PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Distribution, habitat suitability, conservation state and natural history of endangered salamander Bolitoglossa pandi
items: Description of the unusual digestive tract of Platax orbicularis and the potential impact of Tenacibaculum maritimum infection
items: Characterization of a high-resolution breath acetone meter for ketosis monitoring
items: A new species of Scapholeberis Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology
items: A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma
items: The lemur baseline: how lemurs compare to monkeys and apes in the Primate Cognition Test Battery
items: Identification and expression profiles of candidate chemosensory receptors in Histia rhodope (Lepidoptera: Zygaenidae)
items: Saururus chinensis-controlled allergic pulmonary disease through NF-κB/COX-2 and PGE2 pathways
items: Drought stress strengthens the link between chlorophyll fluorescence parameters and photosynthetic traits
items: A comparison of common metrics used to quantify the effectiveness of conservation interventions

Distribution, habitat suitability, conservation state and natural history of endangered salamander Bolitoglossa pandi
type: item
type: AcademicArticle
description: Background Pandi’s mushroom-tongue salamander (Bolitoglossa pandi) is one of the threatened amphibians in South America, as well as a flagship species for the Colombian conservation agenda. This species is endemic to the Andean cloud forests of the western slope of the Cordillera Oriental of Colombia, occurring only in the department of Cundinamarca within a narrow elevational range. At night, B. pandi can be seen perching on the upper side of leaves at heights ranging from ground level to 2.5 m. During the day, it can be found under leaf litter or cover objects. Few studies have provided relevant information that can help the Colombian government to formulate lines of action for the conservation of this species; consequently, its threat assessments so far have been based on very limited information. Methods We conducted surveys for salamanders in four municipalities of Cundinamarca, Colombia, using two approaches: visual encounter surveys (Guaduas and Villeta) and the basic sampling protocol for single-species occupancy modeling (Supatá and Venecia). Multivariate analyses were employed to explore the correlation between habitat structure and natural history traits, abundance, and detection/non-detection of B. pandi. We evaluated the B. pandi activity pattern through kernel density curves for each sampling occasion and explored the variability of salamander abundance during their activity period by performing a nested ANOVA. Results We report the discovery of two new populations of B. pandi, which represent the most northwestern records known. A significant correlation between body length, body mass, and habitat structure was observed. Multivariate analyses indicated that leaf litter depth, mean temperature, percent vegetation cover, and altitude were the habitat variables that together explained 60.3% of the B. pandi abundance variability, as well as the main determinants of its optimal habitat. Bolitoglossa pandi exhibits an activity pattern characterized by two m…
format: application/pdf
format: text/html
creator: Teddy Angarita-Sierra
creator: M. Argenis Bonilla-Gómez
creator: David A. Sánchez
creator: Andres R. Acosta-Galvis
creator: Hefzi Medina-Ovalle
creator: Anggi Solano-Moreno
creator: Simon Ulloa-Rengifo
creator: Daniela Guevara-Guevara
creator: Juan J. Torres-Ramirez
creator: Sebastián Curaca-Fierro
creator: Diego M. Cabrera-Amaya
creator: Jhon A. Infante-Betancour
creator: Luisa F. Londoño-Montaño
creator: Diana X. Albarán-Montoya
creator: Lesly R. Peña-Baez
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9901
publisher: PeerJ Inc.
rights: © 2020 Angarita-Sierra et al.
abstract: Background Pandi’s mushroom-tongue salamander (Bolitoglossa pandi) is one of the threatened amphibians in South America, as well as a flagship species for the Colombian conservation agenda. This species is endemic to the Andean cloud forests of the western slope of the Cordillera Oriental of Colombia, occurring only in the department of Cundinamarca within a narrow elevational range. At night, B. pandi can be seen perching on the upper side of leaves at heights ranging from ground level to 2.5 m. During the day, it can be found under leaf litter or cover objects. Few studies have provided relevant information that can help the Colombian government to formulate lines of action for the conservation of this species; consequently, its threat assessments so far have been based on very limited information. Methods We conducted surveys for salamanders in four municipalities of Cundinamarca, Colombia, using two approaches: visual encounter surveys (Guaduas and Villeta) and the basic sampling protocol for single-species occupancy modeling (Supatá and Venecia). Multivariate analyses were employed to explore the correlation between habitat structure and natural history traits, abundance, and detection/non-detection of B. pandi. We evaluated the B. pandi activity pattern through kernel density curves for each sampling occasion and explored the variability of salamander abundance during their activity period by performing a nested ANOVA. Results We report the discovery of two new populations of B. pandi, which represent the most northwestern records known. A significant correlation between body length, body mass, and habitat structure was observed. Multivariate analyses indicated that leaf litter depth, mean temperature, percent vegetation cover, and altitude were the habitat variables that together explained 60.3% of the B. pandi abundance variability, as well as the main determinants of its optimal habitat. Bolitoglossa pandi exhibits an activity pattern characterized by two m…
bibliographic citation: Angarita-Sierra et al. (2020) Distribution, habitat suitability, conservation state and natural history of endangered salamander Bolitoglossa pandi. PeerJ 8:e9901 https://doi.org/10.7717/peerj.9901
date submitted: 2020-04-20
date accepted: 2020-08-18
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Angarita-Sierra
  given name: Teddy
author list: Agent
  family name: Bonilla-Gómez
  given name: M. Argenis
author list: Agent
  family name: Sánchez
  given name: David A.
