Miracle-dz/UniFAR-FTUs huggingface dataset:
Iron influence on dissolved color in lakes of the Upper Great Lakes States

Colored dissolved organic matter (CDOM), a major component of the dissolved organic carbon (DOC) pool in many lakes, is an important controlling factor in lake ecosystem functioning. Absorption coefficients at 440 nm (a440, m-1), a common measure of CDOM, exhibited strong associations with dissolved iron (Fediss) and DOC in 280 lakes of the Upper Great Lakes States (UGLS: Minnesota, Wisconsin, and Michigan), as has been found in Scandinavia and elsewhere. Linear regressions between the three variables on UGLS lake data typically yielded R2 values of 0.6–0.9, suggesting that some underlying common processes influence organic matter and Fediss. Statistical and experimental evidence, however, supports only a minor role for iron contributions to a440 in UGLS lakes. Although both DOC and Fediss were significant variables in linear and log-log regressions on a440, DOC was the stronger predictor; adding Fediss to the linear a440-DOC model improved the R2 only from 0.90 to 0.93. Furthermore, experimental additions of FeIII to colored lake waters had only small effects on a440 (average increase of 0.242 m-1 per 100 μg/L of added FeIII). For 136 visibly stained waters (with a440 > 3.0 m-1), where allochthonous DOM predominates, DOM accounted for 92.3 ± 5.0% of the measured a440 values, and Fediss accounted for the remainder. In 75% of the lakes, Fediss accounted for < 10% of a440, but contributions of 15–30% were observed for 7 river-influenced lakes. Contributions of Fediss in UGLS lakes to specific UV absorbance at 254 nm (SUVA254) generally were also low. Although Fediss accounted for 5–10% of measured SUVA254 in a few samples, on average, 98.1% of the SUVA254 signal was attributable to DOM and only 1.9% to Fediss. DOC predictions from measured a440 were nearly identical to those from a440 corrected to remove Fediss contributions. Overall, variations in Fediss in most UGLS lakes have very small effects on CDOM optical properties, such as a440 and SUVA254, and negligible effects on the accuracy of DOC estimated from a440, data for which can be obtained at broad regional scales by remote sensing methods.
An anti-Gn glycoprotein antibody from a convalescent patient potently inhibits the infection of severe fever with thrombocytopenia syndrome virus

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease localized to China, Japan, and Korea that is characterized by severe hemorrhage and a high fatality rate. Currently, no specific vaccine or treatment has been approved for this disease. To develop a therapeutic agent for SFTS, we isolated antibodies from a phage-displayed antibody library that was constructed from a patient who recovered from SFTS virus (SFTSV) infection. One antibody, designated as Ab10, was reactive to the Gn envelope glycoprotein of SFTSV and protected host cells and A129 mice from infection in both in vitro and in vivo experiments. Notably, Ab10 protected 80% of mice, even when injected 5 days after inoculation with a lethal dose of SFTSV. Using cross-linker assisted mass spectrometry and alanine scanning, we located the non-linear epitope of Ab10 on the Gn glycoprotein domain II and an unstructured stem region, suggesting that Ab10 may inhibit a conformational alteration that is critical for cell membrane fusion between the virus and host cell. Ab10 reacted to recombinant Gn glycoprotein in Gangwon/Korea/2012, HB28, and SD4 strains. Additionally, based on its epitope, we predict that Ab10 binds the Gn glycoprotein in 247 of 272 reported SFTSV isolates previously reported. Together, these data suggest that Ab10 has potential to be developed into a therapeutic agent that could protect against more than 90% of reported SFTSV isolates. Author summary Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease localized to China, Japan, and Korea. This tick-borne virus has infected more than 5,000 humans with a 6.4% to 20.9% fatality rate. Currently, there are no prophylactic or therapeutic measures against this virus. Historically, antibodies from patients who recovered from viral infection have been used to treat new patients. Until now, one recombinant monoclonal antibody was approved for the prophylaxis of respiratory syntial virus infection. We selected 10 antibodies from a patient who recovered from SFTS and found that one antibody potently inhibited SFTS viral infection in both test tube and animal studies. We determined the binding site of this antibody to SFTS virus, which allowed us to predict that this antibody could bind 247 out of 272 SFTS virus isolates reported up to now. We anticipate that this antibody could be developed into a therapeutic measure against SFTS.
NH3 Solubilities and Physical Properties of Ethylamine Hydrochloride Plus Urea Deep Eutectic Solvents

