PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Multiple propane gas burn rates procedure to determine accuracy and linearity of indirect calorimetry systems: an experimental assessment of a method
items: Morphology and cytochemical patterns of peripheral blood cells of tiger frog (Rana rugulosa)
items: COVID-19 onset reduced the sex ratio at birth in South Africa
items: Effects of exogenous calcium on the drought response of the tea plant (Camellia sinensis (L.) Kuntze)
items: The redescription of the holotype of Nothosaurus mirabilis (Diapsida, Eosauropterygia)—a historical skeleton from the Muschelkalk (Middle Triassic, Anisian) near Bayreuth (southern Germany)
items: A new species of lotic breeding salamander (Amphibia, Caudata, Hynobiidae) from Shikoku, Japan
items: Morphology of inner cell mass: a better predictive biomarker of blastocyst viability
items: Differences in subjective well-being between individuals with distinct Joint Personality (temperament-character) networks in a Bulgarian sample
items: The efficacy of computed tomography scanning versus surface scanning in 3D finite element analysis
items: Evolution of pathogenicity in obligate fungal pathogens and allied genera

Multiple propane gas burn rates procedure to determine accuracy and linearity of indirect calorimetry systems: an experimental assessment of a method
type: item
type: AcademicArticle
description: Objective Indirect calorimetry (IC) systems measure the fractions of expired carbon dioxide (FeCO2), and oxygen (FeO2) recorded at the mouth to estimate whole-body energy production. The fundamental principle of IC relates to the catabolism of high-energy substrates such as carbohydrates and lipids to meet the body’s energy needs through the oxidative process, which are reflected in the measured oxygen uptake rates (V̇O2) and carbon dioxide production rates (V̇CO2). Accordingly, it is important to know the accuracy and validity of V̇O2and V̇CO2 measurements when estimating energy production and substrate partitioning for research and clinical purposes. Although several techniques are readily available to assess the accuracy of IC systems at a single point for V̇CO2 and V̇O2, the validity of such procedures is limited when used in testing protocols that incorporate a wide range of energy production (e.g., basal metabolic rate and maximal exercise testing). Accordingly, we built an apparatus that allowed us to manipulate propane burn rates in such a way as to assess the linearity of IC systems. This technical report aimed to assess the accuracy and linearity of three IC systems using our in-house built validation procedure. Approach A series of trials at different propane burn rates (PBR) (i.e., 200, 300, 400, 500, and 600 mL min−1) were run on three IC systems: Sable, Moxus, and Oxycon Pro. The experimental values for V̇O2 and V̇CO2 measured on the three IC systems were compared to theoretical stoichiometry values. Results A linear relationship was observed between increasing PBR and measured values for V̇O2and V̇CO2 (99.6%, 99.2%, 94.8% for the Sable, Moxus, and Jaeger IC systems, respectively). In terms of system error, the Jaeger system had significantly (p < 0.001) greater V̇O2(mean difference (M) = −0.057, standard error (SE) = 0.004), and V̇CO2(M = −0.048, SE = 0.002) error compared to either the Sable (V̇O2, M = 0.044, SE = 0.004; V̇CO2, M = 0.024, SE = 0.002)…
format: application/pdf
format: text/html
creator: Mohammad Ismail
creator: Sanaa A. Alsubheen
creator: Angela Loucks-Atkinson
creator: Matthew Atkinson
creator: Thamir Alkanani
creator: Liam P. Kelly
creator: Fabien Basset
subject: Bioengineering
subject: Kinesiology
subject: Nutrition
subject: Metabolic Sciences
description: doi:10.7717/peerj.13882
publisher: PeerJ Inc.
rights: © 2022 Ismail et al.
abstract: Objective Indirect calorimetry (IC) systems measure the fractions of expired carbon dioxide (FeCO2), and oxygen (FeO2) recorded at the mouth to estimate whole-body energy production. The fundamental principle of IC relates to the catabolism of high-energy substrates such as carbohydrates and lipids to meet the body’s energy needs through the oxidative process, which are reflected in the measured oxygen uptake rates (V̇O2) and carbon dioxide production rates (V̇CO2). Accordingly, it is important to know the accuracy and validity of V̇O2and V̇CO2 measurements when estimating energy production and substrate partitioning for research and clinical purposes. Although several techniques are readily available to assess the accuracy of IC systems at a single point for V̇CO2 and V̇O2, the validity of such procedures is limited when used in testing protocols that incorporate a wide range of energy production (e.g., basal metabolic rate and maximal exercise testing). Accordingly, we built an apparatus that allowed us to manipulate propane burn rates in such a way as to assess the linearity of IC systems. This technical report aimed to assess the accuracy and linearity of three IC systems using our in-house built validation procedure. Approach A series of trials at different propane burn rates (PBR) (i.e., 200, 300, 400, 500, and 600 mL min−1) were run on three IC systems: Sable, Moxus, and Oxycon Pro. The experimental values for V̇O2 and V̇CO2 measured on the three IC systems were compared to theoretical stoichiometry values. Results A linear relationship was observed between increasing PBR and measured values for V̇O2and V̇CO2 (99.6%, 99.2%, 94.8% for the Sable, Moxus, and Jaeger IC systems, respectively). In terms of system error, the Jaeger system had significantly (p < 0.001) greater V̇O2(mean difference (M) = −0.057, standard error (SE) = 0.004), and V̇CO2(M = −0.048, SE = 0.002) error compared to either the Sable (V̇O2, M = 0.044, SE = 0.004; V̇CO2, M = 0.024, SE = 0.002)…
bibliographic citation: Ismail et al. (2022) Multiple propane gas burn rates procedure to determine accuracy and linearity of indirect calorimetry systems: an experimental assessment of a method. PeerJ 10:e13882 https://doi.org/10.7717/peerj.13882
date submitted: 2019-02-26
date accepted: 2022-07-20
issued: 2022-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ismail
  given name: Mohammad
author list: Agent
  family name: Alsubheen
  given name: Sanaa A.
