Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions.

MOTIVATION: The emergence of COVID-19 (C19) created incredible worldwide challenges but offers unique opportunities to understand the physiology of its risk factors and their interactions with complex disease conditions, such as metabolic syndrome. To address the challenges of discovering clinically relevant interactions, we employed a unique approach for epidemiological analysis powered by redescription-based topological data analysis (RTDA). RESULTS: Here, RTDA was applied to Explorys data to discover associations among severe C19 and metabolic syndrome. This approach was able to further explore the probative value of drug prescriptions to capture the involvement of RAAS and hypertension with C19, as well as modification of risk factor impact by hyperlipidemia (HL) on severe C19. RTDA found higher-order relationships between RAAS pathway and severe C19 along with demographic variables of age, gender, and comorbidities such as obesity, statin prescriptions, HL, chronic kidney failure, and disproportionately affecting Black individuals. RTDA combined with CuNA (cumulant-based network analysis) yielded a higher-order interaction network derived from cumulants that furthered supported the central role that RAAS plays. TDA techniques can provide a novel outlook beyond typical logistic regressions in epidemiology. From an observational cohort of electronic medical records, it can find out how RAAS drugs interact with comorbidities, such as hypertension and HL, of patients with severe bouts of C19. Where single variable association tests with outcome can struggle, TDA's higher-order interaction network between different variables enables the discovery of the comorbidities of a disease such as C19 work in concert. AVAILABILITY AND IMPLEMENTATION: Code for performing TDA/RTDA is available in https://github.com/IBM/Matilda and code for CuNA can be found in https://github.com/BiomedSciAI/Geno4SD/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The impact of forced displacement: trauma, increased levels of inflammation and early presentation of diabetes in women Syrian refugees.

BACKGROUND: Forced displacement and war trauma cause high rates of post-traumatic stress, anxiety disorders and depression in refugee populations. We investigated the impact of forced displacement on mental health status, gender, presentation of type 2 diabetes (T2D) and associated inflammatory markers among Syrian refugees in Lebanon. METHODS: Mental health status was assessed using the Harvard Trauma Questionnaire (HTQ) and the Hopkins Symptom Checklist-25 (HSCL-25). Additional metabolic and inflammatory markers were analyzed. RESULTS: Although symptomatic stress scores were observed in both men and women, women consistently displayed higher symptomatic anxiety/depression scores with the HSCL-25 (2.13 ± 0.58 versus 1.95 ± 0.63). With the HTQ, however, only women aged 35-55 years displayed symptomatic post-traumatic stress disorder (PTSD) scores (2.18 ± 0.43). Furthermore, a significantly higher prevalence of obesity, prediabetes and undiagnosed T2D were observed in women participants (23.43, 14.91 and 15.18%, respectively). Significantly high levels of the inflammatory marker serum amyloid A were observed in women (11.90 ± 11.27 versus 9.28 ± 6.93, P = 0.036). CONCLUSIONS: Symptomatic PTSD, anxiety/depression coupled with higher levels of inflammatory marker and T2D were found in refugee women aged between 35 and 55 years favoring the strong need for psychosocial therapeutic interventions in moderating stress-related immune dysfunction and development of diabetes in this subset of female Syrian refugees.

Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India.

India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics, and demographic factors, we developed Correlation Optimization of Genetics and Geodemographics to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a data set of additional 1,323 individuals from 50 Eurasian populations, we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.

K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses.

Papillomaviruses (PVs) are a heterogeneous group of DNA viruses that can infect fish, birds, reptiles, and mammals. PVs infecting humans (HPVs) phylogenetically cluster into five genera (Alpha-, Beta-, Gamma-, Mu- and Nu-PV), with differences in tissue tropism and carcinogenicity. The evolutionary features associated with the divergence of Papillomaviridae are not well understood. Using a combination of k-mer distributions, genetic metrics, and phylogenetic algorithms, we sought to evaluate the characteristics and differences of Alpha-, Beta- and Gamma-PVs constituting the majority of HPV genomes. A total of 640 PVs including 442 HPV types, 27 non-human primate PV types, and 171 non-primate animal PV types were evaluated. Our analyses revealed the highest genetic diversity amongst Gamma-PVs compared to the Alpha and Beta PVs, suggesting reduced selective pressures on Gamma-PVs. Using a sequence alignment-free trimer (k = 3) phylogeny algorithm, we reconstructed a phylogeny that grouped most HPV types into a monophyletic clade that was further split into three branches similar to alignment-based classifications. Interestingly, a subset of low-risk Alpha HPVs (the species Alpha-2, 3, 4, and 14) split from other HPVs and were clustered with non-human primate PVs. Surprisingly, the trimer-constructed phylogeny grouped the Gamma-6 species types originally isolated from the cervicovaginal region with the main Alpha-HPV clade. These data indicate that characterization of papillomavirus heterogeneity via orthogonal approaches reveals novel insights into the biological understanding of HPV genomes.

