One user's report on Sandia data objects : evaluation of the DOL and PMO for use in feature characterization.

The Feature Characterization project (FCDMF) has the goal of building tools that can extract and analyze coherent features in a terabyte dataset. We desire to extend our feature characterization library (FClib) to support a wider variety of complex ASCI data, and to support parallel algorithms. An attractive alternative to extending the library's internal data structures is to replace them with an externally provided data object. This report is the summary of a quick exploration of two candidate data objects in use at Sandia National Laboratories: the Data Object Library (DOL) and the Parallel Mesh Object (PMO). It is our hope that this report will provide information for potential users of the data objects, as well as feedback for the objects developers. The data objects were evaluated as to whether they (1) supported the same capabilities as the current version of FClib, (2) provided additional required capabilities, and (3) were relatively easy to use. Both data objects met the requirements of having the same capabilities as FClib and support for parallel algorithms. However, the DOL has a richer set of data structures that more closely align with the current data structures of FClib and our planned extensions. Specifically, the DOL can support time changing geometry, which is needed to represent features as datasets. Unfortunately, the DOL did not meet our ease of use requirement. The PMO was easier to learn and use, but did not support time-changing geometry. Given the above results, we will extend the FClib API (Application Programming Interface) to handle time-changing geometry. Then we will replace the internal data structures with the DOL, but we will provide the FClib API in addition to the DOL API to support simplified usage

U1/U2 crib groundwater biological treatment demonstration project

The primary objective of the biological treatment project is to develop and demonstrate a process for Hanford groundwater remediation. Biodenitrification using facultative anaerobic microorganisms is a promising technology for the simultaneous removal of nitrates and organics from contaminated aqueous streams. During FY 1988, a consortium of Hanford groundwater microorganisms was shown to degrade both nitrates and carbon tetrachloride (CC1{sub 4}). A pilot-scale treatment system was designed and constructed based on the results of laboratory-and-bench-scale testing. This report summarizes the results of biological groundwater treatment studies performed during FY 1989 at the pilot-scale. These tests were conducted using a simulated Hanford groundwater with a continuous stirred-tank bioreactor, and a fluidized-bed bioreactor that was added to the pilot-scale treatment system in FY 1989. The pilot-scale system demonstrated continuous degradation of nitrates and CC1{sub 4} in a simulated groundwater. 4 refs., 7 figs., 1 tab

Finding regions of interest on toroidal meshes

Fusion promises to provide clean and safe energy, and a considerable amount of research effort is underway to turn this aspiration intoreality. This work focuses on a building block for analyzing data produced from the simulation of microturbulence in magnetic confinementfusion devices: the task of efficiently extracting regions of interest. Like many other simulations where a large amount of data are produced,the careful study of ``interesting'' parts of the data is critical to gain understanding. In this paper, we present an efficient approach forfinding these regions of interest. Our approach takes full advantage of the underlying mesh structure in magnetic coordinates to produce acompact representation of the mesh points inside the regions and an efficient connected component labeling algorithm for constructingregions from points. This approach scales linearly with the surface area of the regions of interest instead of the volume as shown with bothcomputational complexity analysis and experimental measurements. Furthermore, this new approach is 100s of times faster than a recentlypublished method based on Cartesian coordinates

Polymorphisms of the TUB Gene Are Associated with Body Composition and Eating Behavior in Middle-Aged Women

BACKGROUND: The TUB gene, encoding an evolutionary conserved protein, is highly expressed in the hypothalamus and might act as a transcription factor. Mutations in TUB cause late-onset obesity, insulin-resistance and neurosensory deficits in mice. An association of common variants in the TUB gene with body weight in humans has been reported. METHODS/FINDINGS: The aim was to investigate the relationship of single nucleotide polymorphisms (SNPs) of the TUB gene (rs2272382, rs2272383 and rs1528133) with both anthropometry and self-reported macronutrient intake from a validated food frequency questionnaire. These associations were studied in a population-based, cross-sectional study of 1680 middle-aged Dutch women, using linear regression analysis. The minor allele C of the rs1528133 SNP was significantly associated with increased weight (+1.88 kg, P = 0.022) and BMI (+0.56 units, P = 0.05). Compared with non-carriers, both AG heterozygotes and AA homozygotes of the rs2272382 SNP derived less energy from fat (AG: -0.55+/-0.28%, P = 0.05, AA: -0.95+/-0.48%, P = 0.047). However, both genotypes were associated with an increased energy intake from carbohydrates (0.69+/-0.33%, P = 0.04 and 1.68+/-0.56%, P = 0.003, respectively), mainly because of a higher consumption of mono- and disaccharides. Both these SNPs, rs2272382 and rs1528133, were also associated with a higher glycemic load in the diet. The glycemic load was higher among those with AG and AA genotypes for the variant rs2272382 than among the wild types (+1.49 (95% CI: -0.27-3.24) and +3.89 (95% CI: 0.94-6.85) units, respectively). Carriers of the minor allele C of rs1528133 were associated with an increased glycemic load of 1.85 units compared with non-carriers. CONCLUSIONS: Genetic variation of the TUB gene was associated with both body composition and macronutrient intake, suggesting that TUB might influence eating behavior

FIB patterning of stainless steel for the development of nano-structured stent surfaces for cardiovascular applications