author list: Agent
  family name: Loucks-Atkinson
  given name: Angela
author list: Agent
  family name: Atkinson
  given name: Matthew
author list: Agent
  family name: Alkanani
  given name: Thamir
author list: Agent
  family name: Kelly
  given name: Liam P.
author list: Agent
  family name: Basset
  given name: Fabien
doi: 10.7717/peerj.13882
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-29
copyright: ©2022 Ismail et al.
attribution name: Ismail et al.

Morphology and cytochemical patterns of peripheral blood cells of tiger frog (Rana rugulosa)
type: item
type: AcademicArticle
description: Background Tiger frog (Rana rugulosa) is a national second-class protected amphibian species in China with an important ecological and economic value. In recent years, due to excessive human hunting, pollution and habitat loss, the wild population of tiger frog has declined sharply. To protect wildlife resources, the artificial breeding of tiger frogs has rapidly developed in China. Diseases are increasing and spreading among tiger frogs due to the increasing scale of artificial farming. The blood examination is the most straightforward and less invasive technique to evaluate the animal health condition. Thus, it is essential to obtain the normal hematological indicators of tiger frogs. The objective of this study was to investigate the morphometry, microstructure and cytochemical patterns of peripheral blood cells in tiger frogs. Methods The number of blood cells in tiger frogs was counted on a blood count board, and the cell sizes were measured by a micrometer under light microscope. The morphology and classification of blood cells were studied by Wright-Giemsa staining, and the cytochemical pateerns was investigated by various cytochemical staining including periodic acid-Schiff (PAS), Sudan black B (SBB), peroxidase (POX), alkaline phosphatase (AKP), acid phosphatase (ACP), chloroacetic acid AS-D naphthol esterase (CAE) and α-naphthol acetate esterase (ANAE) staining. Results Besides erythrocytes and thrombocytes, five types of leukocytes were identified in tiger frogs: neutrophils, eosinophils, basophils, lymphocytes and monocytes. The mean erythrocyte, leukocyte and thrombocyte counts were 1.33 ± 0.15 million/mm3, 3.73 ± 0.04 × 104/mm3 and 1.7 ± 0.01 × 104/mm3, respectively. Small lymphocytes were the most abundant leukocytes, followed by large lymphocytes, Neutrophils, eosinophils and monocytes, basophils were the fewest. Eosinophils were strongly positive for PAS, positive for SBB, POX, ACP, CAE, ANAE, while weakly positive for AKP staining; basophils were s…
format: application/pdf
format: text/html
creator: Xianxian Chen
creator: Yu Wu
creator: Lixin Huang
creator: Xue Cao
creator: Misbah Hanif
creator: Fei Peng
creator: Xiaobing Wu
creator: Shengzhou Zhang
subject: Cell Biology
subject: Veterinary Medicine
subject: Zoology
subject: Hematology
description: doi:10.7717/peerj.13915
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Background Tiger frog (Rana rugulosa) is a national second-class protected amphibian species in China with an important ecological and economic value. In recent years, due to excessive human hunting, pollution and habitat loss, the wild population of tiger frog has declined sharply. To protect wildlife resources, the artificial breeding of tiger frogs has rapidly developed in China. Diseases are increasing and spreading among tiger frogs due to the increasing scale of artificial farming. The blood examination is the most straightforward and less invasive technique to evaluate the animal health condition. Thus, it is essential to obtain the normal hematological indicators of tiger frogs. The objective of this study was to investigate the morphometry, microstructure and cytochemical patterns of peripheral blood cells in tiger frogs. Methods The number of blood cells in tiger frogs was counted on a blood count board, and the cell sizes were measured by a micrometer under light microscope. The morphology and classification of blood cells were studied by Wright-Giemsa staining, and the cytochemical pateerns was investigated by various cytochemical staining including periodic acid-Schiff (PAS), Sudan black B (SBB), peroxidase (POX), alkaline phosphatase (AKP), acid phosphatase (ACP), chloroacetic acid AS-D naphthol esterase (CAE) and α-naphthol acetate esterase (ANAE) staining. Results Besides erythrocytes and thrombocytes, five types of leukocytes were identified in tiger frogs: neutrophils, eosinophils, basophils, lymphocytes and monocytes. The mean erythrocyte, leukocyte and thrombocyte counts were 1.33 ± 0.15 million/mm3, 3.73 ± 0.04 × 104/mm3 and 1.7 ± 0.01 × 104/mm3, respectively. Small lymphocytes were the most abundant leukocytes, followed by large lymphocytes, Neutrophils, eosinophils and monocytes, basophils were the fewest. Eosinophils were strongly positive for PAS, positive for SBB, POX, ACP, CAE, ANAE, while weakly positive for AKP staining; basophils were s…
bibliographic citation: Chen et al. (2022) Morphology and cytochemical patterns of peripheral blood cells of tiger frog (Rana rugulosa). PeerJ 10:e13915 https://doi.org/10.7717/peerj.13915
date submitted: 2022-01-24
date accepted: 2022-07-28
issued: 2022-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xianxian
author list: Agent
  family name: Wu
  given name: Yu
author list: Agent
  family name: Huang
  given name: Lixin
author list: Agent
  family name: Cao
  given name: Xue
author list: Agent
  family name: Hanif
  given name: Misbah
author list: Agent
  family name: Peng
  given name: Fei
author list: Agent
  family name: Wu
  given name: Xiaobing
author list: Agent
  family name: Zhang
  given name: Shengzhou
doi: 10.7717/peerj.13915
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-29
copyright: ©2022 Chen et al.
attribution name: Chen et al.