In the present work, the solubilities of NH3 in deep eutectic solvents formulated by ethylamine chloride (EaCl) and urea were determined at (313.2–353.2) K and (0–300.0) kPa. It is found that the isotherms for NH3 absorption display slightly nonideal profiles, and EaCl contributes slightly more than urea to the absorption of NH3 in EaCl + urea mixtures. Overall, EaCl + urea mixtures possess quite promising absorption capacities for NH3, with the values of (4.179–4.573) mol·kg–1 at 313.2 K and ∼100.0 kPa. The Krichevsky–Kasarnovsky (K–K) equation was used for the correlation of NH3 solubilities, and Henry’s constants and infinite-dilution partial molar volumes of NH3 in EaCl + urea mixtures were obtained. The thermodynamic functions of the NH3 absorption process were also calculated based on the relationship between Henry’s constants and temperatures. Considering that the physical properties are basic data for liquid solvents, the densities, viscosities, glass transition temperatures, melting temperatures,.
Quantification of the Photocatalytic Self-Cleaning Ability of Non-Transparent Materials

The photo-induced reactivity of compounds at the surface of photocatalytic materials is used to maintain the cleanliness of the surface of glass, concretes and paints. A standard method to quantify the photocatalytic self-cleaning (SC) properties of non-transparent materials was recently published. It is based on the covering of the sample surface with a defined amount of dye and on the evaluation of the reflectance spectra of the coloured surface under irradiation. The calibration of the spectral changes allowed the quantification of the surface residual dye and the evaluation of the self-cleaning kinetics. The method was tested on seven white and coloured photocatalytic materials using methylene blue (MB), rhodamine B (RhB) and metanil yellow (MY). The main by-products of the MB photocatalytic degradation at the solid/solid interface were identified, showing that MB degradation in solution follows a path quite different from that at the solid/solid interface. Also MY showed a different order of photoreactivity. Furthermore, experiments at the solid/solid interface are more trustworthy than tests in solution for evaluating the self-cleaning ability. The differences of the photocatalytic phenomena at the solid/solid interface in comparison with the most studied photoactivated processes at the solid/liquid interface are outlined. Furthermore, photocatalytic materials showed selectivity toward some specific dyes. This encourages the use of more than one dye for the evaluation of the self-cleaning ability of a photocatalytic material.
The Effect of FG-Nup Phosphorylation on NPC Selectivity: A One-Bead-Per-Amino-Acid Molecular Dynamics Study

Nuclear pore complexes (NPCs) are large protein complexes embedded in the nuclear envelope separating the cytoplasm from the nucleoplasm in eukaryotic cells. They function as selective gates for the transport of molecules in and out of the nucleus. The inner wall of the NPC is coated with intrinsically disordered proteins rich in phenylalanine-glycine repeats (FG-repeats), which are responsible for the intriguing selectivity of NPCs. The phosphorylation state of the FG-Nups is controlled by kinases and phosphatases. In the current study, we extended our one-bead-per-amino-acid (1BPA) model for intrinsically disordered proteins to account for phosphorylation. With this, we performed molecular dynamics simulations to probe the effect of phosphorylation on the Stokes radius of isolated FG-Nups, and on the structure and transport properties of the NPC. Our results indicate that phosphorylation causes a reduced attraction between the residues, leading to an extension of the FG-Nups and the formation of a significantly less dense FG-network inside the NPC. Furthermore, our simulations show that upon phosphorylation, the transport rate of inert molecules increases, while that of nuclear transport receptors decreases, which can be rationalized in terms of modified hydrophobic, electrostatic, and steric interactions. Altogether, our models provide a molecular framework to explain how extensive phosphorylation of FG-Nups decreases the selectivity of the NPC.
Rapid prediction of yellow tea free amino acids with hyperspectral images

