Impact Of Low-Frequency HIV-1 Drug Resistance Mutations On Antiretroviral Therapy Outcomes.

BACKGROUND: The association between low-frequency HIV-1 drug resistance mutations (DRMs) and treatment failure (TF) is controversial. We explore this association using NGS methods that accurately sample low-frequency DRMs. METHODS: We enrolled women with HIV-1 in Malawi who were either ART naïve (A), had ART failure (B), or had discontinued ART (C). At entry, A and C began an NNRTI-based regimen and B started a PI-based regimen. We used Primer ID MiSeq to identify regimen-relevant DRMs in entry and TF plasma samples, and a Cox proportional hazards model to calculate hazard ratios (HRs) for entry DRMs. Low-frequency DRMs were defined as ≤ 20%. RESULTS: We sequenced 360 participants. Cohort B and C participants were more likely to have TF than Cohort A participants. The presence of K103N at entry significantly increased TF risk among A and C participants at both high and low frequency, with HR of 3.12 [1.58-6.18, 95% CI] and 2.38 [1.00-5.67, 95% CI] respectively. At TF, 45% of participants showed selection of DRMs while in the remaining participants there was an apparent lack of selective pressure from ART. CONCLUSIONS: Using accurate NGS for DRM detection may benefit an additional 10% of the patients by identifying low-frequency K103N mutations.

Two-Year Outcomes of Novel Dual-Mobility Implant in Primary Total Hip Arthroplasty.

Introduction: Dual-mobility (DM) implants for total hip arthroplasty (THA) have gained popularity due to their potential to reduce hip instability and dislocation events that may lead to revision surgery. These implants consist of a femoral head articulated within a polyethylene liner, which articulates within an outer acetabular shell, creating a dual-bearing surface. Our study aimed to report our observations on the survivorship of a novel DM implant for primary total hip arthroplasty at two years. Methods: We conducted a retrospective, multicenter study to assess the clinical outcomes of patients undergoing a THA with a novel DM implant (OR3O acetabular system™, Smith & Nephew, Inc., Memphis, TN) from January 2020 to September 2021. Patient demographics, surgical information, and survivorship data were collected from medical records for patients with a minimum of two years of follow-up. Primary outcomes included overall implant survivorship at two years as well as aseptic survivorship, revision rates of the DM acetabular shell, and average time to revision. Patient-reported outcomes were collected in the form of HOOS JR. Results: A total of 250 hips in 245 patients had a minimum two-year follow-up. Primary osteoarthritis (80%) was the most common indication for index THA. The average aseptic survivorship of the DM acetabular components at two years for the cohort was 98.4% and survivorship of the acetabular implants overall was 97.6%. There were a total of four (1.6%) aseptic revisions of the DM acetabular component. Reasons for aseptic acetabular revision included one case of instability, one intraprosthetic dislocation, one periprosthetic acetabular fracture, and one malpositioned acetabular cup resulting in impingement. The mean time of follow-up was 893.9 days. Eighty-seven patients had preoperative and two-year HOOS JR available. HOOS JR improved by an average of 38.5 points. Conclusion: This novel DM acetabular implant demonstrates excellent survivorship at two years follow-up with low rates of instability and intraprosthetic dislocation and no episodes of metal-on-metal corrosion. Use of the DM implant demonstrated clinically relevant improvements in patient-reported outcomes at two years.

N4 -Hydroxycytidine/Molnupiravir Inhibits RNA-Virus Induced Encephalitis by Producing Mutated Viruses with Reduced Fitness.

A diverse group of RNA viruses including Rabies, Polio, La Crosse, West Nile, Zika, Nipah, Eastern and Western equine encephalitis, Venezuelan equine encephalitis, Japanese encephalitis, and tick-borne encephalitis viruses have the ability to gain access to and replicate in the central nervous system (CNS), causing severe neurological disease. Current treatment for these patients is generally limited to supportive care. To address the need for a generalizable antiviral, we utilized a strategy of mutagenesis to limit virus replication. We evaluated ribavirin (RBV), favipiravir (FAV) and N 4 -hydroxycytidine (NHC) against La Crosse virus (LACV) which is the primary cause of pediatric arboviral encephalitis cases in North America. NHC was more potent than RBV or FAV in neuronal cells. Oral administration of molnupiravir (MOV), the 5'-isobutyryl prodrug of NHC, decreased neurological disease development by 32% following intraperitoneal (IP) infection of LACV. MOV also reduced disease by 23% when virus was administered intranasally (IN). NHC and MOV produced less fit viruses by incorporating predominantly G-to-A or C-to-U mutations. Furthermore, NHC also inhibited two other orthobunyaviruses, Jamestown Canyon virus and Cache Valley virus. Collectively, these studies indicate that NHC/MOV has therapeutic potential to inhibit virus replication and subsequent neurological disease caused by this neurotropic RNA virus.

