title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=44 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Predictive performance of clinical scores and survival outcomes in critically ill patients with sepsis: a prospective longitudinal study at a tertiary medical centre in Ethiopia link: https://peerj.com/articles/20109 last-modified: 2025-10-02 description: BackgroundClinical scores such as quick sequential organ failure assessment (qSOFA), early warning score (EWS), and universal vital assessment (UVA) are commonly used as screening and prognostic tools in sepsis. However, consistent findings across different regions and hospital settings remain limited. This study aims to evaluate the performance of these clinical scores and identify predictors of survival in septic adults admitted to the ICU.MethodsA prospective longitudinal study was conducted from October 10, 2023, to October 9, 2024, involving adults admitted to the intensive care unit (ICU). Clinical scores were calculated on the first, third, and fifth days of admission. Their performance in detecting sepsis, identifying culture-positive cases, and predicting mortality was assessed using receiver operating characteristic (ROC) curves. Kaplan–Meier survival analysis was used to estimate survival probabilities, and a Cox proportional hazards model was applied to identify predictors of survival in sepsis patients.ResultsOf the ICU-admitted patients, 148 (51.9%) were septic, and 54 (36.5%) of them died in the ICU. The modified early warning score (MEWS) showed good performance in identifying sepsis (area under the curve (AUC) = 0.67; 95% confidence interval (CI) [0.61–0.73]) and culture-positive cases (AUC = 0.65; 95% CI [0.50–0.80]) on the day of admission. MEWS also performed better in predicting mortality on day five (AUC = 0.75; 95% CI [0.57–0.93]). Patients with sepsis had significantly lower survival probabilities than those without sepsis (log-rank test, p < 0.001). Each additional point in the Glasgow Coma Scale (GCS) score reduced the hazard of death by 10% (HR = 0.90; 95% CI [0.84–0.97]; p = 0.005).ConclusionThe MEWS score outperformed other clinical scores in identifying sepsis, detecting culture-positive cases, and predicting mortality. Sepsis was associated with higher mortality, which decreased with increasing GCS scores. MEWS may support early identification of sepsis and mortality risk, and its use could help improve ICU survival through timely intervention. creator: Girum Tesfaye Kiya creator: Zeleke Mekonnen creator: Elsah Tegene Asefa creator: Edosa Kejela creator: Edosa Tadasa creator: Esayas Kebede Gudina creator: Tilahun Yemane creator: Gemeda Abebe uri: https://doi.org/10.7717/peerj.20109 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kiya et al. title: Barriers to cervical cancer prevention and triage strategies: a study of knowledge, attitudes, and p16/Ki-67 dual-staining utility among high-risk women in Tuoli and Fuyun counties, Xinjiang link: https://peerj.com/articles/20100 last-modified: 2025-10-02 description: ObjectiveTo investigate cervical cancer screening knowledge, attitudes, and practices among high-risk women in remote western China, and to identify socioeconomic and systemic barriers influencing screening participation. Additionally, to evaluate the comparative effectiveness of p16 staining versus p16/Ki-67 dual-staining immunocytochemistry in triaging women with cytological abnormalities or HPV-positive results, aiming to reduce unnecessary colposcopy referrals in resource-limited settings.MethodsThis cross-sectional study enrolled 260 women (aged 20–65 years) with cytological abnormalities or HPV-positive results from two remote counties in Xinjiang Province (January–December 2023). Participants completed structured questionnaires assessing cervical cancer knowledge, screening attitudes, and healthcare access. Cervical specimens collected via liquid-based cytology underwent parallel testing: conventional cytology, p16 staining, and p16/Ki-67 dual-staining, with all analyses performed by blinded pathologists.ResultsAmong 260 high-risk women in Xinjiang, cervical cancer awareness (67.31%, 95% CI [61.50–72.90]) and screening rates (56.15%, 95% CI [50.23–62.17]) remained suboptimal. Multivariable analyses revealed significant disparities: college-educated women had 7.58-fold higher odds of awareness (95% CI [2.32–24.75]) compared to those with primary education, while public servants showed the strongest employment-based association (aOR = 11.23, 95% CI [2.64–47.83]). Mediation analysis demonstrated that health awareness fully mediated the effect of education (128.8% mediation) and nearly fully mediated the effect of employment (93.8%). Notably, 93.98% (95% CI [90.85–96.27]) expressed willingness to rescreen, and 82.95% (95% CI [78.33–86.84]) supported HPV vaccination. Biomarker analysis showed that p16/Ki-67 dual-staining positivity increased progressively with lesion