PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Tribe reassessment of the subhimalayan leafhopper genus Pseudosubhimalus (Homoptera: Cicadellidae) based on molecular phylogeny
items: Cyclodipeptides from Pseudomonas aeruginosa modulate the maize (Zea mays L.) root system and promote S6 ribosomal protein kinase activation
items: Early Agenian rhinocerotids from Wischberg (Canton Bern, Switzerland) and clarification of the systematics of the genus Diaceratherium
items: Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents
items: The effect of modulating the quantity of enzymes in a model ethanol pathway on metabolic flux in Synechocystis sp. PCC 6803
items: Endogenous testosterone correlates with parochial altruism in relation to costly punishment in different social settings
items: A real-world study on clinical predictors of relapse after hospitalized detoxification in a Chinese cohort with alcohol dependence
items: HiLDA: a statistical approach to investigate differences in mutational signatures
items: Nicotinamide riboside exerts protective effect against aging-induced NAFLD-like hepatic dysfunction in mice
items: Testing the function of dromaeosaurid (Dinosauria, Theropoda) ‘sickle claws’ through musculoskeletal modelling and optimization

Tribe reassessment of the subhimalayan leafhopper genus Pseudosubhimalus (Homoptera: Cicadellidae) based on molecular phylogeny
type: item
type: AcademicArticle
description: The phylogeny of the Pseudosubhimalus were investigated using of two different data sets, including 91 taxa and 3853 aligned nucleotide positions from the histone H3, 28S rDNA (D2 & D9–10 region). The results suggest the placement of genus in the tribe Ciacadulini, as it was clustered with Cicadulini genera. Relationships between genera of the Cicadulini were strongly supported and leads placement to tribe Cicadulini from Athysanini. Along with this, genus Pseudosubhimalus Ghauri is revised, and P. trilobatus sp. nov. (Himachal Pradesh: Katrain) is added, described from Indian subcontinent and deposited to National Pusa Collection, IARI, New Delhi, with repository number RRS1.
format: application/pdf
format: text/html
creator: GN Niranjana
creator: Naresh M. Meshram
creator: Pathour R. Shashank
creator: Stuti
creator: Tahseen Raza Hashmi
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.7162
publisher: PeerJ Inc.
rights: © 2019 Niranjana et al.
abstract: The phylogeny of the Pseudosubhimalus were investigated using of two different data sets, including 91 taxa and 3853 aligned nucleotide positions from the histone H3, 28S rDNA (D2 & D9–10 region). The results suggest the placement of genus in the tribe Ciacadulini, as it was clustered with Cicadulini genera. Relationships between genera of the Cicadulini were strongly supported and leads placement to tribe Cicadulini from Athysanini. Along with this, genus Pseudosubhimalus Ghauri is revised, and P. trilobatus sp. nov. (Himachal Pradesh: Katrain) is added, described from Indian subcontinent and deposited to National Pusa Collection, IARI, New Delhi, with repository number RRS1.
bibliographic citation: Niranjana et al. (2019) Tribe reassessment of the subhimalayan leafhopper genus Pseudosubhimalus (Homoptera: Cicadellidae) based on molecular phylogeny. PeerJ 7:e7162 https://doi.org/10.7717/peerj.7162
date submitted: 2019-01-24
date accepted: 2019-05-22
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niranjana
  given name: GN
author list: Agent
  family name: Meshram
  given name: Naresh M.
author list: Agent
  family name: Shashank
  given name: Pathour R.
author list: Agent
  family name: Stuti
author list: Agent
  family name: Hashmi
  given name: Tahseen Raza
doi: 10.7717/peerj.7162
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Niranjana et al.
attribution name: Niranjana et al.

