gebhart/patrepeval huggingface dataset:
Octrees for faster isosurface generation (1992)

The large size of many volume data sets often prevents visualization algorithms from providing interactive rendering. The use of hierarchical data structures can ameliorate this problem by storing summary information to prevent useless exploration of regions of little or no current interest within the volume. This paper discusses research into the use of the octree hierarchical data structure when the regions of current interest can vary during the application, and are not known a priori . Octrees are well suited to the six-sided cell structure of many volumes. A new space-efficient design is introduced for octree representations of volumes whose resolutions are not conveniently a power of two; octrees following this design are called branch-on-need octrees (BONOs). Also, a caching method is described that essentially passes information between octree neighbors whose visitation times may be quite different, then discards it when its useful life is over. Using the application of octrees to isosurface generation as a focus, space and time comparisons for octree-based versus more traditional “marching” methods are presented.
Mechanobiology in the development, maintenance, and degeneration of articular cartilage. (2000)

During skeletal development, the establishment of a layer of cartilage at the ends of long bones is intimately linked to the process of endochondral ossification. Previous in vivo studies and computer models suggest that mechanobiological factors can play a key role in modulating cartilage growth and ossification. Specifically, intermittent hydrostatic pressure is thought to maintain cartilage, and shear stresses encourage cartilage destruction and ossification. In the present investigation we examined the combined effects of hydrostatic pressure and shear stress--in the form of an osteogenic index--on the development of a layer of articular cartilage, using an idealized finite element computer model. The results of our analyses provide further support for the view that mechanobiological factors play a key role in regulating the distribution of cartilage thickness and in maintaining a stable cartilage layer at maturity. The model predicts that joints that experience higher contact pressures will have thicker cartilage layers. These predictions are consistent with observations of cartilage thickness in both humans and animals. Variations in articular mechanical load are predicted to modulate cartilage thickness. These results are consistent with the view that the mechanobiological factors responsible for the development of diarthrodial joints eventually lead to cartilage degeneration and osteoarthritis (OA) with aging.
A 100-MHz, 50-Ω, -45-dB distortion, 3.3-V CMOS line driver for Ethernet and fast Ethernet networking applications (1999)

A fast line driver has been developed for networking applications in a 0.4-/spl mu/ digital CMOS process. It is intended to drive cables with large, low-distortion sinewaves for 10BASE-T and sharp-edged pulses for 100BASE-T-type data communications. The driver has a fully differential architecture and uses a current-feedback approach to achieve small- as well as large-signal closed-loop bandwidths in excess of 100 MHz. It can drive a 10-MHz, 5-V/sub pp/ sinewave across a 50-/spl Omega/ load from a 3.3-V power supply with a total harmonic distortion of -43 dB. The quiescent power consumption of the driver is 25 mW, while its area is 0.15 mm/sup 2/.
Enhanced Viral Intergenic Region–Specific Short Interfering RNA Accumulation and DNA Methylation Correlates with Resistance Against a Geminivirus (2011)

RNA silencing mediated by short-interfering RNA (siRNA) is used by plants as a defense against viruses. In the case of geminiviruses, viral DNA is targeted at the transcriptional level, while virus-derived transcripts are targeted by posttranscriptional silencing. Mungbean yellow mosaic India virus (MYMIV), a bipartite geminivirus, causes yellow mosaic disease in soybean (Glycine max). A soybean variety resistant to this disease has been identified (line PK416). To understand the molecular mechanism underlying this resistance, distribution of MYMIV-derived siRNAs along the viral genome was compared in resistant and susceptible plants, using samples obtained in the first few days following inoculation. We observed that, in the resistant soybean variety, most of the virus-derived siRNAs were complementary to the intergenic region (IR), while in the susceptible variety (line JS335), a majority of the siRNAs corresponded to coding regions of the viral genome. Most of the IR-specific siRNA molecules produced in the resistant plants were 24 nt in size. Bisulfite sequencing showed that, in the resistant plants, a higher level of methylation occurred in the IR of viral DNA.
Inactivation of the <i>srtA</i> Gene in <i>Streptococcus gordonii</i> Inhibits Cell Wall Anchoring of Surface Proteins and Decreases In Vitro and In Vivo Adhesion (2001)

