title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=455 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Development and validation of a personalized classifier to predict the prognosis and response to immunotherapy in glioma based on glycolysis and the tumor microenvironment link: https://peerj.com/articles/16066 last-modified: 2023-09-19 description: BackgroundGlycolysis is closely associated with cancer progression and treatment outcomes. However, the role of glycolysis in the immune microenvironment, prognosis, and immunotherapy of glioma remains unclear.MethodsThis study investigated the role of glycolysis on prognosis and its relationship with the tumor microenvironment (TME). Subsequently, we developed and validated the glycolysis-related gene signature (GRS)-TME classifier using multiple independent cohorts. Furthermore, we also examined the prognostic value, somatic alterations, molecular characteristics, and potential benefits of immunotherapy based on GRS-TME classifier. Lastly, the effect of kinesin family member 20A (KIF20A) on the proliferation and migration of glioma cells was evaluated in vitro.ResultsGlycolysis was identified as a significant prognostic risk factor in glioma, and closely associated with an immunosuppressive microenvironment characterized by altered distribution of immune cells. Furthermore, a personalized GRS-TME classifier was developed and validated by combining the glycolysis (18 genes) and TME (seven immune cells) scores. Patients in the GRSlow/TMEhigh subgroup exhibited a more favorable prognosis compared to other subgroups. Distinct genomic alterations and signaling pathways were observed among different subgroups, which are closely associated with cell cycle, epithelial—mesenchymal transition, p53 signaling pathway, and interferon-alpha response. Additionally, we found that patients in the GRSlow/TMEhigh subgroup exhibit a higher response rate to immunotherapy, and the GRS-TME classifier can serve as a novel biomarker for predicting immunotherapy outcomes. Finally, high expression of KIF20A is associated with an unfavorable prognosis in glioma, and its knockdown can inhibit the proliferation and migration of glioma cells.ConclusionsOur study developed a GRS-TME classifier for predicting the prognosis and potential benefits of immunotherapy in glioma patients. Additionally, we identified KIF20A as a prognostic and therapeutic biomarker for glioma. creator: Pengfei Fan creator: Jinjin Xia creator: Meifeng Zhou creator: Chao Zhuo creator: Hui He uri: https://doi.org/10.7717/peerj.16066 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Fan et al. title: Energy flow in men’s javelin throw and its relationship to joint load and performance link: https://peerj.com/articles/16081 last-modified: 2023-09-19 description: BackgroundPerformance in javelin throwing is dependent on the release speed and therefore the energy transferred to the javelin. Little is known about the flow of mechanical energy in javelin throwing and whether there is a connection to joint loading and throwing performance. The purpose of the study was therefore to investigate (1) the energy flow within the kinetic chain of the throwing arm, (2) how it is related to performance and joint loads and (3) how joint forces and torques are used to transfer, generate and absorb mechanical energy.MethodsThe kinematics of 10 experienced javelin throwers were recorded using a 12-camera infrared system. 16 markers were placed on the athlete’s body, five on the javelin to track the movement of each segment. A segmental power analysis was carried out to calculate energy flow between upper body, upper arm, forearm and hand. Stepwise regression analysis was used to calculate the variable that best predicts release speed and joint loads.ResultsThe results indicate that the higher the peak rate of energy transfer from the thorax to the humerus, the higher the release speed and the joint loads. While there were no differences between the peak rate of energy transfer in the different joints, the energy transferred differed depending on whether joint forces or torques were used. It can be further shown that higher joint torques and thus higher rotational kinetics at the shoulder are linked to higher release speeds. Thus, the movements of the upper body can be of great influence on the result in javelin throwing. Furthermore, the data show that athletes who are able to transfer more energy through the shoulder, rather than generate it, experience a smaller joint loading. An effective technique for improved energy transfer can thus help perform at the same level while lowering joint stress or have higher performance at the same joint loading. creator: Hans-Peter Köhler creator: Maren Witt uri: https://doi.org/10.7717/peerj.16081 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Köhler and Witt title: Essential role of multi-element data in interpreting elevated element concentrations in areas impacted by both natural and anthropogenic influences link: https://peerj.com/articles/15904 last-modified: 2023-09-18 description: BackgroundThis article presents a detailed analysis of a dataset consisting of 27 elements found in soils, soil eluates, and vegetables from private gardens in a region with a long history of coal mining and burning. With coal being one of the world’s most significant energy sources, and previous studies highlighting elevated element levels in vegetables from this region, the objective of this study was to identify the factors that impact soil geochemistry and metal(loid) uptake in plants.MethodsTotal major and trace element concentrations were analyzed in soils, soil eluates and vegetables by high resolution inductively coupled plasma mass spectrometry. The vegetable samples included six species: fennel, garlic, lettuce, parsley, onion, and radicchio. Each plant was divided into roots, stems, leaves, and/or bulbs and analyzed separately. In addition, the soil pollution status, bioavailable fractions and transfer factors from soil and soil eluates to different plant parts were determined.ResultsThe comprehensive dataset revealed that, apart from the substrate enriched with various elements (Al, As, Co, Cr, Mo, Ni, Pb, Sb, Sn, Ti, U, V, and Zn), other anthropogenic factors such as the legacy of coal mining and combustion activities, associated industries in the area, transport, and agricultural practices, also influence the elevated element concentrations (Cd, Cu, Fe, Mn, and Se) in locally grown vegetables. The transfer factors based on element concentrations in aqueous soil eluates and element bioavailable fractions confirmed to be an effective tool for evaluating metal uptake in plants, emphazising to some extent the effects of plant species and revealing unique patterns for