Cyclodipeptides from Pseudomonas aeruginosa modulate the maize (Zea mays L.) root system and promote S6 ribosomal protein kinase activation
type: item
type: AcademicArticle
description: Background Pseudomonas aeruginosa is an opportunistic and pathogenic bacterium with the ability to produce cyclodipeptides (CDPs), which belong to a large family of molecules with important biological activities. Excessive amounts of CDPs produced by Pseudomonas strains can activate an auxin response in Arabidopsis thaliana and promote plant growth. Target of rapamycin (TOR) is an evolutionarily conserved eukaryotic protein kinase that coordinates cell growth and metabolic processes in response to environmental and nutritional signals. Target of rapamycin kinase phosphorylates various substrates, of which S6 ribosomal protein kinase (S6K) is particularly well known. The PI3K/Akt/mTOR/S6K signaling pathway has been studied extensively in mammals because of its association with fundamental biological processes including cell differentiation. However, evidences suggest that this pathway also has specific and conserved functions in plants and may thus be conserved, as are several of its components like TOR complex 1 and S6K proteins. In plants, TOR-S6K signaling has been shown to be modulated in response to plant growth promoters or stressors. Methods In this study, we evaluated the effects of P. aeruginosa CDPs on the growth and root development of maize plants (Zea mays L.) by adding different CDPs concentrations on culture plant media, as well as the effect on the phosphorylation of the maize S6K protein (ZmS6K) by protein electrophoresis and western blot. Results Our results showed that P. aeruginosa CDPs promoted maize growth and development, including modifications in the root system architecture, correlating with the increased ZmS6K phosphorylation and changes induced in electrophoretic mobility, suggesting post-translational modifications on ZmS6K. These findings suggest that the plant growth-promoting effect of the Pseudomonas genus, associated with the CDPs production, involves the TOR/S6K signaling pathway as a mechanism of plant growth and root development i…
format: application/pdf
format: text/html
creator: Iván Corona-Sánchez
creator: Cesar Arturo Peña-Uribe
creator: Omar González-López
creator: Javier Villegas
creator: Jesus Campos-Garcia
creator: Homero Reyes de la Cruz
subject: Agricultural Science
subject: Biochemistry
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.7494
publisher: PeerJ Inc.
rights: © 2019 Corona-Sánchez et al.
abstract: Background Pseudomonas aeruginosa is an opportunistic and pathogenic bacterium with the ability to produce cyclodipeptides (CDPs), which belong to a large family of molecules with important biological activities. Excessive amounts of CDPs produced by Pseudomonas strains can activate an auxin response in Arabidopsis thaliana and promote plant growth. Target of rapamycin (TOR) is an evolutionarily conserved eukaryotic protein kinase that coordinates cell growth and metabolic processes in response to environmental and nutritional signals. Target of rapamycin kinase phosphorylates various substrates, of which S6 ribosomal protein kinase (S6K) is particularly well known. The PI3K/Akt/mTOR/S6K signaling pathway has been studied extensively in mammals because of its association with fundamental biological processes including cell differentiation. However, evidences suggest that this pathway also has specific and conserved functions in plants and may thus be conserved, as are several of its components like TOR complex 1 and S6K proteins. In plants, TOR-S6K signaling has been shown to be modulated in response to plant growth promoters or stressors. Methods In this study, we evaluated the effects of P. aeruginosa CDPs on the growth and root development of maize plants (Zea mays L.) by adding different CDPs concentrations on culture plant media, as well as the effect on the phosphorylation of the maize S6K protein (ZmS6K) by protein electrophoresis and western blot. Results Our results showed that P. aeruginosa CDPs promoted maize growth and development, including modifications in the root system architecture, correlating with the increased ZmS6K phosphorylation and changes induced in electrophoretic mobility, suggesting post-translational modifications on ZmS6K. These findings suggest that the plant growth-promoting effect of the Pseudomonas genus, associated with the CDPs production, involves the TOR/S6K signaling pathway as a mechanism of plant growth and root development i…
bibliographic citation: Corona-Sánchez et al. (2019) Cyclodipeptides from Pseudomonas aeruginosa modulate the maize (Zea mays L.) root system and promote S6 ribosomal protein kinase activation. PeerJ 7:e7494 https://doi.org/10.7717/peerj.7494
date submitted: 2019-04-10
date accepted: 2019-07-16
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Corona-Sánchez
  given name: Iván
author list: Agent
  family name: Peña-Uribe
  given name: Cesar Arturo
author list: Agent
  family name: González-López
  given name: Omar
author list: Agent
  family name: Villegas
  given name: Javier
author list: Agent
  family name: Campos-Garcia
  given name: Jesus
author list: Agent
  family name: Reyes de la Cruz
  given name: Homero
doi: 10.7717/peerj.7494
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: © 2019 Corona-Sánchez et al.
attribution name: Corona-Sánchez et al.

Early Agenian rhinocerotids from Wischberg (Canton Bern, Switzerland) and clarification of the systematics of the genus Diaceratherium
type: item
type: AcademicArticle
description: Background Wischberg is a Swiss locality in Bern Canton which has yielded numerous vertebrates remains from the earliest Miocene (= MN1). It has a very rich faunal diversity, one of the richest in Switzerland for this age. Among all the mammals reported in the original faunal list 70 years ago, three rhinocerotid species were identified. The material consists of two fragmentary skulls, cranial fragments, several mandibles, teeth and postcranial bones, in a rather good state of preservation. Results After reexamination of the material from this locality (curated in three different Swiss museums) and comparison with holotype specimens, we show that all rhinocerotid specimens from Wischberg can be referred to two species only. Most of the material can be attributed to the large-sized teleoceratine Diaceratherium lemanense, while only a few specimens, including a skull and mandible, belong to the much smaller sized Pleuroceros pleuroceros. We describe and illustrate for the first time most of these fossil remains. However, the systematics of the genus Diaceratherium is currently controversial, and based on our new observations we consider seven species as valid, though a large-scale phylogenetic study should be done in the future to resolve it. The rhinocerotid association found in Wischberg is nonetheless typical of the MN1 biozone, which results from a faunal renewal occurring just before the end of the Oligocene.
