PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Inconsistent effects of components as evidence for non-compositionality in chimpanzee face-gesture combinations? A response to Oña et al (2019)
items: Would future climate warming cause zoonotic diseases to spread over long distances?
items: Adherence to the WHO recommendation of three weekly days of vigorous intensity activities in children: an accelerometry study of vigorous physical activity bouts
items: Heavy metal movement through insect food chains in pristine thermal springs of Yellowstone National Park
items: DNA mini-barcoding reveals the mislabeling rate of canned cat food in Taiwan
items: Arthrological reconstructions of the pterosaur neck and their implications for the cervical position at rest
items: Organic fertilizer type and dose affect growth, morphological and physiological parameters, and mineral nutrition of watermelon seedlings
items: Repair protocols for indirect monolithic restorations: a literature review
items: Biological and growth parameters of Plotosus lineatus in the Mediterranean Sea
items: MX1 and UBE2L6 are potential metaflammation gene targets in both diabetes and atherosclerosis

Inconsistent effects of components as evidence for non-compositionality in chimpanzee face-gesture combinations? A response to Oña et al (2019)
type: item
type: AcademicArticle
description: Using field observations from a sanctuary, Oña and colleagues (DOI: 10.7717/peerj.7623) investigated the semantics of face-gesture combinations in chimpanzees (Pan troglodytes). The response of the animals to these signals was encoded as a binary measure: positive interactions such as approaching or grooming were considered affiliative; ignoring or attacking was considered non-affiliative. The relevant signals are illustrated in Fig. 1 (https://doi.org/10.7717/peerj.7623/fig-1), together with the outcome in terms of average affiliativeness. The authors observe that there seems to be no systematicity in the way the faces modify the responses to the gestures, sometimes reducing affiliativeness, sometimes increasing it. A strong interpretation of this result would be that the meaning of a gesture-face combination cannot be derived from the meaning of the gesture and the meaning of the face, that is, the interpretation of chimpanzees’ face-gesture combinations are non compositional in nature. We will revisit this conclusion: we will exhibit simple compositional systems which, after all, may be plausible. At the methodological level, we argue that it is critical to lay out the theoretical options explicitly for a complete comparison of their pros and cons.
format: application/pdf
format: text/html
creator: Maxime Cauté
creator: Emmanuel Chemla
creator: Philippe Schlenker
subject: Animal Behavior
subject: Anthropology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.16800
publisher: PeerJ Inc.
rights: © 2024 Cauté et al.
abstract: Using field observations from a sanctuary, Oña and colleagues (DOI: 10.7717/peerj.7623) investigated the semantics of face-gesture combinations in chimpanzees (Pan troglodytes). The response of the animals to these signals was encoded as a binary measure: positive interactions such as approaching or grooming were considered affiliative; ignoring or attacking was considered non-affiliative. The relevant signals are illustrated in Fig. 1 (https://doi.org/10.7717/peerj.7623/fig-1), together with the outcome in terms of average affiliativeness. The authors observe that there seems to be no systematicity in the way the faces modify the responses to the gestures, sometimes reducing affiliativeness, sometimes increasing it. A strong interpretation of this result would be that the meaning of a gesture-face combination cannot be derived from the meaning of the gesture and the meaning of the face, that is, the interpretation of chimpanzees’ face-gesture combinations are non compositional in nature. We will revisit this conclusion: we will exhibit simple compositional systems which, after all, may be plausible. At the methodological level, we argue that it is critical to lay out the theoretical options explicitly for a complete comparison of their pros and cons.
bibliographic citation: Cauté et al. (2024) Inconsistent effects of components as evidence for non-compositionality in chimpanzee face-gesture combinations? A response to Oña et al (2019). PeerJ 12:e16800 https://doi.org/10.7717/peerj.16800
date submitted: 2023-06-22
date accepted: 2023-12-26
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cauté
  given name: Maxime
author list: Agent
  family name: Chemla
  given name: Emmanuel
author list: Agent
  family name: Schlenker
  given name: Philippe
doi: 10.7717/peerj.16800
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: © 2024 Cauté et al.
attribution name: Cauté et al.

Would future climate warming cause zoonotic diseases to spread over long distances?
type: item
type: AcademicArticle
description: Dipus sagitta is a major rodent found in arid environments and desert areas. They feed on plant seeds, young branches and some small insects, and have hibernating habits. Peak Dipus sagitta numbers impact the construction of the plant community in the environment, but also have a human impact as these rodents carry a variety of parasitic fleas capable of spreading serious diseases to humans. Based on 216 present distribution records of Dipus sagitta and seven environmental variables, this article simulates the potential distribution of Dipus sagitta during the Last Glacial Maximum, the mid-Holocene, the present and the future (2070s, RCP4.5, RCP8.5). This study also analyzes the geographic changes of the population distribution and evaluates the importance of climate factors by integrating contribution rate, replacement importance value and the jackknife test using the MaxEnt model. In this study, we opted to assess the predictive capabilities of our model using the receiver operating characteristic (ROC) and partial receiver operating characteristic (pROC) metrics. The findings indicate that the AUC value exceeds 0.9 and the AUC ratio is greater than 1, indicating superior predictive performance by the model. The results showed that the main climatic factors affecting the distribution of the three-toed jerboa were precipitation in the coldest quarter, temperature seasonality (standard deviation), and mean annual temperature. Under the two warming scenarios of the mid-Holocene and the future, there were differences in the changes in the distribution area of the three-toed jerboa. During the mid-Holocene, the suitable distribution area of the three-toed jerboa expanded, with a 93.91% increase in the rate of change compared to the Last Glacial Maximum. The size of the three-toed jerboa’s habitat decreases under both future climate scenarios. Compared to the current period, under the RCP4.5 emission scenario, the change rate is −2.96%, and under the RCP8.5 emission sce…
format: application/pdf
format: text/html
creator: Fan Bu
creator: Xiuxian Yue
creator: Shanshan Sun
creator: Yongling Jin
creator: Linlin Li
creator: Xin Li
creator: Rong Zhang
creator: Zhenghaoni Shang
creator: Haiwen Yan
creator: Haoting Zhang
creator: Shuai Yuan
creator: Xiaodong Wu
creator: Heping Fu
subject: Biogeography
subject: Ecology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.16811
publisher: PeerJ Inc.
