Molecular evolution of primate immunodeficiency viruses and hepatitis delta virus

Primate immunodeficiency viruses, or lentiviruses (HIV-1, HIV-2, and SIV), and hepatitis delta virus (HDV) are RNA viruses characterized by rapid evolution. Infection by primate immunodeficiency viruses usually results in the development of acquired immunodeficiency syndrome (AIDS) in humans and AIDS-like illnesses in Asian macaques. Similarly, hepatitis delta virus infection causes hepatitis and liver cancer in humans. These viruses are heterogeneous within an infected patient and among individuals. Substitution rates in the virus genomes are high and vary in different lineages and among sites. Methods of phylogenetic analysis were applied to study the evolution of primate lentiviruses and the hepatitis delta virus. The following results have been obtained: (1) The substitution rate varies among sites of primate lentivirus genes according to the two parameter gamma distribution, with the shape parameter $\alpha$ being close to 1. (2) Primate immunodeficiency viruses fall into species-specific lineages. Therefore, viral transmissions across primate species are not as frequent as suggested by previous authors. (3) Primate lentiviruses have acquired or lost their pathogenicity several times in the course of evolution. (4) Evidence was provided for multiple infections of a North American patient by distinct HIV-1 strains of the B subtype. (5) Computer simulations indicate that the probability of committing an error in testing HIV transmission depends on the number of virus sequences and their length, the divergence times among sequences, and the model of nucleotide substitution. (6) For future investigations of HIV-1 transmissions, using longer virus sequences and avoiding the use of distant outgroups is recommended. (7) Hepatitis delta virus strains are usually related according to the geographic region of isolation. (8) Evolution of HDV is characterized by the rate of synonymous substitution being lower than the nonsynonymous substitution rate and the rate of evolution of the noncoding region. (9) There is a strong preference for G and C nucleotides at the third codon positions of the HDV coding region. ^

Analysis of recurrent failure times: A time-dependent Yule process approach

Analysis of recurrent events has been widely discussed in medical, health services, insurance, and engineering areas in recent years. This research proposes to use a nonhomogeneous Yule process with the proportional intensity assumption to model the hazard function on recurrent events data and the associated risk factors. This method assumes that repeated events occur for each individual, with given covariates, according to a nonhomogeneous Yule process with intensity function λx(t) = λ 0(t) · exp( x′β). One of the advantages of using a non-homogeneous Yule process for recurrent events is that it assumes that the recurrent rate is proportional to the number of events that occur up to time t. Maximum likelihood estimation is used to provide estimates of the parameters in the model, and a generalized scoring iterative procedure is applied in numerical computation. ^ Model comparisons between the proposed method and other existing recurrent models are addressed by simulation. One example concerning recurrent myocardial infarction events compared between two distinct populations, Mexican-American and Non-Hispanic Whites in the Corpus Christi Heart Project is examined. ^

The Emergency Department: Rising wait times, costs, and possible remedies

Emergency Departments (EDs) and Emergency Rooms (ERs) are designed to manage trauma, respond to disasters, and serve as the initial care for those with serious illnesses. However, because of many factors, the ED has become the doorway to the hospital and a “catch-all net” for patients including those with non-urgent needs. This increase in the population in the ED has lead to an increase in wait times for patients. It has been well documented that there has been a constant and consistent rise in the number of patients that frequent the ED (National Center for Health Statistics, 2002); the wait time for patients in the ED has increased (Pitts, Niska, Xu, & Burt, 2008); and the cost of the treatment in the ER has risen (Everett Clinic, 2008). Because the ED was designed to treat patients who need quick diagnoses and may be in potential life-threatening circumstances, management of time can be the ultimate enemy. If a system was implemented to decrease wait times in the ED, decrease the use of ED resources, and decrease costs endured by patients seeking care, better outcomes for patients and patient satisfaction could be achieved. The goal of this research was to explore potential changes and/or alternatives to relieve the burden endured by the ED. In order to explore these options, data was collected by conducting one-on-one interviews with seven physicians closely tied to a Level 1 ED (Emergency Room physicians, Trauma Surgeons and Primary Care physicians). A qualitative analysis was performed on the responses of one-on-one interviews with the aforementioned physicians. The interviews were standardized, open-ended questions that probe what makes an effective ED, possible solutions to improving patient care in the ED, potential remedies for the mounting problems that plague the ED, and the feasibility of bringing Primary Care Physicians to the ED to decrease the wait times experienced by the patient. From the responses, it is clear that there needs to be more research in this area, several areas need to be addressed, and a variety of solutions could be implemented. The most viable option seems to be making the ED its own entity (similar to the clinic or hospital) that includes urgent clinics as a part of the system, in which triage and better staffing would be the most integral part of its success.^

