Maximum Likelihood Estimation of Genetic Parameters in Cell Populations

In this paper we consider a cell population such as bacteria consisting of two types of cells, mutant and nonmutant. Under the mutation and homogeneous pure birth processes, this paper derives a maximum likelihood estimation procedure for estimating mutation rate and birth rate. The method is applied to Newcombe's data; further some Monte Carlo studies are generated. The numerical results indicate that the method is quite efficient for estimating genetic parameters in cell populations.     

Modeling association among demographic parameters in analysis of open population capture-recapture data

We present a hierarchical extension of the Cormack-Jolly-Seber (CJS) model for open population capture-recapture data. In addition to recaptures of marked animals, we model first captures of animals and losses on capture. The parameter set includes capture probabilities, survival rates, and birth rates. The survival rates and birth rates are treated as a random sample from a bivariate distribution, thus the model explicitly incorporates correlation in these demographic rates. A key feature of the model is that the likelihood function, which includes a CJS model factor, is expressed entirely in terms of identifiable parameters; losses on capture can be factored out of the model. Since the computational complexity of classical likelihood methods is prohibitive, we use Markov chain Monte Carlo in a Bayesian analysis. We describe an efficient candidate-generation scheme for Metropolis-Hastings sampling of CJS models and extensions. The procedure is illustrated using mark-recapture data for the moth Gonodontis bidentata.     

A new perspective on hyperthermia-induced birth defects: The role of activation energy and its relation to obstetric ultrasound

This paper concerns the rate of birth defects that is induced by hyperthermic conditions during gestation. These defects occur with low rates under apparently normal physiologic conditions, but with substantially higher rates with appropriate timing of a hyperthermic event during gestation. The concept of “free energy of activation” is invoked to explain not only the background rate but also the effect of a short-term, acute (additive) thermal dosing at a highly heat-sensitive stage of embryogenesis. In this respect, this paper is both retrospective and prospective in approach. It briefly and retrospectively addresses the historical data in this area and then, following a novel mathematical procedure whereby the activation energy for a specific type of hyperthermia-induced birth defect is determined, prospectively applies this information to predict what the outcomes would be in a clinical situation such as obstetric diagnostic ultrasound where it is known that the clinical procedure can involve a temperature increment for a specific duration. A major outcome of this review is that there appear to be no thresholds for hyperthermic events, that any temperature elevation for any duration during pregnancy has some potential for inducing a deleterious effect. The paper includes an analysis that for the first time allows a calculation of risk for such defined thermal insults, with broader implications for any natural or other clinical situation in which the temperature of the embryo or fetus is raised above the normal physiologic level. The topic of hyperthermia-induced birth defects and related activation energies needs thorough, long-term testing of this prospective position.     

Statistical Analyses of Twins Birth Data from a Nigerian Sample

In this paper, both the linear logistic model and its analogous linear model (weighted least squares) are fitted to twin birth data from a Nigerian sample. The logits of the observed perinatal mortality rates are fitted against the birthweight of breech infants for both first born and second born twins. Results show that a quadratic response model fits the data very well, and that the WLS procedure gives a better fit. The results further show that breech births necessarily result in 7.7% and 11.2% mortality rates respectively for first born and second born twins. The results of a log-linear model analysis on the 2×2×4 contingency table formed by the factors, ‘mode of birth’, and twins with the response variable ‘Apgar Scores’-an index of morbidity-also show that both factors play significant roles in explaining the variation of the response variable. It was found that the most important factor effecting the ability of a twin infant to survive as measured by the Apgar scores is the variable ‘mode of birth’ (vertex or breech). In other words, a vertex first twin infant has the best survival chance.     

Prenatal care demand and its effects on birth outcomes by birth defect status in Argentina

Our objective was to identify determinants of prenatal care demand and evaluate the effects of this demand on low birth weight and preterm birth. Delay in initiating prenatal care was modeled as a function of pregnancy risk indicators, enabling factors, and regional characteristics. Conditional maximum likelihood (CML) estimation was used to model self-selection into prenatal care use when estimating its effectiveness. Birth registry data was collected post delivery on infants with and without common birth defects born in 1995-2002 in Argentina using a standard procedure. Several maternal health and fertility indicators had significant effects on prenatal care use. In the group without birth defects, prenatal care delay increased significantly LBW and preterm birth when accounting for self-selection using the CML model but not in the standard probit model. Prenatal care was found to be ineffective on average in the birth defect group. The self-selection of higher risk women into earlier initiation of prenatal care resulted in underestimation of prenatal care effectiveness when using a standard probit model with several covariates. Large improvements in birth outcomes are suggested with earlier initiation of prenatal care for pregnancies uncomplicated with birth defects in Argentina, implying large opportunity costs from the long waiting time observed in this sample (about 17 weeks on average). The suggested ineffectiveness for pregnancies complicated with common birth defects deserves further research.     