author list: Agent
  family name: Acosta-Galvis
  given name: Andres R.
author list: Agent
  family name: Medina-Ovalle
  given name: Hefzi
author list: Agent
  family name: Solano-Moreno
  given name: Anggi
author list: Agent
  family name: Ulloa-Rengifo
  given name: Simon
author list: Agent
  family name: Guevara-Guevara
  given name: Daniela
author list: Agent
  family name: Torres-Ramirez
  given name: Juan J.
author list: Agent
  family name: Curaca-Fierro
  given name: Sebastián
author list: Agent
  family name: Cabrera-Amaya
  given name: Diego M.
author list: Agent
  family name: Infante-Betancour
  given name: Jhon A.
author list: Agent
  family name: Londoño-Montaño
  given name: Luisa F.
author list: Agent
  family name: Albarán-Montoya
  given name: Diana X.
author list: Agent
  family name: Peña-Baez
  given name: Lesly R.
doi: 10.7717/peerj.9901
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Angarita-Sierra et al.
attribution name: Angarita-Sierra et al.

Description of the unusual digestive tract of Platax orbicularis and the potential impact of Tenacibaculum maritimum infection
type: item
type: AcademicArticle
description: Background Ephippidae fish are characterized by a discoid shape with a very small visceral cavity. Among them Platax orbicularis has a high economic potential due to its flesh quality and flesh to carcass ratio. Nonetheless, the development of its aquaculture is limited by high mortality rates, especially due to Tenacibaculum maritimum infection, occurring one to three weeks after the transfer of fishes from bio-secure land-based aquaculture system to the lagoon cages for growth. Among the lines of defense against this microbial infection, the gastrointestinal tract (GIT) is less studied. The knowledge about the morphofunctional anatomy of this organ in P. orbicularis is still scarce. Therefore, the aims of this study are to characterize the GIT in non-infected P. orbicularis juveniles to then investigate the impact of T. maritimum on this multifunctional organ. Methods In the first place, the morpho-anatomy of the GIT in non-infected individuals was characterized using various histological techniques. Then, infected individuals, experimentally challenged by T. maritimum were analysed and compared to the previously established GIT reference. Results The overlapped shape of the GIT of P. orbicularis is probably due to its constrained compaction in a narrow visceral cavity. Firstly, the GIT was divided into 10 sections, from the esophagus to the rectum. For each section, the structure of the walls was characterized, with a focus on mucus secretions and the presence of the Na+/K+ ATPase pump. An identification key allowing the characterization of the GIT sections using in toto histology is given. Secondly, individuals challenged with T. maritimum exhibited differences in mucus type and proportion and, modifications in the mucosal and muscle layers. These changes could induce an imbalance in the trade-off between the GIT functions which may be in favour of protection and immunity to the disadvantage of nutrition capacities.
format: application/pdf
format: text/html
creator: Maud Alix
creator: Eric Gasset
creator: Agnes Bardon-Albaret
creator: Jean Noel
creator: Nelly Pirot
creator: Valérie Perez
creator: Denis Coves
creator: Denis Saulnier
creator: Jehan-Hervé Lignot
creator: Patricia N. Cucchi
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.9966
publisher: PeerJ Inc.
rights: © 2020 Alix et al.
abstract: Background Ephippidae fish are characterized by a discoid shape with a very small visceral cavity. Among them Platax orbicularis has a high economic potential due to its flesh quality and flesh to carcass ratio. Nonetheless, the development of its aquaculture is limited by high mortality rates, especially due to Tenacibaculum maritimum infection, occurring one to three weeks after the transfer of fishes from bio-secure land-based aquaculture system to the lagoon cages for growth. Among the lines of defense against this microbial infection, the gastrointestinal tract (GIT) is less studied. The knowledge about the morphofunctional anatomy of this organ in P. orbicularis is still scarce. Therefore, the aims of this study are to characterize the GIT in non-infected P. orbicularis juveniles to then investigate the impact of T. maritimum on this multifunctional organ. Methods In the first place, the morpho-anatomy of the GIT in non-infected individuals was characterized using various histological techniques. Then, infected individuals, experimentally challenged by T. maritimum were analysed and compared to the previously established GIT reference. Results The overlapped shape of the GIT of P. orbicularis is probably due to its constrained compaction in a narrow visceral cavity. Firstly, the GIT was divided into 10 sections, from the esophagus to the rectum. For each section, the structure of the walls was characterized, with a focus on mucus secretions and the presence of the Na+/K+ ATPase pump. An identification key allowing the characterization of the GIT sections using in toto histology is given. Secondly, individuals challenged with T. maritimum exhibited differences in mucus type and proportion and, modifications in the mucosal and muscle layers. These changes could induce an imbalance in the trade-off between the GIT functions which may be in favour of protection and immunity to the disadvantage of nutrition capacities.
bibliographic citation: Alix et al. (2020) Description of the unusual digestive tract of Platax orbicularis and the potential impact of Tenacibaculum maritimum infection. PeerJ 8:e9966 https://doi.org/10.7717/peerj.9966
date submitted: 2020-03-24
date accepted: 2020-08-26
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alix
  given name: Maud
author list: Agent
  family name: Gasset
  given name: Eric
author list: Agent
  family name: Bardon-Albaret
  given name: Agnes
author list: Agent
  family name: Noel
  given name: Jean
author list: Agent
  family name: Pirot
  given name: Nelly
author list: Agent
  family name: Perez
  given name: Valérie
author list: Agent
  family name: Coves
  given name: Denis
author list: Agent
  family name: Saulnier
  given name: Denis
author list: Agent
  family name: Lignot
  given name: Jehan-Hervé
author list: Agent
  family name: Cucchi
  given name: Patricia N.
doi: 10.7717/peerj.9966
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Alix et al.
attribution name: Alix et al.

