PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of crude oil on survival and development in embryonated eggs in Callinectes sapidus Rathbun, 1896 (Decapoda, Portunidae)
items: Stress among on-duty firefighters: an ambulatory assessment study
items: Plant-derived chimeric antibodies inhibit the invasion of human fibroblasts by Toxoplasma gondii
items: Behavior problems and personality in Korean high school students
items: Effects of gelsemine on oxidative stress and DNA damage responses of Tetrahymena thermophila
items: Screening of prognostic biomarkers for endometrial carcinoma based on a ceRNA network
items: The recent expansion of Fox Sparrow (Passerella iliaca iliaca) breeding range into the northeastern United States
items: Posture similarity index: a method to compare hand postures in synergy space
items: Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
items: Technology-assisted white cane: evaluation and future directions

Effects of crude oil on survival and development in embryonated eggs in Callinectes sapidus Rathbun, 1896 (Decapoda, Portunidae)
type: item
type: AcademicArticle
description: Blue crabs, Callinectes sapidus Rathbun, 1896, are ubiquitous along the Atlantic and Gulf coasts of the USA. These organisms play an integral role in the ecosystems of the Gulf of Mexico (GOM), where not only are they a keystone species, but are also socioeconomically important. The survival of embryonated eggs is necessary to ensure adequate recruitment into the next generation. Because the 2010 Deepwater Horizon oil spill (DWH) occurred during the peak of the blue crab spawning season, the incident likely impacted blue crab embryos. In order to assess the effect of oil on embryonic growth and development, we collected embryonated eggs from seven different female blue crabs from the GOM throughout the spawning season and exposed them to an oil concentration of 500 ppb (the approximate concentration of oil at the surface water near the site of the Deepwater Horizon oil rig). Exposure to oil at this concentration caused a significantly larger proportion of prezoeae vs. zoeae to hatch from embryonated eggs in experiments lasting longer than 4 days. Exposure to oil did not significantly affect overall survival or development rate. The prezoeal stage is a little-studied stage of blue crab development. Though it may or may not be a normal stage of development, this stage has been found to occur in suboptimal conditions and has lower survival than zoeal stages. The larger proportion of prezoeae following prolonged exposure to oil thus indicates that crude oil at concentrations likely to be experienced by crabs after the DWH spill negatively impacted the development of blue crab embryos. In addition to providing insight into the effects of the DWH, this study sheds light on embryonic development in blue crabs, a critical, but poorly investigated phase of this important species’ life cycle.
format: application/pdf
format: text/html
creator: Kelsie L. Kelly
creator: Caz M. Taylor
subject: Developmental Biology
subject: Marine Biology
subject: Toxicology
subject: Ecotoxicology
subject: Environmental Impacts
description: doi:10.7717/peerj.5985
publisher: PeerJ Inc.
rights: © 2018 Kelly and Taylor
abstract: Blue crabs, Callinectes sapidus Rathbun, 1896, are ubiquitous along the Atlantic and Gulf coasts of the USA. These organisms play an integral role in the ecosystems of the Gulf of Mexico (GOM), where not only are they a keystone species, but are also socioeconomically important. The survival of embryonated eggs is necessary to ensure adequate recruitment into the next generation. Because the 2010 Deepwater Horizon oil spill (DWH) occurred during the peak of the blue crab spawning season, the incident likely impacted blue crab embryos. In order to assess the effect of oil on embryonic growth and development, we collected embryonated eggs from seven different female blue crabs from the GOM throughout the spawning season and exposed them to an oil concentration of 500 ppb (the approximate concentration of oil at the surface water near the site of the Deepwater Horizon oil rig). Exposure to oil at this concentration caused a significantly larger proportion of prezoeae vs. zoeae to hatch from embryonated eggs in experiments lasting longer than 4 days. Exposure to oil did not significantly affect overall survival or development rate. The prezoeal stage is a little-studied stage of blue crab development. Though it may or may not be a normal stage of development, this stage has been found to occur in suboptimal conditions and has lower survival than zoeal stages. The larger proportion of prezoeae following prolonged exposure to oil thus indicates that crude oil at concentrations likely to be experienced by crabs after the DWH spill negatively impacted the development of blue crab embryos. In addition to providing insight into the effects of the DWH, this study sheds light on embryonic development in blue crabs, a critical, but poorly investigated phase of this important species’ life cycle.
bibliographic citation: Kelly et al. (2018) Effects of crude oil on survival and development in embryonated eggs in Callinectes sapidus Rathbun, 1896 (Decapoda, Portunidae). PeerJ 6:e5985 https://doi.org/10.7717/peerj.5985
date submitted: 2017-03-07
date accepted: 2018-10-22
issued: 2018-12-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kelly
  given name: Kelsie L.
