PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Research on the application of a cement and soil aggregate for the ecological restoration of vegetation in artificial soil
items: Systematic identification of smORFs in domestic silkworm (Bombyx mori)
items: A new genus of dance fly (Diptera: Empidoidea: Hybotidae) from Cretaceous Spanish ambers and introduction to the fossiliferous amber outcrop of La Hoya (Castellón Province, Spain)
items: A redescription of Palaeogekko risgoviensis (Squamata, Gekkota) from the Middle Miocene of Germany, with new data on its morphology
items: Characteristics of muscle contraction of the rectus femoris using tensiomyography by sex in healthy college students: a cross-sectional study
items: Blooming plant species diversity patterns in two adjacent Costa Rican highland ecosystems
items: Primate tooth crown nomenclature revisited
items: Models of ultrasonic radiomics and clinical characters for lymph node metastasis assessment in thyroid cancer: a retrospective study
items: The impact of hypertension on the prognosis of patients with hypertrophic cardiomyopathy: a single-center retrospective study
items: Development and validation of a novel risk model in newly diagnosed de novo bone metastatic prostate cancer (M1b): a retrospective study

Research on the application of a cement and soil aggregate for the ecological restoration of vegetation in artificial soil
type: item
type: AcademicArticle
description: The construction of high-speed roads has resulted in large amounts of steep and exposed cut slopes, posing more potential hazards in areas with mountains and hills. Vegetation restoration is an effective and environmentally-friendly way to restore exposed slopes using outside soil spray seeding, though it is difficult to establish a vegetation cover. Spraying artificial soil on high and steep slopes is a challenging task as it is difficult to keep the fluid mixture on sloped surfaces. Because of these challenges, this study applied different combinations of cement and soil aggregates in artificial soil, measuring final soil properties after one growing season. Experimental results showed that there were substantial differences in all basic soil parameters and in the soil quality index after different treatments. In particular, adding 5–10% cement content could improve the adhesion of artificial soil without remarkably reducing soil quality; adding 0.09% of soil aggregate was also beneficial to soil nutrient availability. These findings indicate that the combination of cement and soil aggregates could be applied in artificial soils for the ecological restoration of steep slope vegetation. Adding cement to the soil increased the alkaline levels of the soil, so it is important to reduce artificial soil pH in the future. The application of a cement and soil aggregate should be considered in the field for the ecological restoration of slope vegetation, and the impact of this addition on slope stability and vegetation growth should be explored with further research.
format: application/pdf
format: text/html
creator: Zhuxin Mao
creator: Qian Li
creator: Yuchao Wang
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.14657
publisher: PeerJ Inc.
rights: © 2023 Mao et al.
abstract: The construction of high-speed roads has resulted in large amounts of steep and exposed cut slopes, posing more potential hazards in areas with mountains and hills. Vegetation restoration is an effective and environmentally-friendly way to restore exposed slopes using outside soil spray seeding, though it is difficult to establish a vegetation cover. Spraying artificial soil on high and steep slopes is a challenging task as it is difficult to keep the fluid mixture on sloped surfaces. Because of these challenges, this study applied different combinations of cement and soil aggregates in artificial soil, measuring final soil properties after one growing season. Experimental results showed that there were substantial differences in all basic soil parameters and in the soil quality index after different treatments. In particular, adding 5–10% cement content could improve the adhesion of artificial soil without remarkably reducing soil quality; adding 0.09% of soil aggregate was also beneficial to soil nutrient availability. These findings indicate that the combination of cement and soil aggregates could be applied in artificial soils for the ecological restoration of steep slope vegetation. Adding cement to the soil increased the alkaline levels of the soil, so it is important to reduce artificial soil pH in the future. The application of a cement and soil aggregate should be considered in the field for the ecological restoration of slope vegetation, and the impact of this addition on slope stability and vegetation growth should be explored with further research.
bibliographic citation: Mao et al. (2023) Research on the application of a cement and soil aggregate for the ecological restoration of vegetation in artificial soil. PeerJ 11:e14657 https://doi.org/10.7717/peerj.14657
date submitted: 2022-04-21
date accepted: 2022-12-08
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Zhuxin
author list: Agent
  family name: Li
  given name: Qian
author list: Agent
  family name: Wang
  given name: Yuchao
doi: 10.7717/peerj.14657
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: ©2023 Mao et al.
attribution name: Mao et al.

