Unfold: an integrated toolbox for overlap correction, non-linear modeling, and regression-based EEG analysis
Electrophysiological research with event-related brain potentials (ERPs) is increasingly moving from simple, strictly orthogonal stimulation paradigms towards more complex, quasi-experimental designs and naturalistic situations that involve fast, multisensory stimulation and complex motor behavior. As a result, electrophysiological responses from subsequent events often overlap with each other. In addition, the recorded neural activity is typically modulated by numerous covariates, which influence the measured responses in a linear or non-linear fashion. Examples of paradigms where systematic temporal overlap variations and low-level confounds between conditions cannot be avoided include combined electroencephalogram (EEG)/eye-tracking experiments during natural vision, fast multisensory stimulation experiments, and mobile brain/body imaging studies. However, even “traditional,” highly controlled ERP datasets often contain a hidden mix of overlapping activity (e.g., from stimulus onsets, involuntary microsaccades, or button presses) and it is helpful or even necessary to disentangle these components for a correct interpretation of the results. In this paper, we introduce unfold, a powerful, yet easy-to-use MATLAB toolbox for regression-based EEG analyses that combines existing concepts of massive univariate modeling (“regression-ERPs”), linear deconvolution modeling, and non-linear modeling with the generalized additive model into one coherent and flexible analysis framework. The toolbox is modular, compatible with EEGLAB and can handle even large datasets efficiently. It also includes advanced options for regularization and the use of temporal basis functions (e.g., Fourier sets). We illustrate the advantages of this approach for simulated data as well as data from a standard face recognition experiment. In addition to traditional and non-conventional EEG/ERP designs, unfold can also be applied to other overlapping physiological signals, such as pupillary or electrodermal responses. It is available as open-source software at http://www.unfoldtoolbox.org.
Ehinger et al. (2019) Unfold: an integrated toolbox for overlap correction, non-linear modeling, and regression-based EEG analysis. PeerJ 7:e7838 https://doi.org/10.7717/peerj.7838
Gender differences on medical students’ attitudes toward patient-centred care: a cross-sectional survey conducted in Heilongjiang, China
Objectives Assessing medical students’ attitudes toward patient-centred care is essential to bettering medical education. Based on doctor-patient relationships and the medical system in China, it is important to explore the impact of gender differences and other background factors on patient-centred attitudes and to provide references for medical education reform. Methods A cross-sectional study was conducted on fourth-year medical undergraduate students from November 2017 to March 2018 in Heilongjiang Province, Northeast China. The Chinese-revised Patient-Practitioner Orientation Scale (CR-PPOS), which has been validated in previous research, was used to measure the medical students’ attitudes. The medical students’ demographic data was collected, including their gender, age, information on whether they have siblings, family residence location, doctor(s) for parents, year in which the student first experienced clinical practice, and student category. Results A total of 513 students (91.12%) completed the survey. The Chinese medical students scored considerably higher for ‘Caring’ (including patients’ preferences into the decision-making process) than for ‘Sharing’ (sharing information/responsibility with patients). These students tended to have patient-centred attitudes, as measured by an average overall CR-PPOS score of 3.63 (scores higher than 3.5 indicate patient-centred attitudes), which is higher than Malian (3.38) and Pakistani (3.40) medical students but lower than American (4.57) and Brazilian (4.66) students. Female students (P < 0.05) were significantly associated with more patient-centred attitudes and with higher ‘Sharing’ and ‘Caring’ subscale scores. Student category (P < 0.05) was associated with ‘Sharing’ and ‘Caring’ scores. Clinical hospital students (P < 0.05) were associated with more patient-centred attitudes and with higher ‘Sharing’ and ‘Caring’ subscale scores, Students without siblings (p < 0.07) were associated with the higher ‘Sharing’ subscale scores. Conclusions In China, gender has a significant impact on medical students’ patient-centred attitudes, which is similar to findings from other countries. If medical schools want to raise patient-centred attitudes across the board and bridge the gap between male and female patient-centred attitudes, gender, student category, and other factors should be incorporated into medical education.
