Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent Advances in Silver Nanowires Electrodes for Flexible Organic/Perovskite Light-Emitting Diodes

Flexible organic light-emitting diodes and perovskite light-emitting diodes (PeLEDs) have been investigated as an innovative category of revolutionary LED devices for next-generation flat display and lighting applications. A transparent conductive electrode is a key component in flexible OLEDs and PeLEDs, and has been the limitation of the development in this area. Silver nanowires (AgNWs) have been regarded as the most suitable alternative material in TCEs, due to the economical solution synthesis and compatibility with roll-to-roll technology. This mini-review addresses the advances in silver nanowires electrodes for flexible organic/perovskite light-emitting diodes, and the relationship between electrode optimization and device performance is demonstrated. Moreover, the potential strategies and perspectives for their further development of AgNWs-based flexible OLEDs and PeLEDs are presented.
Global Landscape of m6A Methylation of Differently Expressed Genes in Muscle Tissue of Liaoyu White Cattle and Simmental Cattle

Liaoyu white cattle (LYWC) is a local breed in Liaoning Province, China. It has the advantages of grow quickly, high slaughter ratew, high meat quality and strong anti-stress ability. N6 methyladenosine (m6A) is a methylation modification of N6 position of RNA adenine, which is an important modification mechanism affecting physiological phenomena. In this study, we used the longissimus dorsi muscle of LYWC and SIMC for m6A-seq and RNA-seq high-throughput sequencing, and identified the key genes involved in muscle growth and m6A modification development by bioinformatics analysis. There were 31532 m6A peaks in the whole genome of LYWC and 47217 m6A peaks in the whole genome of SIMC. Compared with Simmental cattle group, LYWC group had 17,351 differentially expressed genes: 10,697 genes were up-regulated, 6,654 genes were down regulated, 620 differentially expressed genes were significant, while 16,731 differentially expressed genes were not significant. Among the 620 significantly differentially expressed genes, 295 genes were up-regulated and 325 genes were down regulated. In order to explore the relationship between m6A and mRNA expression in the muscles of LYWC and SIMC, the combined analysis of MeRIP-seq and RNA-seq revealed that 316 genes were m6A modified with mRNA expression. To identify differentially methylated genes related to muscle growth, four related genes were selected for quantitative verification in LYWC and SIMC. GO enrichment and KEGG analysis showed that the differentially expressed genes modified by m6A are mainly involved in skeletal muscle contraction, steroid biosynthesis process, redox process, PPAR pathway and fatty acid metabolism, and galactose metabolism. These results provide a theoretical basis for further research on the role of m6A in muscle growth and development.
Identification of circRNA Biomarker for Gastric Cancer through Integrated Analysis

Gastric cancer (GC) is one of the most common malignant tumors and ranks third in cancer mortality globally. Although, a lot of advancements have been made in diagnosis and treatment of gastric cancer, there is still lack of ideal biomarker for the diagnosis and treatment of gastric cancer. Due to the poor prognosis, the survival rate is not improved much. Circular RNAs (circRNAs) are single-stranded RNAs with a covalently closed loop structure that don’t have the 5′-3′ polarity and a 3′ polyA tail. Because of their circular structure, circRNAs are more stable than linear RNAs. Previous studies have found that circRNAs are involved in several biological processes like cell cycle, proliferation, apoptosis, autophagy, migration and invasion in different cancers, and participate in some molecular mechanisms including sponging microRNAs (miRNAs), protein translation and binding to RNA-binding proteins. Several studies have reported that circRNAs play crucial role in the occurrence and development of different types of cancers. Although, some studies have reported several circRNAs in gastric cancer, more studies are needed in searching new biomarkers for gastric cancer diagnosis and treatment. Here, we investigated potential circRNA biomarkers for GC using next-generation sequencing (NGS) data collected from 5 paired GC samples. A total of 45,783 circRNAs were identified in all samples and among them 478 were differentially expressed (DE). The gene ontology (GO) analysis of the host genes of the DE circRNAs showed that some genes were enriched in several important biological processes, molecular functions and cellular components. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed that some host genes were enriched in several GC related pathways. The circRNA-miRNA-gene interaction network analysis showed that two circRNAs circCEACAM5 and circCOL1A1 were interacted with gastric cancer related miRNAs, and their host genes were also the important therapeutic and prognostic biomarkers for GC. The experimental results also validated that these two circRNAs were DE in GC compared to adjacent normal tissues. Overall, our findings suggest that these two circRNAs circCEACAM5 and circCOL1A1 might be the potential biomarkers for the diagnosis and treatment of GC.
The Influence of CYP3A4 Genetic Polymorphism and Proton Pump Inhibitors on Osimertinib Metabolism