COVID-19 onset reduced the sex ratio at birth in South Africa
type: item
type: AcademicArticle
description: Background The sex ratio at birth (defined as male/(male+female) live births) is anticipated to approximate 0.510 with a slight male excess. This ratio has been observed to decrease transiently around 3–5 months following sudden unexpected stressful events. We hypothesised that stress engendered by the onset of the COVID-19 pandemic may have caused such a decrease in South Africa 3–5 months after March 2020 since in this month, South Africa reported its first COVID-19 case, death and nationwide lockdown restrictions were instituted. Methods We used publicly available, recorded monthly live birth data from Statistics South Africa. The most recent month for which data was available publicly was December 2020. We analysed live births for a 100-month period from September 2012 to December 2020, taking seasonality into account. Chi-squared tests were applied. Results Over this 100-month period, there were 8,151,364 live births. The lowest recorded monthly sex ratio at birth of 0.499 was in June 2020, 3 months after March 2020. This June was the only month during this period where the sex ratio inverted i.e., fewer male live births occurred. The predicted June 2020 ratio was 0.504. The observed June 2020 decrease was statistically significant p = 0.045. Conclusions The sex ratio at birth decreased and inverted in South Africa in June 2020, for the first time, during the most recent 100-month period. This decline occurred 3 months after the March 2020 onset of COVID-19 in South Africa. As June 2020 is within the critical window when population stressors are known to impact the sex ratio at birth, these findings suggest that the onset of the COVID-19 pandemic engendered population stress with notable effects on pregnancy and public health in South Africa. These findings have implications for future pandemic preparedness and social policy.
format: application/pdf
format: text/html
creator: Gwinyai Masukume
creator: Margaret Ryan
creator: Rumbidzai Masukume
creator: Dorota Zammit
creator: Victor Grech
creator: Witness Mapanga
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Public Health
subject: Women’s Health
subject: COVID-19
description: doi:10.7717/peerj.13985
publisher: PeerJ Inc.
rights: © 2022 Masukume et al.
abstract: Background The sex ratio at birth (defined as male/(male+female) live births) is anticipated to approximate 0.510 with a slight male excess. This ratio has been observed to decrease transiently around 3–5 months following sudden unexpected stressful events. We hypothesised that stress engendered by the onset of the COVID-19 pandemic may have caused such a decrease in South Africa 3–5 months after March 2020 since in this month, South Africa reported its first COVID-19 case, death and nationwide lockdown restrictions were instituted. Methods We used publicly available, recorded monthly live birth data from Statistics South Africa. The most recent month for which data was available publicly was December 2020. We analysed live births for a 100-month period from September 2012 to December 2020, taking seasonality into account. Chi-squared tests were applied. Results Over this 100-month period, there were 8,151,364 live births. The lowest recorded monthly sex ratio at birth of 0.499 was in June 2020, 3 months after March 2020. This June was the only month during this period where the sex ratio inverted i.e., fewer male live births occurred. The predicted June 2020 ratio was 0.504. The observed June 2020 decrease was statistically significant p = 0.045. Conclusions The sex ratio at birth decreased and inverted in South Africa in June 2020, for the first time, during the most recent 100-month period. This decline occurred 3 months after the March 2020 onset of COVID-19 in South Africa. As June 2020 is within the critical window when population stressors are known to impact the sex ratio at birth, these findings suggest that the onset of the COVID-19 pandemic engendered population stress with notable effects on pregnancy and public health in South Africa. These findings have implications for future pandemic preparedness and social policy.
bibliographic citation: Masukume et al. (2022) COVID-19 onset reduced the sex ratio at birth in South Africa. PeerJ 10:e13985 https://doi.org/10.7717/peerj.13985
date submitted: 2022-05-17
date accepted: 2022-08-10
issued: 2022-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Masukume
  given name: Gwinyai
author list: Agent
  family name: Ryan
  given name: Margaret
author list: Agent
  family name: Masukume
  given name: Rumbidzai
author list: Agent
  family name: Zammit
  given name: Dorota
author list: Agent
  family name: Grech
  given name: Victor
author list: Agent
  family name: Mapanga
  given name: Witness
doi: 10.7717/peerj.13985
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-29
copyright: ©2022 Masukume et al.
attribution name: Masukume et al.

