The prevalence and associated factors of sleep deprivation among healthy college students in China: a cross-sectional survey
Background The prevalence of sleep deprivation among college students is increasing and has a few associated factors. Methods The present study analyzed 2,142 college students from 28 provinces in China. The Chinese version of the Pittsburgh Sleep Quality Index (PSQI) was used to assess sleep duration. Binary logistic regression was conducted to explore the sleep deprivation related factors. Age and gender were controlled as covariates. Results Among the 2,142 college students (27.7% male, 72.3% female), 1,620 (75.6%) reported the average sleep duration was below 7 h per day for one month, 49.3% (1,055/2,142) slept 6∼7 h (contains 6 h), 21.0% (449/2,142) slept 5∼6 h (contains 5 h), and 5.4% (116/2,142) slept <5 h. Age increased the risk of sleep deprivation, the adjusted odds ratio = 1.05 (95% CI [1.01∼1.10]). The adjusted odds ratio (A-OR) for sleep deprivation was higher for students of more than 60 min nap duration per day (A-OR = 2.35, 95% CI [1.45∼3.80]), and age growth (A-OR = 1.05, 95% CI [1.01∼1.10]). In contrast, A-ORs were lower among sleeping inconsistency between work and rest days (A-OR = 0.61, 95% CI [0.49∼0.75]), accustomed to staying up late (A-OR = 0.45, 95% CI [0.36∼0.57]), staying up late to work or study (A-OR = 0.62, 95% CI [0.49∼0.78]), stress (A-OR = 0.75, 95% CI [0.58∼0.98]), and repeated thoughts in bed had (A-OR = 0.79, 95% CI [0.62∼0.99]). Conclusions Sleep deprivation is extremely common among healthy college students in China. It is necessary to perform methods maintaining enough sleep due to the current high incidence of sleep deprivation. Controlling the nap duration and getting enough sleep on rest days to replace missing hours of sleep on workdays might improve college students’ sleep.
Guo et al. (2023) The prevalence and associated factors of sleep deprivation among healthy college students in China: a cross-sectional survey. PeerJ 11:e16009 https://doi.org/10.7717/peerj.16009
Robustness of genetic diversity measures under spatial sampling and a new frequency-independent measure
The genetic diversity of a taxon has often been estimated by genetic diversity measures. However, they assume random sampling of individuals which is often inapplicable. Except when the distribution of the taxon is limited, researchers conventionally choose several sampling locations from the known distribution and then collect individuals from each location. Spatial sampling is a formalized version of the conventional sampling, which objectively provides geographically even sampling locations to cover genetic variation in a taxon assuming isolation by distance. To evaluate the validity of the spatial sampling in estimating genetic diversity, we conducted coalescent simulation experiments. The sampling locations were selected by spatial sampling and one sample was collected from each location for the sake of theoretical simplicity. We also devised a new measure of genetic diversity, ς, which assumes spatial sampling and is independent of allele frequency. This new measure places an emphasis on rare and phylogenetically distant alleles which have relatively small effect on nucleotide diversity. Therefore, it can complementarily serve for conservation studies although it cannot be used to estimate population mutation rate. We compared ς with the other diversity measures in the experiments. Nucleotide diversity, expected heterozygosity and ς showed within 3% relative biases on average while Watterson’s theta was 31% overestimation on average. Thus, genetic diversities other than Watterson’s theta held good robustness under the spatial sampling.
Aoki et al. (2023) Robustness of genetic diversity measures under spatial sampling and a new frequency-independent measure. PeerJ 11:e16027 https://doi.org/10.7717/peerj.16027
Expression profiles of circular RNAs and interaction networks of competing endogenous RNAs in neurogenic bladder of rats following suprasacral spinal cord injury
Background Neurogenic bladder (NB) following suprasacral spinal cord injury (SSCI) is an interstitial disease with the structural remodeling of bladder tissue and matrix over-deposition. Circular RNAs (circRNAs) are involved in fibrotic disease development through their post-transcriptional regulatory functions. This study aimed to use transcriptome high-throughput sequencing to investigate the process of NB and bladder fibrosis after SSCI. Methods Spinal cord transection at the T10–T11 level was used to construct the SSCI model in rats (10–week–old female Wistar rats, weighing 200 ± 20 g). The bladders were collected without (sham group) and with (SSCI 1–3 groups) NB status. Morphological examination was conducted to assess the extent of bladder fibrosis. Additionally, RNA sequencing was utilized to determine mRNAs and circRNAs expression patterns. The dynamic changes of differentially expressed mRNAs (DEMs) and circRNAs (DECs) in different periods of SSCI were further analyzed. Results Bladder weight, smooth muscle cell hypertrophy, and extracellular matrix gradually increased after SSCI. Compared with the sham group, 3,255 DEMs and 1,339 DECs, 3,449 DEMs and 1,324 DECs, 884 DEMs, and 1,151 DECs were detected in the SSCI 1–3 groups, respectively. Specifically, circRNA3621, circRNA0617, circRNA0586, and circRNA4426 were significant DECs common to SSCI 1–3 groups compared with the sham group. Moreover, Gene Ontology (GO) enrichment suggested that inflammatory and chronic inflammatory responses were the key events in NB progression following SSCI. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment associated with the “Chemokine signaling pathway”, the “IL-17 signaling pathway”, and the “TGF-beta signaling pathway” suggests their potential involvement in regulating biological processes. The circRNA–miRNA–mRNA interaction networks of DECs revealed rno-circ-2239 (micu2) as the largest node, indicating that the rno-circ-2239–miRNA–mRNA–mediated network may play a critical role in the pathogenesis of SSCI-induced NB. Conclusions This study offers a comprehensive outlook on the possible roles of DEMs and DECs in bladder fibrosis and NB progression following SSCI. These findings have the potential to serve as novel biomarkers and therapeutic targets.