The aim of this study was to 1) investigate the effects of 27 CYP3A4 variants on the metabolism of osimertinib and 2) study the interactions between osimertinib and others as well as the underlying mechanism. A recombinant human CYP3A4 enzymatic incubation system was developed and employed to determine the kinetic profile of CYP3A4 variants. Ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) was applied to detect the concentration of the main metabolite, AZ5104. The results demonstrated that the relative clearance rates of CYP3A4.19, 10, 18, 5, 16, 14, 11, 2, 13, 12, 7, 8, and 17 in catalyzing osimertinib were significantly reduced to a minimum of 25.68% compared to CYP3A4.1, while those of CYP3A4.29, 32, 33, 28, 15, 34, and 3 were obviously enhanced, ranging from 114.14% to 284.52%. The activities of the remaining variants were almost equal to those of CYP3A4.1. In addition, 114 drugs were screened to determine the potential interaction with osimertinib based on the rat liver microsome (RLM) reaction system. Sixteen of them inhibited the production of AZ5104 to 20% or less, especially proton pump inhibitors, among which the IC50 of rabeprazole was 6.49 ± 1.17 μM in RLM and 20.39 ± 2.32 μM in human liver microsome (HLM), with both following competitive and non-competitive mixed mechanism. In an in vivo study, Sprague–Dawley (SD) rats were randomly divided into groups, with six animals per group, receiving osimertinib with or without rabeprazole, omeprazole, and lansoprazole. We found that the AUC(0–t), AUC(0–∞), and Cmax of osimertinib decreased significantly after co-administration with rabeprazole orally, but they increased remarkably when osimertinib was administered through intraperitoneal injection. Taken together, our data demonstrate that the genetic polymorphism and proton pump inhibitors remarkably influence the disposition of osimertinib, thereby providing basic data for the precise application of osimertinib.
Real-Time Quaking- Induced Conversion Assays for Prion Diseases, Synucleinopathies, and Tauopathies

Prion diseases, synucleinopathies and tauopathies are neurodegenerative disorders characterized by deposition of abnormal protein aggregates in brain and other tissues. These aggregates consist of misfolded forms of prion, α-synuclein (αSyn), or tau proteins that cause neurodegeneration and represent hallmarks of these disorders. A main challenge in the management of these diseases is the accurate detection and differentiation of these abnormal proteins during the early stages of disease before the onset of severe clinical symptoms. Unfortunately, many clinical manifestations may occur only after neuronal damage is already advanced and definite diagnoses typically require post-mortem neuropathological analysis. Over the last decade, several methods have been developed to increase the sensitivity of prion detection with the aim of finding reliable assays for the accurate diagnosis of prion disorders. Among these, the real-time quaking-induced conversion (RT–QuIC) assay now provides a validated diagnostic tool for human patients, with positive results being accepted as an official criterion for a diagnosis of probable prion disease in multiple countries. In recent years, applications of this approach to the diagnosis of other prion-like disorders, such as synucleinopathies and tauopathies, have been developed. In this review, we summarize the current knowledge on the use of the RT-QuIC assays for human proteopathies.
Microarray Analysis Reveals the Changes in Circular RNA Expression and Molecular Mechanisms in Mice With Ventilator-Induced Lung Injury

