Miracle-dz/UniFAR-FTUs huggingface dataset:
Intragastrically Applicated CCl4-Thiopental Sodium Enhanced Lipid Peroxidation and Liver Fibrosis (Cirrhosis) in Rat: Malonedialdehyde as a Parameter of Lipid Peroxidation Correlated with Hydroxyproline as a Parameter of Collagen Synthesis (Deposition)

We investigated the pathogenesis of liver tissue damage during the lipid peroxidation and fibrogenesis with the observation of correlations between the parameters of collagen synthesis (and deposition) and lipid peroxidation in liver fibrosis (cirrhosis) rats. Rats were randomly divided into two groups, normal and CCl_4-thiopental sod. intoxicated group. And the one group was treated intragastrically with the mixture of CCl_4-thiopental sod. 3 times per week for 3 weeks. The liver tissue and sera were used for the measurement of hydroxyproline (HYP), malonedialdehyde (MDA) and superoxide dismutase (SOD). Biochemical parameters such as aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), total-bilirubin and blood urea nitrogen (BUN) were measured. Additionally, the expression of collagen α1(III) and β-actin mRNA was observed by RT-PCR. The histological change in liver tissue was also observed by Masson’s trichrome and H&E staining. Correlation analysis was carried by Spearman’s rho method. All biochemical parameters except total-bilirubin were significantly higher in the CCl_4-thiopental sod. treated group than that of the normal group ( p < 0.01). In the CCl_4-thiopental sod. treated group, Hyp as a parameter of collagen synthesis (deposition) and MDA as a metabolite of lipid peroxidation, were significantly elevated by 1.98 and 2.11 times higher than that of the normal group ( p > 0.001) respectively. The activity of SOD in the CCl_4-thiopental sod. treated group is decreased significantly by 44.8% ( p > 0.001). And collagen α1(III) mRNA was more expressed in the CCl_4-thiopental sod. treated group than that of the normal group. However, the expression of β-actin mRNA is showed similar in both of groups. A good correlation was observed between the content of hyp and MDA concentration (r = 0.70, n = 40) in the two groups. And the correlation between the levels of hyp and SOD (r = −0.71, n = 25) is also reliable. However, no correlation were observed between MDA concentration and SOD (r = −0.40, n = 25) in the two groups. Elevated levels of MDA in CCl_4-thiopental sod. treated rats indicated enhancement of lipid peroxidation, which is accompanied by a decrease in SOD activity. Moreover, we could confirm that the parameters of collagen synthesis (and deposition) is in good correlation with the metabolite of lipid peroxidation (MDA) and the lipid peroxidation antagonizing enzyme (SOD). Hence, we propose that ➀ lipid peroxidation and collagen synthesis (and deposition) could be enhanced by intragastrically application of CCl_4-thiopental sod. during a short terms. And ➁ the intoxication of CCl_4-thiopental sod. could be used for monitoring of lipid peroxidation and collagen synthesis (and depositon) for test of antioxidant and antifibrotic agent.
Comparison of Five Different Irrigation Techniques on Smear Layer Removal in Apical Thirds of Root Canals of Mandibular First Premolar: A Scanning Electron Microscopic Study

Aim: This study was conducted to compare smear layer removal by five different irrigation techniques—conventional needle irrigation (CI), manual dynamic activation (MDA), passive ultrasonic irrigation (PUI), sonic irrigation (SI), and negative apical pressure (NAP). Materials and Methods: Fifty freshly extracted mandibular first premolars were cleaned and shaped by One Curve rotary files and 3% sodium hypochlorite and 17% ethylenediaminetetraacetic acid. The samples were divided into five equal groups (n = 10), according to the final irrigation activation technique: Group I, CI; Group II, MDA; Group III, PUI; Group IV, SI; and Group V, NAP. The samples were prepared and observed under a scanning electron microscope. The photomicrographs were recorded and evaluated with a scoring system. Results: Group I and Group II had the highest scores, which showed a statistically significant difference between the other groups (P < 0.05). This was followed by PUI, NAP, and SI. Conclusion: Final irrigation activation with SI and NAP resulted in the better removal of smear layer when compared to that with other groups.
Study on the Colorimetry Properties of Transparent Wood Prepared from Six Wood Species