Effects of exogenous calcium on the drought response of the tea plant (Camellia sinensis (L.) Kuntze)
type: item
type: AcademicArticle
description: Background Drought is one of the major factors reducing the yield of many crops worldwide, including the tea crop (Camellia sinensis (L.) Kuntze). Calcium participates in most of cellular signaling processes, and its important role in stress detection and triggering a response has been shown in many crops. The aim of this study was to evaluate possible effects of calcium on the tea plant response to drought. Methods Experiments were conducted using 3-year-old potted tea plants of the best local cultivar Kolkhida. Application of ammonium nitrate (control treatment) or calcium nitrate (Ca treatment) to the soil was performed before drought induction. Next, a 7-day drought was induced in both groups of plants. The following physiological parameters were measured: relative electrical conductivity, pH of cell sap, and concentrations of cations, sugars, and amino acids. In addition, relative expression levels of 40 stress-related and crop quality–related genes were analyzed. Results Under drought stress, leaf electrolyte leakage differed significantly, indicating greater damage to cell membranes in control plants than in Ca-treated plants. Calcium application resulted in greater pH of cell sap; higher accumulation of tyrosine, methionine, and valine; and a greater Mg2+ content as compared to control plants. Drought stress downregulated most of the quality-related genes in both groups of tea plants. By contrast, significant upregulation of some genes was observed, namely CRK45, NAC26, TPS11, LOX1, LOX6, Hydrolase22, DREB26, SWEET2, GS, ADC, DHN2, GOLS1, GOLS3, and RHL41. Among them, three genes (LOX1, RHL41, and GOLS1) showed 2–3 times greater expression in Ca-treated plants than in control plants. Based on these results, it can be speculated that calcium affects galactinol biosynthesis and participates in the regulation of stomatal aperture not only through activation of abscisic-acid signaling but also through jasmonic-acid pathway activation. These findings clarify calc…
format: application/pdf
format: text/html
creator: Lyudmila S. Malyukova
creator: Natalia G. Koninskaya
creator: Yuriy L. Orlov
creator: Lidiia S. Samarina
subject: Agricultural Science
subject: Biotechnology
subject: Genetics
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13997
publisher: PeerJ Inc.
rights: © 2022 Malyukova et al.
abstract: Background Drought is one of the major factors reducing the yield of many crops worldwide, including the tea crop (Camellia sinensis (L.) Kuntze). Calcium participates in most of cellular signaling processes, and its important role in stress detection and triggering a response has been shown in many crops. The aim of this study was to evaluate possible effects of calcium on the tea plant response to drought. Methods Experiments were conducted using 3-year-old potted tea plants of the best local cultivar Kolkhida. Application of ammonium nitrate (control treatment) or calcium nitrate (Ca treatment) to the soil was performed before drought induction. Next, a 7-day drought was induced in both groups of plants. The following physiological parameters were measured: relative electrical conductivity, pH of cell sap, and concentrations of cations, sugars, and amino acids. In addition, relative expression levels of 40 stress-related and crop quality–related genes were analyzed. Results Under drought stress, leaf electrolyte leakage differed significantly, indicating greater damage to cell membranes in control plants than in Ca-treated plants. Calcium application resulted in greater pH of cell sap; higher accumulation of tyrosine, methionine, and valine; and a greater Mg2+ content as compared to control plants. Drought stress downregulated most of the quality-related genes in both groups of tea plants. By contrast, significant upregulation of some genes was observed, namely CRK45, NAC26, TPS11, LOX1, LOX6, Hydrolase22, DREB26, SWEET2, GS, ADC, DHN2, GOLS1, GOLS3, and RHL41. Among them, three genes (LOX1, RHL41, and GOLS1) showed 2–3 times greater expression in Ca-treated plants than in control plants. Based on these results, it can be speculated that calcium affects galactinol biosynthesis and participates in the regulation of stomatal aperture not only through activation of abscisic-acid signaling but also through jasmonic-acid pathway activation. These findings clarify calc…
bibliographic citation: Malyukova et al. (2022) Effects of exogenous calcium on the drought response of the tea plant (Camellia sinensis (L.) Kuntze). PeerJ 10:e13997 https://doi.org/10.7717/peerj.13997
date submitted: 2022-03-16
date accepted: 2022-08-12
issued: 2022-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malyukova
  given name: Lyudmila S.
author list: Agent
  family name: Koninskaya
  given name: Natalia G.
author list: Agent
  family name: Orlov
  given name: Yuriy L.
author list: Agent
  family name: Samarina
  given name: Lidiia S.
doi: 10.7717/peerj.13997
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-29
copyright: © 2022 Malyukova et al.
attribution name: Malyukova et al.

The redescription of the holotype of Nothosaurus mirabilis (Diapsida, Eosauropterygia)—a historical skeleton from the Muschelkalk (Middle Triassic, Anisian) near Bayreuth (southern Germany)
type: item
type: AcademicArticle
description: In 2009, the historical mount of the holotype of Nothosaurus mirabilis from the Upper Muschelkalk of Oschenberg (Laineck Mountain Range, near Bayreuth, southern Germany) was disassembled and the original postcranial skeleton was reworked and remounted in find position. Its morphology is described and figured for the first time in detail. Further on, a thorough overview of the sedimentary environment and the historical activities around the Upper Muschelkalk quarries in the vicinity of Bayreuth is given. The holotype of N. mirabilis is one out of only two fairly complete nothosaur skeletons known from the Bayreuth Upper Muschelkalk and greatly emends our knowledge of the morphology of the species and the genus. It will further allow an assignment of isolated elements to this taxon. The specimen consists of an articulated and complete neck and anterior trunk vertebral column as well as several articulated parts of the anterior tail region. The sacral region is partially preserved but disarticulated. Besides vertebrae, ribs and gastral fragments, both humeri, the right femur, few zeugopodial and autopodial elements, and the right pelvic girdle are preserved. The very high neural spines of the holotype are stabilized by a supersized zygosphene-zygantrum articulation reaching far dorsally. Together with the large intercentral spaces this character suggests lateral undulation of the trunk region during fast swimming whereas propelling with the broad and wing-shaped humerus and the flat ulna was used during slower swimming. The total body length for this not fully grown individual is reconstructed as between 290 to 320 cm. Preservation, degree of completeness, and articulation of the individual is unique. The skull and shoulder girdle are both lost, whereas articulated strings of the vertebral column have turned and appendicular bones have shifted posteriorly or anteriorly, respectively, indicating water movements and possibly also scavenging.
