Investigation of genetic determinants of cognitive change in later life.

Cognitive decline is a major health concern and identification of genes that may serve as drug targets to slow decline is important to adequately support an aging population. Whilst genetic studies of cross-sectional cognition have been carried out, cognitive change is less well-understood. Here, using data from the TOMMORROW trial, we investigate genetic associations with cognitive change in a cognitively normal older cohort. We conducted a genome-wide association study of trajectories of repeated cognitive measures (using generalised estimating equation (GEE) modelling) and tested associations with polygenic risk scores (PRS) of potential risk factors. We identified two genetic variants associated with change in attention domain scores, rs534221751 (p = 1 × 10-8 with slope 1) and rs34743896 (p = 5 × 10-10 with slope 2), implicating NCAM2 and CRIPT/ATP6V1E2 genes, respectively. We also found evidence for the association between an education PRS and baseline cognition (at >65 years of age), particularly in the language domain. We demonstrate the feasibility of conducting GWAS of cognitive change using GEE modelling and our results suggest that there may be novel genetic associations for cognitive change that have not previously been associated with cross-sectional cognition. We also show the importance of the education PRS on cognition much later in life. These findings warrant further investigation and demonstrate the potential value of using trial data and trajectory modelling to identify genetic variants associated with cognitive change.

Genomic landscape and actionable mutations of brain metastases derived from non-small cell lung cancer: A systematic review.

Background: Brain metastases derived from non-small cell lung cancer (NSCLC) represent a significant clinical problem. We aim to characterize the genomic landscape of brain metastases derived from NSCLC and assess clinical actionability. Methods: We searched Embase, MEDLINE, Web of Science, and BIOSIS from inception to 18/19 May 2022. We extracted information on patient demographics, smoking status, genomic data, matched primary NSCLC, and programmed cell death ligand 1 expression. Results: We found 72 included papers and data on 2346 patients. The most frequently mutated genes from our data were EGFR (n = 559), TP53 (n = 331), KRAS (n = 328), CDKN2A (n = 97), and STK11 (n = 72). Common missense mutations included EGFR L858R (n = 80) and KRAS G12C (n = 17). Brain metastases of ever versus never smokers had differing missense mutations in TP53 and EGFR, except for L858R and T790M in EGFR, which were seen in both subgroups. Of the top 10 frequently mutated genes that had primary NSCLC data, we found 37% of the specific mutations assessed to be discordant between the primary NSCLC and brain metastases. Conclusions: To our knowledge, this is the first systematic review to describe the genomic landscape of brain metastases derived from NSCLC. These results provide a comprehensive outline of frequently mutated genes and missense mutations that could be clinically actionable. These data also provide evidence of differing genomic landscapes between ever versus never smokers and primary NSCLC compared to the BM. This information could have important consequences for the selection and development of targeted drugs for these patients.

Higher HIV-1 Env gp120-Specific Antibody-Dependent Cellular Cytotoxicity (ADCC) Activity Is Associated with Lower Levels of Defective HIV-1 Provirus.

A cure for HIV-1 (HIV) remains unrealized due to a reservoir of latently infected cells that persist during antiretroviral therapy (ART), with reservoir size associated with adverse health outcomes and inversely with time to viral rebound upon ART cessation. Once established during ART, the HIV reservoir decays minimally over time; thus, understanding factors that impact the size of the HIV reservoir near its establishment is key to improving the health of people living with HIV and for the development of novel cure strategies. Yet, to date, few correlates of HIV reservoir size have been identified, particularly in pediatric populations. Here, we employed a cross-subtype intact proviral DNA assay (CS-IPDA) to quantify HIV provirus between one- and two-years post-ART initiation in a cohort of Kenyan children (n = 72), which had a median of 99 intact (range: 0-2469), 1340 defective (range: 172-3.84 × 104), and 1729 total (range: 178-5.11 × 104) HIV proviral copies per one million T cells. Additionally, pre-ART plasma was tested for HIV Env-specific antibody-dependent cellular cytotoxicity (ADCC) activity. We found that pre-ART gp120-specific ADCC activity inversely correlated with defective provirus levels (n = 68, r = -0.285, p = 0.0214) but not the intact reservoir (n = 68, r = -0.0321, p-value = 0.800). Pre-ART gp41-specific ADCC did not significantly correlate with either proviral population (n = 68; intact: r = -0.0512, p-value = 0.686; defective: r = -0.109, p-value = 0.389). This suggests specific host immune factors prior to ART initiation can impact proviruses that persist during ART.

phippery: a software suite for PhIP-Seq data analysis.

