Aged polymorphonuclear leukocytes cause fibrotic interstitial lung disease in the absence of regulation by B cells.

Pulmonary immunity requires tight regulation, as interstitial inflammation can compromise gas exchange and lead to respiratory failure. Here we found a greater number of aged CD11bhiL-selectinloCXCR4+ polymorphonuclear leukocytes (PMNs) in lung vasculature than in the peripheral circulation. Using pulmonary intravital microscopy, we observed lung PMNs physically interacting with B cells via ß2 integrins; this initiated neutrophil apoptosis, which led to macrophage-mediated clearance. Genetic deletion of B cells led to the accumulation of aged PMNs in the lungs without systemic inflammation, which caused pathological fibrotic interstitial lung disease that was attenuated by the adoptive transfer of B cells or depletion of PMNs. Thus, the lungs are an intermediary niche in the PMN lifecycle wherein aged PMNs are regulated by B cells, which restrains their potential to cause pulmonary pathology.

The microRNA-183/96/182 cluster inhibits lung cancer progression and metastasis by inducing an interleukin-2-mediated antitumor CD8+ cytotoxic T-cell response.

One of the mechanisms by which cancer cells acquire hyperinvasive and migratory properties with progressive loss of epithelial markers is the epithelial-to-mesenchymal transition (EMT). We have previously reported that in different cancer types, including nonsmall cell lung cancer (NSCLC), the microRNA-183/96/182 cluster (m96cl) is highly repressed in cells that have undergone EMT. In the present study, we used a novel conditional m96cl mouse to establish that loss of m96cl accelerated the growth of Kras mutant autochthonous lung adenocarcinomas. In contrast, ectopic expression of the m96cl in NSCLC cells results in a robust suppression of migration and invasion in vitro, and tumor growth and metastasis in vivo. Detailed immune profiling of the tumors revealed a significant enrichment of activated CD8+ cytotoxic T lymphocytes (CD8+ CTLs) in m96cl-expressing tumors, and m96cl-mediated suppression of tumor growth and metastasis was CD8+ CTL-dependent. Using coculture assays with naïve immune cells, we show that m96cl expression drives paracrine stimulation of CD8+ CTL proliferation and function. Using tumor microenvironment-associated gene expression profiling, we identified that m96cl elevates the interleukin-2 (IL2) signaling pathway and results in increased IL2-mediated paracrine stimulation of CD8+ CTLs. Furthermore, we identified that the m96cl modulates the expression of IL2 in cancer cells by regulating the expression of transcriptional repressors Foxf2 and Zeb1, and thereby alters the levels of secreted IL2 in the tumor microenvironment. Last, we show that in vivo depletion of IL2 abrogates m96cl-mediated activation of CD8+ CTLs and results in loss of metastatic suppression. Therefore, we have identified a novel mechanistic role of the m96cl in the suppression of lung cancer growth and metastasis by inducing an IL2-mediated systemic CD8+ CTL immune response.

Structural mechanism of mitochondrial membrane remodelling by human OPA1.

Distinct morphologies of the mitochondrial network support divergent metabolic and regulatory processes that determine cell function and fate1-3. The mechanochemical GTPase optic atrophy 1 (OPA1) influences the architecture of cristae and catalyses the fusion of the mitochondrial inner membrane4,5. Despite its fundamental importance, the molecular mechanisms by which OPA1 modulates mitochondrial morphology are unclear. Here, using a combination of cellular and structural analyses, we illuminate the molecular mechanisms that are key to OPA1-dependent membrane remodelling and fusion. Human OPA1 embeds itself into cardiolipin-containing membranes through a lipid-binding paddle domain. A conserved loop within the paddle domain inserts deeply into the bilayer, further stabilizing the interactions with cardiolipin-enriched membranes. OPA1 dimerization through the paddle domain promotes the helical assembly of a flexible OPA1 lattice on the membrane, which drives mitochondrial fusion in cells. Moreover, the membrane-bending OPA1 oligomer undergoes conformational changes that pull the membrane-inserting loop out of the outer leaflet and contribute to the mechanics of membrane remodelling. Our findings provide a structural framework for understanding how human OPA1 shapes mitochondrial morphology and show us how human disease mutations compromise OPA1 functions.

Microbes and the fate of neutrophils.