format: application/pdf
format: text/html
creator: Claire Jame
creator: Jérémy Tissier
creator: Olivier Maridet
creator: Damien Becker
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.7517
publisher: PeerJ Inc.
rights: © 2019 Jame et al.
abstract: Background Wischberg is a Swiss locality in Bern Canton which has yielded numerous vertebrates remains from the earliest Miocene (= MN1). It has a very rich faunal diversity, one of the richest in Switzerland for this age. Among all the mammals reported in the original faunal list 70 years ago, three rhinocerotid species were identified. The material consists of two fragmentary skulls, cranial fragments, several mandibles, teeth and postcranial bones, in a rather good state of preservation. Results After reexamination of the material from this locality (curated in three different Swiss museums) and comparison with holotype specimens, we show that all rhinocerotid specimens from Wischberg can be referred to two species only. Most of the material can be attributed to the large-sized teleoceratine Diaceratherium lemanense, while only a few specimens, including a skull and mandible, belong to the much smaller sized Pleuroceros pleuroceros. We describe and illustrate for the first time most of these fossil remains. However, the systematics of the genus Diaceratherium is currently controversial, and based on our new observations we consider seven species as valid, though a large-scale phylogenetic study should be done in the future to resolve it. The rhinocerotid association found in Wischberg is nonetheless typical of the MN1 biozone, which results from a faunal renewal occurring just before the end of the Oligocene.
bibliographic citation: Jame et al. (2019) Early Agenian rhinocerotids from Wischberg (Canton Bern, Switzerland) and clarification of the systematics of the genus Diaceratherium. PeerJ 7:e7517 https://doi.org/10.7717/peerj.7517
date submitted: 2019-05-16
date accepted: 2019-07-19
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jame
  given name: Claire
author list: Agent
  family name: Tissier
  given name: Jérémy
author list: Agent
  family name: Maridet
  given name: Olivier
author list: Agent
  family name: Becker
  given name: Damien
doi: 10.7717/peerj.7517
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: © 2019 Jame et al.
attribution name: Jame et al.

Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents
type: item
type: AcademicArticle
description: In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ∼70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents.
format: application/pdf
format: text/html
creator: Jianzhou Qu
creator: Shutu Xu
creator: Xiaokang Tian
creator: Ting Li
creator: Licheng Wang
creator: Yuyue Zhong
creator: Jiquan Xue
creator: Dongwei Guo
subject: Developmental Biology
subject: Plant Science
description: doi:10.7717/peerj.7528
publisher: PeerJ Inc.
rights: © 2019 Qu et al.
abstract: In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ∼70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents.
bibliographic citation: Qu et al. (2019) Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents. PeerJ 7:e7528 https://doi.org/10.7717/peerj.7528
date submitted: 2019-03-08
date accepted: 2019-07-22
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qu
  given name: Jianzhou
author list: Agent
  family name: Xu
  given name: Shutu
author list: Agent
  family name: Tian
  given name: Xiaokang
author list: Agent
  family name: Li
  given name: Ting
author list: Agent
  family name: Wang
  given name: Licheng
author list: Agent
  family name: Zhong
  given name: Yuyue
author list: Agent
  family name: Xue
  given name: Jiquan
author list: Agent
  family name: Guo
  given name: Dongwei
doi: 10.7717/peerj.7528
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Qu et al.
attribution name: Qu et al.