Systematic identification of smORFs in domestic silkworm (Bombyx mori)
type: item
type: AcademicArticle
description: The silkworm (Bombyx mori) is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides. However, the smORFs in silkworm had been poorly identified and studied. To further study the smORFs in silkworm, systematic genome-wide identification is essential. Here, we identified and analyzed smORFs in the silkworm using comprehensive methods. Our results showed that at least 738 highly reliable smORFs were found in B. mori and that 34,401 possible smORFs were partially supported. We also identified some differentially expressed and tissue-specific-expressed smORFs, which may be closely related to the characteristics and functions of the tissues. This article provides a basis for subsequent research on smORFs in silkworm, and also hopes to provide a reference point for future research methods for smORFs in other species.
format: application/pdf
format: text/html
creator: Linrong Wan
creator: Wenfu Xiao
creator: Ziyan Huang
creator: Anlian Zhou
creator: Yaming Jiang
creator: Bangxing Zou
creator: Binbin Liu
creator: Cao Deng
creator: Youhong Zhang
subject: Agricultural Science
subject: Bioinformatics
subject: Entomology
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.14682
publisher: PeerJ Inc.
rights: © 2022 Wan et al.
abstract: The silkworm (Bombyx mori) is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides. However, the smORFs in silkworm had been poorly identified and studied. To further study the smORFs in silkworm, systematic genome-wide identification is essential. Here, we identified and analyzed smORFs in the silkworm using comprehensive methods. Our results showed that at least 738 highly reliable smORFs were found in B. mori and that 34,401 possible smORFs were partially supported. We also identified some differentially expressed and tissue-specific-expressed smORFs, which may be closely related to the characteristics and functions of the tissues. This article provides a basis for subsequent research on smORFs in silkworm, and also hopes to provide a reference point for future research methods for smORFs in other species.
bibliographic citation: Wan et al. (2023) Systematic identification of smORFs in domestic silkworm (Bombyx mori). PeerJ 11:e14682 https://doi.org/10.7717/peerj.14682
date submitted: 2022-10-12
date accepted: 2022-12-13
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Linrong
author list: Agent
  family name: Xiao
  given name: Wenfu
author list: Agent
  family name: Huang
  given name: Ziyan
author list: Agent
  family name: Zhou
  given name: Anlian
author list: Agent
  family name: Jiang
  given name: Yaming
author list: Agent
  family name: Zou
  given name: Bangxing
author list: Agent
  family name: Liu
  given name: Binbin
author list: Agent
  family name: Deng
  given name: Cao
author list: Agent
  family name: Zhang
  given name: Youhong
doi: 10.7717/peerj.14682
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: ©2022 Wan et al.
attribution name: Wan et al.

A new genus of dance fly (Diptera: Empidoidea: Hybotidae) from Cretaceous Spanish ambers and introduction to the fossiliferous amber outcrop of La Hoya (Castellón Province, Spain)
type: item
type: AcademicArticle
description: Hybotidae fly species, also known as dance flies, in Cretaceous ambers have been described from Lebanon, France, Myanmar, Russia, and Canada. Here we describe Grimaldipeza coelica gen. et sp. n., and recognize another two un-named species, in Spanish amber from the middle Albian El Soplao and lower Cenomanian La Hoya outcrops. The fore tibial gland is present in the new genus, which is characteristic of the family Hybotidae. We compare Grimaldipeza coelica gen. et sp. n. with the holotypes of Trichinites cretaceus Hennig, 1970 and Ecommocydromia difficilis Schlüter, 1978, and clarify some morphological details present in the latter two species. Further taxonomic placement beyond family of the here described new genus was not possible and remains incertae sedis within Hybotidae until extant subfamilies are better defined. We provide new paleoecological data of the hybotids, together with paleogeographical and life paleoenvironmental notes. A table with the known Cretaceous Hybotidae is provided. Furthermore, the La Hoya amber-bearing outcrop is described in detail, filling the information gap for this deposit.
format: application/pdf
format: text/html
creator: Mónica M. Solórzano-Kraemer
creator: Bradley J. Sinclair
creator: Antonio Arillo
creator: Sergio Álvarez-Parra
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.14692
publisher: PeerJ Inc.
rights: © 2023 Solórzano-Kraemer et al.
abstract: Hybotidae fly species, also known as dance flies, in Cretaceous ambers have been described from Lebanon, France, Myanmar, Russia, and Canada. Here we describe Grimaldipeza coelica gen. et sp. n., and recognize another two un-named species, in Spanish amber from the middle Albian El Soplao and lower Cenomanian La Hoya outcrops. The fore tibial gland is present in the new genus, which is characteristic of the family Hybotidae. We compare Grimaldipeza coelica gen. et sp. n. with the holotypes of Trichinites cretaceus Hennig, 1970 and Ecommocydromia difficilis Schlüter, 1978, and clarify some morphological details present in the latter two species. Further taxonomic placement beyond family of the here described new genus was not possible and remains incertae sedis within Hybotidae until extant subfamilies are better defined. We provide new paleoecological data of the hybotids, together with paleogeographical and life paleoenvironmental notes. A table with the known Cretaceous Hybotidae is provided. Furthermore, the La Hoya amber-bearing outcrop is described in detail, filling the information gap for this deposit.
bibliographic citation: Solórzano-Kraemer et al. (2023) A new genus of dance fly (Diptera: Empidoidea: Hybotidae) from Cretaceous Spanish ambers and introduction to the fossiliferous amber outcrop of La Hoya (Castellón Province, Spain). PeerJ 11:e14692 https://doi.org/10.7717/peerj.14692
date submitted: 2022-09-23
date accepted: 2022-12-14
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Solórzano-Kraemer
  given name: Mónica M.
author list: Agent
  family name: J. Sinclair
  given name: Bradley
author list: Agent
  family name: Arillo
  given name: Antonio
author list: Agent
  family name: Álvarez-Parra
  given name: Sergio
doi: 10.7717/peerj.14692
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Solórzano-Kraemer et al.
attribution name: Solórzano-Kraemer et al.