Neutrophils or polymorphonuclear neutrophils (PMNs) are an important component of innate host defense. These phagocytic leukocytes are recruited to infected tissues and kill invading microbes. There are several general characteristics of neutrophils that make them highly effective as antimicrobial cells. First, there is tremendous daily production and turnover of granulocytes in healthy adults-typically 1011 per day. The vast majority (~95%) of these cells are neutrophils. In addition, neutrophils are mobilized rapidly in response to chemotactic factors and are among the first leukocytes recruited to infected tissues. Most notably, neutrophils contain and/or produce an abundance of antimicrobial molecules. Many of these antimicrobial molecules are toxic to host cells and can destroy host tissues. Thus, neutrophil activation and turnover are highly regulated processes. To that end, aged neutrophils undergo apoptosis constitutively, a process that contains antimicrobial function and proinflammatory capacity. Importantly, apoptosis facilitates nonphlogistic turnover of neutrophils and removal by macrophages. This homeostatic process is altered by interaction with microbes and their products, as well as host proinflammatory molecules. Microbial pathogens can delay neutrophil apoptosis, accelerate apoptosis following phagocytosis, or cause neutrophil cytolysis. Here, we review these processes and provide perspective on recent studies that have potential to impact this paradigm.

Declining autozygosity over time: An exploration in over 1 million individuals from three diverse cohorts.

Previous studies have hypothesized that autozygosity is decreasing over generational time. However, these studies were limited to relatively small samples (n < 11,000) lacking in diversity, which may limit the generalizability of their findings. We present data that partially support this hypothesis from three large cohorts of diverse ancestries, two from the US (All of Us, n = 82,474; the Million Veteran Program, n = 622,497) and one from the UK (UK Biobank, n = 380,899). Our results from a mixed-effect meta-analysis demonstrate an overall trend of decreasing autozygosity over generational time (meta-analyzed slope = -0.029, SE = 0.009, p = 6.03e-4). On the basis of our estimates, we would predict FROH to decline 0.29% for every 20-year increase in birth year. We determined that a model including an ancestry-by-country interaction term fit the data best, indicating that ancestry differences in this trend differ by country. We found further evidence to suggest a difference between the US and UK cohorts by meta-analyzing within country, observing a significant negative estimate in the US cohorts (meta-analyzed slope = -0.058, SE = 0.015, p = 1.50e-4) but a non-significant estimate in the UK (meta-analyzed slope = -0.001, SE = 0.008, p = 0.945). The association between autozygosity and birth year was substantially attenuated when accounting for educational attainment and income (meta-analyzed slope = -0.011, SE = 0.008, p = 0.167), suggesting they may partially account for decreasing autozygosity over time. Overall, we demonstrate decreasing autozygosity over time in a large, modern sample and speculate that this trend can be attributed to increases in urbanization and panmixia and differences in sociodemographic processes lead to country-specific differences in the rate of decline.

Ischemic Stroke with Comorbid Cancer Has Specific miRNA-mRNA Networks in Blood That Vary by Ischemic Stroke Mechanism.

OBJECTIVE: Approximately half of ischemic strokes (IS) in cancer patients are cryptogenic, with many presumed cardioembolic. We evaluated whether there were specific miRNA and mRNA transcriptome architectures in peripheral blood of IS patients with and without comorbid cancer, and between cardioembolic versus noncardioembolic IS etiologies in comorbid cancer. METHODS: We studied patients with cancer and IS (CS; n = 42), stroke only (SO; n = 41), and cancer only (n = 28), and vascular risk factor-matched controls (n = 30). mRNA-Seq and miRNA-Seq data, analyzed with linear regression models, identified differentially expressed genes in CS versus SO and in cardioembolic versus noncardioembolic CS, and miRNA-mRNA regulatory pairs. Network-level analyses identified stroke etiology-specific responses in CS. RESULTS: A total of 2,085 mRNAs and 31 miRNAs were differentially expressed between CS and SO. In CS, 122 and 35 miRNA-mRNA regulatory pairs, and 5 and 3 coexpressed gene modules, were associated with cardioembolic and noncardioembolic CS, respectively. Complement, growth factor, and immune/inflammatory pathways showed differences between IS etiologies in CS. A 15-gene biomarker panel assembled from a derivation cohort (n = 50) correctly classified 81% of CS and 71% of SO participants in a validation cohort (n = 33). Another 15-gene panel correctly identified etiologies for 13 of 13 CS-cardioembolic and 11 of 11 CS-noncardioembolic participants upon cross-validation; 11 of 16 CS-cryptogenic participants were predicted cardioembolic. INTERPRETATION: We discovered unique mRNA and miRNA transcriptome architecture in CS and SO, and in CS with different IS etiologies. Cardioembolic and noncardioembolic etiologies in CS showed unique coexpression networks and potential master regulators. These may help distinguish CS from SO and identify IS etiology in cryptogenic CS patients. ANN NEUROL 2024.

