Helistat absorbable collagen hemostatic sponges in cutaneous surgery in HIV-1+ patients. Military Medical Consortium for the Advancement of Military Medicine (MMCAR)

BACKGROUND: While biopsies are often required for adequate diagnosis of skin lesions in HIV-1 infected patients, these procedures result in the possible exposure of medical personnel to blood and contaminated instruments. To reduce exposure of medical personnel to contaminated needles we have used collagen sponges instead of sutures to control bleeding from punch biopsy sites in HIV-1 infected patients. METHODS: A collagen sponge was placed in all punch biopsy sites in HIV-1 infected patients. In cases where there was clinical evidence of local infection the sponges were removed 5-6 minutes after hemostasis was obtained. RESULTS: In over 500 biopsies in which Helistat collagen sponges were used, there have been no cases of secondary infection, and there have been no delays in healing. CONCLUSIONS: We believe that the use of these sponges provides a high degree of safety for the physician, which may assure that the commonly atypical clinical lesions seen in HIV-1 disease are biopsied. In addition, these sponges provide hemostasis, particularly significant in this patient population, and convenience, without a significant risk of secondary infection, and may provide some benefit in healing.     

Identification of lead and other elements in ceramic glazes and housewares by 109Cd-induced X-ray fluorescence emission spectrometry

Hepatitis C virus (HCV) has been reported to conform to a quasispecies nature, which is most evident in hypervariable regions of the putative envelope 2 domain. The aim of this study was to determine the relationship between the nucleotide complexity and diversity of hypervariable region 1 and various stages of the carrier states. The subjects studied were 20 HCV carriers with normal alanine aminotransferase (ALT) levels, 50 patients with chronic hepatitis who showed elevated ALT levels, 22 with cirrhosis, and 24 with hepatocellular carcinoma. The quasispecies complexity was analyzed by means of polymerase chain reaction-mediated single strand conformation polymorphism (PCR-SSCP). The value of nucleotide diversity was calculated by PCR cloning and sequencing. The number of SSCP bands ranged from 1 to 7, with no significant differences in the mean numbers among the stages of HCV infection. There was no correlation between the amounts of serum HCV RNA and the numbers of SSCP bands. No significant difference was found in the values of nucleotide diversity between carriers with normal ALT levels (mean, 6.6 x 10(-2) per site) and patients with chronic hepatitis (7.7 x 10(-2). These findings suggest that the quasispecies complexity of hypervariable region 1 is independent of the stage of chronic HCV infection.     

Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme

In order to determine the thermodynamic cost of introducing a polar group within the core of a protein, a series of nine Ala-->Ser and 3 Val-->Thr substitutions was constructed in T4 lysozyme. The sites were all within alpha-helices but ranged from fully solvent-exposed to totally buried. The range of destabilization incurred by the Ala-->Ser substitutions was found to be very similar to that for the Val-->Thr replacements. For the solvent-exposed and partly exposed sites the destabilization was modest (approximately less than 0.5 kcal/mol). For the completely buried sites the destabilization was larger, but variable (approximately 1-3 kcal/mol). Crystal structure determinations showed that the Ala-->Ser mutant structures were, in general, very similar to their wild-type counterparts, even though the replacements introduce a hydroxyl group. This is in part because the introduced serines are all within alpha-helices and at congested sites can avoid steric clashes with surrounding atoms by making a hydrogen bond to a backbone carbonyl oxygen in the preceding turn of the helix. The three substituted threonine side chains essentially superimpose on their valine counterparts but display somewhat larger conformational adjustments. The results illustrate how a protein structure will adapt in different ways to avoid the presence of an unsatisfied hydrogen bond donor or acceptor. In the most extreme case, Val 149-->Thr, which is also the most destabilizing variant (delta delta G = 2.8 kcal/mol), a water molecule is incorporated in the mutant structure in order to provide a hydrogen-bonding partner. The results are consistent with the view that many hydrogen bonds within proteins contribute only marginally to stability but that noncharged polar groups that lack a hydrogen-bonding partner are very destabilizing (delta delta G approximately greater than 3 kcal/mol). Supportive of other studies, the alpha-helix propensity of alanine is seen to be higher than that of serine (delta delta G = 0.46 +/- 0.04 kcal/mol), while threonine and valine are similar in alpha-helix propensity.     

Simplified estimation technique for organic contaminant transport in groundwater

The analytical solution for one-dimensional dispersive—advective transport of a single solute in a saturated soil accompanied by adsorption onto soil surfaces and first-order reaction rate kinetics for degradation can be used to evaluate the suitability of potential sites for burial of organic chemicals. The technique can be used to the greatest advantage with organic chemicals that are present in groundwaters in small amounts. The steady-state solution provides a rapid method for chemical landfill site evaluation because it contains the important variables that describe interactions between hydrodynamics and chemical transformation. With this solution, solute concentration, at a specified distance from the landfill site, is a function of the initial concentration and two dimensionless groups. In the first group, the relative weights of advective and dispersive variables are compared, and in the second group the relative weights of hydrodynamic and degradation variables are compared. The ratio of hydr odynamic to degradation variables can be rearranged and written as (a_L·λ)/(q/ε), where a_L is the dispersivity of the soil, λ is the reaction rate constant, q is groundwater flow velocity, and ε is the soil porosity. When this term has a value less than 0.01, the degradation process is occurring at such a slow rate relative to the hydrodynamics that it can be neglected. Under these conditions the site is unsuitable because the chemicals are unreactive, and concentrations in groundwaters will change very slowly with distance away from the landfill site.     