The srtA gene product, SrtA, has been shown to be required for cell wall anchoring of protein A as well as virulence in the pathogenic bacterium Staphylococcus aureus. There are five major mechanisms for displaying proteins at the surface of gram-positive bacteria (P. Cossart and R. Jonquieres, Proc. Natl. Acad. Sci. USA 97:5013-5015, 2000). However, since many of the known surface proteins of gram-positive bacteria are believed to be exported and anchored via the sortase pathway, it was of interest to determine if srtA plays a similar role in other gram-positive bacteria. To that end, the srtA gene in the human oral commensal organism Streptococcus gordonii was insertionally inactivated. The srtA mutant S. gordonii exhibited a marked reduction in quantity of a specific anchored surface protein. Furthermore, the srtA mutant had reduced binding to immobilized human fibronectin and had a decreased ability to colonize the oral mucosa of mice. Taken together, these results suggest that the activity of SrtA plays an important role in the biology of nonpathogenic as well as pathogenic gram-positive cocci.
Exclusive Free Radical Mechanisms of Cellular Photosensitization (1998)

In order to determine the specific effects of radical-induced reactions in the absence of complicating excited-state pathways, four different thiohydroxamic esters and their parent molecule, N-hydroxypyridine-2(1H)-thione, have been studied in murine L1210 leukemia cells for their ability to produce photobiological damage. Irradiation (Xexc= 355 nm) of cells in the presence of thiopyridone esters, specific photolytic precursors of sulfur-, carbon- and oxygen-centered radicals, caused toxicity that was unambiguously demonstrated to result from radical photosensitization mechanisms. Cellular morphological changes were observed following irradiation but apoptosis was not found to take place. A good correlation was evident between lipid peroxidation, measured by the thiobarbituric acid method, and phototoxicity, assessed by the trypan blue exclusion assay, indicating that the ester derivatives exert their effects mainly in plasma and/ or subcellular membranes. Irradiation performed under deaerated conditions also induced significant phototoxicity but the effects of deaeration were dependent on the ester used and are discussed in terms of the nature of the primary radical species generated in each case. Irradiation of L1210 cells in the presence of N-hydroxypyridine-2(1H)-thione, a nonspecific, photochemical source of hydroxyl radical, was also found to trigger phototoxicity and lipid peroxidation. However in this case, photodamage cannot yet be definitely attributed to a radical or type II mechanism although the apparent oxygen independence of phototoxicity would indicate that type II contribution is not significant.
Glycerophospholipid:cholesterol acyltransferase complexed with lipopolysaccharide (LPS) is a major lethal exotoxin and cytolysin of Aeromonas salmonicida: LPS stabilizes and enhances toxicity of the enzyme (1990)

An extracellular lethal toxin produced by Aeromonas salmonicida was purified by fast-protein liquid ion-exchange chromatography. The toxin is composed of glycerophospholipid:cholesterol acyltransferase (GCAT) (molecular mass, 25 kilodaltons) aggregated with lipopolysaccharide (LPS), the GCAT/LPS complex having a molecular mass of about 2,000 kilodaltons, estimated by gel filtration chromatography. The toxin is lethal for Atlantic salmon (Salmo salar L.) at a concentration of 0.045 micrograms of protein per g of body weight. The toxin is a hemolysin (T-lysin, active on fish erythrocytes), leukocytolysin, and cytotoxin. Antiserum to the purified toxin neutralized the lethal toxicity of the crude extracellular toxins, indicating this toxin to be the major lethal factor produced by A. salmonicida. In the crude extracellular products, small amounts of free GCAT were also present. This has been purified, and its activities and properties have been compared with those of the GCAT/LPS complex. The presence of LPS did not influence the GCAT activity of the enzyme with egg yolk or phosphatidylcholine (lecithin) as a substrate, but the specific hemolytic activity and lethal toxicity was about eightfold higher in the complexed form. Furthermore, the free GCAT was more susceptible to proteolytic and heat inactivation than was the GCAT/LPS complex. Recombination of LPS (phenol extracted from extracellular products of A. salmonicida) with free GCAT enhanced the hemolytic activity, lethal toxicity, and heat stability of the latter but did not influence its lecithinase activity. In native polyacrylamide gel electrophoresis, the GCAT/LPS complex and the recombined GCAT-LPS both showed a high-molecular-mass band which did not enter the gel, while the free GCAT produced a single band with low molecular mass. In isoelectric focusing gels, the GCAT/LPS and recombined GCAT-LPS produced a nonfocusing smear with pIs from pI 5.0 to 5.8, while the free GCAT produced a single band with pI 4.3. These data show that free GCAT can combine with LPS to produce a high-molecular-mass complex with enhanced toxicity and heat stability compared with those of free GCAT, similar to the preexisting GCAT/LPS complex, and indicate that the LPS moiety of the toxin plays an active role in toxicity.
Fade countermeasures in Ka band: application of frequency diversity to a satellite system (1995)