rights: © 2024 Bu et al.
abstract: Dipus sagitta is a major rodent found in arid environments and desert areas. They feed on plant seeds, young branches and some small insects, and have hibernating habits. Peak Dipus sagitta numbers impact the construction of the plant community in the environment, but also have a human impact as these rodents carry a variety of parasitic fleas capable of spreading serious diseases to humans. Based on 216 present distribution records of Dipus sagitta and seven environmental variables, this article simulates the potential distribution of Dipus sagitta during the Last Glacial Maximum, the mid-Holocene, the present and the future (2070s, RCP4.5, RCP8.5). This study also analyzes the geographic changes of the population distribution and evaluates the importance of climate factors by integrating contribution rate, replacement importance value and the jackknife test using the MaxEnt model. In this study, we opted to assess the predictive capabilities of our model using the receiver operating characteristic (ROC) and partial receiver operating characteristic (pROC) metrics. The findings indicate that the AUC value exceeds 0.9 and the AUC ratio is greater than 1, indicating superior predictive performance by the model. The results showed that the main climatic factors affecting the distribution of the three-toed jerboa were precipitation in the coldest quarter, temperature seasonality (standard deviation), and mean annual temperature. Under the two warming scenarios of the mid-Holocene and the future, there were differences in the changes in the distribution area of the three-toed jerboa. During the mid-Holocene, the suitable distribution area of the three-toed jerboa expanded, with a 93.91% increase in the rate of change compared to the Last Glacial Maximum. The size of the three-toed jerboa’s habitat decreases under both future climate scenarios. Compared to the current period, under the RCP4.5 emission scenario, the change rate is −2.96%, and under the RCP8.5 emission sce…
bibliographic citation: Bu et al. (2024) Would future climate warming cause zoonotic diseases to spread over long distances?. PeerJ 12:e16811 https://doi.org/10.7717/peerj.16811
date submitted: 2023-04-05
date accepted: 2023-12-29
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bu
  given name: Fan
author list: Agent
  family name: Yue
  given name: Xiuxian
author list: Agent
  family name: Sun
  given name: Shanshan
author list: Agent
  family name: Jin
  given name: Yongling
author list: Agent
  family name: Li
  given name: Linlin
author list: Agent
  family name: Li
  given name: Xin
author list: Agent
  family name: Zhang
  given name: Rong
author list: Agent
  family name: Shang
  given name: Zhenghaoni
author list: Agent
  family name: Yan
  given name: Haiwen
author list: Agent
  family name: Zhang
  given name: Haoting
author list: Agent
  family name: Yuan
  given name: Shuai
author list: Agent
  family name: Wu
  given name: Xiaodong
author list: Agent
  family name: Fu
  given name: Heping
doi: 10.7717/peerj.16811
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: ©2024 Bu et al.
attribution name: Bu et al.

Adherence to the WHO recommendation of three weekly days of vigorous intensity activities in children: an accelerometry study of vigorous physical activity bouts
type: item
type: AcademicArticle
description: Background The World Health Organization (WHO) recommends that children and adolescents incorporate vigorous intensity activities (VIAs) at least three days a week. This recommendation has not been sufficiently studied using objective methods, such as accelerometry. Physical education classes and extracurricular sports activities are optimal opportunities for compliance with this recommendation. Objective To identify VIAs through bouts of vigorous physical activity (VPA-Bouts) evaluated with accelerometry and, with this, to know the compliance with the recommendation on VIAs. Methods A cross-sectional study of the habitual physical activity of 353 children (8–9 years old) was carried out using accelerometry and participation in organized extracurricular sports activities was asked through a questionnaire. School days with and without physical education class, weekends, and the average weekly day were identified, as well as school time and out-of-school time. A VPA-Bout was defined as an interval of at least 60 minutes with a proportion of VPA of at least 16.7% in boys and 12.5% in girls (10.0 and 7.5 minutes/hour of VPA, respectively). Results The average daily time in organized extracurricular sports activities declared by questionnaire and the average daily duration of the VPA-Bouts evaluated with accelerometers in the extracurricular period was 21.3 (SD 19.8) and 23.9 (SD 31.2) minutes, respectively, in boys, whereas, in girls it was 20.2 (SD 17.4) and 11.0 (SD 16.9) minutes, respectively. In school time including a physical education class, there was a higher proportion of VPA-Bouts than without these classes (with: 28.6%, without: 2.1%, p < 0.001). Children who reported at least three weekly hours of organized extracurricular sports activities accumulated a higher proportion of school afternoons with VPA-Bouts than those with fewer weekly hours of this type of activities (≥3 hours/week: 27.5%, <3 hours/week: 9.3%, p < 0.001). On the weekend, boys who reported a…
format: application/pdf
format: text/html
creator: Juan Carlos Benavente-Marín
creator: Francisco Javier Barón-López
creator: Begoña Gil Barcenilla
creator: Guadalupe Longo Abril
creator: José M. Rumbao Aguirre
creator: Napoleón Pérez-Farinós
creator: Julia Wärnberg
subject: Epidemiology
subject: Pediatrics
subject: Public Health
subject: Obesity
subject: Sports Medicine
description: doi:10.7717/peerj.16815
publisher: PeerJ Inc.
