Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive Analysis of Clinically Significant Hepatitis B Virus Mutations in Relation to Genotype, Subgenotype and Geographic Region

Hepatitis B virus (HBV) is a highly variable DNA virus due to its unique life cycle, which involves an error-prone reverse transcriptase. The high substitution rate drives the evolution of HBV by generating genetic variants upon which selection operates. HBV mutants with clinical implications have been documented worldwide, indicating the potential for spreading and developing their own epidemiology. However, the prevalence of such mutants among the different HBV genotypes and subgenotypes has not been systematically analyzed. In the current study, we performed large-scale analysis of 6,479 full-length HBV genome sequences from genotypes A-H, with the aim of gaining comprehensive insights into the relationships of relevant mutations associated with immune escape, antiviral resistance and hepatocellular carcinoma (HCC) development with HBV (sub)genotypes and geographic regions. Immune escape mutations were detected in 10.7% of the sequences, the most common being I/T126S (1.8%), G145R (1.2%), M133T (1.2%), and Q129R (1.0%). HBV genotype B showed the highest rate of escape mutations (14.7%) while genotype H had no mutations (P < 0.001). HCC-associated mutations were detected in 33.7% of the sequences, with significantly higher frequency of C1653T, T1753V and A1762T/G1764A in genotype G than C (P < 0.001). The overall frequencies of lamivudine-, telbivudine-, adefovir-, and entecavir-resistant mutants were 7.3, 7.2, 0.5, and 0.2%, respectively, while only 0.05% showed reduced susceptibility to tenofovir. In particular, the highest frequency of lamivudine-resistant mutations was observed in genotype G and the lowest frequency in genotype E (32.5 and 0.3%; P < 0.001). The prevalence of HBV mutants was also biased by geographic location, with North America identified as one of the regions with the highest rates of immune escape, antiviral resistance, and HCC-associated mutants. The collective findings were discussed in light of natural selection and the known characteristics of HBV (sub)genotypes. Our data provide relevant information on the prevalence of clinically relevant HBV mutations, which may contribute to further improvement of diagnostic procedures, immunization programs, therapeutic protocols, and disease prognosis.
Surface Tension of Structured Colloidal Suspensions of Polystyrene and Silica Spheres at the Air-Water Interface

Abstract Surface tensions, γ, of 19 kinds of colloidal spheres of monodispersed polystyrene and silica (6-460 nm in diameter) in crystal-like, liquid-like, and gas-like suspensions are studied systematically at the air-water interface by the Wilhelmy method. γ-values of the aqueous suspensions of colloidal silica spheres are close to that of pure water, though very weak surface activity [maximum in Δγ (surface tension of suspension minus that of water) is ca. -2 mN/m only] is detected for silica spheres of diameters ranging from 100 to 200 nm. The surface activity of polystyrene spheres, on the other hand, is high especially for spheres of diameters between 100 and 200 nm. The maximum in - Δγ is ca. 20 mN/m. The large difference in the surface activity between the two kinds of spheres is due to the difference in surface characters, i.e., highly polar and strongly hydrophobic for silica and polystyrene spheres, respectively. Furthermore, surface tension lowering of the crystal-like suspensions is substantial when compared with that of the liquid-like or gas-like suspensions. It is highly plausible that the intersphere distance in the two-dimensional colloidal crystals at the interface is shorter compared with that in the bulk phase by the shortened electrical double layers at the interface.
Platelets and Regulatory T Cells May Induce a Type 2 Immunity That Is Conducive to the Progression and Fibrogenesis of Endometriosis