Liu et al. (2019) Gender differences on medical students’ attitudes toward patient-centred care: a cross-sectional survey conducted in Heilongjiang, China. PeerJ 7:e7896 https://doi.org/10.7717/peerj.7896
Selection of appropriate reference genes for RT-qPCR analysis under abiotic stress and hormone treatment in celery
Celery is one of the most important vegetable crop and its yield and quality is influenced by many environmental factors. Researches on gene expression not only help to unravel the molecular regulatory mechanism but also identify the key genes in the biological response. RT-qPCR is a commonly used technology to quantify the gene expression. Selecting an appropriate reference gene is an effective approach to improve the accuracy of RT-qPCR assay. To our knowledge, the evaluation of reference genes under different treatments in celery has not been reported yet. In this study, the expression stabilities of eight candidate reference genes (ACTIN, eIF-4α, GAPDH, TBP, TUB-A, UBC, TUB-B, and EF-1α) under abiotic stresses (heat, cold, drought, and salt) and hormone treatments (SA, MeJA, GA, and ABA) were detected. The expression stabilities of candidate genes were compared and ranked by geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder programs. The results calculated by different programs were not completely consistent. Considering the comprehensive analysis results, ACTIN was the most stable reference gene and TUB-B showed the worst expression stabilities under the selected abiotic stress and hormone treatments in celery. The reliability of reference genes was further confirmed by the normalization of CAT1 gene under drought stress. This study presented evidences and basis to select the appropriate reference genes under different treatments in celery.
Feng et al. (2019) Selection of appropriate reference genes for RT-qPCR analysis under abiotic stress and hormone treatment in celery. PeerJ 7:e7925 https://doi.org/10.7717/peerj.7925
Delayed evoked potentials in zebra finch (Taeniopygia guttata) under midazolam-butorphanol-isoflurane anesthesia
Avian animals are visually inclined, which has caused them to attract increasing attention for visual neurophysiology or electrophysiology studies, including the study of the visual evoked potential (VEP). VEP has developed into an investigative tool for understanding the physiology and the pathology of the visual pathway. Chemical restraint is a common method to minimize motion artifacts in animals when acquiring VEP data, but little is known about its influence on the signal in an avian animal. In addition, it is difficult to make comparisons between conscious state data when the animals are ultimately under anesthesia. Therefore, finding drugs and developing protocols that have an acceptable effect is valuable. We compared the local field potentials of physically and chemically restrained zebra finches (Taeniopygia guttata), a small avian species, to simulate a relatively challenging recording condition. Finches were sedated with midazolam-butorphanol, and anesthesia was maintained by isoflurane. Electrodes were implanted into the left nucleus rotundus, which is a visual nucleus in birds. The VEPs of the control group (N = 3) were recorded after they fully recovered and were restrained by towels. The other birds (N = 3) were recorded under anesthesia. The results show that without the visual stimuli, anesthesia generally suppressed the overall power of field potentials. However, by focusing on the spectra during VEPs, visual stimuli still triggered significant VEPs in frequencies below 30.8 Hz, which were even stronger than towel-restrained birds. The drugs also prolonged the latency of the VEP, increased the duration of the VEP when compared to towel-restrained birds. As regard to towel-restrained zebra finches, the field potentials were less synchronized and may need data preprocessing to have clear VEPs. In conclusion, the current study presents evidence of basic VEP for zebra finch under midazolam-butorphanol-isoflurane anesthesia with a protocol that is a safe and feasible anesthetic combination for chemical restraint, which is particularly useful for small animals when obtaining evoked potentials.
Yu et al. (2019) Delayed evoked potentials in zebra finch (Taeniopygia guttata) under midazolam-butorphanol-isoflurane anesthesia. PeerJ 7:e7937 https://doi.org/10.7717/peerj.7937
Cloninger’s TCI associations with adaptive and maladaptive emotion regulation strategies
Background Cognitive emotion regulation plays a crucial role in psychopathology, resilience and well-being by regulating response to stress situations. However, the relationship between personality and adaptive and maladaptive regulation has not been sufficiently examined. Methods Adaptive and maladaptive cognitive emotion regulation strategies of 247 university students were measured using the Cognitive Emotion Regulation Questionnaire (CERQ) and their temperament and character characteristics were analyzed with the Temperament and Character Inventory—Revised Short (TCI-RS). Two-step hierarchical multiple regression analyses were used to analyze whether TCI-RS explains the use of adaptive and maladaptive cognitive emotion regulation strategies. The latent classes of cognitive emotion regulation strategies were extracted with Latent Class Analysis (LCA) and significant differences in the subscales of CERQ and TCI-RS were examined with Analysis of Covariance (ANCOVA) and Profile Analysis after controlling for sex and age. Results The two-step hierarchical multiple regression model using the seven TCI-RS subscales explained 32.30% of the adaptive and 41.70% of the maladaptive CERQ subscale scores when sex and age were introduced in the first step as covariates. As for temperament, Novelty Seeking (NS) and Persistence (PS) were pivotal for adaptive and Harm Avoidance (HA) and PS for maladaptive CERQ total scores. In addition, the character traits Self-Directedness (SD) and Cooperativeness (CO) were critical for high adaptive and low maladaptive CERQ scores. Four latent emotion regulation classes were confirmed through LCA, and distinct TCI-RS profiles were found. The temperament trait HA and character trait SD were significantly different among the four latent emotion regulation classes. Discussion This study demonstrated that SD and CO are related to cognitive emotion regulation strategies along with psychological health and well-being, and that PS exhibits dualistic effects when combined with NS or HA on response to stressful situations. The importance of developing mature character represented by higher SD and CO in regard to mental health and its clinical implementation was discussed.