format: application/pdf
format: text/html
creator: Nicole Klein
creator: Stefan Eggmaier
creator: Hans Hagdorn
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.13818
publisher: PeerJ Inc.
rights: © 2022 Klein et al.
abstract: In 2009, the historical mount of the holotype of Nothosaurus mirabilis from the Upper Muschelkalk of Oschenberg (Laineck Mountain Range, near Bayreuth, southern Germany) was disassembled and the original postcranial skeleton was reworked and remounted in find position. Its morphology is described and figured for the first time in detail. Further on, a thorough overview of the sedimentary environment and the historical activities around the Upper Muschelkalk quarries in the vicinity of Bayreuth is given. The holotype of N. mirabilis is one out of only two fairly complete nothosaur skeletons known from the Bayreuth Upper Muschelkalk and greatly emends our knowledge of the morphology of the species and the genus. It will further allow an assignment of isolated elements to this taxon. The specimen consists of an articulated and complete neck and anterior trunk vertebral column as well as several articulated parts of the anterior tail region. The sacral region is partially preserved but disarticulated. Besides vertebrae, ribs and gastral fragments, both humeri, the right femur, few zeugopodial and autopodial elements, and the right pelvic girdle are preserved. The very high neural spines of the holotype are stabilized by a supersized zygosphene-zygantrum articulation reaching far dorsally. Together with the large intercentral spaces this character suggests lateral undulation of the trunk region during fast swimming whereas propelling with the broad and wing-shaped humerus and the flat ulna was used during slower swimming. The total body length for this not fully grown individual is reconstructed as between 290 to 320 cm. Preservation, degree of completeness, and articulation of the individual is unique. The skull and shoulder girdle are both lost, whereas articulated strings of the vertebral column have turned and appendicular bones have shifted posteriorly or anteriorly, respectively, indicating water movements and possibly also scavenging.
bibliographic citation: Klein et al. (2022) The redescription of the holotype of Nothosaurus mirabilis (Diapsida, Eosauropterygia)—a historical skeleton from the Muschelkalk (Middle Triassic, Anisian) near Bayreuth (southern Germany). PeerJ 10:e13818 https://doi.org/10.7717/peerj.13818
date submitted: 2022-05-05
date accepted: 2022-07-08
issued: 2022-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klein
  given name: Nicole
author list: Agent
  family name: Eggmaier
  given name: Stefan
author list: Agent
  family name: Hagdorn
  given name: Hans
doi: 10.7717/peerj.13818
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-26
copyright: © 2022 Klein et al.
attribution name: Klein et al.

A new species of lotic breeding salamander (Amphibia, Caudata, Hynobiidae) from Shikoku, Japan
type: item
type: AcademicArticle
description: Background Hynobius hirosei is a lotic-breeding salamander endemic to Shikoku Island in western Japan. Significant allozymic and morphological differences have been found among the populations of this species; however, the degree and pattern of intraspecific variation have not been surveyed using a sufficient number of samples. Methods For the taxonomic revision of H. hirosei, we conducted genetic and morphological surveys using samples collected throughout the distribution. Phylogenetic analysis using the cytochrome b region of mitochondrial DNA and population structure analysis using single nucleotide polymorphisms were conducted to evaluate the population structure within the species and the degree of genetic differentiation. Subsequently, a morphological survey based on multivariate and univariate analyses was performed to assess the morphological variation. Results Genetic analyses revealed three genetic groups (Tsurugi, Central, and Nanyo) within H. hirosei, with the Nanyo group distributed allopatrically from the others, and the Tsurugi and Central groups distributed parapatrically with the formation of a hybrid zone between them. The Nanyo group was morphologically distinguishable from the remaining samples, including the topotype of H. hirosei, based on a smaller body size and several ratio values of characters to snout-vent length, longer axilla-groin distance, shorter tail length, shorter internarial distance, longer upper eyelid length, and larger medial tail width. These results support the notion that the Nanyo group is an undescribed species. However, the remaining genetically differentiated groups could not be divided in the present study. Herein, we described the Nanyo group as a new species.
format: application/pdf
format: text/html
creator: Sally Kanamori
creator: Kanto Nishikawa
creator: Masafumi Matsui
creator: Shingo Tanabe
subject: Biodiversity
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.13891
publisher: PeerJ Inc.
rights: © 2022 Kanamori et al.
abstract: Background Hynobius hirosei is a lotic-breeding salamander endemic to Shikoku Island in western Japan. Significant allozymic and morphological differences have been found among the populations of this species; however, the degree and pattern of intraspecific variation have not been surveyed using a sufficient number of samples. Methods For the taxonomic revision of H. hirosei, we conducted genetic and morphological surveys using samples collected throughout the distribution. Phylogenetic analysis using the cytochrome b region of mitochondrial DNA and population structure analysis using single nucleotide polymorphisms were conducted to evaluate the population structure within the species and the degree of genetic differentiation. Subsequently, a morphological survey based on multivariate and univariate analyses was performed to assess the morphological variation. Results Genetic analyses revealed three genetic groups (Tsurugi, Central, and Nanyo) within H. hirosei, with the Nanyo group distributed allopatrically from the others, and the Tsurugi and Central groups distributed parapatrically with the formation of a hybrid zone between them. The Nanyo group was morphologically distinguishable from the remaining samples, including the topotype of H. hirosei, based on a smaller body size and several ratio values of characters to snout-vent length, longer axilla-groin distance, shorter tail length, shorter internarial distance, longer upper eyelid length, and larger medial tail width. These results support the notion that the Nanyo group is an undescribed species. However, the remaining genetically differentiated groups could not be divided in the present study. Herein, we described the Nanyo group as a new species.