Free amino acids are an important indicator of the freshness of yellow tea. This study investigated a novel procedure for predicting the free amino acid (FAA) concentration of yellow tea. It was developed based on the combined spectral and textural features from hyperspectral images. For the purposes of exploration and comparison, hyperspectral images of yellow tea (150 samples) were captured and analyzed. The raw spectra were preprocessed with Savitzky-Golay (SG) smoothing. To reduce the dimension of spectral data, five feature wavelengths were extracted using the successive projections algorithm (SPA). Five textural features (angular second moment, entropy, contrast, correlation, and homogeneity) were extracted as textural variables from the characteristic grayscale images of the five characteristic wavelengths using the gray-level co-occurrence matrix (GLCM). The FAA content prediction model with different variables was established by a genetic algorithm-support vector regression (GA-SVR) algorithm. The results showed that better prediction results were obtained by combining the feature wavelengths and textural variables. Compared with other data, this prediction result was still very satisfactory in the GA-SVR model, indicating that data fusion was an effective way to enhance hyperspectral imaging ability for the determination of free amino acid values in yellow tea.
Optical Biosensors Based on Silicon-On-Insulator Ring Resonators: A Review

Recent developments in optical biosensors based on integrated photonic devices are reviewed with a special emphasis on silicon-on-insulator ring resonators. The review is mainly devoted to the following aspects: (1) Principles of sensing mechanism, (2) sensor design, (3) biofunctionalization procedures for specific molecule detection and (4) system integration and measurement set-ups. The inherent challenges of implementing photonics-based biosensors to meet specific requirements of applications in medicine, food analysis, and environmental monitoring are discussed.
MUC1 is a receptor for the Salmonella SiiE adhesin that enables apical invasion into enterocytes

The cellular invasion machinery of the enteric pathogen Salmonella consists of a type III secretion system (T3SS) with injectable virulence factors that induce uptake by macropinocytosis. Salmonella invasion at the apical surface of intestinal epithelial cells is inefficient, presumably because of a glycosylated barrier formed by transmembrane mucins that prevents T3SS contact with host cells. We observed that Salmonella is capable of apical invasion of intestinal epithelial cells that express the transmembrane mucin MUC1. Knockout of MUC1 in HT29-MTX cells or removal of MUC1 sialic acids by neuraminidase treatment reduced Salmonella apical invasion but did not affect lateral invasion that is not hampered by a defensive barrier. A Salmonella deletion strain lacking the SiiE giant adhesin was unable to invade intestinal epithelial cells through MUC1. SiiE-positive Salmonella closely associated with the MUC1 layer at the apical surface, but invaded Salmonella were negative for the adhesin. Our findings uncover that the transmembrane mucin MUC1 is required for Salmonella SiiE-mediated entry of enterocytes via the apical route.
SOMAscan-based proteomic measurements of plasma brain natriuretic peptide are decreased in mild cognitive impairment and in Alzheimer's dementia patients

Alzheimer's disease represents the most common age-related neurodegenerative disorder and a leading cause of progressive cognitive impairment. Predicting cognitive decline is challenging but would be invaluable in an increasingly aging population which also experiences a rising cardiovascular risk. In order to examine whether plasma measurements of one of the established biomarkers of heart failure, brain natriuretic peptide (BNP), reflect a decline in cognitive function, associated with Alzheimer's disease neurodegeneration, BNP levels were analysed, by using a novel assay called a SOMAscan, in 1. cognitively healthy, control subjects; 2. subjects with mild cognitive impairment, and 3. subjects with Alzheimer's disease. The results of our study show that the levels of the BNP were significantly different between the three types of diagnoses (p < 0.05), whereby subjects with mild cognitive impairment had the lowest mean BNP value, and healthy subjects had the highest BNP value. Importantly, our results show that the levels of the BNP are influenced by the presence of at least one APOE4 allele in the healthy (p < 0.05) and in the Alzheimer's disease groups of subjects (p < 0.1). As the levels of the BNP appear to be independent of the APOE4 genotype in subjects with mild cognitive impairment, the results of our study support inclusion of measurements of plasma levels of the BNP in the list of the core Alzheimer's disease biomarkers for identification of the mild cognitive impairment group of patients. In addition, the results of our study warrant further investigations into molecular links between Alzheimer's disease-type cognitive decline and cardiovascular disorders.
Proteomics Analysis of E. angustifolia Seedlings Inoculated with Arbuscular Mycorrhizal Fungi under Salt Stress

