Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests

Background  

Chow and Liu showed that the maximum likelihood tree for multivariate discrete distributions may be found using a maximum weight spanning tree algorithm, for example Kruskal's algorithm. The efficiency of the algorithm makes it tractable for high-dimensional problems.     

The Brazilian Preference: Cesarean Delivery among Immigrants in Portugal

Objective

To evaluate how the country of origin affects the probability of being delivered by cesarean section when giving birth at public Portuguese hospitals.

Study Design

Women delivered of a singleton birth (n = 8228), recruited from five public level III maternities (April 2005–August 2006) during the procedure of assembling a birth cohort, were classified according to the country of origin and her migration status as Portuguese (n = 7908), non-Portuguese European (n = 84), African (n = 77) and Brazilian (n = 159). A Poisson model was used to evaluate the association between country of birth and cesarean section that was measured by adjusted prevalence ratio (PR) and respective 95% confidence intervals (95%CI).

Results

The cesarean section rate varied from 32.1% in non-Portuguese European to 48.4% in Brazilian women (p = 0.008). After adjustment for potential confounders and compared to Portuguese women as a reference, Brazilian women presented significantly higher prevalence of cesarean section (PR = 1.26; 95%CI: 1.08–1.47). The effect was more evident among multiparous women (PR = 1.39; 95%CI: 1.12–1.73) and it was observed when cesarean section was performed either before labor (PR = 1.43; 95%CI: 0.99–2.06) or during labor (PR = 1.30; 95%CI: 1.07–1.58).

Conclusions

The rate of cesarean section was significantly higher among Brazilian women and it was independent of the presence of any known risk factors or usual clinical indications, suggesting that cultural background influences the mode of delivery overcoming the expected standard of care and outcomes in public health services.     

Enlarging a training set for genomic selection by imputation of un-genotyped animals in populations of varying genetic architecture

Background

The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped.

Methods

Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets.

Results

Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams.

Conclusions

Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.     

Bacterial colonization of Hydra hatchlings follows a robust temporal pattern

Animals are colonized by complex bacterial communities. The processes controlling community membership and influencing the establishment of the microbial ecosystem during development are poorly understood. Here we aimed to explore the assembly of bacterial communities in Hydra with the broader goal of elucidating the general rules that determine the temporal progression of bacterial colonization of animal epithelia. We profiled the microbial communities in polyps at various time points after hatching in four replicates. The composition and temporal patterns of the bacterial communities were strikingly similar in all replicates. Distinct features included high diversity of community profiles in the first week, a remarkable but transient adult-like profile 2 weeks after hatching, followed by progressive emergence of a stable adult-like pattern characterized by low species diversity and the preponderance of the Betaproteobacterium Curvibacter. Intriguingly, this process displayed important parallels to the assembly of human fecal communities after birth. In addition, a mathematical modeling approach was used to uncover the organizational principles of this colonization process, suggesting that both, local environmental or host-derived factor(s) modulating the colonization rate, as well as frequency-dependent interactions of individual bacterial community members are important aspects in the emergence of a stable bacterial community at the end of development.     

Can Community Health Workers Report Accurately on Births and Deaths? Results of Field Assessments in Ethiopia,Malawi and Mali

Introduction

Most low-income countries lack complete and accurate vital registration systems. As a result, measures of under-five mortality rates rely mostly on household surveys. In collaboration with partners in Ethiopia, Ghana, Malawi, and Mali, we assessed the completeness and accuracy of reporting of births and deaths by community-based health workers, and the accuracy of annualized under-five mortality rate estimates derived from these data. Here we report on results from Ethiopia, Malawi and Mali.

Method

In all three countries, community health workers (CHWs) were trained, equipped and supported to report pregnancies, births and deaths within defined geographic areas over a period of at least fifteen months. In-country institutions collected these data every month. At each study site, we administered a full birth history (FBH) or full pregnancy history (FPH), to women of reproductive age via a census of households in Mali and via household surveys in Ethiopia and Malawi. Using these FBHs/FPHs as a validation data source, we assessed the completeness of the counts of births and deaths and the accuracy of under-five, infant, and neonatal mortality rates from the community-based method against the retrospective FBH/FPH for rolling twelve-month periods. For each method we calculated total cost, average annual cost per 1,000 population, and average cost per vital event reported.

Results

On average, CHWs submitted monthly vital event reports for over 95 percent of catchment areas in Ethiopia and Malawi, and for 100 percent of catchment areas in Mali. The completeness of vital events reporting by CHWs varied: we estimated that 30%-90% of annualized expected births (i.e. the number of births estimated using a FPH) were documented by CHWs and 22%-91% of annualized expected under-five deaths were documented by CHWs. Resulting annualized under-five mortality rates based on the CHW vital events reporting were, on average, under-estimated by 28% in Ethiopia, 32% in Malawi, and 9% in Mali relative to comparable FPHs. Costs per vital event reported ranged from $21 in Malawi to $149 in Mali.