Characterization of a high-resolution breath acetone meter for ketosis monitoring
type: item
type: AcademicArticle
description: Background The ketone bodies beta-hydroxybutyrate (BHB) and acetone are endogenous products of fatty acid metabolism. Although ketone levels can be monitored by measuring either blood BHB or breath acetone, determining the precise correlation between these two measurement methods has been challenging. The purpose of this study is to characterize the performance of a novel portable breath acetone meter (PBAM) developed by Readout, Inc., to compare single versus multiple daily ketone measurements, and to compare breath acetone (BrAce) and blood BHB measurements. Methods We conducted a 14-day prospective observational cohort study of 21 subjects attempting to follow either a low-carbohydrate/ketogenic or a standard diet. Subjects were asked to concurrently measure both blood BHB and BrAce five times per day and report the results using an online data entry system. We evaluated the utility of multiple daily measurements by calculating the coefficient of variation (CV) for each daily group of measurements. We calculated the correlation between coincident BrAce and blood BHB measurements using linear ordinary least squares regression analysis. We assessed the ability of the BrAce measurement to accurately predict blood BHB states using receiver operating characteristic (ROC) analysis. Finally, we calculated a daily ketone exposure (DKE) using the area under the curve (AUC) of a ketone concentration versus time graph and compared the DKE of BrAce and blood BHB using linear ordinary least squares regression. Results BrAce and blood BHB varied throughout the day by an average of 44% and 46%, respectively. The BrAce measurement accurately predicted whether blood BHB was greater than or less than the following thresholds: 0.3 mM (AUC = 0.898), 0.5 mM (AUC = 0.854), 1.0 mM (AUC = 0.887), and 1.5 mM (AUC = 0.935). Coincident BrAce and blood BHB measurements were moderately correlated with R2 = 0.57 (P < 0.0001), similar to literature reported values. However, daily ketone exposu…
format: application/pdf
format: text/html
creator: Donald J. Suntrup III
creator: Timothy V. Ratto
creator: Matt Ratto
creator: James P. McCarter
subject: Diabetes and Endocrinology
subject: Drugs and Devices
subject: Nutrition
subject: Respiratory Medicine
subject: Metabolic Sciences
description: doi:10.7717/peerj.9969
publisher: PeerJ Inc.
rights: © 2020 Suntrup III et al.
abstract: Background The ketone bodies beta-hydroxybutyrate (BHB) and acetone are endogenous products of fatty acid metabolism. Although ketone levels can be monitored by measuring either blood BHB or breath acetone, determining the precise correlation between these two measurement methods has been challenging. The purpose of this study is to characterize the performance of a novel portable breath acetone meter (PBAM) developed by Readout, Inc., to compare single versus multiple daily ketone measurements, and to compare breath acetone (BrAce) and blood BHB measurements. Methods We conducted a 14-day prospective observational cohort study of 21 subjects attempting to follow either a low-carbohydrate/ketogenic or a standard diet. Subjects were asked to concurrently measure both blood BHB and BrAce five times per day and report the results using an online data entry system. We evaluated the utility of multiple daily measurements by calculating the coefficient of variation (CV) for each daily group of measurements. We calculated the correlation between coincident BrAce and blood BHB measurements using linear ordinary least squares regression analysis. We assessed the ability of the BrAce measurement to accurately predict blood BHB states using receiver operating characteristic (ROC) analysis. Finally, we calculated a daily ketone exposure (DKE) using the area under the curve (AUC) of a ketone concentration versus time graph and compared the DKE of BrAce and blood BHB using linear ordinary least squares regression. Results BrAce and blood BHB varied throughout the day by an average of 44% and 46%, respectively. The BrAce measurement accurately predicted whether blood BHB was greater than or less than the following thresholds: 0.3 mM (AUC = 0.898), 0.5 mM (AUC = 0.854), 1.0 mM (AUC = 0.887), and 1.5 mM (AUC = 0.935). Coincident BrAce and blood BHB measurements were moderately correlated with R2 = 0.57 (P < 0.0001), similar to literature reported values. However, daily ketone exposu…
bibliographic citation: Suntrup III et al. (2020) Characterization of a high-resolution breath acetone meter for ketosis monitoring. PeerJ 8:e9969 https://doi.org/10.7717/peerj.9969
date submitted: 2020-04-21
date accepted: 2020-08-26
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Suntrup III
  given name: Donald J.
author list: Agent
  family name: Ratto
  given name: Timothy V.
author list: Agent
  family name: Ratto
  given name: Matt
author list: Agent
  family name: McCarter
  given name: James P.
doi: 10.7717/peerj.9969
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Suntrup III et al.
attribution name: Suntrup III et al.

