Miracle-dz/UniFAR-FTUs huggingface dataset:
Generation of Synthetic Elastin-Mimetic Small Diameter Fibers and Fiber Networks

Elastin-mimetic peptide polymers have been synthesized, and the morphological properties of fabricated small diameter fibers and nonwoven fabrics have been characterized. An 81 kDa recombinant protein based upon the repeating elastomeric peptide sequence of elastin (Val-Pro-Gly-Val-Gly)4(Val-Pro-Gly-Lys-Gly) was obtained through bacterial expression of an oligomerized gene coding for tandem repeats of the monomer. The protein was processed into fibers by an electrospinning technique and morphology defined by SEM and TEM. The choice of processing parameters influenced both fiber diameter and morphology with diameters varying between 200 and 3000 nm and three morphological patterns noted: beaded fibers, thin filaments, and broad ribbonlike structures. Detailed image analysis of nonwoven textile fabrics produced from elastin-mimetic fibers revealed that the distribution of single fiber orientation was isotropic with an associated unimodal distribution of protein fiber diameter. In a dry state, the ultimate .
Antioxidant Phenolic Compounds of Ethanolic and Aqueous Extracts from Pink Cedar (Acrocarpus fraxinifolius Whight & Arn.) Bark at Two Tree Ages

In Central Mexico, commercial plantations of pink cedar (Acrocarpus fraxinifolius Whight & Arn.) from 7 to 15 years old are ready for harvesting to obtain wood products without current bark use. Therefore, the aim of this work was to study ethanolic and hot water extracts from A. fraxinifolius bark of 7-year-old (young) and 13-year-old (mature) trees. Yields, total phenolic, flavonoid, and proanthocyanidin contents, as well radical scavenging activity by 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) radicals, as well by ferric-reducing antioxidant power (FRAP) and low-density lipoprotein inhibition assays were estimated. Extracts of young tree barks showed higher phenolic content and better scavenging activity than extracts from mature tree barks; ethanolic extracts were superior to the aqueous ones. Positive correlations between polyphenol content and scavenging activity were observed. Results suggest that A. fraxinifolius bark loses phenolic content and antiradical activity as it ages. Bioactive phenolics such as gallic acid, catechin, epicatechin, and catechin gallate were identified by HPLC-DAD.
Electrokinetic separations with micellar solutions and open-tubular capillaries

La methode de separation electrocinetique donnee peut etre consideree comme un type de chromatographie de partage liquide-liquide ne necessitant pas de support solide pour maintien de la phase liquide stationnaire, et dans laquelle les micelles sont considerees comme une pseudo-phase
The solvent extraction of metals

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SEEDING THE PREGENETIC EARTH: METEORITIC ABUNDANCES OF NUCLEOBASES AND POTENTIAL REACTION PATHWAYS

Carbonaceous chondrites are a class of meteorite known for having high contents of water and organics. In this study, the abundances of the nucleobases, i.e., the building blocks of RNA and DNA, found in carbonaceous chondrites are collated from a variety of published data and compared across various meteorite classes. An extensive review of abiotic chemical reactions producing nucleobases is then performed. These reactions are then reduced to a list of 15 individual reaction pathways that could potentially occur within meteorite parent bodies. The nucleobases guanine, adenine, and uracil are found in carbonaceous chondrites in amounts of 1–500 ppb. It is currently unknown which reaction is responsible for their synthesis within the meteorite parent bodies. One class of carbonaceous meteorite dominates the abundances of both amino acids and nucleobases—the so-called CM2 (e.g., Murchison meteorite). CR2 meteorites (e.g., Graves Nunataks) also dominate the abundances of amino acids, but are the least abundant in nucleobases. The abundances of total nucleobases in these two classes are 330 ± 250 and 16 ± 13 ppb, respectively. Guanine most often has the greatest abundances in carbonaceous chondrites with respect to the other nucleobases, but is 1–2 orders of magnitude less abundant in CM2 meteorites than glycine (the most abundant amino acid). Our survey of the reaction mechanisms for nucleobase formation suggests that Fischer–Tropsch synthesis (i.e., CO, H2, and NH3 gases reacting in the presence of a catalyst such as alumina or silica) is the most likely candidate for conditions that characterize the early states of planetesimals.
Endothelial dysfunction : mechanisms and reversal in insulin resistance and diabetes mellitus

