gebhart/patrepeval huggingface dataset:
Analytic Approximations for Real-Time Area Light Shading (2017)

We introduce analytic approximations for accurate real-time rendering of surfaces lit by non-occluded area light sources. Our solution leverages the Irradiance Tensors developed by Arvo for the shading of Phong surfaces lit by a polygonal light source. Using a reformulation of the 1D boundary edge integral, we develop a general framework for approximating and evaluating the integral in constant time using simple peak shape functions. To overcome the Phong restriction, we propose a low cost edge splitting strategy that accounts for the spherical warp introduced by the half vector parametrization. Thanks to this novel extension, we accurately approximate common microfacet BRDFs, providing a practical method producing specular stretches that closely match the ground truth in real-time. Finally, using the same approximation framework, we introduce support for spherical and disc area light sources, based on an original polygon spinning method supporting non-uniform scaling operations and horizon clipping. Implemented on a GPU, our method achieves real-time performances without any assumption on area light shape nor surface roughness.
Three‐dimensional augmented reality surgical navigation with hybrid optical and electromagnetic tracking for distal intramedullary nail interlocking (2018)

Our results indicate that the AR-guided distal interlocking method is feasible and has many potential applications in clinic after further evaluation.
Overexpression of IL-32α Increases Natural Killer Cell-mediated Killing through Up-regulation of Fas and UL16-binding protein 2 (ULBP2) Expression in Human Chronic Myeloid Leukemia Cells (2011)

IL-32 was recently identified as a proinflammatory cytokine that is induced by IL-18 in natural killer (NK) cells and is highly correlated with inflammatory disorders. However, the relationship between IL-32 and tumor progression is still unknown. In this study, we investigated whether overexpression of IL-32 affects susceptibility of chronic myeloid leukemia (CML) cells to NK cells. Interestingly, IL-32α-overexpressing CML cell lines, K562, Kcl22, and BV173, showed higher NK cell-mediated killing. Flow cytometry analysis revealed that overexpression of IL-32α induced increased expression of Fas and UL16-binding protein 2 (ULBP2) in CML cells. The direct relationship between overexpression of surface molecules by IL-32α and increased NK cell-mediated killing was confirmed by Fas or ULBP2 siRNA transfection. IL-32α-induced Fas and ULBP2 expression are regulated p38 MAPK. In addition, the transcription factor Ets1 plays a key role in ULBP2 specific expression by IL-32α overexpression in ULBP family members. Taken together, these data show that IL-32α stimulates Fas and ULBP2 expression via activation of p38 MAPK, which increases NK susceptibility of CML cells. Enhanced NK cell susceptibility of CML cells by IL-32α overexpression may improve the efficiency of NK cell-based immunotherapy. IL-32 was recently identified as a proinflammatory cytokine that is induced by IL-18 in natural killer (NK) cells and is highly correlated with inflammatory disorders. However, the relationship between IL-32 and tumor progression is still unknown. In this study, we investigated whether overexpression of IL-32 affects susceptibility of chronic myeloid leukemia (CML) cells to NK cells. Interestingly, IL-32α-overexpressing CML cell lines, K562, Kcl22, and BV173, showed higher NK cell-mediated killing. Flow cytometry analysis revealed that overexpression of IL-32α induced increased expression of Fas and UL16-binding protein 2 (ULBP2) in CML cells. The direct relationship between overexpression of surface molecules by IL-32α and increased NK cell-mediated killing was confirmed by Fas or ULBP2 siRNA transfection. IL-32α-induced Fas and ULBP2 expression are regulated p38 MAPK. In addition, the transcription factor Ets1 plays a key role in ULBP2 specific expression by IL-32α overexpression in ULBP family members. Taken together, these data show that IL-32α stimulates Fas and ULBP2 expression via activation of p38 MAPK, which increases NK susceptibility of CML cells. Enhanced NK cell susceptibility of CML cells by IL-32α overexpression may improve the efficiency of NK cell-based immunotherapy.
Enumeration and Detection of Anaerobic Ferrous Iron-Oxidizing, Nitrate-Reducing Bacteria from Diverse European Sediments (1998)

