Miracle-dz/UniFAR-FTUs huggingface dataset:
Numerical Study of Laminar Natural Convection in an Enclosure with Conjugate Heat Transfer

The study of a laminar natural convection in a square enclosure with conjugate boundary condition is done numerically. The top wall and right side wall of the enclosure are considered to have some finite thickness. The problem is solved using finite volume method and the multi-block method is used for meshing the domain. Various cases are considered by varying the parameters like characteristics Reynolds number, conductivity ratio and the wall thickness to analyse their effect on the heat transfer and flow characteristics. Reynolds number is taken equal to 10e3, 5 * 10e3 and 10e4 to constrain the flow as laminar in enclosure. The result shows some significant dependence on Reynolds number in the flow and temperature field inside the domain. An effect of insulation near the top wall is also studied and compared with the case of without insulation by varying the same parameters. It is to be noted that the average temperature inside the enclosure is reduced considerably due to the insulation.
FOXO3 Deficiency in Neutrophils Drives Colonic Inflammation and Tumorigenesis

Inflammatory bowel disease (IBD), characterized by infiltration of polymorphonuclear neutrophils (PMNs), increases the risk of colon cancer. PMN activation corresponds to the accumulation of intracellular Lipid Droplets (LDs). As increased LDs are negatively regulated by transcription factor Forkhead Box O3 (FOXO3), we aim to determine the significance of this regulatory network in PMN-mediated IBD and tumorigenesis. Affected tissue of IBD and colon cancer patients, colonic and infiltrated immune cells, have increased LDs’ coat protein, PLIN2. Mouse peritoneal PMNs with stimulated LDs and FOXO3 deficiency have elevated transmigratory activity. Transcriptomic analysis of these FOXO3-deficient PMNs showed differentially expressed genes (DEGs; FDR < 0.05) involved in metabolism, inflammation, and tumorigenesis. Upstream regulators of these DEGs, similar to colonic inflammation and dysplasia in mice, were linked to IBD and human colon cancer. Additionally, a transcriptional signature representing FOXO3-deficient PMNs (PMN-FOXO3389) separated transcriptomes of affected tissue in IBD (p = 0.00018) and colon cancer (p = 0.0037) from control. Increased PMN-FOXO3389 presence predicted colon cancer invasion (lymphovascular p = 0.015; vascular p = 0.046; perineural p = 0.03) and poor survival. Validated DEGs from PMN-FOXO3389 (P2RX1, MGLL, MCAM, CDKN1A, RALBP1, CCPG1, PLA2G7) are involved in metabolism, inflammation, and tumorigenesis (p < 0.05). These findings highlight the significance of LDs and FOXO3-mediated PMN functions that promote colonic pathobiology.
Analysis of Biochemical and Antimicrobial Properties of Bioactive Molecules of Argemone mexicana

This study identified phytochemicals in Argemone mexicana (A. mexicana) extracts that are responsible for its medicinal properties, and the best solvent for their extraction. The extracts of the stem, leaves, flowers, and fruits of A. mexicana were prepared at low (corresponding to room temperature) and high temperatures (corresponding to the boiling points) in various solvents, viz., hexane, ethyl acetate, methanol, and H2O. The UV-visible absorption spectra of various phytoconstituents in the isolated extracts were determined through spectrophotometry. Qualitative tests for the screening of phytoconstituents in the extracts were performed to identify various phytochemicals. We identified the presence of terpenoids, alkaloids, cardiac glycosides, and carbohydrates in the plant extracts. The antioxidant and anti-human immunodeficiency virus type 1 reverse transcriptase (anti-HIV-1RT) potential, as well as the antibacterial activity of various A. mexicana extracts were determined. These extracts showed strong antioxidant activities. The extracts exhibited antimicrobial activities against Salmonella typhi, Staphylococcus epidermis, Citrobacter, Neisseria gonorrhoeae, and Shigella flexineri. These extracts significantly inhibited HIV-1 reverse transcriptase activity. The aqueous leaf extract prepared at a temperature equivalent to the boiling point, i.e., 100 °C, was identified to be the most active against pathogenic bacteria and HIV-1 RT.
The Epidermal Transcriptome Analysis of a Novel c.639_642dup LORICRIN Variant-Delineation of the Loricrin Keratoderma Pathology

