Mixture modeling for joint analysis of survival, discrete, and continuous data

Mixture modeling is commonly used to model categorical latent variables that represent subpopulations in which population membership is unknown but can be inferred from the data. In relatively recent years, the potential of finite mixture models has been applied in time-to-event data. However, the commonly used survival mixture model assumes that the effects of the covariates involved in failure times differ across latent classes, but the covariate distribution is homogeneous. The aim of this dissertation is to develop a method to examine time-to-event data in the presence of unobserved heterogeneity under a framework of mixture modeling. A joint model is developed to incorporate the latent survival trajectory along with the observed information for the joint analysis of a time-to-event variable, its discrete and continuous covariates, and a latent class variable. It is assumed that the effects of covariates on survival times and the distribution of covariates vary across different latent classes. The unobservable survival trajectories are identified through estimating the probability that a subject belongs to a particular class based on observed information. We applied this method to a Hodgkin lymphoma study with long-term follow-up and observed four distinct latent classes in terms of long-term survival and distributions of prognostic factors. Our results from simulation studies and from the Hodgkin lymphoma study demonstrated the superiority of our joint model compared with the conventional survival model. This flexible inference method provides more accurate estimation and accommodates unobservable heterogeneity among individuals while taking involved interactions between covariates into consideration.^

Flower and seed biomass, and germination rate of arctic tundra plants in response to long term experimental warming

We provide new information on changes in tundra plant sexual reproduction in response to long-term (12 years) experimental warming in the High Arctic. Open-top chambers (OTCs) were used to increase growing season temperatures by 1-2 °C across a range of vascular plant communities. The warming enhanced reproductive effort and success in most species; shrubs and graminoids appeared to be more responsive than forbs. We found that the measured effects of warming on sexual reproduction were more consistently positive and to a greater degree in polar oasis compared with polar semidesert vascular plant communities. Our findings support predictions that long-term warming in the High Arctic will likely enhance sexual reproduction in tundra plants, which could lead to an increase in plant cover. Greater abundance of vegetation has implications for primary consumers - via increased forage availability, and the global carbon budget - as a function of changes in permafrost and vegetation acting as a carbon sink. Enhanced sexual reproduction in Arctic vascular plants may lead to increased genetic variability of offspring, and consequently improved chances of survival in a changing environment. Our findings also indicate that with future warming, polar oases may play an important role as a seed source to the surrounding polar desert landscape.

Long term low latitude and high elevation cosmogenic 3He production rate inferred from a 107 ka-old lava flow in northern Chile; 22°S-3400 m a.s.l

Available geological calibration sites used to estimate the rate at which cosmogenic 3He is produced at the Earth’s surface are mostly clustered in medium to high latitudes. Moreover, most of them have exposure histories shorter than tens of thousands of years. This lack of sites prevents a qualitative assessment of available production models used to convert cosmogenic 3He concentrations into exposure ages and/or denudation rates. It thus limits our ability to take into account the atmospheric, geomagnetic and solar modulation conditions that might have affected the production of cosmogenic nuclides in the past for longer exposure histories and in low latitude regions. We present the cosmogenic 3He production rate inferred from a new geological calibration site located in northern Chile. Five samples were collected on the surface of the largest and best-preserved lava flow of the San Pedro volcano (21.934°S-68.510°W- 3390 m a.s.l), which displays pristine crease-structure features. 40Ar/39Ar dating yield a reliable plateau age of 107±12 ka for the eruption of this lava flow. Eight pyroxene aliquots separated from the surface samples yield a weighted average cosmogenic 3He concentration of 99.3±1.2 Mat.g-1 from which a local cosmogenic 3He production rate of 928±101 at.g-1.yr-1 is calculated. The local production rate is then scaled to a sea level high latitude (SLHL) reference position using different combinations of geographic spatialization schemes, atmosphere models and geomagnetic field reconstructions, yielding SLHL production rates between 103±11 and 130±14 at.g-1.yr-1 consistent with the most recent estimates available from the literature. Finally, we use the same scaling frameworks to re-evaluate the mean global-scale cosmogenic 3He production rate in olivine and pyroxene minerals at 120±16 at.g-1.yr-1 from the compilation of previously published calibration datasets.

