Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure

Drug resistance in HIV type 1 (HIV-1) is a pervasive problem that affects the lives of millions of people worldwide. Although records of drug-resistant mutations (DRMs) have been extensively tabulated within public repositories, our understanding of the evolutionary kinetics of DRMs and how they evolve together remains limited. Epistasis, the interaction between a DRM and other residues in HIV-1 protein sequences, is key to the temporal evolution of drug resistance. We use a Potts sequence-covariation statistical-energy model of HIV-1 protein fitness under drug selection pressure, which captures epistatic interactions between all positions, combined with kinetic Monte-Carlo simulations of sequence evolutionary trajectories, to explore the acquisition of DRMs as they arise in an ensemble of drug-naive patient protein sequences. We follow the time course of 52 DRMs in the enzymes protease, RT, and integrase, the primary targets of antiretroviral therapy. The rates at which DRMs emerge are highly correlated with their observed acquisition rates reported in the literature when drug pressure is applied. This result highlights the central role of epistasis in determining the kinetics governing DRM emergence. Whereas rapidly acquired DRMs begin to accumulate as soon as drug pressure is applied, slowly acquired DRMs are contingent on accessory mutations that appear only after prolonged drug pressure. We provide a foundation for using computational methods to determine the temporal evolution of drug resistance using Potts statistical potentials, which can be used to gain mechanistic insights into drug resistance pathways in HIV-1 and other infectious agents.

Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants

HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem, and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug-resistant HIV-1 intasomes bound to DTG or 4d, with better than 3-Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms of DTG resistance involving E138K + G140A/S + Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.

Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins

The ability of HIV-1 to rapidly mutate leads to antiretroviral therapy (ART) failure among infected patients. Drug-resistance mutations (DRMs), which cause a fitness penalty to intrinsic viral fitness, are compensated by accessory mutations with favorable epistatic interactions which cause an evolutionary trapping effect, but the kinetics of this overall process has not been well characterized. Here, using a Potts Hamiltonian model describing epistasis combined with kinetic Monte Carlo simulations of evolutionary trajectories, we explore how epistasis modulates the evolutionary dynamics of HIV DRMs. We show how the occurrence of a drug-resistance mutation is contingent on favorable epistatic interactions with many other residues of the sequence background and that subsequent mutations entrench DRMs. We measure the time-autocorrelation of fluctuations in the likelihood of DRMs due to epistatic coupling with the sequence background, which reveals the presence of two evolutionary processes controlling DRM kinetics with two distinct time scales. Further analysis of waiting times for the evolutionary trapping effect to reverse reveals that the sequences which entrench (trap) a DRM are responsible for the slower time scale. We also quantify the overall strength of epistatic effects on the evolutionary kinetics for different mutations and show these are much larger for DRM positions than polymorphic positions, and we also show that trapping of a DRM is often caused by the collective effect of many accessory mutations, rather than a few strongly coupled ones, suggesting the importance of multiresidue sequence variations in HIV evolution. The analysis presented here provides a framework to explore the kinetic pathways through which viral proteins like HIV evolve under drug-selection pressure.

Calculating and Characterizing the Charge Distributions in Solids

Accurate estimation of the partial atomic charges on metal centers is useful for understanding electronic and catalytic properties of materials. However, different methods of calculating these charges may give quite different results; this issue has been more widely studied for molecules than for solids. Here we study the charges on the metal centers of a test set of 18 solids containing transition metals by using density functional theory with several density functionals (PBE, PBE+U, TPSS, revTPSS, HLE17, revM06-L, B3LYP, B3LYP*, and other exchange-modified B3LYP functionals) and four charge models (Bader, Hirshfeld, CM5, and DDEC6). The test set contains 12 systems with nonmagnetic metal centers (eight metal oxides (MO₂), two metal sulfides (MS₂), and two metal selenides (MSe₂)) and six ferromagnetic transition metal complexes. Our study shows that, among the four types of charges, Bader charges are the highest and Hirshfeld charges are the lowest for all the systems, regardless of the functional being used. The CM5 charges are bigger than DDEC6 charges for MX₂ with M = Ti or Mo and X = S or Se, but for the other 14 cases they are lower. We found that the most of the systems are sensitive to the Hubbard U parameters in PBE+U and to the percentage X of Hartree-Fock exchange in exchange-modified B3LYP; as we increase U or X, the charges on the metal atoms in MX₂ increase steadily. Testing different density functionals shows charges calculated with higher Hubbard U parameters in PBE+U are comparable to B3LYP (with 20% Hartree-Fock exchange). Among four meta-GGA functionals studied, the charges with HLE17 have the closest agreement with B3LYP. The variation of charges with choice of charge model is greater than the variation with choice of density functional.

