Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison and Assessment of Different Interatomic Potentials for Simulation of Silicon Carbide

Interatomic potentials play a crucial role in the molecular dynamics (MD) simulation of silicon carbide (SiC). However, the ability of interatomic potentials to accurately describe certain physical properties of SiC has yet to be confirmed, particularly for hexagonal SiC. In this study, the mechanical, thermal, and defect properties of four SiC structures (3C-, 2H-, 4H-, and 6H-SiC) have been calculated with multiple interatomic potentials using the MD method, and then compared with the results obtained from density functional theory and experiments to assess the descriptive capabilities of these interatomic potentials. The results indicate that the T05 potential is suitable for describing the elastic constant and modulus of SiC. Thermal calculations show that the Vashishta, environment-dependent interatomic potential (EDIP), and modified embedded atom method (MEAM) potentials effectively describe the vibrational properties of SiC, and the T90 potential provides a better description of the thermal conductivity of SiC. The EDIP potential has a significant advantage in describing point defect formation energy in hexagonal SiC, and the GW potential is suitable for describing vacancy migration in hexagonal SiC. Furthermore, the T90 and T94 potentials can effectively predict the surface energies of the three low-index surfaces of 3C-SiC, and the Vashishta potential exhibits excellent capabilities in describing stacking fault properties in SiC. This work will be helpful for selecting a potential for SiC simulations.
Significant Differences in the Effects of Nitrogen Doping on Pristine Biochar and Graphene-like Biochar for the Adsorption of Tetracycline

To improve the adsorption efficiency of pollutants by biochar, preparing graphene-like biochar (GBC) or nitrogen-doped biochar are two commonly used methods. However, the difference in the nitrogen doping (N-doping) effects upon the adsorption of pollutants by pristine biochar (PBC) and GBC, as well as the underlying mechanisms, are still unclear. Take the tetracycline (TC) as an example, the present study analyzed the characteristics of the adsorption of TCs on biochars (PBC, GBC, N-PBC, N-GBC), and significant differences in the effects of N-doping on the adsorption of TCs by PBC and GBC were consistently observed at different solution properties. Specifically, N-doping had varied effects on the adsorption performance of PBC, whereas it uniformly improved the adsorption performance of GBC. To interpret the phenomenon, the N-doping upon the adsorption was revealed by the QSAR model, which indicated that the pore filling (VM) and the interactions between TCs with biochars (Ead-v) were found to be the most important two factors. Furthermore, the density functional theory (DFT) results demonstrated that N-doping slightly affects biochar’s chemical reactivity. The van der Waals (vdWs) and electrostatic interactions are the main forces for TCs-biochars interactions. Moreover, N-doping mostly strengthened the electrostatic interactions of TCs-biochars, but the vdWs interactions of most samples remained largely unaffected. Overall, the revealed mechanism of N-doping on TCs adsorption by biochars will enhance our knowledge of antibiotic pollution remediation.
Sustainable Transformation of Two Algal Species of Different Genera to High-Value Chemicals and Bioproducts

This study investigates the potential of two algae species from different genera, namely the recently isolated Scenedesmus obliquus BGP and Porphyridium cruentum, from the perspective of their integral sustainable transformation to valuable substances. Conventional Soxhlet and environmentally friendly supercritical fluid extraction were applied to recover oils from the species. The extracts were characterized through analytical techniques, such as GC-Fid and LC-MS/MS, which allowed their qualitative and quantitative differentiation. Thus, P. cruentum oils contained up to 43% C20:4 and C20:5 fatty acids, while those of S. obliquus BGP had only residual amounts. The LC-MS/MS analysis of phenolic compounds in the S. obliquus BGP and P. cruentum extracts showed higher content of 3-OH-4-methoxybenzoic acid and kaempferol 3-O-glycoside in the former and higher amounts of ferulic acid in the latter. Total phenolic content and antioxidant activity of the oils were also determined and compared. The compositional analysis of the oil extracts revealed significant differences and varying potentialities based on their genera and method of extraction. To the best of our knowledge our work is unique in providing such detailed information about the transformation prospects of the two algae species to high-value chemicals and bioproducts.
Withaferin A and Celastrol Overwhelm Proteostasis

