title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=122 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Development of LAMP assay for early detection of Yersinia ruckeri in aquaculture link: https://peerj.com/articles/19015 last-modified: 2025-02-25 description: Yersinia ruckeri is the causative agent of yersiniosis or enteric red mouth disease (ERM) that causes significant economic losses in the salmonid aquaculture industry. Due to an increasing number of outbreaks, lack of effective vaccines and the bacteria’s ability to survive in the environment for long periods, there is a necessity for novel measures to control ERM. New techniques capable of rapidly detecting Y. ruckeri are critical to aid effective control programs. Molecular methods, like real-time polymerase chain reaction, can detect Y. ruckeri; however, that methodology is not field-deployable and cannot support local decision-making during an outbreak. We present a field-deployable molecular assay using loop mediated isothermal amplification (LAMP) and water filtering method for the detection of Y. ruckeri eDNA from water samples to improve current surveillance methods. The assay was optimised to amplify the glutamine synthetase gene (glnA) of Y. ruckeri in under 20 min. The assay demonstrated high specificity and sensitivity, as it did not amplify any non-target bacteria typically present in water sources. It achieved a limit of detection (LOD) of 0.5 × 10−7 ng/µl, significantly surpassing the LOD of 0.5 × 10−4 ng/µl obtained through conventional polymerase chain reaction (cPCR). When applied to environmental water samples spiked with transformed Escherichia coli containing the G-block of the Yersinia ruckeri (glnA) target gene, the Yr-LAMP method exhibited an analytical sensitivity of 0.08 cells/µl from the initial filtered water sample. Notably, the cumulative time for sample preparation and amplification was under 1 h. The simplicity of the developed field-deployable Yr-LAMP assay makes it suitable as a routine procedure to monitor fish for ERM infection. This will enable informed decision-making on mitigating pathogen prevalence in aquaculture farms. creator: Hoda Abbas creator: Nickala Best creator: Gemma Zerna creator: Travis Beddoe uri: https://doi.org/10.7717/peerj.19015 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Abbas et al. title: Role of contrast-enhanced ultrasound with time-intensity curve analysis about thyroid nodule and parenchyma for differentiating BRAF V600E mutation status link: https://peerj.com/articles/19006 last-modified: 2025-02-25 description: BackgroundThe BRAF V600E mutation was proven associated with papillary thyroid cancer (PTC) which has more aggressive behavior and could affect the outcome of PTC. The objective of this study was to observe more contrast-enhanced ultrasound (CEUS) time-intensity curve (TIC)—based quantitative parameters in nodules and surrounding parenchyma and analyze the association between the TIC-based quantitative parameters and BRAF V600E mutation status in patients with PTC.MethodsA retrospective analysis of 447 PTC patients was conducted. Prior to thyroidectomy or fine needle aspiration (FNA), all patients had CEUS and had their BRAF V600E mutations examined. Based on their mutation status, the patients were split into two groups. The two groups were compared in terms of sex, age, quantitative CEUS characteristics, pathological findings, vascular invasion, capsular invasion, and cervical lymph node metastases.ResultsA total of 240 patients were in the mutation negative group and 207 patients were in the BRAF mutation positive group. The BRAF-positive group exhibited significantly higher arrival time (AT) and time to peak enhancement (TTP) of the nodules, among other direct quantitative characteristics. The BRAF-positive mutant nodules showed significantly higher arrival time change and time to peak change compared to the surrounding parenchyma for indirect quantitative metrics.ConclusionThe time-dependent quantitative parameters of CEUS time intensity curve in nodules and surrounding parenchyma have clinical value in distinguishing BRAF V600E mutation positive nodules from gene mutation negative nodules. Quantitative CEUS characteristics may be beneficial in detecting the BRAF V600E mutation status and informing the subsequent clinical choice. creator: Zhipeng Hu creator: Rong Xue creator: Zhixi Liu creator: Liang Liu creator: Zheli Gong uri: https://doi.org/10.7717/peerj.19006 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hu et al. title: When safety becomes the priority: defensive nursing practice and its associated factors among nurses in Egypt: a cross-sectional study link: https://peerj.com/articles/19005 last-modified: 2025-02-25 description: BackgroundDefensive nursing practices, which prioritize legal protection over patient care, are becoming increasingly common. This study aims to explore the prevalence and factors associated with defensive nursing practices among nurses in Egypt, considering the impact of workplace violence and legal threats.MethodsA descriptive cross-sectional study was conducted from February to April 2024 using a self-report online questionnaire. The target population included clinical nurses working in various hospitals in Egypt. A sample size of 1,267 nurses was achieved through convenience sampling. The questionnaire assessed demographic data, experiences of workplace violence, legal consequences, and defensive nursing practices, categorized into