A redescription of Palaeogekko risgoviensis (Squamata, Gekkota) from the Middle Miocene of Germany, with new data on its morphology
type: item
type: AcademicArticle
description: After its original description, the Middle Miocene gekkotan Palaeogekko risgoviensis remained an enigma for palaeontologists due to a rather poor knowledge of its osteology and relationships. Coming from a single locality in southern Germany, this gecko lived in central Europe during a period when a single gekkotan lineage (i.e., euleptine sphaerodactylids) is confidently reported to have inhabited the continent. However, it is unclear whether P. risgoviensis may represent a member of this same lineage or a second clade of Gekkota. In order to shed light on this issue, the type material of P. risgoviensis is here redescribed, refigured and extensively compared with extinct and extant geckos from Europe. A phylogenetic analysis is also conducted in order to investigate its relationships. The new observations confirm the validity of the German species as a distinct taxon, and exclude the previously-suggested chimeric status of the type material of this gecko (with the exception of a single dentary included in the type series, which clearly belong to a different lizard). Phylogenetic relationships of Palaeogekko are still unclear, though, with different positions within the gekkotan tree recovered for the taxon. Nevertheless, it is confidently supported as a non-eublepharid gekkonoid, in agreement with hypothesys presented by other scholars.
format: application/pdf
format: text/html
creator: Andrea Villa
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14717
publisher: PeerJ Inc.
rights: © 2023 Villa
abstract: After its original description, the Middle Miocene gekkotan Palaeogekko risgoviensis remained an enigma for palaeontologists due to a rather poor knowledge of its osteology and relationships. Coming from a single locality in southern Germany, this gecko lived in central Europe during a period when a single gekkotan lineage (i.e., euleptine sphaerodactylids) is confidently reported to have inhabited the continent. However, it is unclear whether P. risgoviensis may represent a member of this same lineage or a second clade of Gekkota. In order to shed light on this issue, the type material of P. risgoviensis is here redescribed, refigured and extensively compared with extinct and extant geckos from Europe. A phylogenetic analysis is also conducted in order to investigate its relationships. The new observations confirm the validity of the German species as a distinct taxon, and exclude the previously-suggested chimeric status of the type material of this gecko (with the exception of a single dentary included in the type series, which clearly belong to a different lizard). Phylogenetic relationships of Palaeogekko are still unclear, though, with different positions within the gekkotan tree recovered for the taxon. Nevertheless, it is confidently supported as a non-eublepharid gekkonoid, in agreement with hypothesys presented by other scholars.
bibliographic citation: Villa (2023) A redescription of Palaeogekko risgoviensis (Squamata, Gekkota) from the Middle Miocene of Germany, with new data on its morphology. PeerJ 11:e14717 https://doi.org/10.7717/peerj.14717
date submitted: 2022-10-26
date accepted: 2022-12-19
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Villa
  given name: Andrea
doi: 10.7717/peerj.14717
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Villa
attribution name: Villa

Characteristics of muscle contraction of the rectus femoris using tensiomyography by sex in healthy college students: a cross-sectional study
type: item
type: AcademicArticle
description: Background Tensiomyography (TMG) is a non-invasive instrument for measuring mechanical muscle contraction characteristics and measuring the maximum displacement of the muscle belly in the radial direction with respect to the muscle and the time needed to achieve this from electrical stimulation. There have been only been a reports of TMG in healthy adults. A systematic review of TMG reported a low proportion of female participants, with a small sample size. Therefore, it is unclear whether there is a difference in TMG parameters according to sex and between dominant and non-dominant feet. Furthermore, the relationship between TMG parameters and evaluations commonly used in clinical practice has not been clarified. This study aimed to clarify the characteristics of muscle contraction of the rectus femoris using TMG according to sex among healthy college students and its relationship with muscle function evaluation, such as lower limb muscle mass and muscle strength. Methods This cross-sectional study included 91 healthy university students (18–24 years). Five tools were used: TMG, lower-limb muscle mass, rectus femoris thickness, isometric knee joint extension torque, and thigh circumference. Each parameter was compared by the generalized linear mixed model (GLMM) and Bonferroni’s multiple comparison test, with sex as the without-subject factor and dominant/non-dominant foot as the within-subject factor. The correlation between the TMG parameters and other parameters was examined using Pearson’s correlation coefficient for both males and females. Results The results of the GLMM, in terms of the TMG parameters, an interaction was observed for maximum displacement (Dm); in the results of the multiple comparison test, Dm for the non-dominant leg was significantly lower in females than in males. A main effect and interaction were not observed for delay time (Td) and contraction time (Tc) by sex, dominant foot, or non-dominant foot. There was a main effect of sex on muscl…
format: application/pdf
format: text/html
creator: Yasuaki Kusumoto
creator: Hayato Goto
creator: Kohei Chiba
creator: Sakiko Oonishi
creator: Junko Tsuchiya
subject: Kinesiology
subject: Orthopedics
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.14732
publisher: PeerJ Inc.