Anaerobic, nitrate-dependent microbial oxidation of ferrous iron was recently recognized as a new type of metabolism. In order to study the occurrence of three novel groups of ferrous iron-oxidizing, nitrate-reducing bacteria (represented by strains BrG1, BrG2, and BrG3), 16S rRNA-targeted oligonucleotide probes were developed. In pure-culture experiments, these probes were shown to be suitable for fluorescent in situ hybridization, as well as for hybridization analysis of denaturing gradient gel electrophoresis (DGGE) patterns. However, neither enumeration by in situ hybridization nor detection by the DGGE-hybridization approach was feasible with sediment samples. Therefore, the DGGE-hybridization approach was combined with microbiological methods. Freshwater sediment samples from different European locations were used for enrichment cultures and most-probable-number (MPN) determinations. Bacteria with the ability to oxidize ferrous iron under nitrate-reducing conditions were detected in all of the sediment samples investigated. At least one of the previously described types of bacteria was detected in each enrichment culture. MPN studies showed that sediments contained from 1 x 10(5) to 5 x 10(8) ferrous iron-oxidizing, nitrate-reducing bacteria per g (dry weight) of sediment, which accounted for at most 0.8% of the nitrate-reducing bacteria growing with acetate. Type BrG1, BrG2, and BrG3 bacteria accounted for an even smaller fraction (0.2% or less) of the ferrous iron-oxidizing, nitrate-reducing community. The DGGE patterns of MPN cultures suggested that more organisms than those isolated thus far are able to oxidize ferrous iron with nitrate. A comparison showed that among the anoxygenic phototrophic bacteria, organisms that have the ability to oxidize ferrous iron also account for only a minor fraction of the population.
Characterization of an electrogenic sodium/glucose cotransporter in a human colon epithelial cell line (1995)

In this study, we have characterized the Na/glucose transporter in polarized monolayers formed by the clonal human colon carcinoma cell line HT-29-D4. Isotopic tracer flux measurements show that differentiated HT-29-D4 cells possess a sodium-dependent alpha-methyl-D-glucopyranoside (AMG) uptake that is competed for by increasing concentrations of D-glucose, D-galactose, and phlorizin. This transport is exclusively localized on the apical side of the epithelium. Kinetic data demonstrate the existence of a single Michaelian sodium-dependent AMG transporter with a Km of 1.2 +/- 0.12 mM and a Vmax of 3.24 +/- 0.25 nmol/mg of protein per min. Hill analysis reveals a coefficient of 1.9 +/- 0.03, consistent with at least two sodium ions involved in AMG transport. Interestingly, the cotransporter function is not modulated by glucose in the culture medium. Transepithelial electrical parameter measurements show that the transepithelial potential difference (Vt) is glucose dependent and phlorizin sensitive. Antibodies directed against a peptide of the rabbit intestinal glucose cotransporter (Ser402-Lys420) recognize, in western blot experiments, the characteristic bands of the cotransporter on a crude membrane preparation of differentiated HT-29-D4 cells and react strongly with the apical domain of the monolayer in immunofluorescence experiments. We conclude that HT-29-D4 cells express the sodium/glucose cotransporter SGLT1 at their apical membrane and that this transporter generates the basal transepithelial potential difference.
Peptide Sequencing of 2-DE Gel-Isolated Proteins by Nanoelectrospray Tandem Mass Spectrometry (2003)

Shortly after the introduction of electrospray as a viable ionization technique for large molecules (1), electrospray tandem mass spectrometry (ES MS/MS) techniques, such as HPLC-ES MS/MS, were used successfully for peptide sequencing at picomole and subpicomole levels (2–4). In LC-MS/MS, peptide sequence information is generated during the short time, 10–30 s, that a peptide elutes from the HPLC column run at a flow rate of 0.5–5 μL/min. This time frame rarely allows optimization of experimental parameters for MS/MS sequencing of individual peptides unless several LC-MS/MS experiments can be performed on a sample. With the introduction of the nanoelectrospray ion source (5–7), the time constraint of tandem mass spectrometry has been removed, and peptide sequencing has been reliably extended to the femtomole level of gel-isolated protein.
Combinatorial Electrodeposition of Magnetostrictive Fe[sub 1−x]Ga[sub x] (2010)

