OSPRay - A CPU Ray Tracing Framework for Scientific Visualization.

Scientific data is continually increasing in complexity, variety and size, making efficient visualization and specifically rendering an ongoing challenge. Traditional rasterization-based visualization approaches encounter performance and quality limitations, particularly in HPC environments without dedicated rendering hardware. In this paper, we present OSPRay, a turn-key CPU ray tracing framework oriented towards production-use scientific visualization which can utilize varying SIMD widths and multiple device backends found across diverse HPC resources. This framework provides a high-quality, efficient CPU-based solution for typical visualization workloads, which has already been integrated into several prevalent visualization packages. We show that this system delivers the performance, high-level API simplicity, and modular device support needed to provide a compelling new rendering framework for implementing efficient scientific visualization workflows.

Lithium treatment inhibits protein kinase C translocation in rat brain cortex.

RATIONALE: Lithium, an effective psychotropic agent, affects membrane phospholipid metabolism, interferes with phosphoinositide signal transduction, and antagonizes the biological activity of calcium, all major factors of protein kinase C (PKC) activation. Consequently, lithium may interfere with cellular functions requiring PKC. Supporting this hypothesis, lithium was found to inhibit increased neurotransmitter release upon PKC activation and to prevent phorbol ester-mediated PKC translocation. OBJECTIVES: The present study was undertaken to determine whether the frontal cortex of rats treated with lithium exhibits altered PKC activity and translocation in response to phorbol ester, K+, or serotonin (5-HT) receptor stimulation and to determine whether specific PKC isozymes are disproportionately affected. METHODS: Rats were fed either a normal diet or one enriched with LiCl. In cerebrocortical slices or synaptosomes, cytosolic and membranous PKC activity and translocation in response to stimuli were determined after partial purification with anion exchange chromatography. RESULTS: In brain slices, lithium treatment inhibited phorbol 12-myristate, 13-acetate (PMA)-, 5-HT-, or K+-induced PKC translocation from cytosol to membrane without affecting basal membrane or cytosolic PKC activity. In synaptosomes, lithium also attenuated PMA- or K+-evoked translocation of PKC. Immunoblotting with isozyme-specific PKC antibodies revealed that chronic lithium treatment reduced basal cytosolic alphaPKC and deltaPKC but increased membrane-associated zetaPKC immunoreactivities. Stimulation with PMA, 5-HT or K+ elicited translocation of alpha, beta and gammaPKC isozymes and PMA induced translocation of delta and epsilonPKC isozymes. Stimulus-mediated translocation of PKC isozymes was attenuated in cortical tissue obtained from animals that received lithium for 6 weeks. In synaptosomes, PMA- or K+-induced PKC translocation was attenuated by in vitro lithium or chronic lithium treatment. Neither rubidium nor cesium affected PKC activities or PMA-induced translocation. Suppression of PMA-elicited translocation by lithium was partially antagonized by Ca2+. CONCLUSIONS: Lithium treatment reduces PKC translocation induced by either stimulation of a cell surface receptor or by direct enzyme stimulation with phorbol ester. This effect leads to reduced PKC-mediated phosphorylation of cellular proteins and may be responsible for the pharmacotherapeutic action of lithium.

D(4) dopamine receptor differentially regulates Akt/nuclear factor-kappa b and extracellular signal-regulated kinase pathways in D(4)MN9D cells.