Injury to the vascular wall resulting in endothelial dysfunction is recognised as a key early event that initiates and promotes progression of atherosclerosis. Studies have shown that endothelial dysfunction, characterised by impaired endotheliumdependent flow mediated dilatation (FMD), is present from early in life in association with cardiovascular risk factors. This thesis investigates the mechanisms of impaired FMD and describes its relation to risk factors and inflammatory markers in healthy subjects with insulin resistance and type 1 diabetes mellitus. In healthy volunteers, the role of nitric oxide in conduit artery dilatation, in response to flow stimuli with differing dynamic characteristics, was examined. It has been demonstrated that NO is an important mediator of transient flow stimuli, whilst dilatation to sustained flow occurs by a NO independent mechanism. Furthermore, in subjects with hypercholesterolaemia impaired flow-mediated dilatation was confined to the NO pathway. In a large population based cohort, the determinants of vascular dysfunction have been studied with particular reference to the roles of insulin resistance, glucose intolerance and the metabolic syndrome. These studies demonstrate an abnormality of vascular function in association with the metabolic syndrome that is not mediated by insulin resistance per se. In contrast, associations between classical risk factors, inflammation and impaired endothelial function and arterial elasticity are demonstrated. In experimental models reversal of endothelial dysfunction retards the progression of atherosclerosis. Whilst such an approach remains unproven in humans, this thesis describes studies designed to test the effects of specific interventions, on endothelial function in young patients with insulin-dependent diabetes. No benefit has been demonstrated following ACE inhibition or administration of L-arginine, the precursor of NO but significant improvement in FMD was seen after cholesterol reduction. Conclusion The studies presented in this thesis enhance the understanding of conduit artery physiology and the mechanisms of endothelial dysfunction in patients with risk factors for atherosclerosis. Understanding these mechanisms will be important in the development of strategies targeted at retarding atherosclerosis early in its natural history. Using non-invasive techniques, the benefit of such interventions, on arterial physiology, can be demonstrated from an early age.
Passivity of Metals, Alloys, and Semiconductors

The sections in this article are Introduction Definition of Passivity Survey of Systems General Principles of Passivity Thermodynamics and Bond Polarity Experimental Techniques for Characterization of Passive Films Thickness and Stoichiometry of Passive Films Chemistry, Crystal Structure and Aging Chemistry and Crystal Structure Aging Potential Distribution at the Interface Electrochemical and Chemical Reactions in Passive Systems Reactions Current Densities i Ionic Properties, Migration and Ion-Transfer Reactions Electronic Behavior and ETR Band Structure of Oxide Films Electron-Transfer Reactions ETR at Oxide Films Mixed Ionic/Electronic Conductivity Equivalent Circuit Diagrams Growth of Oxide Films and Ionic Migration Survey on the Growth of Oxide Films Insulating Passive Films on Metals: Growth, and Corrosion of Al as Example Thermodynamic Aspects A Survey on Oxide Formation from CVs The Film Formation Factor k Electrochemical Impedance Spectra EIS and Equivalent Circuit Diagram Kinetics of Film Growth Corrosion and Breakdown Porous Aluminum Oxide Other Types of Passive Aluminum Oxide Films, Anof, Modified Aluminum, Alloys Other Systems Other Metals Forming Insulating Oxide Films Semiconducting and Metallic Oxide Films on Metals Duplex Films Passivation with Participation of the Electrolyte Semiconductors Passivation of Alloys ITR at the Homogeneous Oxide/Electrolyte Interface: Corrosion and Modification Passive Corrosion in the Steady State Corrosion during Oxide Growth Oxide Reduction and Oxidation Modification of Oxide Films by ITR of Other Ions Corrosion at Inhomogeneous Films: Breakdown, Pitting and Localized Attack Microscopic and Molecular Reasons for Local Corrosion Dielectric Breakdown Collision ionization model Tunnel model for thin films Pitting Corrosion Cathodic Breakdown Laser Induced Breakdown or Oxide Growth Applications Conclusions Acknowledgments
Uso del residual sólido de biogás en la fertilización del plátano fruta