SUMMARY: We present the phippery software suite for analyzing data from phage display methods that use immunoprecipitation and deep sequencing to capture antibody binding to peptides, often referred to as PhIP-Seq. It has three main components that can be used separately or in conjunction: (i) a Nextflow pipeline, phip-flow, to process raw sequencing data into a compact, multidimensional dataset format and allows for end-to-end automation of reproducible workflows. (ii) a Python API, phippery, which provides interfaces for tasks such as count normalization, enrichment calculation, multidimensional scaling, and more, and (iii) a Streamlit application, phip-viz, as an interactive interface for visualizing the data as a heatmap in a flexible manner. AVAILABILITY AND IMPLEMENTATION: All software packages are publicly available under the MIT License. The phip-flow pipeline: https://github.com/matsengrp/phip-flow. The phippery library: https://github.com/matsengrp/phippery. The phip-viz Streamlit application: https://github.com/matsengrp/phip-viz.

Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers.

Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. Here, we characterize antibody binding and functionality against Wuhan-Hu-1 (B lineage) strain SARS-CoV-2 in convalescent plasma from 36 postpartum women and 14 of their infants infected with SARS-CoV-2 from a vaccine-naïve prospective cohort in Nairobi, Kenya. We find significantly higher antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels in infants versus mothers. Plasma antibodies from mothers and infants bind to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants display higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants have significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, Spike pseudovirus neutralization titers between infants and mothers are similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody activities and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.

Passively Acquired Constant Region 5-Specific Antibodies Associated With Improved Survival in Infants Who Acquire Human Immunodeficiency Virus.

Studying vertical human immunodeficiency virus (HIV) transmission enables the impact of passively transferred antibodies on HIV transmission and pathogenesis to be examined. Using phage display of HIV envelope peptides and peptide enzyme-linked immunosorbent assay (ELISA), we found that, in infants who acquired HIV, passive antibody responses to constant region 5 (C5) were associated with improved survival in 2 cohorts. In a combined analysis, C5 peptide ELISA activity was correlated directly with survival and estimated infection time and inversely with set point viral load. These results suggest that preexisting C5-specific antibodies may be correlated with the survival of infants living with HIV, motivating additional research into their protective potential.

Reconstruction of a polyclonal ADCC antibody repertoire from an HIV-1 non-transmitting mother.

Human natural history and vaccine studies support a protective role of antibody dependent cellular cytotoxicity (ADCC) activity against many infectious diseases. One setting where this has consistently been observed is in HIV-1 vertical transmission, where passively acquired ADCC activity in HIV-exposed infants has correlated with reduced acquisition risk and reduced pathogenesis in HIV+ infants. However, the characteristics of HIV-specific antibodies comprising a maternal plasma ADCC response are not well understood. Here, we reconstructed monoclonal antibodies (mAbs) from memory B cells from late pregnancy in mother MG540, who did not transmit HIV to her infant despite several high-risk factors. Twenty mAbs representing 14 clonal families were reconstructed, which mediated ADCC and recognized multiple HIV Envelope epitopes. In experiments using Fc-defective variants, only combinations of several mAbs accounted for the majority of plasma ADCC of MG540 and her infant. We present these mAbs as evidence of a polyclonal repertoire with potent HIV-directed ADCC activity.

Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers.

Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. We characterized antibody binding and functionality in convalescent plasma from postpartum women and their infants infected with SARS-CoV-2 from a vaccine-naïve prospective cohort in Nairobi, Kenya. Antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels were significantly higher in infants than in mothers. Plasma antibodies from mothers and infants bound to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants displayed higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants had significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, neutralization titers between infants and mothers were similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody repertoires and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.

Socioeconomic Disparities in Method of Anesthesia for Knee Arthroplasties in the US.

INTRODUCTION: Knee arthroplasty (KA) can be performed using general anesthesia (GA), neuraxial anesthesia (NA) or regional anesthesia (RA). We believe proportion of types of anesthetics have changed but that there is a disparity based on socioeconomic factors. METHODS: Unadjusted rates and adjusted odds ratios for the use of RA or PNB were compared between groupings of patients based on socioeconomic status. RESULTS: General anesthesia is the most common (49.7%) while NA (39.4%) and RA (10.9%) were the second and third. University hospitals and patient home ZIP Code median income had the strongest association with RA as a (adjusted odds ratio (AOR) 26.3, 95% confidence interval (95%CI) 22.1-31.3, p<.01 and AOR 7.58, 95% CI 7.20-7.98, p<.01). CONCLUSION: General anesthesia is the most common but the rate of alternative forms of primary anesthesia type have changed over time. Disparities exist in anesthesia care which are associated with income levels.