Endometriosis is a hormonal disease, as well as a chronic inflammatory disease. While various immune cells are documented to be involved in endometriosis, there is a wanton lack of a bigger picture on how these cells are coordinated to work concertedly. Since endometriotic lesions experience cyclical bleeding, they are fundamentally wounds that undergo repeated tissue injury and repair (ReTIAR). In this study, we attempted to characterize the role of platelets and regulatory T cells (Tregs) in modulating the lesional immune microenvironment and its subsequent effects on lesional progression and fibrogenesis. Through two mouse experiments, we show that, by disrupting predominantly a type 2 immune response in lesional microenvironment, both platelets and Tregs depletion decelerated lesional progression and fibrogenesis, likely through the suppression of the TGF-β1/Smad3 and PDGFR-β/PI3K/Akt signaling pathways. In particular, platelet depletion resulted in significantly reduced lesional expression of thymic stromal lymphopoietin (TSLP), leading to reduced aggregation of macrophages and alternatively activated (M2) macrophages, and of Tregs, T helper 2 (Th2) and Th17 cells but increased aggregation of Th1 cells, in lesions, which, in turn, yields retarded fibrogenesis. Similarly, Tregs depletion resulted in suppression of platelet aggregation, and reduced aggregation of M2 macrophages, Th2 and Th17 cells but increased aggregation of Th1 cells, in lesions. Thus, both platelet and Tregs depletion decelerated lesional progression and fibrogenesis by disrupting predominantly a type 2 immunity in lesional microenvironment. Taken together, this suggests that both platelets and Tregs may induce a type 2 immunity in lesional microenvironment that is conducive to lesional progression and fibrogenesis.
Synergistic Effects of Catalyst Mixtures on Biomass Catalytic Pyrolysis

This paper studied the synergistic effects of catalyst mixtures on biomass catalytic pyrolysis in comparison with the single catalyst in a microwave reactor and a TGA. In general, positive synergistic effects were identified based on increased mass loss rate, reduced activation energy, and improved bio-oil quality compared to the case with a single catalyst at higher catalyst loads. 10KP/10Bento (a mixture of 10% K3PO4 and 10% bentonite) increased the mass loss rate by 85 and 45% at heating rates of 100 and 25°C/min, respectively, compared to switchgrass without catalyst. The activation energy for 10KP/10Bento and 10KP/10Clino (a mixture of 10% K3PO4 and 10% clinoptilolite) was slightly lower or similar to other catalysts at 30 wt. % load. The reduction in the activation energy by the catalyst mixture was higher at 100°C/min than 25°C/min due to the improved catalytic activity at higher heating rates. Synergistic effects are also reflected in the improved properties of bio-oil, as acids, aldehydes, and anhydrosugars were significantly decreased, whereas phenol and aromatic compounds were substantially increased. 30KP (30% K3PO4) and 10KP/10Bento increased the content of alkylated phenols by 341 and 207%, respectively, in comparison with switchgrass without catalyst. Finally, the use of catalyst mixtures improved the catalytic performance markedly, which shows the potential to reduce the production cost of bio-oil and biochar from microwave catalytic pyrolysis.
Volatile constituents of the essential oil of Nepeta ucrainica L. ssp. kopetdaghensis from Iran

Composition of the volatile oil of Nepeta ucraininca L. ssp. kopetdaghensis (Lamiaceae) was investigated by GLC and GC-MS. Forty-one compounds representing 89.5% of the total oil were characterized. The main components of the oil were germacrene-D (39.7%), palmitic acid (10.8%), β-bourbonene (5.8%) and spathulenol (5.6%). Nepetalact-one isomers were not present in the essential oil of N. ucrainica L. ssp. kopetdaghensis. Copyright © 2004 John Wiley & Sons, Ltd.
Synthesis and structure control of l‐lactic acid–glycolic acid copolymer by homo‐copolymerization

A two-step direct melt copolymerization process of l-lactic acid (L-LA)/glycolic acid (GA) was developed: poly(l-lactic acid) (PLLA) and poly(glycolic acid) (PGA) with different molecular weight was first synthesized respectively by binary catalyst (tin chloride/p-toluenesulfonic or tin chloride); and then poly(l-lactic-co-glycolic acid) (b-PLGA) was produced by melt polymerization of the as-prepared PLLA and PGA, wherein the composition and chain structure of b-PLGA copolymers could be controlled by the molecular weight of PLLA. The chain structure and thermal properties of copolymers were studied by Wide-angle X-ray diffraction, nuclear magnetic resonance, differential scanning calorimetry, and thermogravimetric analysis. In comparison with the random PLGA (r-PLGA) synthesized by one-step direct melt polymerization, the average l-lactic blocks length (LLA) in b-PLGA was longer while the average glycolic blocks length (LGA) in b-PLGA was shorter which further resulted in the improved crystallinity and thermostability. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41566.
Solvent-Induced Crystallization of Polyarylene Sulfide Sulfone

