Miracle-dz/UniFAR-FTUs huggingface dataset:
Protective Effects of Melatonin Against Aristolochic Acid-Induced Nephropathy in Mice

Melatonin, a pineal hormone, is well known to regulate the sleep–wake cycle. Besides, the hormone has been shown to display pleiotropic effects arising from its powerful anti-oxidant and anti-inflammatory activities. Recent studies have reported that melatonin exerts protective effects in animal models of kidney disease. However, the potential effects of melatonin on aristolochic acid (AA)-induced nephropathy (AAN) have not yet been investigated. Here, we found that the administration of melatonin ameliorated AA-induced renal dysfunction, as evidenced by decreased plasma levels of blood urea nitrogen and creatinine and histopathological abnormalities such as tubular dilatation and cast formation. The upregulation of tubular injury markers after AA injection was reversed by melatonin. Melatonin also suppressed AA-induced oxidative stress, as evidenced by the downregulation of 4-hydroxynonenal and reduced level of malondialdehyde, and modulated expression of pro-oxidant and antioxidant enzymes. In addition, p53-dependent apoptosis of tubular epithelial cells, infiltration of macrophages and CD4+ T cells into damaged kidneys, and renal expression of cytokines and chemokines were inhibited by melatonin. Moreover, melatonin attenuated AA-induced tubulointerstitial fibrosis through suppression of the tumor growth factor-β/Smad signaling pathway. These results suggest that melatonin might be a potential therapeutic agent for AAN.
Direct Patterning and Spontaneous Self-Assembly of Graphene Oxide via Electrohydrodynamic Jet Printing for Energy Storage and Sensing

The macroscopic assembly of two-dimensional materials into a laminar structure has received considerable attention because it improves both the mechanical and chemical properties of the original materials. However, conventional manufacturing methods have certain limitations in that they require a high temperature process, use toxic solvents, and are considerably time consuming. Here, we present a new system for the self-assembly of layer-by-layer (LBL) graphene oxide (GO) via an electrohydrodynamic (EHD) jet printing technique. During printing, the orientation of GO flakes can be controlled by the velocity distribution of liquid jet and electric field-induced alignment spontaneously. Closely-packed GO patterns with an ordered laminar structure can be rapidly realized using an interfacial assembly process on the substrates. The surface roughness and electrical conductivity of the LBL structure were significantly improved compared with conventional dispensing methods. We further applied this technique to fabricate a reduced graphene oxide (r-GO)-based supercapacitor and a three-dimensional (3D) metallic grid hybrid ammonia sensor. We present the EHD-assisted assembly of laminar r-GO structures as a new platform for preparing high-performance energy storage devices and sensors.
The Effect of the Ultra-High-Pressure Homogenization of Protein Encapsulants on the Survivability of Probiotic Cultures after Spray Drying

Interest in probiotic foods and ingredients is increasing as consumers become more aware of their potential health benefits. The production of these products often involves the use of dry culture powders, and the techniques used to produce such powders often suffer from significant losses of viable cells during drying or require the use of expensive drying technologies with limited throughput (e.g., freeze drying). In this study, the authors examined whether culture survivability during spray drying could be increased via the treatment of two common protein encapsulants with ultra-high-pressure homogenization (UHPH). Lactobacillus plantarum NRRL B-1927 (also known as ATCC 10241), a probiotic strain, was suspended in either soy protein isolate (SPI) or whey protein isolate (WPI) which had been either treated with UHPH at 150 Mpa or left untreated as a control. The suspensions were then dried using either concurrent-flow spray drying (CCSD), mixed-flow spray drying (MFSD) or freeze drying (FD) and evaluated for cell survivability, particle size, moisture content and water activity. In all cases, UHPH resulted in equal or greater survivability among spray dried cultures, showed reductions in particle size measures and, except for one marginal case (CCFD SPI), significantly reduced the moisture content of the dried powders. The combination of these findings strongly suggests that UHPH could allow probiotic powder manufacturers to replace freeze drying with spray drying while maintaining or increasing product quality.
A Modular, Reconfigurable Microfabricated Assembly Platform for Microfluidic Transport and Multitype Cell Culture and Drug Testing

