Utility of molecular phylogenetic methods: a critique of immuno-taxonomy

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Elevated fetal steroidogenic activity in autism

Autism affects males more than females, giving rise to the idea that the influence of steroid hormones on early fetal brain development may be one important early biological risk factor. Utilizing the Danish Historic Birth Cohort and Danish Psychiatric Central Register, we identified all amniotic fluid samples of males born between 1993 and 1999 who later received ICD-10 (International Classification of Diseases, 10th Revision) diagnoses of autism, Asperger syndrome or PDD-NOS (pervasive developmental disorder not otherwise specified) (n=128) compared with matched typically developing controls. Concentration levels of Δ4 sex steroids (progesterone, 17α-hydroxy-progesterone, androstenedione and testosterone) and cortisol were measured with liquid chromatography tandem mass spectrometry. All hormones were positively associated with each other and principal component analysis confirmed that one generalized latent steroidogenic factor was driving much of the variation in the data. The autism group showed elevations across all hormones on this latent generalized steroidogenic factor (Cohen's d=0.37, P=0.0009) and this elevation was uniform across ICD-10 diagnostic label. These results provide the first direct evidence of elevated fetal steroidogenic activity in autism. Such elevations may be important as epigenetic fetal programming mechanisms and may interact with other important pathophysiological factors in autism

Immuno-taxonomy and the reconstruction of brachiopod phylogeny

In response to an earlier critique (Cohen 1992), immuno-taxonomy has been defended as providing a timely and practical approach to brachiopod systematics (Curry et al. 1993). Although the concept of applying this methodology to the brachiopod shell is novel and worthwhile, and has the potential importance for palaeobiology, the alternative analysis given here suggests that its practical utility remains highly uncertain because of conceptual and methodological limitations. These limitations cast doubt on, but do not necessarily disprove, systematic relationships inferred from the immuno-taxonomic data (Collins et al. 1991c; (Curry et al. 1991)

Control of dipolar relaxation in external fields

We study dipolar relaxation in both ultra-cold thermal and Bose-condensed chromium atom gases. We show three different ways to control dipolar relaxation, making use of either a static magnetic field, an oscillatory magnetic field, or an optical lattice to reduce the dimensionality of the gas from 3D to 2D. Although dipolar relaxation generally increases as a function of a static magnetic field intensity, we find a range of non-zero magnetic field intensities where dipolar relaxation is strongly reduced. We use this resonant reduction to accurately determine the S=6 scattering length of chromium atoms: $a_6 = 103 \pm 4 a_0$. We compare this new measurement to another new determination of $a_6$, which we perform by analysing the precise spectroscopy of a Feshbach resonance in d-wave collisions, yielding $a_6 = 102.5 \pm 0.4 a_0$. These two measurements provide by far the most precise determination of $a_6$ to date. We then show that, although dipolar interactions are long-range interactions, dipolar relaxation only involves the incoming partial wave $l=0$ for large enough magnetic field intensities, which has interesting consequences on the stability of dipolar Fermi gases. We then study ultra-cold chromium gases in a 1D optical lattice resulting in a collection of independent 2D gases. We show that dipolar relaxation is modified when the atoms collide in reduced dimensionality at low magnetic field intensities, and that the corresponding dipolar relaxation rate parameter is reduced by a factor up to 7 compared to the 3D case. Finally, we study dipolar relaxation in presence of radio-frequency (rf) oscillating magnetic fields, and we show that both the output channel energy and the transition amplitude can be controlled by means of rf frequency and Rabi frequency.Comment: 25 pages, 17 figure

Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classification (the subphylum Phoroniformea nov.)

Molecular phylogenetic analyses of aligned 18S rDNA gene sequences from articulate and inarticulate brachiopods representing all major extant lineages, an enhanced set of phoronids and several unrelated protostome taxa, confirm previous indications that in such data, brachiopod and phoronids form a well-supported clade that (on previous evidence) is unambiguously affiliated with protostomes rather than deuterostomes. Within the brachiopod-phoronid clade, an association between phoronids and inarticulate brachiopods is moderately well supported, whilst a close relationship between phoronids and craniid inarticulates is weakly indicated. Brachiopod-phoronid monophyly is reconciled with the most recent Linnaean classification of brachiopods by abolition of the phylum Phoronida and rediagnosis of the phylum Brachiopoda to include tubiculous, shell-less forms. Recognition that brachiopods and phoronids are close genealogical allies of protostome phyla such as molluscs and annelids, but are much more distantly related to deuterostome phyla such as echinoderms and chordates, implies either (or both) that the morphology and ontogeny of blastopore, mesoderm and coelom formation have been widely misreported or misinterpreted, or that these characters have been subject to extensive homoplasy. This inference, if true, undermines virtually all morphology-based reconstructions of phylogeny made during the past century or more

Population Dynamics on Complex Food Webs

In this work we analyse the topological and dynamical properties of a simple model of complex food webs, namely the niche model. In order to underline competition among species, we introduce "prey" and "predators" weighted overlap graphs derived from the niche model and compare synthetic food webs with real data. Doing so, we find new tests for the goodness of synthetic food web models and indicate a possible direction of improvement for existing ones. We then exploit the weighted overlap graphs to define a competition kernel for Lotka-Volterra population dynamics and find that for such a model the stability of food webs decreases with its ecological complexity.Comment: 11 Pages, 5 Figures, styles enclosed in the submissio