Circular RNA (circRNA) expression profiles in lung tissues from mice with and without ventilator-induced lung injury (VILI) were analyzed using high-throughput sequencing and bioinformatics to clarify their potential role in VILI pathogenesis and provide valuable molecular markers for VILI diagnosis and treatment. A VILI mouse model was established using high-tidal volume ventilation, and lung tissue was stained with HE and TUNEL. The present study used high-throughput sequencing technology to analyze the expression profile of circRNAs in the lung tissue of mice with and without VILI. Bioinformatics was used to analyze the enrichment of differentially expressed circRNAs using Gene Ontology and KEGG to predict function. Among the top 10 circRNAs with significant differential expression, we used real-time quantitative polymerase chain reaction technology (qRT-PCR) to verify the accuracy of the high-throughput sequencing results and constructed the corresponding circRNA-miRNA-mRNA-specific binding network map using software prediction. The most upregulated circRNAs were novel_circ_0000899 and novel_circ_0014815, and the most downregulated circRNAs were novel_circ_0015069. A total of 14,347 circRNAs were detected using high-throughput sequencing. Compared to the control group, 285 circRNAs were abnormally and significantly expressed in the lung tissues of VILI mice (|log2(FC)| > 1, p < 0.05). A total of 171 circRNAs were significantly upregulated, and 114 circRNAs were significantly downregulated. Gene ontology analyses indicated that the differentially expressed circRNAs were involved in multiple biological functions, such as regulation of metabolic processes, protein phosphorylation, and chromatin organization. KEGG pathway analyses revealed that the Ras signaling pathway, rap1 signaling pathway, PI3K − Akt signaling pathway, and ECM receiver interaction were related to the differentially expressed circRNAs. The qRT-PCR verification results were generally consistent with the circRNA expression trends of the high-throughput sequencing data. The circRNA-miRNA-mRNA interaction network suggested that miRNAs and mRNAs related to circRNAs played a key role in VILI. Differentially expressed circRNAs were identified in the tissues of VILI mice using high-throughput sequencing combined with bioinformatics analysis, and the results lay a foundation for further study of the mechanism of circRNAs in the occurrence and development of VILI.
Prevalence and Diversity of Antibiotic Resistant Escherichia coli From Anthropogenic-Impacted Larut River

Aquatic environments, under frequent anthropogenic pressure, could serve as reservoirs that provide an ideal condition for the acquisition and dissemination of antibiotic resistance genetic determinants. We investigated the prevalence and diversity of antibiotic-resistant Escherichia coli by focusing on their genetic diversity, virulence, and resistance genes in anthropogenic-impacted Larut River. The abundance of E. coli ranged from (estimated count) Est 1 to 4.7 × 105 (colony-forming units per 100 ml) CFU 100 ml−1 to Est 1 to 4.1 × 105 CFU 100 ml−1 with phylogenetic group B1 (46.72%), and A (34.39%) being the most predominant. The prevalence of multiple antibiotic resistance phenotypes of E. coli, with the presence of tet and sul resistance genes, was higher in wastewater effluents than in the river waters. These findings suggested that E. coli could be an important carrier of the resistance genes in freshwater river environments. The phylogenetic composition of E. coli and resistance genes was associated with physicochemical properties and antibiotic residues. These findings indicated that the anthropogenic inputs exerted an effect on the E. coli phylogroup composition, diversification of multiple antibiotic resistance phenotypes, and the distribution of resistance genes in the Larut River.
Bioprinting of Decellularized Porcine Cardiac Tissue for Large-Scale Aortic Models

