Unique genetic signatures in HIV-1 subtype A1 and A1D recombinant envelope glycoprotein distinguish contemporary transmitted/founder viruses from historical strains in East Africa.

Introduction: The envelope glycoprotein (Env) of HIV-1 Transmitted/Founder (T/F) viruses in subtypes B and C carries distinct genetic signatures that enhance transmission fitness, augment infectivity and immune evasion. However, there is limited data on such signatures in T/F subtypes A1, D and A1D recombinants that predominate East Africa's HIV epidemic.

Methods: We used phylogenetically corrected approaches to detect distinct genetic signatures by comparing 44 contemporary HIV-1 T/F Envs with 229 historical Envs of the same subtype in East Africa.

Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters.

Motivation: The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference.

Hypermut 3: Identifying specific mutational patterns in a defined nucleotide context that allows multistate characters.

The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference.

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. (p24) and (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994-2018) and four hyperendemic Lake Victoria fishing communities (2011-2018) under continuous surveillance.

Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda.

HIV incidence has been declining in Africa with scale-up of HIV interventions. However, there is limited data on HIV evolutionary trends in African populations with waning epidemics. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-five-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort.

Comprehensive Genetic Characterization of Four Novel HIV-1 Circulating Recombinant Forms (CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx): Insights from Molecular Epidemiology in Cyprus.

Molecular investigations of the HIV-1 region (2253-5250 in the HXB2 genome) were conducted on sequences obtained from 331 individuals infected with HIV-1 in Cyprus between 2017 and 2021. This study unveiled four distinct HIV-1 putative transmission clusters, encompassing 19 previously unidentified HIV-1 recombinants. These recombinants, each comprising eight, three, four, and four sequences, respectively, did not align with previously established Circulating Recombinant Forms (CRFs).

Dielectric characterization of paraelectric particle-loaded polymer matrix composites and commercial photoresins at W-band frequencies.

This work presents W-band (75-110 GHz) dielectric characterization of commercially available photoresins in their neat state, as well as in polymer matrix composite (PMC) mixtures with various loading concentrations of the paraelectric barium strontium titanate (BST). Due to difficulties 3D printing the BST-loaded PMC resins detailed within, a custom curing and casting process was used to fabricate testable PMC samples, which were synthesized to demonstrate the dielectric functionalization of the underlying polymer matrix. Dielectric characterization of the PMCs confirmed the functionalization of our composites when compared to the commercial photoresins.

Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage.

The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.

Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola.

Angola, located in Central Africa, has around 320,000 (270,000-380,000) people living with human immunodeficiency virus (HIV)/AIDS, equivalent to 1% of the country's population at the end of 2021. A previous study conducted in 2012, using Angolan samples collected between 2008 and 2010 revealed a high prevalence of HIV-1 recombinants, around 42% of sequences, with 21% showing the same UH profile in partial pol region which were grouped into a monophyletic cluster with high bootstrap support. Thus, the objective of the present work was to obtain complete genomes of those sequences and characterize them, aiming at a description of a new circulating recombinant form (CRF).

The emergence and transmission dynamics of HIV-1 CRF07_BC in Mainland China.

A total of 1155 partial gene sequences of human immunodeficiency virus (HIV)-1 CRF07_BC were sampled between 1997 and 2015, spanning 13 provinces in Mainland China and risk groups [heterosexual, injecting drug users (IDU), and men who have sex with men (MSM)] to investigate the evolution, adaptation, spatiotemporal and risk group dynamics, migration patterns, and protein structure of HIV-1 CRF07_BC. Due to the unequal distribution of sequences across time, location, and risk group in the complete dataset ('full1155'), subsampling methods were used. Maximum-likelihood and Bayesian phylogenetic analysis as well as discrete trait analysis of geographical location and risk group were carried out.

Origin and evolution of HIV-1 subtype A6.

Background: HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype A6 and other subtype A sub-subtypes.

Methods: For this study, an initial Maximum Likelihood phylogenetic analysis was performed using a total of 553 full-length, publicly available, reverse transcriptase sequences, from A1, A2, A3, A4, A5, and A6 sub-subtypes of subtype A.

