gebhart/patrepeval huggingface dataset:
The Ectodomain of a Novel Member of the Immunoglobulin Subfamily Related to the Poliovirus Receptor Has the Attributes of a Bona Fide Receptor for Herpes Simplex Virus Types 1 and 2 in Human Cells (1998)

We report on the functional cloning of a hitherto unknown member of the immunoglobulin (Ig) superfamily selected for its ability to confer susceptibility to herpes simplex virus (HSV) infection on a highly resistant cell line (J1.1-2 cells), derived by exposure of BHKtk- cells to a recombinant HSV-1 expressing tumor necrosis factor alpha (TNF-alpha). The sequence of herpesvirus Ig-like receptor (HIgR) predicts a transmembrane protein with an ectodomain consisting of three cysteine-bracketed domains, one V-like and two C-like. HIgR shares its ectodomain with and appears to be an alternative splice variant of the previously described protein PRR-1 (poliovirus receptor-related protein). Both HIgR and PRR-1 conferred on J1.1-2 cells susceptibility to HSV-1, HSV-2, and bovine herpesvirus 1. The viral ligand of HIgR and PRR-1 is glycoprotein D, a constituent of the virion envelope long known to mediate viral entry into cells through interaction with cellular receptor molecules. Recently, PRR-1, renamed HveC (herpesvirus entry mediator C), and the related PRR-2, renamed HveB, were reported to mediate the entry of HSV-1, HSV-2, and bovine herpesvirus 1, and the homologous poliovirus receptor was reported to mediate the entry of pseudorabies virus (R. J. Geraghty, C. Krummenacher, G. H. Cohen, R. J. Eisenberg, and P. G. Spear, Science 280:1618-1620, 1998; M. S. Warner, R. J. Geraghty, W. M. Martinez, R. I. Montgomery, J. C. Whitbeck, R. Xu, R. J. Eisenberg, G. H. Cohen, and P. G. Spear, Virology 246:179-189, 1998). Here we further show that HIgR or PRR-1 proteins detected by using a monoclonal antibody to PRR-1 are widely distributed among human cell lines susceptible to HSV infection and commonly used for HSV studies. The monoclonal antibody neutralized virion infectivity in cells transfected with HIgR or PRR-1 cDNA, as well as in the human cell lines, indicating a direct interaction of virions with the receptor molecule, and preliminarily mapping this function to the ectodomain of HIgR and PRR-1. Northern blot analysis showed that HIgR or PRR-1 mRNAs were expressed in human tissues, with the highest expression being detected in nervous system samples. HIgR adds a novel member to the cluster of Ig superfamily members able to mediate the entry of alphaherpesviruses into cells. The wide distribution of HIgR or PRR-1 proteins among human cell lines susceptible to HSV infection, coupled with the neutralizing activity of the antibody in the same cells, provides direct demonstration of the actual use of this cluster of molecules as HSV-1 and HSV-2 entry receptors in human cell lines. The high level of expression in samples from nervous system makes the use of these proteins in human tissues very likely. This cluster of molecules may therefore be considered to constitute bona fide receptors for HSV-1 and HSV-2.
Simultaneous particle counting and detecting on a chip (2008)

This paper reports a lab-on-a-chip device that performs particle detection and number counting by coupling the fluorescent detection and particle counting simultaneously. The particle number counting is realized by a resistive pulse sensor (RPS) and fluorescent particle detection is achieved by a miniaturized laser-fiber optic detection system. By using a single microfluidic channel with two detecting arm channels placed at the two ends of the sensing section, the RPS signal-to-noise ratio is improved significantly. Two-stage differential amplification is used to further increase the signal-to-noise ratio for both the RPS and fluorescent signals. This method is also highly sensitive, so that we were able to realize the RPS and fluorescent detection of 0.9 microm (mean diameter) fluorescent particles. Excellent agreement was achieved by comparing the results obtained by our system with the results from a commercial flow cytometer for a variety of samples of mixed fluorescent and non-fluorescent particles. The method described in this paper is simple and can be applied to develop a compact device without the need of lock-in amplifier or similar bulky supplemental equipment.
LLR-Based Successive Cancellation List Decoding of Polar Codes (2015)

