PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Development of an autophagy-related gene prognostic signature in lung adenocarcinoma and lung squamous cell carcinoma
items: EEG alpha activity increased in response to transcutaneous electrical nervous stimulation in young healthy subjects but not in the healthy elderly
items: Feasibility of assessing ultra-short-term pulse rate variability from video recordings
items: Exercise mode and attentional networks in older adults: a cross-sectional study
items: Risk of phosphorus losses in surface runoff from agricultural land in the Baltic Commune of Puck in the light of assessment performed on the basis of DPS indicator
items: The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico
items: Assessment of a Takagi–Sugeno-Kang fuzzy model assembly for examination of polyphasic loglinear allometry
items: The Rametrix™ PRO Toolbox v1.0 for MATLAB®
items: sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data
items: Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species

Development of an autophagy-related gene prognostic signature in lung adenocarcinoma and lung squamous cell carcinoma
type: item
type: AcademicArticle
description: Purpose There is plenty of evidence showing that autophagy plays an important role in the biological process of cancer. The purpose of this study was to establish a novel autophagy-related prognostic marker for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Methods The mRNA microarray and clinical data in The Cancer Genome Atlas (TCGA) were analyzed by using a univariate Cox proportional regression model to select candidate autophagy-related prognostic genes. Bioinformatics analysis of gene function using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) platforms was performed. A multivariate Cox proportional regression model helped to develop a prognostic signature from the pool of candidate genes. On the basis of this prognostic signature, we could divide LUAD and LUSC patients into high-risk and low-risk groups. Further survival analysis demonstrated that high-risk patients had significantly shorter disease-free survival (DFS) than low-risk patients. The signature which contains six autophagy-related genes (EIF4EBP1, TP63, BNIP3, ATIC, ERO1A and FADD) showed good performance for predicting the survival of LUAD and LUSC patients by having a better Area Under Curves (AUC) than other clinical parameters. Its efficacy was also validated by data from the Gene Expression Omnibus (GEO) database. Conclusion Collectively, the prognostic signature we proposed is a promising biomarker for monitoring the outcomes of LUAD and LUSC.
format: application/pdf
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creator: Jie Zhu
creator: Min Wang
creator: Daixing Hu
subject: Bioinformatics
subject: Oncology
description: doi:10.7717/peerj.8288
publisher: PeerJ Inc.
rights: © 2020 Zhu et al.
abstract: Purpose There is plenty of evidence showing that autophagy plays an important role in the biological process of cancer. The purpose of this study was to establish a novel autophagy-related prognostic marker for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Methods The mRNA microarray and clinical data in The Cancer Genome Atlas (TCGA) were analyzed by using a univariate Cox proportional regression model to select candidate autophagy-related prognostic genes. Bioinformatics analysis of gene function using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) platforms was performed. A multivariate Cox proportional regression model helped to develop a prognostic signature from the pool of candidate genes. On the basis of this prognostic signature, we could divide LUAD and LUSC patients into high-risk and low-risk groups. Further survival analysis demonstrated that high-risk patients had significantly shorter disease-free survival (DFS) than low-risk patients. The signature which contains six autophagy-related genes (EIF4EBP1, TP63, BNIP3, ATIC, ERO1A and FADD) showed good performance for predicting the survival of LUAD and LUSC patients by having a better Area Under Curves (AUC) than other clinical parameters. Its efficacy was also validated by data from the Gene Expression Omnibus (GEO) database. Conclusion Collectively, the prognostic signature we proposed is a promising biomarker for monitoring the outcomes of LUAD and LUSC.
bibliographic citation: Zhu et al. (2020) Development of an autophagy-related gene prognostic signature in lung adenocarcinoma and lung squamous cell carcinoma. PeerJ 8:e8288 https://doi.org/10.7717/peerj.8288
date submitted: 2019-10-21
date accepted: 2019-11-24
issued: 2020-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Jie
author list: Agent
  family name: Wang
  given name: Min
author list: Agent
  family name: Hu
  given name: Daixing
doi: 10.7717/peerj.8288
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-07
copyright: ©2020 Zhu et al.
attribution name: Zhu et al.