Loricrin keratoderma (LK) is a rare autosomal dominant genodermatosis caused by LORICRIN gene mutations. The pathogenesis of the disease is not yet fully understood. So far, only 10 pathogenic variants in LORICRIN have been described, with all of them but one being deletions or insertions. The significance of rare nonsense variants remains unclear. Furthermore, no data regarding the RNA expression in affected patients are available. The aim of this study is to describe the two variants in the LORICRIN gene found in two distinct families: the novel pathogenic variant c. 639_642dup and a rare c.10C > T (p.Gln4Ter) of unknown significance. We also present the results of the transcriptome analysis of the lesional loricrin keratoderma epidermis of a patient with c. 639_642dup. We show that in the LK lesion, the genes associated with epidermis development and keratocyte differentiation are upregulated, while genes engaged in cell adhesion, differentiation developmental processes, ion homeostasis and transport, signaling and cell communication are downregulated. In the context of the p.Gln4Ter clinical significance evaluation, we provide data indicating that LORICRIN haploinsufficiency has no skin consequences. Our results give further insight into the pathogenesis of LK, which may have therapeutic implications in the future and important significance in the context of genetic counseling.
Effect of α-Al2O3 Additive on the Surface Micro-Arc Oxidation Coating of Ti6Al4V Alloy

α-Al2O3 nanoparticles can enter a micro-arc oxidation coating and participate in the coating-formation process through chemical reaction or physical–mechanical combination in the electrolyte. The prepared coating has high strength, good toughness and excellent wear and corrosion resistance. In this paper, 0, 1, 3 and 5 g/L of α-Al2O3 nanoparticles were added to a Na2SiO3-Na(PO4)6 electrolyte to study the effect on the microstructure and properties of a Ti6Al4V alloy micro-arc oxidation coating. The thickness, microscopic morphology, phase composition, roughness, microhardness, friction and wear properties and corrosion resistance were characterized using a thickness meter, scanning electron microscope, X-ray diffractometer, laser confocal microscope, microhardness tester and electrochemical workstation. The results show that surface quality, thickness, microhardness, friction and wear properties and corrosion resistance of the Ti6Al4V alloy micro-arc oxidation coating were improved by adding α-Al2O3 nanoparticles to the electrolyte. The nanoparticles enter the coatings by physical embedding and chemical reaction. The coatings’ phase composition mainly includes Rutile-TiO2, Anatase-TiO2, α-Al2O3, Al2TiO5 and amorphous phase SiO2. Due to the filling effect of α-Al2O3, the thickness and hardness of the micro-arc oxidation coating increase, and the surface micropore aperture size decreases. The roughness decreases with the increase of α-Al2O3 additive concentration, while the friction wear performance and corrosion resistance are improved.
Silent Owl Flight: The Effect of the Leading Edge Comb on the Gliding Flight Noise

The feathers of owls possess three adaptations that are held responsible for their quiet flight. These are a comb-like structure at the leading edge of the wing, fringes at the trailing edge and a soft and porous upper surface of the wing. To investigate the effect of the first adaptation, the leading edge comb, on the aerodynamic performance and the noise generation during gliding flight, wind tunnel measurements were performed on prepared wings of a Barn owl (Tyto alba) with and without the comb. In agreement with existing studies it was found that the leading edge comb causes a small increase in lift. Additionally, at high angles of attack the results from the acoustic measurements indicate that the presence of the comb leads to a reduction in gliding flight noise. Although this reduction is relatively small, it further helps the owl to approach its prey during the final stages of the landing phase.
Correlated biodiversity change between plant and insect assemblages resurveyed after 80 years across a dynamic habitat mosaic

