Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutagenesis of Coronavirus nsp14 Reveals Its Potential Role in Modulation of the Innate Immune Response

ABSTRACT Coronavirus (CoV) nonstructural protein 14 (nsp14) is a 60-kDa protein encoded by the replicase gene that is part of the replication-transcription complex. It is a bifunctional enzyme bearing 3′-to-5′ exoribonuclease (ExoN) and guanine-N7-methyltransferase (N7-MTase) activities. ExoN hydrolyzes single-stranded RNAs and double-stranded RNAs (dsRNAs) and is part of a proofreading system responsible for the high fidelity of CoV replication. nsp14 N7-MTase activity is required for viral mRNA cap synthesis and prevents the recognition of viral mRNAs as “non-self” by the host cell. In this work, a set of point mutants affecting different motifs within the ExoN domain of nsp14 was generated, using transmissible gastroenteritis virus as a model of Alphacoronavirus. Mutants lacking ExoN activity were nonviable despite being competent in both viral RNA and protein synthesis. A specific mutation within zinc finger 1 (ZF-C) led to production of a viable virus with growth and viral RNA synthesis kinetics similar to that of the parental virus. Mutant recombinant transmissible gastroenteritis virus (TGEV) ZF-C (rTGEV-ZF-C) caused decreased cytopathic effect and apoptosis compared with the wild-type virus and reduced levels of dsRNA accumulation at late times postinfection. Consequently, the mutant triggered a reduced antiviral response, which was confirmed by evaluating different stages of the dsRNA-induced antiviral pathway. The expression of beta interferon (IFN-β), tumor necrosis factor (TNF), and interferon-stimulated genes in cells infected with mutant rTGEV-ZF-C was reduced compared to the levels seen with the parental virus. Overall, our data revealed a potential role for CoV nsp14 in modulation of the innate immune response. IMPORTANCE The innate immune response is the first line of antiviral defense that culminates in the synthesis of interferon and proinflammatory cytokines to control viral replication. CoVs have evolved several mechanisms to counteract the innate immune response at different levels, but the role of CoV-encoded ribonucleases in preventing activation of the dsRNA-induced antiviral response has not been described to date. The introduction of a mutation in zinc finger 1 of the ExoN domain of nsp14 led to production of a virus that induced a weak antiviral response, most likely due to the accumulation of lower levels of dsRNA in the late phases of infection. These observations allowed us to propose a novel role for CoV nsp14 ExoN activity in counteracting the antiviral response, which could serve as a novel target for the design of antiviral strategies.
Xenogeneic human umbilical cord-derived mesenchymal stem cells reduce mortality in rats with acute respiratory distress syndrome complicated by sepsis

This study tested the hypothesis that xenogeneic human umbilical cord-derived mesenchymal stem cell (HUCDMSC) therapy would improve survival rates in rats with acute respiratory distress-syndrome (ARDS, induction by 48 h inhalation of 100% oxygen) and sepsis-syndrome (SS, induction by cecal-ligation and puncture) (ARDS-SS). Adult-male Sprague-Dawley rats were categorized into group 1 (sham-controls), group 2 (ARDS-SS), group 3 [ARDS-SS+HUCDMSC (1.2 ×106 cells administered 1 h after SS-induction)], and group 4 [ARDS-SS+HUCDMSC (1.2 ×106 cells administered 24 h after SS-induction)]. The mortality rate was higher in groups 2 and 4 than in groups 1 and 3 (all p<0.0001). The blood pressure after 28 h was lower in groups 2, 3 and 4 (p<0.0001) than in group 1. Albumin levels and percentages of inflammatory cells in broncho-alveolar lavage fluid, and the percentages of inflammatory and immune cells in circulation, were lowest in group 1, highest in group 2, and higher in group 3 than group 4 (all p<0.0001). The percentages of inflammatory cells in ascites and kidney parenchyma showed identical patterns, as did kidney injury scores (all p<0.0001). EarlyHUCDMSC therapy reduced rodent mortality after induced ARDS-SS.
Conductivity and dissociation in liquid metallic hydrogen and implications for planetary interiors