rights: © 2024 Benavente-Marín et al.
abstract: Background The World Health Organization (WHO) recommends that children and adolescents incorporate vigorous intensity activities (VIAs) at least three days a week. This recommendation has not been sufficiently studied using objective methods, such as accelerometry. Physical education classes and extracurricular sports activities are optimal opportunities for compliance with this recommendation. Objective To identify VIAs through bouts of vigorous physical activity (VPA-Bouts) evaluated with accelerometry and, with this, to know the compliance with the recommendation on VIAs. Methods A cross-sectional study of the habitual physical activity of 353 children (8–9 years old) was carried out using accelerometry and participation in organized extracurricular sports activities was asked through a questionnaire. School days with and without physical education class, weekends, and the average weekly day were identified, as well as school time and out-of-school time. A VPA-Bout was defined as an interval of at least 60 minutes with a proportion of VPA of at least 16.7% in boys and 12.5% in girls (10.0 and 7.5 minutes/hour of VPA, respectively). Results The average daily time in organized extracurricular sports activities declared by questionnaire and the average daily duration of the VPA-Bouts evaluated with accelerometers in the extracurricular period was 21.3 (SD 19.8) and 23.9 (SD 31.2) minutes, respectively, in boys, whereas, in girls it was 20.2 (SD 17.4) and 11.0 (SD 16.9) minutes, respectively. In school time including a physical education class, there was a higher proportion of VPA-Bouts than without these classes (with: 28.6%, without: 2.1%, p < 0.001). Children who reported at least three weekly hours of organized extracurricular sports activities accumulated a higher proportion of school afternoons with VPA-Bouts than those with fewer weekly hours of this type of activities (≥3 hours/week: 27.5%, <3 hours/week: 9.3%, p < 0.001). On the weekend, boys who reported a…
bibliographic citation: Benavente-Marín et al. (2024) Adherence to the WHO recommendation of three weekly days of vigorous intensity activities in children: an accelerometry study of vigorous physical activity bouts. PeerJ 12:e16815 https://doi.org/10.7717/peerj.16815
date submitted: 2023-12-18
date accepted: 2023-12-29
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Benavente-Marín
  given name: Juan Carlos
author list: Agent
  family name: Barón-López
  given name: Francisco Javier
author list: Agent
  family name: Gil Barcenilla
  given name: Begoña
author list: Agent
  family name: Longo Abril
  given name: Guadalupe
author list: Agent
  family name: Rumbao Aguirre
  given name: José M.
author list: Agent
  family name: Pérez-Farinós
  given name: Napoleón
author list: Agent
  family name: Wärnberg
  given name: Julia
doi: 10.7717/peerj.16815
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: © 2024 Benavente-Marín et al.
attribution name: Benavente-Marín et al.

Heavy metal movement through insect food chains in pristine thermal springs of Yellowstone National Park
type: item
type: AcademicArticle
description: Yellowstone National Park thermal features regularly discharge various heavy metals and metalloids. These metals are taken up by microorganisms that often form mats in thermal springs. These microbial mats also serve as food sources for invertebrate assemblages. To examine how heavy metals move through insect food webs associated with hot springs, two sites were selected for this study. Dragon-Beowulf Hot Springs, acid-sulfate chloride springs, have a pH of 2.9, water temperatures above 70 °C, and populations of thermophilic bacterial, archaeal, and algal mats. Rabbit Creek Hot Springs, alkaline springs, have a pH of up to 9, some water temperatures in excess of 60 °C, and are populated with thermophilic and phototrophic bacterial mats. Mats in both hydrothermal systems form the trophic base and support active metal transfer to terrestrial food chains. In both types of springs, invertebrates bioaccumulated heavy metals including chromium, manganese, cobalt, nickel, copper, cadmium, mercury, tin and lead, and the metalloids arsenic, selenium, and antimony resulting from consuming the algal and bacterial mat biomass. At least two orders of magnitude increase in concentrations were observed in the ephydrid shore fly Paracoenia turbida, as compared to the mats for all metals except antimony, mercury, and lead. The highest bioaccumulation factor (BAF) of 729 was observed for chromium. At the other end of the food web, the invertebrate apex predator, Cicindelidia haemorrhagica, had at least a 10-fold BAF for all metals at some location-year combinations, except with antimony. Of other taxa, high BAFs were observed with zinc for Nebria sp. (2180) and for Salda littoralis (1080). This accumulation, occurring between primary producer and primary consumer trophic levels at both springs, is biomagnified through the trophic web. These observations suggest trace metals enter the geothermal food web through the microbial mat community and are then transferred through the food cha…
format: application/pdf
format: text/html
creator: Braymond Adams
creator: John Bowley
creator: Monica Rohwer
creator: Erik Oberg
creator: Kelly Willemssens
creator: Wendy Wintersteen
creator: Robert K.D. Peterson
creator: Leon G. Higley
subject: Entomology
subject: Toxicology
subject: Zoology
subject: Ecotoxicology
description: doi:10.7717/peerj.16827
publisher: PeerJ Inc.
