PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Functioning of autobiographical memory specificity and self-defining memories in people with cancer diagnosis
items: Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea
items: Simulating more realistic predation threat using attack playbacks
items: Heatstroke-induced hepatocyte exosomes promote liver injury by activating the NOD-like receptor signaling pathway in mice
items: Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions
items: The effect of pupil size and peripheral brightness on detection and discrimination performance
items: Effect of music listening on hypertonia in neurologically impaired patients—systematic review
items: The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis
items: Biomarker potential of repetitive-element transcriptome in lung cancer
items: Genetic characteristics of non-familial epilepsy

Functioning of autobiographical memory specificity and self-defining memories in people with cancer diagnosis
type: item
type: AcademicArticle
description: Objectives Cognitive and emotional disturbances have been associated with the diagnosis and treatment of cancer. Autobiographical memory is one of the specific cognitive processes affected during this disease. The current study had two main aims: (1) to compare the functioning of autobiographical memory specificity and its related variables (executive functioning, depression and perceived stress) in a group of persons with cancer and a control group; and (2) to analyze whether the experience of cancer evolved into a self-defining memory in the sample of participants diagnosed with this disease. Method The study sample comprised 62 participants, 31 in the group with a cancer diagnosis and 31 in the control group. Autobiographical memory specificity, executive functions, depression, stress and self-defining memory were evaluated in the current study. Results Depressive symptomatology and reduced executive functioning, but not perceived stress levels, are related and are predictors of autobiographical memory specificity. In addition, the identified characteristics of the self-defining memories were associated with the cancer experience as a threat to physical integrity and an awareness of the meaning of life. Conclusion This emerging research line is especially important in view of its possible impacts on patients’ well-being, due to the importance of psychological processes in cancer disease.
format: application/pdf
format: text/html
creator: Marta Nieto
creator: Beatriz Navarro-Bravo
creator: Beatriz Moreno
creator: Alberto Ocana
creator: Juan Pedro Serrano
creator: Clotilde Boix Gras
creator: Jorge Ricarte
creator: Luz Fernández-Aguilar
creator: Laura Ros
creator: Jose Miguel Latorre
subject: Cognitive Disorders
subject: Oncology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8126
publisher: PeerJ Inc.
rights: © 2019 Nieto et al.
abstract: Objectives Cognitive and emotional disturbances have been associated with the diagnosis and treatment of cancer. Autobiographical memory is one of the specific cognitive processes affected during this disease. The current study had two main aims: (1) to compare the functioning of autobiographical memory specificity and its related variables (executive functioning, depression and perceived stress) in a group of persons with cancer and a control group; and (2) to analyze whether the experience of cancer evolved into a self-defining memory in the sample of participants diagnosed with this disease. Method The study sample comprised 62 participants, 31 in the group with a cancer diagnosis and 31 in the control group. Autobiographical memory specificity, executive functions, depression, stress and self-defining memory were evaluated in the current study. Results Depressive symptomatology and reduced executive functioning, but not perceived stress levels, are related and are predictors of autobiographical memory specificity. In addition, the identified characteristics of the self-defining memories were associated with the cancer experience as a threat to physical integrity and an awareness of the meaning of life. Conclusion This emerging research line is especially important in view of its possible impacts on patients’ well-being, due to the importance of psychological processes in cancer disease.
bibliographic citation: Nieto et al. (2019) Functioning of autobiographical memory specificity and self-defining memories in people with cancer diagnosis. PeerJ 7:e8126 https://doi.org/10.7717/peerj.8126
date submitted: 2019-07-09
date accepted: 2019-10-30
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nieto
  given name: Marta
author list: Agent
  family name: Navarro-Bravo
  given name: Beatriz
author list: Agent
  family name: Moreno
  given name: Beatriz
author list: Agent
  family name: Ocana
  given name: Alberto
author list: Agent
  family name: Serrano
  given name: Juan Pedro
author list: Agent
  family name: Boix Gras
  given name: Clotilde
author list: Agent
  family name: Ricarte
  given name: Jorge
author list: Agent
  family name: Fernández-Aguilar
  given name: Luz
author list: Agent
  family name: Ros
  given name: Laura
author list: Agent
  family name: Latorre
  given name: Jose Miguel
doi: 10.7717/peerj.8126
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: © 2019 Nieto et al.
attribution name: Nieto et al.

Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea
type: item
type: AcademicArticle
description: Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.
format: application/pdf
format: text/html
creator: Wuttichai Mhuantong
creator: Handung Nuryadi
creator: Agus Trianto
creator: Agus Sabdono
creator: Sithichoke Tangphatsornruang
creator: Lily Eurwilaichitr
creator: Pattanop Kanokratana
creator: Verawat Champreda
subject: Biodiversity
subject: Microbiology
description: doi:10.7717/peerj.8137
publisher: PeerJ Inc.
rights: © 2019 Mhuantong et al.
abstract: Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.
bibliographic citation: Mhuantong et al. (2019) Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea. PeerJ 7:e8137 https://doi.org/10.7717/peerj.8137
date submitted: 2019-03-15
date accepted: 2019-11-01
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mhuantong
  given name: Wuttichai
author list: Agent
  family name: Nuryadi
  given name: Handung
author list: Agent
  family name: Trianto
  given name: Agus
author list: Agent
  family name: Sabdono
  given name: Agus
author list: Agent
  family name: Tangphatsornruang
  given name: Sithichoke
author list: Agent
  family name: Eurwilaichitr
  given name: Lily
author list: Agent
  family name: Kanokratana
  given name: Pattanop
author list: Agent
  family name: Champreda
  given name: Verawat
doi: 10.7717/peerj.8137
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Mhuantong et al.
attribution name: Mhuantong et al.

Simulating more realistic predation threat using attack playbacks
type: item
type: AcademicArticle
description: Use of virtual proxies of live animals are rapidly gaining ground in studies of animal behaviour. Such proxies help to reduce the number of live experimental animals needed to stimulate the behaviour of experimental individuals and to increase standardisation. However, using too simplistic proxies may fail to induce a desired effect and/or lead to quick habituation. For instance, in a predation context, prey often employ multimodal cues to detect predators or use specific aspects of predator behaviour to assess threat. In a live interaction, predator and prey often show behaviours directed towards each other, which are absent in virtual proxies. Here we compared the effectiveness of chemical and visual predator cues in the cooperatively breeding cichlid Neolamprologus pulcher, a species in which predation pressure has been the evolutionary driver of its sociality. We created playbacks of predators simulating an attack and tested their effectiveness in comparison to a playback showing regular activity and to a live predator. We further compared the effectiveness of predator odour and conspecific skin extracts on behaviours directed towards a predator playback. Regular playbacks of calmly swimming predators were less effective than live predators in stimulating a focal individual’s aggression and attention. However, playbacks mimicking an attacking predator induced responses much like a live predator. Chemical cues did not affect predator directed behaviour.
format: application/pdf
format: text/html
creator: Mukta Watve
creator: Sebastian Prati
creator: Barbara Taborsky
subject: Animal Behavior
description: doi:10.7717/peerj.8149
publisher: PeerJ Inc.
rights: © 2019 Watve et al.
abstract: Use of virtual proxies of live animals are rapidly gaining ground in studies of animal behaviour. Such proxies help to reduce the number of live experimental animals needed to stimulate the behaviour of experimental individuals and to increase standardisation. However, using too simplistic proxies may fail to induce a desired effect and/or lead to quick habituation. For instance, in a predation context, prey often employ multimodal cues to detect predators or use specific aspects of predator behaviour to assess threat. In a live interaction, predator and prey often show behaviours directed towards each other, which are absent in virtual proxies. Here we compared the effectiveness of chemical and visual predator cues in the cooperatively breeding cichlid Neolamprologus pulcher, a species in which predation pressure has been the evolutionary driver of its sociality. We created playbacks of predators simulating an attack and tested their effectiveness in comparison to a playback showing regular activity and to a live predator. We further compared the effectiveness of predator odour and conspecific skin extracts on behaviours directed towards a predator playback. Regular playbacks of calmly swimming predators were less effective than live predators in stimulating a focal individual’s aggression and attention. However, playbacks mimicking an attacking predator induced responses much like a live predator. Chemical cues did not affect predator directed behaviour.
bibliographic citation: Watve et al. (2019) Simulating more realistic predation threat using attack playbacks. PeerJ 7:e8149 https://doi.org/10.7717/peerj.8149
date submitted: 2019-07-18
date accepted: 2019-11-04
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Watve
  given name: Mukta
author list: Agent
  family name: Prati
  given name: Sebastian
author list: Agent
  family name: Taborsky
  given name: Barbara
doi: 10.7717/peerj.8149
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Watve et al.
attribution name: Watve et al.