Improved Predictive Tools for Structural Properties of Metal-Organic Frameworks

The accurate determination of structural parameters is necessary to understand the electronic and magnetic properties of metal-organic frameworks (MOFs) and is a first step toward accurate calculations of electronic structure and function for separations and catalysis. Theoretical structural determination of metal-organic frameworks is particularly challenging because they involve ionic, covalent, and noncovalent interactions, which must be treated in a balanced fashion. Here, we apply a diverse group of local exchange-correlation functionals (PBE, PBEsol, PBE-D2, PBE-D3, vdW-DF2, SOGGA, MN15-L, revM06-L, SCAN, and revTPSS) to a broad test set of MOFs to seek the most accurate functionals to study various structural aspects of porous solids, in particular to study lattice constants, unit cell volume, two types of pore size characteristics, bond lengths, bond angles, and torsional angles). The recently developed meta functionals revM06-L and SCAN, without adding any molecular mechanics terms, are able to predict more accurate structures than previously recommended functionals, both those without molecular mechanics terms (PBE, PBEsol, vdW-DF2, and revTPSS) and those with them (PBE-D2 and PBE-D3). To provide a broader test, these two functionals are also tested for lattice constants and band gaps of unary, binary, and ternary semiconductors.

Ferromagnetism in magnesium chloride monolayer with an unusually large spin-up gap

The primary research target of the rapidly evolving spintronic industry is to design highly efficient novel materials that consume very low power and operate with high speed. Main group based ferromagnetic half-metallic materials are very promising due to their long spin-relaxation time. In recent years, the discovery of superconducting state with high critical temperature in a magnesium based system (MgB₂) invigorated researchers due to its simple crystal structure and intriguing results, leading to its use as a good material for large scale application in electronic devices. Here, we report ferromagnetism and strong half-metallicity in another Mg-based system, which can be a promising material for spintronics based devices rather than for electronic devices (such as MgB₂). Based on the first principle calculations, we report here a series of magnetic half-metallic magnesium chloride based monolayers [Mg_0.89δ_0.11Cl₂, Mg_0.78δ_0.22Cl₂, and Mg_0.67δ_0.33Cl₂ (MgCl₃)]. This MgCl₃ phase has a similar pattern as that in CrI₃, which has drawn remarkable attention worldwide as the first intrinsic 2D magnet. These magnesium chloride monolayer based systems are 100% spin-polarized, and promising for scattering-less transport due to strong half-metallicity and large spin-up gap (∼6.135-6.431 eV). The unusually large spin-up gap in our proposed system may shield spin current leakage even in nanoscale device. Further investigation explores a ferromagnetic ordering in Mg_0.89δ_0.11Cl₂ with a Curie temperature of 250 K, which makes the system viable for operation at temperatures slightly lower than the room temperature. High magnetic anisotropy energy (MAE) in Mg_0.89δ_0.11Cl₂ (452.84 μeV) indicates that the energy required to flip the spin is high, and therefore inhibits spin fluctuation. These results suggest a promising way to discover MgCl₂-based 2D spin valves, GMR, TMR and other spintronics devices.