Chae et al. (2019) Cloninger’s TCI associations with adaptive and maladaptive emotion regulation strategies. PeerJ 7:e7958 https://doi.org/10.7717/peerj.7958
Antibacterial immune functions of subadults and adults in a semelparous spider
Although capacity to mount an efficient immune response plays a critical role in individuals’ survival, its dynamics across ontogenetic stages is still largely unexplored. Life stage-dependent variation in the encountered diversity and prevalence of parasites were proposed to contribute to stage-dependent changes in immunity, but differences in life history objectives between developmental stages may also lead to stage-specific changes in efficiency of given immune mechanisms. The reason for this is that juveniles and subadults are unable to reproduce, therefore they invest resources mainly into survival, while adults have to partition their resources between survival and reproduction. The general trade-off between somatic maintenance and reproductive effort is expected to impair immune function. Especially so in semelparous organisms that only reproduce once throughout their lifetime, hence they do not face the trade-off between current and future reproduction. We hypothesised that in a semelparous species individuals would be characterised by decreased investment into somatic maintenance after maturation, in order to maximise their reproductive output. Accordingly, we predicted that (1) elements of somatic maintenance, such as immunity, should be relatively weaker in adults in comparison to subadults, and (2) increased reproductive investment in adults should be associated with lower immune efficiency. We quantified two markers of immunity in subadult and adult individuals of the semelparous wolf spider Pardosa agrestis (Westring, 1861), namely bacterial growth inhibition power and bacterial cell wall lytic activity. We found that subadults showed significantly higher cell wall lytic activity than adults, but the two life stages did not differ in their capacity to inhibit bacterial growth. Also, we found weaker immune measures in mated females compared to virgins. Furthermore, in mated females bacterial growth inhibition power was negatively associated with fecundity.
Rádai et al. (2019) Antibacterial immune functions of subadults and adults in a semelparous spider. PeerJ 7:e7475 https://doi.org/10.7717/peerj.7475
Influence of temperature on intraspecific, unbalanced dyadic contests between crabs
Intraspecific agonistic interactions are widespread across the animal kingdom, with many individual morphological and physiological characteristics playing important roles in the fate of disputes. Additionally, changes to environmental conditions can influence the outcomes of animal contests. The shore crab (Carcinus maenas) is a globally distributed species, present in numerous coastal and estuarine temperate systems around the world. Although shore crabs are highly tolerant to changes in temperature, this parameter has important physiological effects on the species’ ecology, while its effects on behavior are not fully understood. Our study aims to investigate how different individual characteristics (such as sex, color morphotype, carapace and chela morphology) and temperature conditions affect the dyadic interactions between shore crabs when disputing food resources. In general, the differences in carapace width between opponents, their sexes, color morphotypes and the temperature conditions interacted and were important predictors of the contest fate. We found that the body size and color morphotype of C. maenas determined the fate of dyadic disputes. However, the higher temperatures disrupted the well-established dominance of the larger red color morphotype individuals. Overall, the agonistic contest results suggest higher plasticity than previously acknowledged.
Souza et al. (2019) Influence of temperature on intraspecific, unbalanced dyadic contests between crabs. PeerJ 7:e7845 https://doi.org/10.7717/peerj.7845
Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize
P1B-type ATPases, known as heavy metal ATPases (HMAs), play an important role in the control of cadmium (Cd) accumulation in plants. In this study, a total of 12 ZmHMA genes were identified in the maize genome and particularly classified into six clusters based on their phylogenetic relationship and motif compositions. Furthermore, the expression patterns of different ZmHMA genes varied with developmental stages, and were tissue specific under normal conditions. ZmHMA2 and ZmHMA3 genes exhibited significant up-regulation under Cd treatment. Eventually, the association analysis between 103 inbred lines and alleles in ZmHMA2 and ZmHMA3 revealed that one insertion–deletion (InDel) in the intron from ZmHMA2 was associated with leaf Cd concentration under low Cd condition at the seedling stage. Twenty polymorphisms in ZmHMA3 were significantly associated with leaf Cd concentration under various Cd levels at seedling and maturing stages. Five single nucleotide polymorphisms (SNPs) and two InDels of these significantly associated polymorphic loci from ZmHMA3 caused the amino acid substitutions and insertion or deletion events. Importantly, the proteins encoded by ZmHMA2 and ZmHMA3 genes were located in the plasma membrane. This comprehensive analysis will provide an important theoretical basis for future functional verification of ZmHMA genes to unravel the mechanisms of Cd accumulation in leaves of maize. Additionally, the favorable alleles in ZmHMA3 will lay a foundation for the marker-assisted selection of low Cd accumulation in maize.
