gebhart/patrepeval huggingface dataset:
One sense per discourse (1992)

It is well-known that there are polysemous words like sentence whose "meaning" or "sense" depends on the context of use. We have recently reported on two new word-sense disambiguation systems, one trained on bilingual material (the Canadian Hansards) and the other trained on monolingual material (Roget's Thesaurus and Grolier's Encyclopedia). As this work was nearing completion, we observed a very strong discourse effect. That is, if a polysemous word such as sentence appears two or more times in a well-written discourse, it is extremely likely that they will all share the same sense. This paper describes an experiment which confirmed this hypothesis and found that the tendency to share sense in the same discourse is extremely strong (98%). This result can be used as an additional source of constraint for improving the performance of the word-sense disambiguation algorithm. In addition, it could also be used to help evaluate disambiguation algorithms that did not make use of the discourse constraint.
Class II major histocompatibility complex molecules of murine dendritic cells: synthesis, sialylation of invariant chain, and antigen processing capacity are down-regulated upon culture. (1991)

Dendritic cells (DCs), such as Langerhans cells (LCs) of the epidermis and the DCs of lymphoid organs such as spleen, are potent antigen presenting cells. DCs express high levels of major histocompatibility complex (MHC) class II molecules, but, partly because of the low numbers of primary DCs in any tissue, there has been no detailed study of the biochemistry of their class II molecules. This information may be needed to help explain recent findings that DCs process native protein antigens when freshly isolated from epidermis and spleen. Processing ceases during culture, yet a strong accessory function for activating resting T cells develops. We studied immunoprecipitates of DC class II and invariant chain (Ii) molecules by two-dimensional gel electrophoresis. We found that (i) freshly isolated LCs synthesize large amounts of class II and Ii polypeptides; (ii) Ii molecules that are known to be involved in antigen processing display an unusually large number of sialic acids in fresh LCs; (iii) with culture, class II and Ii synthesis decreases dramatically and has virtually ceased at 3 days; and (iv) the turnover of class II in pulse/chase experiments is slow, being undetectable over a 12- to 32-hr culture period, whereas the turnover of Ii is rapid. We conclude that MHC class II molecules of DCs do not seem to be qualitatively unique. However, the regulation of class II and Ii expression is distinctive in that biosynthesis proceeds vigorously for a short period of time and the newly synthesized class II remains stably on the cell surface, whereas Ii turns over rapidly. This may enable DCs to process and retain antigens in the peripheral tissues such as skin and migrate to the lymphoid organs to activate T cells there.
Stromal cell-associated hematopoiesis: immortalization and characterization of a primate bone marrow-derived stromal cell line (1991)

An elucidation of the interaction between the bone marrow microenvironment and hematopoietic stem cells is critical to the understanding of the molecular basis of stem cell self renewal and differentiation. This interaction is dependent, at least in part, on direct cell to cell contact or cellular adhesion to extracellular matrix proteins. Long-term bone marrow cultures (LTMC) provide an appropriate microenvironment for maintenance of primitive hematopoietic stem cells and a means of analyzing this stem cell-stromal cell interaction in vitro. Although LTMC have been successfully generated from murine and human bone marrow, only limited success has been reported in a primate system. In addition, few permanent stromal cell lines are available from nonmurine bone marrow. Because the primate has become a useful model for large animal bone marrow transplant studies and, more specifically, retroviral-mediated gene transfer analysis, we have generated immortalized bone marrow stromal cell lines from primate bone marrow using gene transfer of the Simian virus large T (SV40 LT) antigen. At least one stromal cell line has demonstrated the capacity to maintain early hematopoietic cells in long-term cultures for up to 4 weeks as measured by in vitro progenitor assays. Studies were undertaken to characterize the products of extracellular matrix biosynthesis and growth factor synthesis of this cell line, designated PU-34. In contrast to most murine bone marrow-derived stromal cell lines capable of supporting hematopoiesis in vitro that have been examined, the extracellular matrix produced by this primate cell line includes collagen types I, laminin. Growth factor production analyzed through RNA blot analysis, bone marrow cell culture data, and factor- dependent cell line proliferation assays includes interleukin-6 (IL-6), IL-7, granulocyte-macrophage colony-stimulating factor (GM-CSF), G-CSF, M-CSF, leukemia inhibitory factor, and a novel cytokine designated IL- 11. This immortalized primate bone marrow stromal cell line may be useful in maintaining early progenitor cells for experimental manipulation without the loss of reconstituting capacity and as a potential source of novel hematopoietic growth factors.
V3-independent determinants of macrophage tropism in a primary human immunodeficiency virus type 1 isolate (1995)