Cardiac competence of the paraxial head mesoderm fades concomitant with a shift towards the head skeletal muscle programme.

The vertebrate head mesoderm provides the heart, the great vessels, some smooth and most head skeletal muscle, in addition to parts of the skull. It has been speculated that the ability to generate cardiac and smooth muscle is the evolutionary ground-state of the tissue. However, whether indeed the entire head mesoderm has generic cardiac competence, how long this may last, and what happens as cardiac competence fades, is not clear. Bone morphogenetic proteins (Bmps) are known to promote cardiogenesis. Using 41 different marker genes in the chicken embryo, we show that the paraxial head mesoderm that normally does not engage in cardiogenesis has the ability to respond to Bmp for a long time. However, Bmp signals are interpreted differently at different time points. Up to early head fold stages, the paraxial head mesoderm is able to read Bmps as signal to engage in the cardiac programme; the ability to upregulate smooth muscle markers is retained slightly longer. Notably, as cardiac competence fades, Bmp promotes the head skeletal muscle programme instead. The switch from cardiac to skeletal muscle competence is Wnt-independent as Wnt caudalises the head mesoderm and also suppresses Msc-inducing Bmp provided by the prechordal plate, thus suppressing both the cardiac and the head skeletal muscle programmes. Our study for the first time suggests a specific transition state in the embryo when cardiac competence is replaced by skeletal muscle competence. It sets the stage to unravel the cardiac-skeletal muscle antagonism that is known to partially collapse in heart failure.

Hearing intervention versus health education control to reduce cognitive decline in older adults with hearing loss in the USA (ACHIEVE): a multicentre, randomised controlled trial.

BACKGROUND: Hearing loss is associated with increased cognitive decline and incident dementia in older adults. We aimed to investigate whether a hearing intervention could reduce cognitive decline in cognitively healthy older adults with hearing loss. METHODS: The ACHIEVE study is a multicentre, parallel-group, unmasked, randomised controlled trial of adults aged 70-84 years with untreated hearing loss and without substantial cognitive impairment that took place at four community study sites across the USA. Participants were recruited from two study populations at each site: (1) older adults participating in a long-standing observational study of cardiovascular health (Atherosclerosis Risk in Communities [ARIC] study), and (2) healthy de novo community volunteers. Participants were randomly assigned (1:1) to a hearing intervention (audiological counselling and provision of hearing aids) or a control intervention of health education (individual sessions with a health educator covering topics on chronic disease prevention) and followed up every 6 months. The primary endpoint was 3-year change in a global cognition standardised factor score from a comprehensive neurocognitive battery. Analysis was by intention to treat. This trial was registered at ClinicalTrials.gov, NCT03243422. FINDINGS: From Nov 9, 2017, to Oct 25, 2019, we screened 3004 participants for eligibility and randomly assigned 977 (32·5%; 238 [24%] from ARIC and 739 [76%] de novo). We randomly assigned 490 (50%) to the hearing intervention and 487 (50%) to the health education control. The cohort had a mean age of 76·8 years (SD 4·0), 523 (54%) were female, 454 (46%) were male, and most were White (n=858 [88%]). Participants from ARIC were older, had more risk factors for cognitive decline, and had lower baseline cognitive scores than those in the de novo cohort. In the primary analysis combining the ARIC and de novo cohorts, 3-year cognitive change (in SD units) was not significantly different between the hearing intervention and health education control groups (-0·200 [95% CI -0·256 to -0·144] in the hearing intervention group and -0·202 [-0·258 to -0·145] in the control group; difference 0·002 [-0·077 to 0·081]; p=0·96). However, a prespecified sensitivity analysis showed a significant difference in the effect of the hearing intervention on 3-year cognitive change between the ARIC and de novo cohorts (pinteraction=0·010). Other prespecified sensitivity analyses that varied analytical parameters used in the total cohort did not change the observed results. No significant adverse events attributed to the study were reported with either the hearing intervention or health education control. INTERPRETATION: The hearing intervention did not reduce 3-year cognitive decline in the primary analysis of the total cohort. However, a prespecified sensitivity analysis showed that the effect differed between the two study populations that comprised the cohort. These findings suggest that a hearing intervention might reduce cognitive change over 3 years in populations of older adults at increased risk for cognitive decline but not in populations at decreased risk for cognitive decline. FUNDING: US National Institutes of Health.

