The simian T-lymphotropic virus STLV-PP1664 from Pan paniscus is distinctly related to HTLV-2 but differs in genomic organization

We have isolated a highly divergent simian T-lymphotropic virus, STLV-PP1664, from a wild-caught bonobo (Pan paniscus). Previous phylogenetic analysis suggested that this virus represents an additional type of STLV but this has now become a matter of discussion. We have now obtained and analyzed the entire genome of STLV-PP1664. All major genes and their corresponding viral messengers were identified. Sequence comparison and phylogenetic analysis indicated that this virus, together with the closely related panp isolate, belongs to an early lineage within the PTLV-2 clade, differing from HTLV-2 by about 25%. In contrast to the HTLV-1 and HTLV-2 LTR, only two 21-bp repeats instead of three were found in the STLV-PP1664 LTR. Additional messengers, resulting from alternative splicing, potentially encode five different accessory proteins from open reading frames in the pX region: prorfI, porfII, ptorfV', and two isoforms of Rex. The amino acid sequences of these proteins are only distinctly related to the accessory proteins from HTLV-2. These data suggest a different genomic organization of the STLV-PP1664 pX region than that of HTLV-2. We conclude that STLV-PP1664, although related to HTLV-2, has some distinct features in the LTR and the pX regions, the impact of which needs further investigation. Although arguments pro and contra a distinct classification are nearly equally balanced, we propose to classify this virus as an STLV-2, designated STLV-2PP1664.     

Thin-skin analysis technique for interaction of arbitrary-shape inducer field with long cracks in ferromagnetic metals

In using the AC field measurement (ACFM) technique for non-destructive evaluation (NDE) of metals, a current-carrying wire structure is used to induce eddy current within a thin layer of the metal and a magnetic field sensor to measure the field perturbations in the vicinity of the metal. The sensitivity of ACFM crack detection and sizing relies on an appropriate design of the wire structure geometry together with a dully placement of the sensor. This paper presents an analytical modeling technique for evaluating the electromagnetic field interaction of an ACFM probe with a long uniform crack in a ferromagnetic metallic slab. The probe in the proposed model can have an arbitrary-shape wire inducer with no restrictions on its relative sensor position. The technique is accurate and very efficient computationally. It first uses the two-dimensional Fourier transform to obtain the field distribution at the metal surface. The Laplacian field distribution above the metal is then determined by satisfying the so-obtained boundary condition at air–metal interface. To demonstrate the accuracy of the model, we consider the special case of a rhombic wire inducer. The comparison of our results with those obtained using the conventional algorithm in the literature validates the accuracy of the model introduced in this paper. To show the generality of the model, we also present theoretical and experimental results associated with a solenoid inducer with a three-dimensional geometry for which no analytical solution is available in the literature. The theoretical prediction of crack signal supported by experimental results is used to develop a model-based method for inverting crack signal into crack depth.     

A modified thermodynamic insight to deliquescence of a void‐containing nanocrystal confirmed by MD simulation

Existence of voids in crystalline structures can affect their physical and chemical properties considerably. When the size of the crystal reaches to nanoscale, experimental determination of its void fraction is difficult. In this work, a molecular dynamics approach is introduced to find equilibrium void fractions of a simple cubic (CsCl) and fcc (KCl) nanocrystals by determination of their deliquescence relative humidity (DRH) for different sizes and void fractions and extrapolation of the results to the bulk limit. To confirm the simulation results, the size dependency of DRH to the nanoparticle size was studied thermodynamically by inclusion of size‐dependent density of water nanodroplet which leads to a simple homographic equation. This method proposes the equilibrium void percents of CsCl and KCl nanoparticles to be 10 and 15%, respectively, which are obtained by extrapolation of the results to the bulk limit. The success of obtained Möbius function was also confirmed by fitting it to experimental data for deliquescence of NaCl nanoparticles which implies the importance of considering density of water nanodroplet as a size dependent quantity. Also, using the mentioned thermodynamic approach, void dependency of deliquescence for the nanoparticles was found to be as a quasi‐linear trend which is compatible with the simulation results. It is noticeable that the approach used this work for determination of equilibrium void fraction is only valid if the utilized force fields are accurate. © 2016 American Institute of Chemical Engineers AIChE J, 62: 4066–4077, 2016     

