Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

Sebastes schlegelii, an important aquaculture species, has been widely cultured in East Asian countries. With the increase in the cultivation scale, various diseases have become major threats to the industry. Evidence has shown that non-coding RNAs (ncRNAs) have remarkable functions in the interactions between pathogens and their hosts. However, little is known about the mechanisms of circular RNAs (circRNAs) and coding RNAs in the process of preventing pathogen infection in the intestine in teleosts. In this study, we aimed to uncover the global landscape of mRNAs, circRNAs, and microRNAs (miRNAs) in response to Edwardsiella tarda infection at different time points (0, 2, 6, 12, and 24 h) and to construct regulatory networks for exploring the immune regulatory mechanism in the intestine of S. schlegelii. In total, 1,794 mRNAs, 87 circRNAs, and 79 miRNAs were differentially expressed. The differentially expressed RNAs were quantitatively validated using qRT-PCR. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most of the differentially expressed mRNA genes and the target genes of ncRNAs were related to immune signaling pathways, such as the NF-κB signal pathway, pathogen recognition receptors related to signaling pathways (Toll-like receptors and Nod-like receptors), and the chemokine signaling pathway. Based on these differentially expressed genes, 624 circRNA-miRNA pairs and 2,694 miRNA-mRNA pairs were predicted using the miRanda software. Integrated analyses generated 25 circRNA-miRNA-mRNA interaction networks. In a novel_circ_0004195/novel-530/IκB interaction network, novel_530 was upregulated, while its two targets, novel_circ_0004195 and IκB, were downregulated after E. tarda infection. In addition, two circRNA-miRNA-mRNA networks related to apoptosis (novel_circ_0003210/novel_152/apoptosis-stimulating of p53 protein 1) and interleukin (novel_circ_0001907/novel_127/interleukin-1 receptor type 2) were also identified in our study. We thus speculated that the downstream NF-κB signaling pathway, p53 signaling pathway, and apoptosis pathway might play vital roles in the immune response in the intestine of S. schlegelii. This study revealed a landscape of RNAs in the intestine of S. schlegelii during E. tarda infection and provided clues for further study on the immune mechanisms and signaling networks based on the circRNA-miRNA-mRNA axis in S. schlegelii.
Hypermethylation of DHRS3 as a Novel Tumor Suppressor Involved in Tumor Growth and Prognosis in Gastric Cancer

Background/Aims The role of DHRS3 in human cancer remains unclear. Our study explored the role of DHRS3 in gastric cancer (GC) and its clinicopathological significance and associated mechanisms. Materials Bisulfite-assisted genomic sequencing PCR and a Mass-Array system were used to evaluate and quantify the methylation levels of the promoter. The expression levels and biological function of DHRS3 was examined by both in vitro and in vivo assays. A two-way hierarchical cluster analysis was used to classify the methylation profiles, and the correlation between the methylation status of the DHRS3 promoter and the clinicopathological characteristics of GC were then assessed. Results The DHRS3 promoter was hypermethylated in GC samples, while the mRNA and protein levels of DHRS3 were significantly downregulated. Ectopic expression of DHRS3 in GC cells inhibited cell proliferation and migration in vitro, decreased tumor growth in vivo. DHRS3 methylation was correlated with histological type and poor differentiation of tumors. GC patients with high degrees of CpG 9.10 methylation had shorter survival times than those with lower methylation. Conclusion DHRS3 was hypermethylated and downregulated in GC patients. Reduced expression of DHRS3 is implicated in gastric carcinogenesis, which suggests DHRS3 is a tumor suppressor.
Genetic Architectures and Cell-of-Origin in Glioblastoma