Variant analysis of SARS-CoV-2 genomes.

OBJECTIVE: To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). METHODS: Between 1 February and 1 May 2020, we downloaded 10 022 SARS CoV-2 genomes from four databases. The genomes were from infected patients in 68 countries. We identified variants by extracting pairwise alignment to the reference genome NC_045512, using the EMBOSS needle. Nucleotide variants in the coding regions were converted to corresponding encoded amino acid residues. For clade analysis, we used the open source software Bayesian evolutionary analysis by sampling trees, version 2.5. FINDINGS: We identified 5775 distinct genome variants, including 2969 missense mutations, 1965 synonymous mutations, 484 mutations in the non-coding regions, 142 non-coding deletions, 100 in-frame deletions, 66 non-coding insertions, 36 stop-gained variants, 11 frameshift deletions and two in-frame insertions. The most common variants were the synonymous 3037C > T (6334 samples), P4715L in the open reading frame 1ab (6319 samples) and D614G in the spike protein (6294 samples). We identified six major clades, (that is, basal, D614G, L84S, L3606F, D448del and G392D) and 14 subclades. Regarding the base changes, the C > T mutation was the most common with 1670 distinct variants. CONCLUSION: We found that several variants of the SARS-CoV-2 genome exist and that the D614G clade has become the most common variant since December 2019. The evolutionary analysis indicated structured transmission, with the possibility of multiple introductions into the population.

Association of waterpipe smoking with myocardial infarction and determinants of metabolic syndrome among catheterized patients.

BACKGROUND: Waterpipe smoking is a rising global public health epidemic perceived by many users to be less harmful, though its toxicity overlaps or even exceeds that of cigarette smoking. Short-term cardiovascular changes due to waterpipe smoking are well established, but longer-term health impacts are still not fully elucidated. OBJECTIVE: We aim to investigate the association of waterpipe smoking with myocardial infarction among patients undergoing cardiac catheterization. METHODS: The study was performed on Lebanese patients referred for cardiac catheterization. Patient's blood was collected for metabolic measures and questionnaires were filled out to include socio-demographic, behavioral and pertinent medical characteristics of the study subjects. RESULTS: Myocardial infarction is significantly and independently associated with waterpipe smoking, with odds ratio (OR) of 1.329 (95% CI: [1.04-1.68]; p = .021), which is lower than that for cigarette smoking (OR = 1.87, 95% CI: [1.63-2.15]; p < .001). Only diabetes showed significant association with waterpipe smoking among MI enrollees (OR = 1.66, 95%CI: [1.04-2.63]; p = .032). CONCLUSION: The study provides yet another evidence for the adverse cardiovascular effects of waterpipe smoking on a clinical level. The harmful effects of waterpipe smoking should be underscored by health care professionals.

Caffeine Impact on Metabolic Syndrome Components Is Modulated by a CYP1A2 Variant.

Cultural, dietary, and lifestyle factors are the main modulators of type 2 diabetes mellitus (T2DM) disease risk. Coffee is one of the most popular worldwide beverages, and recent epidemiological studies have showed that coffee consumption is associated with a lower risk of T2DM. This study investigates the impact of coffee intake on T2DM risk and assesses the effect of CYP variants with caffeine exposures on T2DM. Data from 7,607 study subjects were analyzed by logistic regression models, among whom 3,290 GWAS data were available for CYP variants association studies using Plink analysis. These data suggest a protective relationship for women, but not for men; however, the results were not statistically significant in this dataset and there is a significant interaction in favor of women regarding heavy coffee consumption. The interaction between male gender and heavy coffee consumption becomes significant, thereby tending to cancel the protective effect of coffee for males. CYP rs2470890 allele 'C' increases the odds of T2DM by a factor of around 1.2 but decreases the odds of caffeine boosting T2DM of 1.7 by a factor of 0.77. rs2470890 showed an association with T2DM only when the interaction with coffee was considered, thereby setting an example of genetic activation by dietary changes associating with metabolic syndrome.

