Miracle-dz/UniFAR-FTUs huggingface dataset:
A multi-scale study of enzyme diffusion in macromolecular solutions and physical gels of pectin polysaccharides

Pectin accounts for one of the major polysaccharides of the plant cell wall. Pectin methylesterases (PMEs) are enzymes that are able to alter the pectin structure and affect its gelling properties by de-esterifying galacturonic acid. In this work, the diffusion of two PMEs with different origins and modes of action was characterised with a multi-scale approach in different media consisting of pectin macromolecular solutions and physical gels. Fluorescence Recovery After Photobleaching (FRAP) and Fluorescent Correlation Spectroscopy (FCS) investigations showed similar diffusion behaviour for both enzymes at a microscopic scale. In contrast, their behaviours tended to differ when increasing the observation scale up to mm. Indeed, fungal PMEs diffused faster and in a larger range than plant PMEs. These results are discussed with regard to the respective modes of action, processivity and in vivo roles of the two enzymes.
SET‐LRP of methyl methacrylate initiated with CCl4 in the presence and absence of air

Single electron transfer-living radical polymerization (SET-LRP) represents a robust and versatile method for the rapid synthesis of macromolecules with defined architecture. The synthesis of poly(methyl methacrylate) via SET-LRP in dimethyl sulfoxide (DMSO) by using CCl4 as initiator is demonstrated in this work. Resorting to a rather simple Cu(0)/Me6-TREN catalyst a method was established that allowed for the straightforward design of well-defined poly(methyl methacrylate). The reactions were performed at various temperatures (25, 50, 60, and 80 °C) and complete monomer conversion could be achieved. The polymerizations obeyed first order kinetic, the molecular weights increased linearly with conversion and the polymers exhibited narrow molecular weight distributions all indicating the livingness of the process. By providing a small amount of hydrazine to the reaction mixture the polymerization could be conducted in presence of air omitting the need for any elaborated deoxygenation procedures. This methodology offers an elegant way to synthesize functionalized poly(methyl methacrylate) with perfect control over the polymerization process as well as molecular architecture. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 2243–2250, 2010
INTEGRATED LINEAR AND NONLINEAR VISCOELASTICITY OF DISCOTIC LIQUID CRYSTALS

Theory and simulation of steady, small-amplitude, and large-amplitude oscillatory capillary Poiseuille flow of discotic mesophases are presented, discussed, and used to provide an integrated framework to characterize the rheology of precursors used in the manufacturing of carbon super-fibers. The underlying microstructural changes responsible for the non-Newtonian rheology are presented and discussed, taking into account dynamic couplings between orientation and velocity fields. Proper scaling of viscoelastic material functions leads to superposition and hence provides a better fundamental understanding of flow processes in steady and oscillatory flows. The relations between shear-thinning behavior in steady flow, elastic storage in small-amplitude oscillatory shear, and flow enhancement in pulsatile flow are established.
Sensor properties of dual core optical fibers

The series of the dual core optical fibers with the same dimensions of cores and nume¬rical apertures but with different distance between cores was manufactured. To characterize these fibers their spectral attenuation, cut-off wavelength, coupling length, temperature sensitivity and pressure sensitivity were measured. The measurements of temperature sensitivity and pressure sensitivity for different polarizations of input light were done.
Behavior of phosphate in soil extracts using weak unbuffered extracting solutions

Abstract Phosphate concentrations in extracts of soil samples using unbuffered 0.01 M calcium chloride (CaCl2) decreased in time, especially in extracts of calcareous soil samples due to phosphate adsorption on walls of tubes and flasks. To overcome these changes in time, extracts were immediately after centrifugation or filtration acidified to pH 2.0 using hydrochloric acid (HC1).
Brillouin Scattering and its Application in Geosciences

