gebhart/patrepeval huggingface dataset:
Platelet-based coding of depth maps for the transmission of multiview images (2006)

Emerging 3-D displays show several views of the scene simultaneously. A direct transmission of a selection of these views is impractical, because various types of displays support a different number of views and the decoder has to interpolate the intermediate views. The transmission of multiview image information can be simplified by only transmitting the texture data for the central view and a corresponding depth map. Additional to the coding of the texture data, this technique requires the efficient coding of depth maps. Since the depth map represents the scene geometry and thereby covers the 3-D perception of the scene, sharp edges corresponding to object boundaries, should be preserved. We propose an algorithm that models depth maps using piecewise-linear functions (platelets). To adapt to varying scene detail, we employ a quadtree decomposition that divides the image into blocks of variable size, each block being approximated by one platelet. In order to preserve sharp object boundaries, the support area of each platelet is adapted to the object boundary. The subdivision of the quadtree and the selection of the platelet type are optimized such that a global rate-distortion trade-off is realized. Experimental results show that the described method can improve the resulting picture quality after compression of depth maps by 1-3 dB when compared to a JPEG-2000 encoder.
Reaction of 4-haloacetoacetate with phenols in the presence of aluminum chloride. (1982)

Reaction of ethyl 4-bromoacetoacetate (1) with phenol in the presence of aluminum chloride gave ethyl 4-bromo-3-hydroxy-3-(2-hydroxyphenyl) butyrate (3a), which can be regarded as an intermediate of the Pechmann reaction. Similar reaction of ethyl 4-chloroacetoacetate (7) with phenol in the presence of aluminum chloride gave the 4-chloroderivative 8a. Compound 3a was treated with either hydrogen chloride in ethanol or triethylamine followed by treatment with p-toluenesulfonic acid to give 4-bromomethylcoumarin (4a) or ethyl 3-benzo [b] furanacetate (6a), respectively. Similarly, reactions of phenol derivatives 2 with 1 gave the corresponding 3-hydroxy-butyrates 3, which were transformed to the coumarins 4 and the 3-benzo [b] furanacetates 6.
Molecular and chemical characterization of the lipopolysaccharide O‐antigen and its role in the virulence of Yersinia enterocolitica serotype O:8 (1997)

The Y. enterocolitica O:8(YeO8) O-antigen repeat units consist of five sugar residues: N-acetyl-D-galactosamine (GalNAc), D-galactose (Gal), D-mannose (Man), L-fucose (Fuc), and 6-deoxy-D-gulose (6d-Gul). The nucleotide sequence of the O-antigen gene cluster of the YeO8 strain 8081-c was determined. Altogether, 18 open reading frames (ORFs) were identified and shown to be essential for O-antigen biosynthesis. We previously characterized the 3'-end of the O-antigen gene cluster and identified four genes: two for GDP-Man biosynthesis, one for UDP-Gal biosynthesis, and one for O-antigen polymerase. Based on sequence similarity, Tn5-insertion phenotypes and chemical analysis, the 14 new genes were assigned the following functions: four genes are involved in the biosynthesis of CDP-6d-Gul and two in GDP-Fuc biosynthesis. Five gene products were assigned sugar transferase functions and one gene product was similar to Wzx, the O-antigen flippase. Two genes remained unassigned. By genetic complementation we also showed that YeO8 O-antigen biosynthesis was dependent on N-acetyl-glucosaminyl:undecaprenylphosphate transferase (GlcNAc transferase), the WecA (formerly known as Rfe) protein. Data obtained from chemical-composition analysis suggest that in addition to being GlcNAc transferase, WecA may also function as a GalNAc transferase. Using a restriction-deficient derivative of Y. enterocolitica O:8 strain 8081, a rough mutant, designated 8081-R2, was isolated. 8081-R2 was complemented in trans with a cloned O-antigen gene cluster restoring surface O-antigen expression. The virulence of the wild-type strain and that of the complemented strain were significantly higher (approx. 100-fold) than that of the rough mutant in an orally infected mouse model, showing that YeO8 O-antigen is a virulence factor.
Identification of the N-Linked Glycosylation Sites of Vitamin K-Dependent Carboxylase and Effect of Glycosylation on Carboxylase Function (2006)