Data compression using antidictionaries

We give a new text-compression scheme based on forbidden words (“antidictionary”). We prove that our algorithms attain the entropy for balanced binary sources. They run in linear time. Moreover, one of the main advantages of this approach is that it produces very fast decompressors. A second advantage is a synchronization property that is helpful to search compressed data and allows parallel compression. The techniques used in this paper are from information theory and finite automata     

Tunable,Grating-Gated,Graphene-On-Polyimide Terahertz Modulators

An electrically switchable graphene terahertz (THz) modulator with a tunable-by-design optical bandwidth is presented and it is exploited to compensate the cavity dispersion of a quantum cascade laser (QCL). Electrostatic gating is achieved by a metal grating used as a gate electrode, with an HfO₂/AlO_x gate dielectric on top. This is patterned on a polyimide layer, which acts as a quarter wave resonance cavity, coupled with an Au reflector underneath. The authors achieve 90% modulation depth of the intensity, combined with a 20 kHz electrical bandwidth in the 1.9–2.7 THz range. The modulator is then integrated with a multimode THz QCL. By adjusting the modulator operational bandwidth, the authors demonstrate that the graphene modulator can partially compensate the QCL cavity dispersion, resulting in an integrated laser behaving as a stable frequency comb over 35% of the operational range, with 98 equidistant optical modes and a spectral coverage ~1.2 THz. This paves the way for applications in the terahertz, such as tunable transformation-optics devices, active photonic components, adaptive and quantum optics, and metrological tools for spectroscopy at THz frequencies.     

The Expression of Lipoprotein Receptors Is Increased in the Infarcted Area After Myocardial Infarction Induced in Rats With Cardiac Dysfunction

Left ventricular (LV) remodeling after myocardial infarction constitutes the structural basis for ventricular dysfunction and heart failure. The characterization underlying the expression of lipoprotein receptors in cardiac dysfunction is scarcely explored. The aim of this study was to analyze the status of lipoprotein receptors on the infarcted and noninfarcted areas of LV and to verify whether nanoparticles that mimic the lipid structure of low‐density lipoprotein (LDL) and have the ability to bind to LDL receptors (LDE) are taken up more avidly by the noninfarcted LV. 13 male Wistar rats with left coronary artery ligation (myocardial infarction [MI]) and 12 animals with SHAM operation (SHAM) were used in this study. 6 weeks after the procedure, the quantification of low‐density lipoprotein receptor (LDLR), LDL receptor‐related protein 1 (LRP1), scavenger receptor‐class B type I (SR‐BI) lipoprotein receptors, and PCNA proliferation marker, and tissue uptake of radioactively labeled LDE were performed. Immunohistochemistry and Western blot analysis showed that LDLR, LRP1, SR‐BI, and PCNA, expression in infarcted area of MI was remarkably higher than SHAM and noninfarcted subendocardial (SEN) and interstitial (INT) areas. In addition, in SEN noninfarcted area of MI, the presence of LDLR was about threefold higher than in SHAM SEN and INT noninfarcted areas. The LDE uptake of noninfarcted LV of MI group was about 30% greater than that of SHAM group. In conclusion, these findings regarding the status of lipoprotein receptors after MI induction could help to establish mechanisms on myocardial repairing. In conclusion, infarcted rats with LV dysfunction showed increased expression of lipoprotein receptors mainly in the infarcted area.     

