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.     

Nutritional suitability of some uni-algal diets for freshwater calanoids: unexpected inadequacies of commonly used edible greens and others

• 1 Naupliar and copepodid development times (Dn and Dc, respectively) of two African freshwater calanoids (Metadiaptomus meridianus and Tropodiaptomus spectabilis) were measured on mono-specific diets of comparably sized Chlamydomonas reinhardii, Scenedesmus acutus, Cryptomonas sp., Rhodomonas minuta, Cyclotella meneghiniana, and Selenastrum capricornutum, to test the nutritional adequacy of these algae. Comparisons were made at a standard temperature (17°C) and food supply level (1 mgCl^?1).
• 2 All diets other than Scenedesmus and Selenastrum supported complete naupliar development at broadly comparable times within and between calanoids, apart from greatly protracted Dn values for M. meridianus on Cyclotella. Dc durations were more variable between diet types, and both Chlamydomonas and Cyclotella were inferior or inadequate for copepodid development.
• 3 Both naupliar and copepodid stages ingested radiolabelled Scenedesmus and Selenastrum readily. Comparative incorporation rate measures of Selenastrum and Cryptomonas respectively exceeded estimated metabolic maintenance needs of stage 3/4 nauplii of T. spectabilis by some 56% and 790%. Scope for growth (‘surplus’ energy) was accordingly fourteen-fold greater on Cryptomonas than on Selenastrum /Scenedesmus. The dietary inadequacy of these two green algae is thus attributed largely to low digestibility, and perhaps some biochemical deficiency.

     

Factors influencing the distributional abundance of two trophic guilds of Peruvian cricetid rodents

The distributional abundance of 13 species of southern Peruvian rodents is significantly correlated with altitude and patterns of vegetation but vegetation is a better predictor than altitude. Coincidental reversals in the altitudinal trends of both vegetation and rodents demonstrate that rodents are responding to vegetation patterns. Abundance and diversity of rodents are greatest around 4000 m elevation which coincides with the region of greatest vegetational abundance and seasonally heavy rainfall.
The rodent communities consist of two separate feeding guilds, omnivores and insectivores and these guilds show distinctly different distributional patterns. Insectivorous species are strongly associated with the zone of seasonally heavy rainfall (4000 m) whereas omnivorous rodents are relatively abundant over a broader spectrum of elevations and habitats. In a previous study of these same communities, we showed a correspondence between rodent morphology and their diets. This study reveals a correspondence between distributional abundance of the various species and their diets. We conclude that the distributional abundance of southern Peruvian rodents is related to the physiological constraints imposed by altitude (climate) and the distributional abundance of food resources.     

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.     

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.     

Stress Response of Working African Elephants to Transportation and Safari Adventures

Abstract: African elephants (Loxodonta africana) are intensively managed in southern Africa and are routinely translocated between reserves. Domesticated elephants are used for elephant-back safaris and interactions with guests. Understanding how elephants respond to such activities is critical because of welfare issues associated with both humans and elephants. We investigated the stress response (i.e., fecal glucocorticoid metabolite secretion [FGM]) of working elephants in Letsatsing Game Reserve, South Africa, over 1 year to evaluate their response to transportation and ecotourism activities. We used free-ranging elephants in adjacent Pilanesburg National Park as controls. Fecal glucocorticoid metabolites were greatest prior to and during translocation and declined over the year. Within 1–2 months of transportation, FGM levels in working elephants became indistinguishable from those in wild elephants. Fecal glucocorticoid metabolite levels were higher during human interaction days than days without interaction. The highest observed FGM levels were associated with transportation and episodic loud noises. Transportation is a stressful activity for elephants, and ≥3 months should be provided to translocated elephants to acclimate to their new surroundings. Although stress levels of elephants increased slightly when interacting with humans in the contexts we studied, evaluating interactions under a wider range of contexts is necessary to minimize danger to elephants and humans.     

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.