rights: © 2023 Kusumoto et al.
abstract: Background Tensiomyography (TMG) is a non-invasive instrument for measuring mechanical muscle contraction characteristics and measuring the maximum displacement of the muscle belly in the radial direction with respect to the muscle and the time needed to achieve this from electrical stimulation. There have been only been a reports of TMG in healthy adults. A systematic review of TMG reported a low proportion of female participants, with a small sample size. Therefore, it is unclear whether there is a difference in TMG parameters according to sex and between dominant and non-dominant feet. Furthermore, the relationship between TMG parameters and evaluations commonly used in clinical practice has not been clarified. This study aimed to clarify the characteristics of muscle contraction of the rectus femoris using TMG according to sex among healthy college students and its relationship with muscle function evaluation, such as lower limb muscle mass and muscle strength. Methods This cross-sectional study included 91 healthy university students (18–24 years). Five tools were used: TMG, lower-limb muscle mass, rectus femoris thickness, isometric knee joint extension torque, and thigh circumference. Each parameter was compared by the generalized linear mixed model (GLMM) and Bonferroni’s multiple comparison test, with sex as the without-subject factor and dominant/non-dominant foot as the within-subject factor. The correlation between the TMG parameters and other parameters was examined using Pearson’s correlation coefficient for both males and females. Results The results of the GLMM, in terms of the TMG parameters, an interaction was observed for maximum displacement (Dm); in the results of the multiple comparison test, Dm for the non-dominant leg was significantly lower in females than in males. A main effect and interaction were not observed for delay time (Td) and contraction time (Tc) by sex, dominant foot, or non-dominant foot. There was a main effect of sex on muscl…
bibliographic citation: Kusumoto et al. (2023) Characteristics of muscle contraction of the rectus femoris using tensiomyography by sex in healthy college students: a cross-sectional study. PeerJ 11:e14732 https://doi.org/10.7717/peerj.14732
date submitted: 2022-05-16
date accepted: 2022-12-20
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kusumoto
  given name: Yasuaki
author list: Agent
  family name: Goto
  given name: Hayato
author list: Agent
  family name: Chiba
  given name: Kohei
author list: Agent
  family name: Oonishi
  given name: Sakiko
author list: Agent
  family name: Tsuchiya
  given name: Junko
doi: 10.7717/peerj.14732
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Kusumoto et al.
attribution name: Kusumoto et al.

Blooming plant species diversity patterns in two adjacent Costa Rican highland ecosystems
type: item
type: AcademicArticle
description: The Costa Rican Paramo is a unique ecosystem with high levels of endemism that is geographically isolated from the Andean Paramos. Paramo ecosystems occur above Montane Forests, below the permanent snow level, and their vegetation differs notably from that of adjacent Montane Forests. We compared the composition and beta diversity of blooming plant species using phenological data from functional plant groups (i.e., insect-visited, bird-visited and insect + bird-visited plants) between a Paramo and a Montane Forest site in Costa Rica and analyzed seasonal changes in blooming plant diversity between the rainy and dry seasons. Species richness was higher in the Montane Forest for all plant categories, except for insect-visited plants, which was higher in the Paramo. Beta diversity and blooming plant composition differed between both ecosystems and seasons. Differences in species richness and beta diversity between Paramo and the adjacent Montane Forest are likely the result of dispersal events that occurred during the last glacial period and subsequent isolation, as climate turned to tropical conditions after the Pleistocene, and to stressful abiotic conditions in the Paramo ecosystem that limit species establishment. Differences in blooming plant composition between both ecosystems and seasons are likely attributed to differential effects of climatic cues triggering the flowering events in each ecosystem, but phylogenetic conservatism cannot be discarded. Analyses of species composition and richness based on flowering phenology data are useful to evaluate potential floral resources for floral visitors (insects and birds) and how these resources change spatially and temporarily in endangered ecosystems such as the Paramo.
