title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=298 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Construction of a nomogram for predicting catheter-related bladder discomfort in patients with end-stage renal disease after renal transplantation: a retrospective study link: https://peerj.com/articles/17530 last-modified: 2024-06-21 description: BackgroundThe incidence of catheter-related bladder discomfort (CRBD) is relatively high in the end-stage renal disease (ESRD) patients who underwent renal transplantation (RT). This study was designed to establish a nomogram for predicting CRBD after RT among ESRD patients.MethodsIn this retrospective study, we collected 269 ESRD patients who underwent RT between September 2019 and August 2023 in our hospital. The patients were divided into training set (n = 215) and test set (n = 54) based on a ratio of 8:2. Univariate and multivariate logistic regression analyses were utilized to identify the risk factors associated with CRBD after RT, and then a nomogram model was constructed. Receiver operating characteristic (ROC) and calibration curve were used to evaluate the predicting efficiency of the established nomogram.ResultsMultivariate logistic regression analysis showed that aberrant body mass index (BMI) (underweight: OR = 5.25; 95% CI [1.25–22.15], P = 0.024; overweight: OR = 2.75; 95% CI [1.17–6.49], P = 0.021), anuria (OR = 2.86; 95% CI [1.33–5.88]) and application of double J (DJ) stent with a diameter of >5Fr (OR = 15.88; 95% CI [6.47–39.01], P < 0.001) were independent risk factors for CRBD after RT. In contrast, sufentanil utilization (>100 µg) [OR = 0.39; 95% CI [0.17–0.88], P = 0.023] was associated with decreased incidence of CRBD. A nomogram was then established based on these parameters for predicting the occurrence of CRBD after RT. Area under the ROC curve (AUC) values and calibration curves confirmed the prediction efficiency of the nomogram.ConclusionA nomogram was established for predicting CRBD after RT in ESRD patients, which showed good prediction efficiency based on AUC and calibration curves. creator: Kao Liu creator: Shengli Liu creator: Zhiguo Peng creator: Na Li creator: Huaibin Sun uri: https://doi.org/10.7717/peerj.17530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: The relationship between low energy availability, injuries, and bone health in recreational female athletes link: https://peerj.com/articles/17533 last-modified: 2024-06-21 description: BackgroundLow energy availability (LEA) causes pathophysiology of the female athlete’s body affecting the bone and reproductive health and was observed to have a high prevalence in recreational female athletes previously. The aim of this study was to analyse the relationship between low energy availability in females questionnaire (LEAF-Q), bone mineral density (BMD), and postural stability in recreational athletes.MethodsRecreational female athletes (n = 24, age: 23.71 ± 2.94, Tier I) completed LEAF-Q, postural stability measurement during quiet stance (Zebris platform FDM; GmbH) and their BMD was measured using DXA (Hologic QDR Horizon A). Non-parametric statistical tests were used to analyse the relationships between LEAF-Q, BMD, and postural stability and to compare differences between participants divided by the LEAF-Q score and its subscales.ResultsRisk of LEA was observed in 50% of recreational athletes participating in this study. Up to 46% of participants perceived menstrual bleeding changes related to training and 37.50% experienced menstrual dysfunction. Body composition and body weight fluctuations were observed to affect postural stability and BMD. With the risk score for LEA, the BMD and postural stability were not negatively affected in recreational athletes. However, the high number of recreational athletes in the risk score for LEA and menstrual dysfunctions highlights the need for public health programs aimed to increase awareness of LEA and its health consequences and for open communication about the menstrual cycle. Future longitudinal studies observing LEA, BMD, menstrual function, postural stability, and their interrelationship in female athletes are needed to increase the knowledge of this topic. creator: Marta Gimunová creator: Michal Bozděch creator: Martina Bernaciková creator: Romulo Fernandes creator: Michal Kumstát creator: Ana Paludo uri: https://doi.org/10.7717/peerj.17533 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gimunová et al. title: Efficacy and safety of Brolucizumab for neovascular age-related macular degeneration: a systematic review and meta-analysis link: https://peerj.com/articles/17561 last-modified: 2024-06-21 description: BackgroundTo evaluate the efficacy and safety of Brolucizumab for neovascular age-related macular degeneration (n-AMD) through a systematic review and meta-analysis.Materials and MethodsCochrane, PubMed, Embase, and Web of Science databases were comprehensively searched for relevant studies. Stata and RevMan5.4 were applied for meta-analysis and risk of bias assessment. Data on the best-corrected visual acuity (BCVA), central subfield thickness (CSFT), presence of intraretinal fluid (IRF) and/or subretinal fluid (SRF), participants with ≥1 serious adverse events, and participants with ≥1 adverse events were analyzed.ResultsSix studies were finally included. Meta-analysis showed statistical differences in BCVA [SMD = −0.65, 95% CI [−0.17 to −0.23], P < 0.05], the presence of IRF and/or SRF [RR = 0.67, 95% CI [0.56–0.79], P < 0.05], and the safety of participants with ≥1 serious adverse events [RR = 0.57, 95% CI [0.39–0.84], P < 0.05] between the experimental group and the control group. However, no statistical differences were observed in CSFT [SMD = −1.16, 95% CI [−2.79 to 0.47], P > 0.05] or the safety of participants with ≥1 adverse events [RR = 1.07, 95% CI [0.97–1.17], P > 0.05].ConclusionsCompared to other anti-VEGF drugs such as Aflibercept and Ranibizumab, intravitreal injection of 6 mg Brolucizumab is more effective and safer for n-AMD, especially in the presence of IRF and/or SRF, and for participants with ≥1 serious adverse events. creator: Ran Dou creator: Jian Jiang uri: https://doi.org/10.7717/peerj.17561 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dou and Jiang title: Retrospective study of a novel hematological parameter for predicting the survival of patients with nasopharyngeal carcinoma link: https://peerj.com/articles/17573 last-modified: 2024-06-21 description: PurposeThis study aims to explore the prognostic values of routine pre-treatment hematological parameters in patients with nasopharyngeal carcinoma (NPC).MethodsThe hematological parameters and clinical data of patients with NPC were collected from January 2012 to December 2013 at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology. The survival statistics were obtained by regularly following-up the patients. The cut-off values for the hematological parameters were calculated using X-tile software. SPSS version 24.0 was used for the statistical analysis. The relationship between the hematological parameters and the prognosis of patients with NPC was analyzed using the Kaplan–Meier method and Cox multivariate regression. The discriminating abilities of the factors, which predict the prognosis, were evaluated by utilizing the receiver operating characteristic (ROC) area under the curve (AUC).ResultsThis study included 179 patients with NPC. Multivariate analysis shows that pretreatment platelet-to-lymphocyte ratio (PLR; hazard ratio; HR = 0.44, 95% CI [0.21–0.91], p = 0.029), serum albumin (ALB; HR = 2.49, 95% CI [1.17–5.30], p = 0.018), and globulin (GLO; HR = 0.44, 95% CI [0.21–0.90], p = 0.024) are independent predictors for 5-year overall survival (OS) in patients with NPC. In addition, pre-treatment PLR (HR = 0.47, 95% CI [0.25–0.90], p = 0.022) and pre-treatment GLO (HR = 0.37, 95% CI [0.19–0.72], p = 0.001) are associated with 5-year progression-free survival (PFS) in patients with NPC. Based on the results of the multivariate analysis, we proposed a new biomarker GLO-PLR, which is observably correlated with the T stage, N stage and clinical stage in patients with NPC. The OS resolving ability of the GLO-PLR evaluated by AUC is 0.714, which is better than those of GLO and PLR. The PFS resolving ability of the GLO-PLR evaluated by AUC was 0.696, which is also better than those of GLO and PLR.ConclusionPre-treatment PLR, ALB, and GLO are independent predictors of 5-year OS in patients with NPC, where PLR and GLO are also independent predictors of 5-year FPS. Compared with other hematological parameters, the proposed GLO-PLR is an inexpensive, effective, objective, and easy-to-measure marker for predicting