Genome-wide diversity in the levant reveals recent structuring by culture.

The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period. Genetic and archeological studies present solid evidence placing the Middle East and the Arabian Peninsula as the first stepping-stone outside Africa. There is, however, little understanding of demographic changes in the Middle East, particularly the Levant, after the first Out-of-Africa expansion and how the Levantine peoples relate genetically to each other and to their neighbors. In this study we analyze more than 500,000 genome-wide SNPs in 1,341 new samples from the Levant and compare them to samples from 48 populations worldwide. Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region. Cultural changes within the last two millennia appear to have facilitated/maintained admixture between culturally similar populations from the Levant, Arabian Peninsula, and Africa. The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations. Consequently, Levant populations today fall into two main groups: one sharing more genetic characteristics with modern-day Europeans and Central Asians, and the other with closer genetic affinities to other Middle Easterners and Africans. Finally, we identify a putative Levantine ancestral component that diverged from other Middle Easterners ∼23,700-15,500 years ago during the last glacial period, and diverged from Europeans ∼15,900-9,100 years ago between the last glacial warming and the start of the Neolithic.

Impact of inflammation, gene variants, and cigarette smoking on coronary artery disease risk.

BACKGROUND: The role of inflammation in coronary artery disease (CAD) pathogenesis is well recognized. Moreover, smoking inhalation increases the activity of inflammatory mediators through an increase in leukotriene synthesis essential in atherosclerosis pathogenesis. AIM: The aim of this study is to investigate the effect of "selected" genetic variants within the leukotriene (LT) pathway and other variants on the development of CAD. METHODS: CAD was detected by cardiac catheterization. Logistic regression was performed to investigate the association of smoking and selected susceptibility variants in the LT pathway including ALOX5AP, LTA4H, LTC4S, PON1, and LTA as well as CYP1A1 on CAD risk while controlling for age, gender, BMI, family history, diabetes, hyperlipidemia, and hypertension. RESULTS: rs4769874 (ALOX5AP), rs854560 (PON1), and rs4646903 (CYP1A1 MspI polymorphism) are significantly associated with an increased risk of CAD with respective odds ratios of 1.53703, 1.67710, and 1.35520; the genetic variant rs9579646 (ALOX5AP) is significantly associated with a decreased risk of CAD (OR 0.76163). Moreover, a significant smoking-gene interaction is determined with CYP1A1 MspI polymorphism rs4646903 and is associated with a decreased risk of CAD in current smokers (OR 0.52137). CONCLUSION: This study provides further evidence that genetic variation of the LT pathway, PON1, and CYP1A1 can modulate the atherogenic processes and eventually increase the risk of CAD in our study population. Moreover, it also shows the effect of smoking-gene interaction on CAD risk, where the CYP1A1 MspI polymorphism revealed a decreased risk in current smokers.

Circulating lipid levels and risk of coronary artery disease in a large group of patients undergoing coronary angiography.

A main underlying pathology of coronary artery disease is the deposition of cholesterol in the arteries supplying blood to the heart that leads to stenosis and myocardial infarction. We tested if dyslipidemia is a risk factor for coronary artery disease in the Lebanese population, and studied the role of the total cholesterol/HDL cholesterol (TC/HDL-C) ratio as a biological marker of coronary artery disease. We recruited 6,180 Lebanese patients undergoing cardiac catheterization. We conducted a cross-sectional association study between TC/HDL-C ratio and the number and type of vessels occluded in catheterized patients by controlling for confounding effects. The TC/HDL-C ratio ≥4 significantly predicts ≥50 % stenosis in all vessels individually with the odds ratio (OR) ranging from 1.22 to 1.92. The OR increased with increasing number of ≥50 % stenotic vessels (1.39 for 2 vessels and 1.64 for 3-4 vessels), as did risk due to diabetes, CAD family history, gender, and age. The younger than average age of onset subgroup shows a pronounced increase in risk for occlusion of the left main coronary artery due to TC/HDL-C ≥4 (OR 3.26). In conclusion, low levels of HDL-cholesterol and high levels TC/HDL-C ratio are strong biological markers of disease occurrence and severity in the Lebanese population.

