Miracle-dz/UniFAR-FTUs huggingface dataset:
Host Range of Carp Edema Virus (CEV) during a Natural Mortality Event in a Minnesota Lake and Update of CEV Associated Mortality Events in the USA

Mass mortality events of common carp (Cyprinus carpio, carp) associated with carp edema virus (CEV) alone or in coinfections with koi herpesvirus (KHV), is an emerging issue. Despite recent outbreaks of CEV in wild carp populations, the host range of North American species has not been well studied. To that end, we intensively sampled carp (n = 106) and co-habiting native fish species (n = 5 species; n = 156 total fish) from a CEV-suspect mass-mortality event of carp in a small Minnesota lake (Lake Swartout). Additionally, fecal and regurgitant samples (n = 73 each) from double-crested cormorants (Phalacrocorax auritus, DCCO) were sampled to test the potential of DCCO to act as a vector for virus transmission. CEV was confirmed to be widespread in the Lake Swartout carp population during the outbreak with high viral loads and histological confirmation, suggesting that CEV was the cause of the mortality event. There were no detections of CEV in any native fish species; however, DCCO regurgitant and fecal samples were positive for CEV DNA. In addition, three CEV-positive and one CEV + KHV-positive mortality events were confirmed with no observed mortality or morbidity of non-carp species in other lakes. This study provides evidence that CEV infection and disease may be specific to carp during mortality events with mixed-species populations, identifies DCCO as a potential vector for CEV, and further expands the known range of CEV, as well as coinfections with KHV, in North America.
Influence of Atmospheric Gases on the Electrical Properties of PbSe Quantum-Dot Films

We report the effects of N2 and O2 on the electrical properties of PbSe quantum-dot (QD) films treated with 1,2-ethanedithiol (EDT) by measuring the changes in the current−voltage characteristics of QD field-effect transistors (FETs). EDT-treated PbSe QD films at a base pressure of ∼10−5 Torr exhibit ambipolar transport. Exposing these films to N2 shifts the transfer characteristics toward negative gate-voltage values and increases the electron mobility. These changes could be reversed entirely by removing the N2 gas over the FET and returning to base pressure. Oxygen exposure shifts the transfer characteristics in the opposite direction toward positive gate-voltage values. Moreover, oxygen exposure reduces charge mobility but increases film conductivity. For exposures up to ∼108 langmuir, these O2-induced changes could be reversed completely by removing the O2 gas over the sample and returning to base pressure. However, after ∼1010 langmuir of O2 exposure, the changes are irreversible. The QD films then .
RAS Nanoclusters: Dynamic Signaling Platforms Amenable to Therapeutic Intervention

RAS proteins are mutated in approximately 20% of all cancers and are generally associated with poor clinical outcomes. RAS proteins are localized to the plasma membrane and function as molecular switches, turned on by partners that receive extracellular mitogenic signals. In the on-state, they activate intracellular signal transduction cascades. Membrane-bound RAS molecules segregate into multimers, known as nanoclusters. These nanoclusters, held together through weak protein–protein and protein–lipid associations, are highly dynamic and respond to cellular input signals and fluctuations in the local lipid environment. Disruption of RAS nanoclusters results in downregulation of RAS-mediated mitogenic signaling. In this review, we discuss the propensity of RAS proteins to display clustering behavior and the interfaces that are associated with these assemblies. Strategies to therapeutically disrupt nanocluster formation or the stabilization of signaling incompetent RAS complexes are discussed.
The Chemical and Biological Properties of Nanohydroxyapatite Coatings with Antibacterial Nanometals, Obtained in the Electrophoretic Process on the Ti13Zr13Nb Alloy

The risk of an early inflammation after implantation surgery of titanium implants has caused the development of different antimicrobial measures. The present research is aimed at characterizing the effects of nanosilver and nanocopper dispersed in the nanohydroxyapatite coatings, deposited on the Ti13Zr13Nb alloy, and on the chemical and biological properties of the coatings. The one-stage deposition process was performed by the electrophoretic method at different contents of nanomaterials in suspension. The surface topography of the coatings was examined with scanning electron microscopy. The wettability was expressed as the water contact angle. The corrosion behavior was characterized by the potentiodynamic technique. The release rate of copper and silver into the simulated body fluid was investigated by atomic absorption spectrometry. The antibacterial efficiency was evaluated as the survivability and adhesion of the bacteria and the growth of the biofilm. The cytotoxicity was assessed for osteoblasts. The results demonstrate that silver and copper increase the corrosion resistance and hydrophilicity. Both elements together effectively kill bacteria and inhibit biofilm growth but appear to be toxic for osteoblasts. The obtained results show that the nanohydroxyapatite coatings doped with nanosilver and nanocopper in a one-stage electrophoretic process can be valuable for antibacterial coatings.
Jet Fuel Exposure in the United States Air Force