Long-term persistence of Mediterranean pine forests in the Duero Basin (central Spain) during the Holocene: The case of Pinus pinaster Aiton

In the southern Duero Basin of central Spain, there are vast areas of aeolian sand sheets and dune fields. A comprehensive survey of the sand quarries in this area identified a number of palaeosols in sedimentary sequences. The identification and AMS radiocarbon dating of soil charcoal fragments collected in these palaeosols indicate the persistence of Pinus pinaster in this area throughout most of the Holocene. Although potential natural vegetation models have usually considered the Pinus pinaster forests in this inland area of artificial origin, soil charcoal analysis provides firm evidence of a natural origin. Our data fit perfectly with the pattern of Holocene vegetation development for inland areas of Iberia, which are characterised by stability of pine forests throughout the Holocene. Finally, the growing body of palaeobotanical evidence from Iberia (macrofossils and pollen) is contributing to improve our knowledge of P. pinaster ecology, showing that this species has been present in most Iberian regions during the Holocene, where it has inhabited areas characterised by a very diverse set of climatic and soil conditions.

Human midbrain precursors activate the expected developmental genetic program and differentiate long-term to functional A9 dopamine neurons in vitro. Enhancement by Bcl-XL

Understanding the molecular programs of the generation of human dopaminergic neurons (DAn) from their ventral mesencephalic (VM) precursors is of key importance for basic studies, progress in cell therapy, drug screening and pharmacology in the context of Parkinson's disease. The nature of human DAn precursors in vitro is poorly understood, their properties unstable, and their availability highly limited. Here we present positive evidence that human VM precursors retaining their genuine properties and long-term capacity to generate A9 type Substantia nigra human DAn (hVM1 model cell line) can be propagated in culture. During a one month differentiation, these cells activate all key genes needed to progress from pro-neural and prodopaminergic precursors to mature and functional DAn. For the first time, we demonstrate that gene cascades are correctly activated during differentiation, resulting in the generation of mature DAn. These DAn have morphological and functional properties undistinguishable from those generated by VM primary neuronal cultures. In addition, we have found that the forced expression of Bcl-XL induces an increase in the expression of key developmental genes (MSX1, NGN2), maintenance of PITX3 expression temporal profile, and also enhances genes involved in DAn long-term function, maintenance and survival (EN1, LMX1B, NURR1 and PITX3). As a result, Bcl-XL anticipates and enhances DAn generation.

Specific therapy regimes could lead to long-term immunological control of HIV

We use mathematical models to study the relationship between HIV and the immune system during the natural course of infection and in the context of different antiviral treatment regimes. The models suggest that an efficient cytotoxic T lymphocyte (CTL) memory response is required to control the virus. We define CTL memory as long-term persistence of CTL precursors in the absence of antigen. Infection and depletion of CD4+ T helper cells interfere with CTL memory generation, resulting in persistent viral replication and disease progression. We find that antiviral drug therapy during primary infection can enable the development of CTL memory. In chronically infected patients, specific treatment schedules, either including deliberate drug holidays or antigenic boosts of the immune system, can lead to a re-establishment of CTL memory. Whether such treatment regimes would lead to long-term immunologic control deserves investigation under carefully controlled conditions.

A joint hazard and time scaling model to compare survival curves.