Ruan et al. (2023) Expression profiles of circular RNAs and interaction networks of competing endogenous RNAs in neurogenic bladder of rats following suprasacral spinal cord injury. PeerJ 11:e16042 https://doi.org/10.7717/peerj.16042
A new gnathosaurine (Pterosauria, Archaeopterodactyloidea) from the Late Jurassic of Portugal
An incomplete, yet remarkably-sized dentated rostrum and associated partial cervical vertebrae of a pterosaur (ML 2554) were recently discovered from the Late Jurassic (Late Kimmeridgian-Early Tithonian) Lourinhã Formation of Praia do Caniçal, of central west Portugal. This specimen exhibits features such as a spatulated anterior expansion of the rostrum, robust comb-like dentition, and pronounced rims of the tooth alveoli, indicating gnathosaurine affinities. Based on its further unique tooth and dentary morphology, a new genus and species, Lusognathus almadrava gen. et spec. nov., is proposed, making this the first named pterosaur species found within Portugal. The presence of this taxon adds yet another element to the fluvio-deltaic lagoonal environment that has been suggested as representative of the Lourinhã Formation in the Late Jurassic, further contributing to the diversity and distribution of gnathosaurines worldwide.
Fernandes et al. (2023) A new gnathosaurine (Pterosauria, Archaeopterodactyloidea) from the Late Jurassic of Portugal. PeerJ 11:e16048 https://doi.org/10.7717/peerj.16048
Performance of multigene testing in cytologically indeterminate thyroid nodules and molecular risk stratification
Objective Thyroid cancer is the third most prevalent cancer among females. Genetic testing based on next-generation sequencing may provide an auxiliary diagnosis to reduce cytologically diagnostic uncertainty. However, commercial multigene tests are not widely available and are not well-tested in the Chinese population. Methods In this study, we designed a multigene testing panel and evaluated its performance in 529 cytologically indeterminate thyroid nodules (Bethesda III, IV and V). The molecular data of the DNA mutations and RNA fusions of fine needle aspiration samples were reviewed in conjunction with a clinical diagnosis, pathological reports, and definitive surgery for retrospective analysis. Then, the molecular risk stratification was investigated for its accuracy in malignant risk prediction. Results The overall combined consistency revealed substantial agreement (Kappa = 0.726) with the sensitivity, specificity, positive predictive value, and negative predictive values of 97.80%, 82.14%, 98.99%, and 67.65%, respectively. The most common aberration was BRAFV600E (82.59%), followed by NRAS mutants (4.07%), RET fusions (3.70%), and KRAS mutants (3.15%). Two cases (0.44%) were categorized into a high-risk group, 426 cases (94.67%) were categorized into a BRAF-like group with totally histopathologic papillary patterned tumors, and 22 cases (4.89%) were categorized into a RAS-like group with 14 papillary and eight follicular patterned tumors when the cohort concurrent aberrations were excluded. Potentially aggressive features may be related to concurrent molecular alterations of BRAFV600E with TERTQ302R, and AKT1L52R, NRASG12C, NRASQ61R, and CCDC6-RET fusions. Conclusions This study provided a multigene panel for identifying benign nodules from cytologically indeterminate thyroid nodules to avoid unnecessary surgery. We provide further evidence for using molecular risk stratification as a promising predictor of disease outcomes. The results of this study may be limited by the extremely high prevalence of cancer in the cohort for clinical reference.
Zhou et al. (2023) Performance of multigene testing in cytologically indeterminate thyroid nodules and molecular risk stratification. PeerJ 11:e16054 https://doi.org/10.7717/peerj.16054
Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides
Background Gardenia jasminoides is a species of Chinese medicinal plant, which has high medicinal and economic value and rich genetic diversity, but the study on its genetic diversity is far not enough. Methods In this study, one wild and one cultivated gardenia materials were resequenced using IlluminaHiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of G. jasminoides. Results After data analysis, the results showed that clean data of 11.77G, Q30 reached 90.96%. The average comparison rate between the sample and reference genome was 96.08%, the average coverage depth was 15X, and the genome coverage was 85.93%. The SNPs of FD and YP1 were identified, and 3,087,176 and 3,241,416 SNPs were developed, respectively. In addition, SNP non-synonymous mutation, InDel mutation, SV mutation and CNV mutation were also detected between the sample and the reference genome, and KEGG, GO and COG database annotations were made for genes with DNA level variation. The structural gene variation in the biosynthetic pathway of crocin and gardenia, the main medicinal substance of G. jasminoides was further explored, which provided basic data for molecular breeding and genetic diversity of G. jasminoides in the future.