Abstract Jet fuel vapor exposures were measured using industrial hygiene sampling techniques at three domestic U.S. Air Force installations. Breathing zone samples were collected from within three general job categories at each location: aircraft maintenance, fuel handling, and flightline positions. These samples were analyzed using gas chromatography and flame ionization detector techniques. Mean exposure concentrations for all samples collected were 0.01 ppm benzene [standard deviation (SD) = 0.01] and 1.33 ppm naphthas/jet fuels (SD = 1.95) for the aircraft maintenance positions (n = 63), 0.01 ppm benzene (SD = 0.01) and 0.61 ppm naphthas/jet fuels (SD = 0.90) for fuel handling positions (n = 16), and 0.004 ppm benzene (SD = 0.005) and 0.33 ppm naphthas/jet fuels (SD = 0.40) for flightline positions (n = 8).
Generation of Reactive Oxygen Species by Mitochondria

Reactive oxygen species (ROS) are series of chemical products originated from one or several electron reductions of oxygen. ROS are involved in physiology and disease and can also be both cause and consequence of many biological scenarios. Mitochondria are the main source of ROS in the cell and, particularly, the enzymes in the electron transport chain are the major contributors to this phenomenon. Here, we comprehensively review the modes by which ROS are produced by mitochondria at a molecular level of detail, discuss recent advances in the field involving signalling and disease, and the involvement of supercomplexes in these mechanisms. Given the importance of mitochondrial ROS, we also provide a schematic guide aimed to help in deciphering the mechanisms involved in their production in a variety of physiological and pathological settings.
Association of Coffee Consumption and Its Types According to Addition of Sugar and Creamer with Metabolic Syndrome Incidence in a Korean Population from the Health Examinees (HEXA) Study

Coffee is widely consumed worldwide, and numerous studies indicate that coffee consumption may potentially affect the development of chronic diseases. Metabolic syndrome (MetS) may constitute a risk factor for chronic diseases. We aimed to prospectively evaluate the association between coffee consumption and MetS incidence. All participants were selected from the Health Examinees study. MetS was defined by the Adult Treatment Panel III criteria of the National Cholesterol Education Program. A multivariate Cox proportional hazards regression model was used to assess the relationship between coffee consumption and MetS incidence. In comparison with non-consumers, male moderate consumers (≤3 cups/day) showed a lower risk for low high-density lipoprotein cholesterol (HDL-C) (≤1 cup/day, hazard ratio (HR): 0.445, 95% confidence interval (CI): 0.254–0.780; 1–3 cups/day, HR: 0.507, 95% CI: 0.299–0.859) and high fasting blood glucose (FPG) (≤1 cup/day, HR: 0.694, 95% CI: 0.538–0.895; 1–3 cups/day, HR: 0.763, 95% CI: 0.598–0.972). Male 3-in-1 coffee (coffee with sugar and creamer) consumers also showed a lower risk for low HDL-C (HR: 0.423, 95% CI: 0.218–0.824) and high FPG (HR: 0.659, 95% CI: 0.497–0.874). These findings indicate a negative association between moderate coffee consumption and low HDL-C and high FPG among Korean male adults.
Potential Utility of Pre-Emptive Germline Pharmacogenetics in Breast Cancer