Metabolomic and transcriptomic analyses of yellow-flowered crocuses to infer alternative sources of saffron metabolites.

BACKGROUND: The increasing demand for saffron metabolites in various commercial industries, including medicine, food, cosmetics, and dyeing, is driven by the discovery of their diverse applications. Saffron, derived from Crocus sativus stigmas, is the most expensive spice, and there is a need to explore additional sources to meet global consumption demands. In this study, we focused on yellow-flowering crocuses and examined their tepals to identify saffron-like compounds. RESULTS: Through metabolomic and transcriptomic approaches, our investigation provides valuable insights into the biosynthesis of compounds in yellow-tepal crocuses that are similar to those found in saffron. The results of our study support the potential use of yellow-tepal crocuses as a source of various crocins (crocetin glycosylated derivatives) and flavonoids. CONCLUSIONS: Our findings suggest that yellow-tepal crocuses have the potential to serve as a viable excessive source of some saffron metabolites. The identification of crocins and flavonoids in these crocuses highlights their suitability for meeting the demands of various industries that utilize saffron compounds. Further exploration and utilization of yellow-tepal crocuses could contribute to addressing the growing global demand for saffron-related products.

Female and male patients have similar outcomes after transcarotid artery revascularization in prospective trials.

OBJECTIVE: Sex disparities in outcomes after carotid revascularization have long been a concern, with several studies demonstrating increased postoperative death and stroke for female patients after either carotid endarterectomy or transfemoral stenting. Adverse events after transfemoral stenting are higher in female patients, particularly in symptomatic cases. Our objective was to investigate outcomes after transcarotid artery revascularization (TCAR) stratified by patient sex hypothesizing that the results would be similar between males and females. METHODS: We analyzed prospectively collected data from the Safety and Efficacy Study for Reverse Flow Used During Carotid Artery Stenting Procedure (ROADSTER)1 (pivotal), ROADSTER2 (US Food and Drug Administration indicated postmarket), and ROADSTER Extended Access TCAR trials. All patients had verified carotid stenosis meeting criteria for intervention (≥80% for asymptomatic patients and ≥50% in patient with symptomatic disease), and were included based on anatomical or clinical high-risk criteria for carotid stenting. Neurological assessments (National Institutes of Health Stroke Scale, Modified Rankin Scale) were obtained before and within 24 hours from procedure end by an independent neurologist or National Institutes of Health Stroke Scale-certified nurse. Patients were stratified by sex (male vs female). Baseline demographics were compared using χ2 and Fisher's exact tests where appropriate; primary outcomes were combination stroke/death (S/D) and S/D/myocardial infarction (S/D/M) at 30 days, and secondary outcomes were the individual components of S/D/M. Univariate logistic regression was conducted. RESULTS: We included 910 patients for analysis (306 female [33.6%], 604 male [66.4%]). Female patients were more often <65 years old (20.6% vs 15%) or ≥80 years old (22.6% vs 20.2%) compared with males, and were more often of Black/African American ethnicity (7.5% vs 4.3%). There were no differences by sex in term of comorbidities, current or prior smoking status, prior stroke, symptomatic status, or prevalence of anatomical and/or clinical high-risk criteria. General anesthetic use, stent brands used, and procedure times did not differ by sex, although flow reversal times were longer in female patients (10.9 minutes male vs 12.4 minutes female; P = .01), as was more contrast used in procedures for female patients (43 mL male vs 48.9 mL female; P = .049). The 30-day S/D and S/D/M rates were similar between male and female patients (S/D, 2.7% male vs 1.6% female [P = .34]; S/D/M, 3.6% male vs 2.6% female [P = .41]), which did not differ when stratified by symptom status. Secondary outcomes did not differ by sex, including stroke rates at 30 days (2.2% male vs 1.6% female; P = .80), nor were differences seen with stratification by symptom status. Univariate analysis demonstrated that history of a prior ipsilateral stroke was associated with increased odds of S/D (odds ratio [OR], 4.19; P = .001) and S/D/M (OR, 2.78; P = .01), as was symptomatic presentation with increased odds for S/D (OR, 2.78; P = .02). CONCLUSIONS: Prospective TCAR trial data demonstrate exceptionally low rates of S/D/MI, which do not differ by patient sex.

Safety and efficacy of mechanical aspiration thrombectomy for patients with acute lower extremity ischemia.