Anatolian genetic ancestry in North Lebanese populations.

Lebanon's rich history as a cultural crossroad spanning millennia has significantly impacted the genetic composition of its population through successive waves of migration and conquests from surrounding regions. Within modern-day Lebanon, the Koura district stands out with its unique cultural foundations, primarily characterized by a notably high concentration of Greek Orthodox Christians compared to the rest of the country. This study investigates whether the prevalence of Greek Orthodoxy in Koura can be attributed to modern Greek heritage or continuous blending resulting from the ongoing influx of refugees and trade interactions with Greece and Anatolia. We analyzed both ancient and modern DNA data from various populations in the region which could have played a role in shaping the current population of Koura using our own and published data. Our findings indicate that the genetic influence stemming directly from modern Greek immigration into the area appears to be limited. While the historical presence of Greek colonies has left its mark on the region's past, the distinctive character of Koura seems to have been primarily shaped by cultural and political factors, displaying a stronger genetic connection mostly with Anatolia, with affinity to ancient but not modern Greeks.

AI-enabled evaluation of genome-wide association relevance and polygenic risk score prediction in Alzheimer's disease.

GWAS focuses on significance loosing false positives; machine learning probes sub-significant features relying on predictivity. Yet, these are far from orthogonal. We sought to explore how these inform each other in sub-genome-wide significant situations to define relevance for predictive features. We introduce the SVM-based RubricOE that selects heavily cross-validated feature sets, and LDpred2 PRS as a strong contrast to SVM, to explore significance and predictivity. Our Alzheimer's test case notoriously lacks strong genetic signals except for few very strong phenotype-SNP associations, which suits the problem we are exploring. We found that the most significant SNPs among ML and PRS-selected SNPs captured most of the predictivity, while weaker associations tend also to contribute weakly to predictivity. SNPs with weak associations tend not to contribute to predictivity, but deletion of these features does not injure it. Significance provides a ranking that helps identify weakly predictive features.

Coronary artery disease patients with rs7904519 (TCF7L2) are at a persistent risk of type 2 diabetes.

AIMS: Type 2 diabetes (T2D) and coronary artery disease (CAD) often coexist and share genetic factors.This study aimed to investigate the common genetic factors underlying T2D and CAD in patients with CAD. METHODS: A three-step association approach was conducted: a) a discovery step involving 943 CAD patients with T2D and 1,149 CAD patients without T2D; b) an eliminating step to exclude CAD or T2D specific variants; and c) a replication step using the UK Biobank data. RESULTS: Ten genetic loci were associated with T2D in CAD patients. Three variants were specific to either CAD or T2D. Five variants lost significance after adjusting for covariates, while two SNPs remained associated with T2D in CAD patients (rs7904519*G: TCF7L2 and rs17608766*C: GOSR2). The T2D susceptibility rs7904519*G was associated with increased T2D risk, while the CAD susceptibility rs17608766*C was negatively associated with T2D in CAD patients. These associations were replicated in a UK Biobank data, confirming the results. CONCLUSIONS: No significant common T2D and CAD susceptibility genetic association was demonstrated indicating distinct disease pathways. However, CAD patients carrying the T2D susceptibility gene TCF7L2 remain at higher risk for developing T2D emphasizing the need for frequent monitoring in this subgroup.

Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers.

Basque people have received considerable attention from anthropologists, geneticists, and linguists during the last century due to the singularity of their language and to other cultural and biological characteristics. Despite the multidisciplinary efforts performed to address the questions of the origin, uniqueness, and heterogeneity of Basques, the genetic studies performed up to now have suffered from a weak study design where populations are not analyzed in an adequate geographic and population context. To address the former questions and to overcome these design limitations, we have analyzed the uniparentally inherited markers (Y chromosome and mitochondrial DNA) of ~900 individuals from 18 populations, including those where Basque is currently spoken and populations from adjacent regions where Basque might have been spoken in historical times. Our results indicate that Basque-speaking populations fall within the genetic Western European gene pool, that they are similar to geographically surrounding non-Basque populations, and also that their genetic uniqueness is based on a lower amount of external influences compared with other Iberians and French populations. Our data suggest that the genetic heterogeneity and structure observed in the Basque region result from pre-Roman tribal structure related to geography and might be linked to the increased complexity of emerging societies during the Bronze Age. The rough overlap of the pre-Roman tribe location and the current dialect limits support the notion that the environmental diversity in the region has played a recurrent role in cultural differentiation and ethnogenesis at different time periods.