A new species of Scapholeberis Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology
type: item
type: AcademicArticle
description: Background The Amazon basin is recognized as one of the most complex and species-rich freshwater environments globally. The diversity of zooplankton here remains unknown, with many species undescribed. Methods Here, we describe a new species of Scapholeberis Schoedler, 1858 (Cladocera: Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon Basin, collected with recently designed light traps. The description is based on detailed morphology (based on SEM and light microscopy) of parthenogenetic females, ephippial females, males, and molecular data based on the COI gene. Results Scapholeberis yahuarcaquensis n. sp. has a combination of characters present in Scapholeberis kingi Sars, 1888 and Scapholeberis armata freyi Dumont & Pensaert, 1983. These are a trilobate rostrum, with the middle lobe well developed with sides straight to relatively rounded, the presence of an elongated slit frontal head pore, a dorsal pore in the juncture of the cephalic shield and the valves, and a single denticulate membrane at the posterior rim of the valves, with stronger setae in the last third. The unique characters of the parthenogenetic females are ventral sucker with delicate triangles. Each has a filament-like projection in the lamellae’s inner side and an external section forming convex folds with denticle-like projections in the middle zone of the sucker-plate. There is a peculiar pitted sculpture in the ephippial females and a strong projection in the front of it. The male hook on the limb I with a blunt tip, a quirky lamella-like outgrow in the proximal side, and a paddle with well-developed spines scattered on its surface. The ventral sucker-lamellae in the male is much more developed than the female. The COI gene sequences showed an interspecific mean genetic divergence of 16.4% between S. yahuarcaquensis n. sp. and the closest species S. freyi from Mexico, supporting our results. A coalescence analysis and Barcode Index Number also support the new species based on …
format: application/pdf
format: text/html
creator: Camilo Andrade-Sossa
creator: Lorena Buitron-Caicedo
creator: Manuel Elías-Gutiérrez
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Taxonomy
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.9989
publisher: PeerJ Inc.
rights: © 2020 Andrade-Sossa et al.
abstract: Background The Amazon basin is recognized as one of the most complex and species-rich freshwater environments globally. The diversity of zooplankton here remains unknown, with many species undescribed. Methods Here, we describe a new species of Scapholeberis Schoedler, 1858 (Cladocera: Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon Basin, collected with recently designed light traps. The description is based on detailed morphology (based on SEM and light microscopy) of parthenogenetic females, ephippial females, males, and molecular data based on the COI gene. Results Scapholeberis yahuarcaquensis n. sp. has a combination of characters present in Scapholeberis kingi Sars, 1888 and Scapholeberis armata freyi Dumont & Pensaert, 1983. These are a trilobate rostrum, with the middle lobe well developed with sides straight to relatively rounded, the presence of an elongated slit frontal head pore, a dorsal pore in the juncture of the cephalic shield and the valves, and a single denticulate membrane at the posterior rim of the valves, with stronger setae in the last third. The unique characters of the parthenogenetic females are ventral sucker with delicate triangles. Each has a filament-like projection in the lamellae’s inner side and an external section forming convex folds with denticle-like projections in the middle zone of the sucker-plate. There is a peculiar pitted sculpture in the ephippial females and a strong projection in the front of it. The male hook on the limb I with a blunt tip, a quirky lamella-like outgrow in the proximal side, and a paddle with well-developed spines scattered on its surface. The ventral sucker-lamellae in the male is much more developed than the female. The COI gene sequences showed an interspecific mean genetic divergence of 16.4% between S. yahuarcaquensis n. sp. and the closest species S. freyi from Mexico, supporting our results. A coalescence analysis and Barcode Index Number also support the new species based on …
bibliographic citation: Andrade-Sossa et al. (2020) A new species of Scapholeberis Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology. PeerJ 8:e9989 https://doi.org/10.7717/peerj.9989
date submitted: 2020-06-25
date accepted: 2020-08-28
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Andrade-Sossa
  given name: Camilo
author list: Agent
  family name: Buitron-Caicedo
  given name: Lorena
author list: Agent
  family name: Elías-Gutiérrez
  given name: Manuel
doi: 10.7717/peerj.9989
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: © 2020 Andrade-Sossa et al.
attribution name: Andrade-Sossa et al.

A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma
type: item
type: AcademicArticle
description: Background The highest rate of cancer-related deaths worldwide is from lung adenocarcinoma (LUAD) annually. Metabolism was associated with tumorigenesis and cancer development. Metabolic-related genes may be important biomarkers and metabolic therapeutic targets for LUAD. Materials and Methods In this study, the gleaned cohort included LUAD RNA-SEQ data from the Cancer Genome Atlas (TCGA) and corresponding clinical data (n = 445). The training cohort was utilized to model construction, and data from the Gene Expression Omnibus (GEO, GSE30219 cohort, n = 83; GEO, GSE72094, n = 393) were regarded as a testing cohort and utilized for validation. First, we used a lasso-penalized Cox regression analysis to build a new metabolic-related signature for predicting the prognosis of LUAD patients. Next, we verified the metabolic gene model by survival analysis, C-index, receiver operating characteristic (ROC) analysis. Univariate and multivariate Cox regression analyses were utilized to verify the gene signature as an independent prognostic factor. Finally, we constructed a nomogram and performed gene set enrichment analysis to facilitate subsequent clinical applications and molecular mechanism analysis. Result Patients with higher risk scores showed significantly associated with poorer survival. We also verified the signature can work as an independent prognostic factor for LUAD survival. The nomogram showed better clinical application performance for LUAD patient prognostic prediction. Finally, KEGG and GO pathways enrichment analyses suggested several especially enriched pathways, which may be helpful for us investigative the underlying mechanisms.