Modular microfluidics offer the opportunity to combine the precise fluid control, rapid sample processing, low sample and reagent volumes, and relatively lower cost of conventional microfluidics with the flexible reconfigurability needed to accommodate the requirements of target applications such as drug toxicity studies. However, combining the capabilities of fully adaptable modular microelectromechanical systems (MEMS) assembly with the simplicity of conventional microfluidic fabrication remains a challenge. A hybrid polydimethylsiloxane (PDMS)-molding/photolithographic process is demonstrated to rapidly fabricate LEGO®-like modular blocks. The blocks are created with different sizes that interlock via tongue-and-groove joints in the plane and stack via interference fits out of the plane. These miniature strong but reversible connections have a measured resistance to in-plane and out-of-plane forces of up to >6000× and >1000× the weight of the block itself, respectively. The LEGO®-like interference fits enable O-ring-free microfluidic connections that withstand internal fluid pressures of >120 kPa. A single layer of blocks is assembled into LEGO®-like cell culture plates, where the in vitro biocompatibility and drug toxicity to lung epithelial adenocarcinoma cells and hepatocellular carcinoma cells cultured in the modular microwells are measured. A double-layer block structure is then assembled so that a microchannel formed at the interface between layers connects two microwells. Breast tumor cells and hepatocytes cultured in the coupled wells demonstrate interwell migration as well as the simultaneous effects of a single drug on the two cell types.
Speciation history of European (Anguilla anguilla) and American eel (A. rostrata), analysed using genomic data

Speciation in the ocean could differ from terrestrial environments due to fewer barriers to gene flow. Hence, sympatric speciation might be common, with American and European eel being candidates for exemplifying this. They show disjunct continental distributions on both sides of the Atlantic, but spawn in overlapping regions of the Sargasso Sea from where juveniles are advected to North American, European and North African coasts. Hybridization and introgression are known to occur, with hybrids almost exclusively observed in Iceland. Different speciation scenarios have been suggested, involving either vicariance or sympatric ecological speciation. Using RAD sequencing and whole‐genome sequencing data from parental species and F1 hybrids, we analysed speciation history based on the joint allele frequency spectrum (JAFS) and pairwise sequentially Markovian coalescent (PSMC) plots. JAFS supported a model involving a split without gene flow 150,000–160,000 generations ago, followed by secondary contact 87,000–92,000 generations ago, with 64% of the genome experiencing restricted gene flow. This supports vicariance rather than sympatric speciation, likely associated with Pleistocene glaciation cycles and ocean current changes. Whole‐genome PSMC analysis of F1 hybrids from Iceland suggested divergence 200,000 generations ago and indicated subsequent gene flow rather than strict isolation. Finally, simulations showed that results from both approaches (JAFS and PSMC) were congruent. Hence, there is strong evidence against sympatric speciation in North Atlantic eels. These results reiterate the need for careful consideration of cases of possible sympatric speciation, as even in seemingly barrier‐free oceanic environments palaeoceanographic factors may have promoted vicariance and allopatric speciation.
Gram-Scale Synthesis of Bimetallic ZIFs and Their Thermal Conversion to Nanoporous Carbon Materials

The hybrid metal-organic frameworks (MOFs) with different Zn2+/Co2+ ratios are synthesized at room temperature with deionized water as the solvent. This use of deionized water can increase the yield of hybrid MOFs (up to 65–70%). After the pyrolysis, the obtained nanoporous carbons (NPCs) show a decrease in the surface area, in which the highest surface area is 655 m2 g−1. The as-prepared NPCs are subjected to activation with KOH in order to increase their surface area and convert cobalt nanoparticles (Co NPs) to Co oxides. These activated carbons are applied to electrical double-layer capacitors (EDLCs) and pseudocapacitors due to the presence of CoO and Co3O4 nanoparticles in the carbon framework, leading to significantly enhanced specific capacitance as compared to that of pristine NPCs. This synthetic method can be utilized in future research to enhance pseudocapacitance further while maintaining the maximum surface area of the carbon materials.
PDMAC: A Priority-Based Enhanced TDMA Protocol for Warning Message Dissemination in VANETs

