Sequence analysis: Its past, present, and future.

This article marks the occasion of Social Science Research's 50th anniversary by reflecting on the progress of sequence analysis (SA) since its introduction into the social sciences four decades ago, with focuses on the developments of SA thus far in the social sciences and on its potential future directions. The application of SA in the social sciences, especially in life course research, has mushroomed in the last decade and a half. Using a life course analogy, we examined the birth of SA in the social sciences and its childhood (the first wave), its adolescence and young adulthood (the second wave), and its future mature adulthood in the paper. The paper provides a summary of (1) the important SA research and the historical contexts in which SA was developed by Andrew Abbott, (2) a thorough review of the many methodological developments in visualization, complexity measures, dissimilarity measures, group analysis of dissimilarities, cluster analysis of dissimilarities, multidomain/multichannel SA, dyadic/polyadic SA, Markov chain SA, sequence life course analysis, sequence network analysis, SA in other social science research, and software for SA, and (3) reflections on some future directions of SA including how SA can benefit and inform theory-making in the social sciences, the methods currently being developed, and some remaining challenges facing SA for which we do not yet have any solutions. It is our hope that the reader will take up the challenges and help us improve and grow SA into maturity.

Predicting the stability of early employment with its timing and childhood social and health-related predictors: a mixture Markov model approach.

To extend work careers, it is important to focus on all working-aged people including young adults. The aim of this study was to identify typical patterns of work participation among young adults after their first entry into the labour market and to examine whether the timing of entry together with parental and own socio-economic position and health predict early work participation. More in-depth understanding of early careers and their early determinants is important to plan targeted interventions and to promote more stable work participation among young adults. We used the Finnish Birth Cohort 1987 including data from several registers from all 59,476 children born in 1987 as well as their parents, followed until 2015. We estimated a mixture Markov model that allowed for joint identification of latent classes of labour-market attachment, estimation of labour-market transitions within classes, and prediction of class membership using childhood social and health-related determinants. We observed that the first entry into the labour market as measured by six months in continuous employment was not a permanent entry for many, not only due to negative reasons such as unemployment and ill health but also due to more voluntary reasons such as studies. Individuals entering the labour market at a later age were more likely to be in continuous employment thereafter. More advantaged background predicted exits due to studies or - when following a late entry - stable employment, while disadvantaged background factors predicted more unstable work and long-term exits from the labour market.

Can Visualization Alleviate Dichotomous Thinking? Effects of Visual Representations on the Cliff Effect.

Common reporting styles for statistical results in scientific articles, such as p-values and confidence intervals (CI), have been reported to be prone to dichotomous interpretations, especially with respect to the null hypothesis significance testing framework. For example when the p-value is small enough or the CIs of the mean effects of a studied drug and a placebo are not overlapping, scientists tend to claim significant differences while often disregarding the magnitudes and absolute differences in the effect sizes. This type of reasoning has been shown to be potentially harmful to science. Techniques relying on the visual estimation of the strength of evidence have been recommended to reduce such dichotomous interpretations but their effectiveness has also been challenged. We ran two experiments on researchers with expertise in statistical analysis to compare several alternative representations of confidence intervals and used Bayesian multilevel models to estimate the effects of the representation styles on differences in researchers' subjective confidence in the results. We also asked the respondents' opinions and preferences in representation styles. Our results suggest that adding visual information to classic CI representation can decrease the tendency towards dichotomous interpretations - measured as the 'cliff effect': the sudden drop in confidence around p-value 0.05 - compared with classic CI visualization and textual representation of the CI with p-values. All data and analyses are publicly available at https://github.com/helske/statvis.

Statistical analysis of life history calendar data.

The life history calendar is a data-collection tool for obtaining reliable retrospective data about life events. To illustrate the analysis of such data, we compare the model-based probabilistic event history analysis and the model-free data mining method, sequence analysis. In event history analysis, we estimate instead of transition hazards the cumulative prediction probabilities of life events in the entire trajectory. In sequence analysis, we compare several dissimilarity metrics and contrast data-driven and user-defined substitution costs. As an example, we study young adults' transition to adulthood as a sequence of events in three life domains. The events define the multistate event history model and the parallel life domains in multidimensional sequence analysis. The relationship between life trajectories and excess depressive symptoms in middle age is further studied by their joint prediction in the multistate model and by regressing the symptom scores on individual-specific cluster indices. The two approaches complement each other in life course analysis; sequence analysis can effectively find typical and atypical life patterns while event history analysis is needed for causal inquiries.