The present study was designed to investigate the role of D(4) dopamine receptors in regulating the Akt/nuclear factor-kappa B (NF-kappa B) and extracellular signal-regulated kinase (ERK) signaling pathways. The D(4) dopamine receptor agonist PD168077 induced time- and dose-dependent activation of Akt and ERK in D(4)MN9D cells that stably express D(4) dopamine receptors. Maximal Akt and ERK stimulation was achieved at 1 microM PD168077. The agonist-mediated stimulations of Akt and ERK were abolished when cells were preincubated with 50 ng/ml PTX or with 1 microM L745,870, a D(4) dopamine receptor antagonist, indicating that activation of the Akt or ERK pathways is mediated by D(4) dopamine receptors and require a pertussis toxin-sensitive G protein. We also detected a time- and dose-dependent activation of NF-kappa B. Activation of NF-kappa B by 1 microM PD168077 was attenuated in D(4)MN9D cells that were transfected with a kinase-deficient Akt but not in cells transfected with a dominant negative Ras (N17Ras), suggesting that NF-kappa B activation requires Akt but is independent of Ras. In contrast, the transfection of N17Ras into D(4)MN9D cells blunted D(4) dopamine receptor-mediated ERK activation, indicating a Ras-dependent mechanism. Moreover, PP2 (20 nM), an inhibitor of Src, blocked D(4) receptor-mediated SHC phosphorylation and ERK activation. In contrast, transfection of a kinase-dead Akt did not alter D(4) receptor-stimulated ERK. However, PP2 and the mitogen activated protein kinase kinase inhibitor PD98059 did not change D(4) receptor-mediated Akt/NF-kappa B activation. All these indicate that distinct mechanisms mediate ERK and Akt/NF-kappa B activation by D(4) dopamine receptor stimulation. We also demonstrated that D(4) receptor-stimulated cell proliferation is mediated by the Src/SHC/Ras/ERK pathway.

Constructing and evaluating energy surfaces of crystalline disaccharides.

This paper focuses on the methods used to construct Ramachandran plots for disaccharides. Our recent work based on a hybrid of molecular mechanics and quantum mechanics energies pointed to the need to take extra care when making these maps. Care is also important in the quantitative validation of these energy surfaces with linkage conformations that were determined by crystallography. To successfully predict conformations that have been observed experimentally, the calculation of the energy should include stereoelectronic effects and correctly weight the hydrogen bonding. Technical concerns include the method used to scan the range of conformations, starting geometries, and finding the zero of relative potential energy on a surface where the values were collected at regular intervals. The distributions of observed conformations on energy maps of sucrose, maltose, and laminarabiose at dielectric constants of 1.5 and 7.5 illustrate the effects of an elevated dielectric constant for the MM3 component of the hybrid energy calculations. At dielectric constants of 3.5 and 7.5, the overall average energies of observed conformations of sucrose and seven disaccharides of glucose were less than 1.0 kcal mol-1. The distribution of corresponding energies of the various crystalline conformations conformed well to a Boltzmann-like equation.

A QM/MM analysis of the conformations of crystalline sucrose moieties.

Both ab initio quantum mechanics (QM) and molecular mechanics (MM) were used to produce a hybrid energy surface for sucrose that simultaneously provides low energies for conformations that are observed in crystal structures and high energies for most unobserved structures. HF/6-31G* QM energies were calculated for an analogue based on tetrahydropyran (THP) and tetrahydrofuran (THF). Remaining contributions to the potential energy of sucrose were calculated with MM. To do this, the MM surface for the analogue was subtracted from the MM surface for the disaccharide, and the QM surface for the analogue was added. Prediction of the distribution of observable geometries was enhanced by reducing the strength of the hydrogen bonding. Reduced hydrogen-bonding strength is probably useful because many crystalline sucrose moieties do not have intramolecular hydrogen bonds between the fructose and glucose residues. Therefore, hydrogen bonding does not play a large role in determining the molecular conformation. On the hybrid energy surface that was constructed with a dielectric constant of 3.5, the average potential energy of 23 sucrose moieties from crystal structures is 1.16 kcal/mol, and the population of observed structures drops off exponentially as the energy increases.

Age-associated impairment in brain MAPK signal pathways and the effect of caloric restriction in Fischer 344 rats.