The effect of modulating the quantity of enzymes in a model ethanol pathway on metabolic flux in Synechocystis sp. PCC 6803
type: item
type: AcademicArticle
description: Synthetic metabolism allows new metabolic capabilities to be introduced into strains for biotechnology applications. Such engineered metabolic pathways are unlikely to function optimally as initially designed and native metabolism may not efficiently support the introduced pathway without further intervention. To develop our understanding of optimal metabolic engineering strategies, a two-enzyme ethanol pathway consisting of pyruvate decarboxylase and acetaldehyde reductase was introduced into Synechocystis sp. PCC 6803. We characteriseda new set of ribosome binding site sequences in Synechocystis sp. PCC 6803 providing a range of translation strengths for different genes under test. The effect of ribosome-bindingsite sequence, operon design and modifications to native metabolism on pathway flux was analysed by HPLC. The accumulation of all introduced proteins was also quantified using selected reaction monitoring mass spectrometry. Pathway productivity was more strongly dependent on the accumulation of pyruvate decarboxylase than acetaldehyde reductase. In fact, abolishment of reductase over-expression resulted in the greatest ethanol productivity, most likely because strains harbouringsingle-gene constructs accumulated more pyruvate decarboxylase than strains carrying any of the multi-gene constructs. Overall, several lessons were learned. Firstly, the expression level of the first gene in anyoperon influenced the expression level of subsequent genes, demonstrating that translational coupling can also occur in cyanobacteria. Longer operons resulted in lower protein abundance for proximally-encoded cistrons. And, implementation of metabolic engineering strategies that have previously been shown to enhance the growth or yield of pyruvate dependent products, through co-expression with pyruvate kinase and/or fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase, indicated that other factors had greater control over growth and metabolic flux under the tested con…
format: application/pdf
format: text/html
creator: Paulina Bartasun
creator: Nicole Prandi
creator: Marko Storch
creator: Yarin Aknin
creator: Mark Bennett
creator: Arianna Palma
creator: Geoff Baldwin
creator: Yumiko Sakuragi
creator: Patrik R. Jones
creator: John Rowland
subject: Biotechnology
subject: Synthetic Biology
description: doi:10.7717/peerj.7529
publisher: PeerJ Inc.
rights: © 2019 Bartasun et al.
abstract: Synthetic metabolism allows new metabolic capabilities to be introduced into strains for biotechnology applications. Such engineered metabolic pathways are unlikely to function optimally as initially designed and native metabolism may not efficiently support the introduced pathway without further intervention. To develop our understanding of optimal metabolic engineering strategies, a two-enzyme ethanol pathway consisting of pyruvate decarboxylase and acetaldehyde reductase was introduced into Synechocystis sp. PCC 6803. We characteriseda new set of ribosome binding site sequences in Synechocystis sp. PCC 6803 providing a range of translation strengths for different genes under test. The effect of ribosome-bindingsite sequence, operon design and modifications to native metabolism on pathway flux was analysed by HPLC. The accumulation of all introduced proteins was also quantified using selected reaction monitoring mass spectrometry. Pathway productivity was more strongly dependent on the accumulation of pyruvate decarboxylase than acetaldehyde reductase. In fact, abolishment of reductase over-expression resulted in the greatest ethanol productivity, most likely because strains harbouringsingle-gene constructs accumulated more pyruvate decarboxylase than strains carrying any of the multi-gene constructs. Overall, several lessons were learned. Firstly, the expression level of the first gene in anyoperon influenced the expression level of subsequent genes, demonstrating that translational coupling can also occur in cyanobacteria. Longer operons resulted in lower protein abundance for proximally-encoded cistrons. And, implementation of metabolic engineering strategies that have previously been shown to enhance the growth or yield of pyruvate dependent products, through co-expression with pyruvate kinase and/or fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase, indicated that other factors had greater control over growth and metabolic flux under the tested con…
bibliographic citation: Bartasun et al. (2019) The effect of modulating the quantity of enzymes in a model ethanol pathway on metabolic flux in Synechocystis sp. PCC 6803. PeerJ 7:e7529 https://doi.org/10.7717/peerj.7529
date submitted: 2019-04-10
date accepted: 2019-07-22
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bartasun
  given name: Paulina
author list: Agent
  family name: Prandi
  given name: Nicole
author list: Agent
  family name: Storch
  given name: Marko
author list: Agent
  family name: Aknin
  given name: Yarin
author list: Agent
  family name: Bennett
  given name: Mark
author list: Agent
  family name: Palma
  given name: Arianna
author list: Agent
  family name: Baldwin
  given name: Geoff
author list: Agent
  family name: Sakuragi
  given name: Yumiko
author list: Agent
  family name: Jones
  given name: Patrik R.
author list: Agent
  family name: Rowland
  given name: John
doi: 10.7717/peerj.7529
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Bartasun et al.
attribution name: Bartasun et al.

