Miracle-dz/UniFAR-FTUs huggingface dataset:
Recombination Marks the Evolutionary Dynamics of a Recently Endogenized Retrovirus

All vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. While endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term co-evolution of ERV and host because germline infections are rare and expansion is slow, because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed. Because we have locus-specific data on the distribution of cervid endogenous retrovirus (CrERV) in populations of mule deer, in this study we determine the molecular evolutionary processes acting on CrERV at each locus in the context of phylogenetic origin, genome location, and population prevalence. A mule deer genome was de novo assembled from short and long insert mate pair reads and CrERV sequence generated at each locus. CrERV composition and diversity have recently measurably increased by horizontal acquisition of a new retrovirus lineage. This new lineage has further expanded CrERV burden and CrERV genomic diversity by activating and recombining with existing CrERV. Resulting inter-lineage recombinants endogenized and subsequently retrotransposed. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion by retrotransposition of one recombinant CrERV lineage. Thus, in mule deer, retroviral colonization is a dynamic period in the molecular evolution of CrERV that also provides a burst of genomic diversity to the host population.
Complexation of selenium to (R)‐Rh2(MTPA)4: thermodynamics and stoichiometry

Variable‐temperature 1H and 77Se NMR data for 3‐phenylselenenyl‐1‐phenyl‐1‐propene (1) in the presence of Rh2(MTPA)4 (Rh*) prove that the equilibria are strongly shifted towards the adduct Rh*···1; free selenide molecules cannot be detected as long as uncomplexed rhodium atoms are available. In the case of excess Rh*, both 1 : 2 and 1 : 1 adducts (Rh* vs 1) are formed, and the latter is slightly favoured. With excess selenide, the system strongly favours the complexation of two selenide molecules (1 : 2 adduct), i.e. one at each rhodium atom. In this situation, intermolecular selenide exchange can be monitored by variable‐temperature 1H NMR spectroscopy and the energy barrier is estimated to be 54–55 kJ mol−1. Copyright © 2001 John Wiley & Sons, Ltd.
Photochemical transformations of surface and deep marine dissolved organic matter: Effects on bacterial growth

The effects of photochemical transformations on the bioavailability of marine dissolved organic matter (DOM) were investigated in surface and deep water from the Gulf of Mexico. Seawater samples were collected from eight depths (15–1,000 m), passed through 0.2‐µm pore‐size filters, and exposed to sunlight in quartz bottles in a flowing seawater deck incubator for 5‐9 h. Following sunlight exposure, samples were inoculated (1:10) with unfiltered seawater from 15‐m depth, and bacterial growth rates were estimated from rates of 3H‐leucine incorporation in dark incubations. Exposure of surface‐water DOM to sunlight resulted in a 75% reduction in bacterial production, whereas exposure of deep‐water DOM resulted in a 40% enhancement in bacterial production. Photomineralization of bioreactive DOM likely contributed to the reduction of bacterial growth in surface water, but the photoproduction of biorefractory DOM also appeared to contribute to reduced bacterial growth. Enhanced bacterial growth in irradiated deep water was consistent with previous studies demonstrating the photoproduction of bioavailable substrates from deep‐water DOM. Phototransformations of DOM appeared to be multifaceted and to play a critical role in the cycling of DOM in the ocean.
High-temperature breakdown of the synthetic iodine analogue of vanadinite, Pb5(VO4)3I: an apatite-related compound for iodine radioisotope immobilization?

Abstract The thermal stability of the synthetic iodine analogue of vanadinite, Pb5(VO4)3I, in air has been investigated by in situ high temperature X-ray powder diffraction between 300 and 1070 K. Rietveld refinement of phase fractions shows that breakdown to lead orthovanadate, Pb3(VO4)2, begins at temperatures above 540 K, with complete loss of iodine above 680 K. More than 50 K below the onset of breakdown, the unit-cell parameters of Pb5(VO4)3I show anomalous contraction in the crystallographic x−y plane (reduction of a) which we associate with movement of iodine within the [0001] channels of the structure. The implications of these results for immobilization of 129I in potential apatite-related crystalline radioactive waste forms are discussed.
Freeze-Drying of Pharmaceutical Proteins in Vials: Modeling of Freezing and Sublimation Steps