author list: Agent
  family name: Taylor
  given name: Caz M.
doi: 10.7717/peerj.5985
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-11
copyright: © 2018 Kelly and Taylor
attribution name: Kelly and Taylor

Stress among on-duty firefighters: an ambulatory assessment study
type: item
type: AcademicArticle
description: Background Stress at work has been broadly acknowledged as a worldwide problem and has been the focus of concern for many researchers. Firefighting, in particular, is frequently reported as a highly stressful occupation. In order to investigate firefighters’ occupational health in terms of stress events, perceptions, symptoms, and physiological reactions under real-world conditions, an ambulatory assessment protocol was developed. Methods Seventeen firefighters’ cardiac signal was continuously monitored during an average of three shifts within a working week with medical clinically certified equipment (VitalJacket®), which allows for continuous electrocardiogram (ECG) and actigraphy measurement. Psychological data were collected with a software application running on smartphones, collecting potential stressful events, stress symptoms, and stress appraisal. Results A total of 450.56 h of medical-quality ECG were collected, and heart rate variability (HRV) analysis was performed. Findings suggest that although ‘fire’ situations are more common, ‘accidents’ are more stressful. Additionally, firefighters showed high levels of physiological stress (based on AVNN and LF/HF HRV metrics) when compared to normative healthy population values that may not be diagnosed using merely self-reports. Discussion The proposed ambulatory study seems to be useful for the monitoring of stress levels and its potential impact on health of first responders. Additionally, it could also be an important tool for the design and implementation of efficient interventions and informed management resolutions in real time. Potential applications of this research include the development of quantified occupational health (qOHealth) devices for real life monitoring of emergency personnel stress reactions.
format: application/pdf
format: text/html
creator: Susana Rodrigues
creator: Joana S. Paiva
creator: Duarte Dias
creator: João Paulo S. Cunha
subject: Bioengineering
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.5967
publisher: PeerJ Inc.
rights: © 2018 Rodrigues et al.
abstract: Background Stress at work has been broadly acknowledged as a worldwide problem and has been the focus of concern for many researchers. Firefighting, in particular, is frequently reported as a highly stressful occupation. In order to investigate firefighters’ occupational health in terms of stress events, perceptions, symptoms, and physiological reactions under real-world conditions, an ambulatory assessment protocol was developed. Methods Seventeen firefighters’ cardiac signal was continuously monitored during an average of three shifts within a working week with medical clinically certified equipment (VitalJacket®), which allows for continuous electrocardiogram (ECG) and actigraphy measurement. Psychological data were collected with a software application running on smartphones, collecting potential stressful events, stress symptoms, and stress appraisal. Results A total of 450.56 h of medical-quality ECG were collected, and heart rate variability (HRV) analysis was performed. Findings suggest that although ‘fire’ situations are more common, ‘accidents’ are more stressful. Additionally, firefighters showed high levels of physiological stress (based on AVNN and LF/HF HRV metrics) when compared to normative healthy population values that may not be diagnosed using merely self-reports. Discussion The proposed ambulatory study seems to be useful for the monitoring of stress levels and its potential impact on health of first responders. Additionally, it could also be an important tool for the design and implementation of efficient interventions and informed management resolutions in real time. Potential applications of this research include the development of quantified occupational health (qOHealth) devices for real life monitoring of emergency personnel stress reactions.
bibliographic citation: Rodrigues et al. (2018) Stress among on-duty firefighters: an ambulatory assessment study. PeerJ 6:e5967 https://doi.org/10.7717/peerj.5967
date submitted: 2018-07-03
date accepted: 2018-10-19
issued: 2018-12-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodrigues
  given name: Susana
author list: Agent
  family name: Paiva
  given name: Joana S.
author list: Agent
  family name: Dias
  given name: Duarte
author list: Agent
  family name: Cunha
  given name: João Paulo S.
doi: 10.7717/peerj.5967
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-11
copyright: ©2018 Rodrigues et al.
attribution name: Rodrigues et al.