Lymphangiogenesis in aortic valve stenosis--novel regulatory roles for valvular myofibroblasts and mast cells.

OBJECTIVE: To investigate mechanisms of lymphangiogenesis in aortic valve stenosis (AS). METHODS: Lymphatic vessels were visualized with LYVE-1 staining in 20 control, 5 sclerotic, and 40 stenotic human aortic valves. Vascular endothelial growth factors (VEGFs) VEGF-C and VEGF-D, and their lymphangiogenic receptor VEGFR-3, and the angiogenic VEGFR-2 were analysed by quantitative real-time PCR and immunohistochemistry. Cultured myofibroblasts derived from human stenotic aortic valves, and cultured human mast cells were used to study VEGF-C regulation, and VEGF-C and VEGF-A were quantified from cell culture media by enzyme immunoassays. RESULTS: Lymphatic vessels, VEGF-C, VEGF-D, VEGFR-3 and VEGFR-2 all were present in the aortic valves. In AS, the number of lymphatic vessels and the expression of VEGF-D, VEGFR-3, and VEGFR-2 were increased. Moreover, the numbers of lymphatic vessels correlated positively with those of neovessels (r = 0.525, p = 0.001) and mast cells (r = 0.374, p = 0.017). Cultured valvular myofibroblasts produced VEGF-C, and addition of tumour necrosis factor alpha (TNF-α) to the cells augmented its secretion. In contrast, proteases released by activated human mast cells degraded VEGF-C. CONCLUSION: These results show that lymphangiogenesis is induced in advancing AS. Furthermore, valvular myofibroblasts and activated mast cells were identified as novel regulators of lymphangiogenesis in aortic valves.

High-density lipoproteins (HDL) are present in stenotic aortic valves and may interfere with the mechanisms of valvular calcification.

OBJECTIVE: To determine whether differences exist in valvular high density lipoprotein (HDL) content between non-stenotic and stenotic aortic valves, and whether HDL could retard valvular calcification locally. METHODS: Stenotic aortic valves were obtained from valve replacement surgery and non-stenotic control valves from cardiac transplantations or at autopsy. The valvular localization and concentration of apolipoproteinA-I (apoA-I) were analyzed by immunohistochemistry and ELISA. The effects of HDL on the secretion of calcifying mediators and proinflammatory cytokines by cultured aortic valve myofibroblasts were assessed by ELISA and real-time PCR. RESULTS: The concentration of apoA-I was higher in control than in stenotic valves (p < 0.05). ApoA-I surrounded the calcific deposits in stenotic valves, co-localizing with apoB, apoE, and osteoprotegerin (OPG). Incubation of cultured valve myofibroblasts with HDL increased their secretion of OPG (p < 0.001). Furthermore, incubation of myofibroblasts with HDL led to decreased mRNA expression of tumor necrosis factor alpha (TNF-α) (p < 0.05). CONCLUSIONS: The amount of valvular HDL is reduced in aortic valve stenosis. HDL both induces the secretion of OPG and reduces the expression of TNF-α in vitro. Since OPG is known to inhibit and TNF-α to promote aortic valve calcification, HDL may have an anti-calcifying effect in human aortic valves.

[Stenosis of the aortic valve]. / Aorttaläipan ahtauma.

The disease condition underlying the stenosis of the aortic valve resembles atherosclerosis and is dominated by activation of inflammatory cells, and accumulation of cholesterol and involves progressive fibrosis and calcification. Stenosis of the aortic valve may remain asymptomatic for long. Characteristic symptoms include exertional dyspnea and asthenia, angina pectoris type chest pain or loss of consciousness on exertion. The essential clinical finding on examination is a systolic murmur of the heart. Doppler ultrasonography of the heart is the diagnostic cornerstone. Stenosis of the aortic valve is treated with prosthetic valve surgery.

Transcardiac gradients of circulating apelin: extraction by normal hearts vs. release by hearts failing due to pressure overload.

