PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparison of machine learning approaches for enhancing Alzheimer’s disease classification
items: Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar
items: Genetic structure and historical and contemporary gene flow of Astyanaxmexicanus in the Gulf of Mexico slope: a microsatellite-based analysis
items: Phenotype characteristics of gastric epithelial mucus in patients with different gastric diseases: from superficial gastritis to gastric cancer
items: Comparison of microleakage between different restorative materials to restore marginal gap at crown margin
items: Sheath-tailed bats (Chiroptera: Emballonuridae) from the early Pleistocene Rackham’s Roost Site, Riversleigh World Heritage Area, and the distribution of northern Australian emballonurid species
items: The Doublesex/Mab-3 domain transcription factor DMD-10 regulates ASH-dependent behavioral responses
items: Resistance training with different repetition duration to failure: effect on hypertrophy, strength and muscle activation
items: A community perspective on the concept of marine holobionts: current status, challenges, and future directions
items: Towards a multi-basin SWAT model for the migration of nutrients and pesticides to Puck Bay (Southern Baltic Sea)

Comparison of machine learning approaches for enhancing Alzheimer’s disease classification
type: item
type: AcademicArticle
description: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, accounting for nearly 60% of all dementia cases. The occurrence of the disease has been increasing rapidly in recent years. Presently about 46.8 million individuals suffer from AD worldwide. The current absence of effective treatment to reverse or stop AD progression highlights the importance of disease prevention and early diagnosis. Brain structural Magnetic Resonance Imaging (MRI) has been widely used for AD detection as it can display morphometric differences and cerebral structural changes. In this study, we built three machine learning-based MRI data classifiers to predict AD and infer the brain regions that contribute to disease development and progression. We then systematically compared the three distinct classifiers, which were constructed based on Support Vector Machine (SVM), 3D Very Deep Convolutional Network (VGGNet) and 3D Deep Residual Network (ResNet), respectively. To improve the performance of the deep learning classifiers, we applied a transfer learning strategy. The weights of a pre-trained model were transferred and adopted as the initial weights of our models. Transferring the learned features significantly reduced training time and increased network efficiency. The classification accuracy for AD subjects from elderly control subjects was 90%, 95%, and 95% for the SVM, VGGNet and ResNet classifiers, respectively. Gradient-weighted Class Activation Mapping (Grad-CAM) was employed to show discriminative regions that contributed most to the AD classification by utilizing the learned spatial information of the 3D-VGGNet and 3D-ResNet models. The resulted maps consistently highlighted several disease-associated brain regions, particularly the cerebellum which is a relatively neglected brain region in the present AD study. Overall, our comparisons suggested that the ResNet model provided the best classification performance as well as more accurate localization of disease-associate…
format: application/pdf
format: text/html
creator: Qi Li
creator: Mary Qu Yang
subject: Bioinformatics
subject: Cognitive Disorders
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.10549
publisher: PeerJ Inc.
rights: © 2021 Li and Yang
abstract: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, accounting for nearly 60% of all dementia cases. The occurrence of the disease has been increasing rapidly in recent years. Presently about 46.8 million individuals suffer from AD worldwide. The current absence of effective treatment to reverse or stop AD progression highlights the importance of disease prevention and early diagnosis. Brain structural Magnetic Resonance Imaging (MRI) has been widely used for AD detection as it can display morphometric differences and cerebral structural changes. In this study, we built three machine learning-based MRI data classifiers to predict AD and infer the brain regions that contribute to disease development and progression. We then systematically compared the three distinct classifiers, which were constructed based on Support Vector Machine (SVM), 3D Very Deep Convolutional Network (VGGNet) and 3D Deep Residual Network (ResNet), respectively. To improve the performance of the deep learning classifiers, we applied a transfer learning strategy. The weights of a pre-trained model were transferred and adopted as the initial weights of our models. Transferring the learned features significantly reduced training time and increased network efficiency. The classification accuracy for AD subjects from elderly control subjects was 90%, 95%, and 95% for the SVM, VGGNet and ResNet classifiers, respectively. Gradient-weighted Class Activation Mapping (Grad-CAM) was employed to show discriminative regions that contributed most to the AD classification by utilizing the learned spatial information of the 3D-VGGNet and 3D-ResNet models. The resulted maps consistently highlighted several disease-associated brain regions, particularly the cerebellum which is a relatively neglected brain region in the present AD study. Overall, our comparisons suggested that the ResNet model provided the best classification performance as well as more accurate localization of disease-associate…
bibliographic citation: Li et al. (2021) Comparison of machine learning approaches for enhancing Alzheimer’s disease classification. PeerJ 9:e10549 https://doi.org/10.7717/peerj.10549
date submitted: 2020-04-06
date accepted: 2020-11-20
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Qi
author list: Agent
  family name: Yang
  given name: Mary Qu
doi: 10.7717/peerj.10549
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: ©2021 Li and Yang
attribution name: Li and Yang

Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar
type: item
type: AcademicArticle
description: Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) divides the mass flux to H, G and S units in monolignol biosynthesis and affects lignin content. Ten HCT homologs were identified in the Populus trichocarpa (Torr. & Gray) genome. Both genome duplication and tandem duplication resulted in the expansion of HCT orthologs in Populus. Comprehensive analysis including motif analysis, phylogenetic analysis, expression profiles and co-expression analysis revealed the divergence and putative function of these candidate PoptrHCTs. PoptrHCT1 and 2 were identified as likely involved in lignin biosynthesis. PoptrHCT9 and 10- are likely to be involved in plant development and the response to cold stress. Similar functional divergence was also identified in Populus tomentosa Carr. Enzymatic assay of PtoHCT1 showed that PtoHCT1 was able to synthesize caffeoyl shikimate using caffeoyl-CoA and shikimic acid as substrates.
format: application/pdf
format: text/html
creator: Nan Chao
creator: Qi Qi
creator: Shuang Li
creator: Brent Ruan
creator: Xiangning Jiang
creator: Ying Gai
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10741
publisher: PeerJ Inc.
rights: © 2021 Chao et al.
abstract: Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) divides the mass flux to H, G and S units in monolignol biosynthesis and affects lignin content. Ten HCT homologs were identified in the Populus trichocarpa (Torr. & Gray) genome. Both genome duplication and tandem duplication resulted in the expansion of HCT orthologs in Populus. Comprehensive analysis including motif analysis, phylogenetic analysis, expression profiles and co-expression analysis revealed the divergence and putative function of these candidate PoptrHCTs. PoptrHCT1 and 2 were identified as likely involved in lignin biosynthesis. PoptrHCT9 and 10- are likely to be involved in plant development and the response to cold stress. Similar functional divergence was also identified in Populus tomentosa Carr. Enzymatic assay of PtoHCT1 showed that PtoHCT1 was able to synthesize caffeoyl shikimate using caffeoyl-CoA and shikimic acid as substrates.
bibliographic citation: Chao et al. (2021) Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar. PeerJ 9:e10741 https://doi.org/10.7717/peerj.10741
date submitted: 2020-02-24
date accepted: 2020-12-18
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chao
  given name: Nan
author list: Agent
  family name: Qi
  given name: Qi
author list: Agent
  family name: Li
  given name: Shuang
author list: Agent
  family name: Ruan
  given name: Brent
author list: Agent
  family name: Jiang
  given name: Xiangning
author list: Agent
  family name: Gai
  given name: Ying
doi: 10.7717/peerj.10741
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: ©2021 Chao et al.
attribution name: Chao et al.

Genetic structure and historical and contemporary gene flow of Astyanaxmexicanus in the Gulf of Mexico slope: a microsatellite-based analysis
type: item
type: AcademicArticle
description: Background Astyanax mexicanus from the river basins of the Gulf of Mexico slope are small freshwater fish that usually live in large groups in different freshwater environments. The group is considered successful due to its high capacity for dispersal and adaptation to different habitats, and the species present high morphological variability throughout their distribution in Mexico. This has produced the most extreme morphotype of the group; the hypogeous or troglobite, which has no eyes or coloration, and is probably the cause of taxonomic uncertainty in the recognition of species across the entire range. Most studies of A. mexicanus have mainly focused on cave individuals, as well as their adjacent surface locations, providing an incomplete evolutionary history, particularly in terms of factors related to dispersal and the potential corridors used, barriers to gene flow, and distribution of genetic variability. The aim of the present study is to determine the population structure and the degree and direction of genetic flow in this complex taxonomic group, incorporating geographic locations not previously included in analyses using microsatellite loci. Our aim is to contribute to the knowledge of the intricate evolutionary history of A. mexicanus throughout most of its range. Methods The present study included a set of several cave and surface locations of A. mexicanus, which have been widely sampled along the Gulf of Mexico slope, in a genetic population analysis using 10 microsatellite loci. Results Ten genetic populations or lineages were identified. In these populations, gene flow was recorded at two time periods. Historical gene flow, both inter and intra-basin, was observed among surface populations, from surface to cave populations, and among cave populations, whereas recording of contemporary gene flow was limited to intra-basin exchanges and observed among surface populations, surface to cave populations, and cave populations.
format: application/pdf
format: text/html
creator: Rodolfo Pérez-Rodríguez
creator: Sarai Esquivel-Bobadilla
creator: Adonaji Madeleine Orozco-Ruíz
creator: José Luis Olivas-Hernández
creator: Francisco Javier García-De León
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.10784
publisher: PeerJ Inc.
rights: © 2021 Pérez-Rodríguez et al.
abstract: Background Astyanax mexicanus from the river basins of the Gulf of Mexico slope are small freshwater fish that usually live in large groups in different freshwater environments. The group is considered successful due to its high capacity for dispersal and adaptation to different habitats, and the species present high morphological variability throughout their distribution in Mexico. This has produced the most extreme morphotype of the group; the hypogeous or troglobite, which has no eyes or coloration, and is probably the cause of taxonomic uncertainty in the recognition of species across the entire range. Most studies of A. mexicanus have mainly focused on cave individuals, as well as their adjacent surface locations, providing an incomplete evolutionary history, particularly in terms of factors related to dispersal and the potential corridors used, barriers to gene flow, and distribution of genetic variability. The aim of the present study is to determine the population structure and the degree and direction of genetic flow in this complex taxonomic group, incorporating geographic locations not previously included in analyses using microsatellite loci. Our aim is to contribute to the knowledge of the intricate evolutionary history of A. mexicanus throughout most of its range. Methods The present study included a set of several cave and surface locations of A. mexicanus, which have been widely sampled along the Gulf of Mexico slope, in a genetic population analysis using 10 microsatellite loci. Results Ten genetic populations or lineages were identified. In these populations, gene flow was recorded at two time periods. Historical gene flow, both inter and intra-basin, was observed among surface populations, from surface to cave populations, and among cave populations, whereas recording of contemporary gene flow was limited to intra-basin exchanges and observed among surface populations, surface to cave populations, and cave populations.
bibliographic citation: Pérez-Rodríguez et al. (2021) Genetic structure and historical and contemporary gene flow of Astyanaxmexicanus in the Gulf of Mexico slope: a microsatellite-based analysis. PeerJ 9:e10784 https://doi.org/10.7717/peerj.10784
date submitted: 2020-08-12
date accepted: 2020-12-23
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pérez-Rodríguez
  given name: Rodolfo
author list: Agent
  family name: Esquivel-Bobadilla
  given name: Sarai
author list: Agent
  family name: Orozco-Ruíz
  given name: Adonaji Madeleine
author list: Agent
  family name: Olivas-Hernández
  given name: José Luis
author list: Agent
  family name: García-De León
  given name: Francisco Javier
doi: 10.7717/peerj.10784
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: ©2021 Pérez-Rodríguez et al.
attribution name: Pérez-Rodríguez et al.