Transparent wood (TW) was prepared by directly impregnating the wood cell wall and cavity with index-matched prepolymerized methyl methacrylate (MMA). In this process, lignin is retained compared with the preparation of transparent wood in the past, making the production faster and more energy-efficient. The innovation lies in that the prepared transparent wood retains the natural color and texture of the wood while transmitting light, especially under the illumination of a specific light source, which exist as the special visual effects. In order to enhance the practicality of the research and effectively expand the types of home decoration materials, six common wood species with different densities were selected in the experiment. Then the characteristics and mechanisms of wood, that is, color difference, light transmittance, microstructure, changes of chemical functional groups, and tensile strength, before and after PMMA impregnating were compared and analyzed. It is concluded that the light transmittance and mechanical properties of the wood have been improved, and a good synergistic effect between wood and PMMA has been confirmed by the analysis of scanning electron microscopy and infrared spectroscopy. The above highlights make pervious to transparent wood, which has the potential as an excellent functional decorative material.
Discovery of Lonafarnib-Like Compounds: Pharmacophore Modeling and Molecular Dynamics Studies

Progeria is a globally noticed rare genetic disorder manifested by premature aging with no effective treatment. Under these circumstances, farnesyltransferase inhibitors (FTIs) are marked as promising drug candidates. Correspondingly, a pharmacophore model was generated exploiting the features of lonafarnib. The selected pharmacophore model was allowed to screen the InterBioScreen natural compound database to retrieve the potential lead candidates. A series of filtering steps were applied to assess the drug-likeness of the compounds. The obtained compounds were advanced to molecular docking employing the CDOCKER module available with Discovery Studio (DS). Subsequently, three compounds (Hits) have displayed a higher dock score and demonstrated key residue interactions with stable molecular dynamics simulation results compared to the reference compound. Taken together, we therefore put forth three identified Hits as FTIs that may further serve as chemical spaces in designing new compounds.
Magnetic Ring Multi-Defect Stereo Detection System Based on Multi-Camera Vision Technology †

Magnetic rings are the most widely used magnetic material product in industry. The existing manual defect detection method for magnetic rings has high cost, low efficiency and low precision. To address this issue, a magnetic ring multi-defect stereo detection system based on multi-camera vision technology is developed to complete the automatic inspection of magnetic rings. The system can detect surface defects and measure ring height simultaneously. Two image processing algorithms are proposed, namely, the image edge removal algorithm (IERA) and magnetic ring location algorithm (MRLA), separately. On the basis of these two algorithms, connected domain filtering methods for crack, fiber and large-area defects are established to complete defect inspection. This system achieves a recognition rate of 100% for defects such as crack, adhesion, hanger adhesion and pitting. Furthermore, the recognition rate for fiber and foreign matter defects attains 92.5% and 91.5%, respectively. The detection speed exceeds 120 magnetic rings per minutes, and the precision is within 0.05 mm. Both precision and speed meet the requirements of real-time quality inspection in actual production.
Taking the Pressure Off the Patient – Understanding Digital Rectal Examinations on a Real Subject

Better understanding of palpation techniques during unsighted physical examinations has mostly been limited to qualitative and quantitative studies of performance of experts whilst conducting examinations on plastic benchtop models. However, little is known about their performance when conducting such examinations on real subjects. Objective: The aim of this paper is to better understand palpation techniques of experts whilst conducting a Digital Rectal Examination on a real subject. Methods: We recruited four consultants from relevant specialties and asked them to conduct two DREs on a Rectal Teaching Assistant whilst wearing small position and pressure sensors on their examining finger. We segmented the relevant anatomy from an MRI taken of the pelvic region, registered 3D models and analysed retrospectively performance in relation to executed tasks, supination/pronation, palpation convex hull and pressure applied. Results: Primary care consultants examined the anatomy more holistically compared to secondary care experts, the maximum pressure applied across experiments is 3.3N, overall the pressure applied on the prostate is higher than that applied to rectal walls, and the urologist participant not only applied the highest pressure but also did so with the highest most prominent frequency (15.4 and 25.3 Hz). Conclusions: The results of our research allow for better understanding of experts’ technical performance from relevant specialities when conducting a DRE, and suggest the range of pressure applied whilst palpating anatomy. Significance: This research will be valuable in improving the design of haptics-based learning tools, as well as in encouraging reflection on palpation styles across different specialities to develop metrics of performance.
TmSpz6 Is Essential for Regulating the Immune Response to Escherichia coli and Staphylococcus aureus Infection in Tenebrio molitor