In this paper, N-methyl-2-pyrrolidone (NMP) induced crystallization behavior of PASS was found and studied. To study NMP induced crystallization of PASS, Differential Scanning Calorimeter (DSC), X-Ray Powder Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR) and Thermogravimetric Analysis (TGA) were employed. The results showed that the crystal induced by NMP was consistent with precipitates obtained in solution, and was the eutectic of PASS and NMP. With the induction time increased, crystalline region continued to improve and the crystal size became bigger.
Structural aspects of [NiFe]-hydrogenases

Abstract Enzymes that naturally contain an organometallic complex are highly rare. Hydrogenases commonly include iron carbonyl(s) at the active site and play central roles in the hydrogen metabolism of microorganisms. [NiFe]-hydrogenases that harbor an Ni-Fe(CN)2CO complex at the active site most widely exist among organisms, compared with the other two types, [FeFe]- and [Fe]-hydrogenases. Since the first crystal structure report in 1995, structural information of the Ni-Fe cluster with various redox/substrate-bound states has been obtained, although details of the reaction mechanisms are poorly understood. While the subunit composition, physiological function, and spectroscopic/biochemical properties of [NiFe]-hydrogenases are diverse, structural information of only a limited group of the enzymes is available so far. In this paper, structural aspects of [NiFe]-hydrogenases are reviewed and recent progresses in understanding the mechanism of an O2-tolerant property of limited members and active site assembling of [NiFe]-hydrogenases are described.
Thermal Gelation of Methylcellulose in Water: Scaling and Thermoreversibility

Thermally induced gelation was studied for aqueous solutions of methylcellulose with a substitution degree of 1.8 and molecular weight of 310 000. The dynamic viscoelastic and microcalorimetric properties were measured as functions of temperature and polymer concentration. An attempt was made to elucidate the validity of scaling laws and the mechanism involved in the thermoreversible gelation of methylcellulose. For a given high concentration of methlycellulose, the gel elasticity evolved with temperature, but it did not obey a single scaling law. At the gelation temperature of 70 °C, the gel elasticity increased with polymer concentration, and it could be expressed with a two-step scaling, from which the weak gels and the strong gels could be defined. For the weak gels (c ≤ 1 wt %), the elasticity Ge at 70 °C scaled with polymer concentration c as Ge ∼ c1.34, while Ge scaled with c as Ge ∼ c3.03 for the strong gels (c > 1 wt %). The thermoreversibility was examined through a cycle of heating to cooling, .
The hydration mechanism in plant polysaccharides: a physicochemical and dielectric study

Polysaccharides play a vitally important part in the lives of plants and animals, both as structural elements and in the maintenance of functional activity. In this work, we investigate the hydration mechanism of various polysaccharides of plant origin and concentrate, more particularly, in the comparison between results obtained with starches of various origin, on the one hand, and cellulose samples, on the other, using equilibrium and dynamic water sorption isotherms, thermally stimulated depolarization currents (TSDC) techniques in the temperature range 77-300 K and dielectric relaxation spectroscopy in the frequency range 10-10/sup 7/ Hz. The dependence of the characteristics of dielectric spectra on the water content and on the nature of the polysaccharide is investigated and their origin is interpreted on the basis of the nature of the polysaccharide and of results obtained in the first part of the work.
Recycling of waste poly(ethylene terephthalate) into flame‐retardant rigid polyurethane foams

Waste poly(ethylene terephthalate) (PET) textiles were effectively chemical recycling into flame-retardant rigid polyurethane foams (PUFs). The PET textile wastes were glycolytically depolymerized to bis(2-hydroxyethyl) terephthalate (BHET) by excess ethylene glycol as depolymerizing agent and zinc acetate dihydrate as catalyst. The PUFs were produced from BHET and polymeric methane diphenyl diisocyanate. The structures of BHET and PUFs were identified by FTIR spectra. The limiting oxygen index (LOI) of the PUFs (≥23.27%) was higher than that of common PUFs (16–18%), because the aromatic substituent in the depolymerized products improved the flame retardance. To improve the LOI of the PUFs, dimethyl methylphosphonate doped PUFs (DMMP-PUFs) were produced. The LOI of DMMP-PUFs was approached to 27.69% with the increasing of the doped DMMP. The influences of the flame retardant on the foams density, porosity, and compression properties were studied. Furthermore, the influences of foaming agent, catalyst, and flame retardant on the flame retardation were also investigated. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40857.
hBMSC-Derived Extracellular Vesicles Attenuate IL-1β-Induced Catabolic Effects on OA-Chondrocytes by Regulating Pro-inflammatory Signaling Pathways