GaO-on-SiC Composite Wafer for Thermal Management of Ultrawide Bandgap Electronics.

β-phase gallium oxide (GaO) is an emerging ultrawide bandgap (UWBG) semiconductor ( ∼ 4.8 eV), which promises generational improvements in the performance and manufacturing cost over today's commercial wide bandgap power electronics based on GaN and SiC. However, overheating has been identified as a major bottleneck to the performance and commercialization of GaO device technologies.

Thermal Conductivity of β-Phase GaO and (AlGa)O Heteroepitaxial Thin Films.

Heteroepitaxy of β-phase gallium oxide (β-GaO) thin films on foreign substrates shows promise for the development of next-generation deep ultraviolet solar blind photodetectors and power electronic devices. In this work, the influences of the film thickness and crystallinity on the thermal conductivity of (2̅01)-oriented β-GaO heteroepitaxial thin films were investigated. Unintentionally doped β-GaO thin films were grown on -plane sapphire substrates with off-axis angles of 0° and 6° toward ⟨112̅0⟩ via metal-organic vapor phase epitaxy (MOVPE) and low-pressure chemical vapor deposition.

Prevalence of gp160 polymorphisms known to be related to decreased susceptibility to temsavir in different subtypes of HIV-1 in the Los Alamos National Laboratory HIV Sequence Database.

Background: Fostemsavir, a prodrug of the gp120-directed attachment inhibitor temsavir, is indicated for use in heavily treatment-experienced individuals with MDR HIV-1. Reduced susceptibility to temsavir in the clinic maps to discrete changes at amino acid positions in gp160: S375, M426, M434 and M475.

Objectives: To query the Los Alamos National Laboratory (LANL) HIV Sequence Database for the prevalence of polymorphisms at gp160 positions of interest.

Steady-state methods for measuring in-plane thermal conductivity of thin films for heat spreading applications.

The development of high thermal conductivity thin film materials for the thermal management of electronics requires accurate and precise methods for characterizing heat spreading capability, namely, in-plane thermal conductivity. However, due to the complex nature of thin film thermal property measurements, resolving the in-plane thermal conductivity of high thermal conductivity anisotropic thin films with high accuracy is particularly challenging. Capable transient techniques exist; however, they usually measure thermal diffusivity and require heat capacity and density to deduce thermal conductivity.

HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens.

Humanity is currently facing the challenge of two devastating pandemics caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, multi-base insertions and deletions, recombination, and variation in surface glycans all generate the variability that, guided by natural selection, enables both HIV-1's extraordinary diversity and SARS-CoV-2's slower pace of mutation accumulation.

Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years.

We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing.

Thermal Conductivity of Aluminum Scandium Nitride for 5G Mobile Applications and Beyond.

Radio frequency (RF) microelectromechanical systems (MEMS) based on AlScN are replacing AlN-based devices because of their higher achievable bandwidths, suitable for the fifth-generation (5G) mobile network. However, overheating of AlScN film bulk acoustic resonators (FBARs) used in RF MEMS filters limits power handling and thus the phone's ability to operate in an increasingly congested RF environment while maintaining its maximum data transmission rate. In this work, the ramifications of tailoring of the piezoelectric response and microstructure of AlScN films on the thermal transport have been studied.

Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda.

Objective: Dolutegravir (DTG) is now a preferred component of first-line antiretroviral therapy (ART). However, prevalence data on natural resistance to integrase inhibitors [integrase strand transfer inhibitors (INSTIs)] in circulating non-subtype B HIV-1 in sub-Saharan Africa is scarce. Our objective is to report prevalence of pre-treatment integrase polymorphisms associated with resistance to INSTIs in an ART-naive cohort with diverse HIV-1 subtypes.

Emergence of SARS-CoV-2 through recombination and strong purifying selection.

COVID-19 has become a global pandemic caused by the novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis, discovering new drugs, and developing a vaccine. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike and other genes among bat, pangolin, and human coronaviruses, suggesting similar evolutionary constraints in different host species.