Estimation of the correlation between nutrient intake measures under restricted sampling

Food frequency questionnaires (FFQs) are commonly used to assess dietary intake in epidemiologic research. To evaluate the FFQ reliability, the commonly used approach is to estimate the correlation coefficient between the data given in FFQ and those in food records (for example, 4-day food records [4DFR]) for nutrients of interest. However, in a dietary intervention study, a criterion for eligibility may be to select participants who have baseline FFQ-measured dietary intake of percent energy from fat above a prespecified quantity. Other instruments, such as the 4DFR, may be subsequently administrated only to eligible participants. Under these circumstances, analysis without adjusting for the restricted population will usually lead to biased estimation of correlation coefficients and other parameters of interest. In this paper, we apply likelihood-based and multiple imputation (MI) methods to accommodate such incomplete data obtained as a result of the study design. A simulation study is conducted to examine finite sample performance of various estimators. We note that both the MI estimate and the maximum likelihood (ML) estimate based on a bivariate-normal model are not sensitive to departures from this normality assumption. This led us to investigate robustness properties of the ML estimator analytically. We present some data analyses from a dietary assessment study from the Women's Health Initiative to illustrate the methods.     

Efficacy and safety of long-term continuous growth hormone treatment of children born small for gestational age

Twelve years of growth hormone (GH) therapy of short children born small for gestational age (SGA) have demonstrated that GH is an effective and well-tolerated therapy. Most children will reach a normal adult height (AH). AH of 55 SGA adolescents was comparable for those treated with a GH dose of 1 or 2 mg/m2 (approximately 0.033 or 0.066 mg/kg) per day, mean (SD) AH SDS being -1.2 (0.7) and -0.8 (0.7), respectively. GH therapy had no influence on the age at onset, the progression of puberty, duration of puberty and pubertal height gain. GH therapy induced higher fasting and glucose-stimulated insulin levels after 1 and 6 years, but 6 months after GH stop, all levels returned to normal. At baseline mean systolic blood pressure was significantly increased, but both systolic and diastolic blood pressure decreased significantly during 6 years of GH and remained so after GH stop. GH therapy demonstrated a beneficial effect on serum lipid profiles, body composition, bone mineral density and head growth. Treatment with 2 mg GH/m2 per day induced mean serum IGF-I levels of +2 SDS, whereas IGF-I levels remained within the normal range with 1 mg GH/m2 per day. In conclusion, long-term GH therapy of short SGA children with 1 mg/m2 per day appears to be effective and safe. Since the future consequences of high serum IGF-I levels during long-term GH therapy with 2 mg/m2 per day are as yet unknown, it seems safer to treat short prepubertal SGA children with a GH dose of 1 mg/m2 per day when children are to be treated continuously for many years.     

Simple methods to obtain preliminary growth estimates for fishes

Explored were methods to derive preliminary information on growth from other known life history parameters such as maximum size and size and age at first maturity. Use was made of the fact that with asymptotic length known, only one point is needed to determine the general shape of a von Bertalanffy growth curve. An empirical relationship was used to predict asymptotic length from maximum observed length. We used mean size reached at age 1 or 2 or mean age and size at first maturity, as is often provided in the literature, to derive preliminary von Bertalanffy growth curves. Results of this approach were then compared with published growth estimates. We used an empirical relationship to predict length at first maturity from asymptotic length when only the age at first maturity was given in the literature. Temperate fishes usually have restricted spawning periods lasting a few months per year and maturity is typically reached in the first, second, third, or later year, i.e. in steps of 12 months, with larger species maturing later. We used data in FishBase ( http://www.fishbase.org ) to establish typical ranges for age at first maturity and growth performance of temperate fishes as a function of maximum size. We present an approach that uses this framework to derive preliminary growth estimates for species of which only the maximum size is known.     