The vitamin K-dependent carboxylase is an integral membrane protein which is required for the post-translational modification of a variety of vitamin K-dependent proteins. Previous studies have suggested carboxylase is a glycoprotein with N-linked glycosylation sites. In this study, we identify the N-glycosylation sites of carboxylase by mass spectrometric peptide mapping analyses combined with site-directed mutagenesis. Our mass spectrometric results show that the N-linked glycosylation in carboxylase occurs at positions N459, N550, N605, and N627. Eliminating these glycosylation sites by changing asparagine to glutamine caused the mutant carboxylase to migrate faster on SDS-PAGE gels, adding further evidence that these sites are glycosylated. In addition, the mutation studies identified N525, a site that cannot be recovered by mass spectroscopy analysis, as a glycosylation site. Furthermore, the potential glycosylation site at N570 is glycosylated only if all five natural glycosylation sites are simultaneously mutated. Removal of the oligosaccharides by glycosidase from wild-type carboxylase or by elimination of the functional glycosylation sites by site-directed mutagenesis did not affect either the carboxylation or epoxidation activity when the small FLEEL pentapeptide was used as a substrate, suggesting that N-linked glycosylation is not required for the enzymatic function of carboxylase. In contrast, when site N570 and the five natural glycosylation sites were mutated simultaneously, the resulting carboxylase protein was degraded. Our results suggest that N-linked glycosylation is not essential for carboxylase enzymatic activity but is important for protein folding and stability.
Antiphosphatidylserine Antibody Combined with Irradiation Damages Tumor Blood Vessels and Induces Tumor Immunity in a Rat Model of Glioblastoma (2009)

Bavituximab combined with radiotherapy holds promise as a vascular targeting and immune enhancement strategy for the treatment of human glioblastoma.
Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives (1993)

A new multisolution phasing method based on entropy maximization and likelihood ranking, proposed for the specific purpose of extending probabilistic direct methods to the field of macromolecules, has been implemented in two different computer programs and applied to a wide variety of problems. The latter comprise the determination of small crystal structures from X-ray diffraction data obtained from single crystals or from powders, and from electron diffraction data partially phased by image processing of electron micrographs, the ab initio generation and ranking of phase sets for small proteins; and the improvement of poor quality phases for a larger protein at medium resolution under constraint of solvent flatness. These applications show that the primary goal of this new method - namely increasing the accuracy and sensitivity of probabilistic phase indications compared with conventional direct methods - has been achieved. The main components of the method are (1) a tree-directed search through a space of trial phase sets; (2) the saddle-point method for calculating joint probabilities of structure factors, using entropy maximization; (3) likelihood-based scores to rank trial phase sets and prune the search tree; (4) efficient schemes, based on error-correcting codes, for sampling trial phase sets; (5) a statistical analysis of the scores for automatically selecting reliable phase indications. They have been implemented to varying degrees of completeness in a computer program (BUSTER) and tested on two small structures as well as on the small protein crambin. The main obstructions to successful ab initio phasing in the latter case seem to reside in the accumulation of phase sampling errors and in the lack of a properly defined molecular envelope, both of which can be remedied within the methods proposed. A review of the Bayesian statistical theory encompassing all phasing procedures, proposed earlier as an extension of the initial theory, shows that the techniques now available in BUSTER bring closer a number of major enhancements of standard macromolecular phasing techniques, namely isomorphous replacement, molecular replacement, solvent flattening and non-crystallographic symmetry averaging. The gradual implementation of the successive stages of this 'Bayesian programme' should lead to an increasingly integrated, effective and dependable phasing procedure for macromolecular structure determination.
Two human monoclonal antibodies reacting with the major gangliosides of human melanomas and comparison with corresponding mouse monoclonal antibodies. (1989)

