Browse Articles

Nanopore sequencing reveals the genomic diversity of the variants of concern of SARS-CoV-2 during 2021 disease outbreak in Pakistan

Fibrosis-4 index as a predictor of all-cause and cardiovascular mortality in patients with chronic kidney disease

This study utilized data from the National Health and Nutrition Examination Survey (NHANES) 2005–2020 (n = 28,231, including 4,907 chronic kidney disease (CKD) patients) with weighted analyses and, through variance inflation factor (VIF) assessment to verify covariate selection, supported model validity, to demonstrate for the first time that the Fibrosis-4 (FIB4) index serves as an independent predictor of all-cause and cardiovascular disease (CVD)-related mortality in CKD patients. Weighted logistic regression confirmed FIB4 index as a significant independent predictor of CKD risk (fully adjusted odds ratios (OR) 1.85, 95% confidence interval (CI) 1.64–2.08), with strong dose-response gradient (Q4 OR 3.51–6.02). Multivariable Cox proportional hazards regression models revealed that each 1-unit increase in the FIB4 index was associated with a 34% elevated risk of all-cause mortality (hazard ratio (HR) = 1.34, 95%CI: 1.27–1.41, p < 0.001) and a 34% increased risk of CVD mortality (HR = 1.34, 95% CI: 1.24–1.44, p < 0.001). Restricted cubic spline (RCS) analysis identified nonlinear threshold effects at inflection points of 1.84 (all-cause mortality) and 1.74 (CVD mortality), with mortality risks escalating sharply beyond these thresholds (all-cause HR = 2.57; CVD HR = 2.85). Receiver operating characteristic (ROC) curve analysis demonstrated robust predictive performance (area under the curve (AUC): 0.799 for all-cause mortality; 0.801 for CVD mortality). Subgroup analyses highlighted heightened risks among non-Hispanic Black individuals, older adults, and those with low physical activity. Mediation analysis indicated that neutrophil-to-lymphocyte ratio (NLR) mediated 5.48% of the FIB4–all-cause mortality association and 5.83% of the CVD mortality association, though direct effects predominated (94.52% and 94.17%, respectively). These findings establish the FIB4 index as a practical, evidence-based tool for risk stratification in CKD patients, offering critical insights for personalized clinical management.

Critical velocity criterion of explosive charges initiated by fragment impact considering impact angle and charge radius

Detection of false position attacks in VANETs through bagging ensemble learning

Vehicular Ad-hoc Networks (VANETs) are critical to Intelligent Transportation Systems (ITS), enabling vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I) communication to improve road safety and traffic flow. However, VANETs face significant security threats, particularly position falsification attacks, where malicious nodes disseminate false Basic Safety Messages (BSMs). This study proposes an ensemble learning framework to detect such attacks, leveraging Decision Tree (CART), Random Forest, K-Nearest Neighbors (KNN), and Multilayer Perceptron (MLP) classifiers enhanced with bagging. Using the VeReMi dataset, our RSU-level detection system analyzes sequential BSMs to detect malicious behavior. Results demonstrate that KNN with bagging achieves perfect precision, recall, accuracy, and F1 score (100%) for Attack 1, while maintaining near-perfect performance for complex attacks like Attack 2 (99.87% accuracy) and Attack 16 (97.85% accuracy). Decision Tree with bagging also performs well for simpler attacks but experiences a slight decline for highly complex scenarios. Random Forest with bagging excels in simpler attacks but struggles with complex patterns. MLP with bagging shows strong results for simpler attacks but underperforms in complex scenarios. The proposed framework highlights the effectiveness of ensemble techniques, particularly KNN with bagging, in safeguarding VANET communication systems, offering a scalable, efficient, and robust solution for VANET security.

