gebhart/patrepeval huggingface dataset:
QUALIFIER In TREC-12 QA Main Task. (2003)

This paper describes a question answering system and its various modules to solve definition, factoid and list questions defined in the TREC12 Main task. In particular, we tackle the factoid QA task by Event-based Question Answering. Each QA event comprises of elements describing different facets like time, location, object, action etc. By analyzing the external knowledge from pre-retrieved TREC documents, Web documents, WordNet and Ontology to discover the QA event structure, we explore the inherent associations among QA elements and then obtain the answers. There are three subsystems working parallel to handle definition, factoid, and list questions separately. We highlight the shared modules, fine-grained named entity recognition, anaphora resolution and canonicalization co-reference resolution, among the three subsystems as well.
Zero-copy TCP in Solaris (1996)

This paper describes a new feature in Solaris that uses virtual memory remapping combined with checksumming support from the networking hardware, to eliminate data-touching overhead from the TCP/IP protocol stack. By implementing page remapping operations at the right level of the operating system, and caching MMU mappings to take advantage of locality of reference, significant performance gain is attained on certain hardware platforms. Nevertheless, the performance improvement over CPU copying varies, depending on the host memory cache architecture, MMU design, and application behavior. We begin by comparing different zero-copy schemes, and explain our preference for page remapping and copy-on-write (COW) techniques. We then describe our implementation, and present its performance characteristics under a number of different parameters. We conclude with ideas for future improvements.
Human primitive hematopoietic progenitor cells are more enriched in KITlow cells than in KIThigh cells (1993)

To clarify the phenotypes of various classes of human hematopoietic progenitor cells, we used a multicolor staining protocol in conjunction with CD34 and a newly developed mouse antihuman c-kit proto-oncogene product (KIT) monoclonal antibody (MoAb). We characterized three cell fractions in CD34+ cells that express KITlow and KIThigh cells in addition to KIT- cells. A clonogenic assay showed that most granulocyte-macrophage colony-forming cells (GM-CFC) were present in CD34+KIThigh populations, whereas erythroid burst-forming cells (BFU-E) were detected mainly in the CD34+KITlow population. CD34(+)-KIT- fraction contained a small number of BFU-E. Morphologic analysis showed that blast-like cells were more enriched in the CD34+KITlow fraction. KITlow cells contained CD34+CD38- cells that were considered to be very primitive progenitor cells, as determined by a replating assay. To clarify the biologic differences between both fractions, we examined the more primitive progenitor cell functions by assessing long-term culture-initiating cells (LTC-IC) on the stromal cells. At week 2, more CFC recovered from the culture in the fraction initiated with a CD34+KIThigh population. However, more LTC-IC were present during weeks 5 to 9 in the CD34+KITlow population. These results indicate that primitive progenitors are more enriched in the KITlow population and that the KIThigh population contains many GM-committed progenitor cells. We also showed that anti-KIT MoAb inhibited the ability of CD34+ cells to generate CFC on the stromal layer in the LTC system. This suppressive effect was more evident in the generation of BFU-E by CD34+KITlow cells. Moreover, we confirmed that CD34+KIThigh cells emerged from CD34+KITlow cells during coculture with allogeneic stromal cells or from liquid culture in the presence of stem cell factor (SCF), interleukin-6, and erythropoietin. These results emphasize the pivotal role of the KIT and SCF interaction in hematopoiesis and indicate that KITlow cells are more primitive than KIThigh cells.
Differential regulation by cytokines of human astrocyte nitric oxide production (1995)

Reactive nitrogen intermediates, such as nitric oxide (NO), play an important role in host-defense and injury. Human astrocytes released abundant NO upon stimulation with the pro-inflammatory cytokine interleukin (IL)-1 beta, which was potentiated by interferon (IFN)-gamma and tumor necrosis factor (TNF)-alpha. IL-1 receptor antagonist protein markedly attenuated astrocyte NO production. The anti-inflammatory cytokines IL-4 and IL-10 potently suppressed IL-1 beta plus IFN-gamma-stimulated NO, while transforming growth factor-beta preferentially inhibited IL-1 beta plus TNF-alpha-stimulated production of NO. These findings suggest that while IL-1 plays a key role in inducing astrocyte NO production, anti-inflammatory cytokines have the capacity to downregulate NO production by IL-1-stimulated astrocytes.
Rational Design, Synthesis, and X-ray Structure of Selective Noncovalent Thrombin Inhibitors (1998)