Model life table fitting by maximum likelihood estimation: a procedure to reconstruct paleodemographic characteristics from skeletal age distributions

A procedure is presented that uses the regression coefficients for the Coale and Demeny west model life tables to model selected demographic characteristics from skeletal age-at-death distributions. Model death distributions were constructed and compared to a given skeletal distribution, using methods of maximum likelihood estimation to determine the best fit. Two chi-square tests are employed to evaluate the degree of fit. The resulting model includes estimates of demographic characteristics including gross reproductive rate, crude birth rate and life expectancy. The procedure is applied to three archaeological skeletal samples as test cases: two from eastern North America and one from Mexico. These display a range of correspondence (between the best fitting model and the data) from good to poor. The proposed procedure is a potentially powerful tool for both reconstructing paleodemographic rates and illuminating differences between typical human patterns and those found in archaeological populations.     

Health of children born after the infertility treatment with Assisted Reproduction Technology

Since the birth of Louise Brown in July 1978 and the birth of the first intracytoplasmic sperm injection (ICSI) child in January 1992 many couples with female-factor or male-factor infertility can be helped to overcome their infertility resulting in a delivery and birth of a child. Over a million children have been born from assisted conception worldwide. Newer techniques being introduced appear less and less 'natural', such as intracytoplasmic sperm injection (ICSI), but there is little information on these children beyond the neonatal period. This risk varied according to the patient's age, the type of ART procedure performed, the number of embryos transferred, and embryo availability. ART is associated with low increase risk of congenital malformations, major birth defects and genetic and imprinting disorders.     

Analysis of culling probability in dairy buffalo using survival models

In order to contribute to the genetic breeding programs of buffaloes, this study aimed to determine the influence of environmental effects on the stayability (ST) of dairy female Murrah buffalo in the herd. Data from 1016 buffaloes were used. ST was defined as the ability of the female to remain in the herd for 1, 2, 3, 4, 5 or 6 years after the first calving. Environmental effects were studied by survival analysis, adjusted to the fixed effects of farm, year and season of birth, class of first-lactation milk yield and age at first calving. The data were analyzed using the LIFEREG procedure of the SAS program that fits parametric models to failure time data (culling or ST = 0), and estimates parameters by maximum likelihood estimation. Breeding farm, year of birth and first-lactation milk yield significantly influenced (P < 0.0001) the ST to the specific ages (1 to 6 years after the first calving). Buffaloes that were older at first calving presented higher probabilities of being culled 1 year after the first calving, without any effect on culling at older ages. Buffaloes with a higher milk yield at first calving presented a lower culling probability and remained for a longer period of time in the herd. The effects of breeding farm, year of birth and first-lactation milk yield should be included in models used for the analysis of ST in buffaloes.     

Determination of free aspartic acid enantiomers in rat brain by capillary electrophoresis with laser-induced fluorescence detection

Quantification of aspartic acid enantiomers in rat brain by using a chiral capillary electrophoresis procedure is described. Amino acids were pre-column derivatized with naphthalene-2,3-dialdehyde. Enantiomeric separation was achieved by micellar electrokinetic chromatography in the presence of methanol and β-cyclodextrin as chiral selector. The chiral separation was coupled with laser-induced fluorescence detection. Contents of d- and l-aspartic acids in rats at different stages of growth (from 1 day before birth to 90 days after birth) were determined. d-Aspartic acid was detected in all the brain tissue samples tested, but at different levels. In the cerebrum of rats 1 day before birth, d-aspartic acid was found to be at the highest concentration of 81 nmol/g wet tissue. The level of d-aspartic acid in rat brain falls rapidly after birth, while the l-aspartic acid level increases with age.     