Heatstroke-induced hepatocyte exosomes promote liver injury by activating the NOD-like receptor signaling pathway in mice
type: item
type: AcademicArticle
description: Background Liver injury is a common and important clinical issue of severe heat stress (HS), which has toxic effects and promotes subsequent multiple organ failure. The pathogenesis of HS-induced liver injury has not been fully elucidated. Passively injured hepatocytes also drive liver injury. Exosomes, extracellular vesicles secreted by hepatocytes as “danger signals,” mediate the intercellular transportation of diverse functional protein cargoes and modulate the biological processes of target cells. However, whether hepatocyte exosomes are involved in HS-induced liver injury has not been reported. The purpose of the current study was to clarify the release of hepatocyte exosomes under HS conditions and to explore their role in mediating HS-induced liver injury. Methods HS was induced in hepatocytes or mice by hyperthermic treatment at 43.0 °C for 1 h. Exosomes from control and HS-exposed hepatocytes were isolated by standard differential ultracentrifugation. The hepatocyte exosomes were characterized, and the differentially expressed proteins of the control and HS exosomes were identified by isobaric tags for relative and absolute quantitation (iTRAQ) mass spectrometry and subjected to Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Recipient hepatocytes were treated with control or HS exosomes, whereas in vivo, the exosomes were infused into mice. The internalization of HS hepatocyte exosomes by hepatocytes or the liver was tracked. The effect of HS exosomes on the activation of the NOD-like receptor signaling pathway and liver injury was demonstrated in vitro and in vivo. Results HS induced an increase in the release of exosomes from hepatocytes, which were internalized by recipient liver cells in vitro and taken up by the liver in vivo. HS significantly changed the proteomic profiles of hepatocyte exosomes based on the iTRAQ analysis. The KEGG pathway analysis revealed the enrichment of proteins associated with injury and inflammatory signaling…
format: application/pdf
format: text/html
creator: Yue Li
creator: Xintao Zhu
creator: Ming Zhang
creator: Huasheng Tong
creator: Lei Su
subject: Emergency and Critical Care
subject: Gastroenterology and Hepatology
subject: Hematology
description: doi:10.7717/peerj.8216
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Liver injury is a common and important clinical issue of severe heat stress (HS), which has toxic effects and promotes subsequent multiple organ failure. The pathogenesis of HS-induced liver injury has not been fully elucidated. Passively injured hepatocytes also drive liver injury. Exosomes, extracellular vesicles secreted by hepatocytes as “danger signals,” mediate the intercellular transportation of diverse functional protein cargoes and modulate the biological processes of target cells. However, whether hepatocyte exosomes are involved in HS-induced liver injury has not been reported. The purpose of the current study was to clarify the release of hepatocyte exosomes under HS conditions and to explore their role in mediating HS-induced liver injury. Methods HS was induced in hepatocytes or mice by hyperthermic treatment at 43.0 °C for 1 h. Exosomes from control and HS-exposed hepatocytes were isolated by standard differential ultracentrifugation. The hepatocyte exosomes were characterized, and the differentially expressed proteins of the control and HS exosomes were identified by isobaric tags for relative and absolute quantitation (iTRAQ) mass spectrometry and subjected to Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Recipient hepatocytes were treated with control or HS exosomes, whereas in vivo, the exosomes were infused into mice. The internalization of HS hepatocyte exosomes by hepatocytes or the liver was tracked. The effect of HS exosomes on the activation of the NOD-like receptor signaling pathway and liver injury was demonstrated in vitro and in vivo. Results HS induced an increase in the release of exosomes from hepatocytes, which were internalized by recipient liver cells in vitro and taken up by the liver in vivo. HS significantly changed the proteomic profiles of hepatocyte exosomes based on the iTRAQ analysis. The KEGG pathway analysis revealed the enrichment of proteins associated with injury and inflammatory signaling…
bibliographic citation: Li et al. (2019) Heatstroke-induced hepatocyte exosomes promote liver injury by activating the NOD-like receptor signaling pathway in mice. PeerJ 7:e8216 https://doi.org/10.7717/peerj.8216
date submitted: 2019-07-24
date accepted: 2019-11-14
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yue
author list: Agent
  family name: Zhu
  given name: Xintao
author list: Agent
  family name: Zhang
  given name: Ming
author list: Agent
  family name: Tong
  given name: Huasheng
author list: Agent
  family name: Su
  given name: Lei
doi: 10.7717/peerj.8216
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Li et al.