Discussion

Our findings in Mali suggest that CHWs can collect complete and high-quality vital events data useful for monitoring annual changes in under-five mortality rates. Both the supervision of CHWs in Mali and the rigor of the associated field-based data quality checks were of a high standard, and the size of the pilot area in Mali was small (comprising of approximately 53,205 residents in 4,200 households). Hence, there are remaining questions about whether this level of vital events reporting completeness and data quality could be maintained if the approach was implemented at scale. Our experience in Malawi and Ethiopia suggests that, in some settings, establishing and maintaining the completeness and quality of vital events reporting by CHWs over time is challenging. In this sense, our evaluation in Mali falls closer to that of an efficacy study, whereas our evaluations in Ethiopia and Malawi are more akin to an effectiveness study. Our overall findings suggest that no one-size-fits-all approach will be successful in guaranteeing complete and accurate reporting of vital events by CHWs.     

Does small-sided-games’ court area influence metabolic,perceptual, and physical performance parameters of young elite basketball players?

The purpose of this study was to investigate the effect of court size on physiological responses and physical performance of young elite basketball players. Twelve male basketball players (18.6 ± 0.5 years; 88.8 ± 14.5 kg; 192.6 ± 6.5 cm) from an under-19 team performed two small-sided games (matches) with different court areas (28x15 m and 28x9 m; 28x15 and 28x9 protocols). The number of players (3x3) was kept the same in each protocol. The players performed a repeated-sprint ability (RSA) test before and after each match. Blood lactate concentration was collected before (pre) and after (post) the matches, and the session rating of perceived exertion (session-RPE) was determined 30 minutes after the match. Best and mean time in the RSA test were not different between the 28x15 and the 28x9 match protocols (p > 0.05). A significant difference was observed for lactate concentration from pre- to post-match (p < 0.05) in both protocols (28x15 and 28x9); however, there was no significant interaction between protocols. A similar session-RPE mean score (28x15: 7.2 ± 1.4 and 28x9: 6.6 ± 1.4) was detected for both protocols (p > 0.05, ES=0.41). In summary, the results of the current study suggest that the different court areas induced similar responses. Although there was no significant difference in effort perception, players tended to perceive a greater effort in the larger court size.     

Stringent and reproducible tetracycline-regulated transgene expression by site-specific insertion at chromosomal loci with pre-characterised induction characteristics

Background  

The ability to regulate transgene expression has many applications, mostly concerning the analysis of gene function. Desirable induction characteristics, such as low un-induced expression, high induced expression and limited cellular heterogeneity, can be seriously impaired by chromosomal position effects at the site of transgene integration. Many clones may therefore need to be screened before one with optimal induction characteristics is identified. Furthermore, such screens must be repeated for each new transgene investigated, and comparisons between clones with different transgenes is complicated by their different integration sites.     

An IGF-I promoter polymorphism modifies the relationships between birth weight and risk factors for cardiovascular disease and diabetes at age 36

BACKGROUND: Biochemical testing for pheochromocytoma by measurement of fractionated plasma metanephrines is limited by false positive rates of up to 18% in people without known genetic predisposition to the disease. The plasma normetanephrine fraction is responsible for most false positives and plasma normetanephrine increases with age. The objective of this study was to determine if we could improve the specificity of fractionated plasma measurements, by statistically adjusting for age. METHODS: An age-adjusted metanephrine score was derived using logistic regression from 343 subjects (including 33 people with pheochromocytoma) who underwent fractionated plasma metanephrine measurements as part of investigations for suspected pheochromocytoma at Mayo Clinic Rochester (derivation set). The performance of the age-adjusted score was validated in a dataset of 158 subjects (including patients 23 with pheochromocytoma) that underwent measurements of fractionated plasma metanephrines at Mayo Clinic the following year (validation dataset). None of the participants in the validation dataset had known genetic predisposition to pheochromocytoma. RESULTS: The sensitivity of the age-adjusted metanephrine score was the same as that of traditional interpretation of fractionated plasma metanephrine measurements, yielding a sensitivity of 100% (23/23, 95% confidence interval [CI] 85.7%, 100%). However, the false positive rate with traditional interpretation of fractionated plasma metanephrine measurements was 16.3% (22/135, 95% CI, 11.0%, 23.4%) and that of the age-adjusted score was significantly lower at 3.0% (4/135, 95% CI, 1.2%, 7.4%) (p < 0.001 using McNemar's test). CONCLUSION: An adjustment for age in the interpretation of results of fractionated plasma metanephrines may significantly decrease false positives when using this test to exclude sporadic pheochromocytoma. Such improvements in false positive rate may result in savings of expenditures related to confirmatory imaging.     

A theory of germinal center B cell selection, division, and exit

High-affinity antibodies are generated in germinal centers in a process involving mutation and selection of B cells. Information processing in germinal center reactions has been investigated in a number of recent experiments. These have revealed cell migration patterns, asymmetric cell divisions, and cell-cell interaction characteristics, used here to develop a theory of germinal center B cell selection, division, and exit (the LEDA model). According to this model, B cells selected by T follicular helper cells on the basis of successful antigen processing always return to the dark zone for asymmetric division, and acquired antigen is inherited by one daughter cell only. Antigen-retaining B cells differentiate to plasma cells and leave the germinal center through the dark zone. This theory has implications for the functioning of germinal centers because compared to previous models, high-affinity antibodies appear one day earlier and the amount of derived plasma cells is considerably larger.