Vehicular ad hoc networks (VANETs) are the key enabling technology for intelligent transportation systems. Carrier-sense multiple access with collision avoidance (CSMA/CA) is the de facto media access standard for inter-vehicular communications, but its performance degrades in high-density networks. Time-division multiple access (TDMA)-based protocols fill this gap to a certain extent, but encounter inefficient clock synchronization and lack of prioritized message delivery. Therefore, we propose a priority-based direction-aware media access control (PDMAC) as a novel protocol for intra-cluster and inter-cluster clock synchronization. Furthermore, PDMAC pioneers a three-tier priority assignment technique to enhance warning messages delivery by taking into account the direction component, message type, and severity level on each tier. Analytical and simulation results validate the improved performance of PDMAC in terms of clock synchronization, channel utilization, message loss rate, end-to-end delays, and network throughput, as compared with eminent VANET MAC protocols.
Characterization of p53 Family Homologs in Evolutionary Remote Branches of Holozoa

The p53 family of transcription factors plays key roles in development, genome stability, senescence and tumor development, and p53 is the most important tumor suppressor protein in humans. Although intensively investigated for many years, its initial evolutionary history is not yet fully elucidated. Using bioinformatic and structure prediction methods on current databases containing newly-sequenced genomes and transcriptomes, we present a detailed characterization of p53 family homologs in remote members of the Holozoa group, in the unicellular clades Filasterea, Ichthyosporea and Corallochytrea. Moreover, we show that these newly characterized homologous sequences contain domains that can form structures with high similarity to the human p53 family DNA-binding domain, and some also show similarities to the oligomerization and SAM domains. The presence of these remote homologs demonstrates an ancient origin of the p53 protein family.
Peroxiredoxin 5 Silencing Sensitizes Dopaminergic Neuronal Cells to Rotenone via DNA Damage-Triggered ATM/p53/PUMA Signaling-Mediated Apoptosis

Peroxiredoxins (Prxs) are a family of thioredoxin peroxidases. Accumulating evidence suggests that changes in the expression of Prxs may be involved in neurodegenerative diseases pathology. However, the expression and function of Prxs in Parkinson’s disease (PD) remains unclear. Here, we showed that Prx5 was the most downregulated of the six Prx subtypes in dopaminergic (DA) neurons in rotenone-induced cellular and rat models of PD, suggesting possible roles in regulating their survival. Depletion of Prx5 sensitized SH-SY5Y DA neuronal cells to rotenone-induced apoptosis. The extent of mitochondrial membrane potential collapse, cytochrome c release, and caspase activation was increased by Prx5 loss. Furthermore, Prx5 knockdown enhanced the induction of PUMA by rotenone through a p53-dependent mechanism. Using RNA interference approaches, we demonstrated that the p53/PUMA signaling was essential for Prx5 silencing-exacerbated mitochondria-driven apoptosis. Additionally, downregulation of Prx5 augmented rotenone-induced DNA damage manifested as induction of phosphorylated histone H2AX (γ-H2AX) and activation of ataxia telangiectasia mutated (ATM) kinase. The pharmacological inactivation of ATM revealed that ATM was integral to p53 activation by DNA damage. These findings provided a novel link between Prx5 and DNA damage-triggered ATM/p53/PUMA signaling in a rotenone-induced PD model. Thus, Prx5 might play an important role in protection against rotenone-induced DA neurodegeneration.
Electroencephalogram Profiles for Emotion Identification over the Brain Regions Using Spectral, Entropy and Temporal Biomarkers

Identifying emotions has become essential for comprehending varied human behavior during our daily lives. The electroencephalogram (EEG) has been adopted for eliciting information in terms of waveform distribution over the scalp. The rationale behind this work is twofold. First, it aims to propose spectral, entropy and temporal biomarkers for emotion identification. Second, it aims to integrate the spectral, entropy and temporal biomarkers as a means of developing spectro-spatial (SS), entropy-spatial (ES) and temporo-spatial (TS) emotional profiles over the brain regions. The EEGs of 40 healthy volunteer students from the University of Vienna were recorded while they viewed seven brief emotional video clips. Features using spectral analysis, entropy method and temporal feature were computed. Three stages of two-way analysis of variance (ANOVA) were undertaken so as to identify the emotional biomarkers and Pearson’s correlations were employed to determine the optimal explanatory profiles for emotional detection. The results evidence that the combination of applied spectral, entropy and temporal sets of features may provide and convey reliable biomarkers for identifying SS, ES and TS profiles relating to different emotional states over the brain areas. EEG biomarkers and profiles enable more comprehensive insights into various human behavior effects as an intervention on the brain.
Assembly of a G-Quadruplex Repair Complex by the FANCJ DNA Helicase and the REV1 Polymerase