Plant-derived chimeric antibodies inhibit the invasion of human fibroblasts by Toxoplasma gondii
type: item
type: AcademicArticle
description: The parasite Toxoplasma gondii causes an opportunistic infection, that is, particularly severe in immunocompromised patients, infants, and neonates. Current antiparasitic drugs are teratogenic and cause hypersensitivity-based toxic side effects especially during prolonged treatment. Furthermore, the recent emergence of drug-resistant toxoplasmosis has reduced the therapeutic impact of such drugs. In an effort to develop recombinant antibodies as a therapeutic alternative, a panel of affinity-matured, T. gondii tachyzoite-specific single-chain variable fragment (scFv) antibodies was selected by phage display and bioinformatic analysis. Further affinity optimization was attempted by introducing point mutations at hotspots within light chain complementarity-determining region 2. This strategy yielded four mutated scFv sequences and a parental scFv that were used to produce five mouse–human chimeric IgGs in Nicotiana benthamiana plants, with yields of 33–72 mg/kg of plant tissue. Immunological analysis confirmed the specific binding of these plant-derived antibodies to T. gondii tachyzoites, and in vitro efficacy was demonstrated by their ability to inhibit the invasion of human fibroblasts and impair parasite infectivity. These novel recombinant antibodies could therefore be suitable for the development of plant-derived immunotherapeutic interventions against toxoplasmosis.
format: application/pdf
format: text/html
creator: Sherene Swee Yin Lim
creator: Kek Heng Chua
creator: Greta Nölke
creator: Holger Spiegel
creator: Wai Leong Goh
creator: Sek Chuen Chow
creator: Boon Pin Kee
creator: Rainer Fischer
creator: Stefan Schillberg
creator: Rofina Yasmin Othman
subject: Biotechnology
subject: Molecular Biology
subject: Parasitology
subject: Plant Science
subject: Immunology
description: doi:10.7717/peerj.5780
publisher: PeerJ Inc.
rights: © 2018 Lim et al.
abstract: The parasite Toxoplasma gondii causes an opportunistic infection, that is, particularly severe in immunocompromised patients, infants, and neonates. Current antiparasitic drugs are teratogenic and cause hypersensitivity-based toxic side effects especially during prolonged treatment. Furthermore, the recent emergence of drug-resistant toxoplasmosis has reduced the therapeutic impact of such drugs. In an effort to develop recombinant antibodies as a therapeutic alternative, a panel of affinity-matured, T. gondii tachyzoite-specific single-chain variable fragment (scFv) antibodies was selected by phage display and bioinformatic analysis. Further affinity optimization was attempted by introducing point mutations at hotspots within light chain complementarity-determining region 2. This strategy yielded four mutated scFv sequences and a parental scFv that were used to produce five mouse–human chimeric IgGs in Nicotiana benthamiana plants, with yields of 33–72 mg/kg of plant tissue. Immunological analysis confirmed the specific binding of these plant-derived antibodies to T. gondii tachyzoites, and in vitro efficacy was demonstrated by their ability to inhibit the invasion of human fibroblasts and impair parasite infectivity. These novel recombinant antibodies could therefore be suitable for the development of plant-derived immunotherapeutic interventions against toxoplasmosis.
bibliographic citation: Lim et al. (2018) Plant-derived chimeric antibodies inhibit the invasion of human fibroblasts by Toxoplasma gondii. PeerJ 6:e5780 https://doi.org/10.7717/peerj.5780
date submitted: 2017-06-14
date accepted: 2018-09-17
issued: 2018-12-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lim
  given name: Sherene Swee Yin
author list: Agent
  family name: Chua
  given name: Kek Heng
author list: Agent
  family name: Nölke
  given name: Greta
author list: Agent
  family name: Spiegel
  given name: Holger
author list: Agent
  family name: Goh
  given name: Wai Leong
author list: Agent
  family name: Chow
  given name: Sek Chuen
author list: Agent
  family name: Kee
  given name: Boon Pin
author list: Agent
  family name: Fischer
  given name: Rainer
author list: Agent
  family name: Schillberg
  given name: Stefan
author list: Agent
  family name: Othman
  given name: Rofina Yasmin
doi: 10.7717/peerj.5780
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-11
copyright: © 2018 Lim et al.
attribution name: Lim et al.

Behavior problems and personality in Korean high school students
type: item
type: AcademicArticle
description: Introduction Extant studies have examined the effect of psychological characteristics on clinical features that define behavior problems. The purpose of this study was to analyze the effects of temperament and character as both individual factors and complex profiles on behavior problems in a community sample of adolescents. Methods Behavior problems and personality of 670 Korean high school students were measured with the Youth Self-Report (YSR) and Junior version of the Temperament and Character Inventory (JTCI). Stepwise regression analysis analyzed the effects of JTCI character and temperament traits on YSR Total, Internalizing and Externalizing subscale scores, and Profile Analysis examined differences of JTCI personality profiles among three latent YSR subscale profiles acquired from Latent Profile Analysis. Results Seven subscales of the JTCI explained 38% of the YSR total degree of behavior problems, and JTCI Novelty-Seeking and Harm-Avoidance were found to account for vulnerability while JTCI Reward-Dependence and Self-Directedness explained resilience to behavior problems. There were three distinct latent YSR profile groups based on nine YSR subscales, and low behavior problem group showed a resilient personality profile characterized by low Novelty-Seeking and Harm-Avoidance and high Reward-Dependence, Persistence, Self-Directedness and Cooperativeness while high behavior problem group exhibited a vulnerable personality profile of the opposite tendency. Discussion Temperament and character explained behavior problems of Korean high school students as both individual personality traits and a complex personality profile. The results and implications of this study were examined in regard to mental health of adolescents, and the importance of education in the development of mature personality are discussed.