Apelin is a newly discovered inotropic peptide tentatively linked up with the pathophysiology of heart failure (HF). To further assess the role of apelin in HF, we measured its transcardiac arteriovenous gradients in patients with left ventricular pressure overload with or without HF and in patients with structurally normal hearts. Blood samples from the aortic root and coronary sinus were drawn from 49 adult patients undergoing preoperative cardiac catheterization for severe aortic valve stenosis (AS). Similar samples were taken from 12 control patients with structurally normal hearts undergoing electrophysiological studies. Plasma apelin was determined by enzyme immunoassay. In the control group, apelin decreased from a median of 0.39 (0.16-1.94) ng/ml in the aortic root to 0.18 (0.13-1.04) ng/ml in the coronary sinus (P = 0.004). In AS patients free of HF (n = 33), apelin concentration remained unaltered across the heart, but in those with HF (n = 15) apelin rose from a median of 0.26 (0.20-0.82) ng/ml in the aorta to 0.45 (0.24-1.17) ng/ml in the coronary sinus (P = 0.002). The transcardiac apelin gradients differed statistically highly significantly across the three groups (P = 0.00005), and each of the two-group differences was also statistically significant (P < 0.05). In conclusion, left ventricular pressure overload changes the transcardiac arteriovenous differences of circulating apelin. Although normal hearts extract apelin from the coronary blood, hearts failing due to left ventricular pressure overload release apelin into the circulation. Loss of cardiac apelin may be involved in the mechanisms of HF development in AS.

Vascular endothelial growth factor-secreting mast cells and myofibroblasts: a novel self-perpetuating angiogenic pathway in aortic valve stenosis.

OBJECTIVE: To examine the proangiogenic potential of myofibroblasts and mast cells, 2 types of cells present in human aortic valves. METHODS AND RESULTS: Aortic valve stenosis is an active atheroinflammatory disease, characterized by the accumulation of inflammatory cells and the neovascularization of the valves. A total of 85 stenotic valves and 20 control valves were obtained during valve replacement surgery. The results of immunohistochemistry analysis revealed stenotic aortic valves that contained 3 types of neovessels: small microvessels, medium microvessels, and organized arterioles. The distribution density of the neovessels was significantly higher in stenotic valves than in control valves (P<0.001) and correlated positively with valvular calcification gradus (r=0.26, P=0.02) and mast cell density (r=0.38, P<0.001). In the neovascularized areas of stenotic aortic valves, mast cells contained vascular endothelial growth factor and were degranulated, indicating their activation. The stimulation of cultured myofibroblasts derived from aortic valves with a mast cell-preconditioned medium, hypoxic culture conditions, or tobacco smoke all induced vascular endothelial growth factor secretion in the myofibroblasts. Finally, mast cell tryptase was able to degrade the antiangiogenic molecule endostatin in vitro. CONCLUSIONS: Mast cells and myofibroblasts may accelerate the progression of aortic valve stenosis by altering the balance between angiogenic and antiangiogenic factors in the valves, thus promoting valvular neovascularization.

ACE inhibition attenuates uremia-induced aortic valve thickening in a novel mouse model.

BACKGROUND: We examined whether impaired renal function causes thickening of the aortic valve leaflets in hyperlipidemic apoE-knockout (apoE-/-) mice, and whether the putative effect on the aortic valves could be prevented by inhibiting the angiotensin-converting enzyme (ACE) with enalapril. METHODS: Thickening of the aortic valve leaflets in apoE-/- mice was induced by producing mild or moderate chronic renal failure resulting from unilateral nephrectomy (1/2 NX, n = 18) or subtotal nephrectomy (5/6 NX, n = 22), respectively. Additionally, the 5/6 NX mice were randomized to no treatment (n = 8) or enalapril treatment (n = 13). The maximal thickness of each leaflet was measured from histological sections of the aortic roots. RESULTS: Leaflet thickness was significantly greater in the 5/6 NX mice than in the 1/2 NX mice (P = 0.030) or the unoperated mice (P = 0.003). The 5/6 NX mice treated with enalapril had significantly thinner leaflets than did the untreated 5/6 NX mice (P = 0.014). CONCLUSION: Moderate uremia causes thickening of the aortic valves in apoE-/- mice, which can be attenuated by ACE inhibition. The nephrectomized apoE-/- mouse constitutes a new model for investigating the mechanisms of uremia-induced aortic valve disease, and also provides an opportunity to study its pharmacologic prevention.