Prevalence of BRAFV600 in glioma and use of BRAF Inhibitors in patients with BRAFV600 mutation-positive glioma: systematic review.

BACKGROUND: Detailed prevalence estimates of BRAFV600 mutations and BRAF inhibitor (BRAFi) treatment responses in V600-mutant glioma will inform trial development. METHODS: Our systematic review analyzed overall prevalence of BRAFV600 mutations in glioma and BRAFi treatment response. RESULTS: Based on 13 682 patients in 182 publications, the prevalence of BRAFV600 in epithelioid glioblastoma (eGBM) was 69% [95% CI: 45-89%]; pleomorphic xanthoastrocytoma (PXA): 56% [48-64%] anaplastic pleomorphic xanthoastrocytoma (aPXA): 38% [23-54%], ganglioglioma (GG): 40% [33-46%], and anaplastic ganglioglioma (aGG): 46% [18-76%]. Prevalence in astroblastoma was 24% [8-43%], desmoplastic infantile astrocytoma (DIA): 16% [0-57%], subependymal giant cell astrocytoma (SEGA): 8% [0-37%], dysembryoplastic neuroepithelial tumor (DNET): 3% [0-11%], diffuse astrocytoma (DA): 3% [0-9%], and pilocytic astrocytoma (PA): 3% [2-5%]. We reviewed 394 V600-mutant gliomas treated with BRAFi from 130 publications. One hundred and twenty-nine pediatric low-grade gliomas showed 4 (3.1%) complete response (CR); 53 (41.1%) partial response (PR); 64 (49.6%) stable disease (SD) and 8 (6.2%) progressive disease (PD). 25 pediatric high-grade gliomas showed CR; PR; SD; PD in 4 (16.0%); 10 (40.0%), 4 (16.0%); and 7 (28.0%) respectively. Thirty-nine adult low-grade gliomas showed CR; PR; SD; PD of 4 (10.3%); 17 (43.6%); 16 (41.0%) and 2 (5.1%) respectively. Ninety-seven adult high-grade gliomas showed CR; PR; SD; PD of 6 (6.2%); 31 (32.0%); 27 (27.8%); and 33 (34.0%) respectively. CONCLUSIONS: BRAFV600 prevalence is highest in eGBM, PXA, aPXA, GG, aGG, and lower in astroblastoma, DIA, SEGA, DNET, DA, and PA. Our data provide the rationale for adjuvant clinical trials of BRAFi in V600-mutant glioma.

HIV-1 protection: Antibodies move in for the kill.

Identifying the immune responses needed for protection against HIV is critical to finding an effective vaccine. In this issue of Cell Reports Medicine, Thomas and colleagues1 show that antibodies that kill infected cells correlate with infant HIV infection outcomes more so than antibodies that block viral entry.

Improved HIV-positive infant survival is correlated with high levels of HIV-specific ADCC activity in multiple cohorts.

Defining immune responses that protect humans against diverse HIV strains has been elusive. Studying correlates of protection from mother-to-child transmission provides a benchmark for HIV vaccine protection because passively transferred HIV antibodies are present during infant exposure to HIV through breast milk. A previous study by our group illustrated that passively acquired antibody-dependent cellular cytotoxicity (ADCC) activity is associated with improved infant survival whereas neutralization is not. Here, we show, in another cohort and with two effector measures, that passively acquired ADCC antibodies correlate with infant survival. In combined analyses of data from both cohorts, there are highly statistically significant associations between higher infant survival and passively acquired ADCC levels (p = 0.029) as well as dimeric FcγRIIa (p = 0.002) or dimeric FcγRIIIa binding (p < 0.001). These results suggest that natural killer (NK) cell- and monocyte antibody-mediated effector functions may contribute to the observed survival benefit and support a role of pre-existing ADCC-mediating antibodies in clinical outcome.

Synthesis of Graphene Quantum Dots Decorated With Se, Eu and Ag As Photosensitizer and Study of Their Potential to Use in Photodynamic Therapy.