Significance Liquid metallic hydrogen (LMH) is a fundamental system in condensed matter sciences and the main constituent of gas giant planets. Because of exceptional challenges in experimentation and theory, its transport properties remained poorly understood. We have conducted experimental determination of the optical conductivity of bulk LMH using spectrally resolved reflectance measurements on statically compressed and heated hydrogen. Metallic hydrogen’s mechanism of metallization is largely dissociative to an atomic state, rather than the previously held experimental model, ionization of molecules. We find that LMH’s electrical conductivity is substantially higher, a factor of 6–8, than the only experimentally reported value in the literature, measured in the dc limit. The implications of the current results to Jovian giants planetary models are discussed. Liquid metallic hydrogen (LMH) is the most abundant form of condensed matter in our solar planetary structure. The electronic and thermal transport properties of this metallic fluid are of fundamental interest to understanding hydrogen’s mechanism of conduction, atomic or pairing structure, as well as the key input for the magnetic dynamo action and thermal models of gas giants. Here, we report spectrally resolved measurements of the optical reflectance of LMH in the pressure region of 1.4–1.7 Mbar. We analyze the data, as well as previously reported measurements, using the free-electron model. Fitting the energy dependence of the reflectance data yields a dissociation fraction of 65 ± 15%, supporting theoretical models that LMH is an atomic metallic liquid. We determine the optical conductivity of LMH and find metallic hydrogen’s static electrical conductivity to be 11,000–15,000 S/cm, substantially higher than the only earlier reported experimental values. The higher electrical conductivity implies that the Jovian and Saturnian dynamo are likely to operate out to shallower depths than previously assumed, while the inferred thermal conductivity should provide a crucial experimental constraint to heat transport models.
Recovery of West Nile Virus Envelope Protein Domain III Chimeras with Altered Antigenicity and Mouse Virulence

ABSTRACT Flaviviruses are positive-sense, single-stranded RNA viruses responsible for millions of human infections annually. The envelope (E) protein of flaviviruses comprises three structural domains, of which domain III (EIII) represents a discrete subunit. The EIII gene sequence typically encodes epitopes recognized by virus-specific, potently neutralizing antibodies, and EIII is believed to play a major role in receptor binding. In order to assess potential interactions between EIII and the remainder of the E protein and to assess the effects of EIII sequence substitutions on the antigenicity, growth, and virulence of a representative flavivirus, chimeric viruses were generated using the West Nile virus (WNV) infectious clone, into which EIIIs from nine flaviviruses with various levels of genetic diversity from WNV were substituted. Of the constructs tested, chimeras containing EIIIs from Koutango virus (KOUV), Japanese encephalitis virus (JEV), St. Louis encephalitis virus (SLEV), and Bagaza virus (BAGV) were successfully recovered. Characterization of the chimeras in vitro and in vivo revealed differences in growth and virulence between the viruses, with in vivo pathogenesis often not being correlated with in vitro growth. Taken together, the data demonstrate that substitutions of EIII can allow the generation of viable chimeric viruses with significantly altered antigenicity and virulence. IMPORTANCE The envelope (E) glycoprotein is the major protein present on the surface of flavivirus virions and is responsible for mediating virus binding and entry into target cells. Several viable West Nile virus (WNV) variants with chimeric E proteins in which the putative receptor-binding domain (EIII) sequences of other mosquito-borne flaviviruses were substituted in place of the WNV EIII were recovered, although the substitution of several more divergent EIII sequences was not tolerated. The differences in virulence and tissue tropism observed with the chimeric viruses indicate a significant role for this sequence in determining the pathogenesis of the virus within the mammalian host. Our studies demonstrate that these chimeras are viable and suggest that such recombinant viruses may be useful for investigation of domain-specific antibody responses and the more extensive definition of the contributions of EIII to the tropism and pathogenesis of WNV or other flaviviruses.
PR Toxin – Biosynthesis, Genetic Regulation, Toxicological Potential, Prevention and Control Measures: Overview and Challenges