positive and negative behaviors.ResultsThe sample consisted of 1,267 nurses, predominantly female (75.9%), with a mean age of 28.57 years. Positive defensive practices, such as detailed documentation (79%) and thorough explanation of procedures (58.5%), were highly prevalent. Negative practices included avoiding high-risk procedures (15.9%) and patients more likely to file lawsuits (13.6%). Older nurses and those with higher educational qualifications were more likely to engage in positive defensive practices. Nurses who experienced workplace violence or legal threats were significantly more likely to avoid high-complication procedures.ConclusionThe study identified a high engagement in both positive and negative defensive practices among nurses in Egypt. These practices are influenced by factors such as age, education level, and experiences of workplace violence and legal threats. The findings underscore the need for strategies to support nurses, reduce reliance on defensive practices, and ensure better patient outcomes. creator: Ahmed Zaher creator: Yasmine M. Osman creator: Salwa Sayed creator: Sally Mohammed Farghaly Abdelaliem creator: Amany Anwar Saeed Alabdullah creator: Ahmed Hendy creator: Zainab Attia Abdallah creator: Mohammed Musaed Ahmed Al-Jabri creator: Abdelaziz Hendy uri: https://doi.org/10.7717/peerj.19005 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zaher et al. title: Redescription of Aspidosiphon (Paraspidosiphon) steenstrupii Diesing, 1859 (Sipuncula: Aspidosiphonidae) and the reinstatement of three species link: https://peerj.com/articles/19003 last-modified: 2025-02-25 description: Sipuncula, specifically the family Aspidosiphonidae, faces taxonomic challenges due to brief original descriptions and the poor condition or loss of the type material. Detailed standardized redescriptions are essential to understanding the diversification in this group. Herein, a comprehensive redescription of Aspidosiphon (Paraspidosiphon) steenstrupii based on an extensive material collection from the tropical Western Atlantic is provided. Based on morphological data and the analysis of COI sequences, we delimited A. (P.) steenstrupii morphologically, restricting its distribution to the tropical Western Atlantic. Also, the redescriptions and proposals for reinstatement of A. (P.) exostomum, A. (P.) ochrus, and A. (P.) speculator, previously considered junior synonyms of A. (P.) steenstrupii, are included. Furthermore, a comprehensive discussion on diagnostic morphological features to recognize aspidosiphonid species and a detailed revision of synonyms of A. (P.) steenstrupii are included. Notable differences in morphology and genetic data suggest the need for revising the taxonomic status of several synonyms within the family, highlighting underestimated diversity in sipunculans. creator: Itzahi Silva-Morales creator: Luis F. Carrera-Parra uri: https://doi.org/10.7717/peerj.19003 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Silva-Morales and Carrera-Parra title: Prediction of clinical deterioration within one year in chronic obstructive pulmonary disease using the systemic coagulation-inflammation index: a retrospective study employing multiple machine learning method link: https://peerj.com/articles/18989 last-modified: 2025-02-25 description: BackgroundInflammatory response and the coagulation system are pivotal in the pathogenesis of clinical deterioration in chronic obstructive pulmonary disease (COPD), prompting us to hypothesize that the systemic coagulation-inflammation (SCI) index is associated with clinical deterioration in COPD.MethodsA cohort of 957 COPD patients (mean age: 68.4 ± 7.8 years; 74.4% male) from January 2018 to December 2021 was analyzed. Six machine learning models (XGBoost, logistic regression, Random Forest, elastic net (ENT), support vector machine (SVM), and K-nearest neighbors (KNN)) were evaluated using accuracy, precision, recall, F1-score, and the area under the receiver operating characteristic curve (AUC-ROC).ResultsOur study encompassed 957 patients, out of which 171 were classified in the clinical deterioration of COPD (cd-COPD) cohort. Significant disparities in age, comorbidities like respiratory failure, C-reactive protein, lymphocyte count, red blood cell distribution width (RDW), SCI, procalcitonin (PCT), and D-dimer were depicted between the cd-COPD and non-cd-COPD groups. Concerning machine learning and model comparison, the SVM model showcased consistent performance and strong generalization capabilities on both the training and testing sets compared to the other five machine learning (ML) models. The SCI index, as the most influential predictor, demonstrated a median of 93.08 in cd-COPD compared to 81.67 in non-cd-COPD patients.ConclusionThe SCI is markedly elevated in cd-COPD patients compared to COPD patients, and SVM demonstrates reliable performance in cd-COPD prediction. creator: Ling Hou creator: Ming Min creator: Rui Hou creator: Wei Tan creator: Minghua Zhang creator: Qianfei Liu uri: https://doi.org/10.7717/peerj.18989 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hou et al. title: Effects of sex and season (breeding and non-breeding) on microhabitat selection in Stejneger’s bamboo pitviper (Viridovipera stejnegeri) link: https://peerj.com/articles/18970 last-modified: 2025-02-25 description: Habitat quality and availability are crucial for the survival and reproduction of animal species. Intraspecific and seasonal differences in habitat selection reflect