Withaferin A (WA) and celastrol (CEL) are major bioactive components of plants that have been widely employed in traditional medicine. The pleiotropic activities of plant preparations and the isolated compounds in vitro and in vivo have been documented in hundreds of studies. Both WA and CEL were shown to have anticancer activity. Although WA and CEL belong to different chemical classes, our synthesis of the available information suggests that the compounds share basic mechanisms of action. Both WA and CEL bind covalently to numerous proteins, causing the partial unfolding of some of these proteins and of many bystander proteins. The resulting proteotoxic stress, when excessive, leads to cell death. Both WA and CEL trigger the activation of the unfolded protein response (UPR) which, if the proteotoxic stress persists, results in apoptosis mediated by the PERK/eIF-2/ATF4/CHOP pathway or another UPR-dependent pathway. Other mechanisms of cell death may play contributory or even dominant roles depending on cell type. As shown in a proteomic study with WA, the compounds appear to function largely as electrophilic reactants, indiscriminately modifying reachable nucleophilic amino acid side chains of proteins. However, a remarkable degree of target specificity is imparted by the cellular context.
Integrated Bulk and Single-cell RNA Sequencing Data Constructs and Validates a Prognostic Model for Non-small Cell Lung Cancer

Background: Most of the current research on prognostic model construction for non-small cell lung cancer (NSCLC) only involves in bulk RNA-seq data without integration of single-cell RNA-seq (scRNA-seq) data. Besides, most of the prognostic models are constructed by predictive genes, ignoring other predictive variables such as clinical features. Methods: We obtained scRNA-seq data from GEO database and bulk RNA-seq data from TCGA database. We construct a prognostic model through the Least Absolute Shrinkage and Selection Operator (LASSO) and Cox regression. Furthermore, we performed ESTIMATE, CIBERSORT, immune checkpoint-related analyses and compared drug sensitivity using pRRophetic method judged by IC50 between different risk groups. Results: 14 tumor-related genes were extracted for model construction. The AUC for 1-, 3-, and 5 years overall survival prediction in TCGA and three validation cohorts were almost higher than 0.65, some of which were even higher than 0.7, even 0.8. Besides, calibration curves suggested no departure between model prediction and perfect fit. Additionally, immune-related and drug sensitivity results revealed potential targets and strategies for treatment, which can provide clinical guidance. Conclusion: We integrated traditional bulk RNA-seq and scRNA-seq data, along with predictive clinical features to develop a prognostic model for patients with NSCLC. According to the constructed model, patients in different groups can follow precise and individual therapeutic schedules based on immune characteristics as well as drug sensitivity.
Subclinical Hypothyroidism in Patients with Obesity and Metabolic Syndrome: A Narrative Review

The literature on the connection between obesity, metabolic syndrome, and subclinical hypothyroidism is critically analyzed in this narrative review. These conditions are frequently observed among adult populations and various studies and meta-analyses have assessed their association. The prevalence of subclinical hypothyroidism in obese individuals is higher than in non-obese subjects and this trend is more pronounced in unhealthy obesity phenotypes. However, the diagnosis and treatment of subclinical hypothyroidism can be difficult in obese patients. Exaggerated body fat is linked to thyroid hypoechogenicity as evident through ultrasonography and euthyroid obese people have greater TSH, FT3, and FT3/FT4 ratios than non-obese individuals in a euthyroid condition. Moreover, a reduced expression of the TSH receptor and altered function of deiodinases has been found in the adipose tissue of obese patients. Current data do not support the necessity of a pharmacological correction of the isolated hyperthyrotropinemia in euthyroid obese patients because treatment with thyroid hormone does not significantly improve weight loss and the increase in serum TSH can be reversible after hypocaloric diet or bariatric surgery. On the other hand, obesity is linked to elevated leptin levels. Inflammation can raise the risk of Hashimoto thyroiditis, which increases the likelihood that obese patients will experience overt or subclinical hypothyroidism. Both metabolic syndrome and subclinical hypothyroidism are associated with atherosclerosis, liver and kidney disease. Hence, the association of these two illnesses may potentiate the adverse effects noted in each of them. Subclinical hypothyroidism should be identified in patients with obesity and treated with appropriate doses of L-thyroxine according to the lean body mass and body weight. Randomized controlled trials are necessary to verify whether treatment of thyroid deficiency could counteract the expected risks.
The In Vitro Toxicity Profile of ZnS and CdS Quantum Dots in Polysaccharide Carriers (Starch/Chitosan)

