Functional and clinical outcome with modified lateral approach total hip arthroplasty in stiff hips with ankylosing spondylitis.

BACKGROUND: Ankylosing spondylitis at total hip arthroplasty (THA) has significant hip stiffness with flexion deformity, restricted mobility, and function. Range of movement (ROM) improvement with good functional outcome is seen following THA in these hips. The modified Hardinge approach without abductor compromise is helpful in these stiff hips with associated flexion deformity. AIM: To assess improvement in ROM and functional outcomes with a modified lateral approach THA in ankylosing spondylitis with stiff hips. METHODS: A total of 69 hips that underwent THA with a modified Hardinge approach in 40 patients were evaluated at a mean follow-up of 38.33 mo. All individuals ambulated with weight-bearing as tolerated and ROM exercises from the 1st postoperative day. Modified Harris hip score and ROM were assessed during follow-up. Quality of life assessments using the 36-item and 12-item short form health surveys were done along with clinical and functional outcomes at follow-up. SPSS 22.0 was used for statistical analysis. The correlation of ROM and functional score change was performed using Pearson's correlation coefficient. RESULTS: Sixty-nine hips with a significant decrease in ROM preoperatively with 32 clinically fused hips showed significant improvement in flexion range. The mean flexion in 69 hips improved from 29.35 ± 31.38 degrees to 102.17 ± 10.48 degrees. The mean difference of 72.82 with a P value < 0.0001 was significant. In total, 45 out of 69 hips had flexion deformity, with 13 hips having a deformity above 30 degrees. The flexion during the follow-up was below 90 degrees in 3 hips. Eleven hips had flexion of 90 degrees at follow-up, while the remaining 55 hips had flexion above 100 degrees. Modified Harris hip score improved from 17.03 ± 6.02 to 90.66 ± 7.23 (P value < 0.0001). The 36-item short form health survey at the follow-up indicated health status in 40 patients as excellent in 11, very good in 20, good in 5, fair in 3, and poor in 1. The mean mental health score was 84.10 ± 11.58. Pain relief was good in all 69 hips. Altogether, 28/40 patients (70%) had no pain, 9 patients (22%) had occasional pain, and 3 patients (8%) had mild to moderate pain with unusual activity. Heterotopic ossification was seen in 21 hips with Brooker class 1 in 14 hips. CONCLUSION: Modified Hardinge approach THA in ankylosing spondylitis with stiff hips with flexion deformity significantly improved ROM, Harris hip score, and quality of life indicated by the 36-item and 12-item short form health surveys.

Implicit self-consistent electrolyte model in plane-wave density-functional theory.

The ab initio computational treatment of electrochemical systems requires an appropriate treatment of the solid/liquid interfaces. A fully quantum mechanical treatment of the interface is computationally demanding due to the large number of degrees of freedom involved. In this work, we develop a computationally efficient model where the electrode part of the interface is described at the density-functional theory (DFT) level, and the electrolyte part is represented through an implicit solvation model based on the Poisson-Boltzmann equation. We describe the implementation of the linearized Poisson-Boltzmann equation into the Vienna Ab initio Simulation Package, a widely used DFT code, followed by validation and benchmarking of the method. To demonstrate the utility of the implicit electrolyte model, we apply it to study the surface energy of Cu crystal facets in an aqueous electrolyte as a function of applied electric potential. We show that the applied potential enables the control of the shape of nanocrystals from an octahedral to a truncated octahedral morphology with increasing potential.

High-throughput computational X-ray absorption spectroscopy.

X-ray absorption spectroscopy (XAS) is a widely-used materials characterization technique. In this work we present a database of computed XAS spectra, using the Green's formulation of the multiple scattering theory implemented in the FEFF code. With more than 500,000 K-edge X-ray absorption near edge (XANES) spectra for more than 40,000 unique materials, this database constitutes the largest existing collection of computed XAS spectra to date. The data is openly distributed via the Materials Project, enabling researchers across the world to access it for free and use it for comparisons with experiments and further analysis.

Interface-Driven Structural Distortions and Composition Segregation in Two-Dimensional Heterostructures.

The discovery of emergent phenomena in 2D materials has sparked substantial research efforts in the materials community. A significant experimental challenge for this field is exerting atomistic control over the structure and composition of the constituent 2D layers and understanding how the interactions between layers drive both structure and properties. While no segregation for single bilayers was observed, segregation of Pb to the surface of three bilayer thick PbSe-SnSe alloy layers was discovered within [(Pbx Sn1-x Se)1+δ ]n (TiSe2 )1 heterostructures using electron microscopy. This segregation is thermodynamically favored to occur when Pbx Sn1-x Se layers are interdigitated with TiSe2 monolayers. DFT calculations indicate that the observed segregation depends on what is adjacent to the Pbx Sn1-x Se layers. The interplay between interface- and volume-free energies controls both the structure and composition of the constituent layers, which can be tuned using layer thickness.

Computational Screening of 2D Materials for Photocatalysis.

Two-dimensional (2D) materials exhibit a range of extraordinary electronic, optical, and mechanical properties different from their bulk counterparts with potential applications for 2D materials emerging in energy storage and conversion technologies. In this Perspective, we summarize the recent developments in the field of solar water splitting using 2D materials and review a computational screening approach to rapidly and efficiently discover more 2D materials that possess properties suitable for solar water splitting. Computational tools based on density-functional theory can predict the intrinsic properties of potential photocatalyst such as their electronic properties, optical absorbance, and solubility in aqueous solutions. Computational tools enable the exploration of possible routes to enhance the photocatalytic activity of 2D materials by use of mechanical strain, bias potential, doping, and pH. We discuss future research directions and needed method developments for the computational design and optimization of 2D materials for photocatalysis.