The FANCJ helicase unfolds G-quadruplexes (G4s) in human cells to support DNA replication. This action is coupled to the recruitment of REV1 polymerase to synthesize DNA across from a guanine template. The precise mechanisms of these reactions remain unclear. While FANCJ binds to G4s with an AKKQ motif, it is not known whether this site recognizes damaged G4 structures. FANCJ also has a PIP-like (PCNA Interacting Protein) region that may recruit REV1 to G4s either directly or through interactions mediated by PCNA protein. In this work, we measured the affinities of a FANCJ AKKQ peptide for G4s formed by (TTAGGG)4 and (GGGT)4 using fluorescence spectroscopy and biolayer interferometry (BLI). The effects of 8-oxoguanine (8oxoG) on these interactions were tested at different positions. BLI assays were then performed with a FANCJ PIP to examine its recruitment of REV1 and PCNA. FANCJ AKKQ bound tightly to a TTA loop and was sequestered away from the 8oxoG. Reducing the loop length between guanine tetrads increased the affinity of the peptide for 8oxoG4s. FANCJ PIP targeted both REV1 and PCNA but favored interactions with the REV1 polymerase. The impact of these results on the remodeling of damaged G4 DNA is discussed herein.
Feed additive blends fed to nursery pigs challenged with Salmonella

Abstract Salmonella in pigs is a concern for human foodborne salmonellosis. Dietary fungal fermented products, coated butyrate, and organic acids (OAs) may be promising control strategies. The objectives of this study were (i) to evaluate in vitro binding affinity of Salmonella enterica serovar Typhimurium (S. Typh) and Enteritidis (S. Ent), and enterotoxigenic Escherichia coli (ETEC) F4 or F18 to mannan-rich hydrolyzed copra meal (MCM) and fermented rye (FR) with Agaricus subrufescens; and (ii) to assess MCM and FR efficacy to control in vivo S. Typh shedding when combined with OAs and compared with coated butyrate strategy. A 31-d study included 32 pigs [6.29 ± 0.76 kg BW] individually housed and distributed into four dietary treatments: control diet; OA.BU, 4 kg/t OA plus 6 kg/t coated butyrate; OA.MCM, 4 kg/t OA plus 1 kg/t MCM; and OA.FR, 4 kg/t OA plus 2 kg/t FR. All pigs were challenged for 7 d with 1 mL S. Typh (109 colony forming units daily) at 10 d postweaning. Temperature and fecal samples were collected before and after challenge, and fecal Salmonella shedding quantified. Diarrhea scores were monitored daily and growth performance was evaluated weekly. In vitro, culture with MCM and FR showed significant (P < 0.01) binding affinity for both S. Typh and S. Ent, but not for ETEC F4 and F18. In vivo, pigs fed OA.MCM and OA.FR had lower (P < 0.05) shedding and day 3 peak shedding of S. Typh after infections than pigs fed control and OA.BU diets. Pigs fed OA.FR diet tended to have an 18% increase (P = 0.068) in BW on day 14 post first inoculation compared with control and OA.BU, and 19% increased (P = 0.093) final BW at day 21 compared with control. Diarrhea frequency post infection was overall lower (P = 0.006) for OA.FR (18.9%) than OA.BU (44.8%) and OA.MCM (41.7%) while control (28.7%) was not different. In conclusion, FR and MCM show in vitro-binding affinity to Salmonella enterica serovars Typh and Ent. Feeding FR or MCM combined with OA to nursery pigs reduces the peak and averages S. Typh shedding compared with control. Fermented rye with OA tends to improve pig performance after S. Typh challenge.
CD247 expression is associated with differentiation and classification in ovarian cancer

