athletes of strike fighting style in different training load regimes. PeerJ 10:e13827 https://doi.org/10.7717/peerj.13827
date submitted: 2022-05-01
date accepted: 2022-07-11
issued: 2022-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chernozub
  given name: Andrii
author list: Agent
  family name: Manolachi
  given name: Veaceslav
author list: Agent
  family name: Korobeynikov
  given name: Georgiy
author list: Agent
  family name: Potop
  given name: Vladimir
author list: Agent
  family name: Sherstiuk
  given name: Liudmyla
author list: Agent
  family name: Manolachi
  given name: Victor
author list: Agent
  family name: Mihaila
  given name: Ion
doi: 10.7717/peerj.13827
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-03
copyright: ©2022 Chernozub et al.
attribution name: Chernozub et al.

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