Density functional theory study of the electrochemical interface between a Pt electrode and an aqueous electrolyte using an implicit solvent method.

We present a computational study of the interface of a Pt electrode and an aqueous electrolyte employing semi-empirical dispersion corrections and an implicit solvent model within first-principles calculations. The electrode potential is parametrized within the computational hydrogen electrode scheme. Using one explicit layer, we find that the most realistic interface configuration is a water bilayer in the H-up configuration. Furthermore, we focus on the contribution of the dispersion interaction and the presence of water on H, O, and OH adsorption energies. This study demonstrates that the implicit water scheme represents a computationally efficient method to take the presence of an aqueous electrolyte interface with a metal electrode into account.

Damaging the Integrated HIV Proviral DNA with TALENs.

HIV-1 integrates its proviral DNA genome into the host genome, presenting barriers for virus eradication. Several new gene-editing technologies have emerged that could potentially be used to damage integrated proviral DNA. In this study, we use transcription activator-like effector nucleases (TALENs) to target a highly conserved sequence in the transactivation response element (TAR) of the HIV-1 proviral DNA. We demonstrated that TALENs cleave a DNA template with the HIV-1 proviral target site in vitro. A GFP reporter, under control of HIV-1 TAR, was efficiently inactivated by mutations introduced by transfection of TALEN plasmids. When infected cells containing the full-length integrated HIV-1 proviral DNA were transfected with TALENs, the TAR region accumulated indels. When one of these mutants was tested, the mutated HIV-1 proviral DNA was incapable of producing detectable Gag expression. TALEN variants engineered for degenerate recognition of select nucleotide positions also cleaved proviral DNA in vitro and the full-length integrated proviral DNA genome in living cells. These results suggest a possible design strategy for the therapeutic considerations of incomplete target sequence conservation and acquired resistance mutations. We have established a new strategy for damaging integrated HIV proviral DNA that may have future potential for HIV-1 proviral DNA eradication.

Solid-solid phase transformations induced through cation exchange and strain in 2D heterostructured copper sulfide nanocrystals.

We demonstrate dual interface formation in nanocrystals (NCs) through cation exchange, creating epitaxial heterostructures within spherical NCs. The thickness of the inner-disk layer can be tuned to form two-dimensional (2D), single atomic layers (<1 nm). During the cation exchange reaction from copper sulfide to zinc sulfide (ZnS), we observe a solid-solid phase transformation of the copper sulfide phase in heterostructured NCs. As the cation exchange reaction is initiated, Cu ions replaced by Zn ions at the interfaces are accommodated in intrinsic Cu vacancy sites present in the initial roxbyite (Cu1.81S) phase of copper sulfide, inducing a full phase transition to djurleite (Cu1.94S)/low chalcocite (Cu2S), a more thermodynamically stable phase than roxbyite. As the reaction proceeds and reduces the size of the copper sulfide layer, the epitaxial strain at the interfaces between copper sulfide and ZnS increases and is maximized for a copper sulfide disk ∼ 5 nm thick. To minimize this strain energy, a second phase transformation occurs back to the roxbyite phase, which shares a similar sulfur sublattice to wurtzite ZnS. The observation of a solid-solid phase transformation in our unique heterostructured NCs provides a new pathway to control desired phases and an insight into the influence of cation exchange on nanoscale phase transitions in heterostructured materials.

The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis.

There is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. This web system has been used for almost 40,000 searches. We report improvements to HIVToolbox including new functions and workflows, data updates, and updates for ease of use. HIVToolbox2, is an improvement over HIVToolbox with new functions. HIVToolbox2 has new functionalities focused on HIV pathogenesis including drug-binding sites, drug-resistance mutations, and immune epitopes. The integrated, interactive view enables visual mining to generate hypotheses that are not readily revealed by other approaches. Most HIV proteins form multimers, and there are posttranslational modification and protein-protein interaction sites at many of these multimerization interfaces. Analysis of protease drug binding sites reveals an anatomy of drug resistance with different types of drug-resistance mutations regionally localized on the surface of protease. Some of these drug-resistance mutations have a high prevalence in specific HIV-1 M subtypes. Finally, consolidation of Tat functional sites reveals a hotspot region where there appear to be 30 interactions or posttranslational modifications. A cursory analysis with HIVToolbox2 has helped to identify several global patterns for HIV proteins. An initial analysis with this tool identifies homomultimerization of almost all HIV proteins, functional sites that overlap with multimerization sites, a global drug resistance anatomy for HIV protease, and specific distributions of some DRMs in specific HIV M subtypes. HIVToolbox2 is an open-access web application available at [http://hivtoolbox2.bio-toolkit.com].

Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways.

Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent effects. In this work, we implement an implicit solvation model that has a firm theoretical foundation into the widely used density-functional code Vienna ab initio Software Package. The implicit solvation model follows the framework of joint density functional theory. We describe the framework, our algorithm and implementation, and benchmarks for small molecular systems. We apply the solvation model to study the surface energies of different facets of semiconducting and metallic nanocrystals and the SN2 reaction pathway. We find that solvation reduces the surface energies of the nanocrystals, especially for the semiconducting ones and increases the energy barrier of the SN2 reaction.

The Geogenomic Mutational Atlas of Pathogens (GoMAP) web system.

We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼ 502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project/