Use of Diagnostic Codes for Primary Open-Angle Glaucoma Polygenic Risk Score Construction in Electronic Health Record-linked Biobanks.

PURPOSE: Polygenic risk scores (PRSs) likely predict risk and prognosis of glaucoma. We compared the PRS performance for primary open-angle glaucoma (POAG), defined using International Classification of Diseases (ICD) codes versus manual medical record review. DESIGN: Retrospective cohort study METHODS: We identified POAG cases in Mount Sinai BioMe and Mass General Brigham (MGB) biobank using ICD codes. We confirmed POAG based on optical coherence tomograms and visual fields. In a separate 5% sample, the absence of POAG was confirmed with intraocular pressure and cup-disc ratio criteria. We used genotype data and either self-reported glaucoma diagnoses or ICD-10 codes for glaucoma diagnoses from the UK Biobank and the lassosum method to compute a genome-wide POAG PRS. We compared the area under the curve (AUC) for POAG prediction based on ICD codes versus medical records. RESULTS: We reviewed 804 of 996 BioMe and 367 of 1,006 MGB ICD-identified cases. In BioMe and MGB, respectively: positive predictive value was 53% and 55%; negative predictive value was 96% and 97%; sensitivity was 97% and 97%; and specificity was 44% and 53%. Adjusted PRS AUCs for POAG using ICD codes vs. manual record review in BioMe were not statistically different (p≥0.21) by ancestry: 0.77 vs. 0.75 for African, 0.80 vs. 0.80 for Hispanic, and 0.81 vs. 0.81 for European. Results were similar in MGB (p≥0.18): 0.72 vs. 0.80 for African, 0.83 vs. 0.86 for Hispanic, and 0.74 vs. 0.73 for European. CONCLUSIONS: A POAG PRS performed similarly using either manual review or ICD codes in two EHR-linked biobanks; manual assessment of glaucoma status might be unnecessary for some PRS studies. However, caution should be exercised with using ICD codes for glaucoma diagnosis given their low specificity (44-53%) for manually confirmed cases of glaucoma.

Exome sequence analysis identifies rare coding variants associated with a machine learning-based marker for coronary artery disease.

Coronary artery disease (CAD) exists on a spectrum of disease represented by a combination of risk factors and pathogenic processes. An in silico score for CAD built using machine learning and clinical data in electronic health records captures disease progression, severity and underdiagnosis on this spectrum and could enhance genetic discovery efforts for CAD. Here we tested associations of rare and ultrarare coding variants with the in silico score for CAD in the UK Biobank, All of Us Research Program and BioMe Biobank. We identified associations in 17 genes; of these, 14 show at least moderate levels of prior genetic, biological and/or clinical support for CAD. We also observed an excess of ultrarare coding variants in 321 aggregated CAD genes, suggesting more ultrarare variant associations await discovery. These results expand our understanding of the genetic etiology of CAD and illustrate how digital markers can enhance genetic association investigations for complex diseases.

Muesli Intake May Protect Against Coronary Artery Disease: Mendelian Randomization on 13 Dietary Traits.

BACKGROUND: Diet is a key modifiable risk factor of coronary artery disease (CAD). However, the causal effects of specific dietary traits on CAD risk remain unclear. With the expansion of dietary data in population biobanks, Mendelian randomization (MR) could help enable the efficient estimation of causality in diet-disease associations. OBJECTIVES: The primary goal was to test causality for 13 common dietary traits on CAD risk using a systematic 2-sample MR framework. A secondary goal was to identify plasma metabolites mediating diet-CAD associations suspected to be causal. METHODS: Cross-sectional genetic and dietary data on up to 420,531 UK Biobank and 184,305 CARDIoGRAMplusC4D individuals of European ancestry were used in 2-sample MR. The primary analysis used fixed effect inverse-variance weighted regression, while sensitivity analyses used weighted median estimation, MR-Egger regression, and MR-Pleiotropy Residual Sum and Outlier. RESULTS: Genetic variants serving as proxies for muesli intake were negatively associated with CAD risk (OR: 0.74; 95% CI: 0.65-0.84; P = 5.385 × 10-4). Sensitivity analyses using weighted median estimation supported this with a significant association in the same direction. Additionally, we identified higher plasma acetate levels as a potential mediator (OR: 0.03; 95% CI: 0.01-0.12; P = 1.15 × 10-4). CONCLUSIONS: Muesli, a mixture of oats, seeds, nuts, dried fruit, and milk, may causally reduce CAD risk. Circulating levels of acetate, a gut microbiota-derived short-chain fatty acid, could be mediating its cardioprotective effects. These findings highlight the role of gut flora in cardiovascular health and help prioritize randomized trials on dietary interventions for CAD.