A non-canonical fungal peroxisome PTS-1 signal, SYM, and its evolutionary aspects

Abstract Proteins localized to peroxisomes, particularly those expressed under specific conditions or in low abundance, are often undetected by routine proteomics methods due to detection sensitivity limits. In silico identification and experimental validation of peroxisomal targeting signals (PTSs) offer a reliable alternative. We demonstrate that SYM, a non-canonical plant PTS-1 signal, functions similarly in Aspergillus nidulans, as GFP tagged with a SYM C-terminal tripeptide localizes to peroxisomes. One of two native A. nidulans proteins with C-terminal SYM tripeptide shows weak peroxisomal localization alongside cytoplasmic presence, indicating that only a subset of proteins with non-canonical signals access peroxisomes. In silico analysis of 1,010 fungal genomes identified diverse SYM-proteins with variable functions, suggesting that non-canonical PTS-1 signals may evolve spontaneously. Two-thirds of SYM-proteins are predicted to localize to specific intracellular compartments other than the peroxisome. We propose that despite their predicted localization, these proteins possessing SYM as a non-canonical peroxisomal signal might also have peroxisomal presence. Among SYM-proteins, pectinesterases, known plant pathogen virulence factors, were frequent. Notably, 25% of fungal pectinesterases harbor non-canonical PTS-1 signals, suggesting that partial peroxisomal localization of pectinesterases has evolved convergently. This suggests that partial peroxisomal localization may enhance protein functional flexibility, contributing to the organism’s adaptability.

Locality matters: Variation in the reproductive cycle and population structure of subtropical sea urchins

The life cycle of many Echinoidea species remains poorly understood despite research conducted in temperate and tropical-subtropical regions. Common species in the Central-Eastern Atlantic’s shallow waters include Paracentrotus lividus, Arbacia lixula, and Sphaerechinus granularis. Nevertheless, significant gaps in understanding their life cycles persist. This study discusses the reproductive cycles of three sea urchin species in rocky coastal ecosystems around Gran Canaria Island (Spain) (27º45´N, 15º45´W) from June 2020 to May 2021. Morphological measurements reveal that test length increases without a corresponding weight gain. The average size at first maturity (L50) was greater in females (A. lixula 46.26 mm; P. lividus 46.03 mm; S. granularis 49.67 mm SL) than in males (A. lixula 43.55 mm; P. lividus 42.82 mm; S. granularis 48.57 mm SL). The gonadosomatic index in females exceeded that of males. Histological analysis showed oocytes at various developmental stages, indicating asynchronous ovarian development with successive batch spawning seasons. Reproductive activity was generally observed during the warm season for all three species, likely coinciding with increased nutrient availability in Canarian waters. Notably, P. lividus was the only species to show two reproductive seasons annually in San Cristobal. DNA analysis confirmed species identification and provided new fragments of the COI gene, now available in GenBank for future population analysis. These findings represent the first reproductive data for these species in the North Atlantic region, offering valuable insights into their populations and establishing baseline information for managing sea urchin populations.

Effects of inpatient treatment of adolescents with anorexia nervosa are associated with body representation: a monocentric pilot study

Abstract This monocentric pilot study investigates the relationship between nutritional treatment and body representation distortion in adolescents with Anorexia Nervosa (AN) using the Rubber Hand Illusion (RHI) task. A total of 28 adolescents participated, including 14 patients with restrictive AN and 14 healthy controls. The RHI and Robot Hand Illusion (RoHI) tasks were conducted, with assessments taken at admission and discharge for the AN group. Sense of Ownership (SO) and Sense of Agency (SA) rated via 7-item Likert; proprioceptive drift was millimetre shift in perceived hand position after stimulation vs baseline under congruent (sync/in-phase) or incongruent (async/out-of-phase) feedback. Results showed that all groups exhibited higher SO scores in the synchronous condition compared to the asynchronous condition in the RHI task. In the RoHI task, AN patients at admission displayed significantly higher SA scores in the in-phase than in the out-of-phase condition. Notably, SO scores in the RHI task at discharge were positively correlated with weight recovery one month post-discharge (ρ = 0.59). These findings suggest that inpatient treatment influences body representation in adolescents with AN and that changes in body perception may serve as an indicator of treatment effectiveness.