To reveal the mechanism of salinity stress alleviation by arbuscular mycorrhizal fungi (AMF), we investigated the growth parameter, soluble sugar, soluble protein, and protein abundance pattern of E. angustifolia seedlings that were cultured under salinity stress (300 mmol/L NaCl) and inoculated by Rhizophagus irregularis (RI). Furthermore, a label-free quantitative proteomics approach was used to reveal the stress-responsive proteins in the leaves of E. angustifolia. The result indicates that the abundance of 75 proteins in the leaves was significantly influenced when E. angustifolia was inoculated with AMF, which were mainly involved in the metabolism, signal transduction, and reactive oxygen species (ROS) scavenging. Furthermore, we identified chorismate mutase, elongation factor mitochondrial, peptidyl-prolyl cis-trans isomerase, calcium-dependent kinase, glutathione S-transferase, glutathione peroxidase, NADH dehydrogenase, alkaline neutral invertase, peroxidase, and other proteins closely related to the salt tolerance process. The proteomic results indicated that E. angustifolia seedlings inoculated with AMF increased the secondary metabolism level of phenylpropane metabolism, enhanced the signal transduction of Ca2+ and ROS scavenging ability, promoted the biosynthesis of protein, accelerated the protein folding, and inhibited the degradation of protein under salt stress. Moreover, AMF enhanced the synthesis of ATP and provided sufficient energy for plant cell activity. This study implied that symbiosis of halophytes and AMF has potential as an application for the improvement of saline-alkali soils.
Emerging Regulatory Roles of Dual-Specificity Phosphatases in Inflammatory Airway Disease

Inflammatory airway disease, such as asthma and chronic obstructive pulmonary disease (COPD), is a major health burden worldwide. These diseases cause large numbers of deaths each year due to airway obstruction, which is exacerbated by respiratory viral infection. The inflammatory response in the airway is mediated in part through the MAPK pathways: p38, JNK and ERK. These pathways also have roles in interferon production, viral replication, mucus production, and T cell responses, all of which are important processes in inflammatory airway disease. Dual-specificity phosphatases (DUSPs) are known to regulate the MAPKs, and roles for this family of proteins in the pathogenesis of airway disease are emerging. This review summarizes the function of DUSPs in regulation of cytokine expression, mucin production, and viral replication in the airway. The central role of DUSPs in T cell responses, including T cell activation, differentiation, and proliferation, will also be highlighted. In addition, the importance of this protein family in the lung, and the necessity of further investigation into their roles in airway disease, will be discussed.
SIRT5 deficiency suppresses mitochondrial ATP production and promotes AMPK activation in response to energy stress

Sirtuin 5 (SIRT5) is a member of the NAD+-dependent sirtuin family of protein deacylase that catalyzes removal of post-translational modifications, such as succinylation, malonylation, and glutarylation on lysine residues. In light of the SIRT5's roles in regulating mitochondrion function, we show here that SIRT5 deficiency leads to suppression of mitochondrial NADH oxidation and inhibition of ATP synthase activity. As a result, SIRT5 deficiency decreases mitochondrial ATP production, increases AMP/ATP ratio, and subsequently activates AMP-activated protein kinase (AMPK) in cultured cells and mouse hearts under energy stress conditions. Moreover, Sirt5 knockout attenuates transverse aortic constriction (TAC)-induced cardiac hypertrophy and cardiac dysfunction in mice, which is associated with decreased ATP level, increased AMP/ATP ratio and enhanced AMPK activation. Our study thus uncovers an important role of SIRT5 in regulating cellular energy metabolism and AMPK activation in response to energy stress.
Fluoxetine Induces Apoptosis through Extrinsic/Intrinsic Pathways and Inhibits ERK/NF-κB-Modulated Anti-Apoptotic and Invasive Potential in Hepatocellular Carcinoma Cells In Vitro