Spätzle is an extracellular protein that activates the Toll receptor during embryogenesis and immune responses in Drosophila. However, the functions of the spätzle proteins in the innate immune response against bacteria or fungi in T. molitor are not well understood. Therefore, in this study, the open reading frame (ORF) of TmSpz6 was identified and its function in the response to bacterial and fungal infections in T. molitor was investigated using RNAi. The highest expression of TmSpz6 was in prepupae, and 3- and 6-day-old pupae, while remarkable expression was also observed in other stages. The tissue-specific expression analysis showed that TmSpz6 expression was highest in the hemocytes of larvae. TmSpz6 expression was highly induced when challenged with Escherichia coli, Staphylococcus aureus, or Candida albicans at 6 h post-injection; however, TmSpz6-silenced larvae were significantly more susceptible to only E. coli and S. aureus infection. The antimicrobial peptides (AMPs) gene expression analysis results show that TmSpz6 mainly positively regulated the expression of TmTencin-2 and -3 in response to E. coli and S. aureus infection. Collectively, these results suggest that TmSpz6 plays an important role in regulating AMP expression and increases the survival of T. molitor against E. coli and S. aureus.
Preparation of Porous Carbon Nanofibers with Tailored Porosity for Electrochemical Capacitor Electrodes

Porous carbon electrodes that accumulate charges at the electrode/electrolyte interface have been extensively investigated for use as electrochemical capacitor (EC) electrodes because of their great attributes for driving high-performance energy storage. Here, we report porous carbon nanofibers (p-CNFs) for EC electrodes made by the formation of a composite of monodisperse silica nanoparticles and polyacrylonitrile (PAN), oxidation/carbonization of the composite, and then silica etching. The pore features are controlled by changing the weight ratio of PAN to silica nanoparticles. The electrochemical performances of p-CNF as an electrode are estimated by measuring cyclic voltammetry and galvanostatic charge/discharge. Particularly, the p-CNF electrode shows exceptional areal capacitance (13 mF cm−2 at a current of 0.5 mA cm−2), good rate-retention capability (~98% retention of low-current capacitance), and long-term cycle stability for at least 5000 charge/discharge cycles. Based on the results, we believe that this electrode has potential for use as high-performance EC electrodes.
A Deep Siamese Convolution Neural Network for Multi-Class Classification of Alzheimer Disease

Alzheimer’s disease (AD) may cause damage to the memory cells permanently, which results in the form of dementia. The diagnosis of Alzheimer’s disease at an early stage is a problematic task for researchers. For this, machine learning and deep convolutional neural network (CNN) based approaches are readily available to solve various problems related to brain image data analysis. In clinical research, magnetic resonance imaging (MRI) is used to diagnose AD. For accurate classification of dementia stages, we need highly discriminative features obtained from MRI images. Recently advanced deep CNN-based models successfully proved their accuracy. However, due to a smaller number of image samples available in the datasets, there exist problems of over-fitting hindering the performance of deep learning approaches. In this research, we developed a Siamese convolutional neural network (SCNN) model inspired by VGG-16 (also called Oxford Net) to classify dementia stages. In our approach, we extend the insufficient and imbalanced data by using augmentation approaches. Experiments are performed on a publicly available dataset open access series of imaging studies (OASIS), by using the proposed approach, an excellent test accuracy of 99.05% is achieved for the classification of dementia stages. We compared our model with the state-of-the-art models and discovered that the proposed model outperformed the state-of-the-art models in terms of performance, efficiency, and accuracy.
DREB1A/CBF3 Is Repressed by Transgene-Induced DNA Methylation in the Arabidopsis ice1-1 Mutant[OPEN]