Human immunodeficiency virus type 1 isolates differ in their ability to productively infect macrophages, and several groups have mapped the genetic basis for macrophage tropism to regions of env that include the third hypervariable region (V3 loop). We recently described a primary isolate (89.6) which is highly macrophage tropic and yet differs from other macrophage-tropic strains studied in that it is cytopathic in T cells. Genetic mapping of macrophage tropism determinants in this virus was done by using chimeras generated with the prototypic non-macrophage-tropic strain HXB2. Replacement of a 2.7-kb env-containing region of HXB with corresponding sequences from 89.6 conferred the macrophage-tropic phenotype, but insertion of the 89.6 V3 loop along with V4/V5 sequences did not. Conversely, placement of HXB sequences that included V3 into 89.6 did not impair this strain's ability to replicate in macrophages. Sequence analysis of V3 shows that 89.6 differs markedly from previously described macrophage-tropic consensus sequences and that it is more similar to highly charged non-macrophage-tropic strains. This suggests either that macrophage tropism is defined by structural determinants resulting from complex interactions among multiple env regions rather than V3 sequence-specific requirements or that there are multiple mechanisms by which different strains may establish productive macrophage infection. In addition, because the HXB V3 loop supports productive macrophage infection in the background of 89.6, phenotypic characterization of V3 sequences should be considered specific to the viral context in which they are placed.
The Use of a Continuous Popliteal Sciatic Nerve Block After Surgery Involving the Foot and Ankle: Does It Improve the Quality of Recovery? (2003)

A continuous infusion of bupivacaine 0.25% (versus saline) at the popliteal fossa by using a simple elastomeric pump is an effective method of decreasing postoperative pain, reducing the opioid analgesic requirement, and increasing patient satisfaction with pain management after orthopedic surgery involving the foot and ankle. More importantly, the use of the continuous sciatic nerve block in the popliteal fossa facilitated an earlier discharge after lower extremity surgery.
Analyzing glycoproteins separated by two‐dimensional gel electrophoresis (1998)

Two-dimensional (2-D) electrophoresis is the preferred method for separating the glycoforms of proteins. The isoforms usually present as 'trains' of spots in the first dimension and may also differ in molecular weight. The primary goal for analyzing the carbohydrate content of glycoprotein spots is to understand the 'rules' which govern the migration of glycoproteins in 2-D electrophoresis. These rules can then be used to produce predictive vectors to interpret changes in glycosylation patterns. Techniques for the analysis of oligosaccharides released from glycoproteins which have been electroblotted to PVDF membrane after one-dimensional (1-D) and 2-D preparative gel electrophoresis are described. The oligosaccharides are removed enzymatically (PNGase F of N-linked oligosaccharides) or chemically (beta-elimination of O-linked oligosaccharides) and separated by high performance anion exchange chromatography (HPAEC-PAD) and identified by electrospray ionization mass spectrometry (ESI-MS) or analyzed directly by ESI-MS. After enzymic removal of the N-linked oligosaccharides the protein spots can be further analyzed by Edman sequence tagging for identification and quantitation of the protein and by acid hydrolysis for monosaccharide analysis of the O-linked oligosaccharides. These approaches have been proved on 1-D PAGE electroblotted bovine fetuin and human glycophorin A and then used to analyze two abundant proteins which separate as glycoforms on 2-D PAGE preparative narrow range (pH 4.5-5.5) blots of human plasma: alpha2-HS glycoprotein (human fetuin) and alpha1-antitrypsin (alpha1-protease inhibitor). It is apparent that both the macroheterogeneity (site occupation) and microheterogeneity (diversity of structures) of the glycosylation contribute to the separation of protein isoforms in 2-D PAGE.
Quantitative Comparison of the Sensitivity of Detection of Fluorescent and Bioluminescent Reporters in Animal Models (2004)