the prognosis of NPC. creator: Wenhua Tang creator: Guoxian Long uri: https://doi.org/10.7717/peerj.17573 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tang and Long title: Lokiceratops rangiformis gen. et sp. nov. (Ceratopsidae: Centrosaurinae) from the Campanian Judith River Formation of Montana reveals rapid regional radiations and extreme endemism within centrosaurine dinosaurs link: https://peerj.com/articles/17224 last-modified: 2024-06-20 description: The Late Cretaceous of western North America supported diverse dinosaur assemblages, though understanding patterns of dinosaur diversity, evolution, and extinction has been historically limited by unequal geographic and temporal sampling. In particular, the existence and extent of faunal endemism along the eastern coastal plain of Laramidia continues to generate debate, and finer scale regional patterns remain elusive. Here, we report a new centrosaurine ceratopsid, Lokiceratops rangiformis, from the lower portion of the McClelland Ferry Member of the Judith River Formation in the Kennedy Coulee region along the Canada-USA border. Dinosaurs from the same small geographic region, and from nearby, stratigraphically equivalent horizons of the lower Oldman Formation in Canada, reveal unprecedented ceratopsid richness, with four sympatric centrosaurine taxa and one chasmosaurine taxon. Phylogenetic results show that Lokiceratops, together with Albertaceratops and Medusaceratops, was part of a clade restricted to a small portion of northern Laramidia approximately 78 million years ago. This group, Albertaceratopsini, was one of multiple centrosaurine clades to undergo geographically restricted radiations, with Nasutuceratopsini restricted to the south and Centrosaurini and Pachyrostra restricted to the north. High regional endemism in centrosaurs is associated with, and may have been driven by, high speciation rates and diversity, with competition between dinosaurs limiting their geographic range. High speciation rates may in turn have been driven in part by sexual selection or latitudinally uneven climatic and floral gradients. The high endemism seen in centrosaurines and other dinosaurs implies that dinosaur diversity is underestimated and contrasts with the large geographic ranges seen in most extant mammalian megafauna. creator: Mark A. Loewen creator: Joseph J. W. Sertich creator: Scott Sampson creator: Jingmai K. O’Connor creator: Savhannah Carpenter creator: Brock Sisson creator: Anna Øhlenschlæger creator: Andrew A. Farke creator: Peter J. Makovicky creator: Nick Longrich creator: David C. Evans uri: https://doi.org/10.7717/peerj.17224 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Loewen et al. title: Gypenosides exert cardioprotective effects by promoting mitophagy and activating PI3K/Akt/GSK-3β/Mcl-1 signaling link: https://peerj.com/articles/17538 last-modified: 2024-06-20 description: BackgroundGynostemma pentaphyllum (Thunb.) Makino, a well-known edible and medicinal plant, has anti-aging properties and is used to treataging-associated conditions such as diabetes, metabolic syndrome, and cardiovascular diseases. Gypenosides (GYPs) are the primary constituents of G. pentaphyllum. Increasing evidence indicates that GYPs are effective at preserving mitochondrial homeostasis and preventing heart failure (HF). This study aimed to uncover the cardioprotective mechanisms of GYPs related to mitochondrial regulation.MethodsThe bioactive components in GYPs and the potential targets in treating HF were obtained and screened using the network pharmacology approach, followed by drug-disease target prediction and enrichment analyses. The pharmacological effects of GYPs in cardioprotection, mitochondrial function, mitochondrial quality control, and underlying mechanisms were further investigated in Doxorubicin (Dox)-stimulated H9c2 cardiomyocytes.ResultsA total of 88 bioactive compounds of GYPs and their respective 71 drug-disease targets were identified. The hub targets covered MAPK, EGFR, PI3KCA, and Mcl-1. Enrichment analysis revealed that the pathways primarily contained PI3K/Akt, MAPK, and FoxO signalings, as well as calcium regulation, protein phosphorylation, apoptosis, and mitophagy process. In Dox-stimulated H9c2 rat cardiomyocytes, pretreatment with GYPs increased cell viability, enhanced cellular ATP content, restored basal oxygen