We show that successive cancellation list decoding can be formulated exclusively using log-likelihood ratios. In addition to numerical stability, the log-likelihood ratio based formulation has useful properties that simplify the sorting step involved in successive cancellation list decoding. We propose a hardware architecture of the successive cancellation list decoder in the log-likelihood ratio domain which, compared with a log-likelihood domain implementation, requires less irregular and smaller memories. This simplification, together with the gains in the metric sorter, lead to <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$ 56\%$</tex></formula> to <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$137\%$</tex></formula> higher throughput per unit area than other recently proposed architectures. We then evaluate the empirical performance of the CRC-aided successive cancellation list decoder at different list sizes using different CRCs and conclude that it is important to adapt the CRC length to the list size in order to achieve the best error-rate performance of concatenated polar codes. Finally, we synthesize conventional successive cancellation decoders at large block-lengths with the same block-error probability as our proposed CRC-aided successive cancellation list decoders to demonstrate that, while our decoders have slightly lower throughput and larger area, they have a significantly smaller decoding latency.
On the Use of the Dual-Process Langmuir Model for Correlating Unary Equilibria and Predicting Mixed-Gas Adsorption Equilibria (2011)

A new model has been developed for predicting mixed-gas adsorption equilibria from multicomponent gas mixtures based on the dual-process Langmuir (DPL) formulation. It predicts ideal, nonideal, and azeotropic adsorbed solution behavior from a knowledge of only single-component adsorption isotherms and the assertion that each binary pair in the gas mixture correlates in either a perfect positive (PP) or perfect negative (PN) fashion on each of the two Langmuir sites. The strictly PP and strictly PN formulations thus provide a simple means for determining distinct and absolute bounds of the behavior of each binary pair, and the PP or PN behavior can be confirmed by comparing predictions to binary experimental adsorption equilibria or from intuitive knowledge of binary pairwise adsorbate-adsorbent interactions. The extension to ternary and higher-order systems is straightforward on the basis of the pairwise additivity of the binary adsorbent-adsorbate interactions and two rules that logically restrict the combinations of PP and PN behaviors between binary pairs in a multicomponent system. Many ideal and nonideal binary systems and two ternary systems were tested against the DPL model. Each binary adsorbate-adsorbent pair exhibited either PP or PN behavior but nothing in between. This binary information was used successfully to predict ternary adsorption equilibria based on binary pairwise additivity. Overall, predictions from the DPL model were comparable to or significantly better than those from other models in the literature, revealing that its correlative and predictive powers are universally applicable. Because it is loading-explicit, simple to use, and also accurate, the DPL model may be one of the best equilibrium models to use in gas-phase adsorption process simulation.
Liquid-crystal blazed-grating beam deflector (2000)

A transmission-type nonmechanical multiple-angle beam-steering device that uses liquid-crystal blazed grating has been developed. Sixteen steering angles with a contrast ratio of 18 has been demonstrated. A detailed analysis of the liquid-crystal and poly(methyl methacrylate) blazed-grating deflector was carried out to provide guidance during the deflector's development. A manufacturing offset compensation technique is proposed to improve the device's performance greatly. A hybrid approach utilizing electrically generated blazed grating combined with the cascading approach described here yields in excess of 500 deflecting angles.
Structural and Immunochemical Studies on D-Arabino-D-Mannans and D-Mannans of Mycobacterium tuberculosis and Other Mycobacterium Species1 (1977)