Abstract Historical data on co‐occurring taxa are extremely rare. As such, the extent to which distinct co‐occurring taxa experience similar long‐term patterns in species richness and compositional change (e.g., when exposed to a changing environment) is not clear. Using data from a diverse ecological community surveyed in the 1930s and resurveyed in the 2010s, we investigated whether local plant and insect assemblages displayed cross‐taxon congruence—that is, spatiotemporal correlation in species richness and compositional change—across six co‐occurring taxa: vascular plants, non‐vascular plants, grasshoppers and crickets (Orthoptera), ants (Hymenoptera: Formicinae), hoverflies (Diptera: Syrphidae), and dragonflies and damselflies (Odonata). All taxa exhibited high levels of turnover across the ca. 80‐year time period. Despite minimal observed changes at the level of the whole study system, species richness displayed widespread cross‐taxon congruence (i.e., correlated temporal change) across local assemblages within the study system. Hierarchical logistic regression models suggest a role for shared responses to environmental change underlying cross‐taxon correlations and highlight stronger correlations between vascular plants and their direct consumers, suggesting a possible role for biotic interactions between these groups. These results provide an illustration of cross‐taxon congruence in biodiversity change using data unique in its combination of temporal and taxonomic scope, and highlight the potential for cascading and comparable effects of environmental change (abiotic and biotic) on co‐occurring plant and insect communities. However, analyses of historical resurveys based on currently available data come with inherent uncertainties. As such, this study highlights a need for well‐designed experiments, and monitoring programs incorporating co‐occurring taxa, to determine the underlying mechanisms and prevalence of congruent biodiversity change as anthropogenic environmental change accelerates apace.
Synergistic Effects of Kaolin and Silicon Nanoparticles for Ameliorating Deficit Irrigation Stress in Maize Plants by Upregulating Antioxidant Defense Systems

Water deficit is a significant environmental stress that has a negative impact on plant growth and yield. In this research, the positive significance of kaolin and SiO2 nanoparticles in moderating the detrimental effects of water deficit on maize plant growth and yield is investigated. The foliar application of kaolin (3 and 6%) and SiO2 NPs (1.5 and 3 mM) solutions increased the growth and yield variables of maize plants grown under normal conditions (100% available water) and drought stress conditions (80 and 60% available water (AW)). In addition, plants treated with SiO2 NPs (3 mM) demonstrated increased levels of important osmolytes, such as proline and phenol, and maintained more of their photosynthetic pigments (net photosynthetic rate (PN), stomatal conductance (gs), intercellular CO2 concentration (Ci), and transpiration rate (E)) than with other applied treatments under either stress or non-stress conditions. Furthermore, the exogenous foliar application of kaolin and SiO2 NPs also reduced the amounts of hydroxyl radicals (OH), superoxide anions (O2), hydrogen peroxide (H2O2), and lipid peroxidation in maize plants experiencing a water deficit. In contrast, the treatments led to an increase in the activity of antioxidant enzymes such as peroxidase (POX), ascorbate peroxidase (APX), glutathione peroxidase (GR), catalase (CAT), and superoxide dismutase (SOD). Overall, our findings indicate the beneficial impact of the application of kaolin and silicon NPs, particularly the impact of SiO2 NPs (3 mM) on managing the negative, harmful impacts of soil water deficit stress in maize plants.
Multi-Omics Analysis Revealed Increased De Novo Synthesis of Serine and Lower Activity of the Methionine Cycle in Breast Cancer Cell Lines

A pipeline for metabolomics, based on UPLC-ESI-MS, was tested on two malignant breast cancer cell lines of the sub-types ER(+), PR(+), and HER2(3+) (MCF-7 and BCC), and one non-malignant epithelial cancer cell line (MCF-10A). This allowed us to quantify 33 internal metabolites, 10 of which showed a concentration profile associated with malignancy. Whole-transcriptome RNA-seq was also carried out for the three mentioned cell lines. An integrated analysis of metabolomics and transcriptomics was carried out using a genome-scale metabolic model. Metabolomics revealed the depletion of several metabolites that have homocysteine as a precursor, which was consistent with the lower activity of the methionine cycle caused by lower expression of the AHCY gene in cancer cell lines. Increased intracellular serine pools in cancer cell lines appeared to result from the over-expression of PHGDH and PSPH, which are involved in intracellular serine biosynthesis. An increased concentration of pyroglutamic acid in malignant cells was linked to the overexpression of the gene CHAC1.
Protective effect of IAXO-102 on renal ischemia-reperfusion injury in rats