adaptations to changing biological requirements and environmental factors. To investigate the effects of season (breeding and non-breeding) and sex on microhabitat selection in snakes, here we employed field surveys to analyze microhabitat selection data for Stejneger’s bamboo pitviper (Viridovipera stejnegeri) across different sexes and seasons. Results indicated that although no significant difference was observed between groups, marked differences in certain microhabitat factors were noted. Specifically: (1) Non-breeding season females (NBF) displayed distinct differences in altitude, slope position, distance from roads compared to other groups. (2) Temperature exerted a lesser effect on non-breeding season individuals compared to breeding season individuals. Additionally, distance from roads only significantly impacted breeding season males, not females. (3) Regarding sexual differences, males and females differed in slope position and distance from residential sites, reflecting their distinct ecological requirements. Regarding seasons, differences in habitat selection between breeding and non-breeding seasons were primarily related to temperature, indicating behavioral changes linked to seasons. (4) Non-breeding season females exhibited the narrowest microhabitat niche width and the least microhabitat niche overlap with other groups, potentially due to their pronounced foraging requirements, which compel them to explore limited habitats with higher human disturbance but richer food sources. This study contributes novel insights into the habitat selection behaviors of snakes. creator: Songwen Tan creator: Yayong Wu creator: Jiajun Wang creator: Bing Lyu creator: Min Yu creator: He Zhang creator: Peng Guo creator: Lei Shi uri: https://doi.org/10.7717/peerj.18970 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tan et al. title: Computational modelling reveals the influence of object similarity and proximity on visually guided movements link: https://peerj.com/articles/18953 last-modified: 2025-02-25 description: The paper aims to understand how humans reach for a single target object in multi-object scenes. In a previous empirical study, human subjects were asked to execute reaches to a single target among non-targets (choice reaching task). In the current work, we re-analysed the human data and implemented a neurobiologically-plausible cognitive robotics model (choice reaching with a LEGO arm robot, CoRLEGO) that mimics human reaches in the choice reaching task. The results from the experiment confirmed the commonly made assumption that proximity and similarity between objects (also termed perceptual grouping) affect the quality of the reaches. However, what was novel here was that modelling the reaches also allowed to temporally separate these factors, as the start of the movement was affected by both factors while the reach trajectory was affected only by proximity between target and distractor objects indicating that human information processing of visual stimuli applies these factors in a serial fashion. In particular, our model architecture and the optimised parameter settings suggest that object proximity directly influences the movement onset. In addition, our computational model confirmed this interpretation but also revealed that the relationship between the two factors may be affected by how the participants balanced speed (starting time of the movement) and accuracy of reaching (straightness of reaches). Future research will need to test whether this plausible prediction is correct. creator: Mandar Manjunath Patil creator: Dietmar Heinke creator: Fan Zhang uri: https://doi.org/10.7717/peerj.18953 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Patil et al. title: Analysis of biopsies of gastric cancer, intestinal and diffuse, and non-atrophic gastritis: an overview of loss of heterozygosity in Mexican patients link: https://peerj.com/articles/18928 last-modified: 2025-02-25 description: This study analyzed the loss of heterozygosity (LOH) effect on gastric cancer (GC) tumor samples from 21 Mexican patients, including diffuse (DGC) and intestinal (IGC) subtypes, as well as non-atrophic gastritis (NAG, control). Whole-genome high-density arrays were performed, and LOH regions were identified among the tissue samples. The differences in affected chromosomes were established among groups, with chromosomes 6 and 8 primarily affected in DGC and chromosomes 3, 16, and 17 in IGC. Functional pathway analysis revealed involvement in cancer-associated processes, such as signal transduction, immune response, and cellular metabolism. Five LOH-genes (IRAK1, IKBKG, PAK3, TKTL1, PRPS1) shared between GC and NAG suggest an early role in carcinogenesis. Specific genes were highlighted for Hallmarks of Cancer NAG-related genes (PTPRJ and NDUFS) were linked to cell proliferation and growth; IGC genes (GNAI2, RHOA, MAPKAPK3, MST1R) to genomic instability, metastasis, and arrest of cell death; and DGC genes to energy metabolism and immune evasion. These findings emphasize the role of LOH in GC pathogenesis and underscore the need for further research to understand LOH-affected genes and their diagnostic or evolution potential in cancer management. Portions of this text were previously published as part of a preprint (https://www.medrxiv.org/content/10.1101/2024.07.29.24311063v1). creator: Violeta Larios-Serrato creator: Hilda A. Valdez-Salazar creator: Javier Torres creator: Margarita Camorlinga creator: Patricia Piña-Sánchez