EEG alpha activity increased in response to transcutaneous electrical nervous stimulation in young healthy subjects but not in the healthy elderly
type: item
type: AcademicArticle
description: Transcutaneous Electrical Nerve Stimulation (TENS) is used not only in the treatment of pain but also in the examination of sensory functions. With aging, there is decreased sensitivity to somatosensory stimuli. It is essential to examine the effect of TENS application on the sensory functions in the brain by recording the spontaneous electroencephalogram (EEG) activity and the effect of aging on the sensory functions of the brain during the application. The present study aimed to investigate the effect of the application of TENS on the brain’s electrical activity and the effect of aging on the sensory functions of the brain during application of TENS. A total of 15 young (24.2 ± 3.59) and 14 elderly (65.64 ± 4.92) subjects were included in the study. Spontaneous EEG was recorded from 32 channels during TENS application. Power spectrum analysis was performed by Fast Fourier Transform in the alpha frequency band (8–13 Hz) for all subjects. Repeated measures of analysis of variance was used for statistical analysis (p < 0.05). Young subjects had increased alpha power during the TENS application and had gradually increased alpha power by increasing the current intensity of TENS (p = 0.035). Young subjects had higher alpha power than elderly subjects in the occipital and parietal locations (p = 0.073). We can, therefore, conclude that TENS indicated increased alpha activity in young subjects. Young subjects had higher alpha activity than elderly subjects in the occipital and somatosensory areas. To our knowledge, the present study is one of the first studies examining the effect of TENS on spontaneous EEG in healthy subjects. Based on the results of the present study, TENS may be used as an objective method for the examination of sensory impairments, and in the evaluative efficiency of the treatment of pain conditions.
format: application/pdf
format: text/html
creator: Ebru Yıldırım
creator: Bahar Güntekin
creator: Lütfü Hanoğlu
creator: Candan Algun
subject: Neuroscience
subject: Geriatrics
description: doi:10.7717/peerj.8330
publisher: PeerJ Inc.
rights: © 2020 Yıldırım et al.
abstract: Transcutaneous Electrical Nerve Stimulation (TENS) is used not only in the treatment of pain but also in the examination of sensory functions. With aging, there is decreased sensitivity to somatosensory stimuli. It is essential to examine the effect of TENS application on the sensory functions in the brain by recording the spontaneous electroencephalogram (EEG) activity and the effect of aging on the sensory functions of the brain during the application. The present study aimed to investigate the effect of the application of TENS on the brain’s electrical activity and the effect of aging on the sensory functions of the brain during application of TENS. A total of 15 young (24.2 ± 3.59) and 14 elderly (65.64 ± 4.92) subjects were included in the study. Spontaneous EEG was recorded from 32 channels during TENS application. Power spectrum analysis was performed by Fast Fourier Transform in the alpha frequency band (8–13 Hz) for all subjects. Repeated measures of analysis of variance was used for statistical analysis (p < 0.05). Young subjects had increased alpha power during the TENS application and had gradually increased alpha power by increasing the current intensity of TENS (p = 0.035). Young subjects had higher alpha power than elderly subjects in the occipital and parietal locations (p = 0.073). We can, therefore, conclude that TENS indicated increased alpha activity in young subjects. Young subjects had higher alpha activity than elderly subjects in the occipital and somatosensory areas. To our knowledge, the present study is one of the first studies examining the effect of TENS on spontaneous EEG in healthy subjects. Based on the results of the present study, TENS may be used as an objective method for the examination of sensory impairments, and in the evaluative efficiency of the treatment of pain conditions.
bibliographic citation: Yıldırım et al. (2020) EEG alpha activity increased in response to transcutaneous electrical nervous stimulation in young healthy subjects but not in the healthy elderly. PeerJ 8:e8330 https://doi.org/10.7717/peerj.8330
date submitted: 2019-06-27
date accepted: 2019-12-02
issued: 2020-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yıldırım
  given name: Ebru
author list: Agent
  family name: Güntekin
  given name: Bahar
author list: Agent
  family name: Hanoğlu
  given name: Lütfü
author list: Agent
  family name: Algun
  given name: Candan
doi: 10.7717/peerj.8330
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-07
copyright: © 2020 Yıldırım et al.
attribution name: Yıldırım et al.