The Application of Fluorescence In Situ Hybridization in the Prescreening of Veronica Hybrids.

Fluorescence in situ hybridization (FISH), a molecular cytogenetic technique that enables the visualization and identification of specific DNA sequences within chromosomes, has emerged as a pivotal tool in plant breeding programs, particularly in the case of Veronica species. Veronica, a genus with a complex reproductive system, often poses challenges in accurately identifying hybrids because of its tendency to hybridize, which leads to intricate genetic variation. This study focused on the use of FISH as a prescreening method to identify true hybrids in Veronica breeding programs. FISH analysis was first performed on the parents to identify their 45S and 5S rDNA signals, along with their respective chromosome numbers. The signals were then compared with those of the twenty progenies with reference to their supposed parents. Five true hybrids, seven self-pollinated progenies, and eight false hybrids were identified through FISH. The findings highlight the significance of FISH as a screening method that contributes significantly to the efficiency of Veronica breeding programs by ensuring the preservation of desired genetic traits and minimizing the inadvertent inclusion of misidentified hybrids. To conclude, this study underscores the vital role of FISH in enhancing the precision and success of breeding programs and opens new avenues for improved breeding strategies and crop development.

Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People With Type 2 Diabetes.

OBJECTIVE: To identify genetic risk factors for incident cardiovascular disease (CVD) among people with type 2 diabetes (T2D). RESEARCH DESIGN AND METHODS: We conducted a multiancestry time-to-event genome-wide association study for incident CVD among people with T2D. We also tested 204 known coronary artery disease (CAD) variants for association with incident CVD. RESULTS: Among 49,230 participants with T2D, 8,956 had incident CVD events (event rate 18.2%). We identified three novel genetic loci for incident CVD: rs147138607 (near CACNA1E/ZNF648, hazard ratio [HR] 1.23, P = 3.6 × 10-9), rs77142250 (near HS3ST1, HR 1.89, P = 9.9 × 10-9), and rs335407 (near TFB1M/NOX3, HR 1.25, P = 1.5 × 10-8). Among 204 known CAD loci, 5 were associated with incident CVD in T2D (multiple comparison-adjusted P < 0.00024, 0.05/204). A standardized polygenic score of these 204 variants was associated with incident CVD with HR 1.14 (P = 1.0 × 10-16). CONCLUSIONS: The data point to novel and known genomic regions associated with incident CVD among individuals with T2D.

Genome-first evaluation with exome sequence and clinical data uncovers underdiagnosed genetic disorders in a large healthcare system.

Population-based genomic screening may help diagnose individuals with disease-risk variants. Here, we perform a genome-first evaluation for nine disorders in 29,039 participants with linked exome sequences and electronic health records (EHRs). We identify 614 individuals with 303 pathogenic/likely pathogenic or predicted loss-of-function (P/LP/LoF) variants, yielding 644 observations; 487 observations (76%) lack a corresponding clinical diagnosis in the EHR. Upon further investigation, 75 clinically undiagnosed observations (15%) have evidence of symptomatic untreated disease, including familial hypercholesterolemia (3 of 6 [50%] undiagnosed observations with disease evidence) and breast cancer (23 of 106 [22%]). These genetic findings enable targeted phenotyping that reveals new diagnoses in previously undiagnosed individuals. Disease yield is greater with variants in penetrant genes for which disease is observed in carriers in an independent cohort. The prevalence of P/LP/LoF variants exceeds that of clinical diagnoses, and some clinically undiagnosed carriers are discovered to have disease. These results highlight the potential of population-based genomic screening.