rights: © 2024 Adams et al.
abstract: Yellowstone National Park thermal features regularly discharge various heavy metals and metalloids. These metals are taken up by microorganisms that often form mats in thermal springs. These microbial mats also serve as food sources for invertebrate assemblages. To examine how heavy metals move through insect food webs associated with hot springs, two sites were selected for this study. Dragon-Beowulf Hot Springs, acid-sulfate chloride springs, have a pH of 2.9, water temperatures above 70 °C, and populations of thermophilic bacterial, archaeal, and algal mats. Rabbit Creek Hot Springs, alkaline springs, have a pH of up to 9, some water temperatures in excess of 60 °C, and are populated with thermophilic and phototrophic bacterial mats. Mats in both hydrothermal systems form the trophic base and support active metal transfer to terrestrial food chains. In both types of springs, invertebrates bioaccumulated heavy metals including chromium, manganese, cobalt, nickel, copper, cadmium, mercury, tin and lead, and the metalloids arsenic, selenium, and antimony resulting from consuming the algal and bacterial mat biomass. At least two orders of magnitude increase in concentrations were observed in the ephydrid shore fly Paracoenia turbida, as compared to the mats for all metals except antimony, mercury, and lead. The highest bioaccumulation factor (BAF) of 729 was observed for chromium. At the other end of the food web, the invertebrate apex predator, Cicindelidia haemorrhagica, had at least a 10-fold BAF for all metals at some location-year combinations, except with antimony. Of other taxa, high BAFs were observed with zinc for Nebria sp. (2180) and for Salda littoralis (1080). This accumulation, occurring between primary producer and primary consumer trophic levels at both springs, is biomagnified through the trophic web. These observations suggest trace metals enter the geothermal food web through the microbial mat community and are then transferred through the food cha…
bibliographic citation: Adams et al. (2024) Heavy metal movement through insect food chains in pristine thermal springs of Yellowstone National Park. PeerJ 12:e16827 https://doi.org/10.7717/peerj.16827
date submitted: 2023-11-20
date accepted: 2024-01-03
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adams
  given name: Braymond
author list: Agent
  family name: Bowley
  given name: John
author list: Agent
  family name: Rohwer
  given name: Monica
author list: Agent
  family name: Oberg
  given name: Erik
author list: Agent
  family name: Willemssens
  given name: Kelly
author list: Agent
  family name: Wintersteen
  given name: Wendy
author list: Agent
  family name: Peterson
  given name: Robert K.D.
author list: Agent
  family name: Higley
  given name: Leon G.
doi: 10.7717/peerj.16827
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: ©2024 Adams et al.
attribution name: Adams et al.

DNA mini-barcoding reveals the mislabeling rate of canned cat food in Taiwan
type: item
type: AcademicArticle
description: Background Domestic cats are important companion animals in modern society that live closely with their owners. Mislabeling of pet food can not only harm pets but also cause issues in areas such as religious beliefs and natural resource management. Currently, the cat food market is booming. However, despite the risk that mislabeling poses to cats and humans, few studies have focused on species misrepresentation in cat food products. Methods To address this issue, we used DNA barcoding, a highly effective identification methodology that can be applied to even highly processed products. We targeted a short segment (~85 basepairs) of the mitochondrial 16S rRNA (16S) gene as a barcode and employed Sanger or next generation sequencing (NGS) to inspect 138 canned cat food products in the Taiwanese market. Results We discovered that the majority of mislabeling incidents were related to replacement of tuna with other species. Moreover, our metabarcoding revealed that numerous undeclared ingredients were present in all examined canned products. One product contained CITES Appendix II-listed shortfin mako shark (Isurus oxyrinchus). Overall, we uncovered a mislabeling rate of at least 28.99%. To verify cases of mislabeling, an official standardized list of vernacular names, along with the corresponding scientific species names, as well as a dependable barcoding reference sequence database are necessary.
format: application/pdf
format: text/html
creator: Yu-Chun Wang
creator: Shih-Hui Liu
creator: Hsuan Ching Ho
creator: Hsiao-Yin Su
creator: Chia-Hao Chang
subject: Food Science and Technology
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.16833
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Background Domestic cats are important companion animals in modern society that live closely with their owners. Mislabeling of pet food can not only harm pets but also cause issues in areas such as religious beliefs and natural resource management. Currently, the cat food market is booming. However, despite the risk that mislabeling poses to cats and humans, few studies have focused on species misrepresentation in cat food products. Methods To address this issue, we used DNA barcoding, a highly effective identification methodology that can be applied to even highly processed products. We targeted a short segment (~85 basepairs) of the mitochondrial 16S rRNA (16S) gene as a barcode and employed Sanger or next generation sequencing (NGS) to inspect 138 canned cat food products in the Taiwanese market. Results We discovered that the majority of mislabeling incidents were related to replacement of tuna with other species. Moreover, our metabarcoding revealed that numerous undeclared ingredients were present in all examined canned products. One product contained CITES Appendix II-listed shortfin mako shark (Isurus oxyrinchus). Overall, we uncovered a mislabeling rate of at least 28.99%. To verify cases of mislabeling, an official standardized list of vernacular names, along with the corresponding scientific species names, as well as a dependable barcoding reference sequence database are necessary.