format: application/pdf
format: text/html
creator: Zhenyu Zhao
creator: Boxue He
creator: Qidong Cai
creator: Pengfei Zhang
creator: Xiong Peng
creator: Yuqian Zhang
creator: Hui Xie
creator: Xiang Wang
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.10008
publisher: PeerJ Inc.
rights: © 2020 Zhao et al.
abstract: Background The highest rate of cancer-related deaths worldwide is from lung adenocarcinoma (LUAD) annually. Metabolism was associated with tumorigenesis and cancer development. Metabolic-related genes may be important biomarkers and metabolic therapeutic targets for LUAD. Materials and Methods In this study, the gleaned cohort included LUAD RNA-SEQ data from the Cancer Genome Atlas (TCGA) and corresponding clinical data (n = 445). The training cohort was utilized to model construction, and data from the Gene Expression Omnibus (GEO, GSE30219 cohort, n = 83; GEO, GSE72094, n = 393) were regarded as a testing cohort and utilized for validation. First, we used a lasso-penalized Cox regression analysis to build a new metabolic-related signature for predicting the prognosis of LUAD patients. Next, we verified the metabolic gene model by survival analysis, C-index, receiver operating characteristic (ROC) analysis. Univariate and multivariate Cox regression analyses were utilized to verify the gene signature as an independent prognostic factor. Finally, we constructed a nomogram and performed gene set enrichment analysis to facilitate subsequent clinical applications and molecular mechanism analysis. Result Patients with higher risk scores showed significantly associated with poorer survival. We also verified the signature can work as an independent prognostic factor for LUAD survival. The nomogram showed better clinical application performance for LUAD patient prognostic prediction. Finally, KEGG and GO pathways enrichment analyses suggested several especially enriched pathways, which may be helpful for us investigative the underlying mechanisms.
bibliographic citation: Zhao et al. (2020) A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma. PeerJ 8:e10008 https://doi.org/10.7717/peerj.10008
date submitted: 2020-05-14
date accepted: 2020-08-31
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Zhenyu
author list: Agent
  family name: He
  given name: Boxue
author list: Agent
  family name: Cai
  given name: Qidong
author list: Agent
  family name: Zhang
  given name: Pengfei
author list: Agent
  family name: Peng
  given name: Xiong
author list: Agent
  family name: Zhang
  given name: Yuqian
author list: Agent
  family name: Xie
  given name: Hui
author list: Agent
  family name: Wang
  given name: Xiang
doi: 10.7717/peerj.10008
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Zhao et al.
attribution name: Zhao et al.

The lemur baseline: how lemurs compare to monkeys and apes in the Primate Cognition Test Battery
type: item
type: AcademicArticle
description: Primates have relatively larger brains than other mammals even though brain tissue is energetically costly. Comparative studies of variation in cognitive skills allow testing of evolutionary hypotheses addressing socioecological factors driving the evolution of primate brain size. However, data on cognitive abilities for meaningful interspecific comparisons are only available for haplorhine primates (great apes, Old- and New World monkeys) although strepsirrhine primates (lemurs and lorises) serve as the best living models of ancestral primate cognitive skills, linking primates to other mammals. To begin filling this gap, we tested members of three lemur species (Microcebus murinus, Varecia variegata, Lemur catta) with the Primate Cognition Test Battery, a comprehensive set of experiments addressing physical and social cognitive skills that has previously been used in studies of haplorhines. We found no significant differences in cognitive performance among lemur species and, surprisingly, their average performance was not different from that of haplorhines in many aspects. Specifically, lemurs’ overall performance was inferior in the physical domain but matched that of haplorhines in the social domain. These results question a clear-cut link between brain size and cognitive skills, suggesting a more domain-specific distribution of cognitive abilities in primates, and indicate more continuity in cognitive abilities across primate lineages than previously thought.
format: application/pdf
format: text/html
creator: Claudia Fichtel
creator: Klara Dinter
creator: Peter M. Kappeler
subject: Animal Behavior
subject: Anthropology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.10025
publisher: PeerJ Inc.
rights: © 2020 Fichtel et al.
abstract: Primates have relatively larger brains than other mammals even though brain tissue is energetically costly. Comparative studies of variation in cognitive skills allow testing of evolutionary hypotheses addressing socioecological factors driving the evolution of primate brain size. However, data on cognitive abilities for meaningful interspecific comparisons are only available for haplorhine primates (great apes, Old- and New World monkeys) although strepsirrhine primates (lemurs and lorises) serve as the best living models of ancestral primate cognitive skills, linking primates to other mammals. To begin filling this gap, we tested members of three lemur species (Microcebus murinus, Varecia variegata, Lemur catta) with the Primate Cognition Test Battery, a comprehensive set of experiments addressing physical and social cognitive skills that has previously been used in studies of haplorhines. We found no significant differences in cognitive performance among lemur species and, surprisingly, their average performance was not different from that of haplorhines in many aspects. Specifically, lemurs’ overall performance was inferior in the physical domain but matched that of haplorhines in the social domain. These results question a clear-cut link between brain size and cognitive skills, suggesting a more domain-specific distribution of cognitive abilities in primates, and indicate more continuity in cognitive abilities across primate lineages than previously thought.
bibliographic citation: Fichtel et al. (2020) The lemur baseline: how lemurs compare to monkeys and apes in the Primate Cognition Test Battery. PeerJ 8:e10025 https://doi.org/10.7717/peerj.10025
date submitted: 2020-05-04
date accepted: 2020-09-02
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fichtel
  given name: Claudia
author list: Agent
  family name: Dinter
  given name: Klara
author list: Agent
  family name: Kappeler
  given name: Peter M.
doi: 10.7717/peerj.10025
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Fichtel et al.
attribution name: Fichtel et al.