Brillouin spectroscopy is an optical technique that allows one to determine the directional dependence of acoustic velocities in minerals and materials subject to a wide range of environmental conditions. It is based on the inelastic scattering of light by spontaneous collective motions of particles in a material in the frequency range between 10−2 to 10 GHz. Brillouin spectroscopy is used to determine acoustic velocities and elastic properties of a number of crystalline solids, glasses, and liquids. It is most commonly performed on transparent single crystals where the complete elastic tensor of the sample material can be derived. However, Brillouin spectra can be also measured from opaque materials, from which partial or complete information on the elastic tensor can be determined. It is a very flexible technique with many possible areas of application in research disciplines from condensed matter physics to biophysics to materials sciences to geophysics. Brillouin scattering can be performed on very small samples and it can be easily combined with the diamond anvil cell and carried out at high pressures and temperatures (see reviews by Grimsditch and Polian 1989 and Eremets 1996). This makes this technique the method of choice to study the elastic properties of deep Earth materials, relevant to construct a mineralogical model of the interior of our planet that is consistent with the constraints from seismology. Several of the candidate minerals of the Earth’s interior are not stable at ambient conditions, and only recently has there been substantial progress in their synthesis. Unfortunately, those deep earth minerals that can be metastably preserved at ambient pressure and temperature are only available as single crystals with sizes of the order of several tens of microns at most. However, crystals of this size are large enough for Brillouin scattering to be performed. In addition, more sophisticated methods …
Changes in the content of selected heavy metals in groundwater exposed to the impact of a municipal landfill site

Landfilling is the most popular method of waste treatment in Poland. Old and usually uninsulated landfills constitute a major source of contaminants, which are leached by precipitation waters. As rainwater percolates through a landfill, suspended and dissolved components, waste decomposition products and various microorganisms are leached. Given the lack of any protection against leachate contacting groundwater, contaminants spread over a distance ranging from dozens of meters to several kilometers. The purpose of this paper was to determine the degree of contamination of leachate and groundwater with heavy metals (manganese, iron, nickel, chromium, zinc, copper, lead and cadmium) in the surroundings of the Maœlice municipal landfill site in Wroc³aw. The landfill was created without prior insulation of its base, and it has accumulated ca 2.4 mln m3 of waste in over thirty years of its use. Studies on the groundwater were carried out from 1995 to 2008, and the examination of the leachate was concluded in 2004. The analysis of the results shows that the groundwater flowing to the research object is already contaminated. While water percolates through the uninsulated base of the landfill, its quality continues to deteriorate. A large quantity of accumulated waste contributes to the severe contamination of the groundwater. Leachate from the insulated part of the landfill displayed properties that correspond to “old” landfills. Inside such landfills, the processes occurring during the methanogenic phase of waste decomposition are abundant. Concentrations of heavy metals found during
LARGE PLATE LYSIMETER LEACHATE COLLECTION EFFICIENCY FOR WATER BEING TRANSPORTED FROM SOIL TO GROUND WATER

A large, zero-tension, plate lysimeter (3.05 × 2.13 m) was installed to intercept percolating soil water at Bikini Atoll (11° 35′N, 165° 25′E), a former nuclear test-site. The purpose of the very large plate size was to increase the water collection efficiency of the lysimeter, thus providing larger volumes of water per cm of rainfall to measure the concentration of various radionuclides. In two experiments, controlled amounts of irrigation water were applied over the lysimeter and leachate water was collected. Evapotranspiration calculations were made using the Penman-Monteith equation and climate data collected at the atoll. The water balance efficiency of the lysimeter was essentially 100%, in contrast to low efficiencies (10–50%) reported for smaller plate lysimeters.
Aqueous solution properties of poly(trimethyl acrylamido propyl ammonium iodide) [poly(TMAAI)]

The aqueous solution properties of a cationic poly(trimethyl acrylamido propyl ammonium iodide) [poly(TMAAI)] were studied by measurements of reduced viscosity, intrinsic viscosity, and flocculation test. The reduced viscosity and intrinsic viscosity of this cationic polyelectrolyte were related to the types and concentration of added salt. “Soft” salt anions were more easily bound on the quaternary ammonium (R4N+) of poly(TMAAI) than those of “hard” salt anions. Halide anions are hard anions; consequently, hard cations were more easily attracted to halide anions for reducing the binding degree of halide anion on the quaternary ammonium group (R4N+). Some salt ions were observed to strongly attract the quaternary ammonium of the cationic polymeric side chain for coagulation of the polymers. This effect would make the polymeric aqueous solution become turbid. The intrinsic viscosity behavior for cationic polyelectrolyte resulting from the electrostatic repulsive force of the polymer chain is contrasted with polyampholyte. A comparison of various flocculants as to the effect of flocculation was also studied. © 1994 John Wiley & Sons, Inc.
Understanding the folding and stability of a designed WW domain protein with replica exchange molecular dynamics simulations