Serologically active D-arabino-D-mannas ([alpha]D, +82 degrees approximately 89 degrees; ratio of D-arabinose to D-mannose, 1-2:1) were isolated from the soluble fraction of disintegrated cells of M. tuberculosis, M. smegmatis, and several other Mycobacterium species. These arabinomannans had similar structures, consisting of alpha-(1 leads to 5)-linked D-arabinose residues and alpha-(1 leads to 6)-, and (1 leads to 2)-linked D-mannose residues. Methylation and enzymic degradation studies using Arthrobacter sp. alpha-D-mannosidase and M-2 enzyme (D-arabinan hydrolase) indicated that the arabinomannan of M. tuberculosis Aoyama B possesses short side chains built up from alpha-(1 leads to 2)-D-mannosidic linkages which are attached to an alpha-(1 leads to 6)-linked mannan back-bone chain. The alpha-(1 leads to 5)-linked D-arabinose residues located in the side chains were shown, by comparison of the immunochemical activities of the native and enzyme-degraded polysaccharides, to be the main immunodeterminants, as in the cell-wall arabinogalactan. There appeared to be variations in the ratio of arabinose and mannose residues, and also in the proportion of (1 leads to 2)-linked D-mannose units, depending on the individual strain; no (1 leads to 2)-mannosidic linkage was found in M. smegmatis arabinomannan. In addition to arabinomannan, a serologically inactive alpha-D-mannan ([alpha)D, +65 degrees approximately 68 degrees), whose structure may resemble that of the core mannan of the arabinomannan, was isolated as a copper hydroxide complex from the soluble fraction of disintegrated mycobacterial cells.
A Chromatographic Approach for Elevating the Antibody-Dependent Cellular Cytotoxicity of Antibody Composites (2009)

Recent studies have shown that antibodies with low fucose content in their oligosaccharides exhibit highly potent antibody-dependent cellular cytotoxicity (ADCC). However, composites of therapeutic antibodies produced by conventional production systems using cell lines such as Chinese hamster ovary (CHO) and SP2/0 do not necessarily contain sufficient amounts of non-fucosylated antibody species. In this study, we combined two lectin-affinity chromatography techniques, Concanavalin A and Lens culinaris agglutinin, to enrich the non-fucosylated species from therapeutic material using the anti-Her2/neu model antibody. Oligosaccharide analysis by matrix-assisted laser desorption/ionization-time of flight MS following peptide-N-glycosidase F digestion suggested that non-fucosylated antibody could be enriched in the purified fraction with efficient removal of high-mannose species. The ADCC activity of the purified fraction was about 100-fold higher than that of the initial material. The chromatographic strategy presented here can be a useful tool to elevate ADCC activity of antibody materials without concentrating high-mannose oligosaccharides.
Cholinergic Regulatory Lymphocytes Re-Establish Neuromodulation of Innate Immune Responses in Sepsis (2011)

Many anti-inflammatory strategies that are successful in treating sepsis in healthy animals fail in clinical trials, in part because sepsis normally involves immunocompromised patients, and massive lymphocyte apoptosis prevents immunomodulation. In this article, we report a new set of regulatory lymphocytes that are able to re-establish the cholinergic anti-inflammatory modulation and to provide therapeutic advantages in sepsis. The vagus nerve controls inflammation in healthy, but not in septic, mice. Likewise, vagus nerve and cholinergic agonists fail to control inflammation in splenectomized and nude animals. Unlike typical suppressor CD25(+) cells, CD4(+)CD25(-) lymphocytes re-establish the anti-inflammatory potential of the vagus nerve and cholinergic agonists in immunocompromised and septic animals. These cholinergic lymphocytes re-establish splenic protection and the potential of cholinergic agonists to rescue immunocompromised animals from established sepsis. The study results revealed these new regulatory lymphocytes as, to our knowledge, the first known physiological target for neuromodulation of the innate immune responses and a potential therapeutic target for sepsis.
A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21 (1995)

The rice Xa21 gene, which confers resistance to Xanthomonas oryzae pv. oryzae race 6, was isolated by positional cloning. Fifty transgenic rice plants carrying the cloned Xa21 gene display high levels of resistance to the pathogen. The sequence of the predicted protein, which carries both a leucine-rich repeat motif and a serine-threonine kinase-like domain, suggests a role in cell surface recognition of a pathogen ligand and subsequent activation of an intracellular defense response. Characterization of Xa21 should facilitate understanding of plant disease resistance and lead to engineered resistance in rice.
Primary Intraosseous Squamous Cell Carcinoma of the Jaws (2009)

Primary intraosseous squamous cell carcinoma is a high-grade malignancy with frequent, regional lymph node metastasis and high rates of recurrence and mortality. The tumor grading and regional lymph node metastasis may serve as useful indicators for prognosis.
Glucagon-like peptide 2 decreases mortality and reduces the severity of indomethacin-induced murine enteritis (1999)