Identification and expression profiles of candidate chemosensory receptors in Histia rhodope (Lepidoptera: Zygaenidae)
type: item
type: AcademicArticle
description: Insect olfaction and vision play important roles in survival and reproduction. Diurnal butterflies mainly rely on visual cues whereas nocturnal moths rely on olfactory signals to locate external resources. Histia rhodope Cramer (Lepidoptera: Zygaenidae) is an important pest of the landscape tree Bischofia polycarpa in China and other Southeast Asian regions. As a diurnal moth, H. rhodope represents a suitable model for studying the evolutionary shift from olfactory to visual communication. However, only a few chemosensory soluble proteins have been characterized and information on H. rhodope chemoreceptor genes is currently lacking. In this study, we identified 45 odorant receptors (ORs), nine ionotropic receptors (IRs), eight gustatory receptors (GRs) and two sensory neuron membrane proteins (SNMPs) from our previously acquired H. rhodope antennal transcriptomic data. The number of chemoreceptors of H. rhodope was less compared with that found in many nocturnal moths. Some specific chemoreceptors such as OR co-receptor (ORco), ionotropic receptors co-receptor, CO2 receptors, sugar receptors and bitter receptors were predicted by phylogenetic analysis. Notably, two candidate pheromone receptors (PRs) were identified within a novel PR lineage. qRT-PCR results showed that almost all tested genes (22/24) were predominantly expressed in antennae, indicating that they may be important in olfactory function. Among these antennae-enriched genes, six ORs, five IRs and two GRs displayed female-biased expression, while two ORs displayed male-biased expression. Additionally, HrhoIR75q.2 and HrhoGR67 were more highly expressed in heads and legs. This study enriches the olfactory gene inventory of H. rhodope and provides the foundation for further research of the chemoreception mechanism in diurnal moths.
format: application/pdf
format: text/html
creator: Haibo Yang
creator: Junfeng Dong
creator: Ya-Lan Sun
creator: Zhenjie Hu
creator: Qi-Hui Lyu
creator: Dingxu Li
subject: Bioinformatics
subject: Entomology
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10035
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Insect olfaction and vision play important roles in survival and reproduction. Diurnal butterflies mainly rely on visual cues whereas nocturnal moths rely on olfactory signals to locate external resources. Histia rhodope Cramer (Lepidoptera: Zygaenidae) is an important pest of the landscape tree Bischofia polycarpa in China and other Southeast Asian regions. As a diurnal moth, H. rhodope represents a suitable model for studying the evolutionary shift from olfactory to visual communication. However, only a few chemosensory soluble proteins have been characterized and information on H. rhodope chemoreceptor genes is currently lacking. In this study, we identified 45 odorant receptors (ORs), nine ionotropic receptors (IRs), eight gustatory receptors (GRs) and two sensory neuron membrane proteins (SNMPs) from our previously acquired H. rhodope antennal transcriptomic data. The number of chemoreceptors of H. rhodope was less compared with that found in many nocturnal moths. Some specific chemoreceptors such as OR co-receptor (ORco), ionotropic receptors co-receptor, CO2 receptors, sugar receptors and bitter receptors were predicted by phylogenetic analysis. Notably, two candidate pheromone receptors (PRs) were identified within a novel PR lineage. qRT-PCR results showed that almost all tested genes (22/24) were predominantly expressed in antennae, indicating that they may be important in olfactory function. Among these antennae-enriched genes, six ORs, five IRs and two GRs displayed female-biased expression, while two ORs displayed male-biased expression. Additionally, HrhoIR75q.2 and HrhoGR67 were more highly expressed in heads and legs. This study enriches the olfactory gene inventory of H. rhodope and provides the foundation for further research of the chemoreception mechanism in diurnal moths.
bibliographic citation: Yang et al. (2020) Identification and expression profiles of candidate chemosensory receptors in Histia rhodope (Lepidoptera: Zygaenidae). PeerJ 8:e10035 https://doi.org/10.7717/peerj.10035
date submitted: 2020-05-14
date accepted: 2020-09-03
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Haibo
author list: Agent
  family name: Dong
  given name: Junfeng
author list: Agent
  family name: Sun
  given name: Ya-Lan
author list: Agent
  family name: Hu
  given name: Zhenjie
author list: Agent
  family name: Lyu
  given name: Qi-Hui
author list: Agent
  family name: Li
  given name: Dingxu
doi: 10.7717/peerj.10035
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Saururus chinensis-controlled allergic pulmonary disease through NF-κB/COX-2 and PGE2 pathways
type: item
type: AcademicArticle
description: Saururus chinensis is a perennial herb found in the northeastern regions of Asia, including Korea, China, and Japan, and is used in traditional medicine. Studies have identified the four major constituents in Saururus chinensis water extract (LHF618®) as miquelianin (11.75 ± 0.092 mg/g), rutin (1.20 ± 0.008 mg/g), quercitrin (2.38 ± 0.389 mg/g), and quercetin (0.068 ± 0.017 mg/g). Saururus chinensis can improve the symptoms of ovalbumin- or fine dust-induced allergic pulmonary disease by suppressing the effects of WBCs and neutrophils in BALF and IgE in the serum. Saururus chinensis dose-dependently recovered morphological changes such as mucous hyper secretion (from 2.7 ± 0.46 to 0.6 ± 0.65), pulmonary epithelial cell hyperplasia (from 2.4 ± 0.55 to 0.7 ± 0.67), and inflammatory cell infiltration (from 2.3 ± 0.45 to 0.6 ± 0.43), and effectively controlled cDNA levels and protein levels of IL-13. It inhibited NF-κB translocation and COX-2 protein synthesis and suppressed the expression of PGE2. Our results show that Saururus chinensis controlled allergic pulmonary disease via the anti-inflammatory pathways, NF-κB/COX-2 and PGE2. Saururus chinensis may be a promising drug candidate against fine dust-induced allergic pulmonary disease.