OBJECTIVE: Acute limb ischemia (ALI) is associated with high rates of amputation and consequent morbidity and mortality. The objective of this study is to report on the safety and efficacy of aspiration thrombectomy using the Indigo Aspiration System in patients with lower extremity (LE) ALI. METHODS: The STRIDE study was an international, multicenter, prospective, study that enrolled 119 participants presenting with LE-ALI. Patients were treated firstline with mechanical thrombectomy using the Indigo Aspiration System, before stenting or angioplasty, or other therapies as determined by treating physician. The primary end point was target limb salvage at 30 days after the procedure. Secondary end points within 30 days included technical success, defined as core laboratory-adjudicated Thrombolysis in Myocardial Infarction (TIMI) 2/3 flow rate immediately after the procedure, changes in modified Society for Vascular Surgery runoff score, improvement of Rutherford classification compared with before the procedure, patency, rate of device-related serious adverse events, and major periprocedural bleeding. Secondary end points that will be evaluated at 12 months include target limb salvage and mortality. RESULTS: Of the 119 participants enrolled at 16 sites, the mean age was 66.3 years (46.2% female). At baseline (n = 119), ischemic severity was classified as Rutherford I in 10.9%, Rutherford IIa in 54.6%, and Rutherford IIb in 34.5%. The mean target thrombus length was 125.7 ± 124.7 mm. Before the procedure, 93.0% (of patients 107/115) had no flow (TIMI 0) through the target lesion. The target limb salvage rate at 30 days was 98.2% (109/111). The rate of periprocedural major bleed was 4.2% (5/119) and device-related serious adverse events was 0.8% (1/119). Restoration of flow (TIMI 2/3) was achieved in 96.3% of patients (105/109) immediately after the procedure. The median improvement in the modified Society for Vascular Surgery runoff score (before vs after the procedure) was 6.0 (interquartile range, 0.0-11.0). Rutherford classifications also improved after discharge in 86.5% of patients (83/96), as compared with preprocedural scores. Patency at 30 days was achieved in 89.4% of patients (101/113). CONCLUSIONS: In the STRIDE (A Study of Patients with Lower Extremity Acute Limb Ischemia to Remove Thrombus with the Indigo Aspiration System) study, aspiration thrombectomy with the Indigo System provided a safe and effective endovascular treatment for patients with LE-ALI, resulting in a high rate (98.2%) of successful limb salvage at 30 days, with few periprocedural complications.

One-year limb salvage and quality of life following mechanical aspiration thrombectomy in patients with acute lower extremity ischemia.

OBJECTIVE: Lower extremity acute limb ischemia (LE-ALI) is associated with high morbidity and mortality rates, and a burden on patient quality of life (QoL). There is limited medium- to long-term evidence on mechanical aspiration thrombectomy (MT) in patients with LE-ALI. The STRIDE study was designed to assess safety and efficacy of MT using the Indigo Aspiration System in patients with LE-ALI. Thirty-day primary and secondary endpoints and additional outcomes were previously published. Here, we report 365-day secondary endpoints and QoL data from STRIDE. METHODS: STRIDE was a multicenter, prospective, single-arm, observational cohort study that enrolled 119 patients across 16 sites in the United States and Europe. Patients were treated first-line with MT using the Indigo Aspiration System (Penumbra, Inc). The study completed follow-up in October 2023. Secondary endpoints at 365 days included target limb salvage and mortality. Additionally, the VascuQoL-6 questionnaire, developed for evaluating patient-centered QoL outcomes for peripheral arterial disease, was assessed at baseline and follow-up through 365 days. RESULTS: Seventy-three percent of patients (87/119) were available for 365-day follow-up. Mean age of these patients was 65.0 ± 13.3 years, and 44.8% were female. Baseline ischemic severity was classified as Rutherford I in 12.6%, Rutherford IIa in 51.7%, and Rutherford IIb in 35.6%. In general, baseline and disease characteristics (demographics, medical history, comorbidities, target thrombus) of these patients are similar to the enrolled cohort of 119 patients. The secondary endpoints at 365 days for target limb salvage was 88.5% (77/87) and mortality rate was 12.0% (12/100). VascuQoL-6 improved across all domains, with a median total score improvement from 12.0 (interquartile range, 9.0-15.0) at baseline to 19.0 (interquartile range, 16.0-22.0) at 365 days. CONCLUSIONS: These 365-day results from STRIDE demonstrate that first-line MT with the Indigo Aspiration System for LE-ALI portray continued high target limb salvage rates and improved patient-reported QoL. These findings indicate Indigo as a safe and effective therapeutic option for LE-ALI.

Characterizing the polygenic architecture of complex traits in populations of East Asian and European descent.