bibliographic citation: Kanamori et al. (2022) A new species of lotic breeding salamander (Amphibia, Caudata, Hynobiidae) from Shikoku, Japan. PeerJ 10:e13891 https://doi.org/10.7717/peerj.13891
date submitted: 2022-05-02
date accepted: 2022-07-21
issued: 2022-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kanamori
  given name: Sally
author list: Agent
  family name: Nishikawa
  given name: Kanto
author list: Agent
  family name: Matsui
  given name: Masafumi
author list: Agent
  family name: Tanabe
  given name: Shingo
doi: 10.7717/peerj.13891
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-26
copyright: © 2022 Kanamori et al.
attribution name: Kanamori et al.

Morphology of inner cell mass: a better predictive biomarker of blastocyst viability
type: item
type: AcademicArticle
description: Background Transfer of embryos at the blastocyst stage is one of the best approaches for achieving a higher success rate in In vitro fertilization (IVF) treatment as it demonstrates an improved uterine and embryonic synchrony at implantation. Despite novel biochemical and genetic markers proposed for the prediction of embryo viability in recent years, the conventional morphological grading of blastocysts remains the classical way of selection in routine practice. This study aims to investigate the association between the morphological features of blastocysts and pregnancy outcomes. Methods This prospective study included women undergoing single or double frozen blastocyst transfers following their autologous cycles in a period between October 2020 and September 2021. The morphological grades (A—good, B—average, and C—poor) of inner cell mass (ICM) and trophectoderm (TE) of blastocysts with known implantation were compared to assess their predictive potential of pregnancy outcome. It was further explored by measuring the relationship between the two variables using logistic regression and receiver operating characteristic (ROC) analysis. Results A total of 1,972 women underwent frozen embryo transfer (FET) cycles with a total of 3,786 blastocysts. Known implantation data (KID) from 2,060 blastocysts of 1,153 patients were subjected to statistical analysis, the rest were excluded. Implantation rates (IR) from transfer of ICM/TE grades AA, AB, BA, BB were observed as 48.5%, 39.4%, 23.4% and 25% respectively. There was a significantly higher IR observed in blastocysts with ICM grade A (p < 0.001) than those with B irrespective of their TE scores. The analysis of the interaction between the two characteristics confirmed the superiority of ICM over TE as a predictor of the outcome. The rank biserial correlation value for ICM was also greater compared to that of TE (0.11 vs 0.05). Conclusion This study confirms that the morphology of ICM of the blastocyst is a stronger pre…
format: application/pdf
format: text/html
creator: Sargunadevi Sivanantham
creator: Mahalakshmi Saravanan
creator: Nidhi Sharma
creator: Jayashree Shrinivasan
creator: Ramesh Raja
subject: Cell Biology
subject: Developmental Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.13935
publisher: PeerJ Inc.
rights: © 2022 Sivanantham et al.
abstract: Background Transfer of embryos at the blastocyst stage is one of the best approaches for achieving a higher success rate in In vitro fertilization (IVF) treatment as it demonstrates an improved uterine and embryonic synchrony at implantation. Despite novel biochemical and genetic markers proposed for the prediction of embryo viability in recent years, the conventional morphological grading of blastocysts remains the classical way of selection in routine practice. This study aims to investigate the association between the morphological features of blastocysts and pregnancy outcomes. Methods This prospective study included women undergoing single or double frozen blastocyst transfers following their autologous cycles in a period between October 2020 and September 2021. The morphological grades (A—good, B—average, and C—poor) of inner cell mass (ICM) and trophectoderm (TE) of blastocysts with known implantation were compared to assess their predictive potential of pregnancy outcome. It was further explored by measuring the relationship between the two variables using logistic regression and receiver operating characteristic (ROC) analysis. Results A total of 1,972 women underwent frozen embryo transfer (FET) cycles with a total of 3,786 blastocysts. Known implantation data (KID) from 2,060 blastocysts of 1,153 patients were subjected to statistical analysis, the rest were excluded. Implantation rates (IR) from transfer of ICM/TE grades AA, AB, BA, BB were observed as 48.5%, 39.4%, 23.4% and 25% respectively. There was a significantly higher IR observed in blastocysts with ICM grade A (p < 0.001) than those with B irrespective of their TE scores. The analysis of the interaction between the two characteristics confirmed the superiority of ICM over TE as a predictor of the outcome. The rank biserial correlation value for ICM was also greater compared to that of TE (0.11 vs 0.05). Conclusion This study confirms that the morphology of ICM of the blastocyst is a stronger pre…
bibliographic citation: Sivanantham et al. (2022) Morphology of inner cell mass: a better predictive biomarker of blastocyst viability. PeerJ 10:e13935 https://doi.org/10.7717/peerj.13935
date submitted: 2022-06-07
date accepted: 2022-08-02
issued: 2022-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sivanantham
  given name: Sargunadevi
author list: Agent
  family name: Saravanan
  given name: Mahalakshmi
author list: Agent
  family name: Sharma
  given name: Nidhi
author list: Agent
  family name: Shrinivasan
  given name: Jayashree
author list: Agent
  family name: Raja
  given name: Ramesh
doi: 10.7717/peerj.13935
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-26
copyright: ©2022 Sivanantham et al.
attribution name: Sivanantham et al.

