Browsing by Subject "Likelihood Functions"
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Item Open Access A new predictive model for an improved respiratory isolation strategy in HIV-infected patients with PTB.(The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease, 2014-07) Carugati, M; Schiroli, C; Zanini, F; Vanoni, N; Galli, M; Adorni, F; Franzetti, FSetting
Luigi Sacco Hospital, Milan, Italy, 1 January 2000-31 December 2010.Objectives
To develop a predictive score for identifying human immunodeficiency virus (HIV) infected patients with pulmonary tuberculosis (PTB).Design
Retrospective study based on the medical charts of HIV-infected patients admitted consecutively on presumption of PTB. Patients with culture-positive TB were included in the TB group. Culture-negative subjects formed the non-TB group. Risk factors for PTB were identified and a predictive model was developed. The diagnostic test accuracy of the derived score and that of previously developed scores were analysed.Results
A total of 65 patients were included in the TB group and 505 subjects in the non-TB group. An eight-variable model (age, origin, alcohol use, respiratory rate, weight loss, haemoglobin, white blood cell count, typical chest X-ray) was derived. When compared with the different scores, this model showed the greatest area under the receiver operating characteristic curve (0.880). This score was the only one to present a negative likelihood ratio of <0.2, which is the threshold for giving strong diagnostic evidence against TB.Conclusions
This model may be useful in predicting PTB in HIV patients in low-endemic countries. A validation study is necessary.Item Open Access Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation.(Journal of visualized experiments : JoVE, 2019-01-16) Jones, Edward G; Landstrom, Andrew PAdvancements in the cost and speed of next generation genetic sequencing have generated an explosion of clinical whole exome and whole genome testing. While this has led to increased identification of likely pathogenic mutations associated with genetic syndromes, it has also dramatically increased the number of incidentally found genetic variants of unknown significance (VUS). Determining the clinical significance of these variants is a major challenge for both scientists and clinicians. An approach to assist in determining the likelihood of pathogenicity is signal-to-noise analysis at the protein sequence level. This protocol describes a method for amino acid-level signal-to-noise analysis that leverages variant frequency at each amino acid position of the protein with known protein topology to identify areas of the primary sequence with elevated likelihood of pathologic variation (relative to population "background" variation). This method can identify amino acid residue location "hotspots" of high pathologic signal, which can be used to refine the diagnostic weight of VUSs such as those identified by next generation genetic testing.Item Open Access Effects of FOXO genotypes on longevity: a biodemographic analysis.(J Gerontol A Biol Sci Med Sci, 2010-12) Zeng, Y; Cheng, L; Chen, H; Cao, H; Hauser, ER; Liu, Y; Xiao, Z; Tan, Q; Tian, XL; Vaupel, JWBased on data from 760 centenarians and 1060 middle-age controls (all Han Chinese), this article contributes biodemographic insights and syntheses concerning the magnitude of effects of the FOXO genotypes on longevity. We also estimate independent and joint effects of the genotypes of FOXO1A and FOXO3A genes on long-term survival, considering carrying or not-carrying the minor allele of the single-nucleotide polymorphism of another relevant gene. We found substantial gender differences in the independent effects; positive effects of FOXO3A and negative effects of FOXO1A largely compensate each other if one carries both, although FOXO3A has a stronger impact. Ten-year follow-up cohort analysis shows that at very advanced ages 92-110, adjusted for various confounders, positive effects of FOXO3A on survival remain statistically significant, but no significant effects of FOXO1A alone; G × G interactions between FOXO1A-209 and FOXO3A-310 or FOXO3A-292 decrease survival likelihood by 32%-36% (p < .05); G × E interactions between FOXO1A-209 and regular exercise increase survival likelihood by 31%-32% (p < .05).Item Open Access Estimation and validation of a multiattribute model of Alzheimer disease progression.