consumption rate (OCR), and improved mitochondrial membrane potential (MMP). Furthermore, GYPs improved PINK1/parkin-mediated mitophagy without influencing mitochondrial fission/fusion proteins and the autophagic LC3 levels. Mechanistically, the phosphorylation of PI3K, Akt, GSK-3β, and the protein level of Mcl-1 was upregulated by GYP treatment.ConclusionOur findings reveal that GYPs exert cardioprotective effects by rescuing the defective mitophagy, and PI3K/Akt/GSK-3β/Mcl-1 signaling is potentially involved in this process. creator: Yizhe Zheng creator: Wei Wei creator: Yukun Wang creator: Tingting Li creator: Yundong Wei creator: Si Gao uri: https://doi.org/10.7717/peerj.17538 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zheng et al. title: Mitochondrial DNA and Y chromosome reveal the genetic structure of the native Polish Konik horse population link: https://peerj.com/articles/17549 last-modified: 2024-06-20 description: Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a conservation program, while their Polish population consists of about 3,480 individuals, representing 16 dam and six sire lines. To define the population’s genetic structure, mitochondrial DNA and Y chromosome sequence variables were identified. The mtDNA whole hypervariable region analysis was carried out using the Sanger sequencing method on 233 Polish Koniks belonging to all dam lines, while the Y chromosome analysis was performed with the competitive allele-specific PCR genotyping method on 36 horses belonging to all sire lines. The analysis of the mtDNA hypervariable region detected 47 SNPs, which assigned all tested horses to 43 haplotypes. Most dam lines presented more than one haplotype; however, five dam lines were represented by only one haplotype. The haplotypes were classified into six (A, B, E, J, G, R) recognized mtDNA haplogroups, with most horses belonging to haplogroup A, common among Asian horse populations. Y chromosome analysis allocated Polish Koniks in the Crown group, condensing all modern horse breeds, and divided them into three haplotypes clustering with coldblood breeds (28 horses), warmblood breeds (two horses), and Duelmener Pony (six horses). The clustering of all Wicek sire line stallions with Duelmener horses may suggest a historical relationship between the breeds. Additionally, both mtDNA and Y chromosome sequence variability results indicate crossbreeding before the studbooks closure or irregularities in the pedigrees occurred before the DNA testing introduction. creator: Adrianna Dominika Musiał creator: Lara Radović creator: Monika Stefaniuk-Szmukier creator: Agnieszka Bieniek creator: Barbara Wallner creator: Katarzyna Ropka-Molik uri: https://doi.org/10.7717/peerj.17549 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Musiał et al. title: Identifying the source rookery of green turtles (Chelonia mydas) found in feeding grounds around the Korean Peninsula link: https://peerj.com/articles/17560 last-modified: 2024-06-20 description: Determining the genetic diversity and source rookeries of sea turtles collected from feeding grounds can facilitate effective conservation initiatives. To ascertain the genetic composition and source rookery, we examined a partial sequence of the mitochondrial control region (CR, 796 bp) of 40 green turtles (Chelonia mydas) collected from feeding grounds around the Korean Peninsula between 2014 and 2022. We conducted genetic and mixed-stock analyses (MSA) and identified 10 CR haplotypes previously reported in Japanese populations. In the haplotype network, six, three, and one haplotype(s) grouped with the Japan, Indo-Pacific, and Central South Pacific clades, respectively. The primary rookeries of the green turtles were two distantly remote sites, Ogasawara (OGA) and Central Ryukyu Island (CRI), approximately 1,300 km apart from each other. Comparing three parameters (season, maturity, and specific feeding ground), we noted that OGA was mainly associated with summer and the Jeju Sea, whereas CRI was with fall and the East (Japan) Sea ground. The maturity did not show a distinct pattern. Our results indicate that green turtles in the feeding grounds around the Korean Peninsula originate mainly from the Japan MU and have genetic origins in the Japan, Indo-Pacific, and Central South Pacific clades. Our results provide crucial insights into rookeries and