Nanocomposites are an emerging technology for ensuring food safety and quality. Their unique properties, attributed to nanoparticle presence, facilitate the development of sophisticated sensors and biosensors for detecting harmful substances, microbial growth, and environmental changes in food products. Smart and/or active food packaging development also benefits from the use of nanocomposites. This packaging, or portions of it, provide active protection for its contents and serve as sensors to promptly, simply, and safely identify any detrimental changes in stored food, without elaborate techniques or analyses. Films made from potato starch and chitosan were produced and quantum dots of zinc sulfide (ZnS) and cadmium sulfide (CdS)were synthesized in them for this study. The presence and dimensions of the QDs (quantum dots) were examined with scanning electron microscopy (SEM) and ultraviolet-visible (UV-VIS) spectroscopy. The study aimed to establish the toxicity profile of a starch–chitosan bionanocomposite integrated with ZnS and CdS quantum dots. Cytotoxic and genotoxic features were assessed through cytogenetic instability assessments, consisting of the alkaline comet assay, erythrocyte micronucleus assay, and peripheral blood cell viability analysis of a laboratory mouse model.
Current Research Status and Implication for Further Study of Real-World Data on East Asian Traditional Medicine for Heart Failure: A Scoping Review

This study used real-world data (RWD) to explore the long-term effects of East Asian traditional medicine (EATM) on heart failure (HF). A comprehensive search was conducted across five databases to identify relevant studies, which were then reviewed using the Arksey and O’Malley scoping review framework. The analysis focused on a descriptive examination of the long-term outcomes associated with EATM intervention. Methodologically, the study explored various aspects, including study subjects, interventions, applied clinical outcomes, and statistical methods. Out of 258 studies, 12 were selected. Eight studies involved patients with HF, while the others used HF as an outcome. Datasets from the National Health Insurance Research Database were used in Taiwan, while electronic medical record data were used in China and Japan. EATM interventions have been found to be associated with lower mortality and readmission rates. One study indicated that an increased dose of Fuzi, a botanical drug, or prompt use of Fuzi after diagnosis led to a decreased mortality hazard ratio. In two studies examining readmission rates, a significant increase was observed in the non-exposed group, with odds ratios of 1.28 and 1.18. Additionally, in patients with breast cancer, the subdistribution hazard ratio for the occurrence of doxorubicin-induced HF was reduced to 0.69. Although cohort studies with survival analysis were common, methodological flaws, such as issues with statistical methods and HF diagnosis, were identified. Despite these challenges, the study observed an association between EATM and improved clinical outcomes in patients with HF, emphasizing the potential of RWD studies to complement randomized controlled trials, especially for longer-term follow-ups. These results provide foundational data for future RWD research.
Structural basis for the ligand recognition and signaling of free fatty acid receptors