Endogenous testosterone correlates with parochial altruism in relation to costly punishment in different social settings
type: item
type: AcademicArticle
description: Testosterone plays a key role in shaping human social behavior. Recent findings have linked testosterone to altruistic behavior in economic decision tasks depending on group membership and intergroup competition. The preferential treatment of ingroup members, while aggression and discrimination is directed towards outgroup members, has been referred to as parochial altruism. Here we investigated in two consecutive studies, whether testosterone is associated with parochial altruism depending on individual tendency for costly punishment. In the first study, 61 men performed a single-shot ultimatum game (UG) in a minimal group context, in which they interacted with members of an ingroup and outgroup. In the second study, 34 men performed a single-shot UG in a more realistic group context, in which they responded to the proposals of supporters of six political parties during the German election year 2017. Political parties varied in their social distance to the participants’ favorite party as indicated by an individual ranking. Participants of study 2 also performed a cued recall task, in which they had to decide whether they had already encountered a face during the previous UG (old-new decision). In order to make the UG data of study 2 most comparable to the data of study 1, the rejection rates of several parties were combined according to the social distance ranking they achieved. Parties ranked 1 to 3 formed the relatively close and favored ‘ingroup’ that shared similar political values with the participant (e.g., left wing parties), while the ‘outgroup’ consisted of parties ranked from 4 to 6 with more distant or even antagonistic political views (e.g., conservative to right wing parties). In both studies, results showed a parochial pattern with higher rejection rates made in response to outgroup compared to ingroup offers. Interestingly, across studies higher salivary testosterone was associated with higher rejection rates related to unfair outgroup offers in comp…
format: application/pdf
format: text/html
creator: Luise Reimers
creator: Eli Kappo
creator: Lucas Stadler
creator: Mostafa Yaqubi
creator: Esther K. Diekhof
subject: Anthropology
subject: Andrology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.7537
publisher: PeerJ Inc.
rights: © 2019 Reimers et al.
abstract: Testosterone plays a key role in shaping human social behavior. Recent findings have linked testosterone to altruistic behavior in economic decision tasks depending on group membership and intergroup competition. The preferential treatment of ingroup members, while aggression and discrimination is directed towards outgroup members, has been referred to as parochial altruism. Here we investigated in two consecutive studies, whether testosterone is associated with parochial altruism depending on individual tendency for costly punishment. In the first study, 61 men performed a single-shot ultimatum game (UG) in a minimal group context, in which they interacted with members of an ingroup and outgroup. In the second study, 34 men performed a single-shot UG in a more realistic group context, in which they responded to the proposals of supporters of six political parties during the German election year 2017. Political parties varied in their social distance to the participants’ favorite party as indicated by an individual ranking. Participants of study 2 also performed a cued recall task, in which they had to decide whether they had already encountered a face during the previous UG (old-new decision). In order to make the UG data of study 2 most comparable to the data of study 1, the rejection rates of several parties were combined according to the social distance ranking they achieved. Parties ranked 1 to 3 formed the relatively close and favored ‘ingroup’ that shared similar political values with the participant (e.g., left wing parties), while the ‘outgroup’ consisted of parties ranked from 4 to 6 with more distant or even antagonistic political views (e.g., conservative to right wing parties). In both studies, results showed a parochial pattern with higher rejection rates made in response to outgroup compared to ingroup offers. Interestingly, across studies higher salivary testosterone was associated with higher rejection rates related to unfair outgroup offers in comp…
bibliographic citation: Reimers et al. (2019) Endogenous testosterone correlates with parochial altruism in relation to costly punishment in different social settings. PeerJ 7:e7537 https://doi.org/10.7717/peerj.7537
date submitted: 2019-03-01
date accepted: 2019-07-23
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reimers
  given name: Luise
author list: Agent
  family name: Kappo
  given name: Eli
author list: Agent
  family name: Stadler
  given name: Lucas
author list: Agent
  family name: Yaqubi
  given name: Mostafa
author list: Agent
  family name: Diekhof
  given name: Esther K.
doi: 10.7717/peerj.7537
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Reimers et al.
attribution name: Reimers et al.

A real-world study on clinical predictors of relapse after hospitalized detoxification in a Chinese cohort with alcohol dependence
type: item
type: AcademicArticle
description: Background The relapse rate of alcohol dependence (AD) after detoxification is high, but few studies have investigated the clinical predictors of relapse after hospitalized detoxification in real-world clinical practice, especially among Chinese patients. Methods This longitudinal cohort study followed up 122 AD patients who were discharged from January 1, 2016 to January 30, 2018 from their most recent hospitalization for detoxification. These patients were interviewed by telephone from May 20, 2017, to June 30, 2018, at least 6 months after discharge. During the interview, the relapse were assessed by using a revised Chinese version of the Alcohol Use Disorder Identification Test. Candidate predictors, such as therapeutic modalities during hospitalization and at discharge, medical history data related to alcohol use, and demographic information, were obtained from the medical records in the hospital information system. Results During the 6–24 months (with a median of 9 months) follow-up period, the relapse rate was 53.3%. Individuals with a college education level and those who had not been treated with the brief comprehensive cognitive-motivational-behavioural intervention (CCMBI) were more likely than their counterparts to relapse after hospitalized detoxification, and their adjusted HRs (95% CIs) were 1.85 (1.09, 3.16) and 2.00 (1.16, 3.46), respectively. The CCMBI use predicted a reduction in the relapse rate by approximately one-fifth. Conclusion Undergoing the CCMBI during detoxification hospitalization and having less than a college-level education could predict a reduced risk of AD relapse. These findings provide useful information both for further clinical research and for real-world practice.