Lack of functional TCR-epitope interaction is associated with herpes zoster through reduced downstream T cell activation.

The role of T cell receptor (TCR) diversity in infectious disease susceptibility is not well understood. We use a systems immunology approach on three cohorts of herpes zoster (HZ) patients and controls to investigate whether TCR diversity against varicella-zoster virus (VZV) influences the risk of HZ. We show that CD4+ T cell TCR diversity against VZV glycoprotein E (gE) and immediate early 63 protein (IE63) after 1-week culture is more restricted in HZ patients. Single-cell RNA and TCR sequencing of VZV-specific T cells shows that T cell activation pathways are significantly decreased after stimulation with VZV peptides in convalescent HZ patients. TCR clustering indicates that TCRs from HZ patients co-cluster more often together than TCRs from controls. Collectively, our results suggest that not only lower VZV-specific TCR diversity but also reduced functional TCR affinity for VZV-specific proteins in HZ patients leads to lower T cell activation and consequently affects the susceptibility for viral reactivation.

Multivariate Statistical Analysis for the Classification of Sausages Based on Physicochemical Attributes, Using Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) and Inductively Coupled Plasma-Mass Spectrometry (ICP-MS).

Sausage is a convenient food that is widely consumed in the world and in Vietnam. Due to the rapid development of this product, the authenticity of many famous brands has faded by the rise of adulteration. Therefore, in this study, principal component analysis (PCA) was combined with chemical analysis to identify 6 sausage brands. Sausage samples were dried and then ground to a fine powder for both instrumental analyses of attenuated total reflectance-Fourier transform infrared (ATR-FTIR) and inductively coupled plasma-mass spectrometry (ICP-MS). Dried measurements of ATR-FTIR was performed directly on the ZnSe crystal, while elemental data were obtained through microwave digestion before the ICP-MS analysis. Principal component analysis (PCA) within the framework software of XLSTAT and STATISTICA 12 was performed on the spectroscopy and elemental dataset of sausage samples. PCA visualized the distinction of 6 sausage brands on both datasets of ATR-FTIR and ICP-MS. The classification on the spectroscopy profile showed that although more than 90% variation of the dataset was explained on the first two PCs, the difference between several brands was not detected as the distribution of data overlapped with one another. The PCA observation of the elemental composition on PC1 and PC3 has separated the sausage brands into 6 distinctive groups. Besides, several key elements contributed to the brands' identification have been detected, and the most distinctive elements are Na, K, Ca, and Ba. PCA visualization showed the feasibility of the classification of sausage samples from different brands when combined with the results of FT-IR and ICP-MS methods. The experiment was able to differentiate the sausages from the 5 brands using multivariate statistics.

Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas.

Chronic kidney disease is a leading cause of death and disability globally and impacts individuals of African ancestry (AFR) or with ancestry in the Americas (AMS) who are under-represented in genome-wide association studies (GWASs) of kidney function. To address this bias, we conducted a large meta-analysis of GWASs of estimated glomerular filtration rate (eGFR) in 145,732 AFR and AMS individuals. We identified 41 loci at genome-wide significance (p < 5 × 10-8), of which two have not been previously reported in any ancestry group. We integrated fine-mapped loci with epigenomic and transcriptomic resources to highlight potential effector genes relevant to kidney physiology and disease, and reveal key regulatory elements and pathways involved in renal function and development. We demonstrate the varying but increased predictive power offered by a multi-ancestry polygenic score for eGFR and highlight the importance of population diversity in GWASs and multi-omics resources to enhance opportunities for clinical translation for all.

Development of a human genetics-guided priority score for 19,365 genes and 399 drug indications.