The commercial finite element code FEMLAB was used to perform two-dimensional axisymmetric simulations of the temperature profiles and the moving front velocities of standard BSA (bovine serum albumin)-based formulations used to stabilize pharmaceutical proteins during the freeze-drying process. The simulations were validated with both experimental and numerical approaches. In an initial step, the heat transfer phenomena taking place during the cooling of liquid solutions was studied in commercial size glass vials without freezing or sublimation. Then, this model was extended and validated for the freezing process of aqueous BSA-based solutions encountered in the industrial freeze-drying processes with the same vials in order to confirm the identified values of the different thermal conductances between the product and the shelf and between the product and the surroundings. Finally, the conductances between the product and the shelf and between the vial and the surroundings thus determined were used in a dynamic sublimation model with two zones and a moving sublimation front similar to the ones previously proposed in the literature. The simulations showed a satisfactory agreement between experimental and simulated data. The results of this study demonstrated that the freeze-drying process of pharmaceutical proteins in glass vials for standard industrial operating conditions was mainly controlled by the heat transfer from the shelf and the surroundings to the product sublimation front.
Theoretical studies of ligand-free cadmium selenide and related semiconductor clusters

The results of density functional theory potential surface investigations are presented for small ZnS, ZnSe, CdS, and CdSe clusters, up to the heptamer. Clusters of CdSe are investigated further by geometry optimizations of larger crystal structure sections with up to 198 atoms that correspond to the wurtzite modification. In addition to structures and energies of these clusters, we present electron affinities, ionization potentials as well as electronic excitation spectra, obtained from time dependent density functional theory.
Heat transfer in the critical region

Heat transfer coefficients were measured experimentally for carbon dioxide in turbulent flow in an 0.18-in. I.D. pipe. The pressure was 1,200 lb. /sq. in. abs. and the bulk temperature varied from 70° to 120°F. In this critical region the coefficients between fluid and tube wall ranged from 300 to 2,600 B.t. u. /(hr.)(sq. ft./°F.) over a Reynolds number interval of 30,000 to 300,000. Existing empirical and semitheoretical correlations were found inadequate in this region, where the thermal conductivity, viscosity, density, and specific heat are all varying rapidly and nonuniformly with temperature. A method of integrating the heat and momentum transfer equations with variable physical properties, recently proposed by Deissler, was applied to the experimental data and found to fit well. The application required extensive calculations, which were carried out with an Electrodata digital computer. A simplified procedure was proposed for estimating heat transfer coefficients in the critical region by using a semitheoretical equation developed for zero heat flow. Simple rules were suggested for estimating the temperature at which to evaluate the physical properties when this equation is applied to the realt case of finite heat transfer. The method worked well when compared with the computed heat transfer coefficients of Deissler for supercritical wate but showed about 30% deviation when compared with the carbon dioxide results. This discrepancy is believed due to the fact that the carbon dioxide was very close to the critical point (reduced pressure = 1.1) but the water was somewhat further removed (reduced pressure = 1.6).
High-pressure phases of solid nitrogen by Raman and infrared spectroscopy

Raman and infrared spectra of solid nitrogen have been collected between 25 K and room temperature up to 41 GPa. A careful analysis of the spectral band transformations occurring across the high pressure transitions among the δ, δloc, e, and ζ phases allowed to define the phase diagram in the whole P-T region investigated. In particular, the transition between the e and ζ phases has been observed in the range 30–230 K and the corresponding phase-boundary drawn. A significant metastability region (spanning about 10 GPa in pressure) hinders the transformation between the e and ζ phases when pressure is varied at low temperature. Group theory arguments suggest a centrosymmetric structure for the ζ phase and the number of Raman and infrared ν1 and ν2 components can be reproduced both with cubic and tetragonal structures. An appreciable coupling among neighboring molecules is observed, at room temperature, only in the e phase where the relative orientations of the molecules are fixed.
New suitable for tissue reconstruction injectable chitosan/collagen-based hydrogels

The ability of four gel-forming copolymers to act as in situ dermal fillers in plastic and reconstruction surgery was studied. The four hydrogels, which were based on chitosan (CS), included CS/β-GP (β-sodium glycerophosphate), CS–HLC (human-like collagen)/β-GP, CS–AC (animal-derived collagen)/β-GP and CS–Gelatin/β-GP. The potential of the hydrogels as tissue engineering scaffolds was explored by an MTT test and an in vitro degradation assay. The interior morphologies of these hydrogels were also characterized before and after degradation. Histocompatibility in vivo was evaluated by hematoxylin and eosin (H&E) staining, immunohistochemical analysis and transmission electron microscopy (TEM). An MTT assay showed that the CS–HLC/β-GP hydrogel was less cytotoxic and could promote marrow stromal cell (MSC) proliferation better than other hydrogels. Data from an in vitro degradation test showed that the CS–HLC/β-GP hydrogel had a longer degradation time and led to a lower weight loss than the other hydrogels. Furthermore, the CS–HLC/β-GP hydrogel rapidly formed a stable gel that maintained its integrity even after 6 weeks in vivo. From TEM, there were found to be a large quantity of macrophages, fibroblasts, fibrocytes, lymphocytes and capillaries in the CS–AC/β-GP and CS–Gelatin/β-GP hydrogels, whilst levels in the CS–HLC/β-GP hydrogel were small. Furthermore, abnormalities of cell morphology were observed in the CS–AC/β-GP and CS–Gelatin/β-GP hydrogels whereas cell morphology in the CS–HLC/β-GP hydrogel was regular. Therefore, the CS–HLC/β-GP hydrogel, with good cytocompatibility and histocompatibility, is suitable for soft tissue defect filling, such as skin patches, wrinkles, and tissue cavities formed by surgery.
Changes in the Trophic Status of Three Mountain Lakes - Natural or Anthropogenic Process?