Endovascular repair of type B acute aortic syndromes involving the left subclavian artery: A retrospective single-centre study

Background The mid-term outcomes of using the Castor single branched stent graft to treat patients with type B acute aortic syndromes (AASs) involving the left subclavian artery (LSA) were unclear. This study aims to evaluate the mid-term efficacy of the Castor single branched stent graft in the treatment of type B AASs involving the LSA. Methods The retrospective study enrolled patients with type B AASs involving the LSA who were consecutively admitted to our hospital between January 1, 2019 and October 30, 2023. Patients underwent thoracic endovascular aortic repair (TEVAR) using the Castor device. The clinical data of these patients were collected, and their outcomes were followed. Results This study included 106 patients, comprising those presenting with aortic dissection (AD) (n = 93), penetrating aortic ulcer (PAU) (n = 9), and intramural haematoma (IMH) (n = 4). All patients achieved the technical success. After a median follow-up period of 454 days (range: 359–771 days), all patients demonstrated survival, with 14 (14.4%) patients experiencing complications, including acute myocardial infarction (AMI, n = 1), endoleaks (n = 7), stenosis of the branched section(n = 3), stent graft-induced new entry tear (SINE, n = 2), and progressive aortic dilation (n = 1). Among the endoleaks, there were 1 Type Ib, 2 Type II, and 4 Type IV cases. Among the enrolled patients, two required re-intervention. No retrograde type A aortic dissection (RTAD), paraplegia or stroke were observed during the follow-up period. Conclusion The Castor device provided an easily manipulated, safe, and effective treatment option for patients with type B AASs involving the LSA.

Systematic analysis of potato MYB family genes and their potential functions in anthocyanin biosynthesis

Interactions of substrates and phosphinyl containing inhibitors with bacterial and human zinc proteases

Inhibitors of bacterial virulence is suggested to be a promising strategy in the fight against bacterial resistance. The zinc metalloproteases (MPs) thermolysin (TLN), pseudolysin (PLN, LasB) and aureolysin (ALN) are bacterial virulence factors from the M4 family of proteases structurally resembling human zinc MPs. Knowledge about the binding modes of substrates and inhibitors with the bacterial and human zinc MPs is therefore fundamental for developing inhibitors without strong off-target effects. In the present paper, we studied the molecular interactions and cleavage of TLN, the prototype enzyme of the M4 family, with the substrate Mca-Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys(Dnp)-OH (ES005) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and molecular dynamics (MD) simulations. Enzyme inhibition kinetic studies were used to test 5 compounds (H-1 - H-5) containing phosphinyl as the zinc binding group for their inhibition of TLN, PLN and ALN and of the human matrix metalloproteases MMP-9 and MMP-14. The MALDI-TOF MS results revealed that TLN cleaves ES005 at three sites. The most abundant cleavages were between Ala and Phe, and between Gly and Phe, while the third was between Ser and Ala. MD simulations with Ala or Gly in the S1 subpocket and Phe in S1’ subpocket gave stable interactions between ES005 and TLN. The MD simulations with Ser in the S1 subpocket and Ala in the S1’ subpocket showed larger movements of the substrate relative to the catalytic site than the others, which may explain that the Ser-Ala cleavage product was less abundant than the cleavage products from Ala-Phe and Gly-Phe. H-1 inhibited MMP-14 and MMP-9 with inhibition constants ranging from 0.89 to 30 μM but did not inhibit the bacterial zinc MPs. Induced fit docking showed that the aromatic group of H-1, that entered the S1’ subpocket of the human MMPs, is too big for the S1’ subpocket of the bacterial zinc MPs. H-2 inhibited the human MMPs with inhibition constants ranging from 0.53 μM (MMP-9) to 3.0 μM (MMP-14) and the bacterial zinc MPs with inhibition constants ranging from 2.5 μM (TLN) to 80 μM (ALN). Induced fit docking indicated that H-2 interacted quite differently with the human and bacterial zinc proteases, but with primed and unprimed subpockets in both. H-3, H-4 and H-5 did not inhibit any of the zinc MPs with inhibition constants < 100 μM. The MD simulations of ES005 with TLN showed that the MALDI-TOF MS results could be explained by that a Phe in S1’ subpocket generate more stable interaction with TLN than an Ala in that subpocket. The docking studies indicated that the size of the S1’ subpocket is an important determinant for inhibitor selectivity between bacterial and human zinc MPs.