ice1-1 is a widely accepted mutant allele known to abolish cold-inducible expression of DREB1A, which encodes a key transcription factor involved in plant cold stress adaptation, but DREB1A repression in ice1-1 is a case of transgene-induced silencing and not genetic regulation by ICE1. DREB1/CBFs are key transcription factors involved in plant cold stress adaptation. The expression of DREB1/CBFs triggers a cold-responsive transcriptional cascade, after which many stress tolerance genes are expressed. Thus, elucidating the mechanisms of cold stress–inducible DREB1/CBF expression is important to understand the molecular mechanisms of plant cold stress responses and tolerance. We analyzed the roles of a transcription factor, INDUCER OF CBF EXPRESSION1 (ICE1), that is well known as an important transcriptional activator in the cold-inducible expression of DREB1A/CBF3 in Arabidopsis (Arabidopsis thaliana). ice1-1 is a widely accepted mutant allele known to abolish cold-inducible DREB1A expression, and this evidence has strongly supported ICE1-DREB1A regulation for many years. However, in ice1-1 outcross descendants, we unexpectedly discovered that ice1-1 DREB1A repression was genetically independent of the ice1-1 allele ICE1(R236H). Moreover, neither ICE1 overexpression nor double loss-of-function mutation of ICE1 and its homolog SCRM2 altered DREB1A expression. Instead, a transgene locus harboring a reporter gene in the ice1-1 genome was responsible for altering DREB1A expression. The DREB1A promoter was hypermethylated due to the transgene. We showed that DREB1A repression in ice1-1 results from transgene-induced silencing and not genetic regulation by ICE1. The ICE1(R236H) mutation has also been reported as scrm-D, which confers constitutive stomatal differentiation. The scrm-D phenotype and the expression of a stomatal differentiation marker gene were confirmed to be linked to the ICE1(R236H) mutation. We propose that the current ICE1-DREB1 regulatory model should be revalidated without the previous assumptions.
Modifier genes in SCN1A‐related epilepsy syndromes

SCN1A is one of the most important epilepsy‐related genes, with pathogenic variants leading to a range of phenotypes with varying disease severity. Different modifying factors have been hypothesized to influence SCN1A‐related phenotypes. We investigate the presence of rare and more common variants in epilepsy‐related genes as potential modifiers of SCN1A‐related disease severity.
Identifying turmeric powder by source and metanil yellow adulteration levels using near infrared spectra and PCA-SIMCA modeling.

Turmeric sourced from six retailers was processed into a powder and adulterated with metanil yellow at concentrations of 0.0-30% w/w. A handheld near infrared (NIR) spectrometer was used to obtain spectral scans of the samples, which were preprocessed using Savitzky-Golay first derivative (SG1) approximation using 61 smoothing points and second order polynomial. The preprocessed spectra were analyzed using principal component analysis (PCA) followed by classification by soft independent modeling class analogy (SIMCA) and used to group the adulterated turmeric powder samples according to the source (i.e., processor) of adulteration. Results showed the first principal component (PC1) of PCA models was sensitive to adulteration level, but when coupled with SIMCA, un-adulterated and adulterated samples could be classified according to their source despite having high levels of metanil yellow. At 5% level of significance, all of the samples were correctly classed for origin during validation. Some samples were classified under two groups, indicating possible inherent similarities. When PCA model was built using only un-adulterated samples, the PCA-SIMCA model could not classify the adulterated samples, but could classify those with very low levels [ 2% (w/w)] of metanil yellow, allowing for segregation of adulterated samples but not identification of sources.The combination of NIR and PCA-SIMCA modeling is a great tool to detect not only adulterated turmeric powder but, potentially, deter it in the future as the source of adulterated food can be traced back to the source of adulteration.
Design and Synthesis of a Compound Library Exploiting 5-Methoxyleoligin as Potential Cholesterol Efflux Promoter

