Development of an autophagy-related gene prognostic signature in lung adenocarcinoma and lung squamous cell carcinoma
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.
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
EEG alpha activity increased in response to transcutaneous electrical nervous stimulation in young healthy subjects but not in the healthy elderly
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.
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
Feasibility of assessing ultra-short-term pulse rate variability from video recordings
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.
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
Exercise mode and attentional networks in older adults: a cross-sectional study
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.
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
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
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 inclination.
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
The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico
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-emulsify PAH. A possible degradation pathway for naphthalene in Pemsol was proposed following the analysis of Pemsol’s genome. ANI and GGDH analysis indicated that Pemsol is likely a new species of Stenotrophomonas. It is the first report on a complete genome sequence analysis of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that make it a good bacterium for genetic engineering and will be an excellent tool for the remediation of crude oil or PAH-contaminated soil.
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
Assessment of a Takagi–Sugeno-Kang fuzzy model assembly for examination of polyphasic loglinear allometry
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. However, according to present fuzzy methods existence of a break point in Huxley’s data could be validated. Conclusions Offered scheme bears reliable analysis of zero intercept allometries based on geometrical space protocols. Endorsed affine structure accommodates either polyphasic or simple allometry if whatever turns required. Interpretation of break points characterizing heterogeneity is intuitive. Analysis can be achieved in an interactive way. This could not have been obtained by relying on customary approaches. Besides, identification of break points in arithmetical scale is straightforward. Present Takagi-Sugeno-Kang arrangement offers a way to overcome the controversy between a school considering a log-transformation necessary and their critics claiming that consistent results can be only obtained through complex allometry models fitted by direct nonlinear regression in the original scales.
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
The Rametrix™ PRO Toolbox v1.0 for MATLAB®
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.
Senger et al. (2020) The Rametrix™ PRO Toolbox v1.0 for MATLAB®. PeerJ 8:e8179 https://doi.org/10.7717/peerj.8179
sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data
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.
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
Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species
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.
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