Browsing by Subject "Epidemiologic Methods"

Now showing 1 - 5 of 5

Open Access
Inference for nonlinear epidemiological models using genealogies and time series.
(PLoS Comput Biol, 2011-08) Rasmussen, David A; Ratmann, Oliver; Koelle, Katia
Phylodynamics - the field aiming to quantitatively integrate the ecological and evolutionary dynamics of rapidly evolving populations like those of RNA viruses - increasingly relies upon coalescent approaches to infer past population dynamics from reconstructed genealogies. As sequence data have become more abundant, these approaches are beginning to be used on populations undergoing rapid and rather complex dynamics. In such cases, the simple demographic models that current phylodynamic methods employ can be limiting. First, these models are not ideal for yielding biological insight into the processes that drive the dynamics of the populations of interest. Second, these models differ in form from mechanistic and often stochastic population dynamic models that are currently widely used when fitting models to time series data. As such, their use does not allow for both genealogical data and time series data to be considered in tandem when conducting inference. Here, we present a flexible statistical framework for phylodynamic inference that goes beyond these current limitations. The framework we present employs a recently developed method known as particle MCMC to fit stochastic, nonlinear mechanistic models for complex population dynamics to gene genealogies and time series data in a Bayesian framework. We demonstrate our approach using a nonlinear Susceptible-Infected-Recovered (SIR) model for the transmission dynamics of an infectious disease and show through simulations that it provides accurate estimates of past disease dynamics and key epidemiological parameters from genealogies with or without accompanying time series data.
Open Access
Learning from 2523 trauma deaths in India- opportunities to prevent in-hospital deaths.
(BMC health services research, 2017-02-16) Roy, Nobhojit; Kizhakke Veetil, Deepa; Khajanchi, Monty Uttam; Kumar, Vineet; Solomon, Harris; Kamble, Jyoti; Basak, Debojit; Tomson, Göran; von Schreeb, Johan
A systematic analysis of trauma deaths is a step towards trauma quality improvement in Indian hospitals. This study estimates the magnitude of preventable trauma deaths in five Indian hospitals, and uses a peer-review process to identify opportunities for improvement (OFI) in trauma care delivery.All trauma deaths that occurred within 30 days of hospitalization in five urban university hospitals in India were retrospectively abstracted for demography, mechanism of injury, transfer status, injury description by clinical, investigation and operative findings. Using mixed methods, they were quantitatively stratified by the standardized Injury Severity Score (ISS) into mild (1-8), moderate (9-15), severe (16-25), profound (26-75) ISS categories, and by time to death within 24 h, 7, or 30 days. Using peer-review and Delphi methods, we defined optimal trauma care within the Indian context and evaluated each death for preventability, using the following categories: Preventable (P), Potentially preventable (PP), Non-preventable (NP) and Non-preventable but care could have been improved (NPI).During the 18 month study period, there were 11,671 trauma admissions and 2523 deaths within 30 days (21.6%). The overall proportion of preventable deaths was 58%, among 2057 eligible deaths. In patients with a mild ISS score, 71% of deaths were preventable. In the moderate category, 56% were preventable, and 60% in the severe group and 44% in the profound group were preventable. Traumatic brain injury and burns accounted for the majority of non-preventable deaths. The important areas for improvement in the preventable deaths subset, inadequacies in airway management (14.3%) and resuscitation with hemorrhage control (16.3%). System-related issues included lack of protocols, lack of adherence to protocols, pre-hospital delays and delays in imaging.Fifty-eight percent of all trauma deaths were classified as preventable. Two-thirds of the deaths with injury severity scores of less than 16 were preventable. This large subgroup of Indian urban trauma patients could possibly be saved by urgent attention and corrective action. Low-cost interventions such as airway management, fluid resuscitation, hemorrhage control and surgical decision-making protocols, were identified as OFI. Establishment of clinical protocols and timely processes of trauma care delivery are the next steps towards improving care.
Open Access
Rates of coalescence for common epidemiological models at equilibrium.