TEMPORAL VARIATION OF ACUTE AND LUNG TUMORIGENIC EFFECTS OF URETHAN ON STRAIN A MICE (CHRONOBIOLOGY, CARCINOGENICITY, ANESTHETIC, DNA SYNTHESIS)

The effect of circadian variation on susceptibility to the chemical induction of cancer was assessed utilizing the mouse pulmonary adenoma bioassay. Different groups of male A/Jax mice (standardized for rhythm analysis with light from 0600-1800 and darkness from 1800-0600) each received a single timed i.p. injection of urethan (Bioassay I: 0.25, 0.5 or 1.0 mg/g body weight; Bioassay II: 0.75, 1.0, 1.25 mg/g body weight; Bioassay III: 1.0 mg/g body weight) at the following times, 0100, 0500, 0900, 1300, 1700 or 2100. Mice were sacrificed 16 weeks after treatment. The tumorigenic effect of urethan on the lungs (lung surface pulmonary adenomas) was assessed. In addition, mortality, body weight changes and the anesthetic effect of urethan were determined. The rhythmic pattern of DNA synthesis in the lung and the comparative rhythmic pattern in the liver were assessed using a tritiated thymidine incorporation assay.^ In the first adenoma bioassay, the lung tumorigenic response in mice given the highest dose of urethan exhibited a 12-hour rhythm with a major peak in tumor yield at 0100 and a secondary peak at 1300; reduced yields occurred at 0500-0900 and 2100. The second adenoma bioassay, studied at a 6-month seasonal divergence in time from the first study showed a peak at 1300 but not at 0100. The mice from the third adenoma bioassay, studied at an 11-month seasonal divergence in time from the 2nd study showed an increase in tumor yield during the rest cycle (0900-1700).^ This study found a definite suggestion of a low amplitude rhythm in susceptibility to urethan induced effects. The acute toxic and pharmacological effects correlated to exhibit a maximal effect during dark hours (activity span). This rhythmicity might be explained by an alteration in the amplitude of hepatic metabolism. The chronic carcinogenic response exhibited an opposite pattern. Urethan induced tumor response was greater during daylight hours (rest cycle). This correlated with the slight elevation in DNA synthetic activity found in the lung and liver which might be responsible for the increase in carcinogenic response. (Abstract shortened with permission of author.) ^

International comparison of wait times and quality of care: A pilot study

During the healthcare reform debate in the United States in 2009/2010, many health policy experts expressed a concern that expanding coverage would increase waiting times for patients to obtain care. Many complained that delays in obtaining care in turn would compromise the quality of healthcare in the United States. Using data from The Commonwealth Fund 2010 International Health Policy Survey in Eleven Countries, this study explored the relationship between wait times and quality of care, employing a wait time scale and several quality of care indicators present in the dataset. The impact of wait times on quality was assessed. Increased wait time was expected to reduce quality of care. However, this study found that wait times correlated with better health outcomes for some measures, and had no association with others. Since this is a pilot study and statistical significance was not achieved for any of the correlations, further research is needed to confirm and deepen the findings. However, if future studies confirm this finding, an emphasis on reducing wait times at the expense of other health system level performance variables may be inappropriate. ^

Decomposition of $\rm R\times C$ contingency table chi -square: Application to binned DNA fragment size data and population structure analysis

The purpose of this research is to develop a new statistical method to determine the minimum set of rows (R) in a R x C contingency table of discrete data that explains the dependence of observations. The statistical power of the method will be empirically determined by computer simulation to judge its efficiency over the presently existing methods. The method will be applied to data on DNA fragment length variation at six VNTR loci in over 72 populations from five major racial groups of human (total sample size is over 15,000 individuals; each sample having at least 50 individuals). DNA fragment lengths grouped in bins will form the basis of studying inter-population DNA variation within the racial groups are significant, will provide a rigorous re-binning procedure for forensic computation of DNA profile frequencies that takes into account intra-racial DNA variation among populations. ^