We have designed, synthesized, and tested in vitro a novel class of noncovalent thrombin inhibitors. The main feature of these inhibitors is a 6,5-fused bicyclic core structure that fills the S2 pocket of the active site of thrombin. The bicycle introduces conformational constraint into the ligand and locks the Xaa-Pro amide bond into the desired trans configuration. Among the known ring systems, we selected by molecular modeling the 7-thiaindolizidinones (BTD) as our basic template. The influence of several structural features was analyzed: the length of the argininal side chain, the stereochemistry at C6, and the importance of making optimal use of the S3 pocket. Finally, an X-ray crystal structure of inhibitor 15 bound to thrombin was obtained at a resolution of 2.3 A. These designed thrombin inhibitors, which were prepared by an efficient synthesis, showed high selectivity over trypsin and other serine proteases. Further derivation based on the information obtained by X-ray crystallography should certainly allow to improve the potency.
Production of biodiesel from side-stream refining products (2009)

The main focus of this review is to offer an overview of different existing processes for converting side-stream refining products (soapstock, acid oil and deodorized distillates) into new generation energy sources. The review article calls for more research around the SSRPs for its efficient conversion into biodiesel/biofuel and outlines drawbacks of the methodologies reported in the literature so far.
Abstract LB-042: MCPIP1 suppresses breast tumor progression by targeting anti-apoptosis pathway (2015)

Abstract The ability to evade apoptosis is a hallmark of cancer and also plays a significant role in cancer resistance to conventional therapy. While recent progress has broadened our understanding of the apoptosis-evasion mechanisms by cancer cells, how apoptosis resistance develops in cancer cells through posttranscriptional mechanisms, especially by the newly discovered RNA-binding protein monocyte chemotactic protein induced protein 1 (MCPIP1), remains unknown. Here, we report that MCPIP1 expression is impaired in breast tumors and breast tumor cell lines, with the severest impairment in highly metastatic tumors. Ectopic expression of MCPIP1 causes apoptosis of breast tumor cells through selectively suppression of anti-apoptotic gene transcripts, including Bcl2L1, Bcl2A1, RelB, Birc3 and Bcl3. This suppression is medicated through a physical interaction between the PIN domain of MCPIP1 and the 3′UTRs of anti-apoptotic transcripts, resulting in mRNA degradation and tumor cell apoptosis. In difference from the RNA-binding protein tristetraprolin which binds to the ARE in the 3′UTR of target genes for mRNA decay, MCPIP1 specially recognizes a stem-loop structure in the 3′UTR of anti-apoptotic genes for binding and mRNA decay. Furthermore, induction of MCPIP not only ameliorates breast tumor formation but also completely shrinks the established tumors within six days. Lung metastasis is also significantly reduced by MCPIP1 induction. The tumor suppressive effect of MCPIP1 acts through activation of apoptosis. Importantly, by analysis of the excised breast tumors of 251 patients, we found that low MCPIP1 levels in tumors are strongly associated with poor survival of patients over 13 years of follow up. Taken together, we demonstrate that MCPIP1 is a novel potent tumor suppressor which induces tumor apoptosis through tipping the balance between pro-apoptotic and anti-apoptotic genes via selectively targeting the mRNAs of anti-apoptotic genes for degradation. MCPIP1 can serve as a new therapeutic target for treatment of breast cancer and other cancers as well. Citation Format: Jianguo Liu, Wenbao Lu, Huan Ning, Hui Peng, Qinghong Wang, Rong Hou. MCPIP1 suppresses breast tumor progression by targeting anti-apoptosis pathway. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-042. doi:10.1158/1538-7445.AM2015-LB-042
THE ROLE OF POLAR SPECIES IN THE AGGREGATION OF ASPHALTENES (1987)