Use of Next-Generation Sequencing in a State-Wide Strategy of HIV-1 Surveillance: Impact of the SARS-COV-2 Pandemic on HIV-1 Diagnosis and Transmission.

BACKGROUND: The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic posed an unpreceded threat to the management of other pandemics such as human immunodeficiency virus-1 (HIV-1) in the United States. The full impact of the SARS-CoV-2 pandemic on the HIV-1 pandemic needs to be evaluated. METHODS: All individuals with newly reported HIV-1 diagnoses from NC State Laboratory of Public Health were enrolled in this prospective observational study, 2018-2021. We used a sequencing-based recency assay to identify recent HIV-1 infections and to determine the days postinfection (DPI) for each person at the time of diagnosis. RESULTS: Sequencing used diagnostic serum samples from 814 individuals with new HIV-1 diagnoses spanning this 4-year period. Characteristics of individuals diagnosed in 2020 differed from those in other years. People of color diagnosed in 2021 were on average 6 months delayed in their diagnosis compared to those diagnosed in 2020. There was a trend that genetic networks were more known for individuals diagnosed in 2021. We observed no major integrase resistance mutations over the course of the study. CONCLUSIONS: SARS-CoV-2 pandemic may contribute to the spread of HIV-1. Public health resources need to focus on restoring HIV-1 testing and interrupting active, ongoing, transmission.

Unique Molecular Identifiers and Multiplexing Amplicons Maximize the Utility of Deep Sequencing To Critically Assess Population Diversity in RNA Viruses.

Next generation sequencing (NGS)/deep sequencing has become an important tool in the study of viruses. The use of unique molecular identifiers (UMI) can overcome the limitations of PCR errors and PCR-mediated recombination and reveal the true sampling depth of a viral population being sequenced in an NGS experiment. This approach of enhanced sequence data represents an ideal tool to study both high and low abundance drug resistance mutations and more generally to explore the genetic structure of viral populations. Central to the use of the UMI/Primer ID approach is the creation of a template consensus sequence (TCS) for each genome sequenced. Here we describe a series of experiments to validate several aspects of the Multiplexed Primer ID (MPID) sequencing approach using the MiSeq platform. We have evaluated how multiplexing of cDNA synthesis and amplicons affects the sampling depth of the viral population for each individual cDNA and amplicon to understand the relationship between broader genome coverage versus maximal sequencing depth. We have validated reproducibility of the MPID assay in the detection of minority mutations in viral genomes. We have also examined the determinants that allow sequencing reads of PCR recombinants to contaminate the final TCS data set and show how such contamination can be limited. Finally, we provide several examples where we have applied MPID to analyze features of minority variants and describe limits on their detection in viral populations of HIV-1 and SARS-CoV-2 to demonstrate the generalizable utility of this approach with any RNA virus.

Spatio-Spectral Ultrasound Characterization of Reflection and Transmission Through Bone With Temperature Dependence.

Transcranial focused ultrasound (tFUS) is a promising approach for the treatment of neurological disorders. It has proven useful in several clinical applications, with promising outcomes reported in the recent literature. Furthermore, it is currently being investigated in a range of neuromodulation (NM) and ablative applications, including epilepsy. In this application, tFUS access through the temporal window is the key to optimizing the treatment safety and efficacy. Traditional approaches have utilized transducers with low operating frequencies for tFUS applications. Modern array transducers and driving systems allow for more intelligent use of the temporal window by exploiting the spatio-spectral transmission bandwidth to a specified target or targets within the brain. To demonstrate the feasibility of this approach, we have investigated the ultrasound reflection and transmission characteristics for different access points within the temporal window of human skull samples ex vivo. Different transmit-receive (Rx) configurations are used for characterization of the spatio-spectral variability in reflection and transmission through the temporal window. In this article, we show results from a dual-piston transducer set up in the frequency range of 2-7 MHz. Broadband pulses as well as synthesized orthogonal frequency division multiplexed (OFDM) waveforms were used. The latter was used to improve the magnitude and phase measurements in 100-kHz subbands within the 2-7 MHz spectral window. A temperature-controlled water bath was used to characterize the change in reflection and transmission characteristics with temperature in the 25°C-43°C range. The measured values of the complex reflection and transmission coefficients exhibited significant variations with space, frequency, and temperature. On the other hand, the measured transmission phase varied more with location and frequency, with smaller sensitivity to temperature. A measurement-based hybrid angular spectrum (HAS) simulation through the human temporal bone was used to demonstrate the dependence of focusing gain on the skull profile and spatial distribution of change of speed of sound (SOS) at different skull temperatures.