Feasibility of assessing ultra-short-term pulse rate variability from video recordings
type: item
type: AcademicArticle
description: Objectives Remote photoplethysmography (rPPG) is a promising non-contact measurement technique for assessing numerous physiological parameters: pulse rate, pulse rate variability (PRV), respiratory rate, pulse wave velocity, blood saturation, blood pressure, etc. To justify its use in ultra-short-term (UST) PRV analysis, which is of great benefit for several healthcare applications, the agreement between rPPG- and PPG-derived UST-PRV metrics was studied. Approach Three time-domain metrics—standard deviation of normal-to-normal (NN) intervals (SDNN), root mean square of successive NN interval differences (RMSSD), and the percentage of adjacent NN intervals that differ from each other by more than 50 ms (pNN50)—were extracted from 56 video recordings in a publicly available data set. The selected metrics were calculated on the basis of three groups of 10 s recordings and their average, two groups of 30 s recordings and their average, and a group of 60 s recordings taken from the full-length recordings and then compared with metrics derived from the corresponding reference (PPG) pulse waveform signals by using correlation and effect size parameters, and Bland–Altman plots. Main results The results show there is stronger agreement as the recording length increases for SDNN and RMSSD, yet there is no significant change for pNN50. The agreement parameters reach r = 0.841 (p < 0.001), r = 0.529 (p < 0.001), and r = 0.657 (p < 0.001), estimated median bias −1.52, −2.28 ms and −1.95% and a small effect size for SDNN, RMSSD, and pNN50 derived from the 60 s recordings, respectively. Significance Remote photoplethysmography-derived UST-PRV metrics manage to capture UST-PRV metrics derived from reference (PPG) recordings well. This feature is highly desirable in numerous applications for the assessment of one’s health and well-being. In future research, the validity of rPPG-derived UST-PRV metrics compared to the gold standard electrocardiography recordings is to be assessed.
format: application/pdf
format: text/html
creator: Miha Finžgar
creator: Primož Podržaj
subject: Anatomy and Physiology
subject: Drugs and Devices
subject: Radiology and Medical Imaging
subject: Computational Science
description: doi:10.7717/peerj.8342
publisher: PeerJ Inc.
rights: © 2020 Finžgar and Podržaj
abstract: Objectives Remote photoplethysmography (rPPG) is a promising non-contact measurement technique for assessing numerous physiological parameters: pulse rate, pulse rate variability (PRV), respiratory rate, pulse wave velocity, blood saturation, blood pressure, etc. To justify its use in ultra-short-term (UST) PRV analysis, which is of great benefit for several healthcare applications, the agreement between rPPG- and PPG-derived UST-PRV metrics was studied. Approach Three time-domain metrics—standard deviation of normal-to-normal (NN) intervals (SDNN), root mean square of successive NN interval differences (RMSSD), and the percentage of adjacent NN intervals that differ from each other by more than 50 ms (pNN50)—were extracted from 56 video recordings in a publicly available data set. The selected metrics were calculated on the basis of three groups of 10 s recordings and their average, two groups of 30 s recordings and their average, and a group of 60 s recordings taken from the full-length recordings and then compared with metrics derived from the corresponding reference (PPG) pulse waveform signals by using correlation and effect size parameters, and Bland–Altman plots. Main results The results show there is stronger agreement as the recording length increases for SDNN and RMSSD, yet there is no significant change for pNN50. The agreement parameters reach r = 0.841 (p < 0.001), r = 0.529 (p < 0.001), and r = 0.657 (p < 0.001), estimated median bias −1.52, −2.28 ms and −1.95% and a small effect size for SDNN, RMSSD, and pNN50 derived from the 60 s recordings, respectively. Significance Remote photoplethysmography-derived UST-PRV metrics manage to capture UST-PRV metrics derived from reference (PPG) recordings well. This feature is highly desirable in numerous applications for the assessment of one’s health and well-being. In future research, the validity of rPPG-derived UST-PRV metrics compared to the gold standard electrocardiography recordings is to be assessed.
bibliographic citation: Finžgar et al. (2020) Feasibility of assessing ultra-short-term pulse rate variability from video recordings. PeerJ 8:e8342 https://doi.org/10.7717/peerj.8342
date submitted: 2019-08-05
date accepted: 2019-12-03
issued: 2020-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Finžgar
  given name: Miha
author list: Agent
  family name: Podržaj
  given name: Primož
doi: 10.7717/peerj.8342
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-07
copyright: © 2020 Finžgar and Podržaj
attribution name: Finžgar and Podržaj

Exercise mode and attentional networks in older adults: a cross-sectional study
type: item
type: AcademicArticle
description: Background Previous studies have indicated that physical exercise enhances attentional function; however, the relationship between exercise mode and attentional networks has not been clarified for older adults (>60 years old). This study aimed to investigate the relationship between attentional networks and different exercise modes in older adults. Methods Two hundred and fifty-nine participants aged between 60 to 81 years were enrolled and classified into three groups (closed-skill group, open-skill group, or sedentary control group) using an exercise-related questionnaire. All participants completed an attention network test (ANT), which measured executive control, orienting, and alerting networks. Results The open-skill group had significantly higher executive network efficiency compared to the closed-skill (p < 0.01) and sedentary (p < 0.01) groups. The closed-skill group had significantly higher values compared to the sedentary control group (p < 0.05). Differences were not detected among groups for alerting and orienting networks (p > 0.05). The open-skill group had significantly higher values compared to the sedentary control group regarding proportion score of executive network (p < 0.01). In comparison, no significant differences were detected among groups for proportion scores of alerting and orienting networks. Conclusion This study extends current knowledge by demonstrating that open-skill exercises selectively enhance the executive control of attentional networks in older adults. Open-skill exercises combines physical exercise and cognitive training, potentially representing a more effective exercise mode to maintain or enhance attentional function in older adults.