The aim of the present study was to verify the effects of fluoxetine on dysregulation of apoptosis and invasive potential in human hepatocellular carcinoma (HCC) SK-Hep1 and Hep3B cells. Cells were treated with different concentrations of fluoxetine for different times. MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide) assays were used for testing the effects of fluoxetine on cell viability. The regulation of apoptosis signaling, and anti-apoptotic, proliferation, and metastasis-associated proteins after fluoxetine treatment were assayed by flow cytometry and Western blotting assay. The detection of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation after fluoxetine treatment was performed by NF-κB reporter gene assay. The results demonstrated that fluoxetine significantly reduced cell viability, cell migration/invasion, NF-κB, extracellular signal-regulated kinases (ERK) activation, and expression of anti-apoptotic (Cellular FLICE (FADD-like IL-1β-converting enzyme)-inhibitory protein (C-FLIP), Myeloid cell leukemia-1 (MCL-1), X-Linked inhibitor of apoptosis protein (XAIP), and Survivin), proliferation (Cyclin-D1), angiogenesis (vascular endothelial growth factor (VEGF)), and metastasis-associated proteins (matrix metalloproteinase-9 (MMP-9)). Fluoxetine also significantly induced apoptosis, unregulated extrinsic (activation of first apoptosis signal protein and ligand (Fas/FasL), and caspase-8) and intrinsic (loss of mitochondrial membrane potential (ΔΨm) pathways and increased Bcl-2 homologous antagonist killer (BAK) apoptosis signaling. Taken together, these results demonstrated that fluoxetine induced apoptosis through extrinsic/intrinsic pathways and diminished ERK/NF-κB-modulated anti-apoptotic and invasive potential in HCC cells in vitro.
Subclinical atherosclerosis in psoriasis. Usefulness of femoral artery ultrasound for the diagnosis, and analysis of its relationship with insulin resistance

Background Psoriasis is associated with an increased risk of cardiovascular disease (CVD) at younger ages that is not identifiable by traditional risk factors. Screening for subclinical atherosclerosis with ultrasound has only been investigated in carotid arteries. Femoral artery ultrasound has never been considered for this purpose. The link between psoriasis and accelerated atherosclerosis has not yet been established. Objective To study the usefulness of femoral artery ultrasound for the detection of subclinical atherosclerosis in psoriasis. We also investigated its possible relationship with changes in insulin resistance. Methods We conducted a cross-sectional study in 140 participants, 70 patients with moderate-to-severe psoriasis and 70 healthy controls, matched 1:1 for age, sex, and BMI. Femoral and carotid atherosclerotic plaques were evaluated by ultrasonography. Insulin resistance was assessed by the homeostasis model assessment method (HOMA-IR). Results Femoral atherosclerotic plaque prevalence was significantly higher in patients with psoriasis (44.64%) than in controls (19.07%) (p<0.005), but no significant difference was found in carotid plaque prevalence (p<0.3). Femoral plaques were significantly more prevalent than carotid plaques (21.42%) among patients with psoriasis (p<0.001). In the regression analysis, insulin resistance was the most influential determinant of atherosclerosis in psoriasis and C-reactive protein the most significant predictor of insulin resistance. Conclusions Ultrasound screening for femoral atherosclerotic plaques improves the detection of subclinical atherosclerosis in patients with psoriasis, whereas the study of carotid arteries is not sufficiently accurate. Insulin resistance appears to play a greater role in the development of atherosclerosis in these patients in comparison to other classical CVD risk factors.
Regional complexity in enteric neuron wiring reflects diversity of motility patterns in the mouse large intestine

The enteric nervous system controls a variety of gastrointestinal functions including intestinal motility. The minimal neuronal circuit necessary to direct peristalsis is well-characterized but several intestinal regions display also other motility patterns for which the underlying circuits and connectivity schemes that coordinate the transition between those patterns are poorly understood. We investigated whether in regions with a richer palette of motility patterns, the underlying nerve circuits reflect this complexity. Using Ca2+ imaging, we determined the location and response fingerprint of large populations of enteric neurons upon focal network stimulation. Complemented by neuronal tracing and volumetric reconstructions of synaptic contacts, this shows that the multifunctional proximal colon requires specific additional circuit components as compared to the distal colon, where peristalsis is the predominant motility pattern. Our study reveals that motility control is hard-wired in the enteric neural networks and that circuit complexity matches the motor pattern portfolio of specific intestinal regions.