The fine specificity analysis of two human monoclonal antibodies (AbFCM1 and AbHJM1) reacting with gangliosides is described and their specificities are compared with analogous mouse monoclonal antibodies (mAbs). These two antibodies were generated from lymphocytes of melanoma patients by Epstein-Barr virus transformation followed by fusion with mouse myeloma NS-1. Using a wide variety of gangliosides, including N-glycolylneuraminic acid (NeuGc)-containing compounds, the precise structures recognized by these two antibodies were elucidated by enzyme-linked immunosorbent assay and immunostaining of thin-layer chromatograms. AbFCM1 reacted with N-acetylneuraminic acid (NeuAc)-type GM3, GD1a, sialylparagloboside, and GT1b in decreasing order of intensity. This antibody also reacted with (NeuAc-NeuGc-)-GD3 and -disialylparagloboside, but did not react with NeuGc-type GM3, GM2, sialylparagloboside, (NeuGc)2-GD3 and -disialylparagloboside. The main epitope structures recognized by AbFCM1 are, therefore, NeuAc alpha 2----3Gal beta 1- and NeuAc alpha 2----8NeuGc alpha 2----Gal beta 1-. These results are similar to the specificity of mouse mAb M2590. AbHJM1 reacted with NeuAc-type GD3 and disialylparagloboside, GD2, GD1b, GM3, and GT1b, in decreasing order of intensity. Among NeuGc-type gangliosides, this antibody reacts with (NeuAc-NeuGc-)-GD3 and -disialylparagloboside, but did not react with gangliosides containing only NeuGc. Consequently the epitope structure recognized by AbHJM1 is probably (R)-(NeuAc alpha 2----8Sialic acid alpha 2----3)Gal beta 1-. Mouse anti-GD3 mAbR24, in contrast, showed strong reactivity only with GD3 and -disialylparagloboside among NeuAc-type gangliosides, but showed a similar pattern to AbHJM1 in its reactivity with NeuGc-containing gangliosides. Although these two human monoclonal antibodies are not highly restricted in their specificities, they reacted best with the major gangliosides, GM3 and GD3, present in the majority of human melanomas.
The Health Care Costs of Diabetic Peripheral Neuropathy in the U.S. (2003)

The total annual cost of DPN and its complications in the U.S. was estimated to be between 4.6 and 13.7 billion US dollars. Up to 27% of the direct medical cost of diabetes may be attributed to DPN.
Select nutrients, progesterone, and interferon tau affect conceptus metabolism and development (2012)

Interferon tau (IFNT), a novel multifunctional type I interferon secreted by trophectoderm, is the pregnancy recognition signal in ruminants that also has antiviral, antiproliferative, and immunomodulatory bioactivities. IFNT, with progesterone, affects availability of the metabolic substrate in the uterine lumen by inducing expression of genes for transport of select nutrients into the uterine lumen that activate mammalian target of rapamycin (mTOR) cell signaling responsible for proliferation, migration, and protein synthesis by conceptus trophectoderm. As an immunomodulatory protein, IFNT induces an anti-inflammatory state affecting metabolic events that decrease adiposity and glutamine:fructose-6-phosphate amidotransferase 1 activity, while increasing insulin sensitivity, nitric oxide production by endothelial cells, and brown adipose tissue in rats. This short review focuses on effects of IFNT and progesterone affecting transport of select nutrients into the uterine lumen to stimulate mTOR cell signaling required for conceptus development, as well as effects of IFNT on the immune system and adiposity in rats with respect to its potential therapeutic value in reducing obesity.
Evolving strategies in the treatment of sepsis and systemic inflammatory response syndrome (SIRS) (1998)

In recent years, much basic science research has investigated the predisposing factors, initiation, propagation, and resolution of Gram-negative sepsis, endotoxaemic shock, and the newly defined entity of systemic inflammatory response syndrome (SIRS). A major cause of morbidity and mortality in the post-surgical, neonatal, and geriatric hospital population, sepsis has proven itself notoriously resistant to classical modes of therapy, including antibiotics, fluid/pressor and respiratory support. Recently, the widespread nosocomial isolation of new antibiotic-resistant strains of endotoxin-producing bacteria has further complicated management. For these reasons, there is much interest in alternative treatment modalities which focus upon the endotoxin molecule itself and the systemic inflammatory response it provokes via the cytokine, complement, and coagulation cascades. In this review, recent experimental approaches to the therapy of sepsis and SIRS are discussed in light of each step in the complex inflammatory cascade and in comparison to traditional approaches to prevention and therapy of Gram-negative bacteraemia and septic shock.
Determination of Submicromolar Concentrations of Formaldehyde by Liquid Chromatography (1999)

Dissolved formaldehyde in aqueous samples was determined at submicromolar levels by derivatization with Nash's reagent followed by liquid chromatography. The method requires little sample preparation, and the chromatogram is simple even in the presence of other aldehydes and ketones. The isocratic HPLC analysis is rapid with a low limit of detection (0.1 μM) and a precision of 1% RSD at 150 μM. The derivative is stable for at least 3 days at room temperature. Accuracy of the method was verified by intercomparison with an alternate, completely independent method, which utilizes another derivatizing agent.
TOXOPLASMIC ENCEPHALITIS IN CHILDREN (1941)