format: application/pdf
format: text/html
creator: Yu-Jie Tao
creator: Li Hu
creator: Ying He
creator: Bing-Rong Cao
creator: Juan Chen
creator: Ying-Hua Ye
creator: Ting Chen
creator: Xia Yang
creator: Jia-Jun Xu
creator: Jing Li
creator: Ya-Jing Meng
creator: Tao Li
creator: Wan-Jun Guo
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.7547
publisher: PeerJ Inc.
rights: © 2019 Tao et al.
abstract: Background The relapse rate of alcohol dependence (AD) after detoxification is high, but few studies have investigated the clinical predictors of relapse after hospitalized detoxification in real-world clinical practice, especially among Chinese patients. Methods This longitudinal cohort study followed up 122 AD patients who were discharged from January 1, 2016 to January 30, 2018 from their most recent hospitalization for detoxification. These patients were interviewed by telephone from May 20, 2017, to June 30, 2018, at least 6 months after discharge. During the interview, the relapse were assessed by using a revised Chinese version of the Alcohol Use Disorder Identification Test. Candidate predictors, such as therapeutic modalities during hospitalization and at discharge, medical history data related to alcohol use, and demographic information, were obtained from the medical records in the hospital information system. Results During the 6–24 months (with a median of 9 months) follow-up period, the relapse rate was 53.3%. Individuals with a college education level and those who had not been treated with the brief comprehensive cognitive-motivational-behavioural intervention (CCMBI) were more likely than their counterparts to relapse after hospitalized detoxification, and their adjusted HRs (95% CIs) were 1.85 (1.09, 3.16) and 2.00 (1.16, 3.46), respectively. The CCMBI use predicted a reduction in the relapse rate by approximately one-fifth. Conclusion Undergoing the CCMBI during detoxification hospitalization and having less than a college-level education could predict a reduced risk of AD relapse. These findings provide useful information both for further clinical research and for real-world practice.
bibliographic citation: Tao et al. (2019) A real-world study on clinical predictors of relapse after hospitalized detoxification in a Chinese cohort with alcohol dependence. PeerJ 7:e7547 https://doi.org/10.7717/peerj.7547
date submitted: 2019-04-18
date accepted: 2019-07-25
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tao
  given name: Yu-Jie
author list: Agent
  family name: Hu
  given name: Li
author list: Agent
  family name: He
  given name: Ying
author list: Agent
  family name: Cao
  given name: Bing-Rong
author list: Agent
  family name: Chen
  given name: Juan
author list: Agent
  family name: Ye
  given name: Ying-Hua
author list: Agent
  family name: Chen
  given name: Ting
author list: Agent
  family name: Yang
  given name: Xia
author list: Agent
  family name: Xu
  given name: Jia-Jun
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Meng
  given name: Ya-Jing
author list: Agent
  family name: Li
  given name: Tao
author list: Agent
  family name: Guo
  given name: Wan-Jun
doi: 10.7717/peerj.7547
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Tao et al.
attribution name: Tao et al.

HiLDA: a statistical approach to investigate differences in mutational signatures
type: item
type: AcademicArticle
description: We propose a hierarchical latent Dirichlet allocation model (HiLDA) for characterizing somatic mutation data in cancer. The method allows us to infer mutational patterns and their relative frequencies in a set of tumor mutational catalogs and to compare the estimated frequencies between tumor sets. We apply our method to two datasets, one containing somatic mutations in colon cancer by the time of occurrence, before or after tumor initiation, and the second containing somatic mutations in esophageal cancer by sex, age, smoking status, and tumor site. In colon cancer, the relative frequencies of mutational patterns were found significantly associated with the time of occurrence of mutations. In esophageal cancer, the relative frequencies were significantly associated with the tumor site. Our novel method provides higher statistical power for detecting differences in mutational signatures.