Out of the various mycotoxigenic food and feed contaminant, the fungal species belonging to Penicillium genera, particularly Penicillium roqueforti is of great economic importance, and well known for its crucial role in the manufacturing of Roquefort and Gorgonzola cheese. The mycotoxicosis effect of this mold is due to secretion of several metabolites, of which PR toxin is of considerable importance, with regard to food quality and safety challenges issues. The food products and silages enriched with PR toxin could lead into damage to vital internal organs, gastrointestinal perturbations, carcinogenicity, immunotoxicity, necrosis, and enzyme inhibition. Moreover, it also has the significant mutagenic potential to disrupt/alter the crucial processes like DNA replication, transcription, and translation at the molecular level. The high genetic diversities in between the various strains of P. roqueforti persuaded their nominations with Protected Geographical Indication (PGI), accordingly to the cheese type, they have been employed. Recently, the biosynthetic mechanism and toxicogenetic studies unraveled the role of ari1 and prx gene clusters that cross-talk with the synthesis of other metabolites or involve other cross-regulatory pathways to negatively regulate/inhibit the other biosynthetic route targeted for production of a strain-specific metabolites. Interestingly, the chemical conversion that imparts toxic properties to PR toxin is the substitution/oxidation of functional hydroxyl group (-OH) to aldehyde group (-CHO). The rapid conversion of PR toxin to the other derivatives such as PR imine, PR amide, and PR acid, based on conditions available reflects their unstability and degradative aspects. Since the PR toxin-induced toxicity could not be eliminated safely, the assessment of dose-response and other pharmacological aspects for its safe consumption is indispensable. The present review describes the natural occurrences, diversity, biosynthesis, genetics, toxicological aspects, control and prevention strategies, and other management aspects of PR toxin with paying special attention on economic impacts with intended legislations for avoiding PR toxin contamination with respect to food security and other biosafety purposes.
Impact of the IVF laboratory environment on human preimplantation embryo phenotype

The phenotype of the human embryo conceived through in vitro fertilization (IVF), that is its morphology, developmental kinetics, physiology and metabolism, can be affected by numerous components of the laboratory and embryo culture system (which comprise the laboratory environment). The culture media formulation is important in determining embryo phenotype, but this exists within a culture system that includes oxygen, temperature, pH and whether an embryo is cultured individually or in a group, all of which can influence embryo development. Significantly, exposure of an embryo to one suboptimal component of the culture system of laboratory typically predisposes the embryo to become more vulnerable to a second stressor, as has been well documented for atmospheric oxygen and individual culture, as well as for oxygen and ammonium. Furthermore, the inherent viability of the human embryo is derived from the quality of the gametes from which it is created. Patient age, aetiology, genetics, lifestyle (as well as ovarian stimulation in women) are all known to affect the developmental potential of gametes and hence the embryo. Thus, as well as considering the impact of the IVF laboratory environment, one needs to be aware of the status of the infertile couple, as this impacts how their gametes and embryos will respond to an in vitro environment. Although far from straight forward, analysing the interactions that exist between the human embryo and its environment will facilitate the creation of more effective and safer treatments for the infertile couple.
Multicenter Assessment of Gram Stain Error Rates