attribution name: Li et al.

Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions
type: item
type: AcademicArticle
description: Ecological factors, host characteristics and/or interactions among microbes may all shape the occurrence of microbes and the structure of microbial communities within organisms. In the past, disentangling these factors and determining their relative importance in shaping within-host microbiota communities has been hampered by analytical limitations to account for (dis)similar environmental preferences (‘environmental filtering’). Here we used a joint species distribution modelling (JSDM) approach to characterize the bacterial microbiota of one of the most important disease vectors in Europe, the sheep tick Ixodes ricinus, along ecological gradients in the Swiss Alps. Although our study captured extensive environmental variation along elevational clines, the explanatory power of such large-scale ecological factors was comparably weak, suggesting that tick-specific traits and behaviours, microhabitat and -climate experienced by ticks, and interactions among microbes play an important role in shaping tick microbial communities. Indeed, when accounting for shared environmental preferences, evidence for significant patterns of positive or negative co-occurrence among microbes was found, which is indicative of competition or facilitation processes. Signals of facilitation were observed primarily among human pathogens, leading to co-infection within ticks, whereas signals of competition were observed between the tick endosymbiont Spiroplasma and human pathogens. These findings highlight the important role of small-scale ecological variation and microbe-microbe interactions in shaping tick microbial communities and the dynamics of tick-borne disease.
format: application/pdf
format: text/html
creator: Tuomas Aivelo
creator: Anna Norberg
creator: Barbara Tschirren
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Parasitology
description: doi:10.7717/peerj.8217
publisher: PeerJ Inc.
rights: © 2019 Aivelo et al.
abstract: Ecological factors, host characteristics and/or interactions among microbes may all shape the occurrence of microbes and the structure of microbial communities within organisms. In the past, disentangling these factors and determining their relative importance in shaping within-host microbiota communities has been hampered by analytical limitations to account for (dis)similar environmental preferences (‘environmental filtering’). Here we used a joint species distribution modelling (JSDM) approach to characterize the bacterial microbiota of one of the most important disease vectors in Europe, the sheep tick Ixodes ricinus, along ecological gradients in the Swiss Alps. Although our study captured extensive environmental variation along elevational clines, the explanatory power of such large-scale ecological factors was comparably weak, suggesting that tick-specific traits and behaviours, microhabitat and -climate experienced by ticks, and interactions among microbes play an important role in shaping tick microbial communities. Indeed, when accounting for shared environmental preferences, evidence for significant patterns of positive or negative co-occurrence among microbes was found, which is indicative of competition or facilitation processes. Signals of facilitation were observed primarily among human pathogens, leading to co-infection within ticks, whereas signals of competition were observed between the tick endosymbiont Spiroplasma and human pathogens. These findings highlight the important role of small-scale ecological variation and microbe-microbe interactions in shaping tick microbial communities and the dynamics of tick-borne disease.
bibliographic citation: Aivelo et al. (2019) Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions. PeerJ 7:e8217 https://doi.org/10.7717/peerj.8217
date submitted: 2019-09-17
date accepted: 2019-11-14
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aivelo
  given name: Tuomas
author list: Agent
  family name: Norberg
  given name: Anna
author list: Agent
  family name: Tschirren
  given name: Barbara
doi: 10.7717/peerj.8217
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Aivelo et al.
attribution name: Aivelo et al.