Bioluminescent and fluorescent reporters are finding increased use in optical molecular imaging in small animals. In the work presented here, issues related to the sensitivity of in vivo detection are examined for standard reporters. A high-sensitivity imaging system that can detect steady-state emission from both bioluminescent and fluorescent reporters is described. The instrument is absolutely calibrated so that animal images can be analyzed in physical units of radiance allowing more quantitative comparisons to be performed. Background emission from mouse tissue, called autoluminescence and autofluorescence, is measured and found to be an important limitation to detection sensitivity of reporters. Measurements of dual-labeled (bioluminescent/fluorescent) reporter systems, including PC-3M-luc/DsRed2-1 and HeLa-luc/PKH26, are shown. The results indicate that although fluorescent signals are generally brighter than bioluminescent signals, the very low autoluminescent levels usually results in superior signal to background ratios for bioluminescent imaging, particularly compared with fluorescent imaging in the green to red part of the spectrum. Fluorescence detection sensitivity improves in the far-red to near-infrared, provided the animals are fed a low-chlorophyll diet to reduce autofluorescence in the intestinal region. The use of blue-shifted excitation filters is explored as a method to subtract out tissue autofluorescence and improve the sensitivity of fluorescent imaging.
Weights for Computing Vertex Normals from Facet Normals (1999)

Abstract I propose a new equation to estimate the normal at a vertex of a polygonal approximation to a smooth surface, as a weighted sum of the normals to the facets surrounding the vertex. The equation accounts for the difference in size of these facets by assigning larger weights for smaller facets. When tested on random cubic polynomial surfaces, the equation is superior to other popular weighting methods.
The role of endothelial cell lateral junctions during leukocyte trafficking (2002)

An essential function of the inflammatory response is selective targeting of appropriate leukocyte types to a site of infection or injury. The past decade has witnessed an explosion in the level of detail concerning the identification and deciphering of the molecular mechanisms that capture leukocytes from flowing blood and promote leukocyte arrest on the vessel wall. In contrast, less information is known about the migration of adherent blood leukocytes through endothelial cell-to-cell borders (transendothelial migration, TEM) and into the underlying tissues. This article reviews the endothelial-dependent mechanisms that coordinate TEM in peripheral vasculature and highlights the role of certain lateral junctional proteins and protein complexes.
Induction of apoptosis in HeLa cells with siRNA expression vector targeted against bcl-2 (2002)

RNA interference (RNAi) is the process by which double-stranded RNA (dsRNA) directs sequence-specific gene silencing in animal and plant cells. In mammalian cells, 21- or 22-nucleotide (nt) RNAs with 2-nt 3' overhangs small inhibitory RNAs (siRNAs) exhibit an RNAi effect. Very recently, we and others have developed a vector-based siRNA expression system that can induce RNAi in mammalian cells. In this report, to apply this system to oncogene therapy, we tried to suppress the expression of the bcl-2 gene, which is known as a key molecule in the regulation of apoptosis or programmed cell death, by using the siRNA expression system. Western blotting analysis revealed that this siRNA expression vector against bcl-2 suppressed the expression of the bcl-2 protein. Furthermore, HeLa cells which were transiently transfected with the siRNA expression vector against bcl-2 and were subsequently treated with doxorubicin efficiently underwent apoptosis, concomitant with the repression of the bcl-2 gene. These results demonstrate that the siRNA expression vector against bcl-2 has a potential as therapeutic agent for a variety of cancers by down-regulating bcl-2 gene expression.
Feasibility of Detecting Human Immunodeficiency Virus Type 1 Drug Resistance in DNA Extracted from Whole Blood or Dried Blood Spots (2007)