format: application/pdf
format: text/html
creator: Soo Jin Lee
creator: Soo Hyun Park
creator: C Robert Cloninger
creator: Han Chae
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.6106
publisher: PeerJ Inc.
rights: © 2018 Lee et al.
abstract: Introduction Extant studies have examined the effect of psychological characteristics on clinical features that define behavior problems. The purpose of this study was to analyze the effects of temperament and character as both individual factors and complex profiles on behavior problems in a community sample of adolescents. Methods Behavior problems and personality of 670 Korean high school students were measured with the Youth Self-Report (YSR) and Junior version of the Temperament and Character Inventory (JTCI). Stepwise regression analysis analyzed the effects of JTCI character and temperament traits on YSR Total, Internalizing and Externalizing subscale scores, and Profile Analysis examined differences of JTCI personality profiles among three latent YSR subscale profiles acquired from Latent Profile Analysis. Results Seven subscales of the JTCI explained 38% of the YSR total degree of behavior problems, and JTCI Novelty-Seeking and Harm-Avoidance were found to account for vulnerability while JTCI Reward-Dependence and Self-Directedness explained resilience to behavior problems. There were three distinct latent YSR profile groups based on nine YSR subscales, and low behavior problem group showed a resilient personality profile characterized by low Novelty-Seeking and Harm-Avoidance and high Reward-Dependence, Persistence, Self-Directedness and Cooperativeness while high behavior problem group exhibited a vulnerable personality profile of the opposite tendency. Discussion Temperament and character explained behavior problems of Korean high school students as both individual personality traits and a complex personality profile. The results and implications of this study were examined in regard to mental health of adolescents, and the importance of education in the development of mature personality are discussed.
bibliographic citation: Lee et al. (2018) Behavior problems and personality in Korean high school students. PeerJ 6:e6106 https://doi.org/10.7717/peerj.6106
date submitted: 2018-07-12
date accepted: 2018-11-14
issued: 2018-12-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Soo Jin
author list: Agent
  family name: Park
  given name: Soo Hyun
author list: Agent
  family name: Cloninger
  given name: C Robert
author list: Agent
  family name: Chae
  given name: Han
doi: 10.7717/peerj.6106
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-10
copyright: ©2018 Lee et al.
attribution name: Lee et al.

Effects of gelsemine on oxidative stress and DNA damage responses of Tetrahymena thermophila
type: item
type: AcademicArticle
description: Gelsemine is an important toxic substance extracted from Gelsemium elegans, which has a lot of biological functions in cells and organisms, but its toxicity has been rarely reported in Tetrahymena thermophila. In this study, we used the protozoan T. thermophila as an experimental model to investigate the potential toxicity-induced mechanism of gelsemine in the unicellular eukaryote. Our results clearly showed gelsemine inhibited T. thermophila growth in a dose-dependent manner. This exposure also resulted in oxidative stress on T. thermophila cells and antioxidant enzyme levels were significantly altered at high gelsemine levels (p < 0.05). Gelsemine produced a slight apoptotic effect at the highest (0.8 mg/mL) gelsemine level used here (p < 0.05). Furthermore, the toxin-induced DNA damage in a dose-dependent manner. The ultrastructural analysis also revealed mitophagic vacuoles at 0.4 and 0.8 mg/mL levels of gelsemine exposure. Moreover, expressions of oxidative stress-related and MAP kinase genes were significantly changed after exposure to 0.8 mg/mL level of gelsemine (p < 0.05). Altogether, our results clearly show that gelsemine from G. elegans can inhibit the growth via inducing oxidative stress and DNA damage in T. thermophila cells.
format: application/pdf
format: text/html
creator: Qiao Ye
creator: Yongyong Feng
creator: Zhenlu Wang
creator: Wenzhao Jiang
creator: Yuexin Qu
creator: Chaonan Zhang
creator: Aiguo Zhou
creator: Shaolin Xie
creator: Jixing Zou
subject: Microbiology
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.6093
publisher: PeerJ Inc.
rights: © 2018 Ye et al.