Differences in subjective well-being between individuals with distinct Joint Personality (temperament-character) networks in a Bulgarian sample
type: item
type: AcademicArticle
description: Background Personality is the major predictor of people’s subjective well-being (i.e., positive affect, negative affect, and life satisfaction). Recent research in countries with high-income and strong self-transcendent values shows that well-being depends on multidimensional configurations of temperament and character traits (i.e., Joint Personality Networks) that regulate the way people learn to adapt their habits to be in accord with their goals and values, rather than individual traits. To evaluate the prevalence and the associations of different Joint Personality (temperament-character) Networks with well-being in a low-income country with weak self-transcendent values, we tested their association in Bulgarian adults, a population known to have strong secular-rationalist values but weak self-transcendent values. Method The sample consisted of 443 individuals from Bulgaria (68.70% females) with a mean age of 34 years (SD = 15.05). Participants self-reported personality (Temperament and Character Inventory), affect (Positive Affect Negative Affect Schedule), and life satisfaction (Satisfaction with Life Scale). The personality scores were used for profiling through latent profile analysis and latent class analysis based on temperament configurations (i.e., Temperament Profiles) of high/low scores of Novelty Seeking (N/n), Harm Avoidance (H/h), Reward Dependence (R/r), and Persistence (P/s); and character configurations (i.e., Character Profiles) of high/low scores of Self-Directedness (S/s), Cooperativeness (C/c), and Self-Transcendence (T/t). Results We found two Temperament Profiles and two Character Profiles that clustered into two distinctive Joint Personality Networks. All individuals in Joint Personality Network 1 had a Reliable (nhRP) Temperament Profile in combination with an Organized (SCt) Character Profile (i.e., a stable temperament and a healthy character configuration). About 71.9% in Joint Personality Network 2 had an Apathetic (sct) Character Prof…
format: application/pdf
format: text/html
creator: Danilo Garcia
creator: Maryam Kazemitabar
creator: Kristina Stoyanova
creator: Drozdstoy Stoyanov
creator: C. Robert Cloninger
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.13956
publisher: PeerJ Inc.
rights: © 2022 Garcia et al.
abstract: Background Personality is the major predictor of people’s subjective well-being (i.e., positive affect, negative affect, and life satisfaction). Recent research in countries with high-income and strong self-transcendent values shows that well-being depends on multidimensional configurations of temperament and character traits (i.e., Joint Personality Networks) that regulate the way people learn to adapt their habits to be in accord with their goals and values, rather than individual traits. To evaluate the prevalence and the associations of different Joint Personality (temperament-character) Networks with well-being in a low-income country with weak self-transcendent values, we tested their association in Bulgarian adults, a population known to have strong secular-rationalist values but weak self-transcendent values. Method The sample consisted of 443 individuals from Bulgaria (68.70% females) with a mean age of 34 years (SD = 15.05). Participants self-reported personality (Temperament and Character Inventory), affect (Positive Affect Negative Affect Schedule), and life satisfaction (Satisfaction with Life Scale). The personality scores were used for profiling through latent profile analysis and latent class analysis based on temperament configurations (i.e., Temperament Profiles) of high/low scores of Novelty Seeking (N/n), Harm Avoidance (H/h), Reward Dependence (R/r), and Persistence (P/s); and character configurations (i.e., Character Profiles) of high/low scores of Self-Directedness (S/s), Cooperativeness (C/c), and Self-Transcendence (T/t). Results We found two Temperament Profiles and two Character Profiles that clustered into two distinctive Joint Personality Networks. All individuals in Joint Personality Network 1 had a Reliable (nhRP) Temperament Profile in combination with an Organized (SCt) Character Profile (i.e., a stable temperament and a healthy character configuration). About 71.9% in Joint Personality Network 2 had an Apathetic (sct) Character Prof…
bibliographic citation: Garcia et al. (2022) Differences in subjective well-being between individuals with distinct Joint Personality (temperament-character) networks in a Bulgarian sample. PeerJ 10:e13956 https://doi.org/10.7717/peerj.13956
date submitted: 2022-05-16
date accepted: 2022-08-06
issued: 2022-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garcia
  given name: Danilo
author list: Agent
  family name: Kazemitabar
  given name: Maryam
author list: Agent
  family name: Stoyanova
  given name: Kristina
author list: Agent
  family name: Stoyanov
  given name: Drozdstoy
author list: Agent
  family name: Cloninger
  given name: C. Robert
doi: 10.7717/peerj.13956
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-26
copyright: ©2022 Garcia et al.
attribution name: Garcia et al.