Accumulation of cholesterol precursors and plant sterols in human stenotic aortic valves.

The pathogenesis of aortic valve stenosis (AS) is characterized by the accumulation of LDL-derived cholesterol in the diseased valves. Since LDL particles also contain plant sterols, we investigated whether plant sterols accumulate in aortic valve lesions. Serum samples were collected from 82 patients with severe AS and from 12 control subjects. Aortic valves were obtained from a subpopulation of 21 AS patients undergoing valve surgery and from 10 controls. Serum and valvular total cholesterol and noncholesterol sterols were measured by gas-liquid chromatography. Noncholesterol sterols, including both cholesterol precursors and sterols reflecting cholesterol absorption, were detected in serum samples and aortic valves. The higher the ratios to cholesterol of the cholesterol precursors and absorption markers in serum, the higher their ratios in the stenotic aortic valves (r=0.74, P<0.001 for lathosterol and r=0.88, P<0.001 for campesterol). The valvular ratio to cholesterol of lathosterol correlated negatively with the aortic valve area (r= -0.47, P=0.045), suggesting attenuation of cholesterol synthesis with increasing severity of AS. The higher the absorption of cholesterol, the higher the plant sterol contents in stenotic aortic valves. These findings suggest that local accumulation of plant sterols and cholesterol precursors may participate in the pathobiology of aortic valve disease.

Complement system is activated in stenotic aortic valves.

OBJECTIVE: To examine the role of the complement system, a source of powerful proinflammatory mediators, in aortic valve stenosis (AS). METHODS AND RESULTS: Stenotic aortic valves (n=24) were obtained at valve replacement surgery, and non-stenotic (n=12) and early sclerotic (n=4) valves at cardiac transplantations. The terminal complement complex C5b-9 was stained by immunohistochemistry. Expression of the anaphylatoxin receptors C3aR and C5aR was studied in the valves by immunohistochemistry and RT-PCR, and in isolated valve myofibroblasts after stimulation with potential AS-accelerating factors (TNF-alpha and cigarette smoke) by RT-PCR. Cultured myofibroblasts were exposed to C3a, and their secretion of proinflammatory cytokines was assessed by ELISA. C5b-9 was found already in early aortic valve lesions, and its deposition was augmented in advanced stenotic valves. In stenotic valves, expression of C3aR mRNA was upregulated (p<0.05) and strong staining of C3aR and C5aR was detected. Myofibroblasts in stenotic, but not in control valves, expressed C3aR, and, in isolated myofibroblasts, TNF-alpha and cigarette smoke induced C3aR mRNA expression (p<0.05 for both). Stimulation of myofibroblasts with C3a resulted in enhanced secretion of MCP-1 (p<0.001), IL-6 (p=0.003), and IL-8 (p=0.03). CONCLUSIONS: In stenotic aortic valves, complement is activated leading to generation of the anaphylatoxins C3a and C5a. Upregulation of C3aR in the valves as a result of inflammation and external risk factors, such as cigarette smoke, leads to an inflammatory response in aortic valve myofibroblasts. Complement activation in stenotic valves emerges as a novel pathogenic component of AS and may serve as a therapeutic target in this disease.

Aortic valve stenosis: an active atheroinflammatory process.

PURPOSE OF REVIEW: To summarize the current understanding of the pathobiology of aortic valve stenosis and portray the major advances in this field. RECENT FINDINGS: Stenotic aortic valves are characterized by atherosclerosis-like lesions, consisting of activated inflammatory cells, including T lymphocytes, macrophages, and mast cells, and of lipid deposits, calcific nodules, and bone tissue. Active mediators of calcification and cells with osteoblast-like activity are present in diseased valves. Extracellular matrix remodeling, including collagen synthesis and elastin degradation by matrix metalloproteinases and cathepsins, contributes to leaflet stiffening. In experimental animals, hypercholesterolemia induces calcification and bone formation in aortic valves, which can be inhibited by statin treatment. The potential of statins to retard progression of aortic valve stenosis has also been recognized in clinical studies; however, further prospective trials are needed. Angiotensin II-forming enzymes are upregulated in stenotic valves. Angiotensin II may participate in profibrotic progression of aortic valve stenosis and may serve as a possible therapeutic target. SUMMARY: Recent findings regarding the interaction of inflammatory cells, lipids, mediators of calcification, and renin-angiotensin system in stenotic valves support the current opinion of aortic valve stenosis being an actively regulated disease, potentially amenable to targeted molecular therapy. Evidence from prospective clinical studies is eagerly awaited.