Bioprinting is an emerging technique used to layer extrudable materials and cells into simple constructs to engineer tissue or arrive at in vitro organ models. Although many examples of bioprinted tissues exist, many lack the biochemical complexity found in the native extracellular matrix. Therefore, the resulting tissues may be less competent than native tissues—this can be especially problematic for tissues that need strong mechanical properties, such as cardiac or those found in the great vessels. Decellularization of native tissues combined with processing for bioprinting may improve the cellular environment for proliferation, biochemical signaling, and improved mechanical characteristics for better outcomes. Whole porcine hearts were decellularized using a series of detergents, followed by lyophilization and mechanical grinding in order to produce a fine powder. Temperature-controlled enzymatic digestion was done to allow for the resuspension of the decellularized extracellular matrix into a pre-gel solution. Using a commercial extrusion bioprinter with a temperature-controlled printhead, a 1:1 scale model of a human ascending aorta and dog bone shaped structures were printed into a reservoir of alginate and xanthium gum then allowed to crosslink at 37C. The bioengineered aortic construct was monitored for cell adhesion, survival, and proliferation through fluorescent microscopy. The dog bone structure was subjected to tensile mechanical testing in order to determine structural and mechanical patterns for comparison to native tissue structures. The stability of the engineered structure was maintained throughout the printing process, allowing for a final structure that upheld the dimensions of the original Computer-Aided Design model. The decellularized ECM (Ē = 920 kPa) exhibited almost three times greater elasticity than the porcine cardiac tissue (Ē = 330 kPa). Similarly, the porcine cardiac tissue displayed two times the deformation than that of the printed decellularized ECM. Cell proliferation and attachment were observed during the in vitro cell survivability assessment of human aortic smooth muscle cells within the extracellular matrix, along with no morphological abnormalities to the cell structure. These observations allow us to report the ability to bioprint mechanically stable, cell-laden structures that serve as a bridge in the current knowledge gap, which could lead to future work involving complex, large-scale tissue models.
Pretreatment DCE-MRI-Based Deep Learning Outperforms Radiomics Analysis in Predicting Pathologic Complete Response to Neoadjuvant Chemotherapy in Breast Cancer

Purpose To compare the performances of deep learning (DL) to radiomics analysis (RA) in predicting pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) based on pretreatment dynamic contrast-enhanced MRI (DCE-MRI) in breast cancer. Materials and Methods This retrospective study included 356 breast cancer patients who underwent DCE-MRI before NAC and underwent surgery after NAC. Image features and kinetic parameters of tumors were derived from DCE-MRI. Molecular information was assessed based on immunohistochemistry results. The image-based RA and DL models were constructed by adding kinetic parameters or molecular information to image-only linear discriminant analysis (LDA) and convolutional neural network (CNN) models. The predictive performances of developed models were assessed by receiver operating characteristic (ROC) curve analysis and compared with the DeLong method. Results The overall pCR rate was 23.3% (83/356). The area under the ROC (AUROC) of the image-kinetic-molecular RA model was 0.781 [95% confidence interval (CI): 0.735, 0.828], which was higher than that of the image-kinetic RA model (0.629, 95% CI: 0.595, 0.663; P < 0.001) and comparable to that of the image-molecular RA model (0.755, 95% CI: 0.708, 0.802; P = 0.133). The AUROC of the image-kinetic-molecular DL model was 0.83 (95% CI: 0.816, 0.847), which was higher than that of the image-kinetic and image-molecular DL models (0.707, 95% CI: 0.654, 0.761; 0.79, 95% CI: 0.768, 0.812; P < 0.001) and higher than that of the image-kinetic-molecular RA model (0.778, 95% CI: 0.735, 0.828; P < 0.001). Conclusions The pretreatment DCE-MRI-based DL model is superior to the RA model in predicting pCR to NAC in breast cancer patients. The image-kinetic-molecular DL model has the best prediction performance.
Assessing the Mediating Role of Safety Communication Between Safety Culture and Employees Safety Performance

The main purpose of this research was to investigate the mediating role of safety communication (SCO) in the relationship between safety culture (SC) and safety performance (SP) amongst employees in the petrochemical industry. Safety communication methods not only enhance working conditions but also have a positive impact on employee's behaviors and attitudes toward safety leading toward reduced incidents in the workplace environment. A stratified sampling method was followed to collect data in the petrochemical industry in Malaysia. Structural equation modeling (SEM) was utilized to analyze the hypothesized model, using data from 320 participants. The findings reveal that safety communication partially mediates the association between safety culture and safety performance. Further, safety culture was found to have a significant and positive effect on safety performance. This -study makes a significant theoretical contribution by providing empirical evidence on the direct and indirect relationship between safety culture and safety performance in the petrochemical industry.
The Role of Paternal Involvement on Behavioral Sensitive Responses and Neurobiological Activations in Fathers: A Systematic Review