An aggressive primary brain cancer, glioblastoma (GBM) is the most common cancer of the central nervous system in adults. However, an inability to identify its cell-of-origin has been a fundamental issue hindering further understanding of the nature and pathogenesis of GBM, as well as the development of novel therapeutic targets. Researchers have hypothesized that GBM arises from an accumulation of somatic mutations in neural stem cells (NSCs) and glial precursor cells that confer selective growth advantages, resulting in uncontrolled proliferation. In this review, we outline genomic perspectives on IDH-wildtype and IDH-mutant GBMs pathogenesis and the cell-of-origin harboring GBM driver mutations proposed by various GBM animal models. Additionally, we discuss the distinct neurodevelopmental programs observed in either IDH-wildtype or IDH-mutant GBMs. Further research into the cellular origin and lineage hierarchy of GBM will help with understanding the evolution of GBMs and with developing effective targets for treating GBM cancer cells.
Modulation of the Gut Microbiota and Liver Transcriptome by Red Yeast Rice and Monascus Pigment Fermented by Purple Monascus SHM1105 in Rats Fed with a High-Fat Diet

Hyperlipidemia can easily cause atherosclerosis and induce cardiovascular and cerebrovascular diseases. Red yeast rice (RYR) contains a variety of active ingredients and is commonly used as medicine and food, and has pharmacological effects such as lowering blood lipids. In this study, we select Monascus strain SHM1105 with a high yield of Monacolin K and monascus pigment (PIG), and studied the effects of the RYR and PIG fermented by this strain on blood lipids, intestinal flora, and liver transcriptome in hyperlipidemia model rats. The experimental results show that, compared with the high-fat model group, the weight growth rate, liver weight ratio, kidney weight ratio, spleen weight ratio, and fat weight ratio of rats in the gavage lovastatin (LOV), RYR, and PIG group were all significantly decreased (p < 0.05). Intervention with RYR and PIG can significantly reduce the serum TC, TG, and LDL-C levels, which has the effect of lowering blood lipids. The 16SrDNA sequencing results showed that the ratio of Firmicutes/Bacteroidetes decreased significantly (p ≤ 0.01) after the intervention of LOV, RYR, and PIG; the abundance of the ratio of Lachnospiraceae, Ruminococcaceae, Prevotellaceae, and Bacteroidales-S24-7-group also changed. The combined analysis of transcriptome and metabolome showed that lovastatin, RYR, and PIG can all improve lipid metabolism in rats by regulating Steroid hormone biosynthesis, Glycerolipid metabolism, and the Arachidonic acid metabolism pathway. In addition, RYR and PIG also have a unique way of regulating blood lipids. Although a lot of research on the lipid-lowering components of Monascus rice and the single pigment component of Monascus has been carried out, the actual application is RYR and pigments as mixtures, as a mixture of RYR and PIG contains a variety of biologically active ingredients, and each component may have a synergistic effect. Hence it has a lipid-lowering mechanism that lovastatin does not have. Therefore, RYR and PIG are effective in reducing lipid potential development and can be utilized in functional foods.
The Fold: Rethinking Interactivity in Data Visualization

We propose the philosophical notion of the fold as an evocative vocabulary for the design and critique of interactive data visualizations. An expanding range of application areas, such as digital art history and literary studies, illustrates the potential of data visualization for research and education in the humanities. Coinciding with the increasing currency of data as evidence in the humanities, this research addresses a growing interest in data visualization for visual analysis and argumentation. For example, cultural collection visualizations promise a range of possibilities for visual and interactive representations of digital cultural heritage, used both for free exploration and focused research. Based on the concept of the fold, prominently advanced by Gilles Deleuze, this paper outlines a critical framework that draws attention towards the complexity of the underlying data. The fold offers a way to analyze and conceptualize visualizations through the lens of three integrated operations: explication, implication, and complication. It is an opportunity to think of interactive visualizations as portals into coherent, elastic, and ultimately infinite information spaces. Accordingly, it rejects the separation between interactivity and visual encoding and draws attention to the transitions between multiple states of a visualization. We identify design patterns of the fold in data visualizations, devise a framework for the critical interpretation of interactivity in data visualization, and demonstrate the implications for the digital humanities.
Inside the Trading Zone: Thinkering in a Digital History Lab