Simple Summary Breast cancer outcomes are variable due to differences in tumor biology, patient biology, and treatment. The likelihood of developing cancer and other diseases increases with age. Thus, many patients with breast cancer have multiple co-morbidities requiring medical management, which increases the probability of polypharmacy and the risk of adverse drug events. Pharmacogenetics is the study of how inherited genetic variants influence drug response. Depending on the genes that a patient inherits, some respond to drugs as expected, some experience debilitating side effects, and others have minimal to no response. In this paper, we discuss the theoretical clinical utility of pharmacogenetics for 225 patients with breast cancer relative to anti-cancer drugs and non-cancer drugs. For this population, 38 drug–gene associations with high levels of evidence for clinical actionability were identified, supporting the concept of pharmacogenetics integration into the routine care of future patients with breast cancer. Abstract Patients with breast cancer often receive many drugs to manage the cancer, side effects associated with cancer treatment, and co-morbidities (i.e., polypharmacy). Drug–drug and drug–gene interactions contribute to the risk of adverse events (AEs), which could lead to non-adherence and reduced efficacy. Here we investigated several well-characterized inherited (germline) pharmacogenetic (PGx) targets in 225 patients with breast cancer. All relevant clinical, pharmaceutical, and PGx diplotype data were aggregated into a single unifying informatics platform to enable an exploratory analysis of the cohort and to evaluate pharmacy ordering patterns. Of the drugs recorded, there were 38 for which high levels of evidence for clinical actionability with PGx was available from the US FDA and/or the Clinical Pharmacogenetics Implementation Consortium (CPIC). These data were associated with 10 pharmacogenes: DPYD, CYP2C9, CYP2C19, CYP2D6, CYP3A5, CYP4F2, G6PD, MT-RNR1, SLCO1B1, and VKORC1. All patients were taking at least one of the 38 drugs and had inherited at least one actionable PGx variant that would have informed prescribing decisions if this information had been available pre-emptively. The non-cancer drugs with PGx implications that were common (prescribed to at least one-third of patients) included anti-depressants, anti-infectives, non-steroidal anti-inflammatory drugs, opioids, and proton pump inhibitors. Based on these results, we conclude that pre-emptive PGx testing may benefit patients with breast cancer by informing drug and dose selection to maximize efficacy and minimize AEs.
Targeting MMP-Regulation of Inflammation to Increase Metabolic Tolerance to COVID-19 Pathologies: A Hypothesis

Many individuals infected with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) develop no or only mild symptoms, but some can go on onto develop a spectrum of pathologies including pneumonia, acute respiratory distress syndrome, respiratory failure, systemic inflammation, and multiorgan failure. Many pathogens, viral and non-viral, can elicit these pathologies, which justifies reconsidering whether the target of therapeutic approaches to fight pathogen infections should be (a) the pathogen itself, (b) the pathologies elicited by the pathogen interaction with the human host, or (c) a combination of both. While little is known about the immunopathology of SARS-CoV-2, it is well-established that the above-mentioned pathologies are associated with hyper-inflammation, tissue damage, and the perturbation of target organ metabolism. Mounting evidence has shown that these processes are regulated by endoproteinases (particularly, matrix metalloproteinases (MMPs)). Here, we review what is known about the roles played by MMPs in the development of COVID-19 and postulate a mechanism by which MMPs could influence energy metabolism in target organs, such as the lung. Finally, we discuss the suitability of MMPs as therapeutic targets to increase the metabolic tolerance of the host to damage inflicted by the pathogen infection, with a focus on SARS-CoV-2.
Estimation of the Path-Loss Exponent by Bayesian Filtering Method

Regarding wireless sensor network parameter estimation of the propagation model is a most important issue. Variations of the received signal strength indicator (RSSI) parameter are a fundamental problem of a system based on signal strength. In the present paper, we propose an algorithm based on Bayesian filtering techniques for estimating the path-loss exponent of the log-normal shadowing propagation model for outdoor RSSI measurements. Furthermore, in a series of experiments, we will demonstrate the usefulness of the particle filter for estimating the RSSI data. The stability of this algorithm and the differences in determined path-loss exponent for both method were also analysed. The proposed method of dynamic estimation results in significant improvements of the accuracy of RSSI values when compared with the experimental measurements. It should be emphasised that the path-loss exponent mainly depends on the RSSI data. Our results also indicate that increasing the number of inserted particles does not significantly raise the quality of the estimated parameters.
Gamma-Chain Receptor Cytokines & PD-1 Manipulation to Restore HCV-Specific CD8+ T Cell Response during Chronic Hepatitis C