The effect of pupil size and peripheral brightness on detection and discrimination performance
type: item
type: AcademicArticle
description: It is easier to read dark text on a bright background (positive polarity) than to read bright text on a dark background (negative polarity). This positive-polarity advantage is often linked to pupil size: A bright background induces small pupils, which in turn increases visual acuity. Here we report that pupil size, when manipulated through peripheral brightness, has qualitatively different effects on discrimination of fine stimuli in central vision and detection of faint stimuli in peripheral vision. Small pupils are associated with improved discrimination performance, consistent with the positive-polarity advantage, but only for very small stimuli that are at the threshold of visual acuity. In contrast, large pupils are associated with improved detection performance. These results are likely due to two pupil-size related factors: Small pupils increase visual acuity, which improves discrimination of fine stimuli; and large pupils increase light influx, which improves detection of faint stimuli. Light scatter is likely also a contributing factor: When a display is bright, light scatter creates a diffuse veil of retinal illumination that reduces perceived image contrast, thus impairing detection performance. We further found that pupil size was larger during the detection task than during the discrimination task, even though both tasks were equally difficult and similar in visual input; this suggests that the pupil may automatically assume an optimal size for the current task. Our results may explain why pupils dilate in response to arousal: This may reflect an increased emphasis on detection of unpredictable danger, which is crucially important in many situations that are characterized by high levels of arousal. Finally, we discuss the implications of our results for the ergonomics of display design.
format: application/pdf
format: text/html
creator: Sebastiaan Mathôt
creator: Yavor Ivanov
subject: Neuroscience
subject: Ophthalmology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8220
publisher: PeerJ Inc.
rights: © 2019 Mathôt and Ivanov
abstract: It is easier to read dark text on a bright background (positive polarity) than to read bright text on a dark background (negative polarity). This positive-polarity advantage is often linked to pupil size: A bright background induces small pupils, which in turn increases visual acuity. Here we report that pupil size, when manipulated through peripheral brightness, has qualitatively different effects on discrimination of fine stimuli in central vision and detection of faint stimuli in peripheral vision. Small pupils are associated with improved discrimination performance, consistent with the positive-polarity advantage, but only for very small stimuli that are at the threshold of visual acuity. In contrast, large pupils are associated with improved detection performance. These results are likely due to two pupil-size related factors: Small pupils increase visual acuity, which improves discrimination of fine stimuli; and large pupils increase light influx, which improves detection of faint stimuli. Light scatter is likely also a contributing factor: When a display is bright, light scatter creates a diffuse veil of retinal illumination that reduces perceived image contrast, thus impairing detection performance. We further found that pupil size was larger during the detection task than during the discrimination task, even though both tasks were equally difficult and similar in visual input; this suggests that the pupil may automatically assume an optimal size for the current task. Our results may explain why pupils dilate in response to arousal: This may reflect an increased emphasis on detection of unpredictable danger, which is crucially important in many situations that are characterized by high levels of arousal. Finally, we discuss the implications of our results for the ergonomics of display design.
bibliographic citation: Mathôt et al. (2019) The effect of pupil size and peripheral brightness on detection and discrimination performance. PeerJ 7:e8220 https://doi.org/10.7717/peerj.8220
date submitted: 2019-05-06
date accepted: 2019-11-15
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mathôt
  given name: Sebastiaan
author list: Agent
  family name: Ivanov
  given name: Yavor
doi: 10.7717/peerj.8220
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Mathôt and Ivanov
attribution name: Mathôt and Ivanov

Effect of music listening on hypertonia in neurologically impaired patients—systematic review
type: item
type: AcademicArticle
description: Background As music listening is able to induce self-perceived and physiological signs of relaxation, it might be an interesting tool to induce muscle relaxation in patients with hypertonia. To this date effective non-pharmacological rehabilitation strategies to treat hypertonia in neurologically impaired patients are lacking. Therefore the aim is to investigate the effectiveness of music listening on muscle activity and relaxation. Methodology The search strategy was performed by the PRISMA guidelines and registered in the PROSPERO database (no. 42019128511). Seven databases were systematically searched until March 2019. Six of the 1,684 studies met the eligibility criteria and were included in this review. Risk of bias was assessed by the PEDro scale. In total 171 patients with a variety of neurological conditions were included assessing hypertonia with both clinicall and biomechanical measures. Results The analysis showed that there was a large treatment effect of music listening on muscle performance (SMD 0.96, 95% CI [0.29–1.63], I2 = 10%, Z = 2.82, p = 0.005). Music can be used as either background music during rehabilitation (dual-task) or during rest (single-task) and musical preferences seem to play a major role in the observed treatment effect. Conclusions Although music listening is able to induce muscle relaxation, several gaps in the available literature were acknowledged. Future research is in need of an accurate and objective assessment of hypertonia.