To provide a more general method for comparing survival experience, we propose a model that independently scales both hazard and time dimensions. To test the curve shape similarity of two time-dependent hazards, h1(t) and h2(t), we apply the proposed hazard relationship, h12(tKt)/ h1(t) = Kh, to h1. This relationship doubly scales h1 by the constant hazard and time scale factors, Kh and Kt, producing a transformed hazard, h12, with the same underlying curve shape as h1. We optimize the match of h12 to h2 by adjusting Kh and Kt. The corresponding survival relationship S12(tKt) = [S1(t)]KtKh transforms S1 into a new curve S12 of the same underlying shape that can be matched to the original S2. We apply this model to the curves for regional and local breast cancer contained in the National Cancer Institute's End Results Registry (1950-1973). Scaling the original regional curves, h1 and S1 with Kt = 1.769 and Kh = 0.263 produces transformed curves h12 and S12 that display congruence with the respective local curves, h2 and S2. This similarity of curve shapes suggests the application of the more complete curve shapes for regional disease as templates to predict the long-term survival pattern for local disease. By extension, this similarity raises the possibility of scaling early data for clinical trial curves according to templates of registry or previous trial curves, projecting long-term outcomes and reducing costs. The proposed model includes as special cases the widely used proportional hazards (Kt = 1) and accelerated life (KtKh = 1) models.

Hippocampal long-term potentiation is impaired in mice lacking brain-derived neurotrophic factor.

Brain-derived neurotrophic factor (BDNF), a member of the nerve growth factor (NGF) gene family, has been shown to influence the survival and differentiation of specific classes of neurons in vitro and in vivo. The possibility that neurotrophins are also involved in processes of neuronal plasticity has only recently begun to receive attention. To determine whether BDNF has a function in processes such as long-term potentiation (LTP), we produced a strain of mice with a deletion in the coding sequence of the BDNF gene. We then used hippocampal slices from these mice to investigate whether LTP was affected by this mutation. Homo- and heterozygous mutant mice showed significantly reduced LTP in the CA1 region of the hippocampus. The magnitude of the potentiation, as well as the percentage of cases in which LTP could be induced successfully, was clearly affected. According to the criteria tested, important pharmacological, anatomical, and morphological parameters in the hippocampus of these animals appear to be normal. These results suggest that BDNF might have a functional role in the expression of LTP in the hippocampus.

Modification of rhodamine staining allows identification of hematopoietic stem cells with preferential short-term or long-term bone marrow-repopulating ability.

We have developed a modified rhodamine (Rho) staining procedure to study uptake and efflux in murine hematopoietic stem cells. Distinct populations of Rho++ (bright), Rho+ (dull), and Rho- (negative) cells could be discriminated. Sorted Rho- cells were subjected to a second Rho staining procedure with the P-glycoprotein blocking agent verapamil (VP). Most cells became Rho positive [Rho-/Rho(VP)+ cells] and some remained Rho negative [Rho-/Rho(VP)- cells]. These cell fractions were characterized by their marrow-repopulating ability in a syngeneic, sex-mismatch transplantation model. Short-term repopulating ability was determined by recipient survival for at least 6 weeks after lethal irradiation and transplantation--i.e., radioprotection. Long-term repopulating ability at 6 months after transplantation was measured by fluorescence in situ hybridization with a Y-chromosome-specific probe, by graft function and recipient survival. Marrow-repopulating cells were mainly present in the small Rho- cell fraction. Transplantation of 30 Rho- cells resulted in 50% radioprotection and > 80% donor repopulation in marrow, spleen, and thymus 6 months after transplantation. Cotransplantation of cells from both fractions in individual mice directly showed that within this Rho- cell fraction, the Rho-/Rho(VP)+ cells exhibited mainly short-term and the Rho-/Rho(VP)- cells exhibited mainly long-term repopulating ability. Our results indicate that hematopoietic stem cells have relatively high P-glycoprotein expression and that the cells responsible for long-term repopulating ability can be separated from cells exhibiting short-term repopulating ability, probably by a reduced mitochondrial Rho-binding capacity.