Background: Human bone marrow-derived mesenchymal stromal cells (hBMSCs) provide a promising therapeutic approach in the cell-based therapy of osteoarthritis (OA). However, several disadvantages evolved recently, including immune responses of the host and regulatory hurdles, making it necessary to search for alternative treatment options. Extracellular vesicles (EVs) are released by multiple cell types and tissues into the extracellular microenvironment, acting as message carriers during intercellular communication. Here, we investigate putative protective effects of hBMSC-derived EVs as a cell-free approach, on IL-1β-stimulated chondrocytes obtained from OA-patients. Methods: EVs were harvested from the cell culture supernatant of hBMSCs by a sequential ultracentrifugation process. Western blot, scanning electron microscopy (SEM), and nanoparticle tracking analysis (NTA) were performed to characterize the purified particles as EVs. Intracellular incorporation of EVs, derived from PHK26-labeled hBMSCs, was tested by adding the labeled EVs to human OA chondrocytes (OA-CH), followed by fluorescence microscopy. Chondrocytes were pre-stimulated with IL-1β for 24 h, followed by EVs treatment for 24 h. Subsequently, proliferation, apoptosis, and migration (wound healing) were analyzed via BrdU assay, caspase 3/7 assay, and scratch assay, respectively. With qRT-PCR, the relative expression level of anabolic and catabolic genes was determined. Furthermore, immunofluorescence microscopy and western blot were performed to evaluate the protein expression and phosphorylation levels of Erk1/2, PI3K/Akt, p38, TAK1, and NF-κB as components of pro-inflammatory signaling pathways in OA-CH. Results: EVs from hBMSCs (hBMSC-EVs) promote proliferation and reduce apoptosis of OA-CH and IL-1β-stimulated OA-CH. Moreover, hBMSC-EVs attenuate IL-1β-induced reduction of chondrocyte migration. Furthermore, hBMSC-EVs increase gene expression of PRG4, BCL2, and ACAN (aggrecan) and decrease gene expression of MMP13, ALPL, and IL1ß in OA-CH. Notably, COL2A1, SOX9, BCL2, ACAN, and COMP gene expression levels were significantly increased in IL-1β+ EV groups compared with those IL-1β groups without EVs, whereas the gene expression levels of COLX, IL1B, MMP13, and ALPL were significantly decreased in IL-1β+ EV groups compared to IL-1β groups without EVs. In addition, the phosphorylation status of Erk1/2, PI3K/Akt, p38, TAK1, and NF-κB signaling molecules, induced by IL-1β, is prevented by hBMSC- EVs. Conclusion: EVs derived from hBMSCs alleviated IL-1β-induced catabolic effects on OA-CH via promoting proliferation and migration and reducing apoptosis, probably via downregulation of IL-1ß-activated pro-inflammatory Erk1/2, PI3K/Akt, p38, TAK1, and NF-κB signaling pathways. EVs released from BMSCs may be considered as promising cell-free intervention strategy in cartilage regenerative medicine, avoiding several adverse effects of cell-based regenerative approaches.
Investigating Pregnancy and Its Complications Using Circulating Cell-Free RNA in Women's Blood During Gestation

In recent years, there have been major advances in the application of non-invasive techniques to predict pregnancy-related complications, for example by measuring cell-free RNA (cfRNA) in maternal blood. In contrast to cell-free DNA (cfDNA), which is already in clinical use to diagnose fetal aneuploidy, circulating RNA levels can correspond with tissue-specific gene expression and provide a snapshot of prenatal health across gestation. Here, we review the physiologic origins of cfRNA and its novel applications and corresponding challenges to monitor fetal and maternal health and predict pregnancy-related complications.
The Evolving Role of Radiation Therapy in the Treatment of Biliary Tract Cancer