format: application/pdf
format: text/html
creator: MiKyung Song
creator: Soon-Young Lee
creator: Minhee Kim
creator: Sangwoug Park
creator: Juyeon Park
creator: Yongbum Kwon
creator: Dae-Hun Park
subject: Biochemistry
subject: Allergy and Clinical Immunology
subject: Drugs and Devices
subject: Respiratory Medicine
description: doi:10.7717/peerj.10043
publisher: PeerJ Inc.
rights: © 2020 Song et al.
abstract: Saururus chinensis is a perennial herb found in the northeastern regions of Asia, including Korea, China, and Japan, and is used in traditional medicine. Studies have identified the four major constituents in Saururus chinensis water extract (LHF618®) as miquelianin (11.75 ± 0.092 mg/g), rutin (1.20 ± 0.008 mg/g), quercitrin (2.38 ± 0.389 mg/g), and quercetin (0.068 ± 0.017 mg/g). Saururus chinensis can improve the symptoms of ovalbumin- or fine dust-induced allergic pulmonary disease by suppressing the effects of WBCs and neutrophils in BALF and IgE in the serum. Saururus chinensis dose-dependently recovered morphological changes such as mucous hyper secretion (from 2.7 ± 0.46 to 0.6 ± 0.65), pulmonary epithelial cell hyperplasia (from 2.4 ± 0.55 to 0.7 ± 0.67), and inflammatory cell infiltration (from 2.3 ± 0.45 to 0.6 ± 0.43), and effectively controlled cDNA levels and protein levels of IL-13. It inhibited NF-κB translocation and COX-2 protein synthesis and suppressed the expression of PGE2. Our results show that Saururus chinensis controlled allergic pulmonary disease via the anti-inflammatory pathways, NF-κB/COX-2 and PGE2. Saururus chinensis may be a promising drug candidate against fine dust-induced allergic pulmonary disease.
bibliographic citation: Song et al. (2020) Saururus chinensis-controlled allergic pulmonary disease through NF-κB/COX-2 and PGE2 pathways. PeerJ 8:e10043 https://doi.org/10.7717/peerj.10043
date submitted: 2020-04-17
date accepted: 2020-09-04
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: MiKyung
author list: Agent
  family name: Lee
  given name: Soon-Young
author list: Agent
  family name: Kim
  given name: Minhee
author list: Agent
  family name: Park
  given name: Sangwoug
author list: Agent
  family name: Park
  given name: Juyeon
author list: Agent
  family name: Kwon
  given name: Yongbum
author list: Agent
  family name: Park
  given name: Dae-Hun
doi: 10.7717/peerj.10043
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Song et al.
attribution name: Song et al.

Drought stress strengthens the link between chlorophyll fluorescence parameters and photosynthetic traits
type: item
type: AcademicArticle
description: Chlorophyll fluorescence (ChlF) has been used to understand photosynthesis and its response to climate change, particularly with satellite-based data. However, it remains unclear how the ChlF ratio and photosynthesis are linked at the leaf level under drought stress. Here, we examined the link between ChlF ratio and photosynthesis at the leaf level by measuring photosynthetic traits, such as net CO2 assimilation rate (An), the maximum carboxylation rate of Rubisco (Vcmax), the maximum rate of electron transport (Jmax), stomatal conductance (gs) and total chlorophyll content (Chlt). The ChlF ratio of the leaf level such as maximum quantum efficiency of PSII (Fv/Fm) is based on fluorescence kinetics. ChlF intensity ratio (LD685/LD740) based on spectrum analysis was obtained. We found that a combination of the stomatal limitation, non-stomatal limitation, and Chlt regulated leaf photosynthesis under drought stress, while Jmax and Chlt governed the ChlF ratio. A significant link between the ChlF ratio and An was found under drought stress while no significant correlation in the control, which indicated that drought stress strengthens the link between the ChlF ratio and photosynthetic traits. These results suggest that the ChlF ratio can be a powerful tool to track photosynthetic traits of terrestrial ecosystems under drought stress.
format: application/pdf
format: text/html
creator: Jie Zhuang
creator: Yonglin Wang
creator: Yonggang Chi
creator: Lei Zhou
creator: Jijing Chen
creator: Wen Zhou
creator: Jun Song
creator: Ning Zhao
creator: Jianxi Ding
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.10046
publisher: PeerJ Inc.
rights: © 2020 Zhuang et al.