format: application/pdf
format: text/html
creator: Biye Wang
creator: Wei Guo
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.8364
publisher: PeerJ Inc.
rights: © 2020 Wang and Guo
abstract: Background Previous studies have indicated that physical exercise enhances attentional function; however, the relationship between exercise mode and attentional networks has not been clarified for older adults (>60 years old). This study aimed to investigate the relationship between attentional networks and different exercise modes in older adults. Methods Two hundred and fifty-nine participants aged between 60 to 81 years were enrolled and classified into three groups (closed-skill group, open-skill group, or sedentary control group) using an exercise-related questionnaire. All participants completed an attention network test (ANT), which measured executive control, orienting, and alerting networks. Results The open-skill group had significantly higher executive network efficiency compared to the closed-skill (p < 0.01) and sedentary (p < 0.01) groups. The closed-skill group had significantly higher values compared to the sedentary control group (p < 0.05). Differences were not detected among groups for alerting and orienting networks (p > 0.05). The open-skill group had significantly higher values compared to the sedentary control group regarding proportion score of executive network (p < 0.01). In comparison, no significant differences were detected among groups for proportion scores of alerting and orienting networks. Conclusion This study extends current knowledge by demonstrating that open-skill exercises selectively enhance the executive control of attentional networks in older adults. Open-skill exercises combines physical exercise and cognitive training, potentially representing a more effective exercise mode to maintain or enhance attentional function in older adults.
bibliographic citation: Wang et al. (2020) Exercise mode and attentional networks in older adults: a cross-sectional study. PeerJ 8:e8364 https://doi.org/10.7717/peerj.8364
date submitted: 2019-08-08
date accepted: 2019-12-06
issued: 2020-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Biye
author list: Agent
  family name: Guo
  given name: Wei
doi: 10.7717/peerj.8364
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-07
copyright: ©2020 Wang and Guo
attribution name: Wang and Guo

Risk of phosphorus losses in surface runoff from agricultural land in the Baltic Commune of Puck in the light of assessment performed on the basis of DPS indicator
type: item
type: AcademicArticle
description: Background In order to counteract the eutrophication of waterways and reservoirs, a basic risk assessment of phosphorus (P) losses in the surface runoff from agricultural land should be included in water management plans. A new method has been developed to assess the risk of P losses by estimating the degree of P saturation (DPS) based on the P concentration of the water extract water-soluble P. Methods The risk of P losses in surface runoff from agricultural land in the Puck Commune on the Baltic Sea Coast was assessed with the DPS method. The results were compared to an agronomic interpretation of the soil test P concentration (STP). Research was conducted on mineral and organic soils from 50 and 11 separate agricultural plots with a total area of 133.82 and 37.23 ha, respectively. Phosphorus was extracted from the collected samples using distilled water on all soil samples, acid ammonium lactate on mineral soils, and an extract of 0.5 mol HCl·dm−3 on organic soils. The organic matter content and pH values were also determined. The results of the P content in the water extracted from the soils were converted into DPS values, which were then classified by appropriate limit intervals. Results and discussion There was a high risk of P losses from the soil via surface runoff in 96.7% of the agricultural parcels tested (96% of plots with mineral soils and 100% of plots with organic soils). Simultaneously, a large deficiency of plant-available P was found in soils from 62% of agricultural plots. These data indicate that the assessment of P concentration in soils made on the basis of an environmental soil P test conflicts with the assessment made based on STP and create a cognitive dissonance. The risk level of P losses through surface runoff from the analyzed plots as determined by the DPS indicator is uncertain. This uncertainty is increased as the DPS index is not correlated with other significant factors in P runoff losses, such as the type of crop and area inclinati…
format: application/pdf
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creator: Stefan Pietrzak
creator: Grażyna Pazikowska-Sapota
creator: Grażyna Dembska
creator: Lidia Anita Dzierzbicka-Glowacka
creator: Dominika Juszkowska
creator: Zuzanna Majewska
creator: Marek Urbaniak
creator: Dominika Ostrowska
creator: Agnieszka Cichowska
creator: Katarzyna Galer-Tatarowicz
subject: Agricultural Science
subject: Environmental Impacts
description: doi:10.7717/peerj.8396
publisher: PeerJ Inc.