Glucagon-like peptides (GLPs) are secreted from enteroendocrine cells in the gastrointestinal tract. GLP-1 actions regulate blood glucose, whereas GLP-2 exerts trophic effects on intestinal mucosal epithelium. Although GLP-1 actions are preserved in diseases such as diabetes, GLP-2 action has not been extensively studied in the setting of intestinal disease. We have now evaluated the biological effects of a human GLP-2 analog in the setting of experimental murine nonsteroidal antiinflammatory drug-induced enteritis. Human (h)[Gly(2)]GLP-2 significantly improved survival whether administered before, concomitant with, or after indomethacin. h[Gly(2)]GLP-2-treated mice exhibited reduced histological evidence of disease activity, fewer intestinal ulcerations, and decreased myeloperoxidase activity in the small bowel (P < 0.05, h[Gly(2)]GLP-2- vs. saline-treated controls). h[Gly(2)]GLP-2 significantly reduced cytokine induction, bacteremia, and the percentage of positive splenic and hepatic bacterial cultures (P < 0.05). h[Gly(2)]GLP-2 enhanced epithelial proliferation (P < 0.05 for increased crypt cell proliferation in h[Gly(2)]GLP-2- vs. saline-treated mice after indomethacin) and reduced apoptosis in the crypt compartment (P < 0.02). These observations demonstrate that a human GLP-2 analog exerts multiple complementary actions that serve to preserve the integrity of the mucosal epithelium in experimental gastrointestinal injury in vivo.
Identification of the histidine residues involved in substrate recognition by a rat H+/peptide cotransporter, PEPT1 (1996)

The LLC‐PK 1 cells stably transfected with a rat PEPT1 cDNA transported ceftibuten (anion) and cephradine (zwitterion), both oral β‐lactam antibiotics, in a H + ‐gradient‐dependent manner. Diethylpyrocarbonate, a histidine residue modifier, abolished ceftibuten uptake. This inhibition was prevented in the presence of glycylsarcosine or cephradine. When expressed in Xenopus oocytes, replacement of either histidine 57 or histidine 121 of the rat PEPT1 with glutamine by site‐directed mutagenesis eliminated ceftibuten and [ 14 C]glycylsarcosine transport activities. Immunostaining of oocyte sections indicated that insertion of the mutant transporters in the plasma membranes was not impaired. These findings suggest that both histidine 57 and histidine 121, which are conserved in the rat, rabbit and human PEPT1, are involved in substrate recognition of this molecule.
Novel Tyrosine Kinase Inhibitors in the Treatment of Cancer (2009)

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Structure of FcγRI in complex with Fc reveals the importance of glycan recognition for high-affinity IgG binding (2015)

Fc gamma receptor I (FcγRI) contributes to protective immunity against bacterial infections, but exacerbates certain autoimmune diseases. The sole high-affinity IgG receptor, FcγRI plays a significant role in immunotherapy. To elucidate the molecular mechanism of its high-affinity IgG binding, we determined the crystal structure of the extracellular domains of human FcγRI in complex with the Fc domain of human IgG1. FcγRI binds to the Fc in a similar mode as the low-affinity FcγRII and FcγRIII receptors. In addition to many conserved contacts, FcγRI forms additional hydrogen bonds and salt bridges with the lower hinge region of Fc. Unique to the high-affinity receptor-Fc complex, however, is the conformation of the receptor D2 domain FG loop, which enables a charged KHR motif to interact with proximal carbohydrate units of the Fc glycans. Both the length and the charge of the FcγRI FG loop are well conserved among mammalian species. Ala and Glu mutations of the FG loop KHR residues showed significant contributions of His-174 and Arg-175 to antibody binding, and the loss of the FG loop-glycan interaction resulted in an ∼ 20- to 30-fold decrease in FcγRI affinity to all three subclasses of IgGs. Furthermore, deglycosylation of IgG1 resulted in a 40-fold loss in FcγRI binding, demonstrating involvement of the receptor FG loop in glycan recognition. These results highlight a unique glycan recognition in FcγRI function and open potential therapeutic avenues based on antibody glycan engineering or small molecular glycan mimics to target FcγRI for certain autoimmune diseases.
Most Early Disseminated Cancer Cells Detected in Bone Marrow of Breast Cancer Patients Have a Putative Breast Cancer Stem Cell Phenotype (2006)