Free fatty acid receptors 1 to 4 (FFA1 to FFA4) are class A G protein–coupled receptors (GPCRs). FFA1 to FFA3 share substantial sequence similarity, whereas FFA4 is unrelated. However, FFA1 and FFA4 are activated by long-chain fatty acids, while FFA2 and FFA3 respond to short-chain fatty acids generated by intestinal microbiota. FFA1, FFA2, and FFA4 are potential drug targets for metabolic and inflammatory conditions. Here, we determined the active structures of FFA1 and FFA4 bound to docosahexaenoic acid, FFA4 bound to the synthetic agonist TUG-891, and butyrate-bound FFA2, each complexed with an engineered heterotrimeric Gq protein (miniGq), by cryo–electron microscopy. Together with computational simulations and mutagenesis studies, we elucidated the similarities and differences in the binding modes of fatty acid ligands to their respective GPCRs. Our findings unveiled distinct mechanisms of receptor activation and G protein coupling. We anticipate that these outcomes will facilitate structure-based drug development and underpin future research on this group of GPCRs.
Evaluation of In Vitro Protein Hydrolysis in Seven Insects Approved by the EU for Use as a Protein Alternative in Aquaculture

Simple Summary In aquaculture, fishmeal and soybean meal have traditionally been used in the formulation of feed to cover the protein demands of fish. More sustainable protein sources, such as algae and insects, are currently being investigated as alternatives. Therefore, this study evaluates the in vitro digestibility of protein from seven insects approved by the European Union for use in animal feed. The study results suggest that Tenebrio molitor had digestibility similar to that of fishmeal, while Acheta domestica and Hermetia illucens obtained similar data to those provided by soybean meal. Abstract Rapid population growth is leading to an increase in the demand for high-quality protein such as fish, which has led to a large increase in aquaculture. However, fish feed is dependent on fishmeal. It is necessary to explore more sustainable protein alternatives that can meet the needs of fish. Insects, due to their high protein content and good amino acid profiles, could be a successful alternative to fishmeal and soybean meal traditionally used in sectors such as aquaculture. In this work, seven species of insects (Hermetia illucens, Tenebrio molitor, Acheta domestica, Alphitobius diaperinus, Gryllodes sigillatus, Gryllus assimilis, and Musca domestica) approved by the European Union (UE) for use as feed for farmed animals (aquaculture, poultry, and pigs) were studied. Their proximate composition, hydrolysis of organic matter (OMd), hydrolysis of crude protein (CPd), degree of hydrolysis (DH/NH2 and DH/100 g DM), and total hydrolysis (TH) were analyzed. The results showed that Tenebrio molitor had digestibility similar to that of fishmeal, while Acheta domestica and Hermetia illucens provided similar digestibility to that of soybean meal. The acid detergent fiber (ADF) data were negatively correlated with all protein digestibility variables. The differences in the degree of hydrolysis (DH) results and the similarity in total hydrolysis (TH) results could indicate the slowing effects of ADF on protein digestibility. Further in vivo studies are needed.
Ensemble Learning Framework for DDoS Detection in SDN-Based SCADA Systems

Supervisory Control and Data Acquisition (SCADA) systems play a crucial role in overseeing and controlling renewable energy sources like solar, wind, hydro, and geothermal resources. Nevertheless, with the expansion of conventional SCADA network infrastructures, there arise significant challenges in managing and scaling due to increased size, complexity, and device diversity. Using Software Defined Networking (SDN) technology in traditional SCADA network infrastructure offers management, scaling and flexibility benefits. However, as the integration of SDN-based SCADA systems with modern technologies such as the Internet of Things, cloud computing, and big data analytics increases, cybersecurity becomes a major concern for these systems. Therefore, cyber-physical energy systems (CPES) should be considered together with all energy systems. One of the most dangerous types of cyber-attacks against SDN-based SCADA systems is Distributed Denial of Service (DDoS) attacks. DDoS attacks disrupt the management of energy resources, causing service interruptions and increasing operational costs. Therefore, the first step to protect against DDoS attacks in SDN-based SCADA systems is to develop an effective intrusion detection system. This paper proposes a Decision Tree-based Ensemble Learning technique to detect DDoS attacks in SDN-based SCADA systems by accurately distinguishing between normal and DDoS attack traffic. For training and testing the ensemble learning models, normal and DDoS attack traffic data are obtained over a specific simulated experimental network topology. Techniques based on feature selection and hyperparameter tuning are used to optimize the performance of the decision tree ensemble models. Experimental results show that feature selection, combination of different decision tree ensemble models, and hyperparameter tuning can lead to a more accurate machine learning model with better performance detecting DDoS attacks against SDN-based SCADA systems.
Antibiotic Exposure Concurrently with Anti-PD1 Blockade Therapy Reduces Overall Survival in Patients with Child–Pugh Class A Advanced Hepatocellular Carcinoma