Phenotype characteristics of gastric epithelial mucus in patients with different gastric diseases: from superficial gastritis to gastric cancer
type: item
type: AcademicArticle
description: Background Gastric gland mucin is important for maintaining the basic function of the gastric mucosa, protecting it from foreign substances and reducing the occurrence of gastric diseases. Exploring the phenotype of gastric gland mucus changes during the progression of gastric disease is of great clinical significance. Methods A total of 483 patients with different gastric diseases were collected in this study, including 82 superficial gastritis (SG), 81 atrophic gastritis (AG), 168 dysplasia (GD), and 152 gastric cancer (GC). Mucin staining was performed using HID-ABpH2.5-PAS method and was further grouped according to the mucin coloration. Results The phenotypic characteristics of mucin during disease progression were divided into neutral, acidic, and mucus-free types. Furthermore, acidic mucus can be divided into type I, type II, and type III. The SG group was dominated by neutral mucus (100%), and the AG was dominated by acid mucus (81.48%), which gradually increased with the severity of atrophy (P < 0.05). The GD and GC groups were dominated by mucus-free (43.45%, 78.29%), and as the degree of GD worsened, neutral and acidic mucus gradually decreased and mucus-free increased (P < 0.001). From the SG, AG, GD, and GC progression, neutral and acidic mucus gradually decreased, and mucus- free gradually increased. Acidic mucin revealed that type III (red-brown black) mucin was predominant in AG, GD, and GC, and increased with the degree of AG, GD, as well as the biological behavior of GC. In the lesion adjacent to high-grade GD or GC, type III acid mucin is predominant. Conclusion There were three mucin phenotypes in the process of gastric diseases. With the disease progression, the trend of phenotypic change was that neutral and acidic mucus gradually decreased and mucus-free increased. The appearance of type III mucin suggested a relatively serious phase of gastric diseases and may be a more suitable candidate for follow-up monitoring of patients with GC risk.
format: application/pdf
format: text/html
creator: Nannan Dong
creator: Rui Guo
creator: Yuehua Gong
creator: Yuan Yuan
subject: Gastroenterology and Hepatology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.10822
publisher: PeerJ Inc.
rights: © 2021 Dong et al.
abstract: Background Gastric gland mucin is important for maintaining the basic function of the gastric mucosa, protecting it from foreign substances and reducing the occurrence of gastric diseases. Exploring the phenotype of gastric gland mucus changes during the progression of gastric disease is of great clinical significance. Methods A total of 483 patients with different gastric diseases were collected in this study, including 82 superficial gastritis (SG), 81 atrophic gastritis (AG), 168 dysplasia (GD), and 152 gastric cancer (GC). Mucin staining was performed using HID-ABpH2.5-PAS method and was further grouped according to the mucin coloration. Results The phenotypic characteristics of mucin during disease progression were divided into neutral, acidic, and mucus-free types. Furthermore, acidic mucus can be divided into type I, type II, and type III. The SG group was dominated by neutral mucus (100%), and the AG was dominated by acid mucus (81.48%), which gradually increased with the severity of atrophy (P < 0.05). The GD and GC groups were dominated by mucus-free (43.45%, 78.29%), and as the degree of GD worsened, neutral and acidic mucus gradually decreased and mucus-free increased (P < 0.001). From the SG, AG, GD, and GC progression, neutral and acidic mucus gradually decreased, and mucus- free gradually increased. Acidic mucin revealed that type III (red-brown black) mucin was predominant in AG, GD, and GC, and increased with the degree of AG, GD, as well as the biological behavior of GC. In the lesion adjacent to high-grade GD or GC, type III acid mucin is predominant. Conclusion There were three mucin phenotypes in the process of gastric diseases. With the disease progression, the trend of phenotypic change was that neutral and acidic mucus gradually decreased and mucus-free increased. The appearance of type III mucin suggested a relatively serious phase of gastric diseases and may be a more suitable candidate for follow-up monitoring of patients with GC risk.
bibliographic citation: Dong et al. (2021) Phenotype characteristics of gastric epithelial mucus in patients with different gastric diseases: from superficial gastritis to gastric cancer. PeerJ 9:e10822 https://doi.org/10.7717/peerj.10822
date submitted: 2020-08-17
date accepted: 2021-01-02
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Nannan
author list: Agent
  family name: Guo
  given name: Rui
author list: Agent
  family name: Gong
  given name: Yuehua
author list: Agent
  family name: Yuan
  given name: Yuan
doi: 10.7717/peerj.10822
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: ©2021 Dong et al.
attribution name: Dong et al.