Spatial‐Temporal Modeling of the Association between Air Pollution Exposure and Preterm Birth: Identifying Critical Windows of Exposure

Summary Exposure to high levels of air pollution during the pregnancy is associated with increased probability of preterm birth (PTB), a major cause of infant morbidity and mortality. New statistical methodology is required to specifically determine when a particular pollutant impacts the PTB outcome, to determine the role of different pollutants, and to characterize the spatial variability in these results. We develop a new Bayesian spatial model for PTB which identifies susceptible windows throughout the pregnancy jointly for multiple pollutants (PM_2.5 , ozone) while allowing these windows to vary continuously across space and time. We geo‐code vital record birth data from Texas (2002–2004) and link them with standard pollution monitoring data and a newly introduced EPA product of calibrated air pollution model output. We apply the fully spatial model to a region of 13 counties in eastern Texas consisting of highly urban as well as rural areas. Our results indicate significant signal in the first two trimesters of pregnancy with different pollutants leading to different critical windows. Introducing the spatial aspect uncovers critical windows previously unidentified when space is ignored. A proper inference procedure is introduced to correctly analyze these windows.     

Genetic analysis of crossfostering data with sire and dam records

A method is presented for the analysis of data from crossfostering experiments in which parts of litters are reciprocally interchanged at birth. Observed variances and covariances of differently related individuals are expressed as functions of theoretical causal components of phenotypic variance (additive direct, dominance direct, additive maternal, dominance maternal, direct-maternal covariance, and environmental). Causal components are estimated by weighted least squares analysis of this system of equations, including a ridge-regression procedure to examine consequences of correlation between observed components. Ridge regression suggests that dominance direct genetic variance is generally underestimated, but that narrow-sense heritability estimates are reliable.     

Birth defects interstate data exchange: a battle worth fighting?

BACKGROUND: Regardless of where infants and children are delivered, diagnosed, or treated, an important aspect of population-based birth defects surveillance is ensuring the inclusion of children with birth defects in the catchment area. However, little is known as to how the lack of interstate birth defects data exchange affects program surveillance, monitoring, prevention, and referral activities. The study objectives were to determine the status of interstate birth defects data exchange agreements and to quantify statewide data on resident births occurring in nonresident states. METHODS: In 2004, surveys were distributed to all population-based birth defects programs in the United States to determine: 1) the types of interstate birth defects data exchange agreements that exist among birth defects programs, 2) perceived barriers in establishing exchange agreements, and 3) the extent to which out-of-state births affect a program's catchment area. The National Center for Health Statistics (NCHS) data for 2002 on live birth residency were used to determine the actual frequency of out-of-state live birth occurrence. RESULTS: Of the 52 states and territories that were surveyed, 65% (n = 34) responded. Approximately 21% (n = 7) of those that responded had an interstate data exchange agreement that allowed sharing of birth defects data with another state or a facility within another state. Approximately 53% (n = 18) of responding states indicated plans to develop an interstate birth defects data exchange agreement with other states, hospitals, or both. The NCHS data showed that the actual percentage of resident out-of-state live births ranged from 0.16 to 11.51. NCHS data also reveal that 78% of states would be able to capture >75% of their out-of-state births by sharing data on out-of-state births with the three neighboring states ranking highest in terms of such occurrences. CONCLUSIONS: Few states have interstate birth defects data exchange agreements, though all states have resident births occurring out of state. While suggestive, data beyond residency of live births are needed to quantify the degree to which the objectives of state-based birth defects programs are compromised. Resources exist to guide programs in establishing interstate data exchange agreements. Efforts to establish such agreements with only a few neighboring states could be a large step toward improving birth defects surveillance on a state, regional, and national level.     

Modelling Survival and Mortality Risk to 15 Years of Age for a National Cohort of Children with Serious Congenital Heart Defects Diagnosed in Infancy

Background

Congenital heart defects (CHDs) are a significant cause of death in infancy. Although contemporary management ensures that 80% of affected children reach adulthood, post-infant mortality and factors associated with death during childhood are not well-characterised. Using data from a UK-wide multicentre birth cohort of children with serious CHDs, we observed survival and investigated independent predictors of mortality up to age 15 years.

Methods

Data were extracted retrospectively from hospital records and death certificates of 3,897 children (57% boys) in a prospectively identified cohort, born 1992–1995 with CHDs requiring intervention or resulting in death before age one year. A discrete-time survival model accounted for time-varying predictors; hazards ratios were estimated for mortality. Incomplete data were addressed through multilevel multiple imputation.