Increased expression of profibrotic neutral endopeptidase and bradykinin type 1 receptors in stenotic aortic valves.

AIMS: In aortic stenosis (AS), adverse remodelling of the valves may depend on altered local regulation of pro- and antifibrotic systems. We have recently shown that angiotensin-converting enzyme (ACE), which generates profibrotic angiotensin II and inactivates antifibrotic bradykinin (BK), is upregulated in stenotic aortic valves. Here, we analyse the expression of neutral endopeptidase (NEP), another profibrotic and BK-degrading enzyme, and of BK receptors in aortic valves in AS. METHODS AND RESULTS: Stenotic aortic valves (n = 86) were obtained at valve replacement surgery and control valves (n = 13) at cardiac transplantation. Expression levels of NEP and BK type 1 and 2 receptors (BK-1R and BK-2R) in aortic valves and in isolated valvular myofibroblasts were analysed by real-time PCR and immunohistochemistry, and NEP activity was quantified by autoradiography. NEP, BK-1R, and BK-2R mRNA levels were higher in stenotic than in non-stenotic valves (P < 0.05 for each) and the respective proteins localized to valvular endothelial cells and myofibroblasts. In stenotic valves, the proteolytic activity of NEP was significantly increased (4.5-fold, P < 0.001), and tumour necrosis factor-alpha induced the expression of NEP in cultured myofibroblasts. Finally, treatment of cultured myofibroblasts with an NEP inhibitor (phosphoramidon) downregulated the expression of profibrotic transforming growth factor-beta1, whereas addition of BK decreased the expression of collagens I and III which was reversed by a BK-2R antagonist. CONCLUSION: NEP activity is increased in stenotic aortic valves in parallel with increased expression of BK-receptors. The upregulation of NEP and BK-1R have the potential to promote valvular fibrosis and remodelling while the increase in BK-2R may represent a compensatory antifibrotic response. These findings add novel pathogenic insight and raise potential new therapeutic targets in AS.

Receptors for the anaphylatoxins C3a and C5a are expressed in human atherosclerotic coronary plaques.

The anaphylatoxins C3a and C5a are potent chemotactic and pro-inflammatory peptides that are released during complement activation, and recent clinical work have suggested them a role in acute coronary events. Here we studied whether human coronary plaques express anaphylatoxin receptors C3aR and C5aR, i.e. whether they have the potential to respond to anaphylatoxins. For this purpose, both normal (n=14) and atherosclerotic (n=20) human coronary artery samples were collected for histological and PCR analyses. Immunohistochemistry demonstrated that in atherosclerotic, but not in normal intimas, C3aR and C5aR were present. Consistently, PCR analysis showed that the expression of both receptors was >5-fold increased in the atherosclerotic plaques (p<0.01). Double immunofluorescence stainings revealed that in the plaques the principal cells expressing both C3aR and C5aR were macrophages. Moreover, T cells expressed C5aR and a small fraction of them also expressed C3aR, the mast cells expressed C5aR, whereas endothelial cells and subendothelial smooth muscle cells expressed both C3aR and C5aR. In conclusion, the presence of receptors for anaphylatoxins in human coronary plaques suggests that anaphylatoxins activate coronary plaques, and points the complement system as a potential therapeutic target in attempts to stabilize them.

Increased circulating concentrations and augmented myocardial extraction of osteoprotegerin in heart failure due to left ventricular pressure overload.