Three sediment cores have been studied from the Morskie Oko (MOK), Przedni Staw Polski (PSP), and Czarny Staw Gąsienicowy (CSG) lakes to examine the recent environmental history of the alpine lakes located in the Polish part of the Tatra Mountains (Carpathians). Changes in the total phosphorus concentration in the water over the past centuries were reconstructed based on diatom data (DI-TP), assuming that diatoms are good indicators of productivity in lakes. The results of the analysis showed significant alterations in the trophic status of the studied lakes over the past 50 years. Clear changes from oligotrophy to mesotrophy occurred in the lakes located close to year-round mountain huts on the shores of MOK and PSP. In contrast, DI-TP decreased in CSG, and the only symptom of higher productivity in the lake was an increase in total organic carbon.
Estudo cinético da decomposição térmica do pentaeretritol-tetranitrado (PETN)

The pentaerythritol-tetranitrate (PETN) is a nitroether used in explosives and propellant formulations. Due to its suitable properties, PETN is used in booster manufacture. Knowing the thermal decomposition behavior of an energetic material is very important for storage and manipulation, and the purpose of this work is to study the kinetic parameters of the decomposition of PETN, compare the results with literature data and to study the decomposition activation energy differences between two crystalline forms of PETN (tetragonal and needle) by means of differential scanning calorimetry (DSC). Fourier transform infrared spectroscopy (FT-IR) is used to study the two crystalline forms.
A Review of Rapid Gas-Solid Separation Techniques

Rapid, effective separation of phases is an essential step in many hydrocarbon conversion gas-solid processes. In heavy oil upgrading, fluid catalytic cracking (FCC) and biomass pyrolysis, for example, very fast separation of reacting gases from catalytic or heat-bearing solids is required to inhibit further reaction. The primary functions of a rapid separator in the context of a gas-solid flow are, first, to terminate contact between the reacting gases and the catalytic or hot solid particles and, second, to recover the isolated product vapors. Uninterrupted vapor-solid contact results in degraded, overcracked and generally less valuable products. Increasing interest in rapid separation has led in the past 25 years to a wide variety of proposed separator designs in the literature.Centrifugal separation is the fundamental principle underlying cyclone operation and most rapid gas-solid separation processes. Traditional cyclones rely on centrifugal separation and are very widely applicable. They are used for the removal of solid particulate matter from gas or liquid streams, for gas demisting, and in hydrocyclones. Most FCC processes employ traditional cyclone configurations for secondary and tertiary separation. The review briefly summarizes important topics studied in reverse flow cyclone operation. For initial separation, however, most fast gas-solid separators in the literature feature only partial cyclone layouts. Separation typically occurs more quickly in these devices relative to traditional cyclones, likely at the expense of separation efficiency.The current review places emphasis on experimental results and novel separation techniques in the context of fast gas-solid separation. Several recent methods of rapid gas-solid separation employ co-current or "uniflow" centrifugal arrangements. Hence, particular attention is directed to co-current centrifugal separators. These devices have been studied much less intensively than their reverse flow counterparts. Fast co-current separators, with their novel, partial cyclone layouts, are interesting for their performance characteristics in relation to popular commercial designs.
Interactions of H2O molecules in ice II. Interaction energies of H2O molecules in ice

The energy of interaction of H2O molecules in ice is calculated by representing each molecule as a series of multipoles. This energy is found to increase when the mutual polarization of the molecules is taken into account. It is also found to depend significantly upon interactions of a molecule with its second and further neighbours. The interaction energy of molecules in the cubic form of ice is found to be essentially the same as that of molecules in the ordinary hexagonal form.
The movement of solids through flighted rotating drums. Part II solids‐gas interaction and model validation