Iterative method for optical modelling of perovskite-based tandem solar cells.

We present an iterative method to model the optical properties of a complete semitransparent perovskite solar cell. It is based on spectroscopic characterizations and accounts for porosity and incoherence effects. We provide the complex refractive indices of each layer, and we identify the main sources of optical losses. The optical model is also coupled to an electrical model of 4T perovskite/silicon tandem solar cells. It allows to evaluate the interplay between the optical and electrical losses, and the balance between the efficiency of the top and bottom cells. These models provide an effective way to design future tandem devices.

Occurrence of (suspected) genotoxic flavoring substances in Belgian alcohol-free beers.

The regulatory landscape of flavorings is evolving, thereby putting pressure on control laboratories to develop analytical methods for a wide range of compounds in various types of food and drinks. In order to improve the monitoring of flavoring substances, a versatile and accurate analytical method using the solvent-assisted flavor evaporation (SAFE) technique coupled to GC-MS(SIM) was developed and validated. Focus was put on authorized flavoring substances requiring specific attention due to a genotoxic concern based on information from European risks assessment reports. Thirty-seven (suspected) genotoxic flavoring substances were analyzed in a selection of ten alcohol-free beers. Five suspected genotoxic compounds (i.e. 1-(2-furyl)-2-propanone, 2-acetylfuran, 2-acetyl-5-methylfuran, 2-acetyl-3,5-dimethylfuran, hex-2-eno-1,4-lactone) as well as two confirmed genotoxic flavoring substances (p-mentha-1,8-dien-7-al, 2,4-pentanedione) were identified and quantified among the selected samples. Low concentrations and natural occurrences of the identified compounds suggested that these were not added as such but rather originated from heat-treatments or from plant-based extracts.

Assessing the added value of group B Streptococcus maternal immunisation in preventing maternal infection and fetal harm: population surveillance study.

OBJECTIVE: To assess the incidence of maternal group B Streptococcus (GBS) infection in England. DESIGN: Population surveillance augmented through data linkage. SETTING: England. POPULATION: All pregnant women accessing the National Health Service (NHS) in England. METHODS: Invasive GBS (iGBS) infections during pregnancy or within 6 weeks of childbirth were identified by linking Public Health England (PHE) national microbiology surveillance data for 2014 to NHS hospital admission records. Capsular serotypes of GBS were determined by reference laboratory typing of clinical isolates from women aged 15-44 years. Post-caesarean section surgical site infection (SSI) caused by GBS was identified in 21 hospitals participating in PHE SSI surveillance (2009-2015). MAIN OUTCOME MEASURES: iGBS rate per 1000 maternities; risk of GBS SSI per 1000 caesarean sections. RESULTS: Of 1601 patients diagnosed with iGBS infections in England in 2014, 185 (12%) were identified as maternal infections, a rate of 0.29 (95% CI 0.25-0.33) per 1000 maternities and representing 83% of all iGBS cases in women aged 18-44 years. Seven (3.8%) were associated with miscarriage. Fetal outcome identified excess rates of stillbirth (3.4 versus 0.5%) and extreme prematurity (<28 weeks of gestation, 3.7 versus 0.5%) compared with national averages (P < 0.001). Caesarean section surveillance in 27 860 women (21 hospitals) identified 47 cases of GBS SSI, with an estimated 4.24 (3.51-5.07) per 1000 caesarean sections, a median time-to-onset of 10 days (IQR 7-13 days) and ten infections that required readmission. Capsular serotype analysis identified a diverse array of strains with serotype III as the most common (43%). CONCLUSIONS: Our assessment of maternal GBS infection in England indicates the potential additional benefit of GBS vaccination in preventing adverse maternal and fetal outcomes.

Effect of Systemic Administration of Granulocyte-Colony Stimulating Factor on Rate of Fracture Healing of Bone Defect in Goats as Animal Model

@#Granulocyte-colony stimulating factor (G-CSF) serves as an important cytokine in haematopoiesis; released at both physiological and pathological conditions by a range of cells. We hypothesized that the systemic administration of G-CSF would produce an accelerated fracture-healing rate in non-union bone defects; thus, potentially leading to useful clinical applications. Ten male adult Katjang goats, weighing about 15-26 kilograms were randomly chosen and a tibial bone defect was induced in each animal. The defect was maintained by internal fixation with a titanium plate and reinforced by an external fiberglass cast. Post-operative radiographs were performed twice weekly and radiographic assessments were performed by evaluating the bridging and union measurements through a validated method. In the treatment group, the time for bridging and union exhibited statistically significant differences when compared with a control group. The outcomes of the present study establishing a notion that administration of G-CSF besides inducing haematopoiesis, promotes healing of fractures and non-union bone defects as well.