Preventing Social Death in Long Term Care: Fostering Social Connectivity in the U.S. and The Netherlands. ACES Working Papers, July 2012

Long term care (LTC) is both costly and of increasing concern as baby boomers age and more people live longer with chronic conditions. Today, people receive formal and informal LTC supports in homes, nursing homes, and alternative settings around the world. Where people live and the way LTC is delivered has an important impact on whether person’s receiving care thrive as they age. This paper is about how different LTC environments in the U.S. and The Netherlands foster or impede social connectivity, suggesting that quality of life will be impeded and types of social death, or disconnection from social life, more often the result in environments that limit choice and self determination, limit access to privacy and social connection, and limit access to reciprocal exchanges, a key component of participating in relationships typical of the concept of “the gift” introduced by anthropologist Marcel Mauss in 1954. Building on ethnographic data from a 15-month study of LTC in The Netherlands and a review of staffing practices in LTC environments in the U.S. and The Netherlands, I will explore concepts of reciprocity and social connectivity impacted by various LTC environments in two countries known to experiment with different models of care. This research builds on social constructivist notions of death and dying explored throughout this edited volume and adds to this effort examination of social death in anthropological perspective.

Long Term Outcomes Following Catheter Ablation of Ventricular Tachycardia in Patients with and without Structural Heart Disease.

BACKGROUND Long-term outcomes following ventricular tachycardia (VT) ablation are sparsely described. OBJECTIVES To describe long term prognosis following VT ablation in patients with no structural heart disease (no SHD), ischemic (ICM) and non-ischemic cardiomyopathy (NICM). METHODS Consecutive patients (n=695; no SHD 98, ICM 358, NICM 239 patients) ablated for sustained VT were followed for a median of 6 years. Acute procedural parameters (complete success [non-inducibility of any VT]) and outcomes after multiple procedures were reported. RESULTS Compared with patients with no SHD or NICM, ICM patients were the oldest, had more males, lowest left ventricular ejection fraction (LVEF), highest drug failures, VT storms and number of inducible VTs. Complete procedure success was highest in no SHD, compared ICM and NICM patients (79%, 56%, 60% respectively, P<0.001). At 6 years, ventricular arrhythmia (VA)-free survival was highest in no SHD (77%) than ICM (54%) and NICM (38%, P<0.001) and overall survival was lowest in ICM (48%), followed by NICM (74%) and no SHD patients (100%, P<0.001). Age, LVEF, presence of SHD, acute procedural success (non-inducibility of any VT), major complications, need for non-radiofrequency ablation modalities, and VA recurrence were independently associated with all cause mortality. CONCLUSIONS Long term follow up following VT ablation shows excellent prognosis in the absence of SHD, highest VA recurrence and transplantation in NICM and highest mortality in patients with ICM. The extremely low mortality for those without SHD suggests that VT in this population is very rarely an initial presentation of a myopathic process.

The 2014 chikungunya virus outbreak in the U.S. Virgin Islands: epidemiology, long-term health outcomes, and economic burden

Thesis (Ph.D.)--University of Washington, 2016-06

Secondary prevention of cardiovascular events with long-term pravastatin in patients with diabetes or impaired fasting glucose - Results from the LIPID trial