It has been abundantly demonstrated in recent years that acute nonsuppurative encephalitis is a syndrome of multiple etiology. My purpose in the present communication is (1) to present evidence that organisms of the genus Toxoplasma can be the cause of such encephalitis in children, (2) to describe the clinical and pathologic appearances and (3) to indicate the steps which can be taken to establish the diagnosis. <h3>PRESENT STATUS OF TOXOPLASMA</h3> Toxoplasma is a genus of protozoan parasites which were first observed in the gondi (North African rodent) in 1908 by Nicolle and Manceaux,<sup>1</sup>who differentiated it from Leishmania, and independently in the same year in the rabbit (Brazil) by Splendore.<sup>2</sup>They are highly organized parasites consisting of distinct cytoplasm and nuclear chromatin and are crescentic, pyriform, oval or round, measuring 6 to 7 microns in length and 2 to 4 microns in width, depending on the stage of
Application of L-DNA as a molecular tag (2005)

Enantiomeric DNA termed as L-DNA has unique properties. One is the ability of hybridizing to the complementary DNA as natural D-DNA. Another property is that the L-DNA could be recognized much more weakly by enzymes than D-DNA. We have focused our attention on these properties and applied L-DNA as a molecular tag. Here, we report that L-D chimera DNA is useful for PCR primers and subsequent separation and hybridization. Precise investigation revealed that in the process of PCR, L-DNA region could not be the PCR template and the polymerase extension reaction stopped at the boundary between L- and D-DNA region. As a result, L-DNA region formed like a "sticky end" and played a role of molecular tag. According to the L-DNA tag sequence, the produced L-DNA-tagged PCR products were easily separated or hybridized on the solid surface where the complementary L-DNA was pre-immobilized.
VACET: Proposed SciDAC2 Visualization and Analytics Center for Enabling Technologies (2006)

This project focuses on leveraging scientific visualization and analytics software technology as an enabling technology for increasing scientific productivity and insight. Advances in computational technology have resulted in an ''information big bang, '' which in turn has created a significant data understanding challenge. This challenge is widely acknowledged to be one of the primary bottlenecks in contemporary science. The vision for our Center is to respond directly to that challenge by adapting, extending, creating when necessary and deploying visualization and data understanding technologies for our science stakeholders. Using an organizational model as a Visualization and Analytics Center for Enabling Technologies (VACET), we are well positioned to be responsive to the needs of a diverse set of scientific stakeholders in a coordinated fashion using a range of visualization, mathematics, statistics, computer and computational science and data management technologies.
Isolation of Rhizobium phaseoli Tn5-induced mutants with altered expression of cytochrome terminal oxidases o and aa3 (1990)

Two Rhizobium phaseoli mutants affected in cytochrome expression were obtained by Tn5-mob mutagenesis of the wild-type strain (CE3). Mutant strain CFN031 expressed sevenfold less cytochrome o in culture, expressed cytochrome aa3 under microaerophilic culture conditions, in contrast to strain CE3, and was affected in its vegetative growth properties and proliferation inside plant host cells. Mutant CFN037 expressed cytochrome aa3 under microaerophilic culture conditions, while bacteroid development and nitrogen fixation occurred earlier than in strain CE3.
PF_KEY Key Management API, Version 2 (1998)

A generic key management API that can be used not only for IP Security [Atk95a] [Atk95b] [Atk95c] but also for other network security services is presented in this document.Version 1 of this API was implemented inside 4.4-Lite BSD as part of the U. S. Naval Research Laboratory's freely distributable and usable IPv6 and IPsec implementation[AMPMC96].It is documented here for the benefit of others who might also adopt and use the API, thus providing increased portability of key management applications (e.g. a manual keying application, an ISAKMP daemon, a GKMP daemon [HM97a][HM97b], a Photuris daemon, or a SKIP certificate discovery protocol daemon).
A rapid reproducible test for determining rabies neutralizing antibody. (1973)