abstract: Gelsemine is an important toxic substance extracted from Gelsemium elegans, which has a lot of biological functions in cells and organisms, but its toxicity has been rarely reported in Tetrahymena thermophila. In this study, we used the protozoan T. thermophila as an experimental model to investigate the potential toxicity-induced mechanism of gelsemine in the unicellular eukaryote. Our results clearly showed gelsemine inhibited T. thermophila growth in a dose-dependent manner. This exposure also resulted in oxidative stress on T. thermophila cells and antioxidant enzyme levels were significantly altered at high gelsemine levels (p < 0.05). Gelsemine produced a slight apoptotic effect at the highest (0.8 mg/mL) gelsemine level used here (p < 0.05). Furthermore, the toxin-induced DNA damage in a dose-dependent manner. The ultrastructural analysis also revealed mitophagic vacuoles at 0.4 and 0.8 mg/mL levels of gelsemine exposure. Moreover, expressions of oxidative stress-related and MAP kinase genes were significantly changed after exposure to 0.8 mg/mL level of gelsemine (p < 0.05). Altogether, our results clearly show that gelsemine from G. elegans can inhibit the growth via inducing oxidative stress and DNA damage in T. thermophila cells.
bibliographic citation: Ye et al. (2018) Effects of gelsemine on oxidative stress and DNA damage responses of Tetrahymena thermophila. PeerJ 6:e6093 https://doi.org/10.7717/peerj.6093
date submitted: 2018-06-06
date accepted: 2018-11-10
issued: 2018-12-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Qiao
author list: Agent
  family name: Feng
  given name: Yongyong
author list: Agent
  family name: Wang
  given name: Zhenlu
author list: Agent
  family name: Jiang
  given name: Wenzhao
author list: Agent
  family name: Qu
  given name: Yuexin
author list: Agent
  family name: Zhang
  given name: Chaonan
author list: Agent
  family name: Zhou
  given name: Aiguo
author list: Agent
  family name: Xie
  given name: Shaolin
author list: Agent
  family name: Zou
  given name: Jixing
doi: 10.7717/peerj.6093
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-10
copyright: © 2018 Ye et al.
attribution name: Ye et al.

Screening of prognostic biomarkers for endometrial carcinoma based on a ceRNA network
type: item
type: AcademicArticle
description: Objective This study aims to reveal the regulation network of lncRNAs-miRNAs-mRNA in endometrial carcinoma (EC), to investigate the underlying mechanisms of EC occurrence and progression, to screen prognostic biomarkers. Methods RNA-seq and miRNA-seq data of endometrial carcinoma were downloaded from the TCGA database. Edge.R package was used to screen differentially expressed genes. A database was searched to determine differentially expressed lncRNA-miRNA and miRNA-mRNA pairs, to construct the topological network of ceRNA, and to elucidate the key RNAs that are for a prognosis of survival. Results We screened out 2632 mRNAs, 1178 lncRNAs and 189 miRNAs that were differentially expressed. The constructed ceRNA network included 97 lncRNAs, 20 miRNAs and 73 mRNAs. Analyzing network genes for associations with prognosies revealed 169 prognosis-associated RNAs, including 92 lncRNAs, 16miRNAs and 61 mRNAs. Conclusion Our results reveal new potential mechanisms underlying the carcinogenesis and progression of endometrial carcinoma.
format: application/pdf
format: text/html
creator: Ming-Jun Zheng
creator: Rui Gou
creator: Wen-Chao Zhang
creator: Xin Nie
creator: Jing Wang
creator: Ling-Ling Gao
creator: Juan-Juan Liu
creator: Xiao Li
creator: Bei Lin
subject: Gynecology and Obstetrics
subject: Oncology
description: doi:10.7717/peerj.6091
publisher: PeerJ Inc.
rights: © 2018 Zheng et al.
abstract: Objective This study aims to reveal the regulation network of lncRNAs-miRNAs-mRNA in endometrial carcinoma (EC), to investigate the underlying mechanisms of EC occurrence and progression, to screen prognostic biomarkers. Methods RNA-seq and miRNA-seq data of endometrial carcinoma were downloaded from the TCGA database. Edge.R package was used to screen differentially expressed genes. A database was searched to determine differentially expressed lncRNA-miRNA and miRNA-mRNA pairs, to construct the topological network of ceRNA, and to elucidate the key RNAs that are for a prognosis of survival. Results We screened out 2632 mRNAs, 1178 lncRNAs and 189 miRNAs that were differentially expressed. The constructed ceRNA network included 97 lncRNAs, 20 miRNAs and 73 mRNAs. Analyzing network genes for associations with prognosies revealed 169 prognosis-associated RNAs, including 92 lncRNAs, 16miRNAs and 61 mRNAs. Conclusion Our results reveal new potential mechanisms underlying the carcinogenesis and progression of endometrial carcinoma.