(Med Decis Making, 2010-11) Stallard, Eric; Kinosian, Bruce; Zbrozek, Arthur S; Yashin, Anatoliy I; Glick, Henry A; Stern, YaakovOBJECTIVES: To estimate and validate a multiattribute model of the clinical course of Alzheimer disease (AD) from mild AD to death in a high-quality prospective cohort study, and to estimate the impact of hypothetical modifications to AD progression rates on costs associated with Medicare and Medicaid services. DATA AND METHODS: The authors estimated sex-specific longitudinal Grade of Membership (GoM) models for AD patients (103 men, 149 women) in the initial cohort of the Predictors Study (1989-2001) based on 80 individual measures obtained every 6 mo for 10 y. These models were replicated for AD patients (106 men, 148 women) in the 2nd Predictors Study cohort (1997-2007). Model validation required that the disease-specific transition parameters be identical for both Predictors Study cohorts. Medicare costs were estimated from the National Long Term Care Survey. RESULTS: Sex-specific models were validated using the 2nd Predictors Study cohort with the GoM transition parameters constrained to the values estimated for the 1st Predictors Study cohort; 57 to 61 of the 80 individual measures contributed significantly to the GoM models. Simulated, cost-free interventions in the rate of progression of AD indicated that large potential cost offsets could occur for patients at the earliest stages of AD. CONCLUSIONS: AD progression is characterized by a small number of parameters governing changes in large numbers of correlated indicators of AD severity. The analysis confirmed that the progression of AD represents a complex multidimensional physiological process that is similar across different study cohorts. The estimates suggested that there could be large cost offsets to Medicare and Medicaid from the slowing of AD progression among patients with mild AD. The methodology appears generally applicable in AD modeling.Item Open Access Genetic evaluation of a proposed introduction: the case of the greater prairie chicken and the extinct heath hen.(Mol Ecol, 2004-07) Palkovacs, EP; Oppenheimer, AJ; Gladyshev, E; Toepfer, JE; Amato, G; Chase, T; Caccone, APopulation introduction is an important tool for ecosystem restoration. However, before introductions should be conducted, it is important to evaluate the genetic, phenotypic and ecological suitability of possible replacement populations. Careful genetic analysis is particularly important if it is suspected that the extirpated population was unique or genetically divergent. On the island of Martha's Vineyard, Massachusetts, the introduction of greater prairie chickens (Tympanuchus cupido pinnatus) to replace the extinct heath hen (T. cupido cupido) is being considered as part of an ecosystem restoration project. Martha's Vineyard was home to the last remaining heath hen population until its extinction in 1932. We conducted this study to aid in determining the suitability of greater prairie chickens as a possible replacement for the heath hen. We examined mitochondrial control region sequences from extant populations of all prairie grouse species (Tympanuchus) and from museum skin heath hen specimens. Our data suggest that the Martha's Vineyard heath hen population represents a divergent mitochondrial lineage. This result is attributable either to a long period of geographical isolation from other prairie grouse populations or to a population bottleneck resulting from human disturbance. The mtDNA diagnosability of the heath hen contrasts with the network of mtDNA haplotypes of other prairie grouse (T. cupido attwateri, T. pallidicinctus and T. phasianellus), which do not form distinguishable mtDNA groupings. Our findings suggest that the Martha's Vineyard heath hen was more genetically isolated than are current populations of prairie grouse and place the emphasis for future research on examining prairie grouse adaptations to different habitat types to assess ecological exchangeability between heath hens and greater prairie chickens.Item Open Access Impact of poor mental health in adult spinal deformity patients with poor physical function: a retrospective analysis with a 2-year follow-up.(Journal of neurosurgery. Spine, 2017-01) Bakhsheshian, Joshua; Scheer, Justin K; Gum, Jeffrey L; Hostin, Richard; Lafage, Virginie; Bess, Shay; Protopsaltis, Themistocles S; Burton, Douglas C; Keefe, Malla Kate; Hart, Robert A; Mundis, Gregory M; Shaffrey, Christopher I; Schwab, Frank; Smith, Justin S; Ames, Christopher P; International Spine Study GroupOBJECTIVE Mental disease burden can have a significant impact on levels of disability and health-related quality of life (HRQOL) measures. Therefore, the authors investigated the significance of mental health status in adults with spinal deformity and poor physical function. METHODS A retrospective analysis of a prospective multicenter database of 365 adult spinal deformity (ASD) patients who had undergone surgical treatment was performed. Health-related QOL variables were examined preoperatively and at the 2-year postoperative follow-up. Patients