A Generic Framework for Hidden Markov Models on Biomedical Data

Background: Biomedical data are usually collections of longitudinal data assessed at certain points in time. Clinical observations assess the presences and severity of symptoms, which are the basis for description and modeling of disease progression. Deciphering potential underlying unknowns solely from the distinct observation would substantially improve the understanding of pathological cascades. Hidden Markov Models (HMMs) have been successfully applied to the processing of possibly noisy continuous signals. The aim was to improve the application HMMs to multivariate time-series of categorically distributed data. Here, we used HHMs to study prediction of the loss of free walking ability as one major clinical deterioration in the most common autosomal dominantly inherited ataxia disorder worldwide. We used HHMs to investigate the prediction of loss of the ability to walk freely, representing a major clinical deterioration in the most common autosomal-dominant inherited ataxia disorder worldwide. Results: We present a prediction pipeline which processes data paired with a configuration file, enabling to construct, validate and query a fully parameterized HMM-based model. In particular, we provide a theoretical and practical framework for multivariate time-series inference based on HMMs that includes constructing multiple HMMs, each to predict a particular observable variable. Our analysis is done on random data, but also on biomedical data based on Spinocerebellar ataxia type 3 disease. Conclusions: HHMs are a promising approach to study biomedical data that naturally are represented as multivariate time-series. Our implementation of a HHMs framework is publicly available and can easily be adapted for further applications

Interactive cohort exploration for spinocerebellar ataxias using synthetic cohort data for visualization

Motivation: Visualization of data is a crucial step to understanding and deriving hypotheses from clinical data. However, for clinicians, visualization often comes with great effort due to the lack of technical knowledge about data handling and visualization. The application offers an easy-to-use solution with an intuitive design that enables various kinds of plotting functions. The aim was to provide an intuitive solution with a low entrance barrier for clinical users. Little to no onboarding is required before creating plots, while the complexity of questions can grow up to specific corner cases. To allow for an easy start and testing with SCAview, we incorporated a synthetic cohort dataset based on real data of rare neurological movement disorders: the most common autosomal-dominantly inherited spinocerebellar ataxias (SCAs) type 1, 2, 3, and 6 (SCA1, 2, 3 and 6). Methods: We created a Django-based backend application that serves the data to a React-based frontend that uses Plotly for plotting. A synthetic cohort was created to deploy a version of SCAview without violating any data protection guidelines. Here, we added normal distributed noise to the data and therefore prevent re-identification while keeping distributions and general correlations. Results: This work presents SCAview, an user-friendly, interactive web-based service that enables data visualization in a clickable interface allowing intuitive graphical handling that aims to enable data visualization in a clickable interface. The service is deployed and can be tested with a synthetic cohort created based on a large, longitudinal dataset from observational studies in the most common SCAs

The DEEP3 Galaxy Redshift Survey: The Impact of Environment on the Size Evolution of Massive Early-type Galaxies at Intermediate Redshift

Using data drawn from the DEEP2 and DEEP3 Galaxy Redshift Surveys, we investigate the relationship between the environment and the structure of galaxies residing on the red sequence at intermediate redshift. Within the massive (10 < log(M*/Msun) < 11) early-type population at 0.4 < z <1.2, we find a significant correlation between local galaxy overdensity (or environment) and galaxy size, such that early-type systems in higher-density regions tend to have larger effective radii (by ~0.5 kpc or 25% larger) than their counterparts of equal stellar mass and Sersic index in lower-density environments. This observed size-density relation is consistent with a model of galaxy formation in which the evolution of early-type systems at z < 2 is accelerated in high-density environments such as groups and clusters and in which dry, minor mergers (versus mechanisms such as quasar feedback) play a central role in the structural evolution of the massive, early-type galaxy population.Comment: 11 pages, 5 figures, 2 tables; resubmitted to MNRAS after addressing referee's comments (originally submitted to journal on August 16, 2011

Variants of Rab GTPase–Effector Binding Protein-2 Cause Variation in the Collateral Circulation and Severity of Stroke

The extent (number and diameter) of collateral vessels varies widely and is a major determinant, along with arteriogenesis (collateral remodeling), of variation in severity of tissue injury following large artery occlusion. Differences in genetic background underlie the majority of the variation in collateral extent in mice, through alterations in collaterogenesis (embryonic collateral formation). In brain and other tissues, ~80% of the variation in collateral extent among different mouse strains has been linked to a region on chromosome 7. We recently used congenic (CNG) fine-mapping of C57BL/6 (B6, high extent) and BALB/cBy (BC, low extent) mice to narrow the region to a 737 Kb locus, Dce1. Herein, we report the causal gene

CANDELS: The correlation between galaxy morphology and star formation activity at z~2