Some of the problems concerning the use of Ka band for satellite systems have been investigated and many fade countermeasures have been described. Frequency diversity has been analyzed and characterized in detail verifying the variability of its performance as a function of several system parameters. A satellite system utilizing frequency diversity has been dimensioned and the advantages in terms of power margin and then of technology have been shown. Among the several operating situations analyzed, the best one, from complexity/benefits point of view, seems to be to utilize a portion of Ku band as shared resource sufficient to assist the 10% of the stations simultaneously, choosing the operating point on probability curves in the first portion of the knee.
Wide-field Fourier ptychographic microscopy using laser illumination source (2016)

Fourier ptychographic (FP) microscope is a coherent imaging method that can synthesize an image with a higher bandwidth using multiple low-bandwidth images captured at different spatial frequency regions. The method's demand for multiple images drives the need for a brighter illumination scheme and a high-frame-rate camera for a faster acquisition. We report the use of a guided laser beam as an illumination source for an FP microscope. It uses a mirror array and a 2-dimensional scanning Galvo mirror system to provide a sample with plane-wave illuminations at diverse incidence angles. The use of a laser presents speckles in the image capturing process due to reflections between glass surfaces in the system. They appear as slowly varying background fluctuations in the final reconstructed image. We are able to mitigate these artifacts by including a phase image obtained by differential phase contrast (DPC) deconvolution in the FP algorithm. We use a 1-Watt laser configured to provide a collimated beam with 150 mW of power and beam diameter of 1 cm to allow for the total capturing time of 0.96 seconds for 96 raw FP input images in our system, with the camera sensor's frame rate being the bottleneck for speed. We demonstrate a factor of 4.25 resolution improvement using a 0.1 NA objective lens over the full camera field-of-view of 2.7 mm by 1.5 mm.
Evaluation of a flow cytometric fluorescence quenching assay of phagocytosis of sensitized sheep erythrocytes by polymorphonuclear leukocytes (1994)

A number of reports have been published describing phagocytosis assays for flow cytometric analysis. In some of these, the fluorescence quenching technique has been used to discriminate between adherent and ingested particles. In this report, we have evaluated the efficacy of a quantitative fluorescence quenching technique with crystal violet and trypan blue for application in a phagocytosis assay with polymorphonuclear leukocytes and sensitized sheep red blood cells. We set the requirements to a high quenching efficiency of the fluorescence of extracellularly bound particles and no intracellular quenching. The latter was determined using polymorphonuclear leukocytes stained with the fluorescent nuclear dye hydroethidine. We observed that both trypan blue and crystal violet efficiently quench the fluorescence of PKH26 (a red fluorescent membrane-associated dye) erythrocytes but that only crystal violet quenches intracellular fluorescence. In testing trypan blue and crystal violet from different manufacturers, there was no real difference between different brands of crystal violet, but only the trypan blue from Merck turned out to be an efficient quencher, whereas the other brands of trypan blue showed low quenching efficiency. Trypan blue at a concentration of 25-50 micrograms/ml proved to be a good quencher of the fluorescent erythrocytes and exerted minimal side effects: over 90% quenching of the erythrocytes, no intracellular quenching, moderate increase in autofluorescence of the polymorphonuclear leukocytes, and no cell loss.
A liquid-phase quartz crystal microbalance for photovoltaics research (2008)