format: application/pdf
format: text/html
creator: E. Jacob Cristóbal-Pérez
creator: Gilbert Barrantes
creator: Alfredo Cascante-Marín
creator: Ruth Madrigal-Brenes
creator: Paul Hanson
creator: Eric J. Fuchs
subject: Biodiversity
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.14445
publisher: PeerJ Inc.
rights: © 2023 Cristóbal-Pérez et al.
abstract: The Costa Rican Paramo is a unique ecosystem with high levels of endemism that is geographically isolated from the Andean Paramos. Paramo ecosystems occur above Montane Forests, below the permanent snow level, and their vegetation differs notably from that of adjacent Montane Forests. We compared the composition and beta diversity of blooming plant species using phenological data from functional plant groups (i.e., insect-visited, bird-visited and insect + bird-visited plants) between a Paramo and a Montane Forest site in Costa Rica and analyzed seasonal changes in blooming plant diversity between the rainy and dry seasons. Species richness was higher in the Montane Forest for all plant categories, except for insect-visited plants, which was higher in the Paramo. Beta diversity and blooming plant composition differed between both ecosystems and seasons. Differences in species richness and beta diversity between Paramo and the adjacent Montane Forest are likely the result of dispersal events that occurred during the last glacial period and subsequent isolation, as climate turned to tropical conditions after the Pleistocene, and to stressful abiotic conditions in the Paramo ecosystem that limit species establishment. Differences in blooming plant composition between both ecosystems and seasons are likely attributed to differential effects of climatic cues triggering the flowering events in each ecosystem, but phylogenetic conservatism cannot be discarded. Analyses of species composition and richness based on flowering phenology data are useful to evaluate potential floral resources for floral visitors (insects and birds) and how these resources change spatially and temporarily in endangered ecosystems such as the Paramo.
bibliographic citation: Cristóbal-Pérez et al. (2023) Blooming plant species diversity patterns in two adjacent Costa Rican highland ecosystems. PeerJ 11:e14445 https://doi.org/10.7717/peerj.14445
date submitted: 2022-09-03
date accepted: 2022-11-01
issued: 2023-01-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cristóbal-Pérez
  given name: E. Jacob
author list: Agent
  family name: Barrantes
  given name: Gilbert
author list: Agent
  family name: Cascante-Marín
  given name: Alfredo
author list: Agent
  family name: Madrigal-Brenes
  given name: Ruth
author list: Agent
  family name: Hanson
  given name: Paul
author list: Agent
  family name: Fuchs
  given name: Eric J.
doi: 10.7717/peerj.14445
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-12
copyright: ©2023 Cristóbal-Pérez et al.
attribution name: Cristóbal-Pérez et al.

Primate tooth crown nomenclature revisited
type: item
type: AcademicArticle
description: Cusp patterning on living and extinct primate molar teeth plays a crucial role in species diagnoses, phylogenetic inference, and the reconstruction of the evolutionary history of the primate clade. These studies rely on a system of nomenclature that can accurately identify and distinguish between the various structures of the crown surface. However, studies at the enamel-dentine junction (EDJ) of some primate taxa have demonstrated a greater degree of cusp variation and expression at the crown surface than current systems of nomenclature allow. In this study, we review the current nomenclature and its applicability across all the major primate clades based on investigations of mandibular crown morphology at the enamel-dentine junction revealed through microtomography. From these observations, we reveal numerous new patterns of lower molar accessory cusp expression in primates. We highlight numerous discrepancies between the expected patterns of variation inferred from the current academic literature, and the new patterns of expected variation seen in this study. Based on the current issues associated with the crown nomenclature, and an incomplete understanding of the precise developmental processes associated with each individual crown feature, we introduce these structures within a conservative, non-homologous naming scheme that focuses on simple location-based categorisations. Until there is a better insight into the developmental and phylogenetic origin of these crown features, these categorisations are the most practical way of addressing these structures. Until then, we also suggest the cautious use of accessory cusps for studies of taxonomy and phylogeny.
format: application/pdf
format: text/html
creator: Simon A. Chapple
creator: Matthew M. Skinner
subject: Anthropology
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14523
publisher: PeerJ Inc.
rights: © 2023 Chapple and Skinner
abstract: Cusp patterning on living and extinct primate molar teeth plays a crucial role in species diagnoses, phylogenetic inference, and the reconstruction of the evolutionary history of the primate clade. These studies rely on a system of nomenclature that can accurately identify and distinguish between the various structures of the crown surface. However, studies at the enamel-dentine junction (EDJ) of some primate taxa have demonstrated a greater degree of cusp variation and expression at the crown surface than current systems of nomenclature allow. In this study, we review the current nomenclature and its applicability across all the major primate clades based on investigations of mandibular crown morphology at the enamel-dentine junction revealed through microtomography. From these observations, we reveal numerous new patterns of lower molar accessory cusp expression in primates. We highlight numerous discrepancies between the expected patterns of variation inferred from the current academic literature, and the new patterns of expected variation seen in this study. Based on the current issues associated with the crown nomenclature, and an incomplete understanding of the precise developmental processes associated with each individual crown feature, we introduce these structures within a conservative, non-homologous naming scheme that focuses on simple location-based categorisations. Until there is a better insight into the developmental and phylogenetic origin of these crown features, these categorisations are the most practical way of addressing these structures. Until then, we also suggest the cautious use of accessory cusps for studies of taxonomy and phylogeny.