bibliographic citation: Wang et al. (2024) DNA mini-barcoding reveals the mislabeling rate of canned cat food in Taiwan. PeerJ 12:e16833 https://doi.org/10.7717/peerj.16833
date submitted: 2023-11-13
date accepted: 2024-01-04
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yu-Chun
author list: Agent
  family name: Liu
  given name: Shih-Hui
author list: Agent
  family name: Ho
  given name: Hsuan Ching
author list: Agent
  family name: Su
  given name: Hsiao-Yin
author list: Agent
  family name: Chang
  given name: Chia-Hao
doi: 10.7717/peerj.16833
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: © 2024 Wang et al.
attribution name: Wang et al.

Arthrological reconstructions of the pterosaur neck and their implications for the cervical position at rest
type: item
type: AcademicArticle
description: The lack of any pterosaur living descendants creates gaps in the knowledge of the biology of this group, including its cervical biomechanics, which makes it difficult to understand their posture and life habits. To mitigate part of this issue, we reconstructed the cervical osteology and arthrology of three pterosaurs, allowing us to make inferences about the position of the neck of these animals at rest. We used scans of three-dimensionally preserved cervical series of Anhanguera piscator, Azhdarcho lancicollis and Rhamphorhynchus muensteri for the reconstructions, thus representing different lineages. For the recognition of ligaments, joint cartilages, and levels of overlapping of the zygapophyses, we applied the Extant Phylogenetic Bracket method, based on various extant birds and on Caiman latirostris. We inferred that pterosaur intervertebral joints were probably covered by a thin layer of synovial cartilage whose thickness varied along the neck, being thicker in the posterior region. Ignoring this cartilage can affect reconstructions. According to the vertebral angulation, their neck was slightly sinuous when in rest position. Our analyses also indicate that pterosaurs had segmented and supra-segmented articular cervical ligaments, which could confer stabilization, execute passive forces on the neck and store elastic energy.
format: application/pdf
format: text/html
creator: Richard Buchmann
creator: Taissa Rodrigues
subject: Biophysics
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.16884
publisher: PeerJ Inc.
rights: © 2024 Buchmann and Rodrigues
abstract: The lack of any pterosaur living descendants creates gaps in the knowledge of the biology of this group, including its cervical biomechanics, which makes it difficult to understand their posture and life habits. To mitigate part of this issue, we reconstructed the cervical osteology and arthrology of three pterosaurs, allowing us to make inferences about the position of the neck of these animals at rest. We used scans of three-dimensionally preserved cervical series of Anhanguera piscator, Azhdarcho lancicollis and Rhamphorhynchus muensteri for the reconstructions, thus representing different lineages. For the recognition of ligaments, joint cartilages, and levels of overlapping of the zygapophyses, we applied the Extant Phylogenetic Bracket method, based on various extant birds and on Caiman latirostris. We inferred that pterosaur intervertebral joints were probably covered by a thin layer of synovial cartilage whose thickness varied along the neck, being thicker in the posterior region. Ignoring this cartilage can affect reconstructions. According to the vertebral angulation, their neck was slightly sinuous when in rest position. Our analyses also indicate that pterosaurs had segmented and supra-segmented articular cervical ligaments, which could confer stabilization, execute passive forces on the neck and store elastic energy.