Hepatitis C virus (HCV)-specific CD8+ T cell response is essential in natural HCV infection control, but it becomes exhausted during persistent infection. Nowadays, chronic HCV infection can be resolved by direct acting anti-viral treatment, but there are still some non-responders that could benefit from CD8+ T cell response restoration. To become fully reactive, T cell needs the complete release of T cell receptor (TCR) signalling but, during exhaustion this is blocked by the PD-1 effect on CD28 triggering. The T cell pool sensitive to PD-1 modulation is the progenitor subset but not the terminally differentiated effector population. Nevertheless, the blockade of PD-1/PD-L1 checkpoint cannot be always enough to restore this pool. This is due to the HCV ability to impair other co-stimulatory mechanisms and metabolic pathways and to induce a pro-apoptotic state besides the TCR signalling impairment. In this sense, gamma-chain receptor cytokines involved in memory generation and maintenance, such as low-level IL-2, IL-7, IL-15, and IL-21, might carry out a positive effect on metabolic reprogramming, apoptosis blockade and restoration of co-stimulatory signalling. This review sheds light on the role of combinatory immunotherapeutic strategies to restore a reactive anti-HCV T cell response based on the mixture of PD-1 blocking plus IL-2/IL-7/IL-15/IL-21 treatment.
Deciphering the Proteotoxic Stress Responses Triggered by the Perturbed Thylakoid Proteostasis in Arabidopsis

Here, we explored heat dependent thylakoid FtsH protease substrates and investigated proteotoxicity induced by thermal damage and processive protease dysfunction on the thylakoid membrane. Through our thylakoid enriched proteome analysis and biochemical experiments, carbonylated stromal proteins were suggested as possible FtsH targets. Furthermore, we observed in the thylakoid fractions in the absence of FtsH stromal reactive oxygen species-detoxifying enzymes, as well as heat shock proteins and chaperones, which are known to be upregulated at the transcriptional level when this protease is absent, which is called the damaged protein response, resembling unfolded protein response in eukaryotic cells. Interestingly, the thylakoid-enriched high-density fractions included stromal translation factors and RNA-binding proteins, along with aminoacyl-tRNA synthetase, reminiscent of the formation of stress granules. Unexpectedly, extraplastid proteins such as mitochondrial chaperones, peroxidase, tricarboxylic acid cycle and respiratory chain enzymes, as well as cytosolic ribosomes, translation factors, heat shock proteins, antioxidants and metabolic enzymes, were also found deposited in the high-density fractions depending on the loss of thylakoid FtsH, with more prominent effects of thermal stress on the cytosolic proteins. This may reflect intracellular adaptation to the proteotoxic influences from the organelle.
Low-Temperature-Induced Controllable Transversal Shell Growth of NaLnF4 Nanocrystals

Highly controllable anisotropic shell growth is essential for further engineering the function and properties of lanthanide-doped luminescence nanocrystals, especially in some of the advanced applications such as multi-mode bioimaging, security coding and three-dimensional (3D) display. However, the understanding of the transversal shell growth mechanism is still limited today, because the shell growth direction is impacted by multiple complex factors, such as the anisotropy of surface ligand-binding energy, anisotropic core–shell lattice mismatch, the size of cores and varied shell crystalline stability. Herein, we report a highly controlled transversal shell growth method for hexagonal sodium rare-earth tetrafluoride (β-NaLnF4) nanocrystals. Exploiting the relationship between reaction temperature and shell growth direction, we found that the shell growth direction could be tuned from longitudinal to transversal by decreasing the reaction temperature from 310 °C to 280 °C. In addition to the reaction temperature, we also discussed the roles of other factors in the transversal shell growth of nanocrystals. A suitable core size and a relative lower shell precursor concentration could promote transversal shell growth, although different shell hosts played a minor role in changing the shell growth direction.
Chimeric VLPs Based on HIV-1 Gag and a Fusion Rabies Glycoprotein Induce Specific Antibodies against Rabies and Foot-and-Mouth Disease Virus