Band gap opening in stanene induced by patterned B-N doping

Stanene is a quantum spin Hall insulator and a promising material for electronic and optoelectronic devices. Density functional theory (DFT) calculations are performed to study the band gap opening in stanene by elemental mono-doping (B, N) and co-doping (B-N). Different patterned B-N co-doping is studied to change the electronic properties of stanene. A patterned B-N co-doping opens the band gap in stanene and its semiconducting nature persists under strain. Molecular dynamics (MD) simulations are performed to confirm the thermal stability of such a doped system. The stress-strain study indicates that such a doped system is as stable as pure stanene. Our work function calculations show that stanene and doped stanene have a lower work function than graphene and thus are promising materials for photocatalysts and electronic devices.

Ferromagnetism and Half-Metallicity in a High-Band-Gap Hexagonal Boron Nitride System

Metal-free half-metallicity is the subject of intense research in the field of spintronics devices. Using density functional theoretical calculations, atom-thin hexagonal boron nitride (h-BN)-based systems are studied for possible spintronics applications. Ferromagnetism is observed in patterned C-doped h-BN systems. Interestingly, such a patterned C-doped h-BN exhibits half-metallicity with a Curie temperature of approximately 324 K at a particular C-doping concentration. It shows half-metallicity more than metal-free systems studied to date. Thus, such a BN-based system can be used to achieve a 100 % spin-polarised current at the Fermi level. Furthermore, this C-doped system shows excellent dynamical, thermal, and mechanical properties. Therefore, a stable metal-free planar ferromagnetic half-metallic h-BN-based system is proposed for use in room-temperature spintronics devices.

High Curie temperature and half-metallicity in an atomically thin main group-based boron phosphide system: long range ferromagnetism

In this work, we have designed a main group-based novel ferromagnetic half-metallic material with a high Curie temperature for spintronics.

Room-Temperature Magneto-dielectric Effect in LaGa0.7Fe0.3O3+γ; Origin and Impact of Excess Oxygen

We report an observation of room-temperature magneto-dielectric (RTMD) effect in LaGa_0.7Fe_0.3O_3+γ compound. The contribution of intrinsic/resistive sources in the presently observed RTMD effect was analyzed by measuring direct-current (dc) magnetoresistance (MR) in four-probe geometry and frequency-dependent MR via impedance spectroscopy (MRIS). Present MRIS analysis reveals that at frequencies corresponding to grain contribution (≥1 × 10⁶ Hz for present sample), the observed MD phenomenon is MR-free/intrinsic, whereas at lower probing frequencies (<1 × 10⁶ Hz), the observed MD coupling appears to be MR-dominated possibly due to oxygen excess, that is, due to coexistence of Fe³⁺ and Fe⁴⁺. The magnetostriction is anticipated as a mechanism responsible for MR-free/intrinsic MD coupling, whereas the MR-dominated part is attributed to hopping charge transport along with Maxwell-Wagner and space charge polarization. The multivalence of Fe ions in LaGa_0.7Fe_0.3O_3+γ was validated through iodometric titration and Fe K-edge X-ray absorption near-edge structure measurements. The excess of oxygen, that is, coexistence of Fe³⁺ and Fe⁴⁺, was understood in terms of stability of Fe⁴⁺ by means of "bond-valence-sum" analysis and density functional theory-based first-principles calculations. The cation vacancies at La/Ga site (or at La and Ga both) were proposed as the possible origin of excess oxygen in presently studied compound. Present investigation suggests that, to justify the intrinsic/resistive origin of MD phenomenon, frequency-dependent MR measurements are more useful than measuring only dc MR or comparing the trends of magnetic-field-dependent change in dielectric constant and tan δ. Presently studied Fe-doped LaGaO₃ can be a candidate for RTMD applications.

Stanene based gas sensors: effect of spin–orbit coupling

B@, N@, and B–N@stanene for NO₂ gas sensors.