Due to high cost, availability of human immunodeficiency virus type 1 (HIV-1) drug resistance testing in resource-poor settings is still limited. We therefore evaluated the usefulness of viral DNA extracted from either whole blood or dried blood spots (DBS). Samples were collected from 50 patients receiving therapy and 10 therapy-naïve patients. Amplification and sequencing of RNA and DNA was performed using an in-house assay. Protease (PR) and reverse transcriptase (RT) sequences of plasma viral RNA were obtained for 96.6% and 89.7%, respectively, of the 29 patients with a detectable viral load. For cellular viral DNA, useful PR and RT sequences were obtained for 96.6% and 93.1% of the whole-blood-cell samples and for 93.1% and 93.1% of the DBS samples, respectively. For the 31 patients with an undetectable viral load, PR and RT sequences were obtained for 67.7% and 61.3% of the whole-blood-cell DNA preparations and for 54.8% and 58.1% of the DBS DNA preparations, respectively. A good correlation between RNA and DNA sequences was found; most discordances were caused by the detection of mixed amino acids. Of the RT drug-resistant mutations, 13 (38.2%) were seen in RNA only, 6 (17.6%) in DNA only, and 15 (44.1%) in both. Repeated amplification and sequencing of DNA extracts revealed a lack of reproducibility for the detection of drug resistance mutations in a number of samples, indicating a possible founder effect. In conclusion, this study shows the feasibility of genotypic drug resistance testing on whole blood cells or DBS and its possible usefulness for HIV-1 subtyping or examining the overall distribution of drug resistance in a population. For individual patients, RNA sequencing was shown to be superior to DNA sequencing, especially for patients who experienced early treatment failure. The use of DNA extracted from whole blood or DBS for the detection of archived drug resistance mutations deserves further study.
Interactive Distributed Ray Tracing of Highly Complex Models (2001)

Many disciplines must handle the creation, visualization, and manipulation of huge and complex 3D environments. Examples include large structural and mechanical engineering projects dealing with entire cars, ships, buildings, and processing plants. The complexity of such models is usually far beyond the interactive rendering capabilities of todays 3D graphics hardware. Previous approaches relied on costly preprocessing for reducing the number of polygons that need to be rendered per frame but suffered from excessive precomputation times often several days or even weeks. In this paper we show that using a highly optimized software ray tracer we are able to achieve interactive rendering performance for models up to 50 million triangles including reflection and shadow computations. The necessary preprocessing has been greatly simplified and accelerated by more than two orders of magnitude. Interactivity is achieved with a novel approach to distributed rendering based on coherent ray tracing. A single copy of the scene database is used together with caching of BSP voxels in the ray tracing clients.
Additives for Stabilizing LiPF[sub 6]-Based Electrolytes Against Thermal Decomposition (2005)

Thermal stability of lithium-ion battery electrolytes composed of LiPF 6 in a mixture of organic carbonates was probed. Generation of PF5 via the thermal dissociation of LiPF6 is the primary source of thermal decomposition. It was found that the addition of low concentrations (3-12%) of Lewis basic additives provides a dramatic increase in the thermal stability of the electrolyte. The increased stability is linked to the formation of base: PF5 complexes which reversibly sequester PF5, preventing the decomposition of the electrolyte. Lewis bases investigated include pyridine, hexamethoxycyclotriphosphazene, and hexamethylphosphoramide. Our results can serve as a valuable model for stabilizing organic electrolytes against thermal decomposition initiated by Lewis acids. © 2005 The Electrochemical Society. All rights reserved.
Changes in interleukin-2 and interleukin-4 production in asymptomatic, human immunodeficiency virus-seropositive individuals. (1993)

Infection with HIV results in an incremental loss of T helper cell (TH) function, which can occur years before CD4 cell numbers are critically reduced and AIDS is diagnosed. All TH function is not affected, however, because B cell activation and hypergammaglobulinema are also characteristic of this period. Recently, in a murine model of AIDS an early loss in production of the CD4 cytokines IL-2 and IFN-gamma was correlated with an increase in the B cell stimulatory cytokines IL-4, IL-5, and IL-10. We therefore assessed the production of IL-4 generated by PBL from HIV-seropositive (HIV+) individuals who did not have AIDS, yet who exhibited different TH functional categories based on their IL-2 production profiles. We observed that the decreases in recall antigen-stimulated IL-2 production were accompanied by an increase in IL-4 production. The loss of recall antigen-stimulated responses in HIV+ individuals could be reversed in vitro by anti-IL-4 antibody. Our results suggest that the TH functions assessed by IL-4 production replace the normally dominant TH function of antigen-stimulated IL-2 production in the progression toward AIDS, and raise the possibility of cytokine cross-regulation in AIDS therapy.
A system for active image-based rendering (2003)