bibliographic citation: Zheng et al. (2018) Screening of prognostic biomarkers for endometrial carcinoma based on a ceRNA network. PeerJ 6:e6091 https://doi.org/10.7717/peerj.6091
date submitted: 2018-05-17
date accepted: 2018-11-09
issued: 2018-12-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Ming-Jun
author list: Agent
  family name: Gou
  given name: Rui
author list: Agent
  family name: Zhang
  given name: Wen-Chao
author list: Agent
  family name: Nie
  given name: Xin
author list: Agent
  family name: Wang
  given name: Jing
author list: Agent
  family name: Gao
  given name: Ling-Ling
author list: Agent
  family name: Liu
  given name: Juan-Juan
author list: Agent
  family name: Li
  given name: Xiao
author list: Agent
  family name: Lin
  given name: Bei
doi: 10.7717/peerj.6091
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-10
copyright: ©2018 Zheng et al.
attribution name: Zheng et al.

The recent expansion of Fox Sparrow (Passerella iliaca iliaca) breeding range into the northeastern United States
type: item
type: AcademicArticle
description: The breeding range of the Eastern Fox Sparrow (Passerella iliaca iliaca) is generally recognized as comprising the boreal forest of Canada. However, recent observations suggest that the species is present during the summer months throughout much of the northeastern US, unexpected for a species characterized as a passage migrant in the region. To clarify, I conducted a literature review to document the historical status of the species in the northeastern US and then analyzed observations submitted to eBird to describe its recent and current status in the region. Historical accounts consistently identify Fox Sparrow as a passage migrant through the region during early spring and late fall. Beginning in the early 1980s, observers began noting regular extralimital records of Fox Sparrow in northern Maine. A single nest was discovered in the state in 1983, and another in northern New Hampshire in 1997. Despite the paucity of breeding records, observations submitted to eBird suggest that the southern limit of the breeding range of Fox Sparrow has expanded rapidly to the south and west in recent years. The proportion of complete checklists submitted to eBird that contained at least one observation of Fox Sparrow grew at an annual rate of 18% from 2003–2016 and was independent of observer effort. Fox Sparrow now occurs regularly on mountaintops and in young stands of spruce (Picea spp.) and balsam fir (Abies balsamea) during the breeding season throughout northern and western Maine and northern New Hampshire, with occasional records from the Green Mountains of Vermont and the Adirondack Mountains of New York. The cause of this rapid expansion of its breeding range is unknown, but may be related to an increase in the amount of young conifer forest in the northeastern US created by commercial timber harvest.
format: application/pdf
format: text/html
creator: John D. Lloyd
subject: Biogeography
subject: Zoology
description: doi:10.7717/peerj.6087
publisher: PeerJ Inc.
rights: © 2018 Lloyd
abstract: The breeding range of the Eastern Fox Sparrow (Passerella iliaca iliaca) is generally recognized as comprising the boreal forest of Canada. However, recent observations suggest that the species is present during the summer months throughout much of the northeastern US, unexpected for a species characterized as a passage migrant in the region. To clarify, I conducted a literature review to document the historical status of the species in the northeastern US and then analyzed observations submitted to eBird to describe its recent and current status in the region. Historical accounts consistently identify Fox Sparrow as a passage migrant through the region during early spring and late fall. Beginning in the early 1980s, observers began noting regular extralimital records of Fox Sparrow in northern Maine. A single nest was discovered in the state in 1983, and another in northern New Hampshire in 1997. Despite the paucity of breeding records, observations submitted to eBird suggest that the southern limit of the breeding range of Fox Sparrow has expanded rapidly to the south and west in recent years. The proportion of complete checklists submitted to eBird that contained at least one observation of Fox Sparrow grew at an annual rate of 18% from 2003–2016 and was independent of observer effort. Fox Sparrow now occurs regularly on mountaintops and in young stands of spruce (Picea spp.) and balsam fir (Abies balsamea) during the breeding season throughout northern and western Maine and northern New Hampshire, with occasional records from the Green Mountains of Vermont and the Adirondack Mountains of New York. The cause of this rapid expansion of its breeding range is unknown, but may be related to an increase in the amount of young conifer forest in the northeastern US created by commercial timber harvest.
bibliographic citation: Lloyd (2018) The recent expansion of Fox Sparrow (Passerella iliaca iliaca) breeding range into the northeastern United States. PeerJ 6:e6087 https://doi.org/10.7717/peerj.6087
date submitted: 2018-09-10
date accepted: 2018-11-08
issued: 2018-12-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lloyd
  given name: John D.