OBJECTIVE- Diabetes, a major health problem worldwide, increases the risk of cardiovascular disease and its associated mortality. Evidence of the overall benefits of lipid modification in this area is needed. RESEARCH DESIGN AND METHODS- The Long-Term Intervention with Pravastatin in Ischemic Disease (LIPID) trial showed that cholesterol-lowering treatment with pravastatin reduced mortality and coronary heart disease (CHD) events in 9,014 patients aged 31-75 years with CHD and total cholesterol 4.0-7.0 mmol/l. We measured the effects of pravastatin therapy, 40 mg/day over 6.0 years, on the risk of CHD death or nonfatal myocardial infarction and other cardiovascular outcomes in 1,077 LIPID patients with diabetes and 940 patients with impaired fasting glucose (IFG). RESULTS- in patients allocated to placebo, the risk of a major CHD event was 61% higher in patients with diabetes and 23% higher in the IFG group than in patients with normal fasting glucose, and the risk of any cardiovascular event was 37% higher in the diabetic group and 19% higher in the IFG group. Pravastatin therapy reduced the risk of a major CHD event overall from 15.9 to 12.3% (relative risk reduction [RRR] 24%, P < 0.001) and from 23.4 to 19.6% in the diabetic group (19%, P = 0.11); in the diabetic group, the reduction was not significantly different from the reductions in the other groups. Pravastatin reduced the risk of any cardiovascular event from 52.7 to 45.2% (21%, P < 0.008) in patients With diabetes and from 45.7 to 37.1% (26%, P = 0.003) in the IFG group. Pravastatin reduced the risk of stroke from 9.9 to 6.3% in the diabetic group (RRR 39%, Cl 7-61%, P = 0.02) and from 5.4 to 3.4% in the IFG group (RRR 42%, Cl -9 to 69%, P = 0.09). Pravastatin did not reduce the incidence of diabetes. Over 6 years, pravastatin therapy prevented one major,CHD event (CHD death or nonfatal myocardial infarction) in 23 patients with IFG and 18 patients with diabetes. A meta-analysis of other major trials confirmed the high absolute risks of diabetes and IFG and the absolute benefits of statin therapy in these patients. CONCLUSIONS- Cholesterol-lowering treatment with pravastatin therapy prevents cardiovascular events, including stroke, in patients with diabetes or IFG and established CHD.

Beyond verbal fluency: Investigating the long-term effects of bilateral subthalamic (STN) deep brain stimulation (DBS) on language in two cases

Cognitive functioning has been described as largely impervious to chronic STN-DBS administered over 12-month periods. In relation to the domain of language, however, the effects of STN-DBS are yet to be thoroughly delineated. Verbal fluency tasks represent an almost exclusively applied index of linguistic proficiency relative to neuropsychological research within this population. Comprehensive investigations of the impact of STN-DBS on language function, however, have never been undertaken. The more precise elucidation of the role of the STN in the mediation of language processes, by way of assessments which probe language comprehension and production mechanisms, served as the primary focus of this research. Longitudinal analysis also afforded consideration of the way in which cognitive-linguistic circuits respond to STN-DBS over time. Bilateral STN-DBS primarily effected clinically reliable fluctuations (i.e., both improvements and declines) in performance in both subjects on tasks demanding cognitive-linguistic flexibility in the formulation and comprehension of complex language. Of particular note, both subjects demonstrated a cumulative increase in the proportion of reliable post-operative improvements achieved over time. The findings of this research lend support to models of subcortical participation in language which endorse a role for the STN, and suggest that bilateral STN-DBS may serve to enhance the proficiency of basal ganglia-thalamocortical linguistic circuits over time.

Increase of a Caribbean leatherback turtle Dermochelys coriacea nesting population linked to long-term nest protection

The leatherback turtle Dermochelys coriacea is considered to be at serious risk of global extinction, despite ongoing conservation efforts. Intensive long-term monitoring of a leatherback nesting population on Sandy Point (St. Croix, US Virgin Islands) offers a unique opportunity to quantify basic population parameters and evaluate effectiveness of nesting beach conservation practices. We report a significant increase in the number of females nesting annually from ca. 18-30 in the 1980s to 186 in 2001, with a corresponding increase in annual hatchling production from ca. 2000 to over 49,000. We then analyzed resighting data from 1991 to 2001 with an open robust-design capture-mark-recapture model to estimate annual nester survival and adult abundance for this population. The expected annual survival probability was estimated at ca. 0.893 (95% CL 0.87-0.92) and the population was estimated to be increasing ca. 13% pa since the early 1990s. Taken together with DNA fingerprinting that identify mother-daughter relations, our findings suggest that the increase in the size of the nesting population since 1991 was probably due to an aggressive program of beach protection and egg relocation initiated more than 20 years ago. Beach protection and egg relocation provide a simple and effective conservation strategy for this Northern Caribbean nesting population as long as adult survival at sea remains relatively high. (c) 2005 Elsevier Ltd. All rights reserved.