format: application/pdf
format: text/html
creator: Zhi Yang
creator: Priyatama Pandey
creator: Darryl Shibata
creator: David V. Conti
creator: Paul Marjoram
creator: Kimberly D. Siegmund
subject: Bioinformatics
subject: Genomics
subject: Statistics
description: doi:10.7717/peerj.7557
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: We propose a hierarchical latent Dirichlet allocation model (HiLDA) for characterizing somatic mutation data in cancer. The method allows us to infer mutational patterns and their relative frequencies in a set of tumor mutational catalogs and to compare the estimated frequencies between tumor sets. We apply our method to two datasets, one containing somatic mutations in colon cancer by the time of occurrence, before or after tumor initiation, and the second containing somatic mutations in esophageal cancer by sex, age, smoking status, and tumor site. In colon cancer, the relative frequencies of mutational patterns were found significantly associated with the time of occurrence of mutations. In esophageal cancer, the relative frequencies were significantly associated with the tumor site. Our novel method provides higher statistical power for detecting differences in mutational signatures.
bibliographic citation: Yang et al. (2019) HiLDA: a statistical approach to investigate differences in mutational signatures. PeerJ 7:e7557 https://doi.org/10.7717/peerj.7557
date submitted: 2019-03-11
date accepted: 2019-07-25
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Zhi
author list: Agent
  family name: Pandey
  given name: Priyatama
author list: Agent
  family name: Shibata
  given name: Darryl
author list: Agent
  family name: Conti
  given name: David V.
author list: Agent
  family name: Marjoram
  given name: Paul
author list: Agent
  family name: Siegmund
  given name: Kimberly D.
doi: 10.7717/peerj.7557
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Yang et al.
attribution name: Yang et al.

Nicotinamide riboside exerts protective effect against aging-induced NAFLD-like hepatic dysfunction in mice
type: item
type: AcademicArticle
description: Background & Aims Aging is one of the risk factors of non-alcoholic fatty liver disease (NAFLD). Yet, the mechanism underlying the aging-associated NAFLD-like syndrome is not fully understood. Nicotinamide adenine dinucleotide (NAD), a ubiquitous coenzyme, has protective effects against aging. Here, we investigated the actions of NAD precursors nicotinamide riboside (NR) on the development of aging-induced NAFLD. Methods NR supplemented food (2.5 g/kg food) was applied to aged mice for three months while normal chow to the other groups. Body weight, food intake, liver weight and fat pat mass were measured. The serum concentrations of lipid content, alanine aminotransferase (ALT), aspartate aminotransferase (AST) and NAD were determined by biochemical assays. Pathological assessment and immunohistochemistry analysis of hepatic tissues were used to evaluate the effect of NR on NAFLD development and inflammatory infiltration. Results NR repletion significantly reduced fat pat mass in aged mice, while not altered the body weight, food intake, and liver weight. NR repletion significantly rescued the NAD reduction in aged mice. The total cholesterol and triglyceride levels could be lowered by NR repletion in aged mice. The AST level was also significantly reduced by NR repletion in aged group, while the ALT level lowered but without significance. Notably, moderate NAFLD phenotypes, including steatosis and hepatic fibrosis could be markedly corrected by NR repletion. In addition, Kupffer cells accumulated and inflammatory infiltration could also be remarkably reversed by NR repletion in aged mice. Conclusion Aging was associated with NAFLD-like phenotypes in mice, which could be reversed by oral NR repletion. Therefore, oral NR uptake might be a promising strategy to halt the progression of NAFLD.
format: application/pdf
format: text/html
creator: Xue Han
creator: Xiaogang Bao
creator: Qi Lou
creator: Xian Xie
creator: Meng Zhang
creator: Shasang Zhou
creator: Honggang Guo
creator: Guojun Jiang
creator: Qiaojuan Shi
subject: Gastroenterology and Hepatology
subject: Pharmacology
description: doi:10.7717/peerj.7568
publisher: PeerJ Inc.
rights: © 2019 Han et al.
abstract: Background & Aims Aging is one of the risk factors of non-alcoholic fatty liver disease (NAFLD). Yet, the mechanism underlying the aging-associated NAFLD-like syndrome is not fully understood. Nicotinamide adenine dinucleotide (NAD), a ubiquitous coenzyme, has protective effects against aging. Here, we investigated the actions of NAD precursors nicotinamide riboside (NR) on the development of aging-induced NAFLD. Methods NR supplemented food (2.5 g/kg food) was applied to aged mice for three months while normal chow to the other groups. Body weight, food intake, liver weight and fat pat mass were measured. The serum concentrations of lipid content, alanine aminotransferase (ALT), aspartate aminotransferase (AST) and NAD were determined by biochemical assays. Pathological assessment and immunohistochemistry analysis of hepatic tissues were used to evaluate the effect of NR on NAFLD development and inflammatory infiltration. Results NR repletion significantly reduced fat pat mass in aged mice, while not altered the body weight, food intake, and liver weight. NR repletion significantly rescued the NAD reduction in aged mice. The total cholesterol and triglyceride levels could be lowered by NR repletion in aged mice. The AST level was also significantly reduced by NR repletion in aged group, while the ALT level lowered but without significance. Notably, moderate NAFLD phenotypes, including steatosis and hepatic fibrosis could be markedly corrected by NR repletion. In addition, Kupffer cells accumulated and inflammatory infiltration could also be remarkably reversed by NR repletion in aged mice. Conclusion Aging was associated with NAFLD-like phenotypes in mice, which could be reversed by oral NR repletion. Therefore, oral NR uptake might be a promising strategy to halt the progression of NAFLD.