rights: © 2020 Pietrzak et al.
abstract: Background In order to counteract the eutrophication of waterways and reservoirs, a basic risk assessment of phosphorus (P) losses in the surface runoff from agricultural land should be included in water management plans. A new method has been developed to assess the risk of P losses by estimating the degree of P saturation (DPS) based on the P concentration of the water extract water-soluble P. Methods The risk of P losses in surface runoff from agricultural land in the Puck Commune on the Baltic Sea Coast was assessed with the DPS method. The results were compared to an agronomic interpretation of the soil test P concentration (STP). Research was conducted on mineral and organic soils from 50 and 11 separate agricultural plots with a total area of 133.82 and 37.23 ha, respectively. Phosphorus was extracted from the collected samples using distilled water on all soil samples, acid ammonium lactate on mineral soils, and an extract of 0.5 mol HCl·dm−3 on organic soils. The organic matter content and pH values were also determined. The results of the P content in the water extracted from the soils were converted into DPS values, which were then classified by appropriate limit intervals. Results and discussion There was a high risk of P losses from the soil via surface runoff in 96.7% of the agricultural parcels tested (96% of plots with mineral soils and 100% of plots with organic soils). Simultaneously, a large deficiency of plant-available P was found in soils from 62% of agricultural plots. These data indicate that the assessment of P concentration in soils made on the basis of an environmental soil P test conflicts with the assessment made based on STP and create a cognitive dissonance. The risk level of P losses through surface runoff from the analyzed plots as determined by the DPS indicator is uncertain. This uncertainty is increased as the DPS index is not correlated with other significant factors in P runoff losses, such as the type of crop and area inclinati…
bibliographic citation: Pietrzak et al. (2020) Risk of phosphorus losses in surface runoff from agricultural land in the Baltic Commune of Puck in the light of assessment performed on the basis of DPS indicator. PeerJ 8:e8396 https://doi.org/10.7717/peerj.8396
date submitted: 2019-05-17
date accepted: 2019-12-13
issued: 2020-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pietrzak
  given name: Stefan
author list: Agent
  family name: Pazikowska-Sapota
  given name: Grażyna
author list: Agent
  family name: Dembska
  given name: Grażyna
author list: Agent
  family name: Dzierzbicka-Glowacka
  given name: Lidia Anita
author list: Agent
  family name: Juszkowska
  given name: Dominika
author list: Agent
  family name: Majewska
  given name: Zuzanna
author list: Agent
  family name: Urbaniak
  given name: Marek
author list: Agent
  family name: Ostrowska
  given name: Dominika
author list: Agent
  family name: Cichowska
  given name: Agnieszka
author list: Agent
  family name: Galer-Tatarowicz
  given name: Katarzyna
doi: 10.7717/peerj.8396
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-07
copyright: © 2020 Pietrzak et al.
attribution name: Pietrzak et al.

The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico
type: item
type: AcademicArticle
description: Background Stenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents. Method Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed. Results Anthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol’s growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol’s possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emul…
format: application/pdf
format: text/html
creator: Temidayo O. Elufisan
creator: Isabel C. Rodríguez-Luna
creator: Omotayo Opemipo Oyedara
creator: Alejandro Sánchez-Varela
creator: Armando Hernández-Mendoza
creator: Edgar Dantán Gonzalez
creator: Alma D. Paz-González
creator: Kashif Muhammad
creator: Gildardo Rivera
creator: Miguel Angel Villalobos-Lopez
creator: Xianwu Guo
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.8102
publisher: PeerJ Inc.
rights: © 2020 Elufisan et al.
abstract: Background Stenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents. Method Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed. Results Anthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol’s growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol’s possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emul…
bibliographic citation: Elufisan et al. (2020) The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico. PeerJ 8:e8102 https://doi.org/10.7717/peerj.8102
date submitted: 2019-03-28
date accepted: 2019-10-25
issued: 2020-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elufisan
  given name: Temidayo O.