Xu et al. (2023) Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides. PeerJ 11:e16056 https://doi.org/10.7717/peerj.16056
In vitro and ex vitro propagation of Turkish myrtles through conventional and plantform bioreactor systems
The myrtle (Myrtus communis) plant naturally grows in the temperate Mediterranean and subtropical regions and is used for various purposes; thus, it is among the promising species of horticultural crops. This study aimed to evaluate and compare the performance of different propagation systems, including rooting, solid media propagation, rooting, and with the Plantform bioreactor system, in achieving healthy and rapid growth of four myrtle genotypes with diverse genetic origins and well-regional adaptation. The selection of myrtle genotypes with distinct genetic backgrounds and proven adaptability to specific regions allowed for a comprehensive assessment of the propagation systems under investigation. Present findings proved that the Plantform system, the new-generation tissue culture system, was quite successful in micropropagation and rooting myrtle genotypes. We succeeded in vitro micropropagation and rooting of diverse wild myrtle genotypes, enabling year-round propagation without reliance on specific seasons or environmental conditions. The process involved initiating cultures from explants and multiplying them through shoot proliferation in a controlled environment. This contributes to sustainable plant propagation, preserving and utilizing genetic resources for conservation and agriculture.
Şimşek et al. (2023) In vitro and ex vitro propagation of Turkish myrtles through conventional and plantform bioreactor systems. PeerJ 11:e16061 https://doi.org/10.7717/peerj.16061
The mediating roles of coping styles and academic burnout in the relationship between stressors and depressive symptoms among Chinese postgraduates
Background Since few studies have incorporated factors like stressors, coping styles, and academic burnout into the same model to analyze their impacts on depressive symptoms, this research attempts to establish an optimal structural model to explore the direct and indirect effects of these factors on depressive symptoms. Methods A total of 266 postgraduates completed questionnaires regarding coping styles, academic burnout, stressors, and depressive symptoms. The path analysis was applied for investigating the roles of coping styles and academic burnout in mediating the relationship between stressors and depressive symptoms. Results The total and direct effects of stressors on depressive symptoms were 0.53 and 0.31, respectively. The proportion of the direct effect of stressors on depressive symptoms to its total effect amounted to 58.50%. The indirect effects of academic burnout, positive coping style, and negative coping style on the association between stressors and depressive symptoms were 0.11, 0.04, and 0.03, taking up 20.75%, 7.55%, and 5.66% of the total effect, respectively. The serial indirect effect of positive coping style and academic burnout was 0.02, accounting for 3.77% of the total effect, while that of negative coping style and academic burnout was 0.02, taking up 3.77% of the total effect. Conclusions Coping styles and academic burnout chain jointly mediate the relationship between stressors and depressive symptoms among postgraduates. Thus, encouraging postgraduates to tackle stress positively may reduce the likelihood of the development of academic burnout and further reduce depressive symptoms.
Shi et al. (2023) The mediating roles of coping styles and academic burnout in the relationship between stressors and depressive symptoms among Chinese postgraduates. PeerJ 11:e16064 https://doi.org/10.7717/peerj.16064
Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study
Background COVID-19 is a worldwide pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various pathological conditions. The aim of this retrospective and observational pilot study was to investigate the range of cfDNA plasma concentrations in hospitalized COVID-19 patients during the first wave of SARS-CoV-2 infection, to relate them to established inflammatory parameters as a correlative biomarker for disease severity, and to compare them with plasma levels in a healthy control group. Methods Lithium-Heparin plasma samples were obtained from COVID-19 patients (n = 21) during hospitalization in the University Medical Centre of Mainz, Germany between March and June 2020, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). The cfDNA levels were compared with those of an uninfected control group (n = 19). Results Plasma cfDNA levels in COVID-19 patients ranged from 247.5 to 6,346.25 ng/ml and the mean concentration was 1,831 ± 1,388 ng/ml (± standard deviation), which was significantly different from the levels of the uninfected control group (p < 0.001). Regarding clinical complications, the highest correlation was found between cfDNA levels and the myositis (p = 0.049). In addition, cfDNA levels correlated with the “WHO clinical progression scale”. D-Dimer and C-reactive protein (CRP) were the clinical laboratory parameters with the highest correlations with cfDNA levels. Conclusion The results of this observational pilot study show a wide range in cfDNA plasma concentrations in patients with COVID-19 during the first wave of infection and confirm that cfDNA plasma concentrations serve as a predictive biomarker of disease severity in COVID-19.
Hoeter et al. (2023) Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study. PeerJ 11:e16072 https://doi.org/10.7717/peerj.16072
Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators
Background Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9. Methods In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed. Results Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1. Conclusion The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.
Jiang et al. (2023) Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators. PeerJ 11:e16103 https://doi.org/10.7717/peerj.16103