each pollution source within its environmental context (e.g., Cd, Mo, S, and Se in this case). The study highlights the crucial importance of utilizing comprehensive datasets that encompass a multitude of factors when interpreting the impacts of element uptake in edible plants. creator: Marija Petrović creator: Gordana Medunić creator: Željka Fiket uri: https://doi.org/10.7717/peerj.15904 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Petrović et al. title: Description of a common stauromedusa on the Pacific Coast of the United States and Canada, Haliclystus sanjuanensis new species (Cnidaria: Staurozoa) link: https://peerj.com/articles/15944 last-modified: 2023-09-18 description: Haliclystus “sanjuanensis” nomen nudum is the most common staurozoan on the west coast of the United States and Canada. This species was described in the M.S. Thesis by Gellermann (1926) and although that name has been in use nearly continuously since that time, no published description exists. Furthermore, the most popular operative name for this species has varied between several related species names over time, resulting in confusion. Herein, we provide a detailed description and synonymy of Haliclystus sanjuanensis n. sp., whose distribution is verified from Unalaska Island in the Aleutians (53.4° N, 166.8° W) in the northwest, to Santa Barbara County, California, just north of Point Conception (34.5° N, 120.5° W), in the south. Haliclystus sanjuanensis n. sp. is compared with the twelve other described species of Haliclystus and illustrations of both macroscopic and microscopic anatomy are provided. Haliclystus sanjuanensis n. sp. is unique among species of Haliclystus in the arrangement of the bright-white nematocyst spots in its calyx and the pattern of dark stripes running the length of the stalk and up the outside of the calyx. creator: Claudia E. Mills creator: Hannah Westlake creator: Yayoi M. Hirano creator: Lucília S. Miranda uri: https://doi.org/10.7717/peerj.15944 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mills et al. title: Comparative efficacy of intraoperative radiotherapy and external boost irradiation in early-stage breast cancer: a systematic review and meta-analysis link: https://peerj.com/articles/15949 last-modified: 2023-09-18 description: External boost radiotherapy (EBRT) and intraoperative radiotherapy (IORT) are shown to be effective in patients with early-stage breast cancer. However, the difference between IORT and EBRT for patients’ prognosis remains to be elucidated. The purpose of this meta-analysis is to investigate differences in local recurrence (LR), distant metastases, disease free survival (DFS), and overall survival (OS) between these two therapies. We searched the Cochrane Library, PubMed, Web of Science and Embase, from inception to Jan 10th, 2022. We used The Cochrane risk-of-bias assessment tool to assess the risk of bias of the included studies, and the STATA15.0 tool was used for the meta-analyses. Eight studies were ultimately included. Meta-analysis demonstrated that there was an inconsistent finding in the long-term risk of LR between the two radiotherapies, and there was no significant difference in short-term risk of LR, the metastasis rate, DFS, and OS IORT would be more convenient, less time-consuming, less costly, and more effective at reducing side effects and toxicity. However, these benefits must be balanced against the potential for increased risk of LR in the long term. creator: Jiaxin Liu creator: Xiaowei Shi creator: Zhenbo Niu creator: Cheng Qian uri: https://doi.org/10.7717/peerj.15949 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: The prevalence and associated factors of sleep deprivation among healthy college students in China: a cross-sectional survey link: https://peerj.com/articles/16009 last-modified: 2023-09-18 description: BackgroundThe prevalence of sleep deprivation among college students is increasing and has a few associated factors.MethodsThe 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.ResultsAmong 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]).ConclusionsSleep 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. creator: Congcong Guo creator: Songzhe Piao creator: Chenyu Wang creator: Lili Yu creator: Kejun Wang creator: Qian Qu creator: Cuiting Zhang creator: Xiaofei Yu uri: https://doi.org/10.7717/peerj.16009 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guo et al. title: Robustness of genetic diversity measures under spatial sampling and a new frequency-independent measure link: https://peerj.com/articles/16027 last-modified: 2023-09-18 description: 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. creator: Satoshi Aoki creator: Fumiko Ishihama creator: Keita Fukasawa uri: https://doi.org/10.7717/peerj.16027 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Aoki et al. title: Expression profiles of circular RNAs and interaction networks of competing endogenous RNAs in neurogenic bladder of rats following suprasacral spinal cord injury link: https://peerj.com/articles/16042 last-modified: 2023-09-18 description: BackgroundNeurogenic 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.MethodsSpinal 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.ResultsBladder 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.ConclusionsThis 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. creator: Jimeng Ruan creator: Xin Cui creator: Hao Yan creator: Chunsong Jia creator: Tongwen Ou creator: Zhenhua Shang uri: https://doi.org/10.7717/peerj.16042 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ruan et al. title: A new gnathosaurine (Pterosauria, Archaeopterodactyloidea) from the Late Jurassic of Portugal link: https://peerj.com/articles/16048 last-modified: 2023-09-18 description: 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. creator: Alexandra E. Fernandes creator: Victor Beccari creator: Alexander W. A. Kellner creator: Octávio Mateus uri: https://doi.org/10.7717/peerj.16048 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Fernandes et al. title: Performance of multigene testing in cytologically indeterminate thyroid nodules and molecular risk stratification link: https://peerj.com/articles/16054 last-modified: 2023-09-18 description: ObjectiveThyroid 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.MethodsIn 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.ResultsThe 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. ConclusionsThis 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. creator: Yuanyuan Zhou creator: Xinping Wu creator: Yuzhi Zhang creator: Zhiqiang Li creator: Xia Ge creator: Hao Chen creator: Yuan Mao creator: Wenbo Ding uri: https://doi.org/10.7717/peerj.16054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhou et al.