PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: The association of wrist circumference with hypertension in northeastern Chinese residents in comparison with other anthropometric obesity indices
items: OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling
items: Healthy eating promoting in a Brazilian sports-oriented school: a pilot study
items: Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement

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

The association of wrist circumference with hypertension in northeastern Chinese residents in comparison with other anthropometric obesity indices
type: item
type: AcademicArticle
description: Background Wrist circumference (WrC) is an easily obtained measure in estimating the body frame and regional fat distribution, and has increasingly used as an obesity index. The aim of our study is to estimate the association of WrC with elevated blood pressure (BP) among northeastern Chinese community-dwelling residents, and compare the strength of this association to other anthropometric obesity indices. Methods A total of 2,331 adult participants (761 male participants, and 1,570 female participants) were included. WrC and other five generally used obesity indices, including body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) and neck circumference (NC) were measured. Hypertension was defined as systolic blood pressure (SBP)/diastolic blood pressure (DBP) ≥140/90 mmHg or anti-hypertensive medication use. Multivariable linear and logistic regression models were performed to identify associations of BP and hypertension with per standard deviation (SD) increase of obesity indices. Areas under receiver operative characteristic curves (AUC) were calculated to compare the predicting capacity of WrC and other obesity indices on hypertension. Results All of the six obesity indices were positively associated with both SBP and DBP after adjustment for age and gender (P-values of associations of SBP with obesity indices were 0.043 for WrC, and <0.001 for other five indices; P-values of associations of DBP with obesity indices were 0.011 for WrC, 0.031 for WHR, and <0.001 for other four indices), while the association between SBP and WrC showed no statistically significant after further adjusted for life-style and metabolic risk factors (P-value was 0.062). The increases of both SBP and DBP per SD increase of BMI were the largest. The positive associations of five obesity indices but WHR with hypertension were observed after adjustment for all risk factors (P-values were 0.024 for WrC, 0.064 for WHR and <0.001 for other fou…
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format: text/html
creator: Yongfang Li
creator: Yuyan Liu
creator: Jing He
creator: Ping Ma
creator: Luyang Yu
creator: Guifan Sun
subject: Epidemiology
subject: Global Health
subject: Health Policy
subject: Public Health
description: doi:10.7717/peerj.7599
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Wrist circumference (WrC) is an easily obtained measure in estimating the body frame and regional fat distribution, and has increasingly used as an obesity index. The aim of our study is to estimate the association of WrC with elevated blood pressure (BP) among northeastern Chinese community-dwelling residents, and compare the strength of this association to other anthropometric obesity indices. Methods A total of 2,331 adult participants (761 male participants, and 1,570 female participants) were included. WrC and other five generally used obesity indices, including body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) and neck circumference (NC) were measured. Hypertension was defined as systolic blood pressure (SBP)/diastolic blood pressure (DBP) ≥140/90 mmHg or anti-hypertensive medication use. Multivariable linear and logistic regression models were performed to identify associations of BP and hypertension with per standard deviation (SD) increase of obesity indices. Areas under receiver operative characteristic curves (AUC) were calculated to compare the predicting capacity of WrC and other obesity indices on hypertension. Results All of the six obesity indices were positively associated with both SBP and DBP after adjustment for age and gender (P-values of associations of SBP with obesity indices were 0.043 for WrC, and <0.001 for other five indices; P-values of associations of DBP with obesity indices were 0.011 for WrC, 0.031 for WHR, and <0.001 for other four indices), while the association between SBP and WrC showed no statistically significant after further adjusted for life-style and metabolic risk factors (P-value was 0.062). The increases of both SBP and DBP per SD increase of BMI were the largest. The positive associations of five obesity indices but WHR with hypertension were observed after adjustment for all risk factors (P-values were 0.024 for WrC, 0.064 for WHR and <0.001 for other fou…
bibliographic citation: Li et al. (2019) The association of wrist circumference with hypertension in northeastern Chinese residents in comparison with other anthropometric obesity indices. PeerJ 7:e7599 https://doi.org/10.7717/peerj.7599
date submitted: 2019-05-29
date accepted: 2019-07-31
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yongfang
author list: Agent
  family name: Liu
  given name: Yuyan
author list: Agent
  family name: He
  given name: Jing
author list: Agent
  family name: Ma
  given name: Ping
author list: Agent
  family name: Yu
  given name: Luyang
author list: Agent
  family name: Sun
  given name: Guifan
doi: 10.7717/peerj.7599
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Li et al.
attribution name: Li et al.

OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling
type: item
type: AcademicArticle
description: With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial. In this paper, we present a tool called OutbreakFinder that can accept a distance matrix in csv format; alignment files from Lyve-SET, Parsnp, and ClustalOmega; and a tree file in Newick format as inputs to compute a cluster-labeled two-dimensional plot based on multidimensional-scaling dimension reduction coupled with affinity propagation clustering. OutbreakFinder can be downloaded for free at https://github.com/skypes/Newton-method-MDS.
format: application/pdf
format: text/html
creator: Ming-Hsin Tsai
creator: Yen-Yi Liu
creator: Chih-Chieh Chen
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.7600
publisher: PeerJ Inc.
rights: © 2019 Tsai et al.
abstract: With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial. In this paper, we present a tool called OutbreakFinder that can accept a distance matrix in csv format; alignment files from Lyve-SET, Parsnp, and ClustalOmega; and a tree file in Newick format as inputs to compute a cluster-labeled two-dimensional plot based on multidimensional-scaling dimension reduction coupled with affinity propagation clustering. OutbreakFinder can be downloaded for free at https://github.com/skypes/Newton-method-MDS.
bibliographic citation: Tsai et al. (2019) OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling. PeerJ 7:e7600 https://doi.org/10.7717/peerj.7600
date submitted: 2019-04-16
date accepted: 2019-08-01
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsai
  given name: Ming-Hsin
author list: Agent
  family name: Liu
  given name: Yen-Yi
author list: Agent
  family name: Chen
  given name: Chih-Chieh
doi: 10.7717/peerj.7600
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: © 2019 Tsai et al.
attribution name: Tsai et al.

Healthy eating promoting in a Brazilian sports-oriented school: a pilot study
type: item
type: AcademicArticle
description: Background Adolescents, particularly athletes, have high exposure to ultra-processed foods, which could be harmful to their health and physical performance. School environments are capable of improving eating patterns. Our study is aimed at capturing changes in students’ food consumption three years after they enrolled at an experimental school, considered a model of health promotion in Rio de Janeiro city. We also aimed to depict the promising nature of the healthy eating promotion program implemented in the school and share the learnings from its implementation. Methods Our pilot study was a follow-up on the implementation of a school garden, experimental kitchen activities, and health promotion classes. We evaluated 83 adolescent athletes’ food consumption twice during the study: at its beginning (2013) and end (2016), by administering a food frequency questionnaire (FFQ) that inquired about the frequency of foods consumed in the past week. To evaluate how effectively the activities were established, integrated, and sustained in schools, the Garden Resources, Education, and Environment Nexus (GREEN) tool was used, and the school’s adherence to the school garden program was classified as high (scored 47 points out of 57). Results In 2013, 89 adolescents (mean ± SD 11.9 ± 0.4 years, 54% male) participated in the study, of which 83 continued until 2016 (14.8 ± 0.5 years, 55% male). In 2013, the mean frequency of raw salad and fruits consumption was 1.4 (CI [1.0–1.9]) and 4.3 (CI [3.8–4.9]) days per week, respectively. Three years later, the frequency of raw salad and fruits consumption was 2.2 (CI [1.6–2.7]) and 5.0 (4.5–5.5), respectively. Considering that five meals were offered at school (five days/week), it may be possible to assume that the program raised awareness on the importance of healthy eating. Conclusion Our results suggest that such integrated healthy eating promotion programs may improve adolescent athletes’ eating habits, by increasing the frequency …
format: application/pdf
format: text/html
creator: Fábia Albernaz Massarani
creator: Marta Citelli
creator: Daniela Silva Canella
creator: Josely Correa Koury
subject: Global Health
subject: Kinesiology
subject: Nutrition
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.7601
publisher: PeerJ Inc.
rights: © 2019 Massarani et al.
abstract: Background Adolescents, particularly athletes, have high exposure to ultra-processed foods, which could be harmful to their health and physical performance. School environments are capable of improving eating patterns. Our study is aimed at capturing changes in students’ food consumption three years after they enrolled at an experimental school, considered a model of health promotion in Rio de Janeiro city. We also aimed to depict the promising nature of the healthy eating promotion program implemented in the school and share the learnings from its implementation. Methods Our pilot study was a follow-up on the implementation of a school garden, experimental kitchen activities, and health promotion classes. We evaluated 83 adolescent athletes’ food consumption twice during the study: at its beginning (2013) and end (2016), by administering a food frequency questionnaire (FFQ) that inquired about the frequency of foods consumed in the past week. To evaluate how effectively the activities were established, integrated, and sustained in schools, the Garden Resources, Education, and Environment Nexus (GREEN) tool was used, and the school’s adherence to the school garden program was classified as high (scored 47 points out of 57). Results In 2013, 89 adolescents (mean ± SD 11.9 ± 0.4 years, 54% male) participated in the study, of which 83 continued until 2016 (14.8 ± 0.5 years, 55% male). In 2013, the mean frequency of raw salad and fruits consumption was 1.4 (CI [1.0–1.9]) and 4.3 (CI [3.8–4.9]) days per week, respectively. Three years later, the frequency of raw salad and fruits consumption was 2.2 (CI [1.6–2.7]) and 5.0 (4.5–5.5), respectively. Considering that five meals were offered at school (five days/week), it may be possible to assume that the program raised awareness on the importance of healthy eating. Conclusion Our results suggest that such integrated healthy eating promotion programs may improve adolescent athletes’ eating habits, by increasing the frequency …
bibliographic citation: Massarani et al. (2019) Healthy eating promoting in a Brazilian sports-oriented school: a pilot study. PeerJ 7:e7601 https://doi.org/10.7717/peerj.7601
date submitted: 2018-12-13
date accepted: 2019-08-01
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Massarani
  given name: Fábia Albernaz
author list: Agent
  family name: Citelli
  given name: Marta
author list: Agent
  family name: Canella
  given name: Daniela Silva
author list: Agent
  family name: Koury
  given name: Josely Correa
doi: 10.7717/peerj.7601
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Massarani et al.
attribution name: Massarani et al.

Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement
type: item
type: AcademicArticle
description: Infant acute lymphoblastic leukemia (ALL) with the mixed lineage leukemia (MLL) gene rearrangement (MLL-R) is considered a distinct leukemia from childhood or non-MLL-R infant ALL. To detect key genes and elucidate the molecular mechanisms of MLL-R infant ALL, microarray expression data were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between MLL-R and non-MLL-R infant ALL were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. Then, we constructed a protein-protein interaction (PPI) network and identified the hub genes. Finally, drug-gene interactions were mined. A total of 139 cases of MLL-R infant ALL including 77 (55.4%) fusions with AF4, 38 (27.3%) with ENL, 14 (10.1%) with AF9, and 10 (7.2%) other gene fusions were characterized. A total of 236 up-regulated and 84 down-regulated DEGs were identified. The up-regulated DEGs were mainly involved in homophilic cell adhesion, negative regulation of apoptotic process and cellular response to drug GO terms, while down-regulated DEGs were mainly enriched in extracellular matrix organization, protein kinase C signaling and neuron projection extension GO terms. The up-regulated DEGs were enriched in seven KEGG pathways, mainly involving transcriptional regulation and signaling pathways, and down-regulated DEGs were involved in three main KEGG pathways including Alzheimer’s disease, TGF-beta signaling pathway, and hematopoietic cell lineage. The PPI network included 297 nodes and 410 edges, with MYC, ALB, CD44, PTPRC and TNF identified as hub genes. Twenty-three drug-gene interactions including four up-regulated hub genes and 24 drugs were constructed by Drug Gene Interaction database (DGIdb). In conclusion, MYC, ALB, CD44, PTPRC and TNF may be potential bio-markers for the diagnosis and therapy of MLL-R infant ALL.
format: application/pdf
format: text/html
creator: Hao Zhang
creator: Juan Cheng
creator: Zijian Li
creator: Yaming Xi
subject: Molecular Biology
subject: Hematology
subject: Oncology
subject: Pediatrics
description: doi:10.7717/peerj.7628
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Infant acute lymphoblastic leukemia (ALL) with the mixed lineage leukemia (MLL) gene rearrangement (MLL-R) is considered a distinct leukemia from childhood or non-MLL-R infant ALL. To detect key genes and elucidate the molecular mechanisms of MLL-R infant ALL, microarray expression data were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between MLL-R and non-MLL-R infant ALL were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. Then, we constructed a protein-protein interaction (PPI) network and identified the hub genes. Finally, drug-gene interactions were mined. A total of 139 cases of MLL-R infant ALL including 77 (55.4%) fusions with AF4, 38 (27.3%) with ENL, 14 (10.1%) with AF9, and 10 (7.2%) other gene fusions were characterized. A total of 236 up-regulated and 84 down-regulated DEGs were identified. The up-regulated DEGs were mainly involved in homophilic cell adhesion, negative regulation of apoptotic process and cellular response to drug GO terms, while down-regulated DEGs were mainly enriched in extracellular matrix organization, protein kinase C signaling and neuron projection extension GO terms. The up-regulated DEGs were enriched in seven KEGG pathways, mainly involving transcriptional regulation and signaling pathways, and down-regulated DEGs were involved in three main KEGG pathways including Alzheimer’s disease, TGF-beta signaling pathway, and hematopoietic cell lineage. The PPI network included 297 nodes and 410 edges, with MYC, ALB, CD44, PTPRC and TNF identified as hub genes. Twenty-three drug-gene interactions including four up-regulated hub genes and 24 drugs were constructed by Drug Gene Interaction database (DGIdb). In conclusion, MYC, ALB, CD44, PTPRC and TNF may be potential bio-markers for the diagnosis and therapy of MLL-R infant ALL.
bibliographic citation: Zhang et al. (2019) Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement. PeerJ 7:e7628 https://doi.org/10.7717/peerj.7628
date submitted: 2019-04-16
date accepted: 2019-08-06
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Cheng
  given name: Juan
author list: Agent
  family name: Li
  given name: Zijian
author list: Agent
  family name: Xi
  given name: Yaming
doi: 10.7717/peerj.7628
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

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