Mitogen-activated protein kinases (MAPKs) play important roles in cell proliferation, differentiation, and apoptosis. Important functional roles for MAPKs in postmitotic cells have recently been suggested. In the present study, we investigated the effect of aging on the brain ERK (extracellular signal-regulated kinase) and p38 MAPK signaling pathways of Fischer 344 rats. The results show that basal tyrosine-phosphorylated ERK1/ERK2 in cortex of 24-month-old rats was reduced by 36%-59%, compared to 6- and 12-month-old rats (p<.05, 24- vs. 12- or 6-month-old rats). Similarly, the phosphotransferase activities of ERK and p38 MAPK, measured by in vitro immunocomplex kinase assays using myelin basic protein (MBP) as substrate, were shown to be reduced approximately 50% and 59% respectively, in the cerebrocortex of 24-month-old rats (p<.01, 24- vs. 12- or 6-month-old rats). The reductions in basal ERK and p38 MAPK activities are not due to altered protein levels of these kinases as assessed by Western analysis. Immunohistochemically, no age-related differences in ERK expression and cellular distribution were observed However, cytosolic ERK tended to aggregate in brain neurons of aged rats. In contrast brain tyrosine-phosphorylated PLCgamma1 did not change with age. Activation of ERK in response to EGF or PMA was also reduced in cortical brain slices of 24-month-old rats. These results demonstrate an age-associated selective impairment in the MAPK signaling pathways. Moreover, lifelong caloric restriction completely prevented the age-related decrease in basal brain ERK activity and diminished the age-related reduction of p38 MAPK activity. Taken together, these data indicate that ERK and p38 MAPK signaling pathways are impaired in the aged brain and that lifelong caloric restriction modulates these defects in brain intracellular signaling pathways.

Femoral neuropathy secondary to the use of a self-retaining retractor. Report of three cases and review of the literature.

PURPOSE: Three recent cases of femoral neuropathy at our institution following colorectal surgery have been ascribed to the use of the self-retaining Bookwalter retractor. The pathophysiology of neural injury includes compression, stretch, transection, ligation, iliopsoas hematoma, ischemia, and cement encapsulation. The aim of this study is to provide a comprehensive review of femoral nerve anatomy and mechanism of retractor injury. METHODS: The relationship of the femoral nerve to the lateral blade of the Bookwalter retractor was evaluated during colorectal surgery and in cadaveric dissections. RESULTS: The lateral blade of the self-retaining retractor was observed to either compress or impinge the intrapelvic portion of the femoral nerve. CONCLUSION: The incidence of postoperative femoral neuropathy is likely underestimated because a majority of cases are self-limited. This debilitating iatrogenic injury can be prevented with a thorough understanding of femoral nerve anatomy and careful placement of self-retaining retractor blades.

An update on the vaccinia virus genome.

This communication is intended as a single source update of the initial report (Goebel et al., 1990a,b) which described the complete DNA sequence of the vaccinia virus genome. We have integrated published information as well as unpublished data. Our understanding of the complexities of the genetic functional organization of poxviruses is increasing at a remarkable rate. While some previously unknown identities have since been elucidated, the fact that the majority of vaccinia-encoded gene products still lack assigned functions lends excitement to the immediate future of poxvirus research.

Treatment of acute diarrhea with norfloxacin during Desert Storm deployment.

A retrospective study on the treatment of diarrhea in a U.S. Air Force Wing deployed to Egypt during Operation Desert Storm was conducted. Two groups of patients were compared for treatment efficacy. One group was treated with norfloxacin 800 mg as a single dose with the onset of symptoms. The other group was treated conservatively. The group treated with norfloxacin was noted to become asymptomatic in one-fourth the time of the group treated conservatively. This was highly significant, statistically, and in practice. It is recommended that diarrhea be treated aggressively during deployments to third world countries.

Vaccinia virus encodes a protein with similarity to glutaredoxins.

Recently, we have reported the complete nucleotide sequence of vaccinia virus (Goebel, S. J., Johnson, G. P., Perkus, M. E., Davis, S. W., Winslow, J. P., and Paoletti, E. 1990, Virology 179, 247-266). Approximately 2.2 kbp leftward of the large subunit of ribonucleotide reductase resides a 108-amino acid open reading frame, O2L (nt 62,851-62,528) with significant similarity to known glutaredoxins. The deduced amino acid sequence of open reading frame O2L is 28.7% identical to the yeast and Escherichia coli proteins and greater than 40% identical to various mammalian glutaredoxins. Similar patterns of hydrophobicity as well as alpha-helix and beta-sheet potentials suggest that O2L and the glutaredoxins share a similar secondary structure. Furthermore, a common function is inferred by the presence of a highly conserved redox-active site.

Deletion of 55 open reading frames from the termini of vaccinia virus.