GQDs decorated with europium (Eu), silver (Ag) and selenium (Se) at molar ratios of 0.1%, 0.3% and 0.5% were produced for the first time at different temperatures of 180 °C, 200 °C and 220 °C. Surface passivation was carried out with polyethylene glycol (PEG) to increase the intensity of photoluminescence (PL) of the produced samples. The prepared quantum dots were characterized by X-Ray diffraction (XRD), Fourier transformed infrared spectroscopy (FTIR), transmission electron microscopy (TEM), PL and ultraviolet-visible spectroscopy. GQDs synthesized at 180 °C and decorated with Se (0.3%) had maximum PL intensity along with long lasted afterglow over 90 min compared with other samples. Excitation wavelength at 360 nm produced maximum emission at 600-900 nm and resulted in high singlet oxygen (1O 2) generation which makes it a good candidate for photodynamic therapy applications.

Effects of advanced age and pituitary pars intermedia dysfunction on components of the acute phase reaction in horses.

Age, neurodegenerative disorders, and dysfunction of insulin secretion may be correlated with increased systemic concentrations of acute phase markers. Thus, the study aimed to determine the effect of age, pituitary pars intermedia dysfunction (PPID), and insulin dysregulation (ID) associated with PPID, on markers of the acute phase reaction. Twenty-nine mix-breed horses of both sexes were classified into groups: (1) healthy adult controls, (2) healthy non-PPID geriatric horses, (3) PPID ID+ horses, and (4) PPID ID- horses. Whole blood proinflammatory cytokine gene expression and serum concentrations of pro- and anti-inflammatory cytokines and acute phase proteins were measured. The data were analyzed using the Mann-Whitney U-test, and correlations between groups of data were assessed using Spearman's correlation coefficient. The tests were statistically significant if P < 0.05. No differences in the whole blood cytokine gene expression, serum cytokine concentrations, or acute phase proteins were noted between the groups. In the PPID ID group, there was a strong correlation between the ACTH concentration after the administration of thyrotropin-releasing hormone and the expression of IL-8 (r = 0.941; P = 0.0321). In the PPID ID+ group, there was a strong correlation between basal insulin concentrations and serum amyloid A (SAA; r = 0.936; P = 0.0083) as well as between postprandial insulin concentrations and SAA (r = 0.965; P = 0.001). These data suggest that neurodegeneration in horses moderately affects circulating markers of inflammation and that ID in horses with PPID influences acute phase inflammatory markers.

Effects of equine metabolic syndrome on inflammation and acute-phase markers in horses.

Obesity and metabolic disorders are associated with systemic low-grade chronic inflammation, both in humans and animals. The aim of the study is to assess the effects of obesity and hyperinsulinemia on individual components of the acute-phase reaction in equine metabolic syndrome (EMS) horses. Eight mixed-breed EMS and six control, age-matched horses of both sexes were included in the study. Animals were classified as EMS or control based on the assessment of BCS, cresty neck score, and basal insulin >50 µU/mL and/or insulin responses to the oral sugar test (OST) >60 µU/mL. Peripheral venous blood was collected. The expression of proinflammatory cytokines, the concentration of circulating cytokines, and acute-phase proteins (serum amyloid A, C-reactive protein, haptoglobin, activin A, and procalcitonin) were measured. The data were analyzed using the Mann-Whitney test, whereas correlations were examined using Spearman's correlation coefficient. The tests were statistically significant if P ≤ 0.05. There were no differences in cytokine gene expression, circulating cytokine concentrations, or concentrations of acute-phase proteins between the EMS and the control groups. There was a strong correlation between the basal concentration of insulin and the serum concentrations of IL-6 (r = 0.71, P < 0.05). Activin A was positively correlated with post-OST insulin concentrations (r = 0.707, P = 0.05), indicating that this marker of inflammation could warrant further investigation in horses with EMS.

Preparation and characterization of selenium-decorated graphene quantum dots with high afterglow for application in photodynamic therapy.

Graphene quantum dots (GQDs) was synthesized using a simple, rapid and affordable method and decorated with selenium at different molar ratios for the first time to obtain an efficient sample for use in photodynamic therapy. Surface modification of GQDs was carried out using polyethylene glycol (PEG) for conjugation with protoporphyrin IX (PpIX). Synthesized GQDs (Se: 0.3%) at 180°C had an emission spectrum that fairly coincided with the absorption profile of PpIX. A relative decrease of about 62.48% in the emission intensity of anthracene was recorded under illumination with UVC light in the presence of GQDs (Se: 0.3%) and the reduction for clung GQDs (Se: 0.3%) and PpIX during 90 min was about 70.68%. Singlet oxygen (1 O2 ) generation was examined using a chemical method that showed significant enhancement in decomposition rate constant in clung GQDs-PEG-PpIX compared with GQDs and PpIX alone. Afterglow over 600 s showed that GQDs (Se: 0.3%) could be effective for near skin and even deep tumours.