Abstract Many properties of heavy oils are Influenced by the presence of asphaltenes. According to solubility studies, asphaltenes are the most polar fraction of heavy oils, but the magnitude of the dlpole moment is not known. We quantified this parameter by applying dielectric spectroscopy to several heavy oils with different asphaitene concentrations, and the response of the permanent dlpoles was measured as a function of concentration and temperature. The asphaltenes have dielectric constants ranging from 5 to 7. Calculations Indicate more than one dlpole per asphaitene molecule. The diameter of the dlpole center was assessed to be 3 to 6 A. The probe was extended to study the Involvement of dlpoles In asphaitene aggregation. As the concentration of asphaltenes exceeds 10%, the dielectric constant exhibits substantial negative deviation from linearity, signifying the onset of Intermolecular Interactions (the pairing of dipoles in head-to-ta1l configurations to form clusters). Raising the temperature Increases the dielectric constant. Indicating dissociation of the aggregates. Based on comparison of these results with the dielectric behavior of model compounds the role of dipoles in the process of asphaitene association has been demonstrated for the first time. Additional informationNotes on contributorsH. Paul Maruska General Electric Space Systems Division, P.O. Box 8555, Philadelphia, PA 19101
Polynucleotide binding to macrophage scavenger receptors depends on the formation of base-quartet-stabilized four-stranded helices. (1993)

Macrophage scavenger receptors exhibit unusually broad, but circumscribed, polyanionic ligand-binding specificity. For example, the polyribonucleotides poly(I) and poly(G) are ligands but poly(A) and poly(C) are not. To further investigate the molecular basis of this polynucleotide-binding specificity, we tested the capacity of various oligodeoxyribonucleic acids to inhibit the scavenger receptor-mediated degradation of 125I-labeled acetylated low density lipoprotein by Chinese hamster ovary cells expressing the type I bovine scavenger receptor. A series of short oligodeoxyriboguanines (dGn, where 5 < or = n < or = 37) were effective inhibitors. The dG6, dG12, and dA5G37 members of this series were shown by circular dichroism and UV spectroscopy to be assembled into four-stranded helices stabilized by G-quartets. [32P]dA5G37 bound directly to scavenger receptors. Partial or complete denaturation of the quadruplex structures of these oligonucleotides by boiling destroyed their inhibitory activity. Receptor activity was also inhibited by d(T4G4)4, a telomere-like oligonucleotide which forms an intramolecular quadruplex. In addition, conversion of the four-stranded potassium salt of poly(I) to the single-stranded lithium salt dramatically reduced its inhibitory activity. Addition of KCl to the Li+ salt resulted in the reformation of poly(I)'s quadruplex structure and restoration of its inhibitory activity. A variety of single-stranded and double-stranded oligo- and polydeoxyribonucleotides (e.g. dA37, HaeIII restriction fragments of phi X174) exhibited very little or no inhibitory activity. Thus, a base-quartet-stabilized four-stranded helix appears to be a necessary structural determinant for polynucleotide binding to and inhibition of scavenger receptors. This conformational requirement accounts for the previously unexplained polyribonucleotide-binding specificity of scavenger receptors. The spatial distribution of the negatively charged phosphates in polynucleotide quadruplexes may form a charged surface which is complementary to the positively charged surface of the collagenous ligand-binding domain of the scavenger receptor.
Bioimmunoassay of Aryl Hydrocarbon (Ah) Receptor Transformation in Vitro by 2,3,7,8- Tetrachlorodibenzo-p-Dioxin(TCDD) (1996)