severity (P < 0.001).ConclusionThis study reveals suboptimal cervical cancer knowledge and screening rates among women in Xinjiang, with socioeconomic disparities—particularly in education and employment—primarily mediated through health awareness. The findings support integrated interventions, including physician-led education, digital health communication for media-dependent populations, simplified visual materials for less-educated women, and active linkage to national screening programs for unemployed populations. High rescreening willingness and parental acceptance of HPV vaccination indicate strong potential for intervention. p16 staining and p16/Ki-67 dual-staining show promise for triage in resource-limited settings. These findings highlight the need for tailored strategies to enhance cervical cancer prevention in western China, with further research needed to address current limitations. creator: Hayuehashi Tali creator: Kunayimu Yeerjiang creator: Bei bei Zeng creator: Tang Rui creator: Buajier Musha creator: Yan Wang uri: https://doi.org/10.7717/peerj.20100 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tali et al. title: Two new free-living marine species of Desmodorella (Nematoda: Desmodoridae) from the continental shelf of northeastern Brazil, with an emended generic diagnosis and a dichotomous key to the species link: https://peerj.com/articles/20094 last-modified: 2025-10-02 description: Two new species of Desmodorella are described from sediment samples collected on the continental shelf of northeastern Brazil. Although the occurrence of the genus has been previously reported in this region, the present study provides the first formal descriptions of Desmodorella species based on material collected from the Brazilian coast. Desmodorella cornuta sp. nov. is characterized by a protuberant horn-shaped cuticular projection positioned dorsally in the pharyngeal region, a unique characteristic among species of the genus. Desmodorella parabalteata sp. nov. is distinguished from other species by the presence of a cephalic capsule and cuticle ornamented with vacuoles, multispiral amphidial fovea, longitudinal rows of ridges that are often indistinct under light microscopy, two pairs of lateral rows of spines that are more prominent than the remaining rows, and thin, nearly straight spicules with a slightly swollen proximal end and lacking a capitulum. An emended diagnosis of the genus and a dichotomous key to species are provided. creator: Alex Manoel creator: Patricia F. Neres creator: André M. Esteves uri: https://doi.org/10.7717/peerj.20094 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Manoel et al. title: Novel monoclonal antibodies for immunodetection of AmpC β-lactamases link: https://peerj.com/articles/20036 last-modified: 2025-10-02 description: BackgroundAccurate and easy-to-perform assays for the detection of antibiotic-resistant bacterial isolates producing AmpC β-lactamases are epidemiologically relevant, leading to more effective use of antibiotics and a comprehensive understanding of β-lactamase prevalence. We describe novel monoclonal antibodies (MAbs) against CMY β-lactamases and their application in immunoassays for the detection of CMY-producing bacterial isolates.MethodsRecombinant CMY-34 was expressed in Escherichia coli and used as an immunogen for MAb generation by hybridoma technology. Selected CMY-34-specific MAbs were comprehensively characterized by various immunoassays, computational analysis, and sequencing of their variable domains. To prove MAb reactivity with CMY β-lactamases, the antibodies were tested with CMY-producing bacterial isolates. For this purpose, the MAbs were applied in sandwich-type assays, such as sandwich enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), and two-photon excitation (TPX) assay for immunodetection of CMY enzymes.ResultsTwo high-affinity MAbs raised against recombinant CMY-34 were characterized in detail. Both MAbs recognized CMY-34 β-lactamase in the Citrobacter portucalensis isolate. The analysis of MAb epitopes revealed their sequence homology among the members of the CMY family, suggesting their potential broad reactivity. Comprehensively characterized MAbs were successfully applied in sandwich ELISA and two rapid immunoassay formats that were tested with CMY-positive bacterial isolates. MAb-based immunoassays detected all analyzed CMY-positive isolates producing CMY-2, CMY-4, CMY-6, CMY-16, and CMY-34 β-lactamases.ConclusionNovel MAbs raised against CMY-34 recognize common epitopes of CMY β-lactamases and can be applied for immunodetection of CMY β-lactamases in bacterial isolates. creator: Karolina Bielskė creator: Martynas Simanavičius creator: Julie Nuttens creator: Julija Armalytė creator: Justas Dapkūnas creator: Lukas Valančauskas creator: Aurelija Žvirblienė uri: https://doi.org/10.7717/peerj.20036 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bielskė et al. title: Aquatic sloths (Thalassocnus) from the Miocene of Chile and the evolution of marine mammal herbivory in the Pacific Ocean link: https://peerj.com/articles/19897 last-modified: 2025-10-02 description: The evolution of marine mammals in South America includes unique and extinct lineages found nowhere else in the world, such as the walrus-convergent whale Odobenocetops and multiple aquatic sloth species belonging to the genus Thalassocnus. Aquatic sloths have been collected from Mio-Pliocene marine deposits in Peru and Chile, and terrestrial deposits in Argentina. In Chile, these occurrences range over 800 km across several basins from the Bahía Inglesa, Coquimbo, and Horcón formations. Here we report aquatic sloth material belonging to the species Thalassocnus natans from a new locality, Norte Bahía Caldera from the Bahía Inglesa Formation in the Atacama Region. We find multiple lines of evidence to support a late Miocene age for this material, which consists of a nearly complete skeleton, including cranial and postcranial remains and associated mandible and postcranial elements that represent the most complete Thalassocnus specimens reported yet from Chile. Based on this finding, we review the stratigraphic origin and geologic age of Thalassocnus species from the western coast of South America and determine that remains from the Upper Pliocene of central Chile represent the youngest known record of this genus to date. Our review also suggests that overlapping stratigraphic ranges for type material of T. antiquus with both T. natans and T. littoralis weakens the proposed argument for Thalassocnus evolution through anagenesis succession. Finally, in the context of Thalassocnus material from Chile and Peru, including other marine mammal herbivores (e.g., sirenians), we demonstrate that one of the most unusual features of this guild is that South American marine mammal herbivores did not reach the body sizes of their analogous counterparts (i.e., desmostylians and sirenians) in the North Pacific. This observation builds on other paleontological evidence about the unusual features of the Peruvian biotic province during the Neogene. creator: Ana M. Valenzuela-Toro creator: Nicholas D. Pyenson creator: Jorge Velez-Juarbe creator: Mario E. Suárez uri: https://doi.org/10.7717/peerj.19897 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Valenzuela-Toro et al. title: Effects of shading stress on endogenous hormone levels in Eleutherococcus giraldii: hormonal dynamics and growth strategy analysis link: https://peerj.com/articles/20135 last-modified: 2025-10-01 description: BackgroundEleutherococcus giraldii (E. giraldii) is a quintessential traditional Chinese medicinal plant with significant developmental potential. Its growth and development are highly responsive to environmental factors, particularly light conditions. However, the endogenous hormonal changes in E. giraldii under shading stress remain unclear, and its adaptive growth strategies require further investigation.MethodsExperimental groups with varying light transmittance (29.12%, 39.68%, and 100%) were established using shade nets, comprising moderate shading, light shading, and control groups. The endogenous hormone contents in apical and lateral leaves of E. giraldii were quantified using the enzyme-linked immunosorbent assay (ELISA). Statistical analysis and graphical presentations were performed using IBM SPSS Statistics 27 and Origin 2022 software.ResultsShading treatment consistently promoted the accumulation of isopentenyl adenine nucleoside (iPA), zeatin riboside (ZR), gibberellic acid 3 (GA3), and abscisic acid (ABA) in both apical and lateral leaves of E. giraldii, while exhibiting differential effects on indoleacetic acid (IAA)-enhancing its content in lateral leaves but reducing it in apical leaves. Quantitative analysis revealed that moderate shading induced: (1) maximal increases in iPA, ZR, and GA3 levels in apical leaves (P < 0.05); (2) maximal increases in ABA, iPA, ZR, and GA3 concentrations as well as the ABA/ZR ratio in lateral leaves; (3) maximal reductions in the ABA/iPA and ABA/GA3 ratios in apical leaves along with the ABA/GA3 ratio in lateral leaves; (4) decreased ABA/IAA and ABA/ZR in apical leaves coupled with increased ABA/iPA in lateral leaves. Under light shading conditions, the most substantial changes included: (1) greatest ABA enhancement in apical leaves and IAA accumulation in lateral leaves; (2) most pronounced declines in IAA content (apical leaves) and ABA/IAA ratio (lateral leaves); (3) elevated ABA/IAA and ABA/ZR ratios in apical leaves with concurrent reduction of ABA/iPA in lateral leaves. Importantly, comprehensive correlation analysis demonstrated positive correlations among all examined hormones (ABA, IAA, iPA, ZR, and GA3) in both leaf types, indicating systemic hormonal coordination during shade adaptation.ConclusionShading stress significantly restructured endogenous hormone