Elevated Lp(a) Levels Correlate with Severe and Multiple Coronary Artery Stenotic Lesions.

Backgrounds and Aims: The role of Lipoprotein(a) (Lp(a)) in increasing the risk of cardiovascular diseases is reported in several populations. The aim of this study is to investigate the correlation of high Lp(a) levels with the degree of coronary artery stenosis. Methods: Two hundred and sixty-eight patients were enrolled for this study. Patients who underwent coronary artery angiography and who had Lp(a) measurements available were included in this study. Binomial logistic regressions were applied to investigate the association between Lp(a) and stenosis in the four major coronary arteries. The effect of LDL and HDL Cholesterol on modulating the association of Lp(a) with coronary artery disease (CAD) was also evaluated. Multinomial regression analysis was applied to assess the association of Lp(a) with the different degrees of stenosis in the four major coronary arteries. Results: Our analyses showed that Lp(a) is a risk factor for CAD and this risk is significantly apparent in patients with HDL-cholesterol ≥35 mg/dL and in non-obese patients. A large proportion of the study patients with elevated Lp(a) levels had CAD even when exhibiting high HDL serum levels. Increased HDL with low Lp(a) serum levels were the least correlated with stenosis. A significantly higher levels of Lp(a) were found in patients with >50% stenosis in at least two major coronary vessels arguing for pronounced and multiple stenotic lesions. Finally, the derived variant (rs1084651) of the LPA gene was significantly associated with CAD. Conclusion: Our study highlights the importance of Lp(a) levels as an independent biological marker of severe and multiple coronary artery stenosis.

Homocysteine levels, H-Hypertension, and the MTHFR C677T genotypes: A complex interaction.

Background and objectives: High homocysteine levels are associated with increased risk of hypertension and stroke. Homocysteine is metabolized by the methylenetetrahydrofolate reductase (MTHFR). We aimed to investigate the levels of homocysteine and their association with hypertension, stroke, and antihypertensive medication usage in patients with different MTHFR C677T genotypes. Methods and results: Genotype frequency of MTHFR polymorphism was performed, and plasma homocysteine levels were measured in 2,640 adult Lebanese patients. Hypertension, history of stroke, and list of medications were documented, among other clinical and demographic parameters. The TT mutant genotype and the T mutant allele of MTHFR were more prevalent in hyperhomocysteinemia (HHcy) and H-hypertensive (H-HTN, defined as hypertension with hyperhomocysteinemia) patients when compared to non-HHcy subjects and non H-HTN patients respectively. Homocysteine levels were significantly higher in hypertensive patients specifically among those on diuretics. A higher level of homocysteine was found in hypertensive patients with the MTHFR T allele compared to patients carrying the C allele. Among the T allele carriers, the average plasma homocysteine level was 13.3 ± 0.193 µmol/L for hypertensive subjects compared to 11.9 ± 0.173 µmol/L (non-hypertensives). Furthermore, homocysteine levels significantly correlated with stroke risk in patients with the T alleles. Conclusions: We found an association of homocysteine with hypertension, hypertensive medication, and stroke risk among patients with the MTHFR T allele and the TT genotype. The association of diuretics therapy with higher homocysteine levels calls for routine measurements and therapeutic control of homocysteine in patients on diuretic, to improve health-related outcomes.

Parallel evolution of genes and languages in the Caucasus region.

We analyzed 40 single nucleotide polymorphism and 19 short tandem repeat Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The data suggested a direct origin of Caucasus male lineages from the Near East, followed by high levels of isolation, differentiation, and genetic drift in situ. Comparison of genetic and linguistic reconstructions covering the last few millennia showed striking correspondences between the topology and dates of the respective gene and language trees and with documented historical events. Overall, in the Caucasus region, unmatched levels of gene-language coevolution occurred within geographically isolated populations, probably due to its mountainous terrain.

mtDNA lineages reveal coronary artery disease-associated structures in the Lebanese population.