AbstractAn assay is described that detects 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) indirectly by quantitating transformation of guinea pig aryl hydrocarbon (Ah) receptor in vitro. Transformed Ah receptor is isolated on an affinity column and measured by dot-blot immunoassay. Antisera were developed against the highly conserved amino-terminal region of mammalian Ah receptor and affinity-purified. Hepatic cytosol from guinea pigs was treated with TCDD. Treatment resulted in the transformation of the Ah receptor to the DNA binding form. Affinity chromatography of the treated cytosol using dioxin-responsive element (DRE) oligonucleotides isolated a single immunoreactive and TCDD treatment-dependent protein with a molecular mass of 105 kDa. The protein was identified as guinea pig Ah receptor based on TCDD treatment dependence, molecular weight, and immunoreactivity. A bioimmunoassay was designed to detect the transformation of guinea pig Ah receptor by TCDD. Transformation of guinea pig Ah receptor by TCDD was dose-dependent. Maximal transformation was seen at doses of 4 and 8 nM TCDD. Half-maximal response was estimated to be 0.548 nM ≤ 0.002 SE from nonlinear curve fitting of the dose-response data to a hyperbolic function. The limit of quantitation was 0.125 nM. A standard curve of 10 to 320 fmol of antigen on dot blots was generated. The limit of antigen quantitation was 10 fmol. Comparison of densities from the TCDD-dose responses to densities of the antigen standard curve indicated that the recovery of transformed Ah receptor was between 1.8 and 14 fmol/mg cytosol protein in the 0.125 to 8-nm TCDD dose range. Seven additional dioxin and furan congeners of TCDD and three PCBs were tested in the assay. Dose responses to 1,2,3,7,8-PCDD; 1,2,3,4,7,8-HCDD; 2-MCDD; 2,3,7,8-TCDF; 1,2,3,7,8-PCDF; 2,3,4,7,8-PCDF; 2,3,4,6,7,8-HCDF; 3,3′,4,4′-TCB; 3,3′,4,4′,5-PCB; and 2,3,3′,4,4′,5-HCB were generated. The half-maximal response of these compounds was proportional to their respective toxic equivalency factors. These results suggest that this assay could be used for detection of TCDD and related congeners, quantitation of transformed Ah receptor, and estimations of toxic equivalency factors in vitro. The potential uses of this assay are discussed.Key Words: : Aryl hydrocarbon receptorDioxinsGuinea pigImmunoassay2,3,7,8-tetrachlorodibenzo-p-dioxinToxic equivalency factors
Hepatocyte transplantation for metabolic disorders, experience at King's College hospital and review of literature. (2006)

Hepatocyte transplantation is emerging as a potential treatment for liver based metabolic disorders and acute liver failure. To date, clinical studies have shown that hepatocyte transplantation could be used as a "bridge" to liver transplantation in a few patients with acute liver failure and has changed the phenotype of metabolic patients in terms of reducing the severity of illness. For many years, research studies have been carried out to optimise conditions for a) hepatocyte isolation in order to obtain the highest possible number of viable hepatocytes isolated from various sources of unused donor liver tissues, and b) cryopreservation and storage of hepatocytes for immediate cell availability in emergency cases. In this review, we summarise the worldwide clinical experience in hepatocyte transplantation for liver based metabolic disorders including the experience of our centre at King's College Hospital, London (United Kingdom). We briefly comment on the possible future developments and improvements needed in this field.
Analysis of phosphofructokinase subunits and isozymes in ascites tumor cells and its original tissue, murine mammary gland (1997)

Phosphofructokinase (PFK) subunits and isozymes have been examined in ascites tumor cells and murine mammary gland, the tissue from where this tumor originated. Ascites tumor was found to contain predominantly the C-type subunit, whereas the L-type subunit was more abundant in mammary gland. An altered M-type subunit of lower electrophoretic mobility was found in both cell types and no M4 homotetramers were detected in either of them. Characteristic regulatory properties of ascites tumor PFK, i.e. insensitivity to fructose-1,6-P2 activation and inhibition by P-enolpyruvate, were also observed in the mammary gland isozyme. The nature of these properties and the contribution of the distinct subunit types to fructose-1,6-P2 activation are discussed.
Mutation analysis of B-RAF gene in human gliomas (2004)

The RAS/RAF/MEK/ERK kinase pathway is pivotal in the transduction of mitogenic stimuli from activated growth factor receptors, which regulates cell proliferation, survival, and differentiation. Up-regulation of this pathway due to RAS mutations is found in approximately 30% of human tumors. Recently, activating mutations of B-RAF were identified in a large proportion of human cancers. Gliomas are the most frequent primary central nervous system tumors and the molecular mechanisms that underlie the development and progression of these tumors are far from being completely understood. The purpose of this study was to clarify the incidence of B-RAF mutations and their possible relation with tumor progression in a series of 82 human gliomas, including 49 astrocytic and 33 oligodendroglial tumors. The analysis of B-RAF hotspot regions, exons 11 and 15, showed presence of B-RAF mutations in only 2 out of 34 (6%) glioblastomas, and absence in the remaining histological types. Both mutations were located in the hotspot residue 600 (V600E) at exon 15, which leads to constitutive B-RAF kinase activity. These data suggest that activating mutations of B-RAF are not a frequent event in gliomas; nevertheless, when present they are associated with high-grade malignant lesions.
Biomechanical and Topographic Considerations for Autologous Osteochondral Grafting in the Knee (2001)