Simple Summary This study examines the role of antibiotic use on the immunotherapeutic response in patients with hepatocellular carcinoma (HCC) treated with an immune checkpoint inhibitor (ICI). HCC is the leading cause of cancer death worldwide. In this work, we examine 59 patients with HCC treated with ICI, 39 patients did not use antibiotics, and 20 patients did use antibiotics concurrent with ICI. We found that patients with Child–Pugh class A advanced HCC who did not take antibiotics during the treatment course had significantly longer overall survival compared to those who did. This work adds to the growing evidence that antibiotic use during the treatment course with ICI might negatively affect survival outcomes. This work along with others suggests the need for a careful prescription of antibiotics to patients with HCC undergoing ICI. Abstract Hepatocellular carcinoma (HCC) is the third leading cause of cancer death worldwide with a poor prognosis. Treatment with immune checkpoint inhibitors (ICIs) has improved overall survival in patients with HCC. However, not all patients benefit from the treatment. In this study, 59 patients with HCC were enrolled from two medical centers in Saudi Arabia, with 34% using antibiotics concurrently with their Nivolumab (anti-PD1 blockade). The impact of antibiotic use on the clinical outcomes of patients with HCC undergoing treatment with anti-PD1 blockade was examined. The patients’ overall survival (OS) was 5 months (95% CI: 3.2, 6.7) compared to 10 months (95% CI: 0, 22.2) (p = 0.08). Notably, patients with Child–Pugh A cirrhosis receiving anti-PD1 blockade treatment without concurrent antibiotic use showed a significantly longer median OS reaching 22 months (95% CI: 6.5, 37.4) compared to those who were given antibiotics with a median OS of 6 months (95% CI: 2.7, 9.2) (p = 0.02). This difference in overall survival was particularly found in Child–Pugh class A patients receiving anti-PD1 blockade. These findings suggest that antibiotic use may negatively affect survival outcomes in HCC patients undergoing anti-PD1 blockade, potentially due to antibiotic-induced alterations to the gut microbiome impacting the anti-PD1 blockade response. This study suggests the need for careful consideration when prescribing antibiotics to patients with HCC receiving anti-PD1 blockade.
Comparative Analysis of Differential Cellular Transcriptome and Proteome Regulation by HIV-1 and HIV-2 Pseudovirions in the Early Phase of Infection

In spite of the similar structural and genomic organization of human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2), striking differences exist between them in terms of replication dynamics and clinical manifestation of infection. Although the pathomechanism of HIV-1 infection is well characterized, relatively few data are available regarding HIV-2 viral replication and its interaction with host–cell proteins during the early phase of infection. We utilized proteo-transcriptomic analyses to determine differential genome expression and proteomic changes induced by transduction with HIV-1/2 pseudovirions during 8, 12 and 26 h time-points in HEK-293T cells. We show that alteration in the cellular milieu was indeed different between the two pseudovirions. The significantly higher number of genes altered by HIV-2 in the first two time-points suggests a more diverse yet subtle effect on the host cell, preparing the infected cell for integration and latency. On the other hand, GO analysis showed that, while HIV-1 induced cellular oxidative stress and had a greater effect on cellular metabolism, HIV-2 mostly affected genes involved in cell adhesion, extracellular matrix organization or cellular differentiation. Proteomics analysis revealed that HIV-2 significantly downregulated the expression of proteins involved in mRNA processing and translation. Meanwhile, HIV-1 influenced the cellular level of translation initiation factors and chaperones. Our study provides insight into the understudied replication cycle of HIV-2 and enriches our knowledge about the use of HIV-based lentiviral vectors in general.