format: application/pdf
format: text/html
creator: Tamaya Van Criekinge
creator: Kristiaan D’Août
creator: Jonathon O’Brien
creator: Eduardo Coutinho
subject: Neuroscience
subject: Kinesiology
subject: Neurology
description: doi:10.7717/peerj.8228
publisher: PeerJ Inc.
rights: © 2019 Van Criekinge et al.
abstract: Background As music listening is able to induce self-perceived and physiological signs of relaxation, it might be an interesting tool to induce muscle relaxation in patients with hypertonia. To this date effective non-pharmacological rehabilitation strategies to treat hypertonia in neurologically impaired patients are lacking. Therefore the aim is to investigate the effectiveness of music listening on muscle activity and relaxation. Methodology The search strategy was performed by the PRISMA guidelines and registered in the PROSPERO database (no. 42019128511). Seven databases were systematically searched until March 2019. Six of the 1,684 studies met the eligibility criteria and were included in this review. Risk of bias was assessed by the PEDro scale. In total 171 patients with a variety of neurological conditions were included assessing hypertonia with both clinicall and biomechanical measures. Results The analysis showed that there was a large treatment effect of music listening on muscle performance (SMD 0.96, 95% CI [0.29–1.63], I2 = 10%, Z = 2.82, p = 0.005). Music can be used as either background music during rehabilitation (dual-task) or during rest (single-task) and musical preferences seem to play a major role in the observed treatment effect. Conclusions Although music listening is able to induce muscle relaxation, several gaps in the available literature were acknowledged. Future research is in need of an accurate and objective assessment of hypertonia.
bibliographic citation: Van Criekinge et al. (2019) Effect of music listening on hypertonia in neurologically impaired patients—systematic review. PeerJ 7:e8228 https://doi.org/10.7717/peerj.8228
date submitted: 2019-07-23
date accepted: 2019-11-18
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Van Criekinge
  given name: Tamaya
author list: Agent
  family name: D’Août
  given name: Kristiaan
author list: Agent
  family name: O’Brien
  given name: Jonathon
author list: Agent
  family name: Coutinho
  given name: Eduardo
doi: 10.7717/peerj.8228
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Van Criekinge et al.
attribution name: Van Criekinge et al.

The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis
type: item
type: AcademicArticle
description: Background The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences. Methods Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups. Results The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.
format: application/pdf
format: text/html
creator: Dan Chen
creator: Jing Liu
creator: Luca Bartolozzi
creator: Xia Wan
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.8274
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences. Methods Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups. Results The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.
bibliographic citation: Chen et al. (2019) The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis. PeerJ 7:e8274 https://doi.org/10.7717/peerj.8274
date submitted: 2019-02-19
date accepted: 2019-11-22
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Dan
author list: Agent
  family name: Liu
  given name: Jing
author list: Agent
  family name: Bartolozzi
  given name: Luca
author list: Agent
  family name: Wan
  given name: Xia
doi: 10.7717/peerj.8274
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: © 2019 Chen et al.
attribution name: Chen et al.

Biomarker potential of repetitive-element transcriptome in lung cancer
type: item
type: AcademicArticle
description: Since repetitive elements (REs) account for nearly 53% of the human genome, profiling its transcription after an oncogenic change might help in the search for new biomarkers. Lung cancer was selected as target since it is the most frequent cause of cancer death. A bioinformatic workflow based on well-established bioinformatic tools (such as RepEnrich, RepBase, SAMTools, edgeR and DESeq2) has been developed to identify differentially expressed RNAs from REs. It was trained and tested with public RNA-seq data from matched sequencing of tumour and healthy lung tissues from the same patient to reveal differential expression within the RE transcriptome. Healthy lung tissues express a specific set of REs whose expression, after an oncogenic process, is strictly and specifically changed. Discrete sets of differentially expressed REs were found for lung adenocarcinoma, for small-cell lung cancer, and for both cancers. Differential expression affects more HERV-than LINE-derived REs and seems biased towards down-regulation in cancer cells. REs behaving consistently in all patients were tested in a different patient cohort to validate the proposed biomarkers. Down-regulation of AluYg6 and LTR18B was confirmed as potential lung cancer biomarkers, while up-regulation of HERVK11D-Int is specific for lung adenocarcinoma and up-regulation of UCON88 is specific for small cell lung cancer. Hence, the study of RE transcriptome might be considered another research target in cancer, making REs a promising source of lung cancer biomarkers.