To investigate the polygenicity of complex traits in populations of East Asian (EAS) and European (EUR) descents, we leveraged genome-wide data from Biobank Japan, UK Biobank, and FinnGen cohorts. Specifically, we analyzed up to 215 outcomes related to 18 health domains, assessing their polygenic architecture via descriptive statistics, such as the proportion of susceptibility SNPs per trait (πc). While we did not observe EAS-EUR differences in the overall distribution of polygenicity parameters across the phenotypes investigated, there were ancestry-specific patterns in the polygenicity differences between health domains. In EAS, pairwise comparisons across health domains showed enrichment for πc differences related to hematological and metabolic traits (hematological fold-enrichment = 4.45, p = 2.15 × 10-7; metabolic fold-enrichment = 4.05, p = 4.01 × 10-6). For both categories, the proportion of susceptibility SNPs was lower than that observed for several other health domains (EAS-hematological median πc = 0.15%, EAS-metabolic median πc = 0.18%) with the strongest πc difference with respect to respiratory traits (EAS-respiratory median πc = 0.50%; hematological-p = 2.26 × 10-3; metabolic-p = 3.48 × 10-3). In EUR, pairwise comparisons showed multiple πc differences related to the endocrine category (fold-enrichment = 5.83, p = 4.76 × 10-6), where these traits showed a low proportion of susceptibility SNPs (EUR-endocrine median πc = 0.01%) with the strongest difference with respect to psychiatric phenotypes (EUR-psychiatric median πc = 0.50%; p = 1.19 × 10-4). Simulating sample sizes of 1,000,000 and 5,000,000 individuals, we also showed that ancestry-specific polygenicity patterns translate into differences across health domains in the genetic variance explained by susceptibility SNPs projected to be genome-wide significant (e.g., EAS hematological-neoplasm p = 2.18 × 10-4; EUR endocrine-gastrointestinal p = 6.80 × 10-4). These findings highlight that traits related to the same health domains may present ancestry-specific variability in their polygenicity.

Modeling the longitudinal changes of ancestry diversity in the Million Veteran Program.

BACKGROUND: The Million Veteran Program (MVP) participants represent 100 years of US history, including significant social and demographic changes over time. Our study assessed two aspects of the MVP: (i) longitudinal changes in population diversity and (ii) how these changes can be accounted for in genome-wide association studies (GWAS). To investigate these aspects, we divided MVP participants into five birth cohorts (N-range = 123,888 [born from 1943 to 1947] to 136,699 [born from 1948 to 1953]). RESULTS: Ancestry groups were defined by (i) HARE (harmonized ancestry and race/ethnicity) and (ii) a random-forest clustering approach using the 1000 Genomes Project and the Human Genome Diversity Project (1kGP + HGDP) reference panels (77 world populations representing six continental groups). In these groups, we performed GWASs of height, a trait potentially affected by population stratification. Birth cohorts demonstrate important trends in ancestry diversity over time. More recent HARE-assigned Europeans, Africans, and Hispanics had lower European ancestry proportions than older birth cohorts (0.010 < Cohen's d < 0.259, p < 7.80 × 10-4). Conversely, HARE-assigned East Asians showed an increase in European ancestry proportion over time. In GWAS of height using HARE assignments, genomic inflation due to population stratification was prevalent across all birth cohorts (linkage disequilibrium score regression intercept = 1.08 ± 0.042). The 1kGP + HGDP-based ancestry assignment significantly reduced the population stratification (mean intercept reduction = 0.045 ± 0.007, p < 0.05) confounding in the GWAS statistics. CONCLUSIONS: This study provides a characterization of ancestry diversity of the MVP cohort over time and compares two strategies to infer genetically defined ancestry groups by assessing differences in controlling population stratification in genome-wide association studies.

Functional and molecular characterization of suicidality factors using phenotypic and genome-wide data.