Each copy of the inverted terminal repeat of vaccinia virus consists of 8 kb of DNA containing 9 ORFS flanked near the terminus of the genome by 4 kb of repetitive DNA which in turn contains blocks of tandem repeats. Using plasmids containing repetitive DNA as the external arm, we have generated deletions at both the left and the right termini of the vaccinia genome. We report here the engineered deletion within a single vaccinia virus of 32.7 kb of DNA (including 38 ORFS) from the left terminus and 14.9 kb of DNA (including 17 ORFS) from the right terminus.

Cases from the aerospace medicine residents' teaching file. Case #39. Ménière's disease.

A case of Ménière's disease in an Air Force pilot is presented. The disease is reviewed in a question and answer format. A record review of all aviators evaluated at USAFSAM during the last 10 years revealed: 1. Only 11 cases of possible Ménière's disease were referred to USAFSAM in the years 1979-88. 2. 100% of fliers with Meniere's disease were recommended to be permanently disqualified from flying status regardless of the treatment or the results. 3. A single case of cochlear hydrops was returned to flying status after one year of observation.

Vaccinia virus host range genes.

A gene encoding an 18-kDa polypeptide (ORF C7L) located in the vaccinia virus HindIII C fragment was shown to be functionally equivalent to previously described host range gene (ORF K1L) spanning the HindIII K/M fragment junction. Either C7L or K1L host range gene is necessary and sufficient by itself to allow replication of vaccinia virus on human cells. Deletion of both C7L and K1L genes from the wild-type vaccinia genome is required to derive a virus deficient for replication on human cells. Further, an ORF encoding a 77-kDa polypeptide derived from cowpox (CP77kDa) and previously shown to allow vaccinia to overcome the restriction for replication on Chinese hamster ovary cells could substitute for the vaccinia host range genes C7L and K1L in permitting replication of the virus on human cells. Additionally, the three unique host range genes C7L, K1L, and CP77kDa were functionally equivalent for vaccinia replication on pig kidney cells, but not on rabbit kidney cells.

The complete DNA sequence of vaccinia virus.

The complete DNA sequence of the genome of vaccinia virus has been determined. The genome consisted of 191,636 bp with a base composition of 66.6% A + T. We have identified 198 "major" protein-coding regions and 65 overlapping "minor" regions, for a total of 263 potential genes. Genes encoded by the virus were located by examination of DNA sequence characteristics and compared with existing vaccinia virus mapping analyses, sequence data, and transcription data. These genes were found to be compactly organized along the genome with relatively few regions of noncoding sequences. Whereas several similarities to proteins of known function were discerned, the function of the majority of proteins encoded by these open reading frames is as yet undetermined.

A DNA ligase gene in the Copenhagen strain of vaccinia virus is nonessential for viral replication and recombination.

Biochemical and genetic analyses have been conducted to determine whether a vaccinia virus open reading frame (orf) with extensive homology to the Saccharomyces cerevisiae DNA ligase gene encodes a functional ligase activity. This orf in HindIII A, designated A50R, is capable of encoding a 552-amino-acid, 63.4-kDa polypeptide. Full-length A50R mRNA produced in vitro directed the synthesis of a polypeptide with an apparent molecular weight of 57 kDa. Significantly, translation reactions programmed with A50R mRNA were capable of ligating a 3-kb Notl restriction fragment into multimers. DNA ligase activity was not detectable when either truncated sense or full-length antisense mRNA was translated in vitro. In extracts prepared from cells infected with wt vaccinia virus, DNA ligase activity was detected as assayed by the formation of a 57 kDa ligase-AMP adduct which was expressed early in the viral replication cycle. In cells infected with a DNA ligase deletion mutant no equivalent AMP-labeled adduct was detected. Relative to wt virus, the DNA ligase deletion mutant exhibited no significant differences in homologous recombination. These results indicate that the vaccinia orf A50R encodes a functional DNA ligase expressed early in infection, but this DNA ligase is nonessential for either recombination or viral replication.

Cases from the aerospace medicine residents' teaching file. Case #38. A navigator with nonischemic central retinal vein occlusion progressing to ischemic central retinal vein occlusion.