bibliographic citation: Buchmann et al. (2024) Arthrological reconstructions of the pterosaur neck and their implications for the cervical position at rest. PeerJ 12:e16884 https://doi.org/10.7717/peerj.16884
date submitted: 2023-10-06
date accepted: 2024-01-12
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buchmann
  given name: Richard
author list: Agent
  family name: Rodrigues
  given name: Taissa
doi: 10.7717/peerj.16884
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: ©2024 Buchmann and Rodrigues
attribution name: Buchmann and Rodrigues

Organic fertilizer type and dose affect growth, morphological and physiological parameters, and mineral nutrition of watermelon seedlings
type: item
type: AcademicArticle
description: Background Organic agriculture has grown rapidly in recent years due to its environmental friendliness, sustainability, and improved farm profitability. Transplants are commonly used for fruits and vegetables to achieve consistent quality, uniformity, and easy field spacing control. The efficacy and optimal amounts of fertilizers for organic transplant production need to be investigated. Methods The effects of three organic fertilizers (Sustane 4-6-4, Nature Safe 7-7-7, and Dramatic 2-4-1) and one conventional fertilizer Peters Professional 20-20-20 (Conventional) with four doses (nitrogen (N) content was matched among fertilizers in each level, as 0.14 g/L, 0.28 g/L, 0.56 g/L, and 0.84 g/L N, respectively) on watermelon seedlings were compared in this study. Results The results showed that all organic fertilizer treatments were not significantly different from the Conventional group in terms of watermelon germination. The only exception was the highest dose of Sustane 4-6-4 (0.84 g/L N) which decreased the germination rate and relative emergence index. Generally, growth index, shoot fresh and dry weights, true leaf number, and stem diameter increased as the amount of N increased within each fertilizer type. The best shoot growth was observed in the highest doses of Conventional and Dramatic 2-4-1 treatments (0.84 g/L N). However, Dramatic 2-4-1 treatments resulted in the lowest root growth when compared to other fertilizers at the same N dose. The second highest fertilization dose (0.56 g/L N) of Sustane 4-6-4 had the best root growth according to root fresh weight, root volume, root area, total root length, as well as the numbers of root tip and crossing when compared to other treatments. For seedlings, a well-developed root system can ensure a good seedling establishment and high survival rate under stressful field conditions after transplanting. Thus, Sustane 4-6-4 at 14 g/L (0.56 g/L N) is recommended to produce high-quality organic watermelon seedlings among t…
format: application/pdf
format: text/html
creator: Qianwen Zhang
creator: Joseph Masabni
creator: Genhua Niu
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.16902
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background Organic agriculture has grown rapidly in recent years due to its environmental friendliness, sustainability, and improved farm profitability. Transplants are commonly used for fruits and vegetables to achieve consistent quality, uniformity, and easy field spacing control. The efficacy and optimal amounts of fertilizers for organic transplant production need to be investigated. Methods The effects of three organic fertilizers (Sustane 4-6-4, Nature Safe 7-7-7, and Dramatic 2-4-1) and one conventional fertilizer Peters Professional 20-20-20 (Conventional) with four doses (nitrogen (N) content was matched among fertilizers in each level, as 0.14 g/L, 0.28 g/L, 0.56 g/L, and 0.84 g/L N, respectively) on watermelon seedlings were compared in this study. Results The results showed that all organic fertilizer treatments were not significantly different from the Conventional group in terms of watermelon germination. The only exception was the highest dose of Sustane 4-6-4 (0.84 g/L N) which decreased the germination rate and relative emergence index. Generally, growth index, shoot fresh and dry weights, true leaf number, and stem diameter increased as the amount of N increased within each fertilizer type. The best shoot growth was observed in the highest doses of Conventional and Dramatic 2-4-1 treatments (0.84 g/L N). However, Dramatic 2-4-1 treatments resulted in the lowest root growth when compared to other fertilizers at the same N dose. The second highest fertilization dose (0.56 g/L N) of Sustane 4-6-4 had the best root growth according to root fresh weight, root volume, root area, total root length, as well as the numbers of root tip and crossing when compared to other treatments. For seedlings, a well-developed root system can ensure a good seedling establishment and high survival rate under stressful field conditions after transplanting. Thus, Sustane 4-6-4 at 14 g/L (0.56 g/L N) is recommended to produce high-quality organic watermelon seedlings among t…
bibliographic citation: Zhang et al. (2024) Organic fertilizer type and dose affect growth, morphological and physiological parameters, and mineral nutrition of watermelon seedlings. PeerJ 12:e16902 https://doi.org/10.7717/peerj.16902
date submitted: 2023-09-28
date accepted: 2024-01-17
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Qianwen
author list: Agent
  family name: Masabni
  given name: Joseph
author list: Agent
  family name: Niu
  given name: Genhua
doi: 10.7717/peerj.16902
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: ©2024 Zhang et al.
attribution name: Zhang et al.

Repair protocols for indirect monolithic restorations: a literature review
type: item
type: AcademicArticle
description: Despite the advancements in indirect monolithic restorations, technical complications may occur during function. To overcome this issues, intraoral repair using resin composite is a practical and low-cost procedure, being able to increase the restoration’s longevity. This review aimed to evaluate the need for repair and suggest a standardized repair protocol to the main indirect restorative materials. For this, studies were surveyed from PubMed with no language or date restriction, to investigate the scientific evidence of indirect monolithic restoration repair with direct resin composite. A classification to guide clinical decisions was made based on the FDI World Dental Federation criteria about defective indirect restorations considering esthetic and functional standards, along with the patient’s view, to decide when polishing, repairing or replacing a defective restoration. Based on 38 surveyed studies, different resin composite intraoral repair protocols, that included mechanical and chemical aspects, were defined depending on the substrate considering resin-based, glass-ceramic or zirconia restorations. The presented criteria and protocols were developed to guide the clinician’s decision-making process regarding defective indirect monolithic restorations, prolonging longevity and increasing clinical success.
format: application/pdf
format: text/html
creator: Lucas Saldanha da Rosa
creator: Rafaela Oliveira Pilecco
creator: Pablo Machado Soares
creator: Marília Pivetta Rippe
creator: Gabriel Kalil Rocha Pereira
creator: Luiz Felipe Valandro
creator: Cornelis Johannes Kleverlaan
creator: Albert J. Feilzer
creator: João Paulo Mendes Tribst
subject: Dentistry
subject: Evidence Based Medicine
description: doi:10.7717/peerj.16942
publisher: PeerJ Inc.
rights: © 2024 da Rosa et al.