(J R Soc Interface, 2012-05-07) Koelle, Katia; Rasmussen, David A
Coalescent theory provides a mathematical framework for quantitatively interpreting gene genealogies. With the increased availability of molecular sequence data, disease ecologists now regularly apply this body of theory to viral phylogenies, most commonly in attempts to reconstruct demographic histories of infected individuals and to estimate parameters such as the basic reproduction number. However, with few exceptions, the mathematical expressions at the core of coalescent theory have not been explicitly linked to the structure of epidemiological models, which are commonly used to mathematically describe the transmission dynamics of a pathogen. Here, we aim to make progress towards establishing this link by presenting a general approach for deriving a model's rate of coalescence under the assumption that the disease dynamics are at their endemic equilibrium. We apply this approach to four common families of epidemiological models: standard susceptible-infected-susceptible/susceptible-infected-recovered/susceptible-infected-recovered-susceptible models, models with individual heterogeneity in infectivity, models with an exposed but not yet infectious class and models with variable distributions of the infectious period. These results improve our understanding of how epidemiological processes shape viral genealogies, as well as how these processes affect levels of viral diversity and rates of genetic drift. Finally, we discuss how a subset of these coalescent rate expressions can be used for phylodynamic inference in non-equilibrium settings. For the ones that are limited to equilibrium conditions, we also discuss why this is the case. These results, therefore, point towards necessary future work while providing intuition on how epidemiological characteristics of the infection process impact gene genealogies.
Open Access
The effect of involuntary job loss on smoking intensity and relapse.
(Addiction, 2005-09) Falba, Tracy; Teng, Hsun-Mei; Sindelar, Jody L; Gallo, William T
AIMS: To assess the impact of involuntary job loss due to plant closure or layoff on relapse to smoking and smoking intensity among older workers. DESIGN, PARTICIPANTS, SAMPLE: Data come from the Health and Retirement Study, a nationally representative survey of older Americans aged 51-61 in 1991 followed every 2 years beginning in 1992. The 3052 participants who were working at the initial wave and had any history of smoking comprise the main sample. METHODS: Primary outcomes are smoking relapse at wave 2 (1994) among baseline former smokers, and smoking quantity at wave 2 among baseline current smokers. As reported at the wave 2 follow-up, 6.8% of the sample experienced an involuntary job loss between waves 1 and 2. FINDINGS: Older workers have over two times greater odds of relapse subsequent to involuntary job loss than those who did not. Further, those who were current smokers prior to displacement that did not obtain new employment were found to be smoking more cigarettes, on average, post-job loss. CONCLUSIONS: The stress of job loss, along with other significant changes associated with leaving one's job, which would tend to increase cigarette consumption, must outweigh the financial hardship which would tend to reduce consumption. This highlights job loss as an important health risk factor for older smokers.
Open Access
The high prevalence of substance use disorders among recent MDMA users compared with other drug users: Implications for intervention.
(Addictive behaviors, 2009-08) Wu, Li-Tzy; Parrott, Andy C; Ringwalt, Christopher L; Patkar, Ashwin A; Mannelli, Paolo; Blazer, Dan G
In light of the resurgence in MDMA use and its association with polysubstance use, we investigated the 12-month prevalence of substance use disorders (SUDs) among adult MDMA users to determine whether they are at risk of other drug-related problems that would call for targeted interventions.Data were drawn from the 2006 National Survey on Drug Use and Health. Past-year adult drug users were grouped into three mutually exclusive categories: 1) recent MDMA users, who had used the drug within the past year; 2) former MDMA users, who had a history of using this drug but had not done so within the past year; and 3) other drug users, who had never used MDMA. Logistic regression procedures were used to estimate the association between respondents' SUDs and MDMA use while adjusting for their socioeconomic status, mental health, age of first use, and history of polydrug use.Approximately 14% of adults reported drug use in the past year, and 24% of those past-year drug users reported a history of MDMA use. Recent MDMA users exhibited the highest prevalence of disorders related to alcohol (41%), marijuana (30%), cocaine (10%), pain reliever/opioid (8%), and tranquilizer (3%) use. Adjusted logistic regression analyses revealed that, relative to other drug users, those who had recently used MDMA were twice as likely to meet criteria for marijuana and pain reliever/opioid use disorders. They were also about twice as likely as former MDMA users to meet criteria for marijuana, cocaine, and tranquilizer use disorders.Seven out of ten recent MDMA users report experiencing an SUD in the past year. Adults who have recently used MDMA should be screened for possible SUDs to ensure early detection and treatment.