were grouped by their 36-Item Short Form Health Survey mental component summary (MCS) and physical component summary (PCS) scores. Both groups had PCS scores ≤ 25th percentile for matched norms; however, the low mental health (LMH) group consisted of patients with an MCS score ≤ 25th percentile, and the high mental health (HMH) group included patients with an MCS score ≥ 75th percentile. RESULTS Of the 264 patients (72.3%) with a 2-year follow-up, 104 (28.5%) met the inclusion criteria for LMH and 40 patients (11.0%) met those for HMH. The LMH group had a significantly higher overall rate of comorbidities, specifically leg weakness, depression, hypertension, and self-reported neurological and psychiatric disease processes, and were more likely to be unemployed as compared with the HMH group (p < 0.05 for all). The 2 groups had similar 2-year postoperative improvements in HRQOL (p > 0.05) except for the greater improvements in the MCS and the Scoliosis Research Society-22r questionnaire (SRS-22r) mental domain (p < 0.05) in the LMH group and greater improvements in PCS and SRS-22r satisfaction and back pain domains (p < 0.05) in the HMH group. The LMH group had a higher rate of reaching a minimal clinically important difference (MCID) on the SRS-22r mental domain (p < 0.01), and the HMH group had a higher rate of reaching an MCID on the PCS and SRS-22r activity domain (p < 0.05). On multivariable logistic regression, having LMH was a significant independent predictor of failure to reach an MCID on the PCS (p < 0.05). At the 2-year postoperative follow-up, 14 LMH patients (15.1%) were categorized as HMH. Two LMH patients (2.2%), and 3 HMH patients (7.7%) transitioned to a PCS score ≥ 75th percentile for age- and sex-matched US norms (p < 0.01). CONCLUSIONS While patients with poor mental and physical health, according to their MCS and PCS scores, have higher medical comorbidity and unemployment rates, they still demonstrate significant improvements in HRQOL measurements postoperatively. Both LMH and HMH patient groups demonstrated similar improvements in most HRQOL domains, except that the LMH patients had difficulties in obtaining improvements in the PCS domain.Item Open Access Importance sampling for the infinite sites model.(Statistical applications in genetics and molecular biology, 2008-01) Hobolth, Asger; Uyenoyama, Marcy K; Wiuf, CarstenImportance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In this paper, we discuss importance sampling for the infinite sites model. The infinite sites assumption is attractive because it constraints the number of possible genealogies, thereby allowing for the analysis of larger data sets. We recall the Griffiths-Tavaré and Stephens-Donnelly proposals and emphasize the relation between the latter proposal and exact sampling from the infinite alleles model. We also introduce a new proposal that takes knowledge of the ancestral state into account. The new proposal is derived from a new result on exact sampling from a single site. The methods are illustrated on simulated data sets and the data considered in Griffiths and Tavaré (1994).Item Open Access Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis.(The Journal of eukaryotic microbiology, 1999-07) Turner, S; Pryer, KM; Miao, VP; Palmer, JDSmall subunit rRNA sequence data were generated for 27 strains of cyanobacteria and incorporated into a phylogenetic analysis of 1,377 aligned sequence positions from a diverse sampling of 53 cyanobacteria and 10 photosynthetic plastids. Tree inference was carried out using a maximum likelihood method with correction for site-to-site variation in evolutionary rate. Confidence in the inferred phylogenetic relationships was determined by construction of a majority-rule consensus tree based on alternative topologies not considered to be statistically significantly different from the optimal tree. The results are in agreement with earlier studies in the assignment of individual taxa to specific sequence groups. Several relationships not previously noted among sequence groups are indicated, whereas other relationships previously supported are contradicted. All plastids cluster as a strongly supported monophyletic group arising near the root of the cyanobacterial line of descent.Item Open Access Likelihoods from summary statistics: recent divergence between species.