author list: Agent
  family name: Rodríguez-Luna
  given name: Isabel C.
author list: Agent
  family name: Oyedara
  given name: Omotayo Opemipo
author list: Agent
  family name: Sánchez-Varela
  given name: Alejandro
author list: Agent
  family name: Hernández-Mendoza
  given name: Armando
author list: Agent
  family name: Dantán Gonzalez
  given name: Edgar
author list: Agent
  family name: Paz-González
  given name: Alma D.
author list: Agent
  family name: Muhammad
  given name: Kashif
author list: Agent
  family name: Rivera
  given name: Gildardo
author list: Agent
  family name: Villalobos-Lopez
  given name: Miguel Angel
author list: Agent
  family name: Guo
  given name: Xianwu
doi: 10.7717/peerj.8102
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-06
copyright: ©2020 Elufisan et al.
attribution name: Elufisan et al.

Assessment of a Takagi–Sugeno-Kang fuzzy model assembly for examination of polyphasic loglinear allometry
type: item
type: AcademicArticle
description: Background The traditional allometric analysis relies on log- transformation to contemplate linear regression in geometrical space then retransforming to get Huxley’s model of simple allometry. Views assert this induces bias endorsing multi-parameter complex allometry forms and nonlinear regression in arithmetical scales. Defenders of traditional approach deem it necessary since generally organismal growth is essentially multiplicative. Then keeping allometry as originally envisioned by Huxley requires a paradigm of polyphasic loglinear allometry. A Takagi-Sugeno-Kang fuzzy model assembles a mixture of weighted sub models. This allows direct identification of break points for transition between phases. Then, this paradigm is seamlessly appropriate for efficient allometric examination of polyphasic loglinear allometry patterns. Here, we explore its suitability. Methods Present fuzzy model embraces firing strength weights from Gaussian membership functions and linear consequents. Weights are identified by subtractive clustering and consequents through recursive least squares or maximum likelihood. Intersection of firing strength factors set criterion to estimate breakpoints. A multi-parameter complex allometry model follows by adapting firing strengths by composite membership functions and linear consequents in arithmetical space. Results Takagi-Sugeno-Kang surrogates adapted complexity depending on analyzed data set. Retransformation results conveyed reproducibility strength of similar proxies identified in arithmetical space. Breakpoints were straightforwardly identified. Retransformed form implies complex allometry as a generalization of Huxley’s power model involving covariate depending parameters. Huxley reported a breakpoint in the log–log plot of chela mass vs. body mass of fiddler crabs (Uca pugnax), attributed to a sudden change in relative growth of the chela approximately when crabs reach sexual maturity. G.C. Packard implied this breakpoint as putative. Ho…
format: application/pdf
format: text/html
creator: Hector A. Echavarria-Heras
creator: Juan R. Castro-Rodriguez
creator: Cecilia Leal-Ramirez
creator: Enrique Villa-Diharce
subject: Ecology
subject: Mathematical Biology
subject: Plant Science
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.8173
publisher: PeerJ Inc.
rights: © 2020 Echavarria-Heras et al.
abstract: Background The traditional allometric analysis relies on log- transformation to contemplate linear regression in geometrical space then retransforming to get Huxley’s model of simple allometry. Views assert this induces bias endorsing multi-parameter complex allometry forms and nonlinear regression in arithmetical scales. Defenders of traditional approach deem it necessary since generally organismal growth is essentially multiplicative. Then keeping allometry as originally envisioned by Huxley requires a paradigm of polyphasic loglinear allometry. A Takagi-Sugeno-Kang fuzzy model assembles a mixture of weighted sub models. This allows direct identification of break points for transition between phases. Then, this paradigm is seamlessly appropriate for efficient allometric examination of polyphasic loglinear allometry patterns. Here, we explore its suitability. Methods Present fuzzy model embraces firing strength weights from Gaussian membership functions and linear consequents. Weights are identified by subtractive clustering and consequents through recursive least squares or maximum likelihood. Intersection of firing strength factors set criterion to estimate breakpoints. A multi-parameter complex allometry model follows by adapting firing strengths by composite membership functions and linear consequents in arithmetical space. Results Takagi-Sugeno-Kang surrogates adapted complexity depending on analyzed data set. Retransformation results conveyed reproducibility strength of similar proxies identified in arithmetical space. Breakpoints were straightforwardly identified. Retransformed form implies complex allometry as a generalization of Huxley’s power model involving covariate depending parameters. Huxley reported a breakpoint in the log–log plot of chela mass vs. body mass of fiddler crabs (Uca pugnax), attributed to a sudden change in relative growth of the chela approximately when crabs reach sexual maturity. G.C. Packard implied this breakpoint as putative. Ho…
bibliographic citation: Echavarria-Heras et al. (2020) Assessment of a Takagi–Sugeno-Kang fuzzy model assembly for examination of polyphasic loglinear allometry. PeerJ 8:e8173 https://doi.org/10.7717/peerj.8173
date submitted: 2019-05-24
date accepted: 2019-11-06
issued: 2020-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Echavarria-Heras
  given name: Hector A.