Improving marginal likelihood estimation for Bayesian phylogenetic model selection

The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be easily computed from the output of a Markov chain Monte Carlo analysis but often greatly overestimates the marginal likelihood. The thermodynamic integration (TI) method is much more accurate than the HM method but requires more computation. In this paper, we introduce a new method, steppingstone sampling (SS), which uses importance sampling to estimate each ratio in a series (the "stepping stones") bridging the posterior and prior distributions. We compare the performance of the SS approach to the TI and HM methods in simulation and using real data. We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed.     

Longitudinal Changes in Clock Drawing Test (CDT) Performance before and after Cognitive Decline

Background

Many scoring systems exist for clock drawing task variants. However, none of them are reliable in evaluating longitudinal changes of cognitive function. The purpose of this study is to create a simple yet optimal scoring procedure to evaluate cognitive decline using a clinic-based sample.

Methods

Clock-drawings from 121 participants (76 individuals with no dementia and later did not develop dementia after a mean 41.2-month follow-up, 45 individuals with no dementia became demented after a mean 42.3-month follow-up) were analyzed using t-test to determine a new and simplified CDT scoring system. The new scoring method was then compared with other commonly used systems.

Results

In the converters, there were only 7 items that are significantly different between the initial visits and the second visits. We propose a new scoring system that includes the seven critical items: numbers are equally spaced (12–3–6–9) (p = 0.031), the other eight numbers are marked (p = 0.022), numbers are clockwise (p = 0.002), all numbers are correct (p = 0.030), distance between numbers is constant (p = 0.016), clock has two hands (p = 0.000), arrows are drawn (p = 0.003). Compared with other traditionally used scoring methods, this based change clock drawing test (BCCDT) has one of the most balanced sensitivities/specificities with a clinic-based sample.

Conclusions

The new CDT scoring system provides further evidence in support of a simple and reliable clock-drawing scoring system in follow-up studies to evaluate cognitive decline, which can be used in assessing the efficacy of medicine.     

Implosion (Flooding)—a New Treatment for Phobias

A new technique is described for the treatment of phobic patients which may be more effective than other available methods to date. Three out of four patients treated by implosion (flooding) became almost symptom-free after a mean of 14 sessions and remained so over six-and-a-half months'' follow-up. The mechanism of action of the method is not yet clear.     

Growth reference charts and the nutritional status of Indian children

We evaluate the growth performance of Indian children of age 0-3 using data from the 1998-1999 National Family and Health Survey, making use of the new child growth standards developed by the World Health Organization’ Multicentre Growth Reference Study. We find that the new charts lead to an increase of 4.2 million in the estimated number of stunted children, and an increase of 2.3 million in the estimated number of wasted children. The estimated number of underweight children decreases instead by 2.1 million. We also use data on ethnic Indians living in the United Kingdom to provide evidence on the height genetic potential of Indians. We find that children of Indian ethnicity who live in the UK have anthropometric outcomes comparable to those in commonly used growth standards and that the height of ethnic South Asian in the sample is negatively related with the amount of time spent outside the United Kingdom.     

Flow cytometry: an alternative method for direct quantification of antigens adsorbed to aluminum hydroxide adjuvant

Flow cytometry (FC) has been widely used in biological research; however, its use for vaccine characterization has been very limited. Here we describe the development of an FC method for the direct quantification of two Neisseria meningitidis vaccine antigens, in mono- and multivalent formulations, while still adsorbed on aluminum hydroxide (AH) suspension. The antibody-based method is specific and sensitive. Because FC allows microscopic particle examination, the entire aluminum suspension carrying adsorbed antigen(s) can be analyzed directly. In addition to determining antigen concentration and identity, the assay is able to determine the distribution of the antigens on AH. High correlation coefficients (r²) were routinely achieved for a broad range of antigen doses from 0 to 150 μg/dose. Traditional assays for quantitative and qualitative antigen characterization on AH particles involve either complete aluminum dissolution or antigen desorption from the adjuvant. Because our direct method uses the whole AH suspension, the cumbersome steps used by traditional methods are not required. Those steps are often inefficient in desorbing the antigens and in some cases can lead to protein denaturation. We believe that this novel FC-based assay could circumvent some of the complex and tedious antigen–adjuvant desorption methods.     