bibliographic citation: Han et al. (2019) Nicotinamide riboside exerts protective effect against aging-induced NAFLD-like hepatic dysfunction in mice. PeerJ 7:e7568 https://doi.org/10.7717/peerj.7568
date submitted: 2019-04-28
date accepted: 2019-07-29
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Xue
author list: Agent
  family name: Bao
  given name: Xiaogang
author list: Agent
  family name: Lou
  given name: Qi
author list: Agent
  family name: Xie
  given name: Xian
author list: Agent
  family name: Zhang
  given name: Meng
author list: Agent
  family name: Zhou
  given name: Shasang
author list: Agent
  family name: Guo
  given name: Honggang
author list: Agent
  family name: Jiang
  given name: Guojun
author list: Agent
  family name: Shi
  given name: Qiaojuan
doi: 10.7717/peerj.7568
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Han et al.
attribution name: Han et al.

Testing the function of dromaeosaurid (Dinosauria, Theropoda) ‘sickle claws’ through musculoskeletal modelling and optimization
type: item
type: AcademicArticle
description: Dromaeosaurids were a clade of bird-like, carnivorous dinosaurs that are well known for their characteristic morphology of pedal digit II, which bore an enlarged, sickle-shaped claw and permitted an extreme range of flexion–extension. Proposed functions for the claw often revolve around predation, but the exact manner of use varies widely. Musculoskeletal modelling provides an avenue to quantitatively investigate the biomechanics of this enigmatic system, and thereby test different behavioural hypotheses. Here, a musculoskeletal model of the hindlimb and pes of Deinonychus was developed, and mathematical optimization was used to assess the factors that maximize production of force at the claw tip. Optimization revealed that more crouched hindlimb postures (i.e., more flexed knees and ankles) and larger flexor muscle volumes consistently increased claw forces, although the optimal degree of digit flexion or extension depended on assumptions of muscle activity and fibre operating range. Interestingly, the magnitude of force capable of being produced at the claw tip was relatively small, arguing against regular transmission of a large proportion of body weight into a substrate principally via the claw tip. Such transmission would therefore likely have needed to occur via more proximal parts of the foot. Collectively, the results best support a grasping function for digit II (e.g., restraint of prey smaller than the dromaeosaurid’s own body size), although other behaviours involving flexed hindlimbs cannot be excluded.
format: application/pdf
format: text/html
creator: Peter J. Bishop
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.7577
publisher: PeerJ Inc.
rights: © 2019 Bishop
abstract: Dromaeosaurids were a clade of bird-like, carnivorous dinosaurs that are well known for their characteristic morphology of pedal digit II, which bore an enlarged, sickle-shaped claw and permitted an extreme range of flexion–extension. Proposed functions for the claw often revolve around predation, but the exact manner of use varies widely. Musculoskeletal modelling provides an avenue to quantitatively investigate the biomechanics of this enigmatic system, and thereby test different behavioural hypotheses. Here, a musculoskeletal model of the hindlimb and pes of Deinonychus was developed, and mathematical optimization was used to assess the factors that maximize production of force at the claw tip. Optimization revealed that more crouched hindlimb postures (i.e., more flexed knees and ankles) and larger flexor muscle volumes consistently increased claw forces, although the optimal degree of digit flexion or extension depended on assumptions of muscle activity and fibre operating range. Interestingly, the magnitude of force capable of being produced at the claw tip was relatively small, arguing against regular transmission of a large proportion of body weight into a substrate principally via the claw tip. Such transmission would therefore likely have needed to occur via more proximal parts of the foot. Collectively, the results best support a grasping function for digit II (e.g., restraint of prey smaller than the dromaeosaurid’s own body size), although other behaviours involving flexed hindlimbs cannot be excluded.
bibliographic citation: Bishop (2019) Testing the function of dromaeosaurid (Dinosauria, Theropoda) ‘sickle claws’ through musculoskeletal modelling and optimization. PeerJ 7:e7577 https://doi.org/10.7717/peerj.7577
date submitted: 2019-06-03
date accepted: 2019-07-29
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bishop
  given name: Peter J.
doi: 10.7717/peerj.7577
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Bishop
attribution name: Bishop

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