author list: Agent
  family name: Castro-Rodriguez
  given name: Juan R.
author list: Agent
  family name: Leal-Ramirez
  given name: Cecilia
author list: Agent
  family name: Villa-Diharce
  given name: Enrique
doi: 10.7717/peerj.8173
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-06
copyright: ©2020 Echavarria-Heras et al.
attribution name: Echavarria-Heras et al.

The Rametrix™ PRO Toolbox v1.0 for MATLAB®
type: item
type: AcademicArticle
description: Background Existing tools for chemometric analysis of vibrational spectroscopy data have enabled characterization of materials and biologicals by their broad molecular composition. The Rametrix™ LITE Toolbox v1.0 for MATLAB® is one such tool available publicly. It applies discriminant analysis of principal components (DAPC) to spectral data to classify spectra into user-defined groups. However, additional functionality is needed to better evaluate the predictive capabilities of these models when “unknown” samples are introduced. Here, the Rametrix™ PRO Toolbox v1.0 is introduced to provide this capability. Methods The Rametrix™ PRO Toolbox v1.0 was constructed for MATLAB® and works with the Rametrix™ LITE Toolbox v1.0. It performs leave-one-out analysis of chemometric DAPC models and reports predictive capabilities in terms of accuracy, sensitivity (true-positives), and specificity (true-negatives). Rametrix™PRO is available publicly through GitHub under license agreement at: https://github.com/SengerLab/RametrixPROToolbox. Rametrix™ PRO was used to validate Rametrix™ LITE models used to detect chronic kidney disease (CKD) in spectra of urine obtained by Raman spectroscopy. The dataset included Raman spectra of urine from 20 healthy individuals and 31 patients undergoing peritoneal dialysis treatment for CKD. Results The number of spectral principal components (PCs) used in building the DAPC model impacted the model accuracy, sensitivity, and specificity in leave-one-out analyses. For the dataset in this study, using 35 PCs in the DAPC model resulted in 100% accuracy, sensitivity, and specificity in classifying an unknown Raman spectrum of urine as belonging to a CKD patient or a healthy volunteer. Models built with fewer or greater number of PCs showed inferior performance, which demonstrated the value of Rametrix™ PRO in evaluating chemometric models constructed with Rametrix™ LITE.
format: application/pdf
format: text/html
creator: Ryan S. Senger
creator: John L. Robertson
subject: Bioengineering
subject: Computational Biology
subject: Nephrology
subject: Urology
subject: Statistics
description: doi:10.7717/peerj.8179
publisher: PeerJ Inc.
rights: © 2020 Senger and Robertson
abstract: Background Existing tools for chemometric analysis of vibrational spectroscopy data have enabled characterization of materials and biologicals by their broad molecular composition. The Rametrix™ LITE Toolbox v1.0 for MATLAB® is one such tool available publicly. It applies discriminant analysis of principal components (DAPC) to spectral data to classify spectra into user-defined groups. However, additional functionality is needed to better evaluate the predictive capabilities of these models when “unknown” samples are introduced. Here, the Rametrix™ PRO Toolbox v1.0 is introduced to provide this capability. Methods The Rametrix™ PRO Toolbox v1.0 was constructed for MATLAB® and works with the Rametrix™ LITE Toolbox v1.0. It performs leave-one-out analysis of chemometric DAPC models and reports predictive capabilities in terms of accuracy, sensitivity (true-positives), and specificity (true-negatives). Rametrix™PRO is available publicly through GitHub under license agreement at: https://github.com/SengerLab/RametrixPROToolbox. Rametrix™ PRO was used to validate Rametrix™ LITE models used to detect chronic kidney disease (CKD) in spectra of urine obtained by Raman spectroscopy. The dataset included Raman spectra of urine from 20 healthy individuals and 31 patients undergoing peritoneal dialysis treatment for CKD. Results The number of spectral principal components (PCs) used in building the DAPC model impacted the model accuracy, sensitivity, and specificity in leave-one-out analyses. For the dataset in this study, using 35 PCs in the DAPC model resulted in 100% accuracy, sensitivity, and specificity in classifying an unknown Raman spectrum of urine as belonging to a CKD patient or a healthy volunteer. Models built with fewer or greater number of PCs showed inferior performance, which demonstrated the value of Rametrix™ PRO in evaluating chemometric models constructed with Rametrix™ LITE.