BACKGROUND: Osteoprotegerin (OPG) and the receptor activator of nuclear factor-kappaB ligand (RANKL), two cytokines regulating bone remodeling, have recently been raised as potential pathogenetic factors in cardiovascular diseases. We have studied circulating and myocardial OPG and RANKL in patients having severe aortic stenosis (AS) with or without heart failure (HF). METHODS: We studied 131 adults with AS. Blood was sampled from the aortic root, coronary sinus, and femoral vein at cardiac catheterization. LV myocardial biopsies were taken at surgery. Plasma OPG and soluble (s)RANKL were analyzed by ELISA, and myocardial OPG and RANKL by RT-PCR and immunohistochemistry. RESULTS: Circulating OPG was elevated in AS patients with HF, the association being independent of age, sex, and presence of coronary artery disease (beta=0.17, p=0.033). Elevated plasma OPG decreased after valve replacement in patients with preoperative HF (p=0.0005). Relative to its concentration in the aortic root, plasma OPG was reduced in the coronary sinus (p<0.05) and in the femoral vein (p<0.001), these arteriovenous gradients being accentuated in HF (p=0.003). CONCLUSIONS: HF due to LV pressure overload in AS increases circulating OPG and augments OPG extraction by the heart and peripheral tissues. OPG may be involved in the pathogenesis of HF and could serve as a useful biomarker in HF due to LV pressure overload.

Increased expression of elastolytic cathepsins S, K, and V and their inhibitor cystatin C in stenotic aortic valves.

OBJECTIVE: To investigate the possible role of elastolytic cathepsins S, K, and V and their endogenous inhibitor cystatin C in adverse extracellular matrix remodeling of stenotic aortic valves. METHODS AND RESULTS: Stenotic aortic valves were collected at valve replacement surgery and control valves at cardiac transplantations. The expression of cathepsins S, K, and V and cystatin C was studied by conventional and real-time polymerase chain reaction and by immunohistochemistry. Total cathepsin activity in the aortic valves was quantified by a fluorometric microassay. When compared with control valves, stenotic valves showed increased mRNA expression of cathepsins S, K, and V (P<0.05 for each) and a higher total cathepsin activity (P<0.001). In stenotic valves, cystatin C mRNA was increased (P<0.05), and cystatin C protein was found particularly in areas with infiltrates of inflammatory cells. Both cathepsin S and cystatin C were present in bony areas of the valves, whereas cathepsin V localized to endothelial cells in areas rich of neovascularization. Incubation of thin sections of aortic valves with cathepsins S, K, and V resulted in severe disruption of elastin fibers, and this cathepsin effect could be blocked by adding cystatin C to the incubation system. CONCLUSIONS: Stenotic aortic valves show increased expression and activity of elastolytic cathepsins S, K, and V. These cathepsins may accelerate the destruction of aortic valvular extracellular matrix, so promoting the progression of aortic stenosis.

Possible role for mast cell-derived cathepsin G in the adverse remodelling of stenotic aortic valves.

AIMS: Aortic stenosis (AS) is characterized by extensive remodelling of the valves, including infiltration of inflammatory cells, extracellular matrix degradation, and fibrosis. The molecular mechanisms behind this adverse remodelling have remained obscure. In this article, we study whether cathepsin G, an angiotensin II (Ang II)-forming elastolytic enzyme, contributes to progression of AS. METHODS AND RESULTS: Stenotic aortic valves (n = 86) and control valves (n = 17) were analysed for cathepsin G, transforming growth factor-beta1 (TGF-beta1), and collagens I and III with RT-PCR and immunohistochemistry. Valvular collagen/elastin ratio was quantified by histochemistry. In stenotic valves, cathepsin G was present in mast cells and showed increased expression (P < 0.001), which correlated positively (P < 0.001) with the expression levels of TGF-beta1 and collagens I and III. TGF-beta1 was also present in mast cell-rich areas and cathepsin G induced losartan-sensitive TGF-beta1 expression in cultured fibroblasts. Collagen/elastin ratio was increased in stenotic valves (P < 0.001) and correlated positively with smoking (P = 0.02). Nicotine in cigarette smoke activated mast cells and induced TGF-beta1 expression in cultured fibroblasts. Fragmented elastin was observed in stenotic valves containing activated cathepsin G-secreting mast cells and in normal valves treated with cathepsin G. CONCLUSION: In stenotic aortic valves, mast cell-derived cathepsin G may cause adverse valve remodelling and AS progression.