The efficacy of computed tomography scanning versus surface scanning in 3D finite element analysis
type: item
type: AcademicArticle
description: Finite element analysis (FEA) is a commonly used application in biomechanical studies of both extant and fossil taxa to assess stress and strain in solid structures such as bone. FEA can be performed on 3D structures that are generated using various methods, including computed tomography (CT) scans and surface scans. While previous palaeobiological studies have used both CT scanned models and surface scanned models, little research has evaluated to what degree FE results may vary when CT scans and surface scans of the same object are compared. Surface scans do not preserve the internal geometries of 3D structures, which are typically preserved in CT scans. Here, we created 3D models from CT scans and surface scans of the same specimens (crania and mandibles of a Nile crocodile, a green sea turtle, and a monitor lizard) and performed FEA under identical loading parameters. It was found that once surface scanned models are solidified, they output stress and strain distributions and model deformations comparable to their CT scanned counterparts, though differing by notable stress and strain magnitudes in some cases, depending on morphology of the specimen and the degree of reconstruction applied. Despite similarities in overall mechanical behaviour, surface scanned models can differ in exterior shape compared to CT scanned models due to inaccuracies that can occur during scanning and reconstruction, resulting in local differences in stress distribution. Solid-fill surface scanned models generally output lower stresses compared to CT scanned models due to their compact interiors, which must be accounted for in studies that use both types of scans.
format: application/pdf
format: text/html
creator: Andre J. Rowe
creator: Emily J. Rayfield
subject: Computational Biology
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.13760
publisher: PeerJ Inc.
rights: © 2022 Rowe and Rayfield
abstract: Finite element analysis (FEA) is a commonly used application in biomechanical studies of both extant and fossil taxa to assess stress and strain in solid structures such as bone. FEA can be performed on 3D structures that are generated using various methods, including computed tomography (CT) scans and surface scans. While previous palaeobiological studies have used both CT scanned models and surface scanned models, little research has evaluated to what degree FE results may vary when CT scans and surface scans of the same object are compared. Surface scans do not preserve the internal geometries of 3D structures, which are typically preserved in CT scans. Here, we created 3D models from CT scans and surface scans of the same specimens (crania and mandibles of a Nile crocodile, a green sea turtle, and a monitor lizard) and performed FEA under identical loading parameters. It was found that once surface scanned models are solidified, they output stress and strain distributions and model deformations comparable to their CT scanned counterparts, though differing by notable stress and strain magnitudes in some cases, depending on morphology of the specimen and the degree of reconstruction applied. Despite similarities in overall mechanical behaviour, surface scanned models can differ in exterior shape compared to CT scanned models due to inaccuracies that can occur during scanning and reconstruction, resulting in local differences in stress distribution. Solid-fill surface scanned models generally output lower stresses compared to CT scanned models due to their compact interiors, which must be accounted for in studies that use both types of scans.
bibliographic citation: Rowe et al. (2022) The efficacy of computed tomography scanning versus surface scanning in 3D finite element analysis. PeerJ 10:e13760 https://doi.org/10.7717/peerj.13760
date submitted: 2022-04-04
date accepted: 2022-06-29
issued: 2022-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rowe
  given name: Andre J.
author list: Agent
  family name: Rayfield
  given name: Emily J.
doi: 10.7717/peerj.13760
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-25
copyright: ©2022 Rowe and Rayfield
attribution name: Rowe and Rayfield

Evolution of pathogenicity in obligate fungal pathogens and allied genera
type: item
type: AcademicArticle
description: Obligate fungal pathogens (ascomycetes and basidiomycetes) and oomycetes are known to cause diseases in cereal crop plants. They feed on living cells and most of them have learned to bypass the host immune machinery. This paper discusses some of the factors that are associated with pathogenicity drawing examples from ascomycetes, basidiomycetes and oomycetes, with respect to their manifestation in crop plants. The comparisons have revealed a striking similarity in the three groups suggesting convergent pathways that have arisen from three lineages independently leading to an obligate lifestyle. This review has been written with the intent, that new information on adaptation strategies of biotrophs, modifications in pathogenicity strategies and population dynamics will improve current strategies for breeding with stable resistance.
format: application/pdf
format: text/html
creator: Moytri RoyChowdhury
creator: Jake Sternhagen
creator: Ya Xin
creator: Binghai Lou
creator: Xiaobai Li
creator: Chunnan Li
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genetics
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.13794
publisher: PeerJ Inc.
rights: © 2022 RoyChowdhury et al.
abstract: Obligate fungal pathogens (ascomycetes and basidiomycetes) and oomycetes are known to cause diseases in cereal crop plants. They feed on living cells and most of them have learned to bypass the host immune machinery. This paper discusses some of the factors that are associated with pathogenicity drawing examples from ascomycetes, basidiomycetes and oomycetes, with respect to their manifestation in crop plants. The comparisons have revealed a striking similarity in the three groups suggesting convergent pathways that have arisen from three lineages independently leading to an obligate lifestyle. This review has been written with the intent, that new information on adaptation strategies of biotrophs, modifications in pathogenicity strategies and population dynamics will improve current strategies for breeding with stable resistance.
bibliographic citation: RoyChowdhury et al. (2022) Evolution of pathogenicity in obligate fungal pathogens and allied genera. PeerJ 10:e13794 https://doi.org/10.7717/peerj.13794
date submitted: 2021-08-06
date accepted: 2022-07-06
issued: 2022-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: RoyChowdhury
  given name: Moytri
author list: Agent
  family name: Sternhagen
  given name: Jake
author list: Agent
  family name: Xin
  given name: Ya
author list: Agent
  family name: Lou
  given name: Binghai
author list: Agent
  family name: Li
  given name: Xiaobai
author list: Agent
  family name: Li
  given name: Chunnan
doi: 10.7717/peerj.13794
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-25
copyright: ©2022 RoyChowdhury et al.
attribution name: RoyChowdhury et al.

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