abstract: Despite the advancements in indirect monolithic restorations, technical complications may occur during function. To overcome this issues, intraoral repair using resin composite is a practical and low-cost procedure, being able to increase the restoration’s longevity. This review aimed to evaluate the need for repair and suggest a standardized repair protocol to the main indirect restorative materials. For this, studies were surveyed from PubMed with no language or date restriction, to investigate the scientific evidence of indirect monolithic restoration repair with direct resin composite. A classification to guide clinical decisions was made based on the FDI World Dental Federation criteria about defective indirect restorations considering esthetic and functional standards, along with the patient’s view, to decide when polishing, repairing or replacing a defective restoration. Based on 38 surveyed studies, different resin composite intraoral repair protocols, that included mechanical and chemical aspects, were defined depending on the substrate considering resin-based, glass-ceramic or zirconia restorations. The presented criteria and protocols were developed to guide the clinician’s decision-making process regarding defective indirect monolithic restorations, prolonging longevity and increasing clinical success.
bibliographic citation: da Rosa et al. (2024) Repair protocols for indirect monolithic restorations: a literature review. PeerJ 12:e16942 https://doi.org/10.7717/peerj.16942
date submitted: 2023-09-07
date accepted: 2024-01-23
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: da Rosa
  given name: Lucas Saldanha
author list: Agent
  family name: Pilecco
  given name: Rafaela Oliveira
author list: Agent
  family name: Soares
  given name: Pablo Machado
author list: Agent
  family name: Rippe
  given name: Marília Pivetta
author list: Agent
  family name: Pereira
  given name: Gabriel Kalil Rocha
author list: Agent
  family name: Valandro
  given name: Luiz Felipe
author list: Agent
  family name: Kleverlaan
  given name: Cornelis Johannes
author list: Agent
  family name: Feilzer
  given name: Albert J.
author list: Agent
  family name: Tribst
  given name: João Paulo Mendes
doi: 10.7717/peerj.16942
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: ©2024 da Rosa et al.
attribution name: da Rosa et al.

Biological and growth parameters of Plotosus lineatus in the Mediterranean Sea
type: item
type: AcademicArticle
description: This study examined the age distribution and growth characteristics of the striped eel catfish (Plotosus lineatus), which is an invasive alien species in the eastern Mediterranean. A total of 1,011 samples were collected from Iskenderun Bay (Turkey), with lengths ranging from 5.1 to 16.8 cm, predominantly comprising females (1:1.92). Age 3 represented the majority in the population (52.03%). The value of the scaling exponent “b” of the length-weight relationship was less than “3” for both sexes (females: 2.28; males: 2.26; combined: 2.27). The results for the von Bertalanffy growth parameters were observed for the combined sexes as, L∞ = 24.9934 cm, k = 0.1718 year−1, and t₀ = −1.7707 years. The striped eel catfish populations in Iskenderun Bay exhibited negative allometric growth patterns and were predominantly composed of adult individuals. This study presents the dataset on the length-weight correlations, age-growth characteristics, and von Bertalanffy growth parameters of Plotosus lineatus in the Mediterranean Sea, thereby significantly contributing to comprehending the stock dynamics. It is anticipated that this study will make a significant contribution to the management of P. lineatus stocks, given its invasive nature.
format: application/pdf
format: text/html
creator: Servet Ahmet Doğdu
creator: Cemal Turan
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.16945
publisher: PeerJ Inc.
rights: © 2024 Doğdu and Turan
abstract: This study examined the age distribution and growth characteristics of the striped eel catfish (Plotosus lineatus), which is an invasive alien species in the eastern Mediterranean. A total of 1,011 samples were collected from Iskenderun Bay (Turkey), with lengths ranging from 5.1 to 16.8 cm, predominantly comprising females (1:1.92). Age 3 represented the majority in the population (52.03%). The value of the scaling exponent “b” of the length-weight relationship was less than “3” for both sexes (females: 2.28; males: 2.26; combined: 2.27). The results for the von Bertalanffy growth parameters were observed for the combined sexes as, L∞ = 24.9934 cm, k = 0.1718 year−1, and t₀ = −1.7707 years. The striped eel catfish populations in Iskenderun Bay exhibited negative allometric growth patterns and were predominantly composed of adult individuals. This study presents the dataset on the length-weight correlations, age-growth characteristics, and von Bertalanffy growth parameters of Plotosus lineatus in the Mediterranean Sea, thereby significantly contributing to comprehending the stock dynamics. It is anticipated that this study will make a significant contribution to the management of P. lineatus stocks, given its invasive nature.