STELLA provides a drug design framework enabling extensive fragment-level chemical space exploration and balanced multi-parameter optimization

Study of the rice yield variations under water saving scenarios using DSSAT crop model

The current instability of water resources poses a major challenge and may lead to a food shortage crisis. To address this issue and to cope with the challenges of future extreme weather events and insufficient water resources, it is imperative to develop water-saving cultivation measures. This study used the long-term historical yield data of three rice varieties, TK9, TNG67 and TCS10, from an agricultural research station in Taiwan, simulated two water-saving cultivation experiments using the DSSAT crop model, and established a yield model based on the water-saving ratio, aiming to recommend appropriate irrigation water for Taiwan rice varieties. The goal was to save water while ensuring that the yield is not affected. Through water-saving cultivation simulation experiments, we estimated that under the condition of maintaining more than 90% of rice yield, water-saving irrigation treatment of rice in two different cropping seasons can save about 48% to 100% and 42% to 61% of irrigation water respectively. For irrigation treatment during sensitive growth stages, significant water-saving effects can be achieved, which are about 40% to 75% and 55% to 91% respectively. This study suggests that in the case of water shortage, it is possible to consider moderately increasing the water-saving ratio and implementing irrigation during sensitive growth periods, so as to effectively cope with future water shortage scenarios and achieve sustainable rice production while saving water resources.

GraphFedAI framework for DDoS attack detection in IoT systems using federated learning and graph based artificial intelligence

A comparative study of machine learning models for automated detection and classification of retinal diseases in Ghana

Introduction: Retinal diseases, a significant global health concern, often lead to severe vision impairment and blindness, resulting in substantial functional and social limitations. This study explored a novel goal of developing and comparing the performance of multiple state-of-the-art convolutional neural network (CNN) models for the automated detection and classification of retinal diseases using optical coherence tomography (OCT) images. Method: The study utilized several models, including DenseNet121, ResNet50, Inception V3, MobileNet, and OCT images obtained from the WATBORG Eye Clinic, to detect and classify multiple retinal diseases such as glaucoma, macular edema, posterior vitreous detachment (PVD), and normal eye cases. The preprocessing techniques employed included data augmentation, resizing, and one-hot encoding. We also used the Gaussian Process-based Bayesian Optimization (GPBBO) approach to fine-tune the hyperparameters. Model performance was evaluated using the F1-Score, precision, recall, and area under the curve (AUC). Result: All the CNN models evaluated in this study demonstrated a strong capability to detect and classify various retinal diseases with high accuracy. MobileNet achieved the highest accuracy at 96% and AUC of 0.975, closely followed by DenseNet121, which had 95% accuracy and an AUC of 0.963. Inception V3 and ResNet50, while not as high in accuracy, showed potential in specific contexts, with 83% and 79% accuracy, respectively. Conclusion: These results underscore the potential of advanced CNN models for diagnosing retinal diseases. With the exception of ResNet50, the other CNN models displayed accuracy levels that are comparable to other state-of-the-art deep learning models. Notably, MobileNet and DenseNet121 showed considerable promise for use in clinical settings, enabling healthcare practitioners to make rapid and accurate diagnoses of retinal diseases. Future research should focus on expanding datasets, integrating multi-modal data, exploring hybrid models, and validating these models in clinical environments to further enhance their performance and real-world applicability.

Trichoderma harzianum-loaded maize biochar enhances Cd–Cu immobilization and reduces bio-accessibility in contaminated soil

Relationships between nitrogen-fixing bacteria community structure in Vicia villosa nodules, soil properties and rocky desertification degree in karst area southwest China

Rocky desertification, a common phenomenon in karst ecosystems, significantly impacts soil fertility and vegetation restoration. Therefore, understanding the relationship between nitrogen-fixing bacteria and soil properties under different degrees of rocky desertification is crucial. Our experiment was conducted to investigate the bacterial community structure and the main environmental factors affecting the distribution of the nitrogen-fixing bacteria in the nodules of V. villosa. Based on nifH gene sequence analysis, we found that the community composition of nitrogen-fixing bacteria in the nodules was significantly correlated with the degree of rocky desertification. The soil physicochemical properties affecting community composition were analyzed. The results revealed that: (1) The soil water content, alkali-hydrolyzable nitrogen content, and total nitrogen content in the slight rocky desertification area GJ4 were significantly higher than those in the moderate rocky desertification areas KY and MZ3. (2) There were significant differences in the community composition of nitrogen-fixing bacteria across the four rocky desertification areas (R2 = 0.448, P = 0.001). Within the same area, the Shannon index in slight rocky desertification was significantly higher than that of moderate rocky desertification. Rhizobium was the dominant genus. (3) In Gejiu, Yunnan Province, it has been observed that there is a clear negative correlation was observed among rocky desertification grade, soil water content, and nitrogen-fixing bacterial diversity in the typical karst ecosystem. Specifically, intensifying rocky desertification significantly reduces soil moisture and bacterial diversity. The degree of soil rocky desertification, total nitrogen content, total phosphorus content, and pH of soil are the main factors that play a key role in the community composition of the nitrogen-fixing bacteria in the nodules of V. villosa. This study provides a theoretical basis for the control of rocky desertification.