bibliographic citation: Chapple et al. (2023) Primate tooth crown nomenclature revisited. PeerJ 11:e14523 https://doi.org/10.7717/peerj.14523
date submitted: 2022-07-11
date accepted: 2022-11-15
issued: 2023-01-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chapple
  given name: Simon A.
author list: Agent
  family name: Skinner
  given name: Matthew M.
doi: 10.7717/peerj.14523
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-12
copyright: ©2023 Chapple and Skinner
attribution name: Chapple and Skinner

Models of ultrasonic radiomics and clinical characters for lymph node metastasis assessment in thyroid cancer: a retrospective study
type: item
type: AcademicArticle
description: Background Preoperative prediction of cervical lymph node metastasis in papillary thyroid carcinoma provided a basis for tumor staging and treatment decision. This study aimed to investigate the utility of machine learning and develop different models to preoperatively predict cervical lymph node metastasis based on ultrasonic radiomic features and clinical characteristics in papillary thyroid carcinoma nodules. Methods Data from 400 papillary thyroid carcinoma nodules were included and divided into training and validation group. With the help of machine learning, clinical characteristics and ultrasonic radiomic features were extracted and selected using randomforest and least absolute shrinkage and selection operator regression before classified by five classifiers. Finally, 10 models were built and their area under the receiver operating characteristic curve, accuracy, sensitivity, specificity, positive predictive value and negative predictive value were measured. Results Among the 10 models, RF-RF model revealed the highest area under curve (0.812) and accuracy (0.7542) in validation group. The top 10 variables of it included age, seven textural features, one shape feature and one first-order feature, in which eight were high-dimensional features. Conclusions RF-RF model showed the best predictive performance for cervical lymph node metastasis. And the importance features selected by it highlighted the unique role of higher-dimensional statistical methods for radiomics analysis.
format: application/pdf
format: text/html
creator: Hui Zhu
creator: Bing Yu
creator: Yanyan Li
creator: Yuhua Zhang
creator: Juebin Jin
creator: Yao Ai
creator: Xiance Jin
creator: Yan Yang
subject: Computational Biology
subject: Oncology
subject: Radiology and Medical Imaging
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.14546
publisher: PeerJ Inc.
rights: © 2023 Zhu et al.
abstract: Background Preoperative prediction of cervical lymph node metastasis in papillary thyroid carcinoma provided a basis for tumor staging and treatment decision. This study aimed to investigate the utility of machine learning and develop different models to preoperatively predict cervical lymph node metastasis based on ultrasonic radiomic features and clinical characteristics in papillary thyroid carcinoma nodules. Methods Data from 400 papillary thyroid carcinoma nodules were included and divided into training and validation group. With the help of machine learning, clinical characteristics and ultrasonic radiomic features were extracted and selected using randomforest and least absolute shrinkage and selection operator regression before classified by five classifiers. Finally, 10 models were built and their area under the receiver operating characteristic curve, accuracy, sensitivity, specificity, positive predictive value and negative predictive value were measured. Results Among the 10 models, RF-RF model revealed the highest area under curve (0.812) and accuracy (0.7542) in validation group. The top 10 variables of it included age, seven textural features, one shape feature and one first-order feature, in which eight were high-dimensional features. Conclusions RF-RF model showed the best predictive performance for cervical lymph node metastasis. And the importance features selected by it highlighted the unique role of higher-dimensional statistical methods for radiomics analysis.
bibliographic citation: Zhu et al. (2023) Models of ultrasonic radiomics and clinical characters for lymph node metastasis assessment in thyroid cancer: a retrospective study. PeerJ 11:e14546 https://doi.org/10.7717/peerj.14546
date submitted: 2022-09-22
date accepted: 2022-11-18
issued: 2023-01-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Hui
author list: Agent
  family name: Yu
  given name: Bing
author list: Agent
  family name: Li
  given name: Yanyan
author list: Agent
  family name: Zhang
  given name: Yuhua
author list: Agent
  family name: Jin
  given name: Juebin
author list: Agent
  family name: Ai
  given name: Yao
author list: Agent
  family name: Jin
  given name: Xiance
author list: Agent
  family name: Yang
  given name: Yan
doi: 10.7717/peerj.14546
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-12
copyright: ©2023 Zhu et al.
attribution name: Zhu et al.