The goal of this article is to critically reflect on the practical and epistemological challenges of doing historical research in the digital age. The analysis is based on a case study of the Doctoral Training Unit (DTU) “Digital History and Hermeneutics”, an interdisciplinary research and training programme that was established at the Luxembourg Centre for Contemporary and Digital History (C ² DH) of the University of Luxembourg. The DTU is designed as interdisciplinary trading zone that applies the method of “thinkering” – the tinkering with technology combined with the critical reflection on the practice of doing digital history. Based on this case study, the article addresses the question of how to constitute an interdisciplinary trading zone in practice and how to situate this trading zone in physical working environments, like a Digital History Lab and shared office space.
Morphology Control in Solution‐Processed Bulk‐Heterojunction Solar Cell Mixtures

The efficiency of bulk‐heterojunction solar cells is very sensitive to the nanoscale structure of the active layer. In the past, the final morphology in solution‐processed devices has been controlled by varying the casting solvent and by curing the layer using heat tempering or solvent soaking. A recipe for making the “best‐performing” morphology can be achieved using these steps. This article presents a review of several new techniques that have been developed to control the morphology in polymer/fullerene heterojunction mixtures. The techniques fall into two broad categories. First, the morphology can be controlled by preparing nanoparticle suspensions of one component. The size and shape of the nanoparticles in solution determine the size and shape of the domain in a mixed layer. Second, the morphology can be controlled by adding a secondary solvent or an additive that more strongly affects one component of the mixture during drying. In both cases, the as‐cast efficiency of the solar cell is improved with respect to the single‐solvent case, which strongly argues that morphology control is an issue that will receive increasing attention in future research.
Diurnal Variation and Chemical Characteristics of Atmospheric Aerosol Particles and Their Source Fingerprints at Xiamen Bay

This study investigated the diurnal variation of mass concentration and chemical composition of atmospheric aerosol particles sampled at Xiamen Bay, located on the west bank of the Taiwan Strait. Atmospheric PM10 samples were collected at ten particulate matter (PM) sampling sites at Xiamen Bay, including five sites at the Kinmen Islands and five sites in urban Xiamen, at both daytime and nighttime during the regular and intensive sampling periods. Regular sampling was conducted to collect PM10 with high-volume samplers three times a month from April 2009 to April 2010, while intensive sampling was conducted to collect PM2.5 and PM2.5–10 with dichotomous samplers in the spring and winter of 2009 and 2010. This study further selected ten major emission sources (e.g., stone processing, power plants, soil dusts, and biomass burning) at Xiamen Bay to collect fugitive particulate samples which were then resuspended in a self-designed resuspension chamber to collect PM2.5 and PM2.5–10 with two separate dichotomous samplers for further chemical analysis. The results from PM10 sampling indicated that atmospheric aerosol particles tended to be accumulated in Xiamen Bay all year round, but especially in spring and winter. A significant diurnal variation of PM10 was observed, with higher PM10 concentrations in the daytime during the regular sampling periods. The chemical analysis results showed that the major chemical components of PM10 were SO4 2– , NO3 – , NH4 + , OC, EC, and crustal elements (Ca, Mg, Fe, and Al), which were usually higher in the daytime than at night at Xiamen Bay. The differences were most pronounced at night, where the concentrations of most anthropogenic elements (Ni, Cu, As, and V) were higher than those in the daytime. The elemental composition of PM emitted from stone processing and the cement industry were dominated by crustal elements, particularly Ca, whereas the profile of top-soil mainly contained Al and Ca. The profiles of industrial sources were dominated by secondary inorganic aerosols and EC. Moreover, construction and road dusts contained large amounts of Fe and Al, while biomass burning released large amounts of K, OC, and SO4 2–
Finite volume and spectral methods applied to Pb-30%TI alloy solidification

Convection developing in the melted alloy Pb-30 %Tl is studied under up-ward directional solidification conditions. Numerical investigation is based on the collocation Chebychev methods and the enthalpy-porosity formulation associated to the finite volume approximation. The method is able to describe properly various convective solutal patterns and transitions according to gravity level (symmetric, asymmetric, time-dependent). Signature of on the solidification front unsteadiness in terme of the striations is exibited.
Effect of Isoalkyl Lactates as Pendant Group on Poly(acrylic acid)