Comparison of microleakage between different restorative materials to restore marginal gap at crown margin
type: item
type: AcademicArticle
description: Background An occurrence of secondary caries around the indirect restoration margin is reported to remain a leading cause of failures. Objective This study aimed to test the interfacial microleakage of conventional glass-ionomer (CGI), resin-modified glass ionomer (RMGI) and Nano-hybrid composite (CR) restorations at a full veneer margin crown. Methods Ninety human extracted molar teeth were divided into three groups (n = 30). Each group was subdivided into three subgroups (n = 10) according to the extent of the structural defects; The structural defect in G1 had a depth of 1.5 mm, width and length at 2 mm and 1 mm intrusion within the crown cervical margin. The corresponding structural defect dimension values for G2 were 2, 5, 4 and 2 mm with defects extending onto the root structure. Meanwhile, G3: structural deficiency of 2 mm depth, 3 mm width and 3 mm length and with 1.5 mm extension into the prepared teeth. These structural defects in each subgroup were restored with CGI, RMGI and CR. Artificial carious lesion formation was induced at the cervical finish line with a demineralizing solution. The artificial carious lesions were restored as per the group distribution. Subsequently, teeth samples were prepared and cemented with Nickel-chromium full coverage restorations utilizing glass-ionomer luting cement. Teeth samples were thermocycled, isolated with nail varnish, and immersed in 0.1% methylene blue for 24 h. The teeth samples were sectioned longitudinally, dye penetration was evaluated with a stereomicroscope. The data were analyzed with Kruskal–Wallis and Mann–Whitney U tests. Results CGI-G1 recorded the highest micro-leakage score at 1.450; while CR-G3 recorded the least score (0.350). At a cementum-restoration interface, CR-G1 (0.850) documented the lowest micro-leakage; RMGI-G3 had a greater value at 1.700. Conclusions The hybrid CR could be effectively used to restore the restoration of a marginal gap around crown margins.
format: application/pdf
format: text/html
creator: Satheesh B. Haralur
creator: Ghaseb Ahmed AL Ghaseb
creator: Norah Ali Alqahtani
creator: Bader Alqahtani
subject: Dentistry
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.10823
publisher: PeerJ Inc.
rights: © 2021 Haralur et al.
abstract: Background An occurrence of secondary caries around the indirect restoration margin is reported to remain a leading cause of failures. Objective This study aimed to test the interfacial microleakage of conventional glass-ionomer (CGI), resin-modified glass ionomer (RMGI) and Nano-hybrid composite (CR) restorations at a full veneer margin crown. Methods Ninety human extracted molar teeth were divided into three groups (n = 30). Each group was subdivided into three subgroups (n = 10) according to the extent of the structural defects; The structural defect in G1 had a depth of 1.5 mm, width and length at 2 mm and 1 mm intrusion within the crown cervical margin. The corresponding structural defect dimension values for G2 were 2, 5, 4 and 2 mm with defects extending onto the root structure. Meanwhile, G3: structural deficiency of 2 mm depth, 3 mm width and 3 mm length and with 1.5 mm extension into the prepared teeth. These structural defects in each subgroup were restored with CGI, RMGI and CR. Artificial carious lesion formation was induced at the cervical finish line with a demineralizing solution. The artificial carious lesions were restored as per the group distribution. Subsequently, teeth samples were prepared and cemented with Nickel-chromium full coverage restorations utilizing glass-ionomer luting cement. Teeth samples were thermocycled, isolated with nail varnish, and immersed in 0.1% methylene blue for 24 h. The teeth samples were sectioned longitudinally, dye penetration was evaluated with a stereomicroscope. The data were analyzed with Kruskal–Wallis and Mann–Whitney U tests. Results CGI-G1 recorded the highest micro-leakage score at 1.450; while CR-G3 recorded the least score (0.350). At a cementum-restoration interface, CR-G1 (0.850) documented the lowest micro-leakage; RMGI-G3 had a greater value at 1.700. Conclusions The hybrid CR could be effectively used to restore the restoration of a marginal gap around crown margins.
bibliographic citation: Haralur et al. (2021) Comparison of microleakage between different restorative materials to restore marginal gap at crown margin. PeerJ 9:e10823 https://doi.org/10.7717/peerj.10823
date submitted: 2020-03-31
date accepted: 2021-01-02
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haralur
  given name: Satheesh B.
author list: Agent
  family name: AL Ghaseb
  given name: Ghaseb Ahmed
author list: Agent
  family name: Alqahtani
  given name: Norah Ali
author list: Agent
  family name: Alqahtani
  given name: Bader
doi: 10.7717/peerj.10823
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: © 2021 Haralur et al.
attribution name: Haralur et al.