Ischemia/reperfusion injury (IRI) is a common cause of kidney damage, characterized by oxidative stress and inflammation. In this study, we investigated the potential protective effects of IAXO-102, a chemical compound, on experimentally induced IRI in male rats. The bilateral renal IRI model was used, with 24 adult male rats randomly divided into four groups (N=6): sham group (laparotomy without IRI induction), control group (laparotomy plus bilateral IRI for 30 minutes followed by 2 hours of reperfusion), vehicle group (same as control but pre-injected with the vehicle), and treatment group (similar to control but pre-injected with IAXO-102). We measured several biomarkers involved in IRI pathophysiology using enzyme-linked immunosorbent assay (ELISA), including High mobility group box1 (HMGB1), nuclear factor kappa b-p65 (NF-κB p65), interleukin beta-1 (IL-1β), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), 8-isoprostane, Bcl-2 associated X protein (BAX), heat shock protein 27 (HSP27), and Bcl-2. Statistical analysis was performed using one-way ANOVA and Tukey post hoc tests. Our results showed that IAXO-102 significantly improved kidney function, reduced histological alterations, and decreased the inflammatory response (IL-1, IL-6, and TNF) caused by IRI. IAXO-102 also decreased apoptosis by reducing pro-apoptotic Bax and increasing anti-apoptotic Bcl-2 without impacting HSP27. In conclusion, our findings suggest that IAXO-102 had a significant protective effect against IRI damage in the kidneys.
Isoscapes of remnant and restored Hawaiian montane forests reveal differences in biological nitrogen fixation and carbon inputs

Deforestation and subsequent land-use conversion has altered ecosystems and led to negative effects on biodiversity. To ameliorate these effects, nitrogen-fixing (N2-fixing) trees are frequently used in the reforestation of degraded landscapes, especially in the tropics; however, their influence on ecosystem properties such as nitrogen (N) availability and carbon (C) stocks are understudied. Here, we use a 30-y old reforestation site of outplanted native N2-fixing trees (Acacia koa) dominated by exotic grass understory, and a neighboring remnant forest dominated by A. koa canopy trees and native understory, to assess whether restoration is leading to similar N and C biogeochemical landscapes and soil and plant properties as a target remnant forest ecosystem. We measured nutrient contents and isotope values (δ15N, δ13C) in soils, A. koa, and non-N2-fixing understory plants (Rubus spp.) and generated δ15N and δ13C isoscapes of the two forests to test for (1) different levels of biological nitrogen fixation (BNF) and its contribution to non-N2-fixing understory plants, and (2) the influence of historic land conversion and more recent afforestation on plant and soil δ13C. In the plantation, A. koa densities were higher and foliar δ15N values for A. koa and Rubus spp. were lower than in the remnant forest. Foliar and soil isoscapes also showed a more homogeneous distribution of low δ15N values in the plantation and greater influence of A. koa on neighboring plants and soil, suggesting greater BNF. Foliar δ13C also indicated higher water use efficiency (WUEi) in the plantation, indicative of differences in plant-water relations or soil water status between the two forest types. Plantation soil δ13C was higher than the remnant forest, consistent with greater contributions of exotic C4-pasture grasses to soil C pools, possibly due to facilitation of non-native grasses by the dense A. koa canopy. These findings are consequential for forest restoration, as they contribute to the mounting evidence that outplanting N2-fixing trees produces different biogeochemical landscapes than those observed in reference ecosystems, thereby influencing plant-soil interactions which can influence restoration outcomes.
Characterization of Chromatin Accessibility in Fetal Bovine Chondrocytes

