Dynamic visualization of coexpression in systems genetics data

Biologists hope to address grand scientific challenges by exploring the abundance of data made available through modern microarray technology and other high-throughput techniques. The impact of this data, however, is limited unless researchers can effectively assimilate such complex information and integrate it into their daily research; interactive visualization tools are called for to support the effort. Specifically, typical studies of gene co-expression require novel visualization tools that enable the dynamic formulation and fine-tuning of hypotheses to aid the process of evaluating sensitivity of key parameters. These tools should allow biologists to develop an intuitive understanding of the structure of biological networks and discover genes residing in critical positions in networks and pathways. By using a graph as a universal representation of correlation in gene expression, our system employs several techniques that when used in an integrated manner provide innovative analytical capabilities. Our tool for interacting with gene co-expression data integrates techniques such as: graph layout, qualitative subgraph extraction through a novel 2D user interface, quantitative subgraph extraction using graph-theoretic algorithms or by compound queries, dynamic level-of-detail abstraction, and template-based fuzzy classification. We demonstrate our system using a real-world workflow from a large-scale, systems genetics study of mammalian gene co-expression.     

Detection of minor constitutents of the stratosphere by far infrared emission spectroscopy

The far infrared (30–110 cm^?1) emission spectrum of the lower stratosphere has been measured from balloon altitudes with a high resolution (0.06 cm^?1) rapid-scanning Michelson interferometer on two flights in 1976. The quality and resolution of the spectra obtained from two altitudes have permitted a careful search for emission lines from environmentally important molecules such as HCl, NO₂, OH, H₂O₂, and CO, among the more prominent and well-known features due to H₂O, O₃ and O₂. Column densities have been determined for H₂O and O₃ and upper limit estimates have been made from tentative identifications of several other constituents. However, the large angular field of view observed by the instrument prevented the determination of concentration profiles from atmospheric limb scans to the horizon. The possible future directions of this technique are outlined on the basis of operating experience over a 6 year programme. The viability of this method of monitoring the concentrations of minor constituents in the stratosphere is discussed with respect to other equivalent techniques.     

Impact of pulmonary vascular stiffness and vasodilator treatment in pediatric pulmonary hypertension: 21 patient-specific fluid-structure interaction studies

Recent clinical studies of pulmonary arterial hypertension (PAH) have found correlations between increased pulmonary vascular stiffness (PVS) and poorer disease outcomes. However, mechanistic questions remain about the relationships amongst PVS, RV power, and vascular hemodynamics in the setting of progressive PAH that are difficult or impossible to answer using direct measurements. Clinically validated patient-specific computational modeling may allow exploration of these issues through perturbation-based predictive testing. Here we use a simple patient-specific model to answer four questions: how do hemodynamics change as PAH worsens? How does increasing PVS impact hemodynamics and RV power? For a patient with moderate PAH, what are the consequences if the pressures increase modestly yet sufficiently to engage collagen in those vessels? What impact does pressure-reducing vasodilator treatment have on hemodynamics? Twenty-one sets of model-predicted impedance and mean PA pressure (mPAP) show good agreement with clinical measurements, thereby validating the model. Worsening was modeled using data from three PAH outcomes groups; these show not only the expected increase in mPAP, but also an increase in pressure pulsatility. Interestingly, chronically increasing mPAP decreased WSS, suggesting that increased PA cross-sectional area affected WSS greater than increased PVS. For a patient with moderately high PVR (12.7 WU) with elastin-based upstream vascular remodeling, moving from elastin-dominant vessel behavior to collagen-dominant behavior caused substantial increases in mPAP, pressure and WSS pulsatility. For the same patient, reducing PVR through a simulated vasodilator to a value equivalent to mild PAH did not decrease pressure pulsatility and dramatically increased WSS pulsatility. Overall, these results suggest a close association between PVS and hemodynamics and that hemodynamics may play an important role in progressing PAH. These support the hypothesis that treatments should target decreasing or reversing upstream vascular remodeling in addition to decreasing mean pressures.     

Measuring hydraulic properties of geotextiles after installation damage

Since geotextiles have been progressively incorporated into coastal protection structures, the influence of installation damage on them has been the primary concern. During installation/construction, geotextiles are repeatedly subjected to high mechanical stresses which often exceed service stress. It is therefore vital to evaluate the mechanical and hydraulic damage and determine the consequences of these damages to better develop criteria for selection of suitable products. As these damages could reduce the material's mechanical strength and hydraulic efficiency, or in the severest form of damage, puncturing, would end the separation function. The properties investigated in this paper include the permittivity and apparent opening size (AOS) of geotextiles. Generally, the greater the drop energy of armour units applied to geotextiles, the greater the potential for damage. Findings show that the residual permittivity could increase significantly, 45% during installation. The preliminary design of coastal structures will be optimised as engineers and designers can better estimate the amount of damage on geotextiles upon installation.     