Findings

By age 15 years, 932 children had died; 144 died without any procedure. Survival to one year was 79.8% (95% confidence intervals [CI] 78.5, 81.1%) and to 15 years was 71.7% (63.9, 73.4%), with variation by cardiac diagnosis. Importantly, 20% of cohort deaths occurred after age one year. Models using imputed data (including all children from birth) demonstrated higher mortality risk as independently associated with cardiac diagnosis, female sex, preterm birth, having additional cardiac defects or non-cardiac malformations. In models excluding children who had no procedure, additional predictors of higher mortality were younger age at first procedure, lower weight or height, longer cardiopulmonary bypass or circulatory arrest duration, and peri-procedural complications; non-cardiac malformations were no longer significant.

Interpretation

We confirm the high mortality risk associated with CHDs in the first year of life and demonstrate an important persisting risk of death throughout childhood. Late mortality may be underestimated by procedure-based audit focusing on shorter-term surgical outcomes. National monitoring systems should emphasise the importance of routinely capturing longer-term survival and exploring the mechanisms of mortality risk in children with serious CHDs.     

On Method of Moments Estimation in Linear Mixed Effects Models with Measurement Error on Covariates and Response with Application to a Longitudinal Study of Gene-Environment Interaction

We study a linear mixed effects model for longitudinal data, where the response variable and covariates with fixed effects are subject to measurement error. We propose a method of moment estimation that does not require any assumption on the functional forms of the distributions of random effects and other random errors in the model. For a classical measurement error model we apply the instrumental variable approach to ensure identifiability of the parameters. Our methodology, without instrumental variables, can be applied to Berkson measurement errors. Using simulation studies, we investigate the finite sample performances of the estimators and show the impact of measurement error on the covariates and the response on the estimation procedure. The results show that our method performs quite satisfactory, especially for the fixed effects with measurement error (even under misspecification of measurement error model). This method is applied to a real data example of a large birth and child cohort study.     

The birth of a wild mountain gorilla (Gorilla gorilla beringei)

The live birth of a wild mountain gorilla is described. Details of the birth process are given along with the mother’s periparturitional behaviour and the responses of others to the birth. The mother, a multiparous female, gave no observable indication that birth was imminent, and delivered her infant quickly and easily. During parturition, a subadult male showed interest in the proceedings. Following delivery, several animals approached the mother, who then left the birth site. The mother cleaned her infant and by two hours postpartum had established ventro-ventral contact and, possibly, nursing. These data are related to relevant observations from the literature and unpublished data on other animals from this study.     

Genetic study of the height and weight process during infancy.

Longitudinal height and weight data from 4649 Dutch twin pairs between birth and 2.5 years of age were analyzed. The data were first summarized into parameters of a polynomial of degree 4 by a mixed-effects procedure. Next, the variation and covariation in the parameters of the growth curve (size at one year of age, growth velocity, deceleration of growth, rate of change in deceleration [i.e., jerk] and rate of change in jerk [i.e., snap]) were decomposed into genetic and nongenetic sources. Additionally, the variation in the estimated size at birth and at 2 years of age interpolated from the polynomial was decomposed into genetic and nongenetic components. Variation in growth was best characterized by a genetic model which included additive genetic, common environmental and specific environmental influences, plus effects of gestational age. The effect of gestational age was largest for size at birth, explaining 39% of the variance. The differences between monozygotic and dizygotic twin correlations were largest for size at 1 and 2 years of age and growth velocity of weight, which suggests that these parameters are more influenced by heritability than size at birth, deceleration and jerk. The percentage of variance explained by additive genetic influences for height at 2 years of age was 52% for females and 58% for males. For weight at 2 years of age, heritability was approximately 58% for both sexes. Variation in snap height for males was also mainly influenced by additive genetic factors, while snap for females was influenced by both additive genetic and common environmental factors. The correlations for the additive genetic and common environmental factors for deceleration and snap are large, indicating that these parameters are almost entirely under control of the same additive genetic and common environmental factors. Female jerk and snap, and also female height at birth and height at 2 years of age, are mostly under control of the same additive genetic factor.     