(Genetics, 2005-11) Leman, Scotland C; Chen, Yuguo; Stajich, Jason E; Noor, Mohamed AF; Uyenoyama, Marcy KWe describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. In this first application, we address the demographic history of closely related members of the Drosophila pseudoobscura group. We base the maximum-likelihood estimation of the time since speciation and the effective population sizes of the extant and ancestral populations on the pattern of nucleotide variation at DPS2002, a noncoding region tightly linked to a paracentric inversion that strongly contributes to reproductive isolation. Consideration of summary statistics rather than entire nucleotide sequences permits a compact description of the genealogy of the sample. We use importance sampling first to propose a genealogical and mutational history consistent with the observed array of summary statistics and then to correct the likelihood with the exact probability of the history determined from a system of recursions. Analysis of a subset of the data, for which recursive computation of the exact likelihood was feasible, indicated close agreement between the approximate and exact likelihoods. Our results for the complete data set also compare well with those obtained through Metropolis-Hastings sampling of fully resolved genealogies of entire nucleotide sequences.Item Open Access Lower likelihood of cardiac procedures after acute coronary syndrome in patients with human immunodeficiency virus/acquired immunodeficiency syndrome.(Medicine, 2018-02) Clement, Meredith E; Lin, Li; Navar, Ann Marie; Okeke, Nwora Lance; Naggie, Susanna; Douglas, Pamela SCardiovascular disease (CVD) is an increasing cause of morbidity and mortality in human immunodeficiency virus (HIV)-infected adults; however, this population may be less likely to receive interventions during hospitalization for acute coronary syndrome (ACS). The degree to which this disparity can be attributed to poorly controlled HIV infection is unknown.In this large cohort study, we used the National Inpatient Sample (NIS) to compare rates of cardiac procedures among patients with asymptomatic HIV-infection, symptomatic acquired immunodeficiency syndrome (AIDS), and uninfected adults hospitalized with ACS from 2009 to 2012. Multivariable analysis was used to compare procedure rates by HIV status, with appropriate weighting to account for NIS sampling design including stratification and hospital clustering.The dataset included 1,091,759 ACS hospitalizations, 0.35% of which (n = 3783) were in HIV-infected patients. Patients with symptomatic AIDS, asymptomatic HIV, and uninfected patients differed by sex, race, and income status. Overall rates of cardiac catheterization and revascularization were 53.3% and 37.4%, respectively. In multivariable regression, we found that relative to uninfected patients, those with symptomatic AIDS were less likely to undergo catheterization (odds ratio [OR] 0.48, confidence interval [CI] 0.43-0.55), percutaneous coronary intervention (OR 0.69, CI 0.59-0.79), and coronary artery bypass grafting (0.75, CI 0.61-0.93). No difference was seen for those with asymptomatic HIV relative to uninfected patients (OR 0.93, CI 0.81-1.07; OR 1.06, CI 0.93-1.21; OR 0.88, CI 0.72-1.06, respectively).We found that lower rates of cardiovascular procedures in HIV-infected patients were primarily driven by less frequent procedures in those with AIDS.Item Open Access Monte Carlo methods for localization of cones given multielectrode retinal ganglion cell recordings.(Network (Bristol, England), 2013-01) Sadeghi, K; Gauthier, JL; Field, GD; Greschner, M; Agne, M; Chichilnisky, EJ; Paninski, LIt has recently become possible to identify cone photoreceptors in primate retina from multi-electrode recordings of ganglion cell spiking driven by visual stimuli of sufficiently high spatial resolution. In this paper we present a statistical approach to the problem of identifying the number, locations, and color types of the cones observed in this type of experiment. We develop an adaptive Markov Chain Monte Carlo (MCMC) method that explores the space of cone configurations, using a Linear-Nonlinear-Poisson (LNP) encoding model of ganglion cell spiking output, while analytically integrating out the functional weights between cones and ganglion cells. This method provides information about our posterior certainty about the inferred cone properties, and additionally leads to improvements in both the speed and quality of the inferred cone maps, compared to earlier "greedy" computational approaches.Item Open Access Phylodynamic inference for structured epidemiological models.