Studies have shown that drug targets with human genetic support are more likely to succeed in clinical trials. Hence, a tool integrating genetic evidence to prioritize drug target genes is beneficial for drug discovery. We built a genetic priority score (GPS) by integrating eight genetic features with drug indications from the Open Targets and SIDER databases. The top 0.83%, 0.28% and 0.19% of the GPS conferred a 5.3-, 9.9- and 11.0-fold increased effect of having an indication, respectively. In addition, we observed that targets in the top 0.28% of the score were 1.7-, 3.7- and 8.8-fold more likely to advance from phase I to phases II, III and IV, respectively. Complementary to the GPS, we incorporated the direction of genetic effect and drug mechanism into a directional version of the score called the GPS with direction of effect. We applied our method to 19,365 protein-coding genes and 399 drug indications and made all results available through a web portal.

Diagnosing Viral Infections Through T-Cell Receptor Sequencing of Activated CD8+ T Cells.

T-cell-based diagnostic tools identify pathogen exposure but lack differentiation between recent and historical exposures in acute infectious diseases. Here, T-cell receptor (TCR) RNA sequencing was performed on HLA-DR+/CD38+CD8+ T-cell subsets of hospitalized coronavirus disease 2019 (COVID-19) patients (n = 30) and healthy controls (n = 30; 10 of whom had previously been exposed to severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]). CDR3α and CDR3ß TCR regions were clustered separately before epitope specificity annotation using a database of SARS-CoV-2-associated CDR3α and CDR3ß sequences corresponding to >1000 SARS-CoV-2 epitopes. The depth of the SARS-CoV-2-associated CDR3α/ß sequences differentiated COVID-19 patients from the healthy controls with a receiver operating characteristic area under the curve of 0.84 ± 0.10. Hence, annotating TCR sequences of activated CD8+ T cells can be used to diagnose an acute viral infection and discriminate it from historical exposure. In essence, this work presents a new paradigm for applying the T-cell repertoire to accomplish TCR-based diagnostics.

Elucidating the Mechanism of Fe Incorporation in In Situ Synthesized Co-Fe Oxygen-Evolving Nanocatalysts.

Ni- and Co-based catalysts with added Fe demonstrate promising activity in the oxygen evolution reaction (OER) during alkaline water electrolysis, with the presence of Fe in a certain quantity being crucial for their enhanced performance. The mode of incorporation, local placement, and structure of Fe ions in the host catalyst, as well as their direct/indirect contribution to enhancing the OER activity, remain under active investigation. Herein, the mechanism of Fe incorporation into a Co-based host was investigated using an in situ synthesized Co-Fe catalyst in an alkaline electrolyte containing Co2+ and Fe3+. Fe was found to be uniformly incorporated, which occurs solely after the anodic deposition of the Co host structure and results in exceptional OER activity with an overpotential of 319 mV at 10 mA cm-2 and a Tafel slope of 28.3 mV dec-1. Studies on the lattice structure, chemical oxidation states, and mass changes indicated that Fe is incorporated into the Co host structure by replacing the Co3+ sites with Fe3+ from the electrolyte. Operando Raman measurements revealed that the presence of doped Fe in the Co host structure reduces the transition potential of the in situ Co-Fe catalyst to the OER-active phase CoO2. The findings of our facile synthesis of highly active and stable Co-Fe particle catalysts provide a comprehensive understanding of the role of Fe in Co-based electrocatalysts, covering aspects that include the incorporation mode, local structure, placement, and mechanistic role in enhancing the OER activity.

Antibacterial Gelatin Composite Hydrogels Comprised of In Situ Formed Zinc Oxide Nanoparticles.

We report the feasibility of using gelatin hydrogel networks as the host for the in situ, environmentally friendly formation of well-dispersed zinc oxide nanoparticles (ZnONPs) and the evaluation of the antibacterial activity of the as-prepared composite hydrogels. The resulting composite hydrogels displayed remarkable biocompatibility and antibacterial activity as compared to those in previous studies, primarily attributed to the uniform distribution of the ZnONPs with sizes smaller than 15 nm within the hydrogel network. In addition, the composite hydrogels exhibited better thermal stability and mechanical properties as well as lower swelling ratios compared to the unloaded counterpart, which could be attributed to the non-covalent interactions between the in situ formed ZnONPs and polypeptide chains. The presence of ZnONPs contributed to the disruption of bacterial cell membranes, the alteration of DNA molecules, and the subsequent release of reactive oxygen species within the bacterial cells. This chain of events culminated in bacterial cell lysis and DNA fragmentation. This research underscores the potential benefits of incorporating antibacterial agents into hydrogels and highlights the significance of preparing antimicrobial agents within gel networks.