As fathering research has flourished, a growing body of studies has focused on behavioral and neurobiological mechanisms, respectively associated with caregiving sensitivity and responsiveness to infant stimuli. However, the association between these aspects and the key concept of paternal involvement in childcare (i.e., contribution in infant care in terms of time, availability, and responsibility) has been poorly investigated. The current work aims to systematically review the role of involvement in childcare on both neural activations and sensitive behaviors in fathers by examining (a) how paternal involvement has been measured and (b) whether paternal involvement has been associated with neurobiological activation and behavioral sensitive responses. Inclusion criteria were peer-reviewed quantitative studies, concerning fathers responding to infant stimuli at neurobiological or behavioral level, and including a quantitative measurement of paternal involvement in childcare. A quality rating for each study has been performed based on the measurements adopted to assess paternal involvement. Of 2,529 articles, 27 studies were included. According to our quality rating, 10 out of 27 studies included fairly good-standard measures for measuring paternal involvement, whereas 17 studies used good-standard measures. In addition, 11 studies provided details of paternal involvement in the context of neurobiological responses to infant stimuli, whereas 16 addressed paternal sensitive behaviors. Overall, only 8 studies reported relevant findings about the relationship between paternal involvement and neurobiological responses or sensitive behaviors in fathers. The present study is the first systematically evaluating the scope of paternal involvement in the field of Paternal Brain and fathers' sensitive responsiveness research. When high-standard measures are used, paternal involvement seems to play a significant role in modulating both the hormonal and the neural pathways associated with paternal behaviors. Remarkably, the role of paternal engagement may underpin an adaptive nurturance that is not dependent on pregnancy and childbirth but on caregiving experience. A promising positive link between paternal involvement and behavioral sensitivity may be expected in further studies, which will need to corroborate our conclusion by adopting detailed and appropriate measures assessing paternal involvement. As a future line of research, the inclusion of gay fathers may be beneficial for the field.
Diffraction Extraction and Least-Squares Reverse Time Migration Imaging for the Fault-Karst Structure With Adaptive Sampling Strategy

The ultra-deep fault-karst structure discovered in the Tarim Basin in Western China is a fractured-vuggy carbonate reservoir with great potential for development. The diffraction generated by fractures, small-scale caves and vugs is often used for reservoir identification and seismic interpretation. Since the diffraction is much weaker than the reflection, it is difficult to separate the diffraction from the full wavefield. We use a plane-wave destruction (PWD) filter to extract the diffraction from the full data. In order to obtain a high-accuracy and amplitude-preserving imaging profile, we use the least-squares reverse time migration (LSRTM) method to image the separated diffraction. The large amount of calculation is the most challenging problem of the LSRTM algorithm. In view of this, we develop an adaptive sampling strategy to improve computing efficiency and reduce memory requirement. We use a fault model, a vugs-fractures model, and a fault-karst model to demonstrate the effectiveness and practicability of the proposed method. The numerical examples show that the proposed method can enhance the imaging resolution of the fault-karst structure and save computing cost without losing accuracy. In addition, a test on field data processing demonstrates the advantages of our algorithm.
From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output

An increasing number of crystal structures available on one side, and the boost of computational power available for computer-aided drug design tasks on the other, have caused that the structure-based drug design tools are intensively used in the drug development pipelines. Docking and molecular dynamics simulations, key representatives of the structure-based approaches, provide detailed information about the potential interaction of a ligand with a target receptor. However, at the same time, they require a three-dimensional structure of a protein and a relatively high amount of computational resources. Nowadays, as both docking and molecular dynamics are much more extensively used, the amount of data output from these procedures is also growing. Therefore, there are also more and more approaches that facilitate the analysis and interpretation of the results of structure-based tools. In this review, we will comprehensively summarize approaches for handling molecular dynamics simulations output. It will cover both statistical and machine-learning-based tools, as well as various forms of depiction of molecular dynamics output.