Transition-metal embedded carbon nitride monolayers: high-temperature ferromagnetism and half-metallicity

High-temperature ferromagnetic materials with planar surfaces are promising candidates for spintronics applications. Using state-of-the-art density functional theory (DFT) calculations, transition metal (TM = Cr, Mn, and Fe) incorporated graphitic carbon nitride (TM@gt-C3N4) systems are investigated as possible spintronics devices. Interestingly, ferromagnetism and half-metallicity were observed in all of the TM@gt-C3N4 systems. We find that Cr@gt-C3N4 is a nearly half-metallic ferromagnetic material with a Curie temperature of ∼450 K. The calculated Curie temperature is noticeably higher than other planar 2D materials studied to date. Furthermore, it has a steel-like mechanical stability and also possesses remarkable dynamic and thermal (500 K) stability. The calculated magnetic anisotropy energy (MAE) in Cr@gt-C3N4 is as high as 137.26 μeV per Cr. Thereby, such material with a high Curie temperature can be operated at high temperatures for spintronics devices.

Fe doped LaGaO3: good white light emitters

Photoluminescence emission spectra from Fe doped LaGaO₃. The luminescence due to ultra violet He–Cd laser is shown in the inset.

Cuboctahedral vs. octahedral platinum nanoclusters: insights into the shape-dependent catalytic activity for fuel cell applications

The shape of a catalyst plays an important role in any catalytic reaction.

A cuboctahedral platinum (Pt79) nanocluster enclosed by well defined facets favours di-sigma adsorption and improves the reaction kinetics for methanol fuel cells

The methanol dehydrogenation steps are studied very systematically on the (111) facet of a cuboctahedral platinum (Pt79) nanocluster enclosed by well-defined facets. The various intermediates formed during the methanol decompositions are adsorbed at the edge and bridge site of the facet either vertically (through C- and O-centres) or in parallel. The di-sigma adsorption (in parallel) on the (111) facet of the nanocluster is the most stable structure for most of the intermediates and such binding improves the interaction between the substrate and the nanocluster and thus the catalytic activity. The reaction thermodynamics, activation barrier, and temperature dependent reaction rates are calculated for all the successive methanol dehydrogenation steps to understand the methanol decomposition mechanism, and these values are compared with previous studies to understand the catalytic activity of the nanocluster. We find the catalytic activity of the nanocluster is excellent while comparing with any previous reports and the methanol dehydrogenation thermodynamics and kinetics are best when the intermediates are adsorbed in a di-sigma manner.

Targeted water soluble copper–tetrazolate complexes: interactions with biomolecules and catecholase like activities

Two new copper–tetrazolate complexes are synthesized and their interaction with DNA, bovine serum albumin (BSA) and catecholase like activity are explored. Interactions of the complexes with DNA are also investigated using DFT.

Direct vs. indirect pathway for nitrobenzene reduction reaction on a Ni catalyst surface: a density functional study

Density functional theory (DFT) calculations are performed to understand and address the previous experimental results that showed the reduction of nitrobenzene to aniline prefers direct over indirect reaction pathways irrespective of the catalyst surface. Nitrobenzene to aniline conversion occurs via the hydroxyl amine intermediate (direct pathway) or via the azoxybenzene intermediate (indirect pathway). Through our computational study we calculated the spin polarized and dispersion corrected reaction energies and activation barriers corresponding to various reaction pathways for the reduction of nitrobenzene to aniline over a Ni catalyst surface. The adsorption behaviour of the substrate, nitrobenzene, on the catalyst surface was also considered and the energetically most preferable structural orientation was elucidated. Our study indicates that the parallel adsorption behaviour of the molecules over a catalyst surface is preferable over vertical adsorption behaviour. Based on the reaction energies and activation barrier of the various elementary steps involved in direct or indirect reaction pathways, we find that the direct reduction pathway of nitrobenzene over the Ni(111) catalyst surface is more favourable than the indirect reaction pathway.

Additives in protic–hydridic hydrogen storage compounds: a molecular study

Listed model compounds having best dehydrogenation properties where ΔE_avg is the average hydrogen removal energy for the complete dehydrogenation.