(PLoS Comput Biol, 2014-04) Rasmussen, David A; Volz, Erik M; Koelle, KatiaCoalescent theory is routinely used to estimate past population dynamics and demographic parameters from genealogies. While early work in coalescent theory only considered simple demographic models, advances in theory have allowed for increasingly complex demographic scenarios to be considered. The success of this approach has lead to coalescent-based inference methods being applied to populations with rapidly changing population dynamics, including pathogens like RNA viruses. However, fitting epidemiological models to genealogies via coalescent models remains a challenging task, because pathogen populations often exhibit complex, nonlinear dynamics and are structured by multiple factors. Moreover, it often becomes necessary to consider stochastic variation in population dynamics when fitting such complex models to real data. Using recently developed structured coalescent models that accommodate complex population dynamics and population structure, we develop a statistical framework for fitting stochastic epidemiological models to genealogies. By combining particle filtering methods with Bayesian Markov chain Monte Carlo methods, we are able to fit a wide class of stochastic, nonlinear epidemiological models with different forms of population structure to genealogies. We demonstrate our framework using two structured epidemiological models: a model with disease progression between multiple stages of infection and a two-population model reflecting spatial structure. We apply the multi-stage model to HIV genealogies and show that the proposed method can be used to estimate the stage-specific transmission rates and prevalence of HIV. Finally, using the two-population model we explore how much information about population structure is contained in genealogies and what sample sizes are necessary to reliably infer parameters like migration rates.Item Open Access Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex.(PLoS One, 2010-12-09) Gryganskyi, AP; Lee, SC; Litvintseva, AP; Smith, ME; Bonito, G; Porter, TM; Anishchenko, IM; Heitman, J; Vilgalys, RThe Rhizopus oryzae species complex is a group of zygomycete fungi that are common, cosmopolitan saprotrophs. Some strains are used beneficially for production of Asian fermented foods but they can also act as opportunistic human pathogens. Although R. oryzae reportedly has a heterothallic (+/-) mating system, most strains have not been observed to undergo sexual reproduction and the genetic structure of its mating locus has not been characterized. Here we report on the mating behavior and genetic structure of the mating locus for 54 isolates of the R. oryzae complex. All 54 strains have a mating locus similar in overall organization to Phycomyces blakesleeanus and Mucor circinelloides (Mucoromycotina, Zygomycota). In all of these fungi, the minus (-) allele features the SexM high mobility group (HMG) gene flanked by an RNA helicase gene and a TP transporter gene (TPT). Within the R. oryzae complex, the plus (+) mating allele includes an inserted region that codes for a BTB/POZ domain gene and the SexP HMG gene. Phylogenetic analyses of multiple genes, including the mating loci (HMG, TPT, RNA helicase), ITS1-5.8S-ITS2 rDNA, RPB2, and LDH genes, identified two distinct groups of strains. These correspond to previously described sibling species R. oryzae sensu stricto and R. delemar. Within each species, discordant gene phylogenies among multiple loci suggest an outcrossing population structure. The hypothesis of random-mating is also supported by a 50:50 ratio of plus and minus mating types in both cryptic species. When crossed with tester strains of the opposite mating type, most isolates of R. delemar failed to produce zygospores, while isolates of R. oryzae produced sterile zygospores. In spite of the reluctance of most strains to mate in vitro, the conserved sex locus structure and evidence for outcrossing suggest that a normal sexual cycle occurs in both species.Item Open Access Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci.(Molecular phylogenetics and evolution, 2006-06) Korall, P; Pryer, KM; Metzgar, JS; Schneider, H; Conant, DSTree ferns are a well-established clade within leptosporangiate ferns. Most of the 600 species (in seven families and 13 genera) are arborescent, but considerable morphological variability exists, spanning the giant scaly tree ferns (Cyatheaceae), the low, erect plants (Plagiogyriaceae), and the diminutive endemics of the Guayana Highlands (Hymenophyllopsidaceae). In this study, we investigate phylogenetic relationships within tree ferns based on analyses of four protein-coding, plastid loci (atpA, atpB, rbcL, and rps4). Our results reveal four well-supported clades, with genera of Dicksoniaceae (sensu ) interspersed among them: (A) (Loxomataceae, (Culcita, Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia, Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with Hymenophyllopsidaceae nested within. How these four groups are related to one other, to Thyrsopteris, or to Metaxyaceae is weakly supported. Our results show that Dicksoniaceae and Cyatheaceae, as currently recognised, are not monophyletic and new circumscriptions for these families are needed.