title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=418 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms link: https://peerj.com/articles/16028 last-modified: 2023-09-19 description: Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets.Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies.PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies). creator: Marcos Suárez Menéndez creator: Vania E. Rivera-León creator: Jooke Robbins creator: Martine Berube creator: Per J. Palsbøll uri: https://doi.org/10.7717/peerj.16028 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Suárez Menéndez et al. title: Forecasting the flooding dynamics of flatwoods salamander breeding wetlands under future climate change scenarios link: https://peerj.com/articles/16050 last-modified: 2023-09-19 description: Ephemeral wetlands are globally important systems that are regulated by regular cycles of wetting and drying, which are primarily controlled by responses to relatively short-term weather events (e.g., precipitation and evapotranspiration). Climate change is predicted to have significant effects on many ephemeral wetland systems and the organisms that depend on them through altered filling or drying dates that impact hydroperiod. To examine the potential effects of climate change on pine flatwoods wetlands in the southeastern United States, we created statistical models describing wetland hydrologic regime using an approximately 8-year history of water level monitoring and a variety of climate data inputs. We then assessed how hydrology may change in the future by projecting models forward (2025–2100) under six future climate scenarios (three climate models each with two emission scenarios). We used the model results to assess future breeding conditions for the imperiled Reticulated Flatwoods Salamander (Ambystoma bishopi), which breeds in many of the study wetlands. We found that models generally fit the data well and had good predictability across both training and testing data. Across all models and climate scenarios, there was substantial variation in the predicted suitability for flatwoods salamander reproduction. However, wetlands with longer hydroperiods tended to have fewer model iterations that predicted at least five consecutive years of reproductive failure (an important metric for population persistence). Understanding potential future risk to flatwoods salamander populations can be used to guide conservation and management actions for this imperiled species. creator: Houston C. Chandler creator: Nicholas M. Caruso creator: Daniel L. McLaughlin creator: Yan Jiao creator: George C. Brooks creator: Carola A. Haas uri: https://doi.org/10.7717/peerj.16050 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chandler et al. title: Expression level and clinical significance of LncRNA PVT1 in the serum of patients with LEASO link: https://peerj.com/articles/16057 last-modified: 2023-09-19 description: ObjectiveOur study aims to investigate the long non-coding RNA plasmacytoma variant translocation 1 (lncRNA PVT1) in lower extremity arteriosclerosis obliterans (LEASO) patient serum and its clinical significance in LEASO.Patients and MethodsFrom July 2021 to April 2022, 133 LEASO patients diagnosed at the Qingdao Municipal Hospital were included. Among them, 44 complicated with coronary artery disease (CAD) were classified as the LEASO with CAD group. The remaining 89 were marked as the LEASO group, which was classified into single (n = 48) and double (n = 41) lower limb groups, with the former being subclassified into the left (n = 28) and right (n = 20) lower limb groups based on the affected sites. Fifty healthy individuals who came to our hospital for physical examination during the same period were randomly included and defined as the Healthy Control group. PVT1 expression was detected in serum samples from each group using a quantitative reverse transcriptase-polymerase chain reaction , and differences in expression levels were calculated. The ankle-brachial index (ABI) of patients in the LEASO group was measured using a sphygmomanometer, and its correlation with PVT1 was analyzed. Clinical data and laboratory test results (including blood routine, liver and renal function, and blood lipids) were collected for all patients upon admission. Logistic regression analyses were performed to determine the influence of PVT1 and laboratory test results on LEASO. The diagnosis and prediction of LEASO were obtained by combing PVT1 with laboratory test indicators.ResultsIt was found that lncRNA PVT1 expression was the highest in the serum of the LEASO with CAD group, followed by the LEASO and control groups (P < 0.05). Within the LEASO group, no significant difference in PVT1 expression was seen between the left and right limbs (P > 0.05), nor between the single and double lower limb groups. Furthermore, the PVT1 expression increased with the Rutherford grades, indicating a negative correlation between PVT1 and ABI. Logistic regression analysis revealed that triglycerides (OR = 2.972, 95% CI [1.159–7.618]), cholesterol (OR = 6.655, 95% CI [1.490–29.723]), C-reactive protein (OR = 1.686, 95% CI [1.218–2.335]), and PVT1 (OR = 2.885, 95% CI [1.350–6.167]) were independent risk factors for LEASO. Finally, strong sensitivity was observed in the receiver operating characteristic curve when combining PVT1 with meaningful laboratory indicators to diagnose and predict LEASO.ConclusionlncRNA PVT1 promotes LEASO occurrence and progression and is related to atherosclerosis severity. The expression of PVT1 was negatively correlated with ABI. Logistic regression analysis suggested that blood lipid levels and inflammatory reactions might be related to LEASO occurrence. PVT1 was incorporated into laboratory indicators to predict LEASO. The subject’s working curve area was large, and the prediction results were highly sensitive. creator: Xiaoxue Su creator: Xiaoqing Yuan creator: Fenghui Li creator: Guinan Yang creator: Liunianbo Du creator: Fule Zhao creator: Rui Zhao creator: Minghui Ou uri: https://doi.org/10.7717/peerj.16057 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Su et al. 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.