Effect of saline intrusion on rice production in the Mekong River Delta.

Saline intrusion is increasingly threatening the rice farming system in The Mekong River Delta (MRD). Identifying the impact of this disaster on rice farming and providing promptly adaptable solutions is an urgent issue. This study evaluates the influence of saline intrusion on rice productivity of households in the MRD. We utilize the quasi-experimental method, the difference-in-difference (DID) method, with farm level panel data on rice farming extracted from the Vietnam Household Living Standards Survey (VHLSS) in 2014 and 2016. The empirical results indicate that households affected by saline intrusion have lower total production and lower productivity compared to the unaffected group. The affected group has lower total revenue of approximately 4969.8 thousand VND per ha and lower net revenue, on an average of 4679.3 thousand VND per ha, compared to the comparable unaffected group. Among the subsamples of different regions, the damage magnitude of households in severely affected regions by salinity intrusion is higher than in less severely affected areas. Some policy implications that can be proposed from this research are that the management agency should continue to update information on weather and climate change scenarios for forecasting and timely information for rice farmers. The agency comprehensively evaluates the effectiveness of transformed models of sustainable agricultural production adapted to salinity intrusion and replicates high-effective production models; restructure rice cultivation following the salinity intrusion level of each locality.

A fluoropolymer bifunctional solid membrane interface for improving the discharge duration in aqueous Al-air batteries.

Herein, a fluoropolymer bifunctional solid membrane interface (SMI) for an aqueous Al-air battery is proposed, which inhibits anodic self-corrosion, while concurrently reducing the accumulation of undesirable by-products. A battery using the SMI exhibits a remarkable anticorrosion efficiency of 81.31% and achieves an astonishing battery lifetime improvement rate of 184.37% under the condition of 5 min intermittent discharge.

Effects of Immune Cell Heterogeneity and Protein Corona on the Cellular Association and Cytotoxicity of Gold Nanoparticles: A Single-Cell-Based, High-Dimensional Mass Cytometry Study.

Understanding how nanoparticles (NPs) interact with biological systems is important in many biomedical research areas. However, the heterogeneous nature of biological systems, including the existence of numerous cell types and multitudes of key environmental factors, makes these interactions extremely challenging to investigate precisely. Here, using a single-cell-based, high-dimensional mass cytometry approach, we demonstrated that the presence of protein corona has significant influences on the cellular associations and cytotoxicity of gold NPs for human immune cells, and those effects vary significantly with the types of immune cells and their subsets. The altered surface functionality of protein corona reduced the cytotoxicity and cellular association of gold NPs in most cell types (e.g., monocytes, dendritic cells, B cells, natural killer (NK) cells, and T cells) and those immune cells selected different endocytosis pathways such as receptor-mediated endocytosis, phagocytosis, and micropinocytosis. However, even slight alterations in the major cell type (phagocytic cells and non-phagocytic cells) and T cell subsets (e.g., memory and naive T cells) resulted in significant protein corona-dependent variations in their cellular dose of gold NPs. Especially, naive T killer cells exhibited additional heterogeneity than memory T killer cells, with clusters exhibiting distinct cellular association patterns in single-cell contour plots. This multi-parametric analysis of mass cytometry data established a conceptual framework for a more holistic understanding of how the human immune system responds to external stimuli, paving the way for the application of precisely engineered NPs as promising tools of nanomedicine under various clinical settings, including targeted drug delivery and vaccine development.

Microplastics in sediments from urban and suburban rivers: Influence of sediment properties.