bibliographic citation: Senger et al. (2020) The Rametrix™ PRO Toolbox v1.0 for MATLAB®. PeerJ 8:e8179 https://doi.org/10.7717/peerj.8179
date submitted: 2019-05-16
date accepted: 2019-11-08
issued: 2020-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Senger
  given name: Ryan S.
author list: Agent
  family name: Robertson
  given name: John L.
doi: 10.7717/peerj.8179
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-06
copyright: ©2020 Senger and Robertson
attribution name: Senger and Robertson

sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data
type: item
type: AcademicArticle
description: Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still poses some practical and computational challenges. We present sv-callers, a highly portable workflow that enables parallel execution of multiple SV detection tools, as well as provide users with example analyses of detected SV callsets in a Jupyter Notebook. This workflow supports easy deployment of software dependencies, configuration and addition of new analysis tools. Moreover, porting it to different computing systems requires minimal effort. Finally, we demonstrate the utility of the workflow by performing both somatic and germline SV analyses on different high-performance computing systems.
format: application/pdf
format: text/html
creator: Arnold Kuzniar
creator: Jason Maassen
creator: Stefan Verhoeven
creator: Luca Santuari
creator: Carl Shneider
creator: Wigard P. Kloosterman
creator: Jeroen de Ridder
subject: Bioinformatics
subject: Genomics
subject: Data Science
description: doi:10.7717/peerj.8214
publisher: PeerJ Inc.
rights: © 2020 Kuzniar et al.
abstract: Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still poses some practical and computational challenges. We present sv-callers, a highly portable workflow that enables parallel execution of multiple SV detection tools, as well as provide users with example analyses of detected SV callsets in a Jupyter Notebook. This workflow supports easy deployment of software dependencies, configuration and addition of new analysis tools. Moreover, porting it to different computing systems requires minimal effort. Finally, we demonstrate the utility of the workflow by performing both somatic and germline SV analyses on different high-performance computing systems.
bibliographic citation: Kuzniar et al. (2020) sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data. PeerJ 8:e8214 https://doi.org/10.7717/peerj.8214
date submitted: 2019-05-15
date accepted: 2019-11-14
issued: 2020-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuzniar
  given name: Arnold
author list: Agent
  family name: Maassen
  given name: Jason
author list: Agent
  family name: Verhoeven
  given name: Stefan
author list: Agent
  family name: Santuari
  given name: Luca
author list: Agent
  family name: Shneider
  given name: Carl
author list: Agent
  family name: Kloosterman
  given name: Wigard P.
author list: Agent
  family name: de Ridder
  given name: Jeroen
doi: 10.7717/peerj.8214
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-06
copyright: © 2020 Kuzniar et al.
attribution name: Kuzniar et al.

Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species
type: item
type: AcademicArticle
description: Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.
format: application/pdf
format: text/html
creator: Zhanjun Wang
creator: Beibei Xu
creator: Bao Li
creator: Qingqing Zhou
creator: Guiyi Wang
creator: Xingzhou Jiang
creator: Chenchen Wang
creator: Zhongdong Xu
subject: Bioinformatics
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.8251
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.
bibliographic citation: Wang et al. (2020) Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species. PeerJ 8:e8251 https://doi.org/10.7717/peerj.8251
date submitted: 2019-06-26
date accepted: 2019-11-20
issued: 2020-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhanjun
author list: Agent
  family name: Xu
  given name: Beibei
author list: Agent
  family name: Li
  given name: Bao
author list: Agent
  family name: Zhou
  given name: Qingqing
author list: Agent
  family name: Wang
  given name: Guiyi
author list: Agent
  family name: Jiang
  given name: Xingzhou
author list: Agent
  family name: Wang
  given name: Chenchen
author list: Agent
  family name: Xu
  given name: Zhongdong
doi: 10.7717/peerj.8251
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-06
copyright: ©2020 Wang et al.
attribution name: Wang et al.

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