A residence time model for a rotating drum with lifting flights which includes axial displacement of airborne particles due to the drag of the gas stream has been developed in Part I of this study (Sherritt et al., 1993). Because the particles fall in curtains, the equations for single particle drag overestimated the effect of the gas stream on the displacement of the falling particles. In this paper, large scale wind tunnel experiments, which involved pouring a curtain of particles into a gas stream, indicated that the shielding effect of the curtain could be represented by a lower-than-average gas velocity within the curtain. The magnitude of the curtain shielding effect is related to the flight discharge rate, the fall distance and the flight length. Incorporating the results of the experiments into the residence time model provides a significant improvement on the effect of the gas velocity, and hence the best model available, especially for industrial-scale equipment. On a etudie dans la premiere partie de cette etude (Sherritt et al., 1993) un modele de temps de sejour pour un tambour rotatif munis de raclettes de levage qui considere le deplacement axial des particules aeriennes provoque par le courant gazeux. En raison de la chute en rideau des particules, les equations de trainee des particules simples surestiment l'effet du courant gazeux sur le deplacement des particules descendantes. Dans cet article, les experiences menees dans une soufflerie a grande echelle, qui consistent Zi deverser un rideau de particules dans un courant gazeux, indiquent que l'effet de protection du rideau pourrait etre represente par une vitesse de gaz inferieure a la moyenne dans le rideau. La grandeur de l'effet de protection du rideau est liee a la vitesse de deversement des raclettes, de la distance de chute et de la longueur des raclettes. L'integration des resultats des experiences au modele de temps de sejour permet une amelioration significative sur l'effet de la vitesse de gaz, et, de cette facon, on obtient le meilleur modele disponible, en particulier pour les equipements a l'echelle industrielle.
Binary permeation through a silicalite‐1 membrane

Permeation of binary gaseous mixtures through a silicalite-1 membrane was studied. Results are reported for the fluxes and separation factors as a function of the feed composition, the pressure and the temperature. For the various cases a comparison is made between the binary and the single-component permeation behavior. For the permeation of the mixtures the stronger adsorbed component is little affected by the presence of the weaker adsorbed component. On the other hand, for the weaker adsorbed component a clear reduction in the flux is observed. As a consequence, the separation factor for mixtures differs considerably from the so-called ideal separation factor, which is the ratio of the one-component permeances. As expected, the separation factor depends on the temperature. The separation factor is also a function of the composition and the feed pressure. This means that the binary equilibrium adsorption cannot be described with the extended Langmuir model. Binary permeation and separation behavior is described using the ideal adsorption solution theory for equilibrium adsorption.
Accurate determination of lithium isotope ratios by MC-ICP-MS without strict matrix-matching by using a novel washing method

The accurate determination of Li isotopic ratios by MC-ICP-MS has traditionally been hampered by the high background and severe memory effect of Li. In this study, a novel method to efficiently reduce the high background and memory effect of Li was developed. It was found that the Li background can be significantly reduced by a factor of 15 to 70 by using a 5% NaCl rinse solution. In addition, the “mismatching effects” reported previously, which are caused by different acid and Li concentrations between the sample and standard, were eliminated once the Li background was efficiently reduced, suggesting that the crux of the two types of matrix effects is actually the high Li instrumental background and memory effect. Applying the background reduction technique, a method without strict matrix-matching was developed for the accurate and precise determination of Li isotopic ratios. The proposed method was validated by the analysis of eight reference materials with satisfactory results, even when the Li concentration in the samples was not matched with that of standards. The external precision of this method is better than ±0.25‰ (2SD) for δ7Li, suitable for the identification of small fractionation of Li isotopes occurring in geological processes. With the proposed method, there is no need to match the Li and acid concentration of the sample and standard, which significantly reduced the sample preparation time and increased the sample throughput.
On mechanisms involved in the propagation of subsonic positive streamers in cyclohexane

This paper presents a study of slow positive streamers in cyclohexane under impulse voltage. A high sensitivity differential technique is used to record the streamer charge, together with high speed visualization. At voltages below the breakdown voltage, streamers stop while the voltage is still applied. It is shown that the first event preceding stopping is the hydrodynamic collapse of streamer filaments close to the point. This collapse "propagates" from the point to the streamer head, and the streamer then totally disappears. As soon as the streamer collapse starts, the streamer current is stopped, no more electrical energy is supplied, and liquid vaporization ceases. However, the streamer head still propagates at a reduced velocity. These observations constitute a direct evidence of the influence of space charges and electric field (i.e. electrostatic pressure) on propagation processes.