Although sediments are considered to be a major sink for microplastics (MP), there is still a relative lack of knowledge on the factors that influence the occurrence and abundance of MP in riverine sediments. The present study investigated the occurrence and distribution of MP in riverine sediments collected at twelve sites representative of different populated and urbanized rivers (To Lich, Nhue and Day Rivers) located in the Red River Delta (RRD, Vietnam, during dry and rainy seasons. MP concentrations ranged from 1600 items kg-1 dw to 94,300 items kg-1dw. Fiber shape dominated and MP were made of polypropylene (PP) and polyethylene (PE) predominantly. An absence of seasonal effect was observed for both fragments and fibers for each rivers. Decreasing MP concentrations trend was evidenced from the To Lich River, to the Nhue River and to the Day River, coupled with a decreasing fiber length and an increasing fragment area in the surface sediment from upstream to downstream. Content of organic matter was correlated to MP concentrations suggesting that, high levels of organic matter could be MP hotspots in urban rivers. Also, high population density as well as in highly residential areas are related to higher MP concentrations in sediments. Finally, a MP high ecological risk (RI: 866 to 4711) was calculated in the RDD.

Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People with Type 2 Diabetes Mellitus.

BACKGROUND: Type 2 diabetes mellitus (T2D) confers a two- to three-fold increased risk of cardiovascular disease (CVD). However, the mechanisms underlying increased CVD risk among people with T2D are only partially understood. We hypothesized that a genetic association study among people with T2D at risk for developing incident cardiovascular complications could provide insights into molecular genetic aspects underlying CVD. METHODS: From 16 studies of the Cohorts for Heart & Aging Research in Genomic Epidemiology (CHARGE) Consortium, we conducted a multi-ancestry time-to-event genome-wide association study (GWAS) for incident CVD among people with T2D using Cox proportional hazards models. Incident CVD was defined based on a composite of coronary artery disease (CAD), stroke, and cardiovascular death that occurred at least one year after the diagnosis of T2D. Cohort-level estimated effect sizes were combined using inverse variance weighted fixed effects meta-analysis. We also tested 204 known CAD variants for association with incident CVD among patients with T2D. RESULTS: A total of 49,230 participants with T2D were included in the analyses (31,118 European ancestries and 18,112 non-European ancestries) which consisted of 8,956 incident CVD cases over a range of mean follow-up duration between 3.2 and 33.7 years (event rate 18.2%). We identified three novel, distinct genetic loci for incident CVD among individuals with T2D that reached the threshold for genome-wide significance (P<5.0×10-8): rs147138607 (intergenic variant between CACNA1E and ZNF648) with a hazard ratio (HR) 1.23, 95% confidence interval (CI) 1.15 - 1.32, P=3.6×10-9, rs11444867 (intergenic variant near HS3ST1) with HR 1.89, 95% CI 1.52 - 2.35, P=9.9×10-9, and rs335407 (intergenic variant between TFB1M and NOX3) HR 1.25, 95% CI 1.16 - 1.35, P=1.5×10-8. Among 204 known CAD loci, 32 were associated with incident CVD in people with T2D with P<0.05, and 5 were significant after Bonferroni correction (P<0.00024, 0.05/204). A polygenic score of these 204 variants was significantly associated with incident CVD with HR 1.14 (95% CI 1.12 - 1.16) per 1 standard deviation increase (P=1.0×10-16). CONCLUSIONS: The data point to novel and known genomic regions associated with incident CVD among individuals with T2D.

Genome-wide association study of thoracic aortic aneurysm and dissection in the Million Veteran Program.

The current understanding of the genetic determinants of thoracic aortic aneurysms and dissections (TAAD) has largely been informed through studies of rare, Mendelian forms of disease. Here, we conducted a genome-wide association study (GWAS) of TAAD, testing ~25 million DNA sequence variants in 8,626 participants with and 453,043 participants without TAAD in the Million Veteran Program, with replication in an independent sample of 4,459 individuals with and 512,463 without TAAD from six cohorts. We identified 21 TAAD risk loci, 17 of which have not been previously reported. We leverage multiple downstream analytic methods to identify causal TAAD risk genes and cell types and provide human genetic evidence that TAAD is a non-atherosclerotic aortic disorder distinct from other forms of vascular disease. Our results demonstrate that the genetic architecture of TAAD mirrors that of other complex traits and that it is not solely inherited through protein-altering variants of large effect size.