A case report of a young USAF navigator with nonischemic central retinal vein occlusion progressing to ischemic central retinal vein occlusion is presented. This young man was treated with hyperbaric oxygen therapy early in the course of his disease with complete resolution of his condition. Two years later his vision remained 20/17. This is the first known case of central retinal vein occlusion being treated with hyperbaric oxygen.

Absorption and motility of the bypassed human ileum.

The authors assessed absorption and motility of the human ileum after a prolonged period of disuse. In eight patients with ulcerative colitis, a manometric-catheter assembly was placed via the ileostomy into the unused portion of distal ileum two months after ileal pouch-anal anastomosis and temporary diverting loop ileostomy. The distal ileum was perfused at 5 ml/min with an isosmotic solution of either sodium chloride or ileal chyme diluted with sodium chloride for three hours before and three hours after a meal on two consecutive days. Absorption was measured, single and clustered pressure waves were identified and quantitated with the aid of a computer program, and a motility index was calculated. Mean absorption +/- S.E.M. of both perfusates was poor on day 1 (-10 +/- 2 ml/25 cm x 30 min), and the meal induced no ileal motor response. By day 2, however, absorption of both perfusates was much improved (-1 +/- 2 ml/25 cm x 30 min; P less than 0.05), and the number of discrete clustered contractions and the motility index now clearly increased after the meal (2.6 +/- 0.6 vs. 7.2 +/- 1.0 clustered waves/hr; 7.5 +/- 0.5 vs. 9.7 +/- 0.2 motility units/30 min; P less than 0.05). The conclusion was that absorption and motility of the human ileum were impaired after two months of disuse, but that ileal absorption and motility improved one day after the introduction of isosmotic ileal perfusates.

Nucleotide sequence analysis of a 10.5 kbp HindIII fragment of fowlpox virus: relatedness to the central portion of the vaccinia virus HindIII D region.

The nucleotide sequence of a 10465 bp HindIII genomic fragment from fowlpox virus (FPV) is presented. Analysis of the nucleotide sequence revealed 10 potential major open reading frames (ORFs). Five of these ORFs are predicted to encode polypeptides with significant homology to hypothetical polypeptides derived from nucleotide sequence analysis of the vaccinia virus (VV) HindIII D region. Interestingly, these homologous ORFs do not occur in the same tandem arrangement in the FPV genome as they do in the VV genome. These results are discussed.

Transducer manometry and the effect of body position on anal canal pressures.

Anal canal manometry is performed conventionally with balloons, sleeves, perfused or nonperfused open-tipped catheters, or with multiport probes. The authors constructed a new manometer with four transducers embedded in a probe (15 mm outside diameter) and oriented radially, 90 degrees apart. The transducer probe was validated in 27 healthy volunteers by comparing its performance to that of a standard four-port perfused manometer and then used to measure anal canal and rectal pressures in body positions more physiologic (standing, sitting) than that usually employed (left lateral) for such measurements. Both devices measured similar anal canal resting pressure in the left lateral position (mid canal, 58 +/- 3 mm Hg perfused vs. 62 +/- 4 mm Hg transducer; P greater than 0.05). The transducer probe, however, recorded higher squeeze pressures (mid canal, 100 +/- 6 mm Hg perfused vs. 143 +/- 14 mm Hg transducer; P less than 0.05). The transducer probe detected higher intrarectal and resting anal canal pressures when subjects were standing or sitting, compared with the left lateral position (rectum, 3 +/- 1 mm Hg left lateral; 17 +/- 2 mm Hg standing; 20 +/- 1 mm Hg sitting; P less than 0.05; mid anal canal, 57 +/- 3 mm Hg left lateral; 86 +/- 4 mm Hg standing; 81 +/- 5 mm Hg sitting, P less than 0.05). The rise in resting anal canal pressure was uniform circumferentially. Neither anal canal length nor squeeze pressure changed with change in position. The authors concluded that 1) transducer manometry recorded similar resting but higher squeeze pressures compared with perfused manometry; 2) transducer manometry recorded the same radial variation in anal canal resting and squeeze pressures as that recorded by the perfused manometer; and 3) standing and sitting caused a four-fold rise in intrarectal pressure, which was associated with a concomitant rise in resting anal canal pressure.