The impact of hypertension on the prognosis of patients with hypertrophic cardiomyopathy: a single-center retrospective study
type: item
type: AcademicArticle
description: Background Hypertrophic cardiomyopathy (HCM) and hypertension coexist fairly frequently in clinical practice. However, the evidence about the impact of hypertension on the prognosis of HCM is limited. The present study aims to investigate the impact of hypertension on the prognosis of HCM patients. Methods A total of 468 HCM patients were enrolled, and patients were divided into hypertension group (31.8%) and non-hypertension group (68.2%). The primary study endpoint was HCM-related death, consisting of heart failure (HF)-related death, stroke-related death and sudden cardiac death (SCD). Associations between hypertension and HCM-related death were analyzed by Cox regression models with the use of propensity score matching (PSM) as primary analysis. Results There were 55 HCM-related death during a median follow-up time of 4.6 years, and the mortality rate was 2.53 per 100 person years. Kaplan-Meier analysis based on the crude cohort or PSM cohort revealed no significant difference regarding the HCM-related death between the two groups. In the crude cohort, both univariable and multivariable Cox regression analysis indicated that hypertension was not significantly associated with HCM-related death with hazard ratios (HR) at 0.74 (95% CI [0.40–1.36], p value: 0.329) and 0.77 (95% CI [0.35–1.71], p value: 0.521), respectively. Similarly, no strong evidence for an association was observed between hypertension and HCM-related death in the PSM cohort with unadjusted HR at 0.90 (95% CI [0.34–2.41]; p value: 0.838) and adjusted HR at 0.77 (95% CI [0.35–1.71]; p value: 0.521), respectively. Other propensity score methods, including overlap weighting and inverse probability treatment weighting demonstrated similar results. Sensitivity analysis also indicated that the concomitant hypertension did not significantly increase the risk of HF-related death, stroke-related death or SCD in HCM patients. Conclusion HCM-related death did not significantly differ between hypertension an…
format: application/pdf
format: text/html
creator: Ziqiong Wang
creator: Yi Zheng
creator: Haiyan Ruan
creator: Liying Li
creator: Muxin Zhang
creator: Linjia Duan
creator: Sen He
subject: Cardiology
subject: Epidemiology
description: doi:10.7717/peerj.14614
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Hypertrophic cardiomyopathy (HCM) and hypertension coexist fairly frequently in clinical practice. However, the evidence about the impact of hypertension on the prognosis of HCM is limited. The present study aims to investigate the impact of hypertension on the prognosis of HCM patients. Methods A total of 468 HCM patients were enrolled, and patients were divided into hypertension group (31.8%) and non-hypertension group (68.2%). The primary study endpoint was HCM-related death, consisting of heart failure (HF)-related death, stroke-related death and sudden cardiac death (SCD). Associations between hypertension and HCM-related death were analyzed by Cox regression models with the use of propensity score matching (PSM) as primary analysis. Results There were 55 HCM-related death during a median follow-up time of 4.6 years, and the mortality rate was 2.53 per 100 person years. Kaplan-Meier analysis based on the crude cohort or PSM cohort revealed no significant difference regarding the HCM-related death between the two groups. In the crude cohort, both univariable and multivariable Cox regression analysis indicated that hypertension was not significantly associated with HCM-related death with hazard ratios (HR) at 0.74 (95% CI [0.40–1.36], p value: 0.329) and 0.77 (95% CI [0.35–1.71], p value: 0.521), respectively. Similarly, no strong evidence for an association was observed between hypertension and HCM-related death in the PSM cohort with unadjusted HR at 0.90 (95% CI [0.34–2.41]; p value: 0.838) and adjusted HR at 0.77 (95% CI [0.35–1.71]; p value: 0.521), respectively. Other propensity score methods, including overlap weighting and inverse probability treatment weighting demonstrated similar results. Sensitivity analysis also indicated that the concomitant hypertension did not significantly increase the risk of HF-related death, stroke-related death or SCD in HCM patients. Conclusion HCM-related death did not significantly differ between hypertension an…
bibliographic citation: Wang et al. (2023) The impact of hypertension on the prognosis of patients with hypertrophic cardiomyopathy: a single-center retrospective study. PeerJ 11:e14614 https://doi.org/10.7717/peerj.14614
date submitted: 2022-09-13
date accepted: 2022-12-01
issued: 2023-01-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ziqiong
author list: Agent
  family name: Zheng
  given name: Yi
author list: Agent
  family name: Ruan
  given name: Haiyan
author list: Agent
  family name: Li
  given name: Liying
author list: Agent
  family name: Zhang
  given name: Muxin
author list: Agent
  family name: Duan
  given name: Linjia
author list: Agent
  family name: He
  given name: Sen
doi: 10.7717/peerj.14614
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-12
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Development and validation of a novel risk model in newly diagnosed de novo bone metastatic prostate cancer (M1b): a retrospective study