Para lograr incremento de los rendimientos en el cultivo del platano fruta, en suelos Ferriticos Rojo Oscuro tipico, se utilizo el residual de biogas en su estado solido, el cual se caracterizo quimica y microbiologicamente. Se estudiaron dosis de (0,1, 2 y 3 kg. planta-1); en un diseno de bloque al azar y 4 replicas. En las mediciones se tuvo en cuenta, el peso del racimo, el numero de manos y el numero de dedos de la segunda mano de cada racimo. Se hicieron muestreos del suelo al inicio y al finalizar el estudio, para determinar pH (KCl), P2 O5, K2 O y materia organica. La caracterizacion del residual sirvio para conocer sus posibilidades de utilizacion como abono, las cuales son muy positivas. La mejor dosis encontrada fue la de 3 kg.planta-1, lograndose rendimientos de 35.00 t.ha-1; alcanzandose un beneficio economico de 1 430.76 $. ha- 1 ; ademas de un aumento de los contenidos de P2 O5 , K2 O y la materia organica al finalizar el estudio con la dosis empleada
The issue of pseudoreplication when applying a statistical exploratory approach to extract relevant features from ToF‐SIMS spectra

The issue of automated peak selection in time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) spectra is examined in relation to the hierarchical nature of the experimental design and the related existence of observations which are not statistically independent. To avoid unreliable results, the presence of pseudoreplication should be taken into account correctly. A combination of the recommended univariate peak selection approach with some multivariate techniques, namely principal component analysis and heat map data representation, is proposed to highlight and analyze obtained results for a set of ToF‐SIMS spectra from copper phthalocyanine thin films grown on TiO2 substrates by a supersonic beam deposition apparatus. New insight is obtained on the effectiveness of the deposition for different working parameters of the process. Copyright © 2013 John Wiley & Sons, Ltd.
Optimierte atom- und aminosäurespezifische Gewichtungsfaktoren für Protein-Docking Methoden

Protein-Protein Docking ist eine bioinformatische Methode, bei der aus zwei Protein Strukturen, von denen bekannt ist, dass sie in vivo aneinander binden, die dreidimensionale Struktur des Komplexes mit atomarer Auflosung vorhergesagt wird. Die Kenntnis der Struktur ist von grosem wissenschaftlichem Interesse, da oft nur so die genaue Funktion der jeweiligen Interaktion studiert werden kann. Komplexstrukturen konnen zwar meistens auch experimentell ermittelt werden, allerdings sind die bekannten Methoden oftmals extrem zeitaufwandig, so dass es einen betrachtlichen Bedarf an in silico Methoden zur Vorhersage von Proteinkomplexstrukturen gibt. Aktuelle Docking Methoden konnen zwar fur die meisten Komplexe eine der nativen Struktur ahnliche Struktur berechnen, allerdings ist diese richtige Vorhersage in der Regel eine von mehreren tausend als moglich vorhergesagten Strukturen. Das Ziel dieser Arbeit war daher die Entwicklung einer Methode zur Identifikation der richtigen, nahe nativen Struktur aus allen als moglich vorhergesagten Strukturen. Um dieses Ziel zu erreichen, wurde die - in den meisten Docking Programmen benutzte - Darstellung der Proteine als 3D-Gitter um Gewichtungsfaktoren erweitert, welche spezifisch fur die jeweils reprasentierten Atome und Aminosauren durch mathematische Methoden optimiert wurden. Die Optimierungen wurden fur drei Komplexklassen (Enzym-Inhibitor, Antikorper-Antigen und "Andere") durchgefuhrt. Die erhaltenen optimierten atom- und aminosaurespezifischen Gewichtungsfaktoren stehen z.T. in Einklang mit zuvor beobachteten Eigenschaften von Protein-Protein Bindungsstellen. So wurden z.B. hohe Gewichtungsfaktoren fur aromatische, hydrophobe und rigide Residuen optimiert, wahrend die Optimierung fur Aminosauren mit langen flexiblen Seitenketten eher niedrige Faktoren ergeben hat. Da die erhaltenen Gewichtungsfaktoren fur Enzym-Inhibitor Komplexe in Relation zu der Anzahl frei drehbarer Seitenketten stehen, ist die in dieser Arbeit vorgestellte Methode eine auserst effiziente Moglichkeit Flexibilitat beim Docking zu berucksichtigen. Durch eine Sortierung der potentiellen Komplexstrukturen nach der mit den Gewichtungsfaktoren berechneten geometrischen Korrelation in Kombination mit Martins umfassender Scoringfunktion kann der Anteil an Komplexen, fur die eine nahe native Struktur unter den ersten 10 vorhergesagten Strukturen liegt, verzehnfacht werden. Fur 80% der Enzym-Inhibitor und der Antikorper-Antigen Komplexe wird nach Anwendung der Gewichtungsfaktoren mindestens eine nahe native Struktur im ersten Prozent der sortierten Vorhersage gefunden. Um fur 80% der "Anderen" Komplexe mindestens eine nahe native Struktur zu finden, mussen die ersten 8% der Vorhersage durchsucht werden.
Studies on kinetics of iron oxide reduction

