Hierarchical Models in the Brain

This paper describes a general model that subsumes many parametric models for continuous data. The model comprises hidden layers of state-space or dynamic causal models, arranged so that the output of one provides input to another. The ensuing hierarchy furnishes a model for many types of data, of arbitrary complexity. Special cases range from the general linear model for static data to generalised convolution models, with system noise, for nonlinear time-series analysis. Crucially, all of these models can be inverted using exactly the same scheme, namely, dynamic expectation maximization. This means that a single model and optimisation scheme can be used to invert a wide range of models. We present the model and a brief review of its inversion to disclose the relationships among, apparently, diverse generative models of empirical data. We then show that this inversion can be formulated as a simple neural network and may provide a useful metaphor for inference and learning in the brain

Pre-Bilaterian Origins of the Hox Cluster and the Hox Code: Evidence from the Sea Anemone, Nematostella vectensis

BACKGROUND: Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone Nematostella vectensis challenge recent claims that the Hox code is a bilaterian invention and that no “true” Hox genes exist in the phylum Cnidaria. METHODOLOGY/PRINCIPAL FINDINGS: Phylogenetic analyses of 18 Hox-related genes from Nematostella identify putative Hox1, Hox2, and Hox9+ genes. Statistical comparisons among competing hypotheses bolster these findings, including an explicit consideration of the gene losses implied by alternate topologies. In situ hybridization studies of 20 Hox-related genes reveal that multiple Hox genes are expressed in distinct regions along the primary body axis, supporting the existence of a pre-bilaterian Hox code. Additionally, several Hox genes are expressed in nested domains along the secondary body axis, suggesting a role in “dorsoventral” patterning. CONCLUSIONS/SIGNIFICANCE: A cluster of anterior and posterior Hox genes, as well as ParaHox cluster of genes evolved prior to the cnidarian-bilaterian split. There is evidence to suggest that these clusters were formed from a series of tandem gene duplication events and played a role in patterning both the primary and secondary body axes in a bilaterally symmetrical common ancestor. Cnidarians and bilaterians shared a common ancestor some 570 to 700 million years ago, and as such, are derived from a common body plan. Our work reveals several conserved genetic components that are found in both of these diverse lineages. This finding is consistent with the hypothesis that a set of developmental rules established in the common ancestor of cnidarians and bilaterians is still at work today

High-accuracy transmission and fluorescence XAFS of zinc at 10 K, 50 K, 100 K and 150 K using the hybrid technique

The most accurate measurements of the mass attenuation coefficient for metals at low temperature for the zinc K-edge from 9.5 keV to 11.5 keV at temperatures of 10 K, 50 K, 100 K and 150 K using the hybrid technique are reported. This is the first time transition metal X-ray absorption fine structure (XAFS) has been studied using the hybrid technique and at low temperatures. This is also the first hybrid-like experiment at the Australian Synchrotron. The measured transmission and fluorescence XAFS spectra are compared and benchmarked against each other with detailed systematic analyses. A recent method for modelling self-absorption in fluorescence has been adapted and applied to a solid sample. The XAFS spectra are analysed using eFEFFIT to provide a robust measurement of the evolution of nanostructure, including such properties as net thermal expansion and mean-square relative displacement. This work investigates crystal dynamics, nanostructural evolution and the results of using the Debye and Einstein models to determine atomic positions. Accuracies achieved, when compared with the literature, exceed those achieved by both relative and differential XAFS, and represent a state-of-the-art for future structural investigations. Bond length uncertainties are of the order of 20–40 fm

Hearing sensitivity in adults with a unilateral cleft lip and palate after two-stage palatoplasty

Objective To evaluate long-term hearing and middle ear status in patients treated for a unilateral complete cleft lip and palate (UCLP) by two-stage palatoplasty. Methods Forty-nine UCLP patients aged 17 years and older were included in this retrospective study. Patients were invited for a multidisciplinary long-term follow-up of their treatment at a tertiary center for craniofacial surgery in the Netherlands. ENT assessment included tympanometry and pure-tone audiometry. Medical files were searched for medical and surgical history. Results In total, 19.4% of the patients had significant long-term hearing loss (PTA > 20 dB), comprising conductive hearing loss in 21.5% of the patients. In the majority (70%), this hearing loss was more pronounced at higher frequencies. In 25% the high fletcher index showed hearing thresholds above 20 dB. Ventilation tubes were placed at least once in 78.7% of the patients. The frequency of tube insertion was positively correlated with the incidence of reduced tympanic compliance (tympanogram type B) and the need for a pharyngoplasty. Conclusion The present study reports long-term hearing outcomes in UCLP patients with hard palate closure at 3 years of age. Persistent hearing loss was observed in 19.4% of our patients (PTA > 20 dB), mainly at the higher frequencies. Ventilation tube placement was associated with reduced tympanic compliance and higher risk on hearing loss (PTA air conduction). Our high incidence of velopharyngeal incompetence during early childhood, which is likely associated with Eustachian tube dysfunction, might have contributed to these results

Rapid PCR amplification of minimal enediyne polyketide synthase cassettes leads to a predictive familial classification model

A universal PCR method for the rapid amplification of minimal enediyne polyketide synthase (PKS) genes and the application of this methodology to clone remaining prototypical genes from producers of structurally determined enediynes in both family types are presented. A phylogenetic analysis of the new pool of bona fide enediyne PKS genes, consisting of three from 9-membered producers (neocarzinostatin, C1027, and maduropeptin) and three from 10-membered producers (calicheamicin, dynemicin, and esperamicin), reveals a clear genotypic distinction between the two structural families from which to form a predictive model. The results from this study support the postulation that the minimal enediyne PKS helps define the structural divergence of the enediyne core and provides the key tools for generating enediyne hybrid genes/molecular scaffolds; by using the model, a classification is also provided for the unknown enediyne PKS genes previously identified via genome scanning