type: item
type: AcademicArticle
description: Background Previous studies suggested that bone metastasis has a significant effect on the time of progression to metastatic castration-resistant prostate cancer (CRPC) for newly diagnosed de novo bone metastatic hormone-sensitive prostate cancer (mHSPC). Nevertheless, the effect of different bone metastasis sites was not fully evaluated. This study aimed to develop and validate a novel bone metastatic risk model. Methods We enrolled 122 patients who were newly diagnosed with de novo bone metastatic prostate cancer following primary androgen deprivation based therapy at our institution from January 2008 to June 2021. The metastatic bone sites were classified into six sites: skull; cervical, thoracic, and lumbar vertebrae; chest (ribs and sternum); pelvis; upper limbs; and lower limbs. We calculated the bone metastatic score (BMS) for each site: 0 points were assigned for non-metastasis and 1 point was assigned for metastasis. The X-tile was adopted to acquire optimal cutoff points of BMS. We defined high-risk group (HRG) as BMS ≥ 3 and low-risk group (LRG) as BMS < 3. The new bone risk stratification was validated by calculating the area under the receiver operating characteristic curve (AUC). Subsequently, the relevant clinical prognostic variables were added to construct a predictive nomogram for predicting CRPC. Results The median patient age was 73 years. Most patients had Gleason score ≤8 (93 cases, 76.2%). The median follow-up duration was 11.5 months (range: 2–92 months). Eighty-six patients progressed to CRPC during the follow-up. The most common bone metastatic site was the pelvis (90.2%). The median BMS was 4. Seventy-six patients had HRG, while forty-six had LRG. The 1-, 2-, and 3-year AUCs for H/LRG were 0.620, 0.754, and 0.793, respectively. The HRG was associated with earlier time to CRPC. A nomogram based on four parameters (Gleason score, H/LRG, prostate-specific antigen [PSA] nadir, and time to PSA nadir) was developed to predict CRPC. Internal vali…
format: application/pdf
format: text/html
creator: Yang Zhang
creator: Junqi Wang
creator: Li Ding
creator: Yuxin Zheng
creator: Chuang Wu
creator: Kun Wang
creator: Wentao Xia
creator: Peng Ge
subject: Epidemiology
subject: Oncology
subject: Orthopedics
subject: Urology
description: doi:10.7717/peerj.14615
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Background Previous studies suggested that bone metastasis has a significant effect on the time of progression to metastatic castration-resistant prostate cancer (CRPC) for newly diagnosed de novo bone metastatic hormone-sensitive prostate cancer (mHSPC). Nevertheless, the effect of different bone metastasis sites was not fully evaluated. This study aimed to develop and validate a novel bone metastatic risk model. Methods We enrolled 122 patients who were newly diagnosed with de novo bone metastatic prostate cancer following primary androgen deprivation based therapy at our institution from January 2008 to June 2021. The metastatic bone sites were classified into six sites: skull; cervical, thoracic, and lumbar vertebrae; chest (ribs and sternum); pelvis; upper limbs; and lower limbs. We calculated the bone metastatic score (BMS) for each site: 0 points were assigned for non-metastasis and 1 point was assigned for metastasis. The X-tile was adopted to acquire optimal cutoff points of BMS. We defined high-risk group (HRG) as BMS ≥ 3 and low-risk group (LRG) as BMS < 3. The new bone risk stratification was validated by calculating the area under the receiver operating characteristic curve (AUC). Subsequently, the relevant clinical prognostic variables were added to construct a predictive nomogram for predicting CRPC. Results The median patient age was 73 years. Most patients had Gleason score ≤8 (93 cases, 76.2%). The median follow-up duration was 11.5 months (range: 2–92 months). Eighty-six patients progressed to CRPC during the follow-up. The most common bone metastatic site was the pelvis (90.2%). The median BMS was 4. Seventy-six patients had HRG, while forty-six had LRG. The 1-, 2-, and 3-year AUCs for H/LRG were 0.620, 0.754, and 0.793, respectively. The HRG was associated with earlier time to CRPC. A nomogram based on four parameters (Gleason score, H/LRG, prostate-specific antigen [PSA] nadir, and time to PSA nadir) was developed to predict CRPC. Internal vali…
bibliographic citation: Zhang et al. (2023) Development and validation of a novel risk model in newly diagnosed de novo bone metastatic prostate cancer (M1b): a retrospective study. PeerJ 11:e14615 https://doi.org/10.7717/peerj.14615
date submitted: 2022-08-25
date accepted: 2022-12-01
issued: 2023-01-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yang
author list: Agent
  family name: Wang
  given name: Junqi
author list: Agent
  family name: Ding
  given name: Li
author list: Agent
  family name: Zheng
  given name: Yuxin
author list: Agent
  family name: Wu
  given name: Chuang
author list: Agent
  family name: Wang
  given name: Kun
author list: Agent
  family name: Xia
  given name: Wentao
author list: Agent
  family name: Ge
  given name: Peng
doi: 10.7717/peerj.14615
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-12
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

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