Esterification of lactic acid with secondary alcohols such as isopropanol and isobutanol followed by acrylic acid was carried out by azeotropic distillation. Mass, Fourier Transform Infrared,1H-Nuclear Magnetic Resonance and proton decoupled 13C-Nuclear Magnetic Resonance spectroscopic techniques confirmed the formation of isoalkyl lactates and isoalkyl lactate acrylates. Poly(isoalkyl lactate acrylate)s were synthesized by free radical solution polymerization technique and molecular weights of the polymers were determined by gel permeation chromatography. Wide angle X-ray Diffraction studies indicated the polymers were amorphous and their average molecular interchain spacing () value was calculated from 2θ value of amorphous halo. Moisture absorption and glass transition temperature of the polymers decreased with increase in number of carbon atoms of isoalkyl groups and value. Moisture absorption of the polymers were in the range of 2 to 6% (w/w) depending upon the isoalkyl lactate group, relative humidity and time. The moisture absorption of polymers followed Fikian process. Two-step thermal degradation was observed in nitrogen atmosphere and the thermal stability trend can be explained on the basis of value.
Ibuprofen microcapsules : the effect of production variables on microcapsule properties

Ibuprofen was microencapsulated with ethylcellulose using the solvent evaporation method. The effect of production variables on the properties of the microcapsules and drug release from them is described. Results show that size distribution, drug loading and the amount of free drug on the surface of the microcapsules is affected by production variables. The release of drug from the microcapsules was observed to be strongly influenced by parameters affecting the presence of uncoated drug on the microcapsule surface.
Diatomics‐in‐molecules potential surfaces for the triatomic rare gas halides: Rg2X

Potential energy surfaces have been calculated for the lowest nine electronic states of Ne2F, Ar2F, Kr2F, and Kr2Cl, including spin–orbit coupling. The diatomics‐in‐molecules (DIM) method used takes advantage of the accurate ab initio potential curves now becoming available for the constituent diatomics. In the case of Ar2F, the DIM results are in close agreement with more elaborate calculations. DIM calculations, for a minimum of effort, supply the potential energy surfaces needed for calculating absorption and emission spectra as well as molecular dynamics.
MICROWAVE ASSISTED SYNTHESIS OF α,α′-BIS(BENZYLIDENE)KETONES IN DRY MEDIA*

ABSTRACT Aromatic aldehydes undergo cross-aldol condensation with ketones in the presence of KF-Al2O3 under microwave irradiation in solvent-free conditions to afford the corresponding α,α′-bis(benzylidene) alkanones in high yields. *IICT Communication No. 4420.
Correlation between material composition, processing, chemical bonding state, and electrochemical migration failure rate in isolating compounds of high density microelectronics systems

Metals can exhibit dendritic short-circuit growth caused by electrochemical migration in conductor-insulator structures, which may result in failures and reliability problems in microcircuits. The classical model of electrochemical migration has been well known for several decades. This process is a transport of metal ions between two metallization stripes under bias through a continuous aqueous electrolyte. Due to the electrodeposition at the cathode, dendrites and dendrite-like deposits are formed. Ultimately, such a deposit can lead to a short circuit in the device and can cause catastrophic failure. A few anomalous and newly discovered phenomena have initiated to perform some revisions and to add supplementary models to the conventional one. Recent investigations have demonstrated that not only metallic components, but also oxides from the isolating layers can take part in the formation of migrated shorts, after a chemical reduction process. Material design aspects need to clarify the correlation between material composition, processing, chemical bonding state, and electrochemical migration failure rate in isolating compounds: this is the scope of the present study.
Direct parameterization of the pressure-dependent volume by using an inverted approximate Vinet equation of state

Parametric refinement is used for the simultaneous modeling of a series of diffraction data, replacing single independent parameters with physical or empirical equations that are valid for the full sequence of data. For the parametric treatment of diffraction data at high pressure, pressure-dependent constraints can be introduced in the form of an equation of state (EoS). However, the parameterization needs inverse functions of the EoS and most of them are not analytically invertible. In order to overcome this drawback, Taylor series expansions of different orders of the Vinet EoS were calculated and analytically inverted. It is shown that the inverted third-order Vinet EoS approximation, in its volume and linearized version, is applicable to a wide range of materials under high pressure.
Molecular dynamics of a model anisotropic system