profiles and their homeostasis in E. giraldii. Under moderate shading conditions, E. giraldii likely adopted a conservative strategy characterized by “apical leaf growth promotion coupled with lateral leaf growth restriction”, whereas mild shading induced an expansive strategy featuring “apical leaf growth inhibition coordinated with moderate lateral leaf expansion”. These findings provide a theoretical foundation for optimizing cultivation protocols and offer new insights into phytohormonal dynamics in shrubs under light limitation. creator: Xu Feng Huang creator: Rui Gu creator: Guo Peng Chen creator: Rong Ding uri: https://doi.org/10.7717/peerj.20135 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Huang et al. title: Electroantennogram and Olfactory behavioral responses of Trabala vishnou gigantina (Lepidoptera: Lasiocampidae) to herbivore induced Hippophae rhamnoides leaf volatiles link: https://peerj.com/articles/20124 last-modified: 2025-10-01 description: The moth Trabala vishnou gigantina Yang, 1978 (Lepidoptera: Lasiocampidae), a leaf-eating pest, had a severe outbreak in the sea buckthorn, Hippophae rhamnoides L. (Elaeagnaceae) plantation in North China. This study aims to investigate the influence of volatiles emitted by T. vishnou gigantina-infested H. rhamnoides on the behavioral responses of T. vishnou gigantina, laying a basis for the development of plant-based elicitors. The chemical basis of herbivore insect host dynamics between these species were investigated, providing information for herbivore insect control methods. After identifying the compounds produced by the differences between healthy and infested plants, six critical volatile compounds were identified to explore their attractions to T. vishnou gigantina imagoes by using electroantennogram (EAG) and olfactory behavioral response experiments. The results showed that the EAG responses of T. vishnou gigantina imagoes did not only vary in these six different herbivore-infested volatiles, but also between different concentrations of the same volatile. The EAG responses to the herbivore-infested volatiles peaked at a stimulus concentration of 100 µg/µL, with Hexyl 2-methyl butyrate having the highest EAG response. The test results of olfactory behavioral responses had significant differences in the olfactory behavioral responses of female and male imagoes to the six herbivore-infested volatiles. Hexyl 2-methyl butyrate had the strongest attraction to female and male imagoes, followed by 2-ethylhexanol and longifolene. 2-ethylhexanol had a significant attraction to female imagoes, while there was no significant attraction to males. creator: Yonghua Liu creator: Kexu An creator: Shuo Tang creator: Jiangshuai Feng creator: Xiongfei Yan uri: https://doi.org/10.7717/peerj.20124 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Establishment and evaluation of a circAdpgk-0001 knockdown method using CRISPR–Cas13d RNA-targeting technology link: https://peerj.com/articles/20123 last-modified: 2025-10-01 description: BackgroundThe small interfering RNA (siRNA) method has been used to knock down circular RNAs (circRNAs). However, issues such as low efficiency and off-target effects have become increasingly recognized. Recent studies have demonstrated that CRISPR-Cas13 can specifically target and cleave RNA. In this study, we established a CRISPR-Cas13d-based RNA-targeting method to specifically knock down circRNAs, such as circAdpgk-0001, and compared its performance with the siRNA method.MethodsFour clustered regularly interspaced short palindromic repeats (CRISPR) RNAs (crRNAs) of different nucleotide lengths spanning the back-splicing junction (BSJ) of circAdpgk-0001 were designed. A CRISPR-RfxCas13d plasmid capable of specifically cleaving circAdpgk-0001 was constructed and transfected into the JS-1 cell line. Knockdown efficiency was assessed using quantitative real-time PCR (qRT-PCR) and compared with that of the siRNA method. The expression of activation-related factors alpha-smooth muscle actin (α-SMA) and collagen I in JS-1 cells was further evaluated using qRT-PCR and Western blot.ResultsCRISPR-Cas13d with a 24-nucleotide crRNA showed the highest knockdown efficiency (∼50%). After further optimization, the knockdown efficiency of CRISPR-Cas13d reached 70%, significantly higher than that of the siRNA method (40%). Knockdown of circAdpgk-0001 using Cas13d reduced the expression of collagen I and α-SMA by approximately 40%, which was greater than the reduction achieved by siRNA-mediated knockdown.ConclusionCRISPR-Cas13d demonstrated higher efficiency than the siRNA method in knocking down circRNAs, providing a promising tool for investigating circRNA functions. creator: Sijia Huang creator: Hailan Qin creator: Bingxin Dai creator: Miao Liu creator: Jijia Shen uri: https://doi.org/10.7717/peerj.20123 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Licinophilus depressus n. gen., sp. n. (Eugregarinida: Stenophoridae) from Licinus depressus (Coleoptera: Carabidae) link: https://peerj.com/articles/20099 last-modified: 2025-10-01 description: The paper focuses on a new species of gregarines—Licinophilus depressus n. gen. sp. n., which was found in Licinus depressus (Paykull, 1790) (Coleoptera, Carabidae). The individuals of L. depressus ground beetle were collected on the bank of the Dnipro River, Ukraine and examined for the presence of gregarines in the guts. In the parasites discovered in the midguts, we measured the morphological parameters and their ratios, analyzing how they change in relation to the age of the specimens. According to our measurements, the species turned out to be incomparable to any of the ones described in the scientific literature. Because the gregarine specimens formed syzygies at late stages, were observed to have monogenous life cycle and a septum between the protomerite and deutomerite at all stages of development, and also rudimentary epimerite, they were classified to the Septatorina suborder, Stenophoricae superfamily, Stenophoridae family, and distinguished into a new genus due to the fluctuating septum between the protomerite and deutomerite.With age, the width of the segments does not change, while the gregarine increases in size due to significant elongation of the deutomerite. The most varying parameters of this species of gregarines were the deutomerite length (DL), the deutomerite length axis (DLA), and the total length of gregarine (TL) for which the coefficient of variation exceeded 30%. All the studied morphometric indices, except for the ratio of the deutomerite length to the deutomerite width (DL/DW), exhibited weak association with the age and sizes of gregarines. The indices such as the ratios of the epimerite length to the length of the protomerite-epimerite complex (EL/PECL), the protomerite length to the protomerite-epimerite complex (PL/PECL), the epimerite length to the epimerite width (EL/EW), the protomerite length to the protomerite width (PL/PW), the protomerite width to the septum width (PW/SW), the deutomerite width to the protomerite width (DW/PW), the nucleus length to nucleus width (NL/NW), and also DLA remained constant in this gregarine during growth, and therefore they can be used as constant diagnostic features. creator: Viktoriia Lazurska creator: Viktor V. Brygadyrenko uri: https://doi.org/10.7717/peerj.20099 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lazurska and Brygadyrenko title: Response of soil nematode community structure, diversity, and ecological network to elevation gradients in wild fruit forest of Tianshan Mountain, China link: https://peerj.com/articles/20090 last-modified: 2025-10-01 description: BackgroundThe Tianshan wild fruit forest is a special deciduous broad-leaved forest located in the mountains of central Asia.MethodsTo reveal how the Tianshan wild fruit forest ecosystem responds to environmental changes along an elevation gradient, we used the soil nematode index, which is widely recognized as a key indicator of soil health. This study focused on the nematode communities beneath Juglans cathayensis and Malus sieversii, two typical constructive species in the Tianshan wild fruit forest. Six elevation levels (1,480, 1,401, 1,351, 1,305, 1,252, and 1,207 m) were selected, and a nematode co-occurrence network was constructed for each elevation. We analyzed the abundance, diversity, ecological indices, and network complexity of soil nematode communities across different elevation gradients. In addition, we explored the relationships among environmental factors, soil multifunctionality, and nematode community characteristics.ResultsOur results showed that: (1) a total of 60,795 nematodes, representing 80 genera were collected. Total abundance, trophic group abundance, and diversity of nematodes peaked at middle elevations. However, in M. sieversii, nematode diversity increased with elevation. (2) The soil food web in the wild fruit forest exhibited a relatively high metabolic rate (nematode channel ratio > 0.5). (3) In J. cathayensis, the nematode ecological network was more complex and tightly interconnected at low elevations. whereas in M. sieversii, greater network complexity was observed at high elevations. (4) Environmental factors (organic matter, pH, total phosphorus, available potassium, total potassium) significantly affected the composition of nematode trophic groups (p < 0.05). Moreover, network complexity was a key factor influencing soil multifunctionality. This study provides a theoretical foundation for long-term monitoring of soil health in Tianshan wild fruit forest. creator: Yulu Zhang creator: Mengyu Yang creator: Wenxin Liu creator: Zhicheng Jiang creator: Yang Zhao creator: Gaofeng Li creator: Jing Cao creator: Minru Zhang creator: Haijun Yang creator: Dong Cui uri: https://doi.org/10.7717/peerj.20090 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al.