abstract: Chlorophyll fluorescence (ChlF) has been used to understand photosynthesis and its response to climate change, particularly with satellite-based data. However, it remains unclear how the ChlF ratio and photosynthesis are linked at the leaf level under drought stress. Here, we examined the link between ChlF ratio and photosynthesis at the leaf level by measuring photosynthetic traits, such as net CO2 assimilation rate (An), the maximum carboxylation rate of Rubisco (Vcmax), the maximum rate of electron transport (Jmax), stomatal conductance (gs) and total chlorophyll content (Chlt). The ChlF ratio of the leaf level such as maximum quantum efficiency of PSII (Fv/Fm) is based on fluorescence kinetics. ChlF intensity ratio (LD685/LD740) based on spectrum analysis was obtained. We found that a combination of the stomatal limitation, non-stomatal limitation, and Chlt regulated leaf photosynthesis under drought stress, while Jmax and Chlt governed the ChlF ratio. A significant link between the ChlF ratio and An was found under drought stress while no significant correlation in the control, which indicated that drought stress strengthens the link between the ChlF ratio and photosynthetic traits. These results suggest that the ChlF ratio can be a powerful tool to track photosynthetic traits of terrestrial ecosystems under drought stress.
bibliographic citation: Zhuang et al. (2020) Drought stress strengthens the link between chlorophyll fluorescence parameters and photosynthetic traits. PeerJ 8:e10046 https://doi.org/10.7717/peerj.10046
date submitted: 2020-02-25
date accepted: 2020-09-04
issued: 2020-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhuang
  given name: Jie
author list: Agent
  family name: Wang
  given name: Yonglin
author list: Agent
  family name: Chi
  given name: Yonggang
author list: Agent
  family name: Zhou
  given name: Lei
author list: Agent
  family name: Chen
  given name: Jijing
author list: Agent
  family name: Zhou
  given name: Wen
author list: Agent
  family name: Song
  given name: Jun
author list: Agent
  family name: Zhao
  given name: Ning
author list: Agent
  family name: Ding
  given name: Jianxi
doi: 10.7717/peerj.10046
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-24
copyright: ©2020 Zhuang et al.
attribution name: Zhuang et al.

A comparison of common metrics used to quantify the effectiveness of conservation interventions
type: item
type: AcademicArticle
description: Background Evidence-based conservation is urgently needed to identify, apply and promote effective interventions for mitigation of threats and recovery of the natural environment. Estimation of intervention effectiveness is subject to robust study design and statistical analysis, and much progress is documented in these fields. In contrast, little is understood about the accuracy and biases (underestimation and overestimation) of different effectiveness metrics and how they are affected by sample size. Methods In this study, a dataset (n = 500 cases) consisting of random, positive, integer numbers was simulated to produce frequency input data for the 2 × 2 contingency table. For each case, three metrics of the relative risk, odds ratio and the magnitude of change were calculated, their disparity was estimated and the characteristics of treatment (with intervention) and control (without intervention) samples significantly affecting this disparity were studied by means of linear regression. Further, four case studies from different conservation interventions are provided to support the results. Results The study has shown that the relative risk and the magnitude of change produce identical estimates of intervention effectiveness only when treatment and control samples are equal, or when the number of target outcomes (e.g., number of livestock killed by predators) in treatment sample reaches zero. In other situations, the magnitude of change gives overestimates or underestimates, depending on relationships between treatment and control sample sizes. The table summarizing the conditions of equalities and biases between these two metrics is provided. These conditions are valid for both reduction-aimed interventions reducing negative target outcomes (e.g., livestock protection to reduce livestock losses to predators) and for addition-aimed interventions increasing positive target outcomes (e.g., establishment of protected areas to increase species presence). No significan…
format: application/pdf
format: text/html
creator: Igor Khorozyan
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.9873
publisher: PeerJ Inc.
rights: © 2020 Khorozyan
abstract: Background Evidence-based conservation is urgently needed to identify, apply and promote effective interventions for mitigation of threats and recovery of the natural environment. Estimation of intervention effectiveness is subject to robust study design and statistical analysis, and much progress is documented in these fields. In contrast, little is understood about the accuracy and biases (underestimation and overestimation) of different effectiveness metrics and how they are affected by sample size. Methods In this study, a dataset (n = 500 cases) consisting of random, positive, integer numbers was simulated to produce frequency input data for the 2 × 2 contingency table. For each case, three metrics of the relative risk, odds ratio and the magnitude of change were calculated, their disparity was estimated and the characteristics of treatment (with intervention) and control (without intervention) samples significantly affecting this disparity were studied by means of linear regression. Further, four case studies from different conservation interventions are provided to support the results. Results The study has shown that the relative risk and the magnitude of change produce identical estimates of intervention effectiveness only when treatment and control samples are equal, or when the number of target outcomes (e.g., number of livestock killed by predators) in treatment sample reaches zero. In other situations, the magnitude of change gives overestimates or underestimates, depending on relationships between treatment and control sample sizes. The table summarizing the conditions of equalities and biases between these two metrics is provided. These conditions are valid for both reduction-aimed interventions reducing negative target outcomes (e.g., livestock protection to reduce livestock losses to predators) and for addition-aimed interventions increasing positive target outcomes (e.g., establishment of protected areas to increase species presence). No significan…
bibliographic citation: Khorozyan (2020) A comparison of common metrics used to quantify the effectiveness of conservation interventions. PeerJ 8:e9873 https://doi.org/10.7717/peerj.9873
date submitted: 2020-07-03
date accepted: 2020-08-14
issued: 2020-09-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khorozyan
  given name: Igor
doi: 10.7717/peerj.9873
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-23
copyright: © 2020 Khorozyan
attribution name: Khorozyan

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