ABSTRACT Gram stains remain the cornerstone of diagnostic testing in the microbiology laboratory for the guidance of empirical treatment prior to availability of culture results. Incorrectly interpreted Gram stains may adversely impact patient care, and yet there are no comprehensive studies that have evaluated the reliability of the technique and there are no established standards for performance. In this study, clinical microbiology laboratories at four major tertiary medical care centers evaluated Gram stain error rates across all nonblood specimen types by using standardized criteria. The study focused on several factors that primarily contribute to errors in the process, including poor specimen quality, smear preparation, and interpretation of the smears. The number of specimens during the evaluation period ranged from 976 to 1,864 specimens per site, and there were a total of 6,115 specimens. Gram stain results were discrepant from culture for 5% of all specimens. Fifty-eight percent of discrepant results were specimens with no organisms reported on Gram stain but significant growth on culture, while 42% of discrepant results had reported organisms on Gram stain that were not recovered in culture. Upon review of available slides, 24% (63/263) of discrepant results were due to reader error, which varied significantly based on site (9% to 45%). The Gram stain error rate also varied between sites, ranging from 0.4% to 2.7%. The data demonstrate a significant variability between laboratories in Gram stain performance and affirm the need for ongoing quality assessment by laboratories. Standardized monitoring of Gram stains is an essential quality control tool for laboratories and is necessary for the establishment of a quality benchmark across laboratories.
Effect of sputtering power on properties and photovoltaic performance of CIGS thin film solar cells

CuInGaS2 (CIGS) thin films were fabricated by DC magnetron sputtering by varying the sputtering power (70, 90, 110 and 130 W). The X-ray diffraction revealed the formation of tetragonal structure with (1 1 2) preferential orientation. The film prepared at 90 W has better crystallinity with minimum dislocation density and strain. From the scanning electron microscopy analysis, it was found to be a denser and larger in grain formation. The elemental quantification and stoichiometric ratio of the CIGS films were confirmed by energy-dispersive spectra. The optical band gap was found using Tauc plot, and it varied from 1.20 to 1.52 eV. The transport conduction mechanism involved in CIGS films was identified from DC four-probe method. Raman studies reveal that all the films composed of CH and CA ordering. The solar cell measurements indicate that high power conversion efficiency (η) of 0.29% and short-circuit current density of (Jsc) of 4.51 mA/cm2 obtained for the film deposited at 90 W.
Frontal Theta Asymmetry as a Biomarker of Depression.

INTRODUCTION Electroencephalography (EEG) has been used extensively to study affective disorders. Quantitative spectral analysis of an EEG scan has been used to assess the biological basis of emotional disorders such as depression as well as to investigate biomarkers of affective disorders. Inter-hemispheric asymmetries in both baseline and stimulus-evoked frequencies (alpha, beta, theta, and delta) are potential biomarkers of depression. The role of frontal alpha asymmetry has been established, but other spectral frequencies such as frontal theta remain elusive. We compared the hemispheric differences in frontal theta power in depressed patients and controls before and during listening to music to study the correlation of frontal theta asymmetry with depression. METHODS To determine whether stimulus-evoked frontal theta asymmetry is a biomarker of depression, we compared 23 patients with mild depression (based on the Hamilton Depression Rating Scale) with 17 age- and sex-matched controls by conducting EEG at rest and after listening to Indian classical music. RESULTS In controls without depression, the mean frontal theta power of the left hemisphere and frontal theta asymmetry increased significantly during music listening. In depressed patients, frontal theta asymmetry was reversed during music listening. CONCLUSION Frontal theta asymmetry is a potential biomarker of depression.
Augmented mixed models for clustered proportion data

Often in biomedical research, we deal with continuous (clustered) proportion responses ranging between zero and one quantifying the disease status of the cluster units. Interestingly, the study population might also consist of relatively disease-free as well as highly diseased subjects, contributing to proportion values in the interval [0, 1]. Regression on a variety of parametric densities with support lying in (0, 1), such as beta regression, can assess important covariate effects. However, they are deemed inappropriate due to the presence of zeros and/or ones. To evade this, we introduce a class of general proportion density, and further augment the probabilities of zero and one to this general proportion density, controlling for the clustering. Our approach is Bayesian and presents a computationally convenient framework amenable to available freeware. Bayesian case-deletion influence diagnostics based on q-divergence measures are automatic from the Markov chain Monte Carlo output. The methodology is illustrated using both simulation studies and application to a real dataset from a clinical periodontology study.
Modeling and CFD Simulation of Abrasive Flow Machining Process