Rabies neutralizing antibody levels in human and animal sera were tested by a rapid fluorescent focus inhibition technique, in which BHK-21 cells were infected with tissue-culture-adapted rabiesvirus. The results, obtained in 24 hours, were comparable with those of the standard mouse neutralization test.
Statistical design and the analysis of gene expression microarray data (2001)

Gene expression microarrays are an innovative technology with enormous promise to help geneticists explore and understand the genome. Although the potential of this technology has been clearly demonstrated, many important and interesting statistical questions persist. We relate certain features of microarrays to other kinds of experimental data and argue that classical statistical techniques are appropriate and useful. We advocate greater attention to experimental design issues and a more prominent role for the ideas of statistical inference in microarray studies.
A data model and query language for EXODUS (1988)

In this paper, we present the design of the EXTRA data model and the EXCESS query language for the EXODUS extensible database system. The EXTRA data model includes support for complex objects with shared subobjects, a novel mix of object- and value-oriented semantics for data, support for persistent objects of any type in the EXTRA type lattice, and user-defined abstract data types (ADTs). The EXCESS query language provides facilities for querying and updating complex object structures, and it can be extended through the addition of ADT functions and operators, procedures and functions for manipulating EXTRA schema types, and generic set functions EXTRA and EXCESS are intended to serve as a test vehicle for tools developed under the EXODUS extensible database system project.
IL-21 Selectively Protects CD62L+ NKT Cells and Enhances Their Effector Functions for Adoptive Immunotherapy (2018)

T cells expressing CD19-specific chimeric Ag receptors (CARs) produce high remission rates in B cell lymphoma, but frequent disease recurrence and challenges in generating sufficient numbers of autologous CAR T cells necessitate the development of alternative therapeutic effectors. Vα24-invariant NKTs have intrinsic antitumor properties and are not alloreactive, allowing for off-the-shelf use of CAR-NKTs from healthy donors. We recently reported that CD62L<sup>+</sup> NKTs persist longer and have more potent antilymphoma activity than CD62L<sup>-</sup> cells. However, the conditions governing preservation of CD62L<sup>+</sup> cells during NKT cell expansion remain largely unknown. In this study, we demonstrate that IL-21 preserves this crucial central memory-like NKT subset and enhances its antitumor effector functionality. We found that following antigenic stimulation with α-galactosylceramide, CD62L<sup>+</sup> NKTs both expressed IL-21R and secreted IL-21, each at significantly higher levels than CD62L<sup>-</sup> cells. Although IL-21 alone failed to expand stimulated NKTs, combined IL-2/IL-21 treatment produced more NKTs and increased the frequency of CD62L<sup>+</sup> cells versus IL-2 alone. Gene expression analysis comparing CD62L<sup>+</sup> and CD62L<sup>-</sup> cells treated with IL-2 alone or IL-2/IL-21 revealed that the latter condition downregulated the proapoptotic protein BIM selectively in CD62L<sup>+</sup> NKTs, protecting them from activation-induced cell death. Moreover, IL-2/IL-21-expanded NKTs upregulated granzyme B expression and produced more T<sub>H</sub>1 cytokines, leading to enhanced in vitro cytotoxicity of nontransduced and anti-CD19-CAR-transduced NKTs against CD1d<sup>+</sup> and CD19<sup>+</sup> lymphoma cells, respectively. Further, IL-2/IL-21-expanded CAR-NKTs dramatically increased the survival of lymphoma-bearing NSG mice compared with IL-2-expanded CAR-NKTs. These findings have immediate translational implications for the development of NKT cell-based immunotherapies targeting lymphoma and other malignancies.
<title>Spatiotemporal discrimination model predicts temporal masking functions</title> (1998)

We present a simplified dual-channel discrimination model with spatio-temporal filters to represent the visual system contrast sensitivity, and masking based on local spatio- temporal contrast energy. The contrast sensitivity filter parameters of the model were based on previous work. The masking and global sensitivity parameters are calibrated to masking data using brief grating target signals masked by a 700 msec grating with the same spatial parameters.
Femtosecond pulse shaping by dynamic holograms in photorefractive multiple quantum wells (1997)

Femtosecond pulses can be shaped in the time domain by diffraction from dynamic holograms in a photorefractive multiple quantum well placed inside a Fourier pulse shaper. We present several examples of shaped pulses obtained by controlling the amplitude or the phase of the hologram writing beams, which modifies the complex spectrum of the femtosecond output.