Challenging the Existing Model of the Hexameric HIV-1 Gag Lattice and MA Shell Superstructure: Implications for Viral Entry

Despite type 1 human immunodeficiency virus (HIV-1) being discovered in the early 1980s, significant knowledge gaps remain in our understanding of the superstructure of the HIV-1 matrix (MA) shell. Current viral assembly models assume that the MA shell originates via recruitment of group-specific antigen (Gag) polyproteins into a hexagonal lattice but fails to resolve and explain lattice overlapping that occurs when the membrane is folded into a spherical/ellipsoidal shape. It further fails to address how the shell recruits, interacts with and encompasses the viral spike envelope (Env) glycoproteins. These Env glycoproteins are crucial as they facilitate viral entry by interacting with receptors and coreceptors located on T-cells. In our previous publication, we proposed a six-lune hosohedral structure, snowflake-like model for the MA shell of HIV-1. In this article, we improve upon the six-lune hosohedral structure by incorporating into our algorithm the recruitment of complete Env glycoproteins. We generated the Env glycoprotein assembly using a combination of predetermined Env glycoprotein domains from X-ray crystallography, nuclear magnetic resonance (NMR), cryoelectron tomography, and three-dimensional prediction tools. Our novel MA shell model comprises 1028 MA trimers and 14 Env glycoproteins. Our model demonstrates the movement of Env glycoproteins in the interlunar spaces, with effective clustering at the fusion hub, where multiple Env complexes bind to T-cell receptors during the process of viral entry. Elucidating the HIV-1 MA shell structure and its interaction with the Env glycoproteins is a key step toward understanding the mechanism of HIV-1 entry.

On the ocean beach—why elliptic pebbles do not become spherical

Among pebbles strewn across a sandy ocean beach, one can find relatively many with a nearly perfect elliptical (ellipsoidal) shape, and one wonders how this shape was attained and whether, during abrasion, the pebbles would remain elliptical or eventually become spherical. Mainly the latter question was addressed in a previous publication which identified frictional sliding and rotation of an elliptic pebble as main abrasion processes in the surf waves. In particular, it was predicted that the ellipticity $$\varepsilon = \left\{ {1 - b^{2} /a^{2} } \right\}^{1/2}$$ ε = 1 - b 2 / a 2 1 / 2 (a > b, principal ellipse axes) converges to a common equilibrium value for elliptic-like pebbles. Unfortunately, the derivation was based on an invalid force expression and a dimensionally unsuitable curvature. In this paper, not only force and curvature but also the contact duration with the sand surface during rotations is taken into account by fairly simple physical arguments, and it is shown that elliptic pebbles neither approach the same ellipticity and nor become more spherical nor more disk-like but rather that the ellipticity $$\varepsilon$$ ε increases.

Methodology for Establishing Segmentation Strategy for Large Metal Components from Nuclear Power Plants with Consideration of Packaging into Containers

A methodology for segmenting large metal components from nuclear power plants has been developed with a view to minimizing the number of containers to emplace segmented pieces. Spherocylinder-type and rectangular prism-type objects are modeled in shapes, and equations to calculate heights, widths, lengths, or angles for segmentation and the number of pieces are derived using geometric theorems, with a hypothetical ‘virtual rectangle’ being introduced for simplification. Applicability of the new methodology is verified through case studies assuming that each segmented piece is packaged into a 200 L container, and a procedure for adjusting potential overestimation of the segmented pieces due to the virtual rectangle is proposed. The new approach results in fewer segmented pieces but more containers than an existing segmentation study using 3D modeling. It is demonstrated that the number of containers can be further reduced, however, if the generalized methodology is followed by 3D modeling. In addition, it is confirmed that the generalized approach is also applicable to a nonstandard shapes such as ellipsoidal shape but only under limited conditions. Sensitivity analyses are conducted by changing dimensions of the objects and container, which brings about an optimal dimension of container as well. The generalized approach would be utilized either alone in decommissioning planning to estimate waste from segmentation of large metal components or combined with 3D modeling to optimize segmentation operation.