doi: 10.7717/peerj.6087
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-10
copyright: ©2018 Lloyd
attribution name: Lloyd

Posture similarity index: a method to compare hand postures in synergy space
type: item
type: AcademicArticle
description: Background The human hand can perform a range of manipulation tasks, from holding a pen to holding a hammer. The central nervous system (CNS) uses different strategies in different manipulation tasks based on task requirements. Attempts to compare postures of the hand have been made for use in robotics and animation industries. In this study, we developed an index called the posture similarity index to quantify the similarity between two human hand postures. Methods Twelve right-handed volunteers performed 70 postures, and lifted and held 30 objects (total of 100 different postures, each performed five times). A 16-sensor electromagnetic tracking system captured the kinematics of individual finger phalanges (segments). We modeled the hand as a 21-DoF system and computed the corresponding joint angles. We used principal component analysis to extract kinematic synergies from this 21-DoF data. We developed a posture similarity index (PSI), that represents the similarity between posture in the synergy (Principal component) space. First, we tested the performance of this index using a synthetic dataset. After confirming that it performs well with the synthetic dataset, we used it to analyze the experimental data. Further, we used PSI to identify postures that are “representative” in the sense that they have a greater overlap (in synergy space) with a large number of postures. Results Our results confirmed that PSI is a relatively accurate index of similarity in synergy space both with synthetic data and real experimental data. Also, more special postures than common postures were found among “representative” postures. Conclusion We developed an index for comparing posture similarity in synergy space and demonstrated its utility by using synthetic dataset and experimental dataset. Besides, we found that “special” postures are actually “special” in the sense that there are more of them in the “representative” postures as identified by our posture similarity index.
format: application/pdf
format: text/html
creator: Nayan Bhatt
creator: Varadhan SKM
subject: Bioengineering
subject: Computational Biology
subject: Neuroscience
subject: Kinesiology
subject: Computational Science
description: doi:10.7717/peerj.6078
publisher: PeerJ Inc.
rights: © 2018 Bhatt and SKM
abstract: Background The human hand can perform a range of manipulation tasks, from holding a pen to holding a hammer. The central nervous system (CNS) uses different strategies in different manipulation tasks based on task requirements. Attempts to compare postures of the hand have been made for use in robotics and animation industries. In this study, we developed an index called the posture similarity index to quantify the similarity between two human hand postures. Methods Twelve right-handed volunteers performed 70 postures, and lifted and held 30 objects (total of 100 different postures, each performed five times). A 16-sensor electromagnetic tracking system captured the kinematics of individual finger phalanges (segments). We modeled the hand as a 21-DoF system and computed the corresponding joint angles. We used principal component analysis to extract kinematic synergies from this 21-DoF data. We developed a posture similarity index (PSI), that represents the similarity between posture in the synergy (Principal component) space. First, we tested the performance of this index using a synthetic dataset. After confirming that it performs well with the synthetic dataset, we used it to analyze the experimental data. Further, we used PSI to identify postures that are “representative” in the sense that they have a greater overlap (in synergy space) with a large number of postures. Results Our results confirmed that PSI is a relatively accurate index of similarity in synergy space both with synthetic data and real experimental data. Also, more special postures than common postures were found among “representative” postures. Conclusion We developed an index for comparing posture similarity in synergy space and demonstrated its utility by using synthetic dataset and experimental dataset. Besides, we found that “special” postures are actually “special” in the sense that there are more of them in the “representative” postures as identified by our posture similarity index.
bibliographic citation: Bhatt et al. (2018) Posture similarity index: a method to compare hand postures in synergy space. PeerJ 6:e6078 https://doi.org/10.7717/peerj.6078
date submitted: 2018-03-04
date accepted: 2018-11-06
issued: 2018-12-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bhatt
  given name: Nayan
author list: Agent
  family name: SKM
  given name: Varadhan
doi: 10.7717/peerj.6078
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-10
copyright: ©2018 Bhatt and SKM
attribution name: Bhatt and SKM

Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
type: item
type: AcademicArticle
description: Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.
format: application/pdf
format: text/html
creator: Alexandra M. Linz
creator: Shaomei He
creator: Sarah L.R. Stevens
creator: Karthik Anantharaman
creator: Robin R. Rohwer
creator: Rex R. Malmstrom
creator: Stefan Bertilsson
creator: Katherine D. McMahon
subject: Ecosystem Science
subject: Genomics
subject: Microbiology
subject: Freshwater Biology
subject: Biogeochemistry
description: doi:10.7717/peerj.6075
publisher: PeerJ Inc.
rights: © 2018 Linz et al.