Population origins and ancestry have previously been found to be important determinants of coronary artery disease (CAD). This study investigates associations of Lebanese mitochondrial DNA lineages with CAD and studies their correlation with other populations, exploring population structures that may infer mitochondria functional associations and reveal population movements and origins. Sequencing the mitochondrial hypervariable sequence 1 (HVS-1) of 363 controls and 448 cases revealed that haplogroup W was more frequent (P = 0.013) in cases compared to controls, and was associated with increased risk of CAD (OR = 5.50, 95% CI = 1.50-35.30, P = 0.026) among Lebanese samples. Haplogroup A was only found in controls (P = 0.029). We have detected stronger geographic correlation between haplogroup W and CAD (Pearson's r = 0.316, P < 0.001) than between haplogroup A and CAD (r = 0.149, P < 0.001). HVS-1 phylogenetic network of haplogroup W shows controls are restricted to European clusters while cases belong mostly to Middle Eastern natives. The network of haplogroup A shows that the controls belong to a cluster dominated by Central Asians. Our results show evidence of a gene flow into Lebanon, creating CAD-associated population structures that are similar to those in the source populations, maintained by limited admixture, and probably encompassing variations on the nuclear and/or the mitochondrial genome that are correlated with the disease.

Diabetes-induced vascular dysfunction involves arginase I.

Arginase can cause vascular dysfunction by competing with nitric oxide synthase for l-arginine and by increasing cell proliferation and collagen formation, which promote vascular fibrosis/stiffening. We have shown that increased arginase expression/activity contribute to vascular endothelial cell (EC) dysfunction. Here, we examined the roles of the two arginase isoforms, arginase I and II (AI and AII, respectively), in this process. Experiments were performed using streptozotocin-induced diabetic mice: wild-type (WT) mice and knockout mice lacking the AII isoform alone (AI(+/+)AII(-/-)) or in combination with partial deletion of AI (AI(+/-)AII (-/-)). EC-dependent vasorelaxation of aortic rings and arterial fibrosis and stiffness were assessed in relation to arginase activity and expression. Diabetes reduced mean EC-dependent vasorelaxation markedly in diabetic WT and AI(+/+)AII(-/-) aortas (53% and 44% vs. controls, respectively) compared with a 27% decrease in AI(+/-)AII (-/-) vessels. Coronary fibrosis was also increased in diabetic WT and AI(+/+)AII(-/-) mice (1.9- and 1.7-fold vs. controls, respectively) but was not altered in AI(+/-)AII (-/-) diabetic mice. Carotid stiffness was increased by 142% in WT diabetic mice compared with 51% in AI(+/+)AII(-/-) mice and 19% in AI(+/-)AII (-/-) mice. In diabetic WT and AI(+/+)AII(-/-) mice, aortic arginase activity and AI expression were significantly increased compared with control mice, but neither parameter was altered in AI(+/-)AII (-/-) mice. In summary, AI(+/-)AII (-/-) mice exhibit better EC-dependent vasodilation and less vascular stiffness and coronary fibrosis compared with diabetic WT and AI(+/+)AII(-/-) mice. These data indicate a major involvement of AI in diabetes-induced vascular dysfunction.

Topology and redescriptions detect multiple alternative biological pathways from clinical phenotypes.

Biological pathways play a crucial role in the properties of diseases and are important in drug discovery. Identifying the logical relationships among distinctive phenotypic clusters could reveal possible connections to the underlying pathways. However, this process is challenging since clinical phenotypes are often available through unstructured electronic health records. Moreover, in the absence of a standardized questionnaire, there could be bias among physicians toward selecting certain medical terms. In this article, we develop an efficient pipeline to address these challenges and help practitioners to reveal the pathways associated with the disease. We use topological data analysis and redescriptions and propose a pipeline of four phases: (1) pre-processing the clinical notes to extract the salient concepts, (2) constructing a feature space of the patients to characterize the extracted concepts, (3) leveraging the topological properties to distill the available knowledge and visualize the extracted features, and finally, (4) investigating the bias in the clinical notes of the selected features and identify possible pathways. Our experiments on a publicly available dataset of COVID-19 clinical notes testify that our pipeline can indeed extract meaningful pathways.