AbstractThis paper is a review of the iron-oxide reduction research that has been in progress for some years at the University of Toronto. Emphasis has been directed toward the kinetics of hydrogen reduction of sintered briquettes made from reagent-grade iron oxide with and without small additions of impurities. For simulation of hematite ores, the ferric oxide was used directly while the same material, reduced to magnetite, was used to simulate magnetite ores.It was found that hematite reduced in a topochemical manner, and that the reduction rate increased with temperature. For magnetite, a pronounced rate minimum was observed around 700°C at which the briquettes reduced uniformly throughout, leaving grains of unreacted wustite in the iron product. A topochemical pattern of reduction was observed at higher and lower temperatures. Some impurities eliminated the rate minimum.The rate mmimum has been singled out for special study and it has been established that it is controlled by solid-state diffusion in .
Function and dynamics of aptamers: A case study on the malachite green aptamer

Aptamers are short single-stranded nucleic acids that can bind to their targets with high specificity and high affinity. To study aptamer function and dynamics, the malachite green aptamer was chosen as a model. Malachite green (MG) bleaching, in which an OH- attacks the central carbon (C1) of MG, was inhibited in the presence of the malachite green aptamer (MGA). The inhibition of MG bleaching by MGA could be reversed by an antisense oligonucleotide (AS) complementary to the MGA binding pocket. Computational cavity analysis of the NMR structure of the MGA-MG complex predicted that the OH{sup -} is sterically excluded from the C1 of MG. The prediction was confirmed experimentally using variants of the MGA with changes in the MG binding pocket. This work shows that molecular reactivity can be reversibly regulated by an aptamer-AS pair based on steric hindrance. In addition to demonstrate that aptamers could control molecular reactivity, aptamer dynamics was studied with a strategy combining molecular dynamics (MD) simulation and experimental verification. MD simulation predicted that the MG binding pocket of the MGA is largely pre-organized and that binding of MG involves reorganization of the pocket and a simultaneous twisting of the MGA terminal stems around the pocket. MD simulation also provided a 3D-structure model of unoccupied MGA that has not yet been obtained by biophysical measurements. These predictions were consistent with biochemical and biophysical measurements of the MGA-MG interaction including RNase I footprinting, melting curves, thermodynamic and kinetic constants measurement. This work shows that MD simulation can be used to extend our understanding of the dynamics of aptamer-target interaction which is not evident from static 3D-structures. To conclude, I have developed a novel concept to control molecular reactivity by an aptamer based on steric protection and a strategy to study the dynamics of aptamer-target interaction by combining MD simulation and experimental verification. The former has potential application in controlling metabolic reactions and protein modifications by small reactants and the latter may serve as a general approach to study the dynamics of aptamer-target interaction for new insights into mechanisms of aptamer-target recognition.
Characterization of Chemical Bath Deposited CdS, CdSe and PbS

CdS, CdSe and PbS films were grown onto glass by chemical bath deposition (CBD). Different constant deposition temperatures (Td) were employed in the range 0-80 °C with subintervals of 10 °C. Concentration of reagents, pH, and stirring were maintained constants. A microcrystalline mixture CdCO3 and CdS were grown. At intermediates Td values a mixture of both materials present. i.e., For Td ൑ 40 °C, the intensity of the main of X-ray Diffraction (XRD) CdS peak is abruptly reduced. By scanning electronic microscopy (SEM) with Td = 80 °C, concentration atomic: Cd = 49.10, S = 51.90, for Td ൑ 70 °C, increase of carbon and oxygen. The CdSe, average grain size (GS) increased monotonic with Td, reaching saturation of 70 °C, with GS values of 5-16 nm. At low Td values (0-20 °C), the structural phase was found, and the high Td = 70 °C on material 5-16 nm was appreciated transition to phase: Wurzite (W)՜ Zinbclende (ZB) and phases mixture: W/ZB, grain size (GS) 9-27 nm. By (XRD), PbS grow in W phase at all films, for Td = 60 °C, was observed preferential orientation in plane (111) with (GS) of 19-26 nm also a Gibbs free energy calculation is included.
Paternal CHH methylation potentiates stress responses against Pseudomonas syringae in Arabidopsis progenies

Systemic acquired resistance (SAR) is an induced immune mechanism in plants, involving epigenetic regulation by chromatin remodeling and DNA methylation, which can be inherited to progeny following stress exposure. Intersexual epigenetic conflict sometimes leads to unequal expression of maternal and paternal alleles in offspring, resulting in parent-of-origin effects of inheritance. To better understand the parental contributions of epialleles in plant defense, isogenic Arabidopsis parental lines were mock-treated (M) and Pseudomonas syringae (Pst)-treated (P) for reciprocal crosses to produce F1 progenies (MP, PM). Together with their self-fertilized F1 descendants (MM, PP), the genome-wide inherited DNA methylation and transcriptomic changes against Pst were analyzed. F1 descendants shared widespread DNA methylation and transcriptional changes at transposable elements (TEs) and genes. The confrontation of epigenomes triggers the reprogramming of DNA methylation in reciprocal crosses, resulting in transgressive segregation that also shows the parental effect of Pst treatment. Compared to PM, the MP (Pst-primed paternal genome) was found to contributes to CHH hypermethylation, which is associated with processes in plant-pathogen interaction, including carbohydrate metabolism, glutathione metabolism and stronger translation process, which potentially contribute to improved disease resistance in MP in response to Pst challenge. Our data suggested a parent-of-origin effect of defense priming that contributes differently toward improved defense response in progenies.
Sustainable Poly(lactide-b-butadiene) Multiblock Copolymers with Enhanced Mechanical Properties

To develop mechanically improved polylactide (PLA)-based sustainable polymers, a series of poly(lactide-b-butadiene) (PLA–PB) multiblock copolymers were synthesized in a two-step procedure: PLA–PB–PLA (LBL) triblock copolymers were prepared using ring-opening polymerization of d,l-lactide, followed by chain extension of LBL triblock polymers with toluene-2,4-diisocyanate (TDI) and terephthaloyl chloride (TCl). Molecular characterization revealed that the synthetic procedures yielded the desired triblock and multiblock copolymers with a composition range of 0.5 ≤ fPLA ≤ 0.9. Differential scanning calorimetry (DSC), small-angle X-ray scattering (SAXS), and transmission electron microscopy (TEM) demonstrated nearly identical, well-ordered, morphologies in the homologous triblock and multiblock copolymer materials, in sharp contrast with the findings of a recent study involving poly(styrene-b-butadiene) (PS–PB) multiblock polymers. These results indicate a transition from classically ordered morphologies to a.
Gas Permeation in SPE Method I . Oxygen Permeation Through Nafion and NEOSEPTA

The permeation of oxygen at atmospheric pressure through Nafion® 120 and NEOSEPTA® ACH‐45T ion‐exchange membranes was investigated by an electrochemical monitoring technique, which utilizes SPE composite electrodes prepared by an electroless plating method. The oxygen diffusion coefficients were almost the same for each material, but the oxygen solubility was much higher in Nafion than in NEOSEPTA. The oxygen solubility in NEOSEPTA could be explained in terms of dissolution in the aqueous component of the membrane, but the oxygen solubility in Nafion was too high for such an explanation, and was postulated to involve the role of the polytetrafluoroethylene backbone.