We discuss the state of the assembly of the Hubble Sequence in the mix of bright galaxies at redshift 1.4< z \le 2.5 with a large sample of 1,671 galaxies down to H_{AB}~26, selected from the HST/ACS and WFC3 images of the GOODS--South field obtained as part of the GOODS and CANDELS observations. We investigate the relationship between the star formation properties and morphology using various parametric diagnostics, such as the Sersic light profile, Gini (G), M_{20}, Concentration (C), Asymmetry (A) and multiplicity parameters. Our sample clearly separates into massive, red and passive galaxies versus less massive, blue and star forming ones, and this dichotomy correlates very well with the galaxies' morphological properties. Star--forming galaxies show a broad variety of morphological features, including clumpy structures and bulges mixed with faint low surface brightness features, generally characterized by disky-type light profiles. Passively evolving galaxies, on the other hand, very often have compact light distribution and morphology typical of today's spheroidal systems. We also find that artificially redshifted local galaxies have a similar distribution with z~2galaxies in a G-M_{20} plane. Visual inspection between the rest-frame optical and UV images show that there is a generally weak morphological k-correction for galaxies at z~2, but the comparison with non-parametric measures show that galaxies in the rest-frame UV are somewhat clumpier than rest-frame optical. Similar general trends are observed in the local universe among massive galaxies, suggesting that the backbone of the Hubble sequence was already in place at z~2.Comment: 22 pages, 19 figures, ApJ accepted (added 3 references

Rationale, description and baseline findings of a community-based prospective cohort study of kidney function amongst the young rural population of Northwest Nicaragua.

BACKGROUND: An epidemic of Mesoamerican Nephropathy (MeN) is killing thousands of agricultural workers along the Pacific coast of Central America, but the natural history and aetiology of the disease remain poorly understood. We have recently commenced a community-based longitudinal study to investigate Chronic Kidney Disease (CKD) in Nicaragua. Although logistically challenging, study designs of this type have the potential to provide important insights that other study designs cannot. In this paper we discuss the rationale for conducting this study and summarize the findings of the baseline visit. METHODS: The baseline visit of the community-based cohort study was conducted in 9 communities in the North Western Nicaragua in October and November 2014. All of the young men, and a random sample of young women (aged 18-30) without a pre-existing diagnosis of CKD were invited to participate. Glomerular filtration rate (eGFR) was estimated with CKD-EPI equation, along with clinical measurements, questionnaires, biological and environmental samples to evaluate participants' exposures to proposed risk factors for MeN. RESULTS: We identified 520 young adults (286 males and 234 females) in the 9 different communities. Of these, 16 males with self-reported CKD and 5 females with diagnoses of either diabetes or hypertension were excluded from the study population. All remaining 270 men and 90 women, selected at random, were then invited to participate in the study; 350 (97%) agreed to participate. At baseline, 29 (11%) men and 1 (1%) woman had an eGFR <90 mL/min/1.73 m2. CONCLUSION: Conducting a community based study of this type requires active the involvement of communities and commitment from local leaders. Furthermore, a research team with strong links to the area and broad understanding of the context of the problem being studied is essential. The key findings will arise from follow-up, but it is striking that 5% of males under aged 30 had to be excluded because of pre-existing kidney disease, and that despite doing so 11% of males had an eGFR <90 mL/min/1.73 m2 at baseline

Structural Evolution of Early-type Galaxies to z=2.5 in CANDELS

Projected axis ratio measurements of 880 early-type galaxies at redshifts 1<z<2.5 selected from CANDELS are used to reconstruct and model their intrinsic shapes. The sample is selected on the basis of multiple rest-frame colors to reflect low star-formation activity. We demonstrate that these galaxies as an ensemble are dust-poor and transparent and therefore likely have smooth light profiles, similar to visually classified early-type galaxies. Similar to their present-day counterparts, the z>1 early-type galaxies show a variety of intrinsic shapes; even at a fixed mass, the projected axis ratio distributions cannot be explained by the random projection of a set of galaxies with very similar intrinsic shapes. However, a two-population model for the intrinsic shapes, consisting of a triaxial, fairly round population, combined with a flat (c/a~0.3) oblate population, adequately describes the projected axis ratio distributions of both present-day and z>1 early-type galaxies. We find that the proportion of oblate versus triaxial galaxies depends both on the galaxies' stellar mass, and - at a given mass - on redshift. For present-day and z<1 early-type galaxies the oblate fraction strongly depends on galaxy mass. At z>1 this trend is much weaker over the mass range explored here (10^10<M*/M_sun<10^11), because the oblate fraction among massive (M*~10^11 M_sun) was much higher in the past: 0.59+-0.10 at z>1, compared to 0.20+-0.02 at z~0.1. In contrast, the oblate fraction among low-mass early-type galaxies (log(M*/M_sun)1 to 0.72+-0.06 at z=0. [Abridged]Comment: accepted for publication in ApJ; 14 pages; 10 figures; 4 table

Prospectus, November 21, 1988

https://spark.parkland.edu/prospectus_1988/1029/thumbnail.jp