The abrasive flow machining (AFM) is a new finishing operation that involves abrasive particles as the tool to remove work material. AFM is broadly known as “no-tool” precision finishing operation and the carrier media containing abrasive particles is called as “self-deformable stone”. In AFM, a semi-solid polymer-based media containing abrasive powders in a particular proportion is flown through the work-piece at a certain pressure. The AFM consists of three major components, i.e. machine, media and tooling or fixture. The machine consists of a frame structure, control system, hydraulic cylinder and the media cylinder. The extrusion pressure for a standard AFM process varies from 10 bars to 100-200 bars. The function of tooling and fixture is to position the work-piece and provide direction to the media flow through the work-piece. The media consists of a carrier, abrasive powder and some additives. The flow of the media can be modeled using finite volume method as it deals with flow of a fluid. In the present work, FLUID FLOW FLUENT available in ANSYS 15 software package was used for the modeling and simulation. A 2D model for a cylindrical work-piece and a 3D model for four rotary swaging dies along with the fixtures have been prepared. Validation has been done for the two models with the existing experimental data. The most affecting flow output parameters like dynamic pressure, velocity and strain rate for different volume fraction and media speed have been analysed. The 3D model was simulated for both the non-granular and granular flow. The effects of different abrasive particles for variable diameter and volume fraction on the flow output parameters like granular pressure and skin friction coefficient have been studied. The flow analysis of the outputs gives a prediction of material removal efficiency.
Cryptococcus neoformans UGT1 encodes a UDP-Galactose/UDP-GalNAc transporter

Cryptococcus neoformans, an opportunistic fungal pathogen, produces a glycan capsule to evade the immune system during infection. This definitive virulence factor is composed mainly of complex polysaccharides, which are made in the secretory pathway by reactions that utilize activated nucleotide sugar precursors. Although the pathways that synthesize these precursors are known, the identity and the regulation of the nucleotide sugar transporters (NSTs) responsible for importing them into luminal organelles remain elusive. The UDP-galactose transporter, Ugt1, was initially identified by homology to known UGTs and glycan composition analysis of ugt1&Dgr; mutants. However, sequence is an unreliable predictor of NST substrate specificity, cells may express multiple NSTs with overlapping specificities, and NSTs may transport multiple substrates. Determining NST activity thus requires biochemical demonstration of function. We showed that Ugt1 transports both UDP-galactose and UDP-N-acetylgalactosamine in vitro. Deletion of UGT1 resulted in growth and mating defects along with altered capsule and cellular morphology. The mutant was also phagocytosed more readily by macrophages than wild-type cells and cleared more quickly in vivo and in vitro, suggesting a mechanism for the lack of virulence observed in mouse models of infection.
Detection of beat-to-beat intervals from wrist photoplethysmography in patients with sinus rhythm and atrial fibrillation after surgery

Wrist photoplethysmography (PPG) allows unobtrusive monitoring of the heart rate (HR). PPG is affected by the capillary blood perfusion and the pumping function of the heart, which generally deteriorate with age and due to the presence of cardiac arrhythmia. The performance of wrist PPG in monitoring beat-to-beat HR in older patients with arrhythmia has not been reported earlier. We monitored PPG from wrist in 18 patients recovering from surgery in the post-anesthesia care unit, and evaluated the inter-beat interval (IBI) detection accuracy against ECG based R-to-R intervals (RRI). Nine subjects had sinus rhythm (SR, 68.0y ± 10.2y, 6 males) and nine subjects had atrial fibrillation (AF, 71.3y ± 7.8y, 4 males) during the recording. For the SR group, 99.44% of the beats were correctly identified, 2.39% extra beats were detected, and the mean absolute error (MAE) was 7.34 ms. For the AF group, 97.49% of the heartbeats were correctly identified, 2.26% extra beats were detected, and the MAE was 14.31 ms. IBI from the PPG were hence in close agreement with the ECG reference in both groups. The results suggest that wrist PPG provides a comfortable alternative to ECG during low motion and can be used for long-term monitoring and screening of AF episodes.