Processes involving solid surfaces and liquid reactants are ubiquitous in the semiconductor industry, and photovoltaics is no exception. Examples include the chemical bath deposition of CdS buffer layers in Cu(In,Ga)Se <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> and CuInS <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> devices, a process that is used in virtually every commercially available CIS-based module. Aqueous etching is used for anti-reflective texturizing of silicon cells, and is also used in the cleaning, defect etching, and native oxide removal for that particular PV material. Research on next generation quantum dot-based solar cells frequently uses simple solution-based methods for the growth and modification of the quantum dots. In all of these examples, a liquid is used to remove or deposit very thin, sometimes atomically thin, layers on the surface of a solid, and the nature of the chemical and physical changes that take place at that interface are critical to the proper functioning of the finished photovoltaic device. Despite the widespread use of liquid processes in research and in industry, there are few characterization techniques suitable for in-situ and real-time investigations of the solid-liquid interface. We have recently finished constructing a new, low-cost tool based on a quartz crystal microbalance for investigations of liquid processes that are of interest to the PV community. The tool consists of a liquid-phase QCM, pumps, valving, reaction vessels, membrane contactors for control of dissolved gases, and a PC-based control system, and can be used in continuous flow cell mode or in a batch reaction scheme. Because the system has been integrated with the NREL Surface Analysis Team's cluster tool, films either grown or modified with this new tool can be transferred without fear of atmospheric contamination to a suite of surface analytical techniques for further study. This paper will describe the new tool, its capabilities, potential pitfalls with its use, initial results, and possible future research directions.
Ultraviolet laser-induced fluorescence of colonic polyps. (1992)

Ultraviolet laser-induced fluorescence was examined in vivo to determine whether the technique can reliably distinguish between hyperplastic and adenomatous polyps of the colon. Spectra from 86 normal colonic sites, 35 hyperplastic polyps, and 49 adenomatous polyps were recorded in vivo. Polyp type was independently determined by two senior pathologists who were unaware of the fluorescence measurement. A multivariate linear regression analysis was used to differentiate spectra from hyperplastic and adenomatous polyps and resulted in a sensitivity, specificity, predictive value positive, and predictive value negative for identifying adenomatous polyps of 86%, 80%, 86%, and 80%, respectively. These values were not significantly different from the accuracy of routine clinical pathology. Thus, ultraviolet laser-induced fluorescence appears to show promise as a means for distinguishing tissue types. However, further experience is needed before its routine clinical use can be recommended. Significant changes in the fluorescence spectra occurred postmortem, suggesting that future studies of laser-induced fluorescence of colonic tissue must use data acquired in vivo.
Correlation of in vitro Immune Defects withImpaired Gamma Interferon Response inHuman-Immunodeficiency-Virus-Infected Individuals (1988)

65 patients belonging to known acquired-immune-deficiency-syndrome (AIDS) risk groups were tested for mitogen responsiveness to pokeweed mitogen, concanavalin A and phytohemagglutinin, percentages of peripheral blood CD4, CD8 and Leu7 lymphocyte subsets, serum neopterin levels, and γ-interferon (γ-IFN) concentrations in cell culture supernatants. Patients with clinical symptoms of human-immunodeficiency-virus infection showed reduced γ-IFN production in vitro. The IFN concentrations were correlated significantly with mitogen-induced blastogenesis. High serum neopterin levels and decreased CD4/CD8 ratios were associated with diminished γ-IFN levels. The percentage of Leu7 lymphocytes was increased in a group of patients with strikingly elevated γ-IFN levels.
Activation of the prolactin receptor gene by promoter insertion in a Moloney murine leukemia virus-induced rat thymoma (1992)

