Multi-Modal Neuroimaging Analysis and Visualization Tool (MMVT)

Sophisticated visualization tools are essential for the presentation and exploration of human neuroimaging data. While two-dimensional orthogonal views of neuroimaging data are conventionally used to display activity and statistical analysis, three-dimensional (3D) representation is useful for showing the spatial distribution of a functional network, as well as its temporal evolution. For these purposes, there is currently no open-source, 3D neuroimaging tool that can simultaneously visualize desired combinations of MRI, CT, EEG, MEG, fMRI, PET, and intracranial EEG (i.e., ECoG, depth electrodes, and DBS). Here we present the Multi-Modal Visualization Tool (MMVT), which is designed for researchers to interact with their neuroimaging functional and anatomical data through simultaneous visualization of these existing imaging modalities. MMVT contains two separate modules: The first is an add-on to the open-source, 3D-rendering program Blender. It is an interactive graphical interface that enables users to simultaneously visualize multi-modality functional and statistical data on cortical and subcortical surfaces as well as MEEG sensors and intracranial electrodes. This tool also enables highly accurate 3D visualization of neuroanatomy, including the location of invasive electrodes relative to brain structures. The second module includes complete stand-alone pre-processing pipelines, from raw data to statistical maps. Each of the modules and module features can be integrated, separate from the tool, into existing data pipelines. This gives the tool a distinct advantage in both clinical and research domains as each has highly specialized visual and processing needs. MMVT leverages open-source software to build a comprehensive tool for data visualization and exploration.Comment: 29 pages, 10 figure

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors

The variation in the expression patterns of the gap genes in the blastoderm of the fruit fly Drosophila melanogaster reduces over time as a result of cross regulation between these genes, a fact that we have demonstrated in an accompanying article in PLoS Biology (see Manu et al., doi:10.1371/journal.pbio.1000049). This biologically essential process is an example of the phenomenon known as canalization. It has been suggested that the developmental trajectory of a wild-type organism is inherently stable, and that canalization is a manifestation of this property. Although the role of gap genes in the canalization process was established by correctly predicting the response of the system to particular perturbations, the stability of the developmental trajectory remains to be investigated. For many years, it has been speculated that stability against perturbations during development can be described by dynamical systems having attracting sets that drive reductions of volume in phase space. In this paper, we show that both the reduction in variability of gap gene expression as well as shifts in the position of posterior gap gene domains are the result of the actions of attractors in the gap gene dynamical system. Two biologically distinct dynamical regions exist in the early embryo, separated by a bifurcation at 53% egg length. In the anterior region, reduction in variation occurs because of stability induced by point attractors, while in the posterior, the stability of the developmental trajectory arises from a one-dimensional attracting manifold. This manifold also controls a previously characterized anterior shift of posterior region gap domains. Our analysis shows that the complex phenomena of canalization and pattern formation in the Drosophila blastoderm can be understood in terms of the qualitative features of the dynamical system. The result confirms the idea that attractors are important for developmental stability and shows a richer variety of dynamical attractors in developmental systems than has been previously recognized

Coastal landscape changes at Unguja Ukuu, Zanzibar: Contextualizing the archaeology of an early Islamic port of trade

Unguja Ukuu, located on the Zanzibar Archipelago, eastern Africa, was an active Indian Ocean trading settlement from the mid-first millennium until the early second millennium AD. As part of recent archaeological excavations aimed at understanding the site’s transregional trade networks, geoarchaeological analyses were undertaken to document the geomorphic context of the ancient settlement. Here, we outline the results of these field and laboratory studies to discuss patterns of anthropogenic sediment deposition. Unguja Ukuu’s deep coastal stratigraphy appears to record progradation of an inhabited back-reef shore from the mid-seventh to the nineth centuries AD, perhaps in the wake of an earlier middle to late Holocene marine transgression. Excavations on the back-beach show that deposits associated with the ancient settlement include interlayered middens, paleofloors, and backshore sands and, in later phases, a peri-urban dump with dark-earth-type anthrosols developed on these deposits. Coastal progradation appears to have been driven in part by the accumulation of anthropogenic detritus and compaction of ancient surfaces. We hypothesize how the inherited, submerged relic Late Pleistocene geomorphology of the intertidal zone and later Holocene sediment supply from the hinterland may have supported the emergence of Unguja Ukuu as a trading locale, and possibly contributed to its decline in the early second millennium AD

Synthesis and Characterization of Ba₂SnTe₅: A New Zintl Phase Containing Unique One-Dimensional Chains of (SnTe₃)^2- and Dimeric Units of (Te₂)^2-

Synthesis and Characterization of Ba2SnTe5: A New Zintl Phase Containing Unique One-Dimensional Chains of (SnTe3)2- and Dimeric Units of (Te2)2-</sup