MUs, which are the focus of conservation efforts of the Republic of Korea and potential parties to collaborate for green turtle conservation. creator: Min-Woo Park creator: Il-Hun Kim creator: Jaejin Park creator: Changho Yi creator: Min-Seop Kim creator: In-Young Cho creator: Il-Kook Park creator: Hee-Jin Noh creator: Sang Hee Hong creator: Daesik Park uri: https://doi.org/10.7717/peerj.17560 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Park et al. title: VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19 link: https://peerj.com/articles/17504 last-modified: 2024-06-19 description: BackgroundThe development of serodiagnostic tests and vaccines for COVID-19 depends on the identification of epitopes from the SARS-CoV-2 genome. An epitope is the specific part of an antigen that is recognized by the immune system and can elicit an immune response. However, when the genetic variants contained in epitopes are used to develop rapid antigen tests (Ag-RDTs) and DNA or RNA vaccines, test sensitivity and vaccine efficacy can be low.MethodsHere, we developed a “variant on epitope (VOE)” software, a new Python script for identifying variants located on an epitope. Variant analysis and sensitivity calculation for seven recommended epitopes were processed by VOE. Variants in 1,011 Omicron SRA reads from two variant databases (BCFtools and SARS-CoV-2-Freebayes) were processed by VOE.ResultsA variant with HIGH or MODERATE impact was found on all epitopes from both variant databases except the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK on the S gene and ORF7a gene. All epitope variants from the BCFtools and SARS-CoV-2 Freebayes variant databases showed about 100% sensitivity except epitopes APGQTGK and DSKVGGNYN on the S gene, which showed respective sensitivities of 28.4866% and 6.8249%, and 87.7349% and 71.1177%.ConclusionsTherefore, the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK may be useful for the development of an epitope-based peptide vaccine and GGDGKMKD on the N gene may be useful for the development of serodiagnostic tests. Moreover, VOE can also be used to analyze other epitopes, and a new variant database for VOE may be further established when a new variant of SARS-CoV-2 emerges. creator: Danusorn Lee creator: Unitsa Sangket uri: https://doi.org/10.7717/peerj.17504 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lee and Sangket title: A quantitative test of the “Ecomorphotype Hypothesis” for fossil true seals (Family Phocidae) link: https://peerj.com/articles/17592 last-modified: 2024-06-19 description: The fossil record of true seals (Family Phocidae) is mostly made up of isolated bones, some of which are type specimens. Previous studies have sought to increase referral of non-overlapping and unrelated fossils to these taxa using the ‘Ecomorphotype Hypothesis’, which stipulates that certain differences in morphology between taxa represent adaptations to differing ecology. On this basis, bulk fossil material could be lumped to a specific ecomorphotype, and then referred to species in that ecomorphotype, even if they are different bones. This qualitative and subjective method has been used often to expand the taxonomy of fossil phocids, but has never been quantitatively tested. We test the proposed ecomorphotypes using morphometric analysis of fossil and extant northern true seal limb bones, specifically principal components analysis and discriminant function analysis. A large amount of morphological overlap between ecomorphotypes, and poor discrimination between them, suggests that the ‘Ecomorphotype Hypothesis’ is not a valid approach. Further, the analysis failed to assign fossils to ecomorphotypes designated in previous studies, with some fossils from the same taxa being designated as different ecomorphotypes. The failure of this approach suggests that all fossils referred using this method should be considered to have unknown taxonomic status. In light of this, and previous findings that phocid limb bones have limited utility as type specimens, we revise the status of named fossil phocid species. We conclude that the majority of named fossil phocid taxa should be considered nomina dubia. creator: James Patrick Rule creator: Gustavo Burin creator: Travis Park uri: https://doi.org/10.7717/peerj.17592 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rule et al.