Biliary tract cancers (BTC) are a disease entity comprising diverse epithelial tumors, which are categorized according to their anatomical location as intrahepatic (iCCA), perihilar (pCCA), distal (dCCA) cholangiocarcinomas, and gallbladder carcinomas (GBC), with distinct epidemiology, biology, and prognosis. Complete surgical resection is the mainstay in operable BTC as it is the only potentially curative treatment option. Nevertheless, even after curative (R0) resection, the 5-year survival rate ranges between 20 and 40% and the disease free survival rates (DFS) is approximately 48–65% after one year and 23–35% after three years without adjuvant treatment. Improvements in adjuvant chemotherapy have improved the DFS, but the role of adjuvant radiotherapy is unclear. On the other hand, more than 50% of the patients present with unresectable disease at the time of diagnosis, which limits the prognosis to a few months without treatment. Herein, we review the role of radiotherapy in the treatment of cholangiocarcinoma in the curative and palliative setting.
Current Insights Into Adrenal Insufficiency in the Newborn and Young Infant

Adrenal insufficiency (AI) is a potentially life-threatening condition that can be difficult to diagnose, especially if it is not considered as a potential cause of a child's clinical presentation or unexpected deterioration. Children who present with AI in early life can have signs of glucocorticoid deficiency (hyperpigmentation, hypoglycemia, prolonged jaundice, poor weight gain), mineralocorticoid deficiency (hypotension, salt loss, collapse), adrenal androgen excess (atypical genitalia), or associated features linked to a specific underlying condition. Here, we provide an overview of causes of childhood AI, with a focus on genetic conditions that present in the first few months of life. Reaching a specific diagnosis can have lifelong implications for focusing management in an individual, and for counseling the family about inheritance and the risk of recurrence.
Relation Between Reading Performance and White-Matter Alteration and Reorganization in Neurosurgical Patients

Reading abilities and diffusion tensor imaging (DTI) parameters were retrospectively analyzed in a group of neurosurgical patients to investigate (Study 1) the role of white matter—in particular the arcuate fasciculus (AF)—in preserved vs. impaired reading; 4 months after surgery, we explored the plasticity processes (Study 2). Study 1 involved 40 patients with brain glioma (23 low-grade and 17 high-grade gliomas). We compared preoperative DTI parameters of language-related fascicles between patients who developed a reading impairment after surgery (n = 23) and patients with preserved reading (n = 17). Besides lower fractional anisotropy (FA), patients with impaired reading also displayed lower number and density of streamlines of a direct (i.e., directly connecting temporal and frontal lobes) AF segment. In Study 2, we longitudinally tested at follow-up-when reading performance had generally improved-13 patients diagnosed with low-grade glioma. The most relevant finding was a significant increase in length of streamlines of the direct AF segments in both hemispheres. From a neurosurgical perspective, our preliminary findings suggest the clinical importance of sparing direct AF segments for the involvement they showed in reading; however, the results also suggest the reorganization potential of these segments, possibly compensating of the right homologs as well.
How the Toxin got its Toxicity

Venom systems are functional and ecological traits, typically used by one organism to subdue or deter another. A predominant subset of their constituent molecules—“toxins”—share this ecological function and are therefore molecules that mediate interactions between organisms. Such molecules have been referred to as “exochemicals. ” There has been debate within the field of toxinology concerning the evolutionary pathways leading to the “recruitment” of a gene product for a toxic role within venom. We review these discussions and the evidence interpreted in support of alternate pathways, along with many of the most popular models describing the origin of novel molecular functions in general. We note that such functions may arise with or without gene duplication occurring and are often the consequence of a gene product encountering a novel “environment,” i.e., a range of novel partners for molecular interaction. After stressing the distinction between “activity” and “function,” we describe in detail the results of a recent study which reconstructed the evolutionary history of a multigene family that has been recruited as a toxin and argue that these results indicate that a pluralistic approach to understanding the origin of novel functions is advantageous. This leads us to recommend that an expansive approach be taken to the definition of “neofunctionalization”—simply the origins of a novel molecular function by any process—and “recruitment”—the “weaponization” of a molecule via the acquisition of a toxic function in venom, by any process. Recruitment does not occur at the molecular level or even at the level of gene expression, but only when a confluence of factors results in the ecological deployment of a physiologically active molecule as a toxin. Subsequent to recruitment, the evolutionary regime of a gene family may shift into a more dynamic form of “birth-and-death. ” Thus, recruitment leads to a form of “downwards causation,” in which a change at the ecological level at which whole organisms interact leads to a change in patterns of evolution at the genomic level.