WW domain proteins are usually regarded as simple models for understanding the folding mechanism of β-sheet. CC45 is an artificial protein that is capable of folding into the same structure as WW domain. In this article, the replica exchange molecular dynamics simulations are performed to investigate the folding mechanism of CC45. The analysis of thermal stability shows that β-hairpin 1 is more stable than β-hairpin 2 during the unfolding process. Free energy analysis shows that the unfolding of this protein substantially proceeds through solvating the smaller β-hairpin 2, followed by the unfolding of β-hairpin 1. We further propose the unfolding process of CC45 and the folding mechanism of two β-hairpins. These results are similar to the previous folding studies of formin binding protein 28 (FBP28). Compared with FBP28, it is found that CC45 has more aromatic residues in N-terminal loop, and these residues contact with C-terminal loop to form the outer hydrophobic core, which increases the stability of CC45. Knowledge about the stability and folding behaviour of CC45 may help in understanding the folding mechanisms of the β-sheet and in designing new WW domains.
As(V)-reduction to As(III) by arsenic-resistant Bacillus spp. bacterial strains isolated from low-contaminated sediments of the Oliveri-Tindari Lagoon, Italy

Five arsenic-resistant bacterial strains designated MT1, MT2, MT3, V1 and V2 were isolated from sediments of the Oliveri-Tindari Lagoon (Italy), which comprises six small lakes whose sediments contain low arsenic concentrations. Phylogenetic analysis of the 16S rRNA gene sequences assigned them to the genus Bacillus. Bacillus sp. strain MT3 showed higher tolerance to As(III) and As(V), as indicated by minimum inhibitory concentrations of 14 and 135 mmol−1, respectively. Bacillus sp. strain V1 showed growth inhibition at 14 mmol−1 in the presence of As(III) and at 68 mmol−1 in the presence of As(V), whereas the arsenic resistance of Bacillus sp. strain MT1 was 10 and 27 mmol−1 for As(III) and As(V), respectively. The strains Bacillus spp. MT2 and V2 showed low levels of As(III) and As(V) resistance, as it was unable to grow at concentrations>7 and 14 mmol−1, respectively. The isolated arsenic-resistant Bacillus spp. strains were able to reduce As(V) to As(III), especially Bacillus spp. strain MT3. This study suggests that the isolated bacterial strains play a role in the arsenic biogeochemical cycle of arsenic-poor sediments in the Oliveri-Tindari Lagoon.
Untersuchung des Reaktionsablaufs in fetten Kohlenwasserstoff‐Sauerstoff‐Flammen III. Optische Untersuchungen an rußenden Flammen

Gleichzeitig mit den in Teil II [1] beschriebenen massenspektrometrischen Messungen uber die Rusbildung in flachen Flammen bei niedrigen Drucken wurden spektroskopische Untersuchungen an diesen Flammen ausgefuhrt. Es wurde die Emission der Radikale C2, CH und OH, der Temperaturverlauf und die OH-Radikal-Konzentration innerhalb der Reaktionszone in Abhangigkeit von der Zusammensetzung des Frischgases gemessen. Daneben wurde die Rusmenge vorwiegend durch ihre Absorption bestimmt. Der Verlauf der Rusteilchengrose konnte optisch aus der Differenz von Gas- und Teilchentemperatur gewonnen werden. Ferner wurde der Einflus der Versuchsbedingungen auf die Menge des gebildeten Ruses untersucht. Simultaneously with the mass-spectrometric measurements on soot formation in flat flames at low pressures, described in Part II [1], spectroscopic investigations of these flames have been carried out. The emission of the radicals C2, CH and OH, the temperature distribution and the OH radical concentration in the reaction zone were measured as a function of the composition of the gas supplied. In addition the quantity of soot was determined, mainly through its absorption. The size distribution of soot particles could be derived optically from the difference between gas and particle temperatures. Furthermore, the influence of experimental conditions on the quantity of soot formed was investigated.
Low voltage organic field effect transistors with a poly(hexylthiophene)–ZnO nanoparticles composite as channel material

We report on solution processable organic field effect transistors prepared using a poly(3‐hexylthiophene)–ZnO nanoparticles composite as channel semiconductor material and cross‐linked polyvinyl alcohol as gate insulator. Our transistors show a field effect mobility of 0.35 ± 0.06 cm2/V s, threshold voltage of –1.30 ± 0.11 V, and Ion/Ioff ratio of (1.0 ± 0.1) × 103. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Natural zeolites and their ion exchange behavior towards chromium