A Secreted Chorismate Mutase from Xanthomonas arboricola pv. juglandis Attenuates Virulence and Walnut Blight Symptoms

Walnut blight is a significant above-ground disease of walnuts caused by Xanthomonas arboricola pv. juglandis (Xaj). The secreted form of chorismate mutase (CM), a key enzyme of the shikimate pathway regulating plant immunity, is highly conserved between plant-associated beta and gamma proteobacteria including phytopathogens belonging to the Xanthomonadaceae family. To define its role in walnut blight disease, a dysfunctional mutant of chorismate mutase was created in a copper resistant strain Xaj417 (XajCM). Infections of immature walnut Juglans regia (Jr) fruit with XajCM were hypervirulent compared with infections with the wildtype Xaj417 strain. The in vitro growth rate, size and cellular morphology were similar between the wild-type and XajCM mutant strains, however the quantification of bacterial cells by dPCR within walnut hull tissues showed a 27% increase in XajCM seven days post-infection. To define the mechanism of hypervirulence, proteome analysis was conducted to compare walnut hull tissues inoculated with the wild type to those inoculated with the XajCM mutant strain. Proteome analysis revealed 3296 Jr proteins (five decreased and ten increased with FDR ≤ 0.05) and 676 Xaj417 proteins (235 increased in XajCM with FDR ≤ 0.05). Interestingly, the most abundant protein in Xaj was a polygalacturonase, while in Jr it was a polygalacturonase inhibitor. These results suggest that this secreted chorismate mutase may be an important virulence suppressor gene that regulates Xaj417 virulence response, allowing for improved bacterial survival in the plant tissues.     

VAD Based on Kernel Smoothed Function of EGARCH Models

An algorithm for a voice activity detector (VAD) is proposed. It is based on the exponential generalized autoregressive conditional heteroscedasticity (EGARCH) filter for generalized hyperbolic (GH), Gaussian random variables, adaptive threshold values and autocorrelation coefficients. EGARCH models are a new variation of GARCH models used especially in economic time series. A speech signal is assumed to have a GH because GH has heavier tails than the Gaussian distribution (GD) covering other heavy tailed distributions like hyperbolic, skewed $t$ , variance gamma (VG), inverse Gaussian (NIG), Cauchy, Student’s $t$ and Laplace distributions. The distribution of noise signal is assumed to be uncorrelated (white noise), but in general, that is not necessary. In the proposed method, heteroscedasticity is modeled by EGARCH. A kernel smoothed function of conditional variances and autocorrelations generate the soft detection vector. Finally, hard detection is the result of comparing the soft detection vector with an adaptive threshold value. The simulation results show that the proposed VAD is able to operate down to $-5$  dB.     

Determination of elastic constants of additive manufactured Inconel 625 specimens using an ultrasonic technique

The nature of additive manufacturing (AM) processes prescribes direction-dependent properties of the final parts. The degree of material anisotropy is high     

Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements

Our evolutionary and structural analyses revealed that the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) spike gene is a complex mosaic resulting from several recombination events. Additionally, the fixation of variants has mainly been driven by purifying selection, suggesting the presence of conserved structural features. Our dynamic simulations identified two main long-range covariant dynamic movements of the novel glycoprotein, and showed that, as a result of the evolutionary duality, they are preserved. The first movement involves the receptor binding domain with the N-terminal domain and the C-terminal domain 2 and is maintained across human, bat and pangolin coronaviruses. The second is a complex network of long-range dynamics specific to SARS-CoV-2 involving the novel PRRA and the conserved KR*SF cleavage sites, as well as conserved segments in C-terminal domain 3. These movements, essential for host cell binding, are maintained by hinges conserved across human, bat, and pangolin coronaviruses glycoproteins. The hinges, located around Threonine 333 and Proline 527 within the N-terminal domain and C-terminal domain 2, represent candidate targets for the future development of novel pan-coronavirus inhibitors. In summary, we show that while recombination created a new configuration that increased the covariant dynamic movements of the SARS-CoV-2 glycoprotein, negative selection preserved its inter-domain structure throughout evolution in different hosts and inter-species transmissions.