format: application/pdf
format: text/html
creator: Macarena Arroyo
creator: Rocío Bautista
creator: Rafael Larrosa
creator: Manuel Ángel Cobo
creator: M. Gonzalo Claros
subject: Bioinformatics
subject: Genomics
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.8277
publisher: PeerJ Inc.
rights: © 2019 Arroyo et al.
abstract: Since repetitive elements (REs) account for nearly 53% of the human genome, profiling its transcription after an oncogenic change might help in the search for new biomarkers. Lung cancer was selected as target since it is the most frequent cause of cancer death. A bioinformatic workflow based on well-established bioinformatic tools (such as RepEnrich, RepBase, SAMTools, edgeR and DESeq2) has been developed to identify differentially expressed RNAs from REs. It was trained and tested with public RNA-seq data from matched sequencing of tumour and healthy lung tissues from the same patient to reveal differential expression within the RE transcriptome. Healthy lung tissues express a specific set of REs whose expression, after an oncogenic process, is strictly and specifically changed. Discrete sets of differentially expressed REs were found for lung adenocarcinoma, for small-cell lung cancer, and for both cancers. Differential expression affects more HERV-than LINE-derived REs and seems biased towards down-regulation in cancer cells. REs behaving consistently in all patients were tested in a different patient cohort to validate the proposed biomarkers. Down-regulation of AluYg6 and LTR18B was confirmed as potential lung cancer biomarkers, while up-regulation of HERVK11D-Int is specific for lung adenocarcinoma and up-regulation of UCON88 is specific for small cell lung cancer. Hence, the study of RE transcriptome might be considered another research target in cancer, making REs a promising source of lung cancer biomarkers.
bibliographic citation: Arroyo et al. (2019) Biomarker potential of repetitive-element transcriptome in lung cancer. PeerJ 7:e8277 https://doi.org/10.7717/peerj.8277
date submitted: 2019-10-02
date accepted: 2019-11-22
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arroyo
  given name: Macarena
author list: Agent
  family name: Bautista
  given name: Rocío
author list: Agent
  family name: Larrosa
  given name: Rafael
author list: Agent
  family name: Cobo
  given name: Manuel Ángel
author list: Agent
  family name: Claros
  given name: M. Gonzalo
doi: 10.7717/peerj.8277
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: ©2019 Arroyo et al.
attribution name: Arroyo et al.