Foot and mouth disease is a livestock acute disease, causing economic losses in affected areas. Currently, control of this disease is performed by mandatory vaccination campaigns using inactivated viral vaccines. In this work, we describe the development of a chimeric VLP-based vaccine candidate for foot-and-mouth disease virus (FMDV), based on the co-expression of the HIV-1 Gag protein and a novel fusion rabies glycoprotein (RVG), which carries in its N-term the FMDV main antigen: the G-H loop. It is demonstrated by confocal microscopy that both Gag-GFP polyprotein and the G-H loop colocalize at the cell membrane and, that the Gag polyprotein of the HIV virus acts as a scaffold for enveloped VLPs that during the budding process acquires the proteins that are being expressed in the cell membrane. The obtained VLPs were spherical particles of 130 ± 40 nm in diameter (analyzed by TEM, Cryo-TEM and NTA) carrying an envelope membrane that efficiently display the GH-RVG on its surface (analyzed by gold immunolabeling). Immunostainings with a FMDV hyperimmune serum showed that the heterologous antigenic site, genetically fused to RVG, is recognized by specific G-H loop antibodies. Additionally, the cVLPs produced expose the G-H loop to the liquid surrounding (analyzed by specific ELISA). Finally, we confirmed that these FMD cVLPs are able to induce a specific humoral immune response, based on antibodies directed to the G-H loop in experimental animals.
Biosensors: A Sneak Peek into Plant Cell’s Immunity

Biosensors are indispensable tools to understand a plant’s immunity as its spatiotemporal dimension is key in withstanding complex plant immune signaling. The diversity of genetically encoded biosensors in plants is expanding, covering new analytes with ever higher sensitivity and robustness, but their assortment is limited in some respects, such as their use in following biotic stress response, employing more than one biosensor in the same chassis, and their implementation into crops. In this review, we focused on the available biosensors that encompass these aspects. We show that in vivo imaging of calcium and reactive oxygen species is satisfactorily covered with the available genetically encoded biosensors, while on the other hand they are still underrepresented when it comes to imaging of the main three hormonal players in the immune response: salicylic acid, ethylene and jasmonic acid. Following more than one analyte in the same chassis, upon one or more conditions, has so far been possible by using the most advanced genetically encoded biosensors in plants which allow the monitoring of calcium and the two main hormonal pathways involved in plant development, auxin and cytokinin. These kinds of biosensor are also the most evolved in crops. In the last section, we examine the challenges in the use of biosensors and demonstrate some strategies to overcome them.
Phloroglucinol Derivatives in Plant-Beneficial Pseudomonas spp.: Biosynthesis, Regulation, and Functions

Plant-beneficial Pseudomonas spp. aggressively colonize the rhizosphere and produce numerous secondary metabolites, such as 2,4-diacetylphloroglucinol (DAPG). DAPG is a phloroglucinol derivative that contributes to disease suppression, thanks to its broad-spectrum antimicrobial activity. A famous example of this biocontrol activity has been previously described in the context of wheat monoculture where a decline in take-all disease (caused by the ascomycete Gaeumannomyces tritici) has been shown to be associated with rhizosphere colonization by DAPG-producing Pseudomonas spp. In this review, we discuss the biosynthesis and regulation of phloroglucinol derivatives in the genus Pseudomonas, as well as investigate the role played by DAPG-producing Pseudomonas spp. in natural soil suppressiveness. We also tackle the mode of action of phloroglucinol derivatives, which can act as antibiotics, signalling molecules and, in some cases, even as pathogenicity factors. Finally, we discuss the genetic and genomic diversity of DAPG-producing Pseudomonas spp. as well as its importance for improving the biocontrol of plant pathogens.
Age-Related Palatal Wound Healing: An Experimental In Vivo Study

We assessed age-related excisional palatal mucoperiosteal wound closure in rats. A 4.2 mm diameter punch was used to create a secondary healing defect in the palate of Wistar rats. Study group—21, 18-month-old vs. control 21, 2-month-old males. The 2-dimensional area, maximum length and width of the soft tissue defect served as clinical outcome parameters. The dynamics of the initial three healing weeks were assessed. Semi-quantitative histomorphometric analysis of inflammation and myofibroblasts served for the evaluation of the inflammatory and proliferative wound healing phases. Complete wound closure was faster in the old rats. A dimensional related wound closure was observed in the young rats versus a symmetrical wound closure in the old rats. Inflammatory response was significantly delayed and of lower intensity in the old rats. Myofibroblastic response, representing the proliferative stage, was delayed and of lower intensity in the old rats, albeit not statistically significant. Reduced initial tissue damage due to decreased and delayed inflammatory response in the old rats ultimately led to faster clinical wound healing compared to the young rats, despite a statistically non-significant lower proliferative response in the old rats.