Sheath-tailed bats (Chiroptera: Emballonuridae) from the early Pleistocene Rackham’s Roost Site, Riversleigh World Heritage Area, and the distribution of northern Australian emballonurid species
type: item
type: AcademicArticle
description: Sheath-tailed bats (Family Emballonuridae) from the early Pleistocene Rackham’s Roost Site cave deposit in the Riversleigh World Heritage Area, north-western Queensland are the oldest recorded occurrence for the family in Australia. The fossil remains consist of maxillary and dentary fragments, as well as isolated teeth, but until now their precise identity has not been assessed. Our study indicates that at least three taxa are represented, and these are distinguished from other Australian emballonurids based on morphometric analysis of craniodental features. Most of the Rackham’s Roost Site emballonurid remains are referrable to the modern species Taphozous georgianus Thomas, 1915, but the extant species T. troughtoni Tate, 1952 also appears to be present, as well as a very large, as-yet undetermined species of Saccolaimus Temminck, 1838. We identify craniodental features that clearly distinguish T. georgianus from the externally very similar T. troughtoni. Results suggest that the distributions of T. georgianus and T. troughtoni may have overlapped in north-western Queensland since at least the early Pleistocene.
format: application/pdf
format: text/html
creator: Tyler R. King
creator: Troy J. Myers
creator: Kyle N. Armstrong
creator: Michael Archer
creator: Suzanne J. Hand
subject: Ecology
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10857
publisher: PeerJ Inc.
rights: © 2021 King et al.
abstract: Sheath-tailed bats (Family Emballonuridae) from the early Pleistocene Rackham’s Roost Site cave deposit in the Riversleigh World Heritage Area, north-western Queensland are the oldest recorded occurrence for the family in Australia. The fossil remains consist of maxillary and dentary fragments, as well as isolated teeth, but until now their precise identity has not been assessed. Our study indicates that at least three taxa are represented, and these are distinguished from other Australian emballonurids based on morphometric analysis of craniodental features. Most of the Rackham’s Roost Site emballonurid remains are referrable to the modern species Taphozous georgianus Thomas, 1915, but the extant species T. troughtoni Tate, 1952 also appears to be present, as well as a very large, as-yet undetermined species of Saccolaimus Temminck, 1838. We identify craniodental features that clearly distinguish T. georgianus from the externally very similar T. troughtoni. Results suggest that the distributions of T. georgianus and T. troughtoni may have overlapped in north-western Queensland since at least the early Pleistocene.
bibliographic citation: King et al. (2021) Sheath-tailed bats (Chiroptera: Emballonuridae) from the early Pleistocene Rackham’s Roost Site, Riversleigh World Heritage Area, and the distribution of northern Australian emballonurid species. PeerJ 9:e10857 https://doi.org/10.7717/peerj.10857
date submitted: 2020-05-22
date accepted: 2021-01-07
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: King
  given name: Tyler R.
author list: Agent
  family name: Myers
  given name: Troy J.
author list: Agent
  family name: Armstrong
  given name: Kyle N.
author list: Agent
  family name: Archer
  given name: Michael
author list: Agent
  family name: Hand
  given name: Suzanne J.
doi: 10.7717/peerj.10857
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: © 2021 King et al.
attribution name: King et al.