Superconducting imprint of magnetic textures in ferromagnets with perpendicular magnetic anisotropy.

Research on proximity effects in superconductor/ferromagnetic hybrids has most often focused on how superconducting properties are affected-and can be controlled-by the effects of the ferromagnet's exchange or magnetic fringe fields. The opposite, namely the possibility to craft, tailor and stabilize the magnetic texture in a ferromagnet by exploiting superconducting effects, has been more seldom explored. Here we show that the magnetic flux trapped in high-temperature superconducting YBa2Cu3O7-δ microstructures can be used to modify the magnetic reversal of a hard ferromagnet-a cobalt/platinum multilayer with perpendicular magnetic anisotropy-and to imprint unusual magnetic domain distributions in a controlled manner via the magnetic field history. The domain distributions imprinted in the superconducting state remain stable, in absence of an external magnetic field, even after increasing the temperature well above the superconducting critical temperature, at variance to what has been observed for soft ferromagnets with in-plane magnetic anisotropy. This opens the possibility of having non-trivial magnetic configuration textures at room temperature after being tailored below the superconducting transition temperature. The observed effects are well explained by micromagnetic simulations that demonstrate the role played by the magnetic field from the superconductor on the nucleation, propagation, and stabilization of magnetic domains.

ß-d-N4-hydroxycytidine Inhibits SARS-CoV-2 Through Lethal Mutagenesis But Is Also Mutagenic To Mammalian Cells.

Mutagenic ribonucleosides can act as broad-based antiviral agents. They are metabolized to the active ribonucleoside triphosphate form and concentrate in genomes of RNA viruses during viral replication. ß-d-N4-hydroxycytidine (NHC, initial metabolite of molnupiravir) is >100-fold more active than ribavirin or favipiravir against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with antiviral activity correlated to the level of mutagenesis in virion RNA. However, NHC also displays host mutational activity in an animal cell culture assay, consistent with RNA and DNA precursors sharing a common intermediate of a ribonucleoside diphosphate. These results indicate highly active mutagenic ribonucleosides may hold risk for the host.

Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome.

Next generations sequencing (NGS) has become an important tool in biomedical research. The Primer ID approach combined with the MiSeq platform overcomes the limitation of PCR errors and reveals the true sampling depth of population sequencing, making it an ideal tool to study mutagenic effects of potential broad-spectrum antivirals on RNA viruses. In this report we describe a protocol using Primer ID sequencing to study the mutations induced by antivirals in a coronavirus genome from an in vitro cell culture model and an in vivo mouse model. Viral RNA or total lung tissue RNA is tagged with Primer ID-containing cDNA primers during the initial reverse transcription step, followed by two rounds of PCR to amplify viral sequences and incorporate sequencing adaptors. Purified and pooled libraries are sequenced using the MiSeq platform. Sequencing data are processed using the template consensus sequence (TCS) web-app. The Primer ID approach provides an accurate sequencing protocol to measure mutation error rates in viral RNA genomes and host mRNA. Sequencing results suggested that ß-D-N4-hydroxycytidine (NHC) greatly increased the transition substitution rate but not the transversion substitution rate in the viral RNA genomes, and cytosine (C) to uridine (U) was found as the most frequently seen mutation.

Low LAL (Lysosomal Acid Lipase) Expression by Smooth Muscle Cells Relative to Macrophages as a Mechanism for Arterial Foam Cell Formation.

[Figure: see text].

Correction: Mechanical rigidity of a shape-memory metal-organic framework increases by crystal downsizing.

Correction for 'Mechanical rigidity of a shape-memory metal-organic framework increases by crystal downsizing' by Al A. Tiba et al., Chem. Commun., 2021, 57, 89-92, DOI: 10.1039/D0CC05684G.

Mechanical rigidity of a shape-memory metal-organic framework increases by crystal downsizing.

Soft porous nanocrystals with a pronounced shape-memory effect exhibit two- to three-fold increase in elastic modulus compared to the microcrystalline counterpart as determined by atomic force microscopy nanoindentation. The increase in rigidity is consistent with the known shape-memory effect displayed by the framework solid at the nanoscale. Crystal downsizing can offer new avenues for tailoring the mechanical properties of metal-organic frameworks.