This study characterizes the donor and recipient sites involved in osteochondral autograft surgery of the knee with respect to articular cartilage contact pressure, articular surface curvature, and cartilage thickness. Five cadaveric knees were tested in an open chain activity simulation and kinematic data were obtained at incremental knee flexion angles from 0 degrees to 110 degrees. Surface curvature, cartilage thickness, and contact pressure were determined using a stereophotogrammetry method. In all knees, the medial trochlea, intercondylar notch, and lateral trochlea demonstrated nonloadbearing regions. Donor sites from the distal-medial trochlea were totally nonloadbeadng. For the intercondylar notch, lateral trochlea, and proximal-medial trochlea, however, the nonloadbearing areas were small, and typical donor sites in these areas partially encroached into adjacent loadbearing areas. The lateral trochlea (77.1 m(-1)) was more highly curved than the typical recipient sites of the central trochlea (23.3 m(-1)), medial femoral condyle (46.8 m(-1)), and lateral femoral condyles (42.9 m(-1)) (P < 0.05). Overall, the donor sites had similar cartilage thickness (average, 2.1 mm) when compared with the typical recipient sites (average, 2.5 mm). The lateral trochlea and medial trochlea curvatures were found to better match the recipient sites on the femoral condyles, while the intercondylar notch better matched the recipient sites of the central trochlea. The distal-medial trochlea was found to have the advantage of being nonloadbearing. Preoperative planning using the data presented will assist in more conforming, congruent grafts, thereby maximizing biomechanical function.
Refining the assessment of pulmonary regurgitation in adults after tetralogy of Fallot repair: should we be measuring regurgitant fraction or regurgitant volume? (2008)

PR(volume) and PR(fraction) are not interchangeable. PR(volume) may be a more accurate reflection of RV preload and may better represent physiologically significant PR as compared with PR(fraction).
A pilot study of high-dose 1-beta-D-arabinofuranosylcytosine for acute leukemia and refractory lymphoma: clinical response and pharmacology. (1982)

1-beta-D-Arabinofuranosylcytosine (ara-C), 2 or 3 g/sq m, was administered as a 1-hr i.v. infusion every 12 hr for 10 or 12 doses to patients with acute leukemia and refractory lymphoma. Four of seven patients with relapsed or refractory acute myelocytic leukemia and two of four patients with previously untreated acute myelocytic leukemia achieved complete remission. Of five treatment failures, two patients had leukemia which was clearly resistant to high-dose ara-C, and three patients died of infections or hemorrhagic complications during periods of pancytopenia. Three patients with acute myelocytic leukemia in remission received high-dose ara-C as consolidation therapy following previous courses of intensive, multiagent consolidation chemotherapy. Two of these three patients had prolonged thrombocytopenia following high-dose ara-C. Five patients with refractory acute lymphocytic leukemia were treated. Three patients achieved partial remission, and two patients had drug-resistant disease. Complete or partial disappearance of measurable disease parameters was seen in three of three patients with refractory lymphoma. Response was seen in five of five patients with meningeal leukemia, including complete response in one patient with extensive meningeal infiltration. Toxicity of this regimen was generally moderate and limited to pancytopenia and mild nausea. Patients who had received prior multiagent consolidation chemotherapy appeared to be at greater risk for hematopoietic toxicity. Patients who had received prior cranial irradiation or intrathecal chemotherapy appeared to be at greater risk for neurological toxicity. Plasma levels of ara-C immediately after completion of the infusion were 17.96 +/- 8.02 (S.D.) and 35.0 +/- 2.8 micrograms/ml for doses of 2 and 3 g/sq m, respectively. From 160 to 720 min following completion of the infusion, the plasma levels of drug were comparable to steady-state levels achieved with a continuous infusion of ara-C at 100 mg/sq m over 24 hr. A high degree of penetration into the central nervous system was demonstrated. High-dose ara-C has substantial activity against leukemic and lymphomatous cell populations, including cell populations resistant to conventional doses