Modeling the activity burst in the initial phase of cellulose hydrolysis by the processive cellobiohydrolase Cel7A

The hydrolysis of cellulose by processive cellulases, such as exocellulase TrCel7A from Trichoderma reesei, is typically characterized by an initial burst of high activity followed by a slowdown, often leading to incomplete hydrolysis of the substrate. The origins of these limitations to cellulose hydrolysis are not yet fully understood. Here, we propose a new model for the initial phase of cellulose hydrolysis by processive cellulases, incorporating a bound but inactive enzyme state. The model, based on ordinary differential equations, accurately reproduces the activity burst and the subsequent slowdown of the cellulose hydrolysis and describes the experimental data equally well or better than the previously suggested model. We also derive steady-state expressions that can be used to describe the pseudo-steady state reached after the initial activity burst. Importantly, we show that the new model predicts the existence of an optimal enzyme-substrate affinity at which the pseudo-steady state hydrolysis rate is maximized. The model further allows the calculation of glucose production rate from the first cut in the processive run and reproduces the second activity burst commonly observed upon new enzyme addition. These results are expected to be applicable also to other processive enzymes.     

Towards clustering of incomplete microarray data without the use of imputation

MOTIVATION: Clustering technique is used to find groups of genes that show similar expression patterns under multiple experimental conditions. Nonetheless, the results obtained by cluster analysis are influenced by the existence of missing values that commonly arise in microarray experiments. Because a clustering method requires a complete data matrix as an input, previous studies have estimated the missing values using an imputation method in the preprocessing step of clustering. However, a common limitation of these conventional approaches is that once the estimates of missing values are fixed in the preprocessing step, they are not changed during subsequent processes of clustering; badly estimated missing values obtained in data preprocessing are likely to deteriorate the quality and reliability of clustering results. Thus, a new clustering method is required for improving missing values during iterative clustering process. RESULTS: We present a method for Clustering Incomplete data using Alternating Optimization (CIAO) in which a prior imputation method is not required. To reduce the influence of imputation in preprocessing, we take an alternative optimization approach to find better estimates during iterative clustering process. This method improves the estimates of missing values by exploiting the cluster information such as cluster centroids and all available non-missing values in each iteration. To test the performance of the CIAO, we applied the CIAO and conventional imputation-based clustering methods, e.g. k-means based on KNNimpute, for clustering two yeast incomplete data sets, and compared the clustering result of each method using the Saccharomyces Genome Database annotations. The clustering results of the CIAO method are more significantly relevant to the biological gene annotations than those of other methods, indicating its effectiveness and potential for clustering incomplete gene expression data. AVAILABILITY: The software was developed using Java language, and can be executed on the platforms that JVM (Java Virtual Machine) is running. It is available from the authors upon request.     

Early palatal changes in complete and incomplete cleft lip and/or palate.

Early palatal development in various complete and incomplete forms of cleft lip and/or palate (CLP) was studied from birth to 3 months of age by means of dental casts. Palatal morphology (shape) and dimensions--based on reproducible reference points--were determined in a group of 128 CLP children and 68 normal children who served as controls. Substantial normal palatal growth during the first 3 months of life was observed. Round arch forms changed into oval arch forms. Growth mainly takes place in the sagittal direction (+4 mm) (transverse: +1 mm). Palates of CLP children differed significantly dependent on the type of cleft and whether the cleft was complete or incomplete. Cleft lip and alveolus children and bilateral cleft lip and palate children had more elongated palatal arches, whereas unilateral cleft lip and palate children and cleft palate children had wider palatal arches than the control group. Incomplete clefts differed from the control group in the same direction as their complete cleft forms, though less distinctly. Preoperative orthopedics used in CLP patients does not stimulate growth. On the contrary, it even restricts growth.     