Cao et al. (2019) Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize. PeerJ 7:e7877 https://doi.org/10.7717/peerj.7877
Osteogenic cells form mineralized particles, a few μm in size, in a 3D collagen gel culture
Osteogenic cells form mineralized matrices in vitro, as well as in vivo. The formation and shape of the mineralized matrices are highly regulated by the cells. In vitro formation of mineralized matrices by osteogenic cells can be a model for in vivo osteogenesis. In this study, using a three-dimensional (3D) collagen gel culture system, we developed a new in vitro model for the formation of mineralized particles, a few µm in size, by the osteogenic cells. Human osteosarcoma (HOS) cells formed spherical mineralized matrices (about 12 µm) at approximately 7 days when cultured with β-glycerophosphate (β-GP)-containing culture media on 2D tissue culture plates. Alternately, when they were cultured in a 3D collagen gel containing β-GP, they formed mineralized particles with about 1.7 µm in the gel at approximately 3 days. Calcium precipitation in the gel was evaluated by measuring the gel turbidity. This type of mineralization of HOS cells, which formed mineralized particles inside the gel, was also observed in a peptide-based hydrogel culture. The mineralized particles were completely diminished by inhibiting the activity of Pit-1, phosphate cotransporter, of the HOS cells. When mouse osteoblast-like MC3T3-E1 cells, which form large and flat mineralized matrices in 2D osteogenic conditions at approximately 3 weeks of culture, were cultured in a 3D collagen gel, they also formed mineralized particles in the gel, similar to those in HOS cells, at approximately 18 days. Thus, osteogenic cells cultured in the 3D collagen gel form mineralized particles over a shorter period, and the mineralization could be easily determined by gel turbidity. This 3D gel culture system of osteogenic cells acts as a useful model for cells forming particle-type mineralized matrices, and we assume that the mineralized particles in the 3D hydrogel are calcospherulites, which are derived from matrix vesicles secreted by osteogenic cells.
Kihara et al. (2019) Osteogenic cells form mineralized particles, a few μm in size, in a 3D collagen gel culture. PeerJ 7:e7889 https://doi.org/10.7717/peerj.7889
Manure application increased denitrifying gene abundance in a drip-irrigated cotton field
Application of inorganic nitrogen (N) fertilizer and manure can increase nitrous oxide (N2O) emissions. We tested the hypothesis that increased N2O flux from soils amended with manure reflects a change in bacterial community structure and, specifically, an increase in the number of denitrifiers. To test this hypothesis, a field experiment was conducted in a drip-irrigated cotton field in an arid region of northwestern China. Treatments included plots that were not amended (Control), and plots amended with urea (Urea), animal manure (Manure) and a 50/50 mix of urea and manure (U+M). Manure was broadcast-incorporated into the soil before seeding while urea was split-applied with drip irrigation (fertigation) over the growing season. The addition treatments did not, as assessed by nextgen sequencing of PCR-amplicons generated from rRNA genes in soil, affect the alpha diversity of bacterial communities but did change the beta diversity. Compared to the Control, the addition of manure (U+M and Manure) significantly increased the abundance of genes associated with nitrate reduction (narG) and denitrfication (nirK and nosZ). Manure addition (U+M and Manure) did not affect the nitrifying enzyme activity (NEA) of soil but resulted in 39–59 times greater denitrifying enzyme activity (DEA). In contrast, urea application had no impact on the abundances of nitrifier and denitrifier genes, DEA and NEA; likely due to a limitation of C availability. DEA was highly correlated (r = 0.70–0.84, P < 0.01) with the abundance of genes narG, nirK and nosZ. An increase in the abundance of these functional genes was further correlated with soil NO3−, dissolved organic carbon, total C, and total N concentrations, and soil C:N ratio. These results demonstrated a positive relationship between the abundances of denitrifying functional genes (narG, nirK and nosZ) and denitrification potential, suggesting that manure application increased N2O emission by increasing denitrification and the population of bacteria that mediated that process.
Yin et al. (2019) Manure application increased denitrifying gene abundance in a drip-irrigated cotton field. PeerJ 7:e7894 https://doi.org/10.7717/peerj.7894