A graph coloring constructive hyper-heuristic for examination timetabling problems

In this work we investigate a new graph coloring constructive hyper-heuristic for solving examination timetabling problems. We utilize the hierarchical hybridizations of four low level graph coloring heuristics, these being largest degree, saturation degree, largest colored degree and largest enrollment. These are hybridized to produce four ordered lists. For each list, the difficulty index of scheduling the first exam is calculated by considering its order in all lists to obtain a combined evaluation of its difficulty. The most difficult exam to be scheduled is scheduled first (i.e. the one with the minimum difficulty index). To improve the effectiveness of timeslot selection, a?roulette wheel selection mechanism is included in the algorithm to probabilistically select an appropriate timeslot for the chosen exam. We test our proposed approach on the most widely used un-capacitated Carter benchmarks and also on the recently introduced examination timetable dataset from the 2007 International Timetabling Competition. Compared against other methodologies, our results demonstrate that the graph coloring constructive hyper-heuristic produces good results and outperforms other approaches on some of the benchmark instances.     

Novel temperature measurement method & thermodynamic investigations of amorphous polymers during high rate deformation

Polymers are frequently used in applications in which they may be exposed to high rate or impact loading, and there is growing industrial importance in understanding their mechanical behavior at different strain rates. An important aspect of this is the temperature rise due to adiabatic conditions in high rate loading. This paper describes research that has been performed to measure the temperature rise that occurs in specimens undergoing rapid deformation. A novel thermocouple design is presented and applied to PMMA and 20 wt% DINP-plasticized PVC, deformed at moderate and high strain rates. The measurements are accompanied by investigations of strain energy.     

Ascorbic acid enhances destruction of Escherichia coli O157:H7 during home-type drying of apple slices

Destruction of Escherichia coli O157:H7 was evaluated on inoculated apple slices dehydrated at two temperatures with and without application of predrying treatments. Half-ring slices (0.6 cm thick) of peeled and cored Gala apples were inoculated by immersion for 30 min in a four-strain composite inoculum of E. coli O157:H7. The inoculated slices (8.7 to 9.4 log CFU/g) either received no predrying treatment (control), were soaked for 15 min in a 3.4% ascorbic acid solution, or were steam blanched for 3 min at 88 degrees C immediately prior to drying at 57.2 or 62.8 degrees C for up to 6 h. Samples were plated on tryptic soy (TSA) and sorbitol MacConkey (SMAC) agar media for direct enumeration of surviving bacterial populations. Steam blanching changed initial inoculation levels by +0.3 to -0.7 log CFU/g, while immersion in the ascorbic acid solution reduced the inoculation levels by 1.4 to 1.6 log CFU/g. Dehydration of control samples for 6 h reduced mean bacterial populations by 2.9 log CFU/g (TSA or SMAC) at 57.2 degrees C and by 3.3 (SMAC) and 3.5 (TSA) log CFU/g at 62.8 degrees C. Mean decreases from initial inoculum levels for steam-blanched slices after 6 h of drying were 2.1 (SMAC) and 2.0 (TSA) log CFU/g at 57.2 degrees C, and 3.6 (TSA or SMAC) log CFU/g at 62.8 degrees C. In contrast, initial bacterial populations on ascorbic acid-pretreated apple slices declined by 5.0 (SMAC) and 5.1 (TSA) log CFU/g after 3 h of dehydration at 57.2 degrees C, and by 7.3 (SMAC) and 6.9 (TSA) log CFU/g after 3 h at 62.8 degrees C. Reductions on slices treated with ascorbic acid were in the range of 8.0 to 8.3 log CFU/g after 6 h of drying, irrespective of drying temperature or agar medium used. The results of immersing apple slices in a 3.4% ascorbic acid solution for 15 min prior to drying indicate that a predrying treatment enhances the destruction of E. coli O157:H7 on home-dried apple products.     

The DOE advanced gas reactor fuel development and qualification program

The high outlet temperatures and high thermal-energy conversion efficiency of modular high-temperature gas-cooled reactors (HTGRs) enable an efficient and cost-effective integration of the reactor system with non-electricity-generation applications, such as process heat and/or hydrogen production, for the many petrochemical and other industrial processes that require temperatures between 300°C and 900°C. The U.S. Department of Energy (DOE) has selected the HTGR concept for the Next Generation Nuclear Plant (NGNP) Project as a transformative application of nuclear energy that will demonstrate emissions-free nuclear-assisted electricity, process heat, and hydrogen production, thereby reducing greenhouse-gas emissions and enhancing energy security. The objective of the DOE Advanced Gas Reactor (AGR) Fuel Development and Qualification program is to qualify tristructural isotropic (TRISO)-coated particle fuel for use in HTGRs. An overview of the program and recent progress is presented.     

Fibre diffraction in the analysis of filamentous virus structure

In many plant and bacterial viruses, a filamentous nucleocapsid makes up the entire virus particle. These viruses usually form fibres naturally, but they do not crystallize. Fibre diffraction has therefore been the method of choice for structural studies, aided in recent years by cryo-electron microscopy (EM) and solid state nuclear magnetic resonance (ssNMR). Filamentous viruses, particularly tobacco mosaic virus (TMV), have been important in developing fibre diffraction methods, and fibre diffraction allowed TMV to be among the first virus structures determined. Structures of several viruses related to TMV and several filamentous bacterial viruses have been determined at resolutions of 3?Å or better, and lower resolution structures have been determined by fibre diffraction, sometimes in conjunction with other methods, for many other, unrelated, filamentous viruses.