Challenges of loss to follow-up in tuberculosis research

Background

In studies evaluating methods for diagnosing tuberculosis (TB), follow-up to verify the presence or absence of active TB is crucial and high dropout rates may significantly affect the validity of the results. In a study assessing the diagnostic performance of the QuantiFERON®-TB Gold In-Tube test in TB suspect children in Tanzania, factors influencing patient adherence to attend follow-up examinations and reasons for not attending were examined.

Methods

In 160 children who attended and 102 children who did not attend scheduled 2-month follow-up baseline health characteristics, demographic data and risk factors for not attending follow-up were determined. Qualitative interviews were used to understand patient and caretakers reasons for not returning for scheduled follow-up.

Results

Being treated for active TB in the DOTS program (OR: 4.14; 95% CI:1.99–8.62;p-value<0.001) and receiving money for the bus fare (OR:129; 95% CI 16->100;P-value<0.001) were positive predictors for attending follow-up at 2 months, and 21/85(25%) of children not attending scheduled follow-up had died. Interviews revealed that limited financial resources, i.e. lack of money for transportation and poor communication, were related to non-adherence.

Conclusion

Patients lost to follow-up is a potential problem for TB research. Receiving money for transportation to the hospital and communication is crucial for adherence to follow-up conducted at a study facility. Strategies to ensure follow-up should be part of any study protocol.     

Multifactor-dimensionality reduction versus family-based association tests in detecting susceptibility loci in discordant sib-pair studies

Complex diseases are generally thought to be under the influence of multiple, and possibly interacting, genes. Many association methods have been developed to identify susceptibility genes assuming a single-gene disease model, referred to as single-locus methods. Multilocus methods consider joint effects of multiple genes and environmental factors. One commonly used method for family-based association analysis is implemented in FBAT. The multifactor-dimensionality reduction method (MDR) is a multilocus method, which identifies multiple genetic loci associated with the occurrence of complex disease. Many studies of late onset complex diseases employ a discordant sib pairs design. We compared the FBAT and MDR in their ability to detect susceptibility loci using a discordant sib-pair dataset generated from the simulated data made available to participants in the Genetic Analysis Workshop 14. Using FBAT, we were able to identify the effect of one susceptibility locus. However, the finding was not statistically significant. We were not able to detect any of the interactions using this method. This is probably because the FBAT test is designed to find loci with major effects, not interactions. Using MDR, the best result we obtained identified two interactions. However, neither of these reached a level of statistical significance. This is mainly due to the heterogeneity of the disease trait and noise in the data.     

Association between Spouse/Child Separation and Migration-Related Stress among a Random Sample of Rural-to-Urban Migrants in Wuhan,China

BackgroundMillions of people move from rural areas to urban areas in China to pursue new opportunities while leaving their spouses and children at rural homes. Little is known about the impact of migration-related separation on mental health of these rural migrants in urban China.MethodsSurvey data from a random sample of rural-to-urban migrants (n = 1113, aged 18–45) from Wuhan were analyzed. The Domestic Migration Stress Questionnaire (DMSQ), an instrument with four subconstructs, was used to measure migration-related stress. The relationship between spouse/child separation and stress was assessed using survey estimation methods to account for the multi-level sampling design.Results16.46% of couples were separated from their spouses (spouse-separation only), 25.81% of parents were separated from their children (child separation only). Among the participants who married and had children, 5.97% were separated from both their spouses and children (double separation). Spouse-separation only and double separation did not scored significantly higher on DMSQ than those with no separation. Compared to parents without child separation, parents with child separation scored significantly higher on DMSQ (mean score = 2.88, 95% CI: [2.81, 2.95] vs. 2.60 [2.53, 2.67], p < .05). Stratified analysis by separation type and by gender indicated that the association was stronger for child-separation only and for female participants.ConclusionChild-separation is an important source of migration-related stress, and the effect is particularly strong for migrant women. Public policies and intervention programs should consider these factors to encourage and facilitate the co-migration of parents with their children to mitigate migration-related stress.     