Genome-wide association studies (GWAS) of suicidal thoughts and behaviors support the existence of genetic contributions. Continuous measures of psychiatric disorder symptom severity can sometimes model polygenic risk better than binarized definitions. We compared two severity measures of suicidal thoughts and behaviors at the molecular and functional levels using genome-wide data. We used summary association data from GWAS of four traits analyzed in 122,935 individuals of European ancestry: thought life was not worth living (TLNWL), thoughts of self-harm, actual self-harm, and attempted suicide. A new trait for suicidal thoughts and behaviors was constructed first, phenotypically, by aggregating the previous four traits (termed "suicidality") and second, genetically, by using genomic structural equation modeling (gSEM; termed S-factor). Suicidality and S-factor were compared using SNP-heritability (h2) estimates, genetic correlation (rg), partitioned h2, effect size distribution, transcriptomic correlations (ρGE) in the brain, and cross-population polygenic scoring (PGS). The S-factor had good model fit (χ2 = 0.21, AIC = 16.21, CFI = 1.00, SRMR = 0.024). Suicidality (h2 = 7.6%) had higher h2 than the S-factor (h2 = 2.54, Pdiff = 4.78 × 10-13). Although the S-factor had a larger number of non-null susceptibility loci (πc = 0.010), these loci had small effect sizes compared to those influencing suicidality (πc = 0.005, Pdiff = 0.045). The h2 of both traits was enriched for conserved biological pathways. The rg and ρGE support highly overlapping genetic and transcriptomic features between suicidality and the S-factor. PGS using European-ancestry SNP effect sizes strongly associated with TLNWL in Admixed Americans: Nagelkerke's R2 = 8.56%, P = 0.009 (PGSsuicidality) and Nagelkerke's R2 = 7.48%, P = 0.045 (PGSS-factor). An aggregate suicidality phenotype was statistically more heritable than the S-factor across all analyses and may be more informative for future genetic study designs interested in common genetic factors among different suicide related phenotypes.

Infrastructure for bioinformatics applications in Tanzania: Lessons from the Sickle Cell Programme.

Sickle cell disease (SCD) is a common genetic disorder in Africa. Some ongoing work in SCD research includes the analysis and comparisons of variation in phenotypic presentations and disease outcomes with the genotypic signatures. This has contributed to the observed growth of molecular and genetic data in SCD. However, while the "omics" data continues to pile, the capacity to interpret and turn the genetic findings into clinical practice is still underdeveloped, especially in the developing region. Building bioinformatics infrastructure and capacity in the region is key to bridging the gap. This paper seeks to illustrate how the Sickle Cell Programme (SCP) at the Muhimbili University of Health and Allied Sciences (MUHAS) in Tanzania, modeled the integration of infrastructure for bioinformatics and clinical research while running day-to-day clinical care for SCD in Tanzania.

Refining and illuminating acetogenic Eubacterium strains for reclassification and metabolic engineering.

BACKGROUND: The genus Eubacterium is quite diverse and includes several acetogenic strains capable of fermenting C1-substrates into valuable products. Especially, Eubacterium limosum and closely related strains attract attention not only for their capability to ferment C1 gases and liquids, but also due to their ability to produce butyrate. Apart from its well-elucidated metabolism, E. limosum is also genetically accessible, which makes it an interesting candidate to be an industrial biocatalyst. RESULTS: In this study, we examined genomic, phylogenetic, and physiologic features of E. limosum and the closest related species E. callanderi as well as E. maltosivorans. We sequenced the genomes of the six Eubacterium strains 'FD' (DSM 3662T), 'Marburg' (DSM 3468), '2A' (DSM 2593), '11A' (DSM 2594), 'G14' (DSM 107592), and '32' (DSM 20517) and subsequently compared these with previously available genomes of the E. limosum type strain (DSM 20543T) as well as the strains 'B2', 'KIST612', 'YI' (DSM 105863T), and 'SA11'. This comparison revealed a close relationship between all eleven Eubacterium strains, forming three distinct clades: E. limosum, E. callanderi, and E. maltosivorans. Moreover, we identified the gene clusters responsible for methanol utilization as well as genes mediating chain elongation in all analyzed strains. Subsequent growth experiments revealed that strains of all three clades can convert methanol and produce acetate, butyrate, and hexanoate via reverse ß-oxidation. Additionally, we used a harmonized electroporation protocol and successfully transformed eight of these Eubacterium strains to enable recombinant plasmid-based expression of the gene encoding the fluorescence-activating and absorption shifting tag (FAST). Engineered Eubacterium strains were verified regarding their FAST-mediated fluorescence at a single-cell level using a flow cytometry approach. Eventually, strains 'FD' (DSM 3662T), '2A' (DSM 2593), '11A' (DSM 2594), and '32' (DSM 20517) were genetically engineered for the first time. CONCLUSION: Strains of E. limosum, E. callanderi, and E. maltosivorans are outstanding candidates as biocatalysts for anaerobic C1-substrate conversion into valuable biocommodities. A large variety of strains is genetically accessible using a harmonized electroporation protocol, and FAST can serve as a reliable fluorescent reporter protein to characterize genetically engineered cells. In total eleven strains have been assigned to distinct clades, providing a clear and updated classification. Thus, the description of respective Eubacterium species has been emended, improved, aligned, and is requested to be implemented in respective databases.