Alloys of iron and gallium were electroplated to produce magnetostrictive Galfenol thin films. A trapezoidal Hull cell was used to control composition via a combinatorial approach where the deposition current density was varied predictably across the cathode. Four parameter spaces were identified in which metallic iron, Galfenol, oxide, and Ga-rich metal films, respectively, were produced. It was found that a broad range of current densities could be used to produce Galfenol by varying the concentration of and its complexing agent, sodium citrate, compared to that of . A novel method employing energy dispersive X-ray spectroscopy (EDS) was used to determine thickness as well as composition at specific points along the cathode. Deposition rates, partial current densities, and deposition efficiencies were determined accurately as a function of current density using the Nohse equation. The EDS results were verified with Rutherford backscattering (RBS). As expected, deposition rates increased with current density, while efficiencies of codeposition decreased. The grain sizes and crystallographic orientations of metallic Galfenol were dependent on deposition rate with fast rates producing small grains of (110) texturing and slow rates primarily producing large (211) oriented cubic crystals.
Carbon monoxide-releasing molecule-2 decreases fibrinolysis in vitro and in vivo in the rabbit (2011)

Administration of carbon monoxide derived from carbon monoxide-releasing molecules (CORMs) have been demonstrated to enhance coagulation and diminish fibrinolysis in vitro at small concentrations (100-200 μmol/l) in human and rabbit plasma, whereas in vivo administration of large concentrations (>1400 μmol/l) of carbon monoxide has mildly increased bleeding time in vivo in rats. We sought to determine whether CORM-2 [tricarbonyldichlororuthenium (II) dimer] would improve coagulation and attenuate tissue-type plasminogen activator (tPA)-mediated fibrinolysis in rabbit whole blood as determined in vitro by thrombelastography and in an in vivo preclinical rabbit model of ear bleeding time administered intravenous tPA (1 mg/kg). Addition of 200, 400 and 600 μmol/l CORM-2 to whole blood significantly improved coagulation and attenuated fibrinolysis compared with blood without CORM-2. Rabbits administered CORM-2 (10 mg/kg, 279 μmol/l) had a small but significant decrease in bleeding time before tPA administration. Administration of tPA resulted in bleeding times more than six-fold greater than baseline in animals not exposed to CORM-2, whereas rabbits administered CORM-2 had significantly smaller (more than five-fold less) bleeding time values after tPA administration. CORM-2 administration significantly decreases fibrinolytic bleeding in the rabbit in vivo. Additional preclinical investigation of the effects of CORM-2 on coagulopathy (e.g. heparin-mediated or clopidogrel-mediated) utilizing this rabbit model are planned.
Uptake and Distribution of Sodium and Potassium by Corn Seedlings (1983)

The distribution of sodium and potassium throughout corn (Zea mays L. [A632 x Crows 3640] x Oh 43) plants is not simply a matter of uptake by cortical cells and irreversible delivery to the xylem for upward transport. We show that sodium, but not potassium, accumulates in the mesocotyl of corn seedlings grown on NaCl medium. Upon transfer to NaCl-free medium, total sodium is reduced by export through the roots but remains at high levels within the mesocotyl. We report experiments which consider uptake from the xylem.Shoots excised at the seed were allowed to transpire solutions containing (22)Na and (42)K. Potassium uptake within the mesocotyl was very sensitive to concentration, increasing 27-fold between 1 and 10 millimolar. Sodium uptake was dependent upon the square root of the concentration suggesting active accumulation. At sodium concentrations below 1 millimolar, more than 80% of the sodium in the plant was retained in the mesocotyl. Both the uptake by and retention within the mesocotyl were dependent upon transpiration rate as well as concentration. We discuss the limitations of measuring uptake from a finite, depletable medium. The mesocotyl is a modified root with a cuticularized epidermis. We discuss the feasibility of using this ;plastic-coated root' as a model for root transport studies.
A former amino terminal signal sequence engineered to an internal location directs translocation of both flanking protein domains. (1985)