Improving case ascertainment of a population-based birth defects registry in New York State using hospital discharge data

BACKGROUND: The assessment of the data quality of population-based registration systems is essential to understanding the reliability and usefulness of disease surveillance and research findings resulting from the use of registry data. Since the New York State Congenital Malformations Registry (CMR) uses passive case ascertainment, the completeness of the registry data is an important aspect of the quality of information. This paper presents the results of hospital audits, which were conducted to capture the unreported cases using hospital discharge files, and evaluates the effectiveness of the audits. METHODS: Children age 2 years or younger and diagnosed with reportable birth defects for the birth years 1998-2000 were selected from hospital discharge files of all reporting hospitals in the New York Statewide Planning and Research Cooperative System (SPARCS) and matched to the CMR database for the same birth year period.The unmatched reports from the SPARCS hospital discharge files that the CMR possibly missed were sent to hospitals, requesting submission of the missed reports. Two audits on all reporting hospitals in New York State were conducted: 1) 1998 and 1999 birth cohorts audited from June 2000 to March 2002, and 2) 2000 birth cohort audited from November 2001 to November 2002. RESULTS: Hospital audits using SPARCS hospital discharge data identified 5,460 reports that the CMR missed for the selected 66 hospitals analyzed. About 86% of these reports had reportable conditions and were added to the CMR, which comprised 21.4% of all reports from the 66 hospitals for the birth years 1998-2000. The number of reports that would have been missed without audits decreased from the 1998 and 1999 birth cohort (25.1%) to the 2000 birth cohort (13.9%). Low reporting rates and, thus, a high percent of added reports, were found for hospitals with a relatively small number of annual reports and for some specific birth defects such as chromosomal anomalies, anencephalus and congenital anomalies of the urinary system. CONCLUSION: The current study demonstrates that using hospital discharge data to improve case ascertainment is a valuable and effective method of enhancing birth defect surveillance, particularly for those hospitals with low reporting rates.     

Modeling of crossbred cattle growth, comparison between cubic and piecewise random regression models

Two analyses, cubic and piecewise random regression, were conducted to model growth of crossbred cattle from birth to about two years of age, investigating the ability of a piecewise procedure to fit growth traits without the complications of the cubic model. During a four-year period (1994-1997) of the Australian "Southern Crossbreeding Project", mature Hereford cows (N = 581) were mated to 97 sires of Angus, Belgian Blue, Hereford, Jersey, Limousin, South Devon, and Wagyu breeds, resulting in 1141 steers and heifers born over four years. Data included 13 (for steers) and eight (for heifers) live body weight measurements, made approximately every 50 days from birth until slaughter. The mixed model included fixed effects of sex, sire breed, age (linear, quadratic and cubic), and their interactions between sex and sire breed with age. Random effects were sire, dam, management (birth location, year, post-weaning groups), and permanent environmental effects and for each of these when possible, their interactions with linear, quadratic and cubic growth. In both models, body weights of all breeds increased over pre-weaning period, held fairly steady (slightly flattening) over the dry season then increased again towards the end of the feedlot period. The number of estimated parameters for the cubic model was 22 while for the piecewise model it was 32. It was concluded that the piecewise model was very similar to the cubic model in the fit to the data; with the piecewise model being marginally better. The piecewise model seems to fit the data better at the end of the growth period.     

Laparoscopy: the method of choice for sterilization and investigation of infertility

The increasing demand for sterilization as a permanent and effective form of birth control leads one to consider the various methods available to achieve this end. Tubal cauterization and excision by laparoscopy appears to be a safe, efficient method.The technique used is carefully reviewed step by step. The absence of major complications in this series of 115 consecutive laparoscopies certainly supports the safety of the procedure. The low morbidity, short hospital stay and minimal time required appeal particularly to the working mother. The absence of an abdominal scar is also much appreciated. The procedure, when used for investigation of infertility, provides far more information than other current methods.     

Birth-weight-specific infant and neonatal mortality: effects of heterogeneity in the birth cohort

Birth-weight-specific infant mortality is examined using a novel statistical procedure, parametric mixtures of logistic regressions. The results indicate that birth cohorts are composed of two or more subpopulations that are heterogeneous with respect to infant mortality. One subpopulation appears to account for the "normal" process of fetal development, while the other, which accounts for the majority of births at both low and high birth weights, may represent fetuses that were "disturbed" during development. Surprisingly, estimates of neonatal and infant mortality indicate that the "disturbed" subpopulation has lower birth-weight-specific mortality, although overall crude mortality rates are higher for this subpopulation. It is hypothesized that this is due to high rates of fetal loss among the "disturbed" subpopulation, resulting in a highly selected group at birth. The heterogeneity identified in the birth cohort could be responsible for recent decelerations in the decline in infant mortality, and might be the cause of unexplained ethnic differences in birth-weight-specific infant mortality. The novel statistical methodology developed here has broad application within human biology. In particular, it could be used in any context where parametric mixture modeling is applied, such as complex segregation analysis.