The prolactin receptor (Prlr) and growth hormone receptor (Ghr) genes and the Moloney murine leukemia virus integration-2 (Mlvi-2) locus were mapped to mouse chromosome 15 and human chromosome 5 bands p12-p14. To examine the potential relationship between Mlvi-2 and the genes encoding the growth hormone receptor and the prolactin receptor, we determined the chromosomal location of all three loci in the rat, using a panel of rat-mouse somatic cell hybrids, and in the mouse, using a panel of (C57BL/6J x Mus spretus)F1 x C57BL/6J interspecific backcross mice. These analyses revealed that Ghr, Prlr, and Mlvi-2 map to chromosome 2 in the rat and to chromosome 15 in the mouse, in close proximity with each other. Pulsed-field gel electrophoresis of rat genomic DNA showed no overlaps between the gene encoding the prolactin receptor and the remaining loci. Moreover, expression of the prolactin receptor was not affected by provirus insertion in Mlvi-2. During these studies, however, we detected one T-cell lymphoma line (2779) in which the prolactin receptor gene was activated by provirus integration. Sequence analysis of polymerase chain reaction-derived cDNA clones showed that the prolactin receptor RNA message initiates at the 5' long terminal repeat and utilizes the splice donor site 5' of the gag gene to splice the viral sequences onto exon 1 of the prolactin receptor. This message is predicted to encode the intact prolactin receptor protein product. Exposure of the T-cell lymphoma line 2779 to prolactin promoted cellular proliferation.
A probabilistic estimation framework for predictive modeling analytics (2002)

IBM ProbE (for probabilistic estimation) is an extensible, embeddable, and scalable modeling engine, particularly well-suited for implementing segmentation-based modeling techniques, wherein data records are partitioned into segments and separate predictive models are developed for each segment. We describe the ProbE framework and discuss two key business solutions that have been built using ProbE: the IBM Underwriting Profitability Analysis for insurance risk management, and the IBM Advanced Targeted Marketing for Single Events for direct mail database marketing.
Fingolimod (FTY720) as an Acute Rescue Therapy for Intraocular Inflammatory Disease (2008)

A short-term, high-dose treatment with fingolimod rapidly reduces ocular infiltrates in experimental autoimmune uveoretinitis, leading to a normal myeloid cell count within the retina. When given at the early stages of intraocular inflammation, fingolimod resolves disease. Clinical Relevance This study directly demonstrates the therapeutic potential of fingolimod and an acute rescue intervention for human noninfectious posterior-segment intraocular inflammatory disease.
Comparison of low‐dose oral pulse methotrexate and placebo in the treatment of rheumatoid arthritis. A Controlled Clinical Trial (1985)

One hundred eighty-nine patients with rheumatoid arthritis were entered into a prospective, controlled, double-blind multicenter trial comparing placebo and methotrexate (MTX). One hundred ten patients completed 18 weeks of therapy. No remissions were seen, but patients able to tolerate low-dose pulse MTX therapy were significantly improved, compared with patients receiving placebo therapy, for all clinical variables measured, including joint pain/tenderness and swelling counts, rheumatoid nodules, and patient and physician assessment of disease activity. MTX treatment demonstrated statistically significant improvement over placebo in patients with anemia, elevated erythrocyte sedimentation rate, and rheumatoid factor. However, nearly one-third of the patients receiving MTX were withdrawn for adverse drug reactions, of which elevated levels of liver enzymes was the most common. Pancytopenia occurred in 2 patients taking MTX. All adverse drug effects resolved without sequelae. MTX appears to be effective in the treatment of active rheumatoid arthritis but requires close monitoring for toxicity.
Design of sonar sensor model for safe landing of an UAV (2015)

In this paper a procedure that creates a three dimensional (3D) virtual map useful for Safe Landing of an UAV Quadcopter [3], through a Ultrasonic Sensor Model is presented. Reflective sound waves produced from sonar sensor were analyzed and managed to generate a constructed plane where the UAV landing is possible and safe. The low-cost sensor gives relatively accurate range readings if there are disregarding angular uncertainty and specular reflections. Application works for an horizontal plane with and without obstacles inside it. Ultrasonic sensor detects obstacles in the landing field and if there are obstacles higher than UAV landing legs, the landing procedure is aborted. A series of ultrasonic sensors installed on UAV are used for low-altitude mapping on an horizontal plane. Experiments were ducted on a model at 150 cm from the landing field.