An audit of the outcome of amblyopia treatment: a retrospective analysis of 322 children

BACKGROUND/AIMS

Little is known about the effectiveness of occlusion therapy in hospital settings. A retrospective analysis was conducted to assess modalities, outcome and hospital costs of children treated for amblyopia with patching in a UK clinic.

METHODS

Notes of 322 children with amblyopia discharged after occlusion treatment were selected consecutively and reviewed. Data collated included age at presentation, amblyopia type, visual acuity (VA; before/after occlusion and at discharge), number of prescribed hours of occlusion, duration of patching treatment, number of glasses prescribed and number of visits attended or failed to attend. Hospital treatment costs were estimated.

RESULTS

Mixed amblyopes were prescribed the longest amount of patching (mean 2815 h over 23 months) followed by strabismic (1984 h) and anisometropic (1238 h) amblyopes. 319 amblyopes received glasses and five atropine treatment. The percentage of patients reaching VA of 6/12 was best in the anisometropic and strabismic groups (>75%) and worse in mixed amblyopia (64%). Average hospital costs were estimated at pound1365.

CONCLUSION

Although the mean duration of treatment was long, involving many hospital visits, the visual outcome was variable, unsatisfactory (<6/9) and more expensive than necessary. As compliance has been identified as a major problem methods to improve amblyopia treatment are needed, possibly by using educational/motivational intervention.

Survey of management of acquired nystagmus in the United Kingdom

PURPOSE

To determine the current management of acquired nystagmus by ophthalmologists and neurologists.

METHODS

Questionnaires were sent to ophthalmologists (850) and neurologists (434) in the United Kingdom. Estimated numbers of patients seen with acquired nystagmus, treatment options used, and the results of treatment of the patients were collected.

RESULTS

Response rate was 37% for ophthalmologists and 34% for neurologists. The most common causes of acquired nystagmus were estimated to be multiple sclerosis and stroke. 58% of ophthalmologists and 94.5% of neurologists reported seeing patients with nystagmus. The most commonly used medical treatment was gabapentin and baclofen. Other drugs used were clonazepam, carbamazepine, benzhexol, ondansetrone, buspirone, memantine, and botulinum toxin (n=3). Eleven ophthalmologists and 52 neurologists noted symptomatic improvement with medical treatment. Eleven ophthalmologists and 44 neurologists noted improvement in visual acuity (VA). Occurrence of side effects noted with baclofen and gabapentin treatments were similar.

CONCLUSION

A variety of drugs are used to treat acquired nystagmus in the UK. Baclofen and gabapentin are the drugs most commonly used and are reported to cause significant improvement in symptoms and VA. Better knowledge of the action of drugs in nystagmus is needed to establish guidelines and to give patients wider access to treatment.

Shape analysis of hippocampal surface structure in patients with unilateral mesial temporal sclerosis

Structural hippocampal magnetic resonance (MR) imaging-based analysis is helpful in the diagnosis and treatment of mesial temporal epileptic seizures. Computational anatomic techniques provide a framework for objective assessment of three-dimensional hippocampal structure. We applied a previously validated technique of deformation-based hippocampal segmentations in 20 subjects with documented unilateral mesial temporal sclerosis (MTS) and temporal lobe epilepsy. Using composite images, we then measured shape differences between the epileptogenic, smaller hippocampus, and contralateral hippocampus. Final shape differences were projected on the contralateral "normal" side. We calculated results for the left MTS group (10 patients) and right MTS group (10 patients) separately. Both groups showed similar regions of maximal inward deformation in the affected hippocampus, which were the medial and lateral aspect of the head, and posterior aspect of the tail. These results suggest that there are specific three-dimensional patterns of volume loss in patients with mesial temporal epilepsy.

Magnetic resonance imaging deformation-based segmentation of the hippocampus in patients with mesial temporal sclerosis and temporal lobe epilepsy

We compared manual and automated segmentations of the hippocampus in patients with mesial temporal sclerosis. This comparison showed good precision of the deformation-based automated segmentations.