Terrain simplification simplified: a general framework for view-dependent out-of-core visualization

We describe a general framework for out-of-core rendering and management of massive terrain surfaces. The two key components of this framework are: view-dependent refinement of the terrain mesh and a simple scheme for organizing the terrain data to improve coherence and reduce the number of paging events from external storage to main memory. Similar to several previously proposed methods for view-dependent refinement, we recursively subdivide a triangle mesh defined over regularly gridded data using longest-edge bisection. As part of this single, per-frame refinement pass, we perform triangle stripping, view frustum culling, and smooth blending of geometry using geomorphing. Meanwhile, our refinement framework supports a large class of error metrics, is highly competitive in terms of rendering performance, and is surprisingly simple to implement. Independent of our refinement algorithm, we also describe several data layout techniques for providing coherent access to the terrain data. By reordering the data in a manner that is more consistent with our recursive access pattern, we show that visualization of gigabyte-size data sets can be realized even on low-end, commodity PCs without the need for complicated and explicit data paging techniques. Rather, by virtue of dramatic improvements in multilevel cache coherence, we rely on the built-in paging mechanisms of the operating system to perform this task. The end result is a straightforward, simple-to-implement, pointerless indexing scheme that dramatically improves the data locality and paging performance over conventional matrix-based layouts.     

SQuad: Compact Representation for Triangle Meshes

The SQuad data structure represents the connectivity of a triangle mesh by its “S table” of about 2 rpt (integer references per triangle). Yet it allows for a simple implementation of expected constant‐time, random‐access operators for traversing the mesh, including in‐order traversal of the triangles incident upon a vertex. SQuad is more compact than the Corner Table (CT), which stores 6 rpt, and than the recently proposed SOT, which stores 3 rpt. However, in‐core access is generally faster in CT than in SQuad, and SQuad requires rebuilding the S table if the connectivity is altered. The storage reduction and memory coherence opportunities it offers may help to reduce the frequency of page faults and cache misses when accessing elements of a mesh that does not fit in memory. We provide the details of a simple algorithm that builds the S table and of an optimized implementation of the SQuad operators.     

Fast and efficient compression of floating-point data

Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, the simulation stalls and the CPUs are idle. Data compression can alleviate this problem by using some CPU cycles to reduce the amount of data needed to be transfered. Most compression schemes, however, are designed to operate offline and seek to maximize compression, not throughput. Furthermore, they often require quantizing floating-point values onto a uniform integer grid, which disqualifies their use in applications where exact values must be retained. We propose a simple scheme for lossless, online compression of floating-point data that transparently integrates into the I/O of many applications. A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids. We achieve state-of-the-art compression rates and speeds, the latter in part due to an improved entropy coder. We demonstrate that this significantly accelerates I/O throughput in real simulation runs. Unlike previous schemes, our method also adapts well to variable-precision floating-point and integer data.     

Perfluorinated compounds in the Cape Fear Drainage Basin in North Carolina

Concern over perfluorinated organic compounds (PFCs), e.g., perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA), is due to a number of recent studies which show that the PFCs are persistent, bioaccumulative, and toxic in animals. Despite sustained interest in this topic, little information is available concerning the environmental distributions of the compounds. In this study, a new method was developed for the analysis of 10 target PFCs and its performance was examined in a systematic evaluation of surface water in the Cape Fear River Basin in North Carolina. One hundred samples from 80 different locations were collected during the spring of 2006. Detectable levels of the target PFCs were found in all samples, and were comparable to values reported previously, with maximum PFOS at 132 ng/L, PFOA at 287 ng/L, perfluorononanoic acid (C9) at 194 ng/L, and perfluoroheptanoic acid (C7) at 329 ng/L. In general, the lowest concentrations of the PFCs were found in the smallest tributaries while the highest levels were found in middle reaches of the Drainage Basin. Variability of PFC concentrations suggests a series of source inputs throughout the Basin. Seventeen sample sites (22%) had PFOS concentrations greater than 43 ng/L, a conservative safe water concentration estimated to be protective of avian life. In addition, a total of 26 sites (32%) had PFOA concentrations above 40 ng/L.     

Evolutionary characteristics of influenza B virus since its first isolation in 1940: dynamic circulation of deletion and insertion mechanism

New antigenic variants of B/Yamagata/16/88-like lineage which appeared in the season of 1997 as a minor strain tended to predominate in the following season. Also, we could observe for the first time, three peaks of activity caused by H3N2 virus and two variants of B influenza virus. Antigenic and phylogenetic analyses revealed that B/Victoria/2/87-like variants appeared again in Japan in 1997 after a nine-year absence. Influenza B viruses evolved into three major lineages, including the earliest strain (I), B/Yamagata/16/88-like variants (II), which comprised of three sublineages (II-(i), II-(ii), II-(iii)), and B/Victoria/2/87-like variants (III). Evolution of influenza B virus hemagglutinin was apparently distinguishable from that of influenza A virus, showing a systematic mechanism of nucleotide deletion and insertion. This phenomenon was observed to be closely related to evolutionary pathways of I, II-(i), II-(ii), II-(iii) and III lineages. It was noteworthy to reveal that the nucleotide deletion and insertion mechanism of influenza B virus completed one cycle over a fifty-year period, and that a three nucleotide deletion was again observed in 1997 strains belonging to lineage II-(iii). It was evident that amino acid substitutions accompanying nucleotide insertions were highly conserved.     

Determination of hydrogen in titanium alloys by cold neutron prompt gamma activation analysis

Cold neutron prompt gamma-ray activation analysis (CNPGAA) has proven useful for the analysis of hydrogen in titanium alloys. The analysis is nondestructive, measures the entire sample, and the results are independent of the chemical form of hydrogen present. We have used the technique to measure H mass fractions as low as 50 mg/kg in titanium-alloy jet-engine compressor blades and to measure hydrogen in standards for neutron tomography.