Age-developmental stage and severity of trauma related symptoms, anxiety and depressive symptoms in participants who lost their fathers during the war in Croatia

Children of different ages will experience a traumatic event in a different ways. The most important in the generalization of research findings is recognizing that children of different ages think differently, act differently and have different emotional functioning. Experiences that are extremely traumatic to an adult may be perceived by a young child as something that is not so frightening. The fear that the child feels will more frequently be a reflection of that of the adult rather than generated by the child's own perception of the event. So, the individual experience of the trauma is age dependent. Our study focused on children who lost their fathers in conditions of war The aim was to explore the association between age-developmental stages and the severity of trauma related symptoms, anxiety and depressive symptoms in participants who lost their fathers during the war. The study included 103 people who lost their fathers during the war in Croatia, who came to the physical and psychiatric examination organized by the Ministry of Family, War Veterans and Intergenerational Solidarity. The sample was consisted of the participants who were children, or not born yet, at the time when they lost their fathers during the war in Croatia. At the time of interview, the participants were aged between 15 and 35 years old. Data was collected using a structured clinical interview which also included socio-demographic data. Data about former and current psychiatric symptoms were collected using the following instruments: Clinician- Administrated PTSD Scale (CAPS), Hamilton anxiety scale (HAMA), Hamilton depression scale (HAMD). Results showed that there was significant correlation between age and results on used scales. The participants who lost their fathers at a very young age or even before they were born showed less trauma symptoms (r=0.249; p < 0.05) less anxiety (r=0.374; p < 0.01) and depressive (r=0.384; p<0.01) symptoms than participants who lost their fathers at an older age. The study confirmed that the individual experience of the trauma of losing a father in war circumstances is associated with age.     

The association between socioeconomic status and exposure to mobile telecommunication networks in children and adolescents

A potential association between socioeconomic status (SES) and self‐reported use of mobile phones has been investigated in a few studies. If measured exposure to mobile phone networks differs by SES in children, it has not yet been studied. Interview data of 1,481 children and 1,505 adolescents on participants' mobile phone use, socio‐demographic characteristics and potential confounders were taken from the German MobilEe‐study. Sociodemographic data was used to stratify participants into three “status groups” (low, middle, high). Using a personal dosimeter, we obtained an exposure profile over 24 h for each of the participants. Exposure levels during waking hours were expressed as mean percentage of the reference level. Children with a low SES were more likely to own a mobile phone (OR 2.1; 95% CI: 1.1–3.9) and also reported to use their mobile phone longer per day (OR 2.4; 95% CI: 1.1–5.4) than children with a high SES. For adolescents, self‐reported duration of mobile phone use per day was also higher with a low SES (OR: 3.4; 95% CI: 1.4–8.4) compared with a high SES. No association between SES and measured exposure to mobile telecommunication networks was seen for children or adolescents. Mobile phone use may differ between status groups with higher use among disadvantaged groups. However, this does not result in higher overall exposure to mobile telecommunication networks. Whether short duration of own mobile phone use or the small numbers of participants with a low SES are causal, have to be investigated in further studies. Bioelectromagnetics 31:20–27, 2010. © 2009 Wiley‐Liss, Inc.     

Using highly efficient nonlinear experimental design methods for optimization of Lactococcus lactis fermentation in chemically defined media