The Doublesex/Mab-3 domain transcription factor DMD-10 regulates ASH-dependent behavioral responses
type: item
type: AcademicArticle
description: The Doublesex/Mab-3 Domain transcription factor DMD-10 is expressed in several cell types in C. elegans, including in the nervous system. We sought to investigate whether DMD-10 is required for normal neuronal function using behavioral assays. We found that mutation of dmd-10 did not broadly affect behavior. dmd-10 mutants were normal in several behavioral assays including a body bends assay for locomotion, egg laying, chemotaxis and response to gentle touch to the body. dmd-10 mutants did have defects in nose-touch responsiveness, which requires the glutamate receptor GLR-1. However, using quantitative fluorescence microscopy to measure levels of a GLR-1::GFP fusion protein in the ventral nerve cord, we found no evidence supporting a difference in the number of GLR-1 synapses or in the amount of GLR-1 present in dmd-10 mutants. dmd-10 mutants did have decreased responsiveness to high osmolarity, which, along with nose-touch, is sensed by the polymodal sensory neuron ASH. Furthermore, mutation of dmd-10 impaired behavioral response to optogenetic activation of ASH, suggesting that dmd-10 promotes neuronal signaling in ASH downstream of sensory receptor activation. Together our results suggest that DMD-10 is important in regulating the frequency of multiple ASH-dependent behavioral responses.
format: application/pdf
format: text/html
creator: Julia Durbeck
creator: Celine Breton
creator: Michael Suter
creator: Eric S. Luth
creator: Annette M. McGehee
subject: Animal Behavior
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Zoology
description: doi:10.7717/peerj.10892
publisher: PeerJ Inc.
rights: © 2021 Durbeck et al.
abstract: The Doublesex/Mab-3 Domain transcription factor DMD-10 is expressed in several cell types in C. elegans, including in the nervous system. We sought to investigate whether DMD-10 is required for normal neuronal function using behavioral assays. We found that mutation of dmd-10 did not broadly affect behavior. dmd-10 mutants were normal in several behavioral assays including a body bends assay for locomotion, egg laying, chemotaxis and response to gentle touch to the body. dmd-10 mutants did have defects in nose-touch responsiveness, which requires the glutamate receptor GLR-1. However, using quantitative fluorescence microscopy to measure levels of a GLR-1::GFP fusion protein in the ventral nerve cord, we found no evidence supporting a difference in the number of GLR-1 synapses or in the amount of GLR-1 present in dmd-10 mutants. dmd-10 mutants did have decreased responsiveness to high osmolarity, which, along with nose-touch, is sensed by the polymodal sensory neuron ASH. Furthermore, mutation of dmd-10 impaired behavioral response to optogenetic activation of ASH, suggesting that dmd-10 promotes neuronal signaling in ASH downstream of sensory receptor activation. Together our results suggest that DMD-10 is important in regulating the frequency of multiple ASH-dependent behavioral responses.
bibliographic citation: Durbeck et al. (2021) The Doublesex/Mab-3 domain transcription factor DMD-10 regulates ASH-dependent behavioral responses. PeerJ 9:e10892 https://doi.org/10.7717/peerj.10892
date submitted: 2020-08-14
date accepted: 2021-01-12
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Durbeck
  given name: Julia
author list: Agent
  family name: Breton
  given name: Celine
author list: Agent
  family name: Suter
  given name: Michael
author list: Agent
  family name: Luth
  given name: Eric S.
author list: Agent
  family name: McGehee
  given name: Annette M.
doi: 10.7717/peerj.10892
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: © 2021 Durbeck et al.
attribution name: Durbeck et al.

Resistance training with different repetition duration to failure: effect on hypertrophy, strength and muscle activation
type: item
type: AcademicArticle
description: Background This study investigated the effects of two 14-week resistance training protocols with different repetition duration (RD) performed to muscle failure (MF) on gains in strength and muscle hypertrophy as well as on normalized electromyographic (EMG) amplitude and force-angle relationships. Methods The left and right legs of ten untrained males were assigned to either one of the two protocols (2-s or 6-s RD) incorporating unilateral knee extension exercise. Both protocols were performed with 3–4 sets, 50–60% of the one-repetition maximum (1RM), and 3 min rest. Rectus femoris and vastus lateralis cross-sectional areas (CSA), maximal voluntary isometric contraction (MVIC) at 30o and 90o of knee flexion and 1RM performance were assessed before and after the training period. In addition, normalized EMG amplitude-angle and force-angle relationships were assessed in the 6th and 39th experimental sessions. Results The 6-s RD protocol induced larger gains in MVIC at 30o of knee angle measurement than the 2-s RD protocol. Increases in MVIC at 90o of knee angle, 1RM, rectus femoris and vastus lateralis CSA were not significant between the 2-s and 6-s RD protocols. Moreover, different normalized EMG amplitude-angle and force-angle values were detected between protocols over most of the angles analyzed. Conclusion Performing longer RD could be a more appropriate strategy to provide greater gains in isometric maximal muscle strength at shortened knee positions. However, similar maximum dynamic strength and muscle hypertrophy gains would be provided by protocols with different RD.
format: application/pdf
format: text/html
creator: Lucas Túlio Lacerda
creator: Rodrigo Otávio Marra-Lopes
creator: Marcel Bahia Lanza
creator: Rodrigo César Ribeiro Diniz
creator: Fernando Vitor Lima
creator: Hugo Cesar Martins-Costa
creator: Gustavo Ferreira Pedrosa
creator: André Gustavo Pereira Andrade
creator: Armin Kibele
creator: Mauro Heleno Chagas
subject: Anatomy and Physiology
subject: Global Health
subject: Kinesiology
description: doi:10.7717/peerj.10909
publisher: PeerJ Inc.
rights: © 2021 Lacerda et al.
abstract: Background This study investigated the effects of two 14-week resistance training protocols with different repetition duration (RD) performed to muscle failure (MF) on gains in strength and muscle hypertrophy as well as on normalized electromyographic (EMG) amplitude and force-angle relationships. Methods The left and right legs of ten untrained males were assigned to either one of the two protocols (2-s or 6-s RD) incorporating unilateral knee extension exercise. Both protocols were performed with 3–4 sets, 50–60% of the one-repetition maximum (1RM), and 3 min rest. Rectus femoris and vastus lateralis cross-sectional areas (CSA), maximal voluntary isometric contraction (MVIC) at 30o and 90o of knee flexion and 1RM performance were assessed before and after the training period. In addition, normalized EMG amplitude-angle and force-angle relationships were assessed in the 6th and 39th experimental sessions. Results The 6-s RD protocol induced larger gains in MVIC at 30o of knee angle measurement than the 2-s RD protocol. Increases in MVIC at 90o of knee angle, 1RM, rectus femoris and vastus lateralis CSA were not significant between the 2-s and 6-s RD protocols. Moreover, different normalized EMG amplitude-angle and force-angle values were detected between protocols over most of the angles analyzed. Conclusion Performing longer RD could be a more appropriate strategy to provide greater gains in isometric maximal muscle strength at shortened knee positions. However, similar maximum dynamic strength and muscle hypertrophy gains would be provided by protocols with different RD.
bibliographic citation: Lacerda et al. (2021) Resistance training with different repetition duration to failure: effect on hypertrophy, strength and muscle activation. PeerJ 9:e10909 https://doi.org/10.7717/peerj.10909
date submitted: 2020-04-07
date accepted: 2021-01-15
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lacerda
  given name: Lucas Túlio
author list: Agent
  family name: Marra-Lopes
  given name: Rodrigo Otávio
author list: Agent
  family name: Lanza
  given name: Marcel Bahia
author list: Agent
  family name: Diniz
  given name: Rodrigo César Ribeiro
author list: Agent
  family name: Lima
  given name: Fernando Vitor
author list: Agent
  family name: Martins-Costa
  given name: Hugo Cesar
author list: Agent
  family name: Pedrosa
  given name: Gustavo Ferreira
author list: Agent
  family name: Gustavo Pereira Andrade
  given name: André
author list: Agent
  family name: Kibele
  given name: Armin
author list: Agent
  family name: Chagas
  given name: Mauro Heleno
doi: 10.7717/peerj.10909
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: ©2021 Lacerda et al.
attribution name: Lacerda et al.