Genetic characteristics of non-familial epilepsy
type: item
type: AcademicArticle
description: Background Knowledge of the genetic etiology of epilepsy can provide essential prognostic information and influence decisions regarding treatment and management, leading us into the era of precision medicine. However, the genetic basis underlying epileptogenesis or epilepsy pharmacoresistance is not well-understood, particularly in non-familial epilepsies with heterogeneous phenotypes that last until or start in adulthood. Methods We sought to determine the contribution of known epilepsy-associated genes (EAGs) to the causation of non-familial epilepsies with heterogeneous phenotypes and to the genetic basis underlying epilepsy pharmacoresistance. We performed a multi-center study for whole exome sequencing-based screening of 178 selected EAGs in 243 non-familial adult patients with primarily focal epilepsy (122 drug-resistant and 121 drug-responsive epilepsies). The pathogenicity of each variant was assessed through a customized stringent filtering process and classified according to the American College of Medical Genetics and Genomics guidelines. Results Possible causal genetic variants of epilepsy were uncovered in 13.2% of non-familial patients with primarily focal epilepsy. The diagnostic yield according to the seizure onset age was 25% (2/8) in the neonatal and infantile period, 11.1% (14/126) in childhood and 14.7% (16/109) in adulthood. The higher diagnostic yields were from ion channel-related genes and mTOR pathway-related genes, which does not significantly differ from the results of previous studies on familial or early-onset epilepsies. These potentially pathogenic variants, which were identified in genes that have been mainly associated with early-onset epilepsies with severe phenotypes, were also linked to epilepsies that start in or last until adulthood in this study. This finding suggested the presence of one or more disease-modifying factors that regulate the onset time or severity of epileptogenesis. The target hypothesis of epilepsy pharmacoresi…
format: application/pdf
format: text/html
creator: Kyung Wook Kang
creator: Wonkuk Kim
creator: Yong Won Cho
creator: Sang Kun Lee
creator: Ki-Young Jung
creator: Wonchul Shin
creator: Dong Wook Kim
creator: Won-Joo Kim
creator: Hyang Woon Lee
creator: Woojun Kim
creator: Keuntae Kim
creator: So-Hyun Lee
creator: Seok-Yong Choi
creator: Myeong-Kyu Kim
subject: Genetics
subject: Neurology
description: doi:10.7717/peerj.8278
publisher: PeerJ Inc.
rights: © 2019 Kang et al.
abstract: Background Knowledge of the genetic etiology of epilepsy can provide essential prognostic information and influence decisions regarding treatment and management, leading us into the era of precision medicine. However, the genetic basis underlying epileptogenesis or epilepsy pharmacoresistance is not well-understood, particularly in non-familial epilepsies with heterogeneous phenotypes that last until or start in adulthood. Methods We sought to determine the contribution of known epilepsy-associated genes (EAGs) to the causation of non-familial epilepsies with heterogeneous phenotypes and to the genetic basis underlying epilepsy pharmacoresistance. We performed a multi-center study for whole exome sequencing-based screening of 178 selected EAGs in 243 non-familial adult patients with primarily focal epilepsy (122 drug-resistant and 121 drug-responsive epilepsies). The pathogenicity of each variant was assessed through a customized stringent filtering process and classified according to the American College of Medical Genetics and Genomics guidelines. Results Possible causal genetic variants of epilepsy were uncovered in 13.2% of non-familial patients with primarily focal epilepsy. The diagnostic yield according to the seizure onset age was 25% (2/8) in the neonatal and infantile period, 11.1% (14/126) in childhood and 14.7% (16/109) in adulthood. The higher diagnostic yields were from ion channel-related genes and mTOR pathway-related genes, which does not significantly differ from the results of previous studies on familial or early-onset epilepsies. These potentially pathogenic variants, which were identified in genes that have been mainly associated with early-onset epilepsies with severe phenotypes, were also linked to epilepsies that start in or last until adulthood in this study. This finding suggested the presence of one or more disease-modifying factors that regulate the onset time or severity of epileptogenesis. The target hypothesis of epilepsy pharmacoresi…
bibliographic citation: Kang et al. (2019) Genetic characteristics of non-familial epilepsy. PeerJ 7:e8278 https://doi.org/10.7717/peerj.8278
date submitted: 2019-06-25
date accepted: 2019-11-22
issued: 2019-12-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kang
  given name: Kyung Wook
author list: Agent
  family name: Kim
  given name: Wonkuk
author list: Agent
  family name: Cho
  given name: Yong Won
author list: Agent
  family name: Lee
  given name: Sang Kun
author list: Agent
  family name: Jung
  given name: Ki-Young
author list: Agent
  family name: Shin
  given name: Wonchul
author list: Agent
  family name: Kim
  given name: Dong Wook
author list: Agent
  family name: Kim
  given name: Won-Joo
author list: Agent
  family name: Lee
  given name: Hyang Woon
author list: Agent
  family name: Kim
  given name: Woojun
author list: Agent
  family name: Kim
  given name: Keuntae
author list: Agent
  family name: Lee
  given name: So-Hyun
author list: Agent
  family name: Choi
  given name: Seok-Yong
author list: Agent
  family name: Kim
  given name: Myeong-Kyu
doi: 10.7717/peerj.8278
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-19
copyright: © 2019 Kang et al.
attribution name: Kang et al.

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