Stent implantation is a percutaneous interventional procedure that mitigates vessel stenosis, providing mechanical support within the artery and as such a very valuable tool in the fight against coronary artery disease. However, stenting causes physical damage to the arterial wall. It is well accepted that a valuable route to reduce in-stent re-stenosis can be based on promoting cell response to nano-structured stainless steel (SS) surfaces such as by patterning nano-pits in SS. In this regard patterning by focused ion beam (FIB) milling offers several advantages for flexible prototyping. On the other hand FIB patterning of polycrystalline metals is greatly influenced by channelling effects and redeposition. Correlative microscopy methods present an opportunity to study such effects comprehensively and derive structure–property understanding that is important for developing improved patterning. In this chapter we present a FIB patterning protocol for nano-structuring features (concaves) ordered in rectangular arrays on pre-polished 316L stainless steel surfaces. An investigation based on correlative microscopy approach of the size, shape and depth of the developed arrays in relation to the crystal orientation of the underlying SS domains is presented. The correlative microscopy protocol is based on cross-correlation of top-view scanning electron microscopy, electron backscattering diffraction, atomic force microscopy and cross-sectional (serial) sectioning. Various FIB tests were performed, aiming at improved productivity by preserving nano-size accuracy of the patterned process. The optimal FIB patterning conditions for achieving reasonably high throughput (patterned rate of about 0.03 mm2/h) and nano-size accuracy in dimensions and shapes of the features are discussed as well

Structural, Metabolic, and Functional Brain Abnormalities as a Result of Prenatal Exposure to Drugs of Abuse: Evidence from Neuroimaging

Prenatal exposure to alcohol and stimulants negatively affects the developing trajectory of the central nervous system in many ways. Recent advances in neuroimaging methods have allowed researchers to study the structural, metabolic, and functional abnormalities resulting from prenatal exposure to drugs of abuse in living human subjects. Here we review the neuroimaging literature of prenatal exposure to alcohol, cocaine, and methamphetamine. Neuroimaging studies of prenatal alcohol exposure have reported differences in the structure and metabolism of many brain systems, including in frontal, parietal, and temporal regions, in the cerebellum and basal ganglia, as well as in the white matter tracts that connect these brain regions. Functional imaging studies have identified significant differences in brain activation related to various cognitive domains as a result of prenatal alcohol exposure. The published literature of prenatal exposure to cocaine and methamphetamine is much smaller, but evidence is beginning to emerge suggesting that exposure to stimulant drugs in utero may be particularly toxic to dopamine-rich basal ganglia regions. Although the interpretation of such findings is somewhat limited by the problem of polysubstance abuse and by the difficulty of obtaining precise exposure histories in retrospective studies, such investigations provide important insights into the effects of drugs of abuse on the structure, function, and metabolism of the developing human brain. These insights may ultimately help clinicians develop better diagnostic tools and devise appropriate therapeutic interventions to improve the condition of children with prenatal exposure to drugs of abuse

Investigations into Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) Surface Properties Causing Delayed Osteoblast Growth

Osteoblast proliferation is sensitive to the topography of material surfaces. In this study, the proliferation of MC3T3 E1-S14 osteoblast cells on poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) films with different surface characteristics was investigated. The solvent cast films were prepared using three different solvents/solvent mixtures; chloroform, DCM and a mixture of chloroform and acetone which produced PHBV films with both a rough (at the air interface) and smooth (at the glass interface) surface. Investigation of the surface characteristics by scanning electron and scanning probe microscopies revealed different surface topographies and degrees of surface roughness ranging from 20 to 200 nm. Mapping of the surface crystallinity index by micro-attenuated total reflectance Fourier transform infrared (ATR-FTIR) showed distinct variations in surface crystallinity between the different film surfaces. Water contact angles were significantly higher on the rough surface compared the smooth surface for a particular substrate, however, all surfaces were hydrophobic in nature (θA was in the range 69 - 80 degrees). MC3T3 E1-S14 osteoblast cells were cultured on the six different surfaces and proliferation was determined. After 2 days cell proliferation on all surfaces was significantly less than on the control substrate, however, after 4 days cell proliferation was optimal on the three surfaces that displayed the highest contact angle and the smallest crystallinity heterogeneity. In addition, the surface roughness and more specifically the surface topography influenced the proliferation of osteoblast cells on the PHBV film surface

Development of a Biological Treatment System for Hanford Groundwater Remediation

The primary objective of the biological treatment program is to develop and demonstrate a biological process for Hanford groundwater remediation that is capable of nitrate (NO {sub 3}{sup {minus}}) and organic contaminant destruction. Biodenitrification using facultative anaerobic microorganisms is a promising technology for the simultaneous removal of NO{sub 3}{sup {minus}} and organics from contaminated aqueous streams. During FY 1989, microbial consortium from the Hanford groundwater was shown to degrade both NO{sub 3}{sup {minus}} and carbon tetrachloride (CC1{sub 4}). A pilot-scale treatment system was subsequently designed and constructed based on the results of laboratory- and bench-scale testing. The pilot-scale system demonstrated continuous degradation of NO{sub 3}{sup {minus}} and CC1{sub 4} in a simulated groundwater. This report summarizes the results of biological groundwater treatment studies performed during FY 1989 at the pilot-, laboratory-, and bench-scales. Pilot-scale test were conducted using a simulate Hanford groundwater with a continuous stirred-tank bioreactor (CSTR) and a fluidized-bed bioreactor that was added to the pilot-scale treatment system in FY 1989. Laboratory test focused on the degradation of CC1{sub 4} and on the microbial toxicity from CC1{sub 4}, hexavalent chromium (Cr{plus} {sup 6}), and cyanide (CN){sup {minus}} 15 refs., 18 figs., 1 tab