Prevalence and severity of ultrasonographic pulmonary findings in horses with asthma - a preliminary study.

Asthma is one of the most common non-infectious respiratory diseases in horses. Ultrasound examination is a widely available non-invasive additional diagnostic tool. To date, there are no studies focusing on ultrasonographic findings in horses with asthma. The aim of this study was to analyse the prevalence and severity of ultrasound lesions in lung tissue in horses with asthma. Lung ultrasonography was carried out on six healthy horses (controls) and 12 horses with asthma (six with mild and six with severe asthma). The sonographic changes in three lung sections were assessed using a scoring system. The most common changes present in all the animals were comet- tail artefacts. More advanced lesions were present in horses with severe asthma. Statistically significant differences in the overall average intensity of the ultrasound changes were seen between the controls and the study group and between the horses with mild and severe asthma. The lesions were usually located in the caudal lung regions, but they were also present in other areas as the disease progressed. Ultrasonography is a useful additional diagnostic tool enabling an assessment of the stage of the asthma progression. It is a very sensitive technique that visualizes minor lesions in the lung tissue even in clinically healthy animals. Due to its low specificity, it cannot replace endoscopy and the bronchoalveolar lavage in horses with asthma.

Assessment of sand accumulation in the gastrointestinal tract and its excretion with stool in silesian foals.

The aim of this study was to assess sand accumulation in the gastrointestinal tract and fecal sand excretion in Silesian foals using three diagnostic methods and taking into account the sex and age of the animals. Another aim of the study was to compare the three diagnostic methods. The study was carried out on 21 clinically healthy Silesian foals (10 females and 11 males) from 9-28 weeks old grazed on permanent pasture. The sand intake was assessed using a sedimentation test, abdominal ultrasonography and a quantitative evaluation of sand per 100 g of stool. In the sedimentation test, the sand was palpable in the stool of 57.1% of the horses, and clearly visible in 42.9% of the animals. The ultrasound examination revealed the presence of sand in the gastrointestinal tract in 66.7% of the horses. It was limited to a single location in 60% of the horses, while it was present in several regions in 40% of the horses. The mean amount of sand was 0.14 ± 0.33 g per 100 g of stool. It did not exceed 0.1g in 71.4% foals, while it ranged from 0.1-0.5 g in 23.8% foals. In 4.8% of the animals, it amounted to 1.6 g per 100 g of stool. There was no correlation between age and gender and the results. There was a positive correlation between the ultrasound examination and the sedimentation test. Sand may be accumulated in the gastrointestinal tract of foals without any clinical signs. The amount of sand excreted in the stool is not an indicator of the amount of sand accumulated in the gastrointestinal tract. An abdominal ultrasound examination should be combined with a sedimentation test for more specific results.

Enhanced intrinsic photovoltaic effect in tungsten disulfide nanotubes.

The photovoltaic effect in traditional p-n junctions-where a p-type material (with an excess of holes) abuts an n-type material (with an excess of electrons)-involves the light-induced creation of electron-hole pairs and their subsequent separation, generating a current. This photovoltaic effect is particularly important for environmentally benign energy harvesting, and its efficiency has been increased dramatically, almost reaching the theoretical limit1. Further progress is anticipated by making use of the bulk photovoltaic effect (BPVE)2, which does not require a junction and occurs only in crystals with broken inversion symmetry3. However, the practical implementation of the BPVE is hampered by its low efficiency in existing materials4-10. Semiconductors with reduced dimensionality2 or a smaller bandgap4,5 have been suggested to be more efficient. Transition-metal dichalcogenides (TMDs) are exemplary small-bandgap, two-dimensional semiconductors11,12 in which various effects have been observed by breaking the inversion symmetry inherent in their bulk crystals13-15, but the BPVE has not been investigated. Here we report the discovery of the BPVE in devices based on tungsten disulfide, a member of the TMD family. We find that systematically reducing the crystal symmetry beyond mere broken inversion symmetry-moving from a two-dimensional monolayer to a nanotube with polar properties-greatly enhances the BPVE. The photocurrent density thus generated is orders of magnitude larger than that of other BPVE materials. Our findings highlight not only the potential of TMD-based nanomaterials, but also more generally the importance of crystal symmetry reduction in enhancing the efficiency of converting solar to electric power.