To determine whether a functional amino terminal signal sequence can be active at an internal position, a hybrid gene was constructed in which the entire coding region of bovine preprolactin cDNA was inserted into chimpanzee alpha-globin cDNA 109 codons downstream from the initiation codon of globin. When RNA synthesized in vitro from this plasmid (pSPGP1) was translated in the rabbit reticulocyte cell-free system, a 32-kD protein was produced that was both prolactin and globin immunoreactive. When microsomal membranes were present during translation (but not when added posttranslationally), a 26-kD and a 14-kD product were also observed. By immunoreactivity and electrophoretic mobility, the 26-kD protein was identical to mature prolactin, and the 14-kD protein appeared to be the globin domain with the prolactin signal sequence attached at its carboxy terminus. From (a) posttranslational proteolysis in the presence and absence of detergent, (b) sedimentation of vesicles in the presence and absence of sodium carbonate pH 11.5, and (c) N-linked glycosylation of the globin-immunoreactive fragment after insertion of an Asn-X-Ser N-linked glycosylation site into the globin coding region of pSPGP1, it appears that all of the 26-kD and some of the 14-kD products, but none of the 32-kD precursor, have been translocated to the lumen of the membrane vesicles. Thus, when engineered to an internal position, the prolactin signal sequence is able to translocate both flanking protein domains. These data have implications for the understanding of translocation of proteins across the membrane of the endoplasmic reticulum.
Aerobic and anaerobic bacteria in subgingival and supragingival plaques of adult patients with periodontal disease. (2006)

1) In adult patients with periodontal disease, Gram-positive anaerobes, including Peptostreptococcus, were the predominant bacteria in the subgingival plaque. 2) While in the supragingival plaque, Gram-positive aerobic cocci (Streptococcus and Staphylococcus) were predominant.
Relationship between time reversal and linear equalization in digital communications (2006)

Iterative time reversal has been suggested as both an efficient method of creating a spatio-temporal focus and for use in telecommunications as a form of equalization. In this paper, the equivalence of a passive, i.e., via computation, iterative time reversal to the Moore-Penrose pseudo-inverse of the propagation matrix is shown. In the context of communications, however, any received signal is corrupted by noise. Therefore, a regularization term is introduced to the iterative equations, causing convergence to the canonical minimum mean-squared error linear equalizer. Hence, a relationship between time reversal and equalization is demonstrated.
Parametric classification of segments in ocular nystagmus (1991)

A method for nystagmus classification that uses system identification techniques is presented. A system is formulated whose input is head position and whose output is eye position. This system is approximated with an autoregressive with exogenous input model which relates the input and output (transfer function) regardless of the temporal profile for the sensory stimulation. The system is then identified using a least squares criteria and three indicators are produced. From these a flag that marks slow and fast phases as well as blinks is produced. Bad data segment classification is remarkably insensitive to recording noise. The method is more robust than previous techniques. Operator intervention is minimal. The method should be applicable for all types of ocular nystagmus. Results are given in the context of the vestibuloocular reflex. How this method can be applied for optokinetic or pursuit nystagmus is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Analysis of <i>PEAM4</i>, the pea <i>AP1</i> functional homologue, supports a model for <i>AP1</i>‐like genes controlling both floral meristem and floral organ identity in different plant species (2001)

APETALA1 (AP1) and its homologue SQUAMOSA (SQUA) are key regulatory genes specifying floral meristem identity in the model plants Arabidopsis and Antirrhinum. Despite many similarities in their sequence, expression and functions, only AP1 appears to have the additional role of specifying sepal and petal identity. No true AP1/SQUA-functional homologues from any other plant species have been functionally studied in detail, therefore the question of how the different functions of AP1-like genes are conserved between species has not been addressed. We have isolated and characterized PEAM4, the AP1/SQUA-functional homologue from pea, a plant with a different floral morphology and inflorescence architecture to that of Arabidopsis or Antirrhinum. PEAM4 encodes for a polypeptide 76% identical to AP1, but lacks the C-terminal prenylation motif, common to AP1 and SQUA, that has been suggested to control the activity of AP1. Nevertheless, constitutive expression of PEAM4 caused early flowering in tobacco and Arabidopsis. In Arabidopsis, PEAM4 also caused inflorescence-to-flower transformations similar to constitutive AP1 expression, and was able to rescue the floral organ defects of the strong ap1-1 mutant. Our results suggest that the control of both floral meristem and floral organ identity by AP1 is not restricted to Arabidopsis, but is extended to species with diverse floral morphologies, such as pea.
Encoding information in chemical chaos by controlling symbolic dynamics (1997)