creator: Fernando Minauro creator: Martha-Eugenia Ruiz-Tachiquín uri: https://doi.org/10.7717/peerj.18928 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Larios-Serrato et al. title: Efficacy and safety of low-molecular-weight-heparin plus citrate in nephrotic syndrome during continuous kidney replacement therapy: retrospective study link: https://peerj.com/articles/18919 last-modified: 2025-02-25 description: BackgroundNephrotic syndrome (NS) is a condition often necessitating continuous kidney replacement therapy (CKRT) due to severe edema and other complications. Anticoagulation is critical in CKRT to prevent filter clotting, with regional citrate anticoagulation (RCA) being the first-line method. However, the hypercoagulable state of NS may require alternative strategies. Optimal anticoagulation therapy in NS patients undergoing CKRT is lacking.MethodsThis retrospective observational study included 251 CKRT sessions from 122 NS patients treated at Nanfang Hospital, Southern Medical University, from January 2019 to December 2022. Patients were divided into three groups based on anticoagulation method: Low-molecular-weight-heparin (LMWH) alone, RCA alone, and RCA plus LMWH. Filter lifespan, incidence of filter clotting, and adverse events were assessed to evaluate the efficacy and safety profiles of each anticoagulation methods.ResultsThe combination of RCA and LMWH demonstrated a significantly longer mean filter lifespan and lower incidence of filter clotting compared to LMWH or RCA alone. RCA plus LMWH also showed a lower incidence of overall adverse events, particularly thrombosis, without an increase in bleeding complications. Multivariate Cox analysis indicated that RCA plus LMWH was particularly effective in patients with normal kidney function.ConclusionsRCA combined with LMWH provides a superior anticoagulation strategy in NS patients undergoing CKRT, with enhanced filter lifespan and reduced clotting and thrombotic events without increasing bleeding risk. Further research is needed to optimize dosing and validate these results in broader populations. creator: Di Wang creator: Mengqin Yang creator: Siyuan Li creator: Can Tang creator: Jun Ai creator: Diankun Liu uri: https://doi.org/10.7717/peerj.18919 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: The avifauna of Ramanathapuram, Tamil Nadu along the Southeast coast of India: waterbird assessments and conservation implications across key sanctuaries and Ramsar sites link: https://peerj.com/articles/18899 last-modified: 2025-02-25 description: BackgroundWetlands, globally, face significant threats from human activities, and waterbirds, as key indicators of wetland health, are essential to maintaining ecological balance. Any long-term conservation measures should prioritize coordinated habitat preservation, wetland restoration, and sustainable management practices involving local communities. Monitoring and analyzing waterbird population trends are critical for understanding restoration, conservation, and management practices.MethodsThe present study was carried out in five bird sanctuaries Chitrangudi, Kanjirankulam (Ramsar sites), Therthangal, Sakkarakottai, and Mel-Kel Selvanoor of Tamil Nadu, Southeast coast of India, over one year (April 2022 to March 2023). Monthly surveys using direct and block methods, with additional fortnightly visits during the breeding season, were conducted from vantage points to record species diversity, nesting activity, and conservation threats. Assessments of the residential status, national status (SOIB), and Convention for Migratory species (CMS) status were done along with the alpha and beta biodiversity profiles, principal component analysis, Pearson correlation and other statistical methods performed to assess breeding waterbirds community structure. Threats to the breeding waterbirds were categorised into high, medium, and low impacts based on degree of severity and irreversibility.ResultsThe avifaunal checklist revealed a diversity of waterbird species utilizing the sanctuaries for breeding. Notable findings include two Near-Threatened species like, Asian Woolly-necked Stork Ciconia episcopus, and Spot-billed Pelican Pelecanus philippensis, where Asian Woolly-necked Stork recorded only in Therthangal Bird Sanctuary. Avifauna of each sanctuary with breeding waterbirds in parenthesis is as follows: Chitragundi 122 (13); Mel-Kel Selvanoor 117 (19); Therthangal 96 (23); Sakkarakottai 116 (17) and Kanjirankulam 123 (14). The breeding activity (incubation in nests) was from November to February except for Glossy Ibis and Oriental Darter whose breeding started in December; Spot-billed Duck and Knob-billed Duck breed only during January and February. Among the 131 species recorded from all the sanctuaries, 78% were resident birds; 27% were breeding waterbirds, and 21% were Winter visitors. The SOIB and CMS statuses underscore the necessity of implementing effective conservation measures to protect breeding habitats amid anthropogenic pressures. Water unavailability and nest tree unavailability in the sanctuaries are found to be the high degree threats to breeding waterbirds than others. This research provides critical baseline data for the forest department’s future wetland management plans. creator: Hameed Byju creator: Hegde Maitreyi creator: Raveendran Natarajan creator: Reshmi Vijayan creator: Balu Alagar Venmathi Maran uri: https://doi.org/10.7717/peerj.18899 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Byju et al.