abstract: Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.
bibliographic citation: Linz et al. (2018) Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ 6:e6075 https://doi.org/10.7717/peerj.6075
date submitted: 2018-07-05
date accepted: 2018-11-05
issued: 2018-12-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Linz
  given name: Alexandra M.
author list: Agent
  family name: He
  given name: Shaomei
author list: Agent
  family name: Stevens
  given name: Sarah L.R.
author list: Agent
  family name: Anantharaman
  given name: Karthik
author list: Agent
  family name: Rohwer
  given name: Robin R.
author list: Agent
  family name: Malmstrom
  given name: Rex R.
author list: Agent
  family name: Bertilsson
  given name: Stefan
author list: Agent
  family name: McMahon
  given name: Katherine D.
doi: 10.7717/peerj.6075
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-10
copyright: © 2018 Linz et al.
attribution name: Linz et al.

Technology-assisted white cane: evaluation and future directions
type: item
type: AcademicArticle
description: Background Several technology-assisted aids are available to help blind and visually impaired people perform their daily activities. The current research uses the state-of-the-art technology to enhance the utility of traditional navigational aids to produce solutions that are more reliable. In this regard, a white cane is no exception, which is supplemented with the existing technologies to design Electronic Travel Aids (ETAs), Electronic Orientation Aids (EOAs), and Position Locator Devices (PLDs). Although several review articles uncover the strengths and limitations of research contributions that extend traditional navigational aids, we find no review article that covers research contributions on a technology-assisted white cane. The authors attempt to fill this literature gap by reviewing the most relevant research articles published during 2010–2017 with the common objective of enhancing the utility of white cane with the existing technology. Methods The authors have collected the relevant literature published during 2010–17 by searching and browsing all the major digital libraries and publishers’ websites. The inclusion/exclusion criteria were applied to select the research articles that are relevant to the topic of this review article, and all other irrelevant papers were excluded. Among the 577 (534 through database searching and 43 through other sources) initially screened papers, the authors collected 228 full-text articles, which after applying exclusion/inclusion criteria resulted in 36 papers that were included in the evaluation, comparison, and discussion. This also includes research articles of commercially available aids published before the specified range. Results The findings show that the research trend is shifting towards developing a technology-assisted white cane solution that is applicable in both indoor and outdoor environments to aid blind users in navigation. In this regard, exploiting smartphones to develop low-cost and user-friendly navi…
format: application/pdf
format: text/html
creator: Izaz Khan
creator: Shah Khusro
creator: Irfan Ullah
subject: Drugs and Devices
subject: Ophthalmology
subject: Human–Computer Interaction
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6058
publisher: PeerJ Inc.
rights: © 2018 Khan et al.
abstract: Background Several technology-assisted aids are available to help blind and visually impaired people perform their daily activities. The current research uses the state-of-the-art technology to enhance the utility of traditional navigational aids to produce solutions that are more reliable. In this regard, a white cane is no exception, which is supplemented with the existing technologies to design Electronic Travel Aids (ETAs), Electronic Orientation Aids (EOAs), and Position Locator Devices (PLDs). Although several review articles uncover the strengths and limitations of research contributions that extend traditional navigational aids, we find no review article that covers research contributions on a technology-assisted white cane. The authors attempt to fill this literature gap by reviewing the most relevant research articles published during 2010–2017 with the common objective of enhancing the utility of white cane with the existing technology. Methods The authors have collected the relevant literature published during 2010–17 by searching and browsing all the major digital libraries and publishers’ websites. The inclusion/exclusion criteria were applied to select the research articles that are relevant to the topic of this review article, and all other irrelevant papers were excluded. Among the 577 (534 through database searching and 43 through other sources) initially screened papers, the authors collected 228 full-text articles, which after applying exclusion/inclusion criteria resulted in 36 papers that were included in the evaluation, comparison, and discussion. This also includes research articles of commercially available aids published before the specified range. Results The findings show that the research trend is shifting towards developing a technology-assisted white cane solution that is applicable in both indoor and outdoor environments to aid blind users in navigation. In this regard, exploiting smartphones to develop low-cost and user-friendly navi…
bibliographic citation: Khan et al. (2018) Technology-assisted white cane: evaluation and future directions. PeerJ 6:e6058 https://doi.org/10.7717/peerj.6058
date submitted: 2018-03-07
date accepted: 2018-11-03
issued: 2018-12-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khan
  given name: Izaz
author list: Agent
  family name: Khusro
  given name: Shah
author list: Agent
  family name: Ullah
  given name: Irfan
doi: 10.7717/peerj.6058
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-10
copyright: ©2018 Khan et al.
attribution name: Khan et al.

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