In this paper we describe a technique of encoding and then decoding symbol sequences containing information into chaotic oscillations of the Belousov-Zhabotinsky reaction. The encoding technique is based on controlling the chaotic oscillations by applying small parameter perturbations and on learning the grammar of corresponding symbol dynamics produced by the free-running chaotic system. The use of small parameter perturbations requires that we respect the grammar of the symbol dynamics which represents the physical dynamical system. We present a method for learning the grammar of a symbol dynamics in terms of allowed transitions between the bins defined by the symbol generating partition. The encoding technique can be easily utilized for targeting and stabilization of any unstable periodic orbit.
Methyl radical etching of compound semiconductors with a secondary afterglow reactor (1990)

While halogen-based dry etching processes are well established for silicon devices, many compound semiconductors have insufficiently volatile halides for successful conventional dry etch processing. These elements, found in groups II B, III A, IV A, V A, and VI A of the Periodic Table, do form volatile organometallic compounds. A secondary afterglow reactor, in which atomic fluorine produced in a microwave discharge is reacted with methane downstream of the discharge, has been used to etch HgCdTe, CdTe, InP, InSb, and GaAs at temperature-dependent rates between 100 Å and 1000 Å/min. This etching is purely chemical and without ion bombardment, and it shows crystallographic orientation dependence on the etch rate. The activation energies for etching in a methyl/atomic hydrogen ambient range from 2.3 and 7.2 kcal/mol. CdTe(111)B etched faster, smoother, and with a higher activation energy than CdTe(100), which produced a surface with submicron texturing. Specular surfaces were observed with CdTe, InP, InSb, and GaAs, although the HgCdTe etched with significant roughness.
On the Properties of Neural Machine Translation: Encoder–Decoder Approaches (2014)

Neural machine translation is a relatively new approach to statistical machine translation based purely on neural networks.The neural machine translation models often consist of an encoder and a decoder.The encoder extracts a fixed-length representation from a variable-length input sentence, and the decoder generates a correct translation from this representation.In this paper, we focus on analyzing the properties of the neural machine translation using two models; RNN Encoder-Decoder and a newly proposed gated recursive convolutional neural network.We show that the neural machine translation performs relatively well on short sentences without unknown words, but its performance degrades rapidly as the length of the sentence and the number of unknown words increase.Furthermore, we find that the proposed gated recursive convolutional network learns a grammatical structure of a sentence automatically.
Two-Component Transcriptional Regulation of N -Acyl-Homoserine Lactone Production in <i>Pseudomonas aureofaciens</i> (1999)

Production of phenazine antibiotics by the biological control bacterium Pseudomonas aureofaciens 30-84 is regulated in part by the PhzI/PhzR N-acyl-homoserine lactone (AHL) response system (L. S. Pierson III, V. D. Keppenne, and D. W. Wood, J. Bacteriol. 176:3966-3974, 1994; D. W. Wood and L. S. Pierson III, Gene 168:49-53, 1996). Two mutants, 30-84W and 30-84.A2, were isolated and were found to be deficient in the production of phenazine, protease, hydrogen cyanide (HCN), and the AHL signal N-hexanoyl-homoserine lactone. These mutants were not complemented by phzI, phzR, or the phenazine biosynthetic genes (phzFABCD) (L. S. Pierson III, T. Gaffney, S. Lam, and F. Gong, FEMS Microbiol. Lett. 134:299-307, 1995). A 2.2-kb region of the 30-84 chromosome which fully restored production of all of these compounds in strain 30-84W was identified. Nucleotide sequence analysis of this region revealed a single open reading frame encoding a predicted 213-amino-acid protein which is very similar to the global response regulator GacA. Strain 30-84.A2 was not complemented by gacA or any cosmid from a genomic library of strain 30-84 but was complemented by gacS (formerly lemA) homologs from Pseudomonas fluorescens Pf-5 (N. Corbel and J. E. Loper, J. Bacteriol. 177:6230-6236, 1995) and Pseudomonas syringae pv. syringae B728a (E. M. Hrabek and D. K. Willis, J. Bacteriol. 174:3011-3020, 1992). Transcription of phzR was not altered in either mutant; however, phzI transcription was eliminated in strains 30-84W and 30-84.A2. These results indicated that the GacS/GacA two-component signal transduction system of P. aureofaciens 30-84 controls the production of AHL required for phenazine production by mediating the transcription of phzI. Addition of exogenous AHL did not complement either mutant for phenazine production, indicating that the GacS/GacA global regulatory system controls phenazine production at multiple levels. Our results reveal for the first time a mechanism by which a two-component regulatory system and an AHL-mediated regulatory system interact.