5-Methoxyleoligin and leoligin are natural occurring lignans derived from Edelweiss (Leontopodium nivale ssp. alpinum), displaying potent pro-angiogenic and pro-arteriogenic activity. Cholesterol efflux from macrophages is associated with reverse cholesterol transport which inhibits the development of cardiovascular disease. Within this study, we developed a modular and stereoselective total synthesis of 5-methoxyleoligin which can be readily used to prepare a novel compound library of related analogs. The target 5-methoxyleoligin was synthesized exploiting a recently disclosed modular route, which allows also rapid synthesis of analogous compounds. All obtained products were tested towards macrophage cholesterol efflux enhancement and the performance was compared to the parent compound leoligin. It was found that variation on the aryl moiety in 2-position of the furan ring allows optimization of the activity profile, whereas the ester-functionality does not tolerate significant alterations.
The histone demethylase JMJD2B regulates endothelial-to-mesenchymal transition

Significance Here we show that the histone demethylase JMJD2B is induced in endothelial cells by EndMT provoking stimuli and thereby contributes to the acquirement of a mesenchymal/smooth muscle phenotype. Silencing of JMJD2B inhibited EndMT in vitro and reduced the induction of EndMT after myocardial infarction in vivo. Inhibition of JMJD2B prevents the demethylation of repressive trimethylated histone H3 at lysine 9 (H3K9me3) at promoters of mesenchymal and EndMT-controlling genes, thereby reducing EndMT. Together, our study reports a crucial role for JMJD2B in controlling histone modifications during the transition of endothelial cells toward a mesenchymal phenotype. Endothelial cells play an important role in maintenance of the vascular system and the repair after injury. Under proinflammatory conditions, endothelial cells can acquire a mesenchymal phenotype by a process named endothelial-to-mesenchymal transition (EndMT), which affects the functional properties of endothelial cells. Here, we investigated the epigenetic control of EndMT. We show that the histone demethylase JMJD2B is induced by EndMT-promoting, proinflammatory, and hypoxic conditions. Silencing of JMJD2B reduced TGF-β2-induced expression of mesenchymal genes, prevented the alterations in endothelial morphology and impaired endothelial barrier function. Endothelial-specific deletion of JMJD2B in vivo confirmed a reduction of EndMT after myocardial infarction. EndMT did not affect global H3K9me3 levels but induced a site-specific reduction of repressive H3K9me3 marks at promoters of mesenchymal genes, such as Calponin (CNN1), and genes involved in TGF-β signaling, such as AKT Serine/Threonine Kinase 3 (AKT3) and Sulfatase 1 (SULF1). Silencing of JMJD2B prevented the EndMT-induced reduction of H3K9me3 marks at these promotors and further repressed these EndMT-related genes. Our study reveals that endothelial identity and function is critically controlled by the histone demethylase JMJD2B, which is induced by EndMT-promoting, proinflammatory, and hypoxic conditions, and supports the acquirement of a mesenchymal phenotype.
Molecular Characterization and Disease Control of Stem Canker on Royal Poinciana (Delonix regia) Caused by Neoscytalidium dimidiatum in the United Arab Emirates

In the United Arab Emirates (UAE), royal poinciana (Delonix regia) trees suffer from stem canker disease. Symptoms of stem canker can be characterized by branch and leaf dryness, bark lesions, discoloration of xylem tissues, longitudinal wood necrosis and extensive gumming. General dieback signs were also observed leading to complete defoliation of leaves and ultimately death of trees in advanced stages. The fungus, Neoscytalidium dimidiatum DSM 109897, was consistently recovered from diseased royal poinciana tissues; this was confirmed by the molecular, structural and morphological studies. Phylogenetic analyses of the translation elongation factor 1-a (TEF1-α) of N. dimidiatum from the UAE with reference specimens of Botryosphaeriaceae family validated the identity of the pathogen. To manage the disease, the chemical fungicides, Protifert®, Cidely® Top and Amistrar® Top, significantly inhibited mycelial growth and reduced conidial numbers of N. dimidiatum in laboratory and greenhouse experiments. The described “apple bioassay” is an innovative approach that can be useful when performing fungicide treatment studies. Under field conditions, Cidely® Top proved to be the most effective fungicide against N. dimidiatum among all tested treatments. Our data suggest that the causal agent of stem canker disease on royal poinciana in the UAE is N. dimidiatum.