Abstract In this work studies have been performed which demonstrate that trivalent chromium cations may be retained by naturally occuring zeolites. The experimental work perfomed on the natural zeolite clinoptilolite, which is found in abudant quantities in Greece, showed that the ion exchange process is quite rapid and high quantities of chromium ions are removed from the aqueous solutions in a short period of time. Also, the actual exchange capacity of the zeolites is much smaller, about 50%, of the theoretical one. Despite the regeneration conditions used, significant amounts of chromium is retained by the zeolite. It was also shown that loading and regenerating the zeolite greatly improves the ion exchange capacity of the zeolite, since a very small amount of chromium is released during regeneration and an almost constant amount is taken after each loading cycle.
$\mathbf{SrVO_{3}}$ electron emission cathodes with stable, >250 mA/cm2 current density

This work reports improved emission performance of bulk, polycrystalline $\mathbf{SrVO_{3}}$ thermionic emitters with low effective work function (2.3 – 2.4 eV) and stable emission properties. We observed that long term vacuum annealing $\boldsymbol{(\sim 5\ \mathrm{x}\ 10^{-10}}$ torr, $\boldsymbol{\sim 1250\ ^{\circ}}\mathbf{C}$, 100–200 hours) of as-prepared polycrystalline $\mathbf{SrVO_{3}}$ cathodes results in the enhanced thermionic emission of > 250 mA/cm2at around 1175 ${}^{\circ}\mathrm{C}$ and emergence of a low work function surface. Vacuum annealing may help to remove any surface contamination and aids the formation of the desired low work function grains on the cathode surface. In addition to the low work function and high emission current density, the perovskite oxide cathode also demonstrates excellent emission current stability which is essential for its practical applications.
Identificação in silico de genes efetores citosólicos a partir do secretoma de Phytophthora parasítica dos citros.

Durante interacoes planta–patogeno, patogenos secretam proteinas efetoras para o apoplasto e citoplasma vegetal, as quais modulam as respostas de doenca ou de resistencia das plantas. Devido a importância de Phytophthora parasitica como agente causal da doenca gomose dos citros, o objetivo deste trabalho foi identificar genes efetores citosolicos a partir do secretoma de Phytophthora parasitica dos citros, por meio de ferramentas computacionais e ensaios biologicos. Usando o Programa Netglycate, um total de 117 genes de P. parasitica foram identificados no CitEST/PP, que possivelmente codificam glicoproteinas secretadas, com homologia a proteinas de Phytophthora spp. Dentre estes, seis genes foram selecionados como candidatos para estudos futuros de expressao genica e por isso primers especificos para amplificacao por PCR quantitativo em tempo real foram desenhados e sintetizados. Os primers foram validados pela amplificacao de DNA total de P. parasitica por PCR, tendo gerado amplicons de tamanhos esperados. Visando os estudos de expressao genica, fases do desenvolvimento assexual in vitro do patogeno foram obtidas em grande quantidade e a condicao de cultivo adequada variou para cada fase. A producao abundante de hifas e clamidosporos foi obtida em meio liquido cenoura-agar sob luz constante a 25 °C, por 12 e 45 dias, respectivamente. Esporângios de P. parasitica in vitro foram produzidos 5 dias apos imersao de discos de micelio em agua destilada esteril. Para a ativacao da patogenicidade e estudos de interacao citros-Phytophthora, P. parasitica foi recuperado de folhas de laranjeiras com sucesso. O RNA total de micelio foi isolado por um metodo de fenol modificado, por trizol e pelo Kit RNeasy (Qiagen). Os efetores do tipo glicoproteinas identificados sao fortes candidatos para estudos de expressao genica e para o entendimento e controle da gomose em citros.
Synthesis of band-gap-reduced p-type ZnO films by Cu incorporation

p-type ZnO thin films with significantly reduced band gaps were synthesized by heavy Cu incorporation at room temperature and followed by postdeposition annealing at 500°C in air for 2h. All the films were synthesized by rf magnetron sputtering on F-doped tin oxide-coated glass. The p-type conductivity was confirmed by Mott-Schottky plots and illuminated I-V analysis. The Cu+1 acceptor states (at substitutional sites) and their band-gap reduction were demonstrated by UV-visible absorption and x-ray excited valence band measurements.
Synthesis of β-amino alcohols using MgO as a new catalyst under solvent-free conditions