High-fidelity elastic Green’s functions for subduction zone models consistent with the global standard geodetic reference system

Green’s functions (GFs) for elastic deformation due to unit slip on the fault plane comprise an essential tool for estimating earthquake rupture and underground preparation processes. These estimation results are often applied to generate important information for public such as seismic and tsunami hazard assessments. So, it is important to minimize the distortion of the estimation results on the numerical models used for calculating GFs to guarantee assessment reliability. For this purpose, we here calculated GFs based on a numerical model that is of high fidelity to obtain realistic topography and subsurface structural models of the Earth. We targeted two well-known subduction zones in Japan, the Nankai Trough and the Japan Trench. For these subduction zones, databases for realistic topography and subsurface structural models of the Earth are available in the “Japan integrated velocity structure model version 1”, which was proposed for earthquake hazard assessments conducted by the Japanese government. Furthermore, we eliminated the inconsistency in processing calculated GFs and space geodetic observation data for surface displacements, which is often overlooked, by using the same coordinate system. The ellipsoidal shape of the Earth, which is often approximated with a projected plane or a spherical shape, was also incorporated by faithfully following the definitions of the coordinate systems in Geodetic Reference System 1980, which is the global standard for space geodesy. To calculate elastic GFs based on such high-fidelity subduction zone databases with the ellipsoidal shape of the Earth, we introduced the finite element (FE) method. In the FE meshes, the resolution of the topography and subsurface structure is the same as that of the original databases. Recent development of the state-of-the-art computation techniques for the rapid calculation of crustal deformation using large-scale FE models allows for GF calculation based on such a high-fidelity model. However, it is generally not easy to perform such calculations. Thus, we released a library for the GFs calculated with 1-km grid spacing on the ground surface in this study to the geoscience community on a web server, aiming to contribute more reliable seismic and tsunami hazard assessment.

A thermophysical and dynamical study of the Hildas (1162) Larissa and (1911) Schubart

The Hilda asteroids are among the least studied populations in the asteroid belt, despite their potential importance as markers of Jupiter’s migration in the early Solar system. We present new mid-infrared observations of two notable Hildas, (1162) Larissa and (1911) Schubart, obtained using the Faint Object infraRed CAmera for the SOFIA Telescope (FORCAST), and use these to characterise their thermal inertia and physical properties. For (1162) Larissa, we obtain an effective diameter of 46.5$^{+2.3}_{-1.7}$ km, an albedo of 0.12 ± 0.02, and a thermal inertia of 15$^{+10}_{-8}$ Jm−2s1/2K−1. In addition, our Larissa thermal measurements are well matched with an ellipsoidal shape with an axis ratio a/b=1.2 for the most-likely spin properties. Our modelling of (1911) Schubart is not as refined, but the thermal data point towards a high-obliquity spin-pole, with a best-fit a/b=1.3 ellipsoidal shape. This spin-shape solution is yielding a diameter of 72$^{+3}_{-4}$ km, an albedo of 0.039± 0.02, and a thermal inertia below 30 Jm−2s1/2K−1 (or 10$^{+20}_{-5}$ Jm−2s1/2K−1). As with (1162) Larissa, our results suggest that (1911) Schubart is aspherical, and likely elongated in shape. Detailed dynamical simulations of the two Hildas reveal that both exhibit strong dynamical stability, behaviour that suggests that they are primordial, rather than captured objects. The differences in their albedos, along with their divergent taxonomical classification, suggests that despite their common origin, the two have experienced markedly different histories.