In this paper, we develop a system for active image-based rendering (IBR). Active IBR is a framework that is capable of estimating the final rendering quality and capturing the next view at the position where the rendering quality can be improved the most. The result is a non-uniform capturing scheme for IBR. Experimental results on synthetic scenes have shown that active IBR outperforms uniformly captured IBR. In this paper, we set up an active IBR system that can capture real objects with off-the-shelf components. We show that our system can capture objects more intelligently than uniform capturing.
Discovery of a Parenteral Small Molecule Coagulation Factor XIa Inhibitor Clinical Candidate (BMS-962212) (2017)

Factor XIa (FXIa) is a blood coagulation enzyme that is involved in the amplification of thrombin generation. Mounting evidence suggests that direct inhibition of FXIa can block pathologic thrombus formation while preserving normal hemostasis. Preclinical studies using a variety of approaches to reduce FXIa activity, including direct inhibitors of FXIa, have demonstrated good antithrombotic efficacy without increasing bleeding. On the basis of this potential, we targeted our efforts at identifying potent inhibitors of FXIa with a focus on discovering an acute antithrombotic agent for use in a hospital setting. Herein we describe the discovery of a potent FXIa clinical candidate, 55 (FXIa K<sub>i</sub> = 0.7 nM), with excellent preclinical efficacy in thrombosis models and aqueous solubility suitable for intravenous administration. BMS-962212 is a reversible, direct, and highly selective small molecule inhibitor of FXIa.
A combination of catalase and trehalose as additives to conventional freezing medium results in improved cryoprotection of human hematopoietic cells with reference to in vitro migration and adhesion properties (2005)

The present data provide evidence that addition of catalase and trehalose to the conventional freezing medium preserves migration- and adhesion-related properties of the hematopoietic graft.
CD163 (2004)

Paraffin-section immunohistochemical analysis was performed using a monoclonal antibody against CD163 to evaluate the antibody’s usefulness in identifying cells of monocyte/macrophage lineage in normal and neoplastic conditions. Normal human tissue samples and samples from 211 hematopoietic disorders and 115 nonhematopoietic neoplasms were examined. The distribution of KP1 and PG-M1, monoclonal antibodies to the macrophage-associated CD68 antigen, also were evaluated for comparison. CD163 immunoreactivity was observed in resident macrophages of all normal tissue samples except splenic white pulp macrophages and germinal center tingible body macrophages. Among hematopoietic disorders and nonhematopoietic neoplasms, CD163 expression was restricted largely to cases of chronic myelomonocytic leukemia, histiocytic sarcoma, sinus histiocytosis with massive lymphadenopathy, and littoral cell angioma. Acute myeloid leukemias (AMLs) with monocytic differentiation were CD163– with the exception of 1 case of acute monoblastic leukemia. Most myeloid sarcomas also were CD163–. Compared with the CD68 antibodies, CD163 demonstrated greater specificity as a marker of disorders of monocyte/macrophage origin. However, immunohistochemical evaluation of CD163 expression does not seem to be a sensitive means of determining monocytic differentiation in AMLs in paraffin sections or establishing a diagnosis of myeloid sarcoma.
Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii (1996)

The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus jannaschii, and its 58- and 16-kilobase pair extrachromosomal elements have been determined by whole-genome random sequencing. A total of 1738 predicted protein-coding genes were identified; however, only a minority of these (38 percent) could be assigned a putative cellular role with high confidence. Although the majority of genes related to energy production, cell division, and metabolism in M. jannaschii are most similar to those found in Bacteria, most of the genes involved in transcription, translation, and replication in M. jannaschii are more similar to those found in Eukaryotes.