A community perspective on the concept of marine holobionts: current status, challenges, and future directions
type: item
type: AcademicArticle
description: Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
format: application/pdf
format: text/html
creator: Simon M. Dittami
creator: Enrique Arboleda
creator: Jean-Christophe Auguet
creator: Arite Bigalke
creator: Enora Briand
creator: Paco Cárdenas
creator: Ulisse Cardini
creator: Johan Decelle
creator: Aschwin H. Engelen
creator: Damien Eveillard
creator: Claire M.M. Gachon
creator: Sarah M. Griffiths
creator: Tilmann Harder
creator: Ehsan Kayal
creator: Elena Kazamia
creator: François H. Lallier
creator: Mónica Medina
creator: Ezequiel M. Marzinelli
creator: Teresa Maria Morganti
creator: Laura Núñez Pons
creator: Soizic Prado
creator: José Pintado
creator: Mahasweta Saha
creator: Marc-André Selosse
creator: Derek Skillings
creator: Willem Stock
creator: Shinichi Sunagawa
creator: Eve Toulza
creator: Alexey Vorobev
creator: Catherine Leblanc
creator: Fabrice Not
subject: Ecology
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.10911
publisher: PeerJ Inc.
rights: © 2021 Dittami et al.
abstract: Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
bibliographic citation: Dittami et al. (2021) A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 9:e10911 https://doi.org/10.7717/peerj.10911
date submitted: 2020-10-06
date accepted: 2021-01-16
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dittami
  given name: Simon M.
author list: Agent
  family name: Arboleda
  given name: Enrique
author list: Agent
  family name: Auguet
  given name: Jean-Christophe
author list: Agent
  family name: Bigalke
  given name: Arite
author list: Agent
  family name: Briand
  given name: Enora
author list: Agent
  family name: Cárdenas
  given name: Paco
author list: Agent
  family name: Cardini
  given name: Ulisse
author list: Agent
  family name: Decelle
  given name: Johan
author list: Agent
  family name: Engelen
  given name: Aschwin H.
author list: Agent
  family name: Eveillard
  given name: Damien
author list: Agent
  family name: Gachon
  given name: Claire M.M.
author list: Agent
  family name: Griffiths
  given name: Sarah M.
author list: Agent
  family name: Harder
  given name: Tilmann
author list: Agent
  family name: Kayal
  given name: Ehsan
author list: Agent
  family name: Kazamia
  given name: Elena
author list: Agent
  family name: Lallier
  given name: François H.
author list: Agent
  family name: Medina
  given name: Mónica
author list: Agent
  family name: Marzinelli
  given name: Ezequiel M.
author list: Agent
  family name: Morganti
  given name: Teresa Maria
author list: Agent
  family name: Núñez Pons
  given name: Laura
author list: Agent
  family name: Prado
  given name: Soizic
author list: Agent
  family name: Pintado
  given name: José
author list: Agent
  family name: Saha
  given name: Mahasweta
author list: Agent
  family name: Selosse
  given name: Marc-André
doi: 10.7717/peerj.10911
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: ©2021 Dittami et al.
attribution name: Dittami et al.