Molecular Parameters and Intrinsic Viscosity of Nettle Seed (Urtica Pilulifera) Gum as a Function of Temperature

This research focused to determine some molecular properties of Nettle seed gum (NSG), as one of novel and natural source of hydrocolloids, at various temperatures (10, 25, 40, 55, and 70°C) in the dilute region. The results displayed that among the models studied, the Higiro 2 model with highest R2 and lowest RMSE values was the most proper model for determining the intrinsic viscosity of the NSG. According to this model, the intrinsic viscosity value of NSG was obtained in the range of 0.15–0.21 dl/g. It was also revealed that, as the temperature raised, the intrinsic viscosity of NSG declined. The shape factor of NSG at 40°C was spherical, however, with increasing the temperature from 40°C to 70°C, it was changed to an ellipsoidal shape. Berry number and master curve slope revealed that NSG solution at all temperatures was within the dilute regime and that no molecular entanglements were present. The parameter b values acquired for NSG at the intended temperatures showed that the molecular conformation of NSG was random coil. The activation energy and chain flexibility parameter calculated for NSG at the studied temperatures were 0.488×107 J/kgmol and 587.2, respectively.

DETERMINATION OF GRAIN MOTION MODE ON A VIBRATORY SURFACE

he use of vibration transport in agricultural production plays a very significant part. Vibratory conveyors have the variety of advantages over traditional transporting ma-chines such as auger and belt type conveyors used at agri-cultural enterprises for transporting mainly loose and granular materials. A rather low wear coefficient of trans-porting body itself - a conveying trough of a vibration-transporting machine may be referred to the advantages, besides, in some constructions of vibration-transporting machines the amount of friction couples is reduced to a minimum. In the design of constructions of vibration-transporting machines a question arises about the determi-nation of motion mode of particles of the transporting mate-rial. Thus, the detection of a predominant component of motion will allow forecasting the wear rate of a transporting surface and the possibility of enlarging the field of techno-logical use of vibration-transporting machines. During the research process for the determination of motion mode of grain material the shape of which was close to spheroid and ellipsoid, the method of mathematical modeling was applied. The system of differential equations of second order was compiled and solved. In the equations the influ-ence of vibration of a transporting surface on the motion of an elliptically shaped body was taken into account. To solve the system the classical method - Runge-Kutta method of the fourth order was used. The program devel-oped in programming language Python allowed identifying the motion mode of the bodies of spheroidal and ellipsoidal shapes on a vibrating surface. As the result, it was deter-mined that the motion of a body of a spheroidal shape on a vibrating surface was possible due to rolling, and the mo-tion of a body of an ellipsoidal shape was achieved be-cause of its sliding on the surface, what follows from wan-ing rotating movements. The suggested method for the determination of motion mode of a body on a vibrating sur-face is rather flexible and may be applied in calculation for larger bodies in comparison with grain seeds.

Sasanian Pseudo-Signet-Ring Excavated at the Palace of Mangup: The Aspects of Its Attribution and Interpretation

In 2006, the excavation of the palace of the rulers of the Principality of Theodoro (1425–1475) in the central area of the ancient town of Mangup (south-western Crimea) uncovered a unique at this site signet-ring of yellowish chalcedony made in the sixth or early seventh century in Sasanian Iran. This find belongs to a group of the so-called pseudo-signet-rings (muhr); it shows an ellipsoidal shape (flattened hemisphere) with a narrow channel for hanging on the neck, wrist, or belt. On the shield of the signet-ring there is an image of a mountain sheep (аrhar) with steeply curved horns, lying to the left, with the legs tucked. It was accompanied with a number of official symbols of the ruling dynasty in the Sassanian State: the royal bow ashkharavand (of a ribbon tied round a front leg of the animal), a crescent with the horns upward (a young Moon, one of the symbols of the dynasty), and atashdan (Zoroastrian temple altar with burning fire). The composition of this image goes back to the legend about the founder of the Sassanian dynasty King Ardashir I (224–240), who defeated the last Parthian ruler Artaban V (213–224) and ascended the throne with the help from the deity of royal power, victory, might, luck, and glory Farr embodied in the mountain ram. Therefore, the first owner of the signet-ring was a member of the privileged part of the Sassanian society, using the ring to make signature or as a sign of ownership when sealing personal documents and items of trade transactions. Considering the circumstances of the discovery of the Sassanian ring in the cultural layer of one of the largest Byzantine fortresses in Taurica obviously constructed at the end of the reign of Emperor Justinian I (527–565), it is hardly worth thinking of direct official correspondence between the local Byzantine administration and someone from Iranian correspondents or the presence of the military contingents from Persia. Most likely, the find in question was simply a trophy of a Byzantine officer who took part in one of the many Byzantine-Sassanian military campaigns of the second half of the sixth or the first third of the seventh centuries and then continued his service in the garrison of Mangup-Doros.