Abstract Ovarian cancer (OC) is one of the most common malignant tumors in female reproductive system and most OC cases are diagnosed at an advanced stage with the overall 5-year survival rate below 40%. The function of CD247 enhances T-cell antigen receptor (TCR) signaling cascade and it is necessary for assembling of the TCR/CD3 complex on the surface of T lymphocytes. It is well established that defective CD247 function leads to impaired activation of T cells upon engagement of the TCR. Flow cytometry was used to examine the difference of CD247+ T lymphocyte between the OC and ovarian cyst, immunohistochemistry analysis was used to investigate the correlation between CD247 expression and clinicopathologic features of epithelial OC patients. Our study showed that the expression of CD247 in peripheral blood lymphocytes from patients with OC is decreased compared with ovarian cyst patients and the expression of CD247 in tumor infiltrating lymphocytes with cancer tissue is decreased compared with adjacent tissues. We showed that abnormal expression of CD247 was related with differentiation and classification in OC. Our findings suggested that CD247-targeted treatment could be used as a potential therapeutic strategy for OC.
Short-term cyclical stretch phosphorylates p38 and ERK1/2 MAPKs in cultured fibroblasts from the hearts of rainbow trout, Oncorhynchus mykiss

ABSTRACT The form and function of the rainbow trout heart can remodel in response to various stressors including changes in environmental temperature and anemia. Previous studies have hypothesized that changes in biomechanical forces experienced by the trout myocardium as result of such physiological stressors could play a role in triggering the remodeling response. However, there has been no work examining the influence of biomechanical forces on the trout myocardium or of the cellular signals that would translate such a stimuli into a biological response. In this study, we test the hypothesis that the application of biomechanical forces to trout cardiac fibroblasts activate the cell signaling pathways associated with cardiac remodeling. This was done by cyclically stretching cardiac fibroblasts to 10% equibiaxial deformation at 0.33 Hz and quantifying the activation of the p38-JNK-ERK mitogen activated protein kinase (MAPK) pathway. After 20 min, p38 MAPK phosphorylation was elevated by 4.2-fold compared to control cells (P<0.05) and after 24 h of stretch, p38 MAPK phosphorylation remained elevated and extracellular-regulated kinase 1/2 was phosphorylated by 2.4-fold compared to control (P<0.05). Together, these results indicate that mechanotransductive pathways are active in cardiac fibroblasts, and lead to the activation of cell signaling pathways involved in cardiac remodeling. Summary: Here we demonstrate that 10% deformation at 0.33 Hz of trout cardiac fibroblasts stimulates p38-JNK-ERK mitogen activated protein kinase pathways. This suggests that mechanotransductive pathways trigger cardiac remodeling in trout.
Epigenetic Regulation in Etiology of Type 1 Diabetes Mellitus

Type 1 diabetes mellitus (T1DM) is caused by an autoimmune destruction of the pancreatic β-cells, a process in which autoreactive T cells play a pivotal role, and it is characterized by islet autoantibodies. Consequent hyperglycemia is requiring lifelong insulin replacement therapy. T1DM is caused by the interaction of multiple environmental and genetic factors. The integrations of environments and genes occur via epigenetic regulations of the genome, which allow adaptation of organism to changing life conditions by alternation of gene expression. T1DM has increased several-fold over the past half century. Such a short time indicates involvement of environment factors and excludes genetic changes. This review summarizes the most current knowledge of epigenetic changes in that process leading to autoimmune diabetes mellitus.
Research on Operation Efficiency and Membrane Fouling of A2/O-MBR in Reclaimed Water Treatment

Taking the public building domestic wastewater as an example, the combination of the MBR (membrane bioreactor) process and the traditional A2/O (anaerobic-anoxic-oxic) process was established and analyzed in terms of the removal effect of the pollutants, the impact of the microbial community changes on the process, the MBR membrane fouling, the cleaning methods, and the cleaning performance. The results indicated that the effluent water quality of the domestic wastewater treated with the A2/O-MBR process was stable and met the emission requirement to the natural water body. There was good microbial diversity in raw water, the anaerobic tank, the anoxic tank, the aerobic MBR tank and the disinfection tank, and the aerobic MBR tank has a wide variety of aerobic microorganisms, which elevates the removal of organics and the nitrification of ammonia nitrogen and ensures the qualification of nitrogen and phosphorus indexes of the system effluent water. For the fouled membrane, the surface of the contaminated membrane was covered by macromolecular contaminants, causing the membrane flux to drop, and after different cleaning methods to the membrane were compared, it was discovered that the combined use of cleaning agents had better effects than the single ones, and the cleaning method of sodium hydroxide followed by hydrochloric acid showed the best effect, achieving a membrane flux restoration ratio above 80% after cleaning.