This is the first evidence of the existence of the putative stem-like phenotype within the DTC in bone marrow in early breast cancer patients. All patients had a putative stem cell phenotype among the DTC and most individual DTC showed such phenotype. Future molecular characterization of these cells is warranted.
Chronic Lymphocytic Leukemia: New Insights into Biology and Therapy (1990)

Major advances in the biologic research of chronic lymphocytic leukemia have resulted in new understanding of this complex disease. New therapies, such as those with intravenous immunoglobulin and fludarabine, may lead to improved outcome.
Thymus and Autoimmunity: Production of CD25+CD4+ Naturally Anergic and Suppressive T Cells as a Key Function of the Thymus in Maintaining Immunologic Self-Tolerance (1999)

This study shows that the normal thymus produces immunoregulatory CD25+4+8- thymocytes capable of controlling self-reactive T cells. Transfer of thymocyte suspensions depleted of CD25+4+8- thymocytes, which constitute approximately 5% of steroid-resistant mature CD4+8- thymocytes in normal naive mice, produces various autoimmune diseases in syngeneic athymic nude mice. These CD25+4+8- thymocytes are nonproliferative (anergic) to TCR stimulation in vitro, but potently suppress the proliferation of other CD4+8- or CD4-8+ thymocytes; breakage of their anergic state in vitro by high doses of IL-2 or anti-CD28 Ab simultaneously abrogates their suppressive activity; and transfer of such suppression-abrogated thymocyte suspensions produces autoimmune disease in nude mice. These immunoregulatory CD25+4+8- thymocytes/T cells are functionally distinct from activated CD25+4+ T cells derived from CD25-4+ thymocytes/T cells in that the latter scarcely exhibits suppressive activity in vitro, although both CD25+4+ populations express a similar profile of cell surface markers. Furthermore, the CD25+4+8- thymocytes appear to acquire their anergic and suppressive property through the thymic selection process, since TCR transgenic mice develop similar anergic/suppressive CD25+4+8- thymocytes and CD25+4+ T cells that predominantly express TCRs utilizing endogenous alpha-chains, but RAG-2-deficient TCR transgenic mice do not. These results taken together indicate that anergic/suppressive CD25+4+8- thymocytes and peripheral T cells in normal naive mice may constitute a common T cell lineage functionally and developmentally distinct from other T cells, and that production of this unique immunoregulatory T cell population can be another key function of the thymus in maintaining immunologic self-tolerance.
Three putative oxylipin biosynthetic genes integrate sexual and asexual development in Aspergillus nidulans (2005)

Oxylipins called psi factors have been shown to alter the ratio of asexual to sexual sporulation in the filamentous fungus Aspergillus nidulans. Analysis of the A. nidulans genome has led to the identification of three fatty acid oxygenases (PpoA, PpoB and PpoC) predicted to produce psi factors. Here, it is reported that deletion of ppoB (DeltappoB) reduced production of the oleic-acid-derived oxylipin psiBbeta and increased the ratio of asexual to sexual spore development. Generation of the triple mutant Delta ppoA Delta ppoB Delta ppoC resulted in a strain deficient in producing oleic- and linoleic-acid-derived 8'-hydroxy psi factor and caused increased and mis-scheduled activation of sexual development. Changes in asexual to sexual spore development were positively correlated to alterations in the expression of brlA and veA, respectively. PpoB and/or its products antagonistically mediate the expression levels of ppoA and ppoC, thus revealing regulatory feedback loops among these three genes. Phylogenetic analyses showed that ppo genes are present in both saprophytic and pathogenic Ascomycetes and Basidiomycetes, suggesting a conserved role for Ppo enzymes in the life cycle of fungi.
Splicing MPEG video streams in the compressed domain (2002)

An algorithm is proposed for efficiently splicing two MPEG-coded video streams. The algorithm only processes the portion of each video stream that contains frames affected by the splice and it operates directly on the DCT coefficients and motion vectors of those frames. The algorithm achieves good visual performance with very low computational complexity, and incorporates rate control to prevent buffer underflow and overflow. If additional processing power is available, it can be used to further improve the quality of the spliced stream.