Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays.

BACKGROUND: Life science research is moving quickly towards large-scale experimental designs that are comprised of multiple tissues, time points, and samples. Omic time-series experiments offer answers to three big questions: what collective patterns do most analytes follow, which analytes follow an identical pattern or synchronize across multiple cohorts, and how do biological functions evolve over time. Existing tools fall short of robustly answering and visualizing all three questions in a unified interface. RESULTS: Functional Heatmap offers time-series data visualization through a Master Panel page, and Combined page to answer each of the three time-series questions. It dissects the complex multi-omics time-series readouts into patterned clusters with associated biological functions. It allows users to identify a cascade of functional changes over a time variable. Inversely, Functional Heatmap can compare a pattern with specific biology respond to multiple experimental conditions. All analyses are interactive, searchable, and exportable in a form of heatmap, line-chart, or text, and the results are easy to share, maintain, and reproduce on the web platform. CONCLUSIONS: Functional Heatmap is an automated and interactive tool that enables pattern recognition in time-series multi-omics assays. It significantly reduces the manual labour of pattern discovery and comparison by transferring statistical models into visual clues. The new pattern recognition feature will help researchers identify hidden trends driven by functional changes using multi-tissues/conditions on a time-series fashion from omic assays.

Centennial record of anthropogenic impacts in Galveston Bay: Evidence from trace metals (Hg, Pb, Ni, Zn) and lignin oxidation products.

During the 20th century the impacts of industrialization and urbanization in Galveston Bay resulted in significant shifts in trace metals (Hg, Pb, Ni, Zn) and vascular plant biomarkers (lignin phenols) recorded within the surface sediments and sediment cores profile. A total of 22 sediment cores were collected in Galveston Bay in order to reconstruct the historical input of Hg, Pb, Ni, Zn and terrestrial organic matter. Total Hg (T-Hg) concentration ranged between 6 and 162 ng g-1 in surface sediments, and showed decreasing concentrations southward from the Houston Ship Channel (HSC) toward the open estuary. Core profiles of T-Hg and trace metals (Ni, Zn) showed substantial inputs starting in 1905, with peak concentrations between 1960 and 1970's, and decreasing thereafter with exception to Pb, which peaked around 1930-1940s. Stable carbon isotopes and lignin phenols showed an increasing input of terrestrial organic matter driven by urban development within the watershed in the early 1940s. Both the enrichment factor and the geoaccumulation index (Igeo) for T-Hg as a measure of the effectiveness of environmental management practices showed substantial improvements since the 1970s. The natural recovery rate in Galveston Bay since the peak input of T-Hg was non-linear and displayed a slow recovery during the twenty-first century.

Synthesis of the new metastable skutterudite compound NiSb(3) from modulated elemental reactants.

A new metastable binary compound with the skutterudite crystal structure has been synthesized from modulated elemental reactants, through an amorphous intermediate, using a novel low-temperature synthesis technique. The amorphous reaction intermediate undergoes nucleation at 87 degrees C, an extremely low temperature for solid-state reactions. When heated above 350 degrees C, the metastable phase NiSb(3) disproportionates into the thermodynamically stable phases NiSb(2) and Sb. Also, if the sum of the individual elemental layer thicknesses is greater than 30 A, a mixture of different phases forms. Simulation of the high-angle powder X-ray diffraction spectrum confirms that NiSb(3) is isostructural with CoSb(3).

Suppression of binary nucleation in amorphous La-Fe-Sb mixtures.

The nucleation energy of a series of La(x)Fe(y)Sb(z) modulated elemental reactants was measured as a function of the Fe/Sb ratio over a large composition range while holding the La content constant. The nucleation energy of the ternary compound La(0.5)Fe(4)Sb(12) with the skutterudite crystal structure was found to depend very strongly on the Fe/Sb ratio in the modulated elemental reactant, with a higher nucleation energy as the Fe/Sb ratio is moved away from the 1:3 stoichiometric value. When the results of this study are compared with those from Fe(y)Sb(z) modulated reactants, the addition of lanthanum was found to suppress the nucleation of FeSb(2), thereby broadening the Fe/Sb composition range in which the ternary skutterudite compound La(x)Fe(4)Sb(12) nucleates. This suppression of nucleation of a binary phase on addition of a ternary component to an amorphous intermediate is in agreement with theoretical arguments. The observed suppression of nucleation also provides rational for the observed nucleation of metastable ternary and higher-order compounds from homogeneous amorphous reactants.

Synthesis of crystalline skutterudite superlattices using the modulated elemental reactant method.

A series of samples ((AB)(x)(CD)(y))(z) were prepared containing both short repeat units (AB and CD) and long repeat units ((AB)(x)(CD)(y)), where the short repeat units were designed to have the composition appropriate to form square M(4)Sb(12) skutterudites (M = Fe, Co, or Ir; square = vacancy, La, or Y). X-ray diffraction and reflectivity were used to follow the evolution of the films from amorphous, layered materials to crystalline skutterudite superlattices as a function of annealing temperature and time. In all cases, the short repeat units interdiffused and crystallized the expected skutterudite, while the long repeat period persisted after annealing. The skutterudites crystallize with random crystallographic orientation with respect to the substrate. The observed splitting of the peaks in the high-angle diffraction data from the IrSb(3)/CoSb(3) sample indicates the formation of a novel superlattice structure with each grain having a random crystallographic orientation of the skutterudite lattice with respect to the superlattice direction.