Towards a multi-basin SWAT model for the migration of nutrients and pesticides to Puck Bay (Southern Baltic Sea)
type: item
type: AcademicArticle
description: Background This paper analyzes the impact of changes in fertilization on crop yields and the runoff of nutrients from a small agricultural catchment (176 km2) to a shallow bay, using the SWAT model. Puck Bay is part of the Gulf of Gdansk and belongs to the Baltic Sea. The whole area of Puck Bay (364 km2) is protected (Natura 2000) yet despite this it suffers from eutrophication problems due to the relatively minimal depth and difficult water exchange. Methods The paper presents a comparison of the calculated yields and the runoff of nutrients and pesticides in the SWAT model, for a small agricultural coastal catchment. Calculations were made for 13 crop scenarios with weather data from 2011 to 2019. For each crop, an agriculture calendar was made. Two variants of fertilization were considered (autofertilization mode and according to the calendar). The nutrient runoff was calculated depending on the adopted scenario. In addition, the fate of selected pesticides was simulated. Results Depending on the crop, the annual load of NO3into the stream ranged from 0.74 to 3.65 kg ha−1. The annual load of organic phosphorous into the stream was between 0.686 and 3.64 kg ha−1. This is lower than in the majority of EU or Baltic countries. The surface runoff of dissolved Glyphosate was equal to 286 mg ha−1. The annual loads of nutrients from the catchment area are equivalent in both fertilization modes. Regardless of the selected fertilization mode, in addition to the dosage, the form of nutrients is important for the model.
format: application/pdf
format: text/html
creator: Paweł Wielgat
creator: Dominika Kalinowska
creator: Adam Szymkiewicz
creator: Piotr Zima
creator: Beata Jaworska-Szulc
creator: Ewa Wojciechowska
creator: Nicole Nawrot
creator: Karolina Matej-Lukowicz
creator: Lidia Anita Dzierzbicka-Glowacka
subject: Agricultural Science
subject: Soil Science
subject: Natural Resource Management
subject: Ecohydrology
subject: Environmental Impacts
description: doi:10.7717/peerj.10938
publisher: PeerJ Inc.
rights: © 2021 Wielgat et al.
abstract: Background This paper analyzes the impact of changes in fertilization on crop yields and the runoff of nutrients from a small agricultural catchment (176 km2) to a shallow bay, using the SWAT model. Puck Bay is part of the Gulf of Gdansk and belongs to the Baltic Sea. The whole area of Puck Bay (364 km2) is protected (Natura 2000) yet despite this it suffers from eutrophication problems due to the relatively minimal depth and difficult water exchange. Methods The paper presents a comparison of the calculated yields and the runoff of nutrients and pesticides in the SWAT model, for a small agricultural coastal catchment. Calculations were made for 13 crop scenarios with weather data from 2011 to 2019. For each crop, an agriculture calendar was made. Two variants of fertilization were considered (autofertilization mode and according to the calendar). The nutrient runoff was calculated depending on the adopted scenario. In addition, the fate of selected pesticides was simulated. Results Depending on the crop, the annual load of NO3into the stream ranged from 0.74 to 3.65 kg ha−1. The annual load of organic phosphorous into the stream was between 0.686 and 3.64 kg ha−1. This is lower than in the majority of EU or Baltic countries. The surface runoff of dissolved Glyphosate was equal to 286 mg ha−1. The annual loads of nutrients from the catchment area are equivalent in both fertilization modes. Regardless of the selected fertilization mode, in addition to the dosage, the form of nutrients is important for the model.
bibliographic citation: Wielgat et al. (2021) Towards a multi-basin SWAT model for the migration of nutrients and pesticides to Puck Bay (Southern Baltic Sea). PeerJ 9:e10938 https://doi.org/10.7717/peerj.10938
date submitted: 2020-09-29
date accepted: 2021-01-21
issued: 2021-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wielgat
  given name: Paweł
author list: Agent
  family name: Kalinowska
  given name: Dominika
author list: Agent
  family name: Szymkiewicz
  given name: Adam
author list: Agent
  family name: Zima
  given name: Piotr
author list: Agent
  family name: Jaworska-Szulc
  given name: Beata
author list: Agent
  family name: Wojciechowska
  given name: Ewa
author list: Agent
  family name: Nawrot
  given name: Nicole
author list: Agent
  family name: Matej-Lukowicz
  given name: Karolina
author list: Agent
  family name: Dzierzbicka-Glowacka
  given name: Lidia Anita
doi: 10.7717/peerj.10938
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-25
copyright: ©2021 Wielgat et al.
attribution name: Wielgat et al.

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

Agent
family name: Skillings
given name: Derek

Agent
family name: Stock
given name: Willem

Agent
family name: Sunagawa
given name: Shinichi

Agent
family name: Toulza
given name: Eve

Agent
family name: Vorobev
given name: Alexey

Agent
family name: Leblanc
given name: Catherine

Agent
family name: Not
given name: Fabrice