The 2017 May 20th stellar occultation by the elongated centaur (95626) 2002 GZ32

We predicted a stellar occultation of the bright star Gaia DR1 4332852996360346368 (UCAC4 385-75921) (mV= 14.0 mag) by the centaur 2002 GZ32 for 2017 May 20th. Our latest shadow path prediction was favourable to a large region in Europe. Observations were arranged in a broad region inside the nominal shadow path. Series of images were obtained with 29 telescopes throughout Europe and from six of them (five in Spain and one in Greece) we detected the occultation. This is the fourth centaur, besides Chariklo, Chiron and Bienor, for which a multi-chord stellar occultation is reported. By means of an elliptical fit to the occultation chords we obtained the limb of 2002 GZ32 during the occultation, resulting in an ellipse with axes of 305 ± 17 km × 146 ± 8 km. From this limb, thanks to a rotational light curve obtained shortly after the occultation, we derived the geometric albedo of 2002 GZ32 (pV = 0.043 ± 0.007) and a 3-D ellipsoidal shape with axes 366 km × 306 km × 120 km. This shape is not fully consistent with a homogeneous body in hydrostatic equilibrium for the known rotation period of 2002 GZ32. The size (albedo) obtained from the occultation is respectively smaller (greater) than that derived from the radiometric technique but compatible within error bars. No rings or debris around 2002 GZ32 were detected from the occultation, but narrow and thin rings cannot be discarded.

High Delity Elastic Green's Functions for Subduction Zone Models Consistent With the Global Standard Geodetic Reference System

Green's functions (GFs) for elastic deformation due to unit slip on the fault plane comprise an essential tool for estimating earthquake rupture and underground preparation processes. These estimation results are often applied to generate important information for public such as seismic and tsunami hazard assessments. So, it is important to minimize the distortion of the estimation results on the numerical models used for calculating GFs to guarantee assessment reliability. For this purpose, we here calculated GFs based on a numerical model that is of high delity to obtain realistic topography and subsurface structural models of the Earth. We targeted two well-known subduction zones in Japan, the Nankai Trough and the Japan Trench. For these subduction zones, databases for realistic topography and subsurface structural models of the Earth are available in the \Japan integrated velocity structure model version 1", which was proposed for earthquake hazard assessments conducted by the Japanese government.Furthermore, in order to eliminate inconsistencies in data processing of the calculated and observed response, we used the same coordinate systems for processing GFs as those adopted widely to process space geodetic observation data for surface displacements. The ellipsoidal shape of the Earth, which is often approximated with a projected plane or a spherical shape, was also incorporated by faithfully following the denitions of the coordinate systems in Geodetic Reference System 1980, which is the global standard for space geodesy. To calculate elastic GFs based on such high delity subduction zone databases with the ellipsoidal shape of the Earth, we introduced the nite element (FE) method. In the FE meshes, the resolution of the topography and subsurface structure is the same as that of the original databases. Recent development of the state-of-the-art computation techniques for the rapid calculation of crustal deformation using large-scale FE models allows for GF calculation based on such a high delity model. However, it is generally not easy to perform such calculations. Thus, we released a library for the GFs calculated in this study to the geoscience community on a web server, aiming to contribute more reliable seismic and tsunami hazard assessment.