Ratcheting fatigue behaviour of advanced structural materials at their service temperatures

When to stop: Understanding the landscape of extreme-duration cardiopulmonary resuscitation practices among pediatricians in Sudan

Background Pediatric cardiopulmonary resuscitation (CPR) is a life-saving intervention, but its effectiveness in extreme durations remains debated. This study aimed to explore the frequency and decision-making regarding prolonged CPR (PCPR) practices in hospitalized Sudanese children. Methods A web-based cross-sectional survey was conducted among pediatricians and pediatric trainees in Sudan. The survey investigated their experience with prolonged, ultra-prolonged, and extreme-duration CPR and factors influencing termination decisions. Results Ninety-six Sudanese pediatricians and trainees responded to the survey, reporting varied experiences with prolonged CPR durations: over half (51%) and 81% of respondents reported encountering extreme-duration (> 12 hours) and ultra-prolonged (> 2 hours) CPR at least once, respectively. Around 5% and 1% reported to have encountered CPR durations of 48–72 hours and more than 72 hours, respectively, while 18% reported a 12–14-hour as their record high CPR duration. Four participants reported encountering extreme-duration (> 12 hours) CPR more than 15 times. Respondents most frequently (41%) cited the absence of a pulse and heartbeat as the primary factor for terminating CPR. A vast majority acknowledged ethical considerations (84%) and a lack of clear protocols (83%) as a barrier to terminating PCPR. Thematic analysis of an open question revealed a critical need for a standardized protocol addressing PCPR, enhanced CPR training, and better post-resuscitation support. Conclusions This study revealed a relatively high frequency of extended-duration CPR in Sudanese pediatric settings. Termination decisions focused on cardiac activity becoming clinically undetectable rather than brain death signs or specific cutoff CPR durations. The absence of a clear protocol on when to terminate CPR seems to contribute the most to this phenomenon. Further research on patient outcomes after prolonged CPR in this context is warranted.

DMM-YOLO: A high efficiency soil fauna detection model based on an adaptive dynamic shuffle mechanism

Protocol for a scoping review investigating success in research capacity building for nurses, midwives and allied health professionals

Objective To identify and describe how success is currently conceptualised in research capacity building in nurses, midwives and allied health professionals in the UK. Introduction Having a research active healthcare workforce is associated with improved patient outcomes as well as staff retention. It is therefore seen as a key target for many healthcare organisations. Nurses, Midwives and Allied Health Professionals form the largest group of healthcare professionals but are traditionally less involved in research than medically trained staff. A variety of schemes have aimed to address this through so called “research capacity building” activities but an understanding of what constitutes success is needed to aid development of future interventions. Inclusion criteria Participants - Any or all of Nurses, Midwives or Allied Health Professionals. Concept- Definition of success or description of aims of activities aimed at research capacity building. Context- Within in the UK. Methods Content from peer reviewed journals will be searched for in: Embase, CINAHL, MEDLINE, AMED, BNI and EMCARE Web of Science Core Collection. Grey Literature will be searched for in Google and Overton as well as key websites of organisations that work in developing research capacity. Website searches will include National Institute for Health and Care Research, all charities that form the Association of Medical Research Charities as of search date and the websites for the recognised professional bodies for Nurses, Midwives and Allied Health Professionals. Screening of titles and abstracts then full text will be undertaken by one person with 20% cross checked by a second reviewer. Data extraction will use a bespoke data extraction tool and will be undertaken by one person, with 20% cross checked with a second reviewer. A narrative synthesis and qualitative content analysis will be used to synthesise the data. Registered OSF Registries: https://doi.org/10.17605/OSF.IO/QVCDX