Simple Summary Cartilage development plays a crucial role in human health and animal agriculture, and fetal development takes on particular importance in this process. In this study, we identified open chromatin regions in bovine fetal chondrocytes and peaks enriched in the promoter region. By integrating chromatin accessibility with transcriptome data and Genome-Wide Association Studies results of bovine stature traits, we further described the regulatory functions of these regulatory elements defined by open chromatin accessibility. Overall, these findings provide valuable information for understanding the regulatory mechanisms in cartilage development and conducting beef cattle genetic improvement programs. Abstract Despite significant advances of the bovine epigenome investigation, new evidence for the epigenetic basis of fetal cartilage development remains lacking. In this study, the chondrocytes were isolated from long bone tissues of bovine fetuses at 90 days. The Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) and transcriptome sequencing (RNA-seq) were used to characterize gene expression and chromatin accessibility profile in bovine chondrocytes. A total of 9686 open chromatin regions in bovine fetal chondrocytes were identified and 45% of the peaks were enriched in the promoter regions. Then, all peaks were annotated to the nearest gene for Gene Ontology (GO) and Kyoto Encylopaedia of Genes and Genomes (KEGG) analysis. Growth and development-related processes such as amide biosynthesis process (GO: 0043604) and translation regulation (GO: 006417) were enriched in the GO analysis. The KEGG analysis enriched endoplasmic reticulum protein processing signal pathway, TGF-β signaling pathway and cell cycle pathway, which are closely related to protein synthesis and processing during cell proliferation. Active transcription factors (TFs) were enriched by ATAC-seq, and were fully verified with gene expression levels obtained by RNA-seq. Among the top50 TFs from footprint analysis, known or potential cartilage development-related transcription factors FOS, FOSL2 and NFY were found. Overall, our data provide a theoretical basis for further determining the regulatory mechanism of cartilage development in bovine.
Quantification of multipartite entanglement with the use of LOCC transformation

Entanglement is known to be a promising resource which enables us to execute various quantum tasks. Its quantification has been successful for bipartite pure states. However, the quantification of entanglement for multipartite states has been in a difficult situation. The difficulty is due to the difference of structures between bipartite and multipartite states. In the present thesis, we introduce a new approach for this problem. We give a necessary and sufficient condition of the possibility of a deterministic LOCC transformation of three-qubit pure states. This condition is expressed as a transformation law of six entanglement parameters jAB, jAC , jBC , jABC , J5 and Qe, where jAB, jAC and jBC are bipartite entanglements, jABC is a tripartite entanglement, J5 is a tripartite parameter which means a kind of phase, and Qe is a new tripartite parameter which means a kind of charge. This fact shows that three-qubit pure states are a partially ordered set parametrized by the six entanglement parameters. The order of the partially ordered set is defined by the possibility of a deterministic LOCC transformation from a state to another state. In this sense, the present condition is an extension of Nielsen’s work [14] to three-qubit pure states. We also clarify the rules of transfer and dissipation of entanglement. These rules guarantee that the tripartite entanglement can be transformed into bipartite entanglements, but that the bipartite entanglements cannot be transformed into the tripartite entanglement. This implies that the tripartite entanglement is a higher entity than the bipartite entanglements. With a new combination of the six entanglement parameters, the present condition can be simplified enough to determine easily whether a deterministic LOCC transformation from an arbitrary state |ψ〉 to another arbitrary state |ψ′〉 is possible or not. Moreover, the minimum number of times of measurements to reproduce an arbitrary deterministic LOCC transformation is given. This is an extension of Horodecki et al.’s work [24] to three-qubit pure states.
Coronary Angiography Upgraded by Imaging Post-Processing: Present and Future Directions

Advances in computer technology and image processing now allow us to obtain from angiographic images a large variety of information on coronary physiology without the use of a guide-wire as a diagnostic information equivalent to FFR and iFR but also information allowing for the performance of a real virtual percutaneous coronary intervention (PCI) and finally the ability to obtain information to optimize the results of PCI. With specific software, it is now possible to have a real upgrading of invasive coronary angiography. In this review, we present the different advances in this field and discuss the future perspectives offered by this technology.