bibliographic citation: Doğdu et al. (2024) Biological and growth parameters of Plotosus lineatus in the Mediterranean Sea. PeerJ 12:e16945 https://doi.org/10.7717/peerj.16945
date submitted: 2023-11-21
date accepted: 2024-01-24
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doğdu
  given name: Servet Ahmet
author list: Agent
  family name: Turan
  given name: Cemal
doi: 10.7717/peerj.16945
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: © 2024 Doğdu and Turan
attribution name: Doğdu and Turan

MX1 and UBE2L6 are potential metaflammation gene targets in both diabetes and atherosclerosis
type: item
type: AcademicArticle
description: Background The coexistence of diabetes mellitus (DM) and atherosclerosis (AS) is widespread, although the explicit metabolism and metabolism-associated molecular patterns (MAMPs) responsible for the correlation are still unclear. Methods Twenty-four genetically wild-type male Ba-Ma mini pigs were randomly divided into five groups distinguished by different combinations of 90 mg/kg streptozotocin (STZ) intravenous injection and high-cholesterol/lipid (HC) or high-lipid (HL) diet feeding for 9 months in total. Pigs in the STZ+HC and STZ+HL groups were injected with STZ first and then fed the HC or HL diet for 9 months. In contrast, pigs in the HC+STZ and HL+STZ groups were fed the HC or HL diet for 9 months and injected with STZ at 3 months. The controls were only fed a regular diet for 9 months. The blood glucose and abdominal aortic plaque observed through oil red O staining were used as evaluation indicators for successful modelling of DM and AS. A microarray gene expression analysis of all subjects was performed. Results Atherosclerotic lesions were observed only in the HC+STZ and STZ+HC groups. A total of 103 differentially expressed genes (DEGs) were identified as common between them. The most significantly enriched pathways of 103 common DEGs were influenza A, hepatitis C, and measles. The global and internal protein–protein interaction (PPI) networks of the 103 common DEGs consisted of 648 and 14 nodes, respectively. The top 10 hub proteins, namely, ISG15, IRG6, IRF7, IFIT3, MX1, UBE2L6, DDX58, IFIT2, USP18, and IFI44L, drive aspects of DM and AS. MX1 and UBE2L6 were the intersection of internal and global PPI networks. The expression of MX1 and UBE2L6 was 507.22 ± 342.56 and 96.99 ± 49.92 in the HC+STZ group, respectively, which was significantly higher than others and may be linked to the severity of hyperglycaemia-related atherosclerosis. Further PPI network analysis of calcium/micronutrients, including MX1 and UBE2L6, consisted of 58 and 18 nodes, respecti…
format: application/pdf
format: text/html
creator: Guisheng Wang
creator: Rongrong Hua
creator: Xiaoxia Chen
creator: Xucheng He
creator: Yao Dingming
creator: Hua Chen
creator: Buhuan Zhang
creator: Yuru Dong
creator: Muqing Liu
creator: Jiaxiong Liu
creator: Ting Liu
creator: Jingwei Zhao
creator: Yu Qiong Zhao
creator: Li Qiao
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.16975
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Background The coexistence of diabetes mellitus (DM) and atherosclerosis (AS) is widespread, although the explicit metabolism and metabolism-associated molecular patterns (MAMPs) responsible for the correlation are still unclear. Methods Twenty-four genetically wild-type male Ba-Ma mini pigs were randomly divided into five groups distinguished by different combinations of 90 mg/kg streptozotocin (STZ) intravenous injection and high-cholesterol/lipid (HC) or high-lipid (HL) diet feeding for 9 months in total. Pigs in the STZ+HC and STZ+HL groups were injected with STZ first and then fed the HC or HL diet for 9 months. In contrast, pigs in the HC+STZ and HL+STZ groups were fed the HC or HL diet for 9 months and injected with STZ at 3 months. The controls were only fed a regular diet for 9 months. The blood glucose and abdominal aortic plaque observed through oil red O staining were used as evaluation indicators for successful modelling of DM and AS. A microarray gene expression analysis of all subjects was performed. Results Atherosclerotic lesions were observed only in the HC+STZ and STZ+HC groups. A total of 103 differentially expressed genes (DEGs) were identified as common between them. The most significantly enriched pathways of 103 common DEGs were influenza A, hepatitis C, and measles. The global and internal protein–protein interaction (PPI) networks of the 103 common DEGs consisted of 648 and 14 nodes, respectively. The top 10 hub proteins, namely, ISG15, IRG6, IRF7, IFIT3, MX1, UBE2L6, DDX58, IFIT2, USP18, and IFI44L, drive aspects of DM and AS. MX1 and UBE2L6 were the intersection of internal and global PPI networks. The expression of MX1 and UBE2L6 was 507.22 ± 342.56 and 96.99 ± 49.92 in the HC+STZ group, respectively, which was significantly higher than others and may be linked to the severity of hyperglycaemia-related atherosclerosis. Further PPI network analysis of calcium/micronutrients, including MX1 and UBE2L6, consisted of 58 and 18 nodes, respecti…
bibliographic citation: Wang et al. (2024) MX1 and UBE2L6 are potential metaflammation gene targets in both diabetes and atherosclerosis. PeerJ 12:e16975 https://doi.org/10.7717/peerj.16975
date submitted: 2023-07-20
date accepted: 2024-01-29
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Guisheng
author list: Agent
  family name: Hua
  given name: Rongrong
author list: Agent
  family name: Chen
  given name: Xiaoxia
author list: Agent
  family name: He
  given name: Xucheng
author list: Agent
  family name: Dingming
  given name: Yao
author list: Agent
  family name: Chen
  given name: Hua
author list: Agent
  family name: Zhang
  given name: Buhuan
author list: Agent
  family name: Dong
  given name: Yuru
author list: Agent
  family name: Liu
  given name: Muqing
author list: Agent
  family name: Liu
  given name: Jiaxiong
author list: Agent
  family name: Liu
  given name: Ting
author list: Agent
  family name: Zhao
  given name: Jingwei
author list: Agent
  family name: Zhao
  given name: Yu Qiong
author list: Agent
  family name: Qiao
  given name: Li
doi: 10.7717/peerj.16975
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: © 2024 Wang et al.
attribution name: Wang et al.

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