The molecular dynamics method has been used to study a model system of 1000 symmetric top particles placed at the sites of a cubic lattice and interacting with the pair potential Uij = - e ij P 2(cos β ij ). Here e ij is a positive constant, e, for neighbouring sites and zero otherwise. The equations of motion are written in the quaternion representation and contact is made with the more familiar Euler parameterization of rotations. In particular, explicit expressions are given for the Wigner rotation matrices in terms of quaternions. The model is known from Monte Carlo simulations to possess an orientational phase transition and this fact is confirmed. Both static and dynamic properties have been calculated for a few selected temperatures. The singlet orientational distribution function has been obtained as a two dimensional histogram and order parameters ⟨P 2⟩, ⟨P 4⟩, ⟨P 6⟩, have been calculated. It is shown that the appropriate way to describe the orientational dynamics in uniaxial systems of cylindric.
Comparison of conventional C-MAC video laryngoscope guided intubation by anesthesia trainees with and without Frova endotracheal introducer: A randomized clinical trial

Background and Aims: Successful intubation with video laryngoscopes necessitates good hand-eye coordination and the use of intubation adjuncts like bougie and stylet. We proposed this study to find whether using Frova introducer with C-MAC video laryngoscope will reduce the intubation time in trainee anesthesiologists. Material and Methods: We enrolled 140 adults without any difficult airway predictors. They were randomly assigned to undergo C-MAC video laryngoscope guided intubation by anesthesia residents using tracheal tube preloaded over Frova introducer (n = 70) or without Frova introducer (n = 70). Primary outcome was the intubation time. Secondary outcomes were the number of redirections of tracheal tube or Frova introducer toward glottis, need for external laryngeal maneuvers (ELMs), first attempt intubation success rate, and ease of intubation. Results: The median actual intubation time (IQR) in Frova and non-Frova group, respectively, were 25.46 (28.11–19.80) and 19.96 (26.59–15.52) s (P = 0.001). The number of redirections of TT or Frova introducer toward glottis, first attempt success rate, and ease of intubation were comparable. The need for ELMs [n (%)] was 15 (21.4) and 26 (37.1) in Frova and non-Frova group, respectively (P = 0.04). Conclusion: Frova introducer guided endotracheal intubation with C-MAC videolaryngoscope in patients with normal airways had a marginally prolonged intubation time with a significant reduction in the need of external laryngeal manoeuvres but with a comparable number of redirections and attempts. Further research is needed to generalize these findings to patients with difficult airways.
Comparison of Five different methods of Working length determination: An ex vivo study

Aim: The aim of the study was to determine the accuracy and reliability of working length determination using tactile sensation method, digital radiographic method, and electronic apex locator (EAL) in lower premolars in vivo and to compare the lengths so measured to the working length measured with cone-beam computed tomography (CBCT) and the actual working length (AWL) with magnifying loupe, ex vivo. Materials and Methods: Thirty mandibular premolars scheduled for orthodontic extraction were selected. Under local anesthesia, access cavities were prepared and the working lengths were determined by two operators after blinding, using the tactile sensation method, digital radiographic method (radiovisiography [RVG]), and EAL, and tabulated. The teeth were then extracted and subjected to CBCT to determine the working length (CBCTWL). The AWL of the teeth was measured with a K-file that was inserted into the root canal until the file tip is visible at the apical foramen which was confirmed using a magnifying loupe (×8). The values were then statistically analyzed. Statistical Analysis: The SPSS version 20 software (IBM Corp., Armonk, NY, USA) was used to perform statistical analyses, and the confidence interval was determined at P < 0.05. Kappa test was used for the determination of the intra-observer agreement for each method. The comparison of the means of the groups was assessed using repeated measures ANOVA with Greenhouse–Geisser correction and post hoc Bonferroni test. Results: There is a significant difference between the methods in determining the working length. Based on the correlation values on reliability, CBCT method has a more positive correlation with AWL measured using magnifying loupe, followed by EAL, RVG, and tactile sensation. Conclusion: Hence, we conclude that the use of EAL technique is clinically effective for measuring the working length which correlates more positively with the CBCTWL and AWL. Diagnostic CBCT scan can be used as a reliable method for determining the working length.