The Effect of One Year Aneurysm Sac Dynamics on Five Year Mortality and Continued Aneurysm Sac Evolution.

OBJECTIVE: One year aneurysm sac dynamics after endovascular abdominal aortic aneurysm repair (EVAR) were independently associated with greater risk of all-cause mortality in prior registry studies but were limited in completeness and granularity. This retrospective analysis aimed to study the impact of sac dynamics on survival within the Endurant Stent Graft Global Registry (ENGAGE) with five year follow up. METHODS: A total of 1 263 subjects were enrolled in the ENGAGE Registry between March 2009 and April 2011. One year aneurysm sac changes were calculated from one month post-operative imaging scans and the scan closest to the time of one year follow up. Sac regression was defined as a sac decrease of ≥ 5 mm and sac expansion as aneurysm sac growth ≥ 5 mm. The primary outcome was rate of five year all-cause mortality. Kaplan-Meier estimates for freedom from all-cause mortality were calculated. Multivariable Cox regression was used to determine the association between sac dynamics and all-cause mortality. RESULTS: At one year, 441 of the 949 study participants with appropriate imaging (46%) had abdominal aortic aneurysm sac regression, 462 (49%) remained stable, and 46 (4.8%) had sac expansion. For patients with sac regression, five year all-cause mortality was 20%, compared with 28% for stable sac (p = .007) and 37% for the sac expansion (p = .010) cohorts. After adjustment, sac expansion and stable sac cohorts were associated with greater all-cause mortality (expansion: hazard ratio [HR] 1.8; 95% CI 1.1 - 3.2; p = .032; stable: HR 1.4; 95% CI 1.1 - 1.9; p = .019). CONCLUSION: In the ENGAGE Global Registry, one year rate of sac regression was 46%, and one year sac regression was observed to be associated with greater five year survival, corroborating prior findings utilising data from vascular registries. Sac regression could become the new standard for success after EVAR.

On Chemical Bonding in ht-Ga3Rh and Its Effect on Structural Organization and Thermoelectric Behavior.

In the course of systematic studies of intermetallic compounds Ga3TM (TM─transition metal), the compound Ga3Rh is synthesized by direct reaction of the elements at 700 °C. The material obtained is characterized as a high-temperature modification of Ga3Rh. Powder and single-crystal X-ray diffraction analyses reveal tetragonal symmetry (space group P42/mnm, No. 146) with a = 6.4808(2) Å and c = 6.5267(2) Å. Large values and strong anisotropy of the atomic displacement parameters of Ga atoms indicate essential disorder in the crystal structure. A split-position technique is applied to describe the real crystal structure of ht-Ga3Rh. Bonding analysis in ht-Ga3Rh performed on ordered models with the space groups P1̅, P42nm, and P42212 shows, besides the omnipresent heteroatomic Ga-Rh bonds in the rhombic prisms ∞3[Ga8/2Rh2], the formation of homoatomic Ga-Ga bonds bridging the Rh-Rh contacts and the absence of significant Rh-Rh bonding. These features are essential reasons for the experimentally observed disorder in the lattice. In agreement with the calculated electronic density of states, ht-Ga3Rh shows temperature-dependent electrical resistivity of a "bad metal". The very low lattice thermal conductivity of less than 0.5 W m-1 K-1 at 300 K, being lower than those for most other Ga3TM compounds, correlates with the enhanced bonding complexity.

Synthesis and Regioselective Functionalization of Tetrafluorobenzo-[α]-Fused BOPYPY Dyes.

The synthesis of a new bis-BF2 tetrafluorobenzo-[α]-fused BOPYPY dye from 4,5,6,7-tetrafluoroisoindole and 2-hydrazinopyrazine is reported. The regioselectivity of nucleophilic substitution reactions at the periphery of the tetrafluorinated BOPYPY and its α-bromo derivative were investigated using N-, O-, S-, and C-based nucleophiles. Among the aromatic fluorine atoms, the F2 atom is consistently regioselectively substituted, except when the α-position contains a thiophenol group; in this case, F4 is substituted instead due to stabilizing π-π-stacking between the two aromatic groups. The α-bromo BOPYPY derivative also reacts under Stille cross-coupling reaction conditions to produce the corresponding α-substituted product. The spectroscopic properties of these new fluorinated BOPYPYs were investigated and compared with nonfluorinated analogs.