Optimization of fermentation media and processes is a difficult task due to the potential for high dimensionality and nonlinearity. Here we develop and evaluate variations on two novel and highly efficient methods for experimental fermentation optimization. The first approach is based on using a truncated genetic algorithm with a developing neural network model to choose the best experiments to run. The second approach uses information theory, along with Bayesian regularized neural network models, for experiment selection. To evaluate these methods experimentally, we used them to develop a new chemically defined medium for Lactococcus lactis IL1403, along with an optimal temperature and initial pH, to achieve maximum cell growth. The media consisted of 19 defined components or groups of components. The optimization results show that the maximum cell growth from the optimal process of each novel method is generally comparable to or higher than that achieved using a traditional statistical experimental design method, but these optima are reached in about half of the experiments (73–94 vs. 161, depending on the variants of methods). The optimal chemically defined media developed in this work are rich media that can support high cell density growth 3.5–4 times higher than the best reported synthetic medium and 72% higher than a commonly used complex medium (M17) at optimization scale. The best chemically defined medium found using the method was evaluated and compared with other defined or complex media at flask‐ and fermentor‐scales. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Identifying molecular markers associated with classification of genotypes by External Logistic Biplots

For characterization of genetic diversity in genotypes several molecular techniques, usually resulting in a binary data matrix, have been used. Despite the fact that in Cluster Analysis (CA) and Principal Coordinates Analysis (PCoA) the interpretation of the variables responsible for grouping is not straightforward, these methods are commonly used to classify genotypes using DNA molecular markers. In this article, we present a novel algorithm that uses a combination of PCoA, CA and Logistic Regression (LR), as a better way to interpret the variables (alleles or bands) associated to the classification of genotypes. The combination of three standard techniques with some new ideas about the geometry of the procedures, allows constructing an External Logistic Biplot (ELB) that helps in the interpretation of the variables responsible for the classification or ordination. An application of the method to study the genetic diversity of four populations from Africa, Asia and Europe, using the HapMap data is included. AVAILABILITY: The Matlab code for implementing the methods may be obtained from the web site: http://biplot.usal.es.     

Analysis of protein composition of rabbit aqueous humor following two different cataract surgery incision procedures using 2-DE and LC-MS/MS

Background  

The aqueous humor (AH), a liquid of the anterior and posterior chamber of the eye, comprises many proteins with various roles and important biological functions. Many of these proteins have not been identified yet and their functions in AH are still unknown. Recently, our laboratory published the protein database of AH obtained from healthy rabbits which expanded known protein identifications by 65%. Our present study extends our previous work and analyses AH following two types of cataract surgery incision procedures (clear corneal and limbal incisions) by using two dimensional gel electrophoresis (2-DE) and liquid chromatography tandem mass spectrometry (LC-MS/MS). Although both incision protocols are commonly used during cataract surgeries, the difference in protein composition and their release into AH following each surgery has never been systematically compared and remains unclear. The first step, which is the focus of this work, is to assess the scale of the protein change, at which time does maximum release occurs and when possible, to identify protein changes.     

Gas dispersion in volume-cycled tube flow. II. Tracer bolus experiments.

We present a new method for rapid measurement of local gas dispersion in volume-cycled tube flow. After a small bolus of tracer gas (argon) was injected into the oscillating flow, the time-averaged effective diffusion coefficient (mean value of Deff/D) for axial transport of a tracer gas is evaluated from local argon concentration measurements taken by a mass spectrometer. Two methods are presented for the evaluation of mean value of Deff/D from the concentration measurements: one uses all the sampled data, and the other uses only the local peaks of the concentration. Experiments were conducted in two tubes (radius = 0.85 or 1.0 cm) over a range of frequencies (0.42 less than or equal to f less than or equal to 8.5 Hz) and tidal volumes (7 less than or equal to VT less than or equal to 48 ml). The experimental results show very good agreement with the theoretical predictions of Elad et al. (J. Appl. Physiol. 72: 312-320, 1992). In the absence of oscillations (static fluid), the resulting mean value of Deff/D converges to that of molecular diffusion. We also show that concentration data may be acquired at any radial or axial position, not necessarily at the tracer gas injection point, and the resulting mean value of Deff/D is independent of the spatial position of the sampling catheter. This method is of similar accuracy and is substantially faster than previous methods for measuring gas dispersion in oscillatory flows. The rapidity of these measurements may permit this method to be used for the in vivo assessment of gas transport properties within the pulmonary system.