MgO catalyzed efficiently the ring opening of epoxides with a range of aromatic and aliphatic amines to produce β-substituted alcohols in high yields under solvent-free conditions. Exclusive trans stereoselectivity is observed for cyclic epoxide.Key words: MgO, β-amino alcohols, solvent-free, epoxide, amine.
A plate count method for aerobic cellulose decomposers in soil by Congo red staining

Abstract The ability of microorganisms to decompose polysaccharides such as cellulose is of considerable importance in terms of the carbon cycle in soil ecosystems. In order to analyze the behavior of cellulose decomposers in soil, a quantitative estimation is indispensable. Someya (1980) modified the plate count method for the enumeration of cellulose decomposers in soil developed by Hankin and Anagnostakis (1977). Carboxymethylcellulose sodium salt (CMC) is used as the substrate which, after incubation, is precipitated with cetyltrimethylammonium bromide (CTAB, 10 g L-1) to visualize the zone of hydrolysis (clear zone) on an agar plate. The method has been widely used for the enumeration of cellulose decomposers in soil. However, one of the shortcomings of the method is that, with the time of incubation, the large clear zones formed by rapidly growing cellulose decomposers overlap with each other and/or mask the small clear zones formed by slower or weaker cellulose decomposers (Someya 1980). Although s.
Computer Vision Technologies for Reconstructing the Trajectory of Human Movements in Three–dimensional Space

Background: The research aims at creating an algorithm for reconstructing complex human movements in three-dimensional space using RGB cameras and neural networks. The contributions of this work are presented as follows: 1) the authors use common RGB cameras that are utilized in smart phones; 2) we also detect the moment the movement starts and ends according to preset criteria and video footage; 3) finally, we reconstruct the trajectory of human body movements in three-dimensional space by analyzing 3D reconstruction of its reference points. Methods: This research focuses on the analysis of the subject's body movements during Double Axel jump. For the purpose of trajectory calculation, we used COCO-18 key-point format for human pose skeleton. We developed an algorithm for reconstructing human body movements which includes: 1) creating video footage using 2 IP cameras; 2) recognizing the moments of the subject's jumping up and landing; 3) 2D reconstructing the points defining the positions of the subject's right and left foot with the use of Openpose library; 4) calculating coordinates of the said reference points in 3D space and building trajectories of the subject's feet movements in 3D space. As a programming language we use Python 3.9. Results: The algorithm was used to reconstruct the trajectory of the subject's feet movements in 3D space during the jump. Conclusions: RGB cameras prove to be a good tool for the purpose of reaching the research goals. Calculating coordinates of the reference points marking human joints makes it possible to build reference curves and to analyze biomechanics of movements.
From nucleation to coalescence of Cu2O islands during in situ oxidation of Cu(001)

The nucleation, growth, and coalescence of Cu2O islands due to oxidation of Cu(001) films were visualized by in situ ultrahigh-vacuum transmission electron microscopy. We have previously demonstrated that the nucleation and initial growth of copper oxides is dominated by oxygen surface diffusion. These surface models have been extended to quantitatively represent the coalescence behavior of copper oxidation in the framework of the Johnson–Mehl–Avrami–Kolmogorov theory. An excellent agreement exists between the experimental data of nucleation to coalescence with the surface model. The implication could be an alternate paradigm for passivation and oxidation, since classic theories assume uniform film growth.
Formation of Metallacyclic Complexes by Activation of an Aryl C−H Bond in a Platinum−Safrole Analogue of Zeiseʼs Salt

Potassium trichloro(safrole)platinate(II), K[Pt(Saf)Cl3] (1), reacts with piperidine to give cis-[Pt(Saf-1H)(Piperidine)Cl] (2). The interaction of 1 with AgNO3, SnCl2, KOH, and ethanol−water solutions leads to formation of the dinuclear chelate ring complex [Pt2(Saf-1H)2Cl2] (3). 1H and 13C NMR spectra and single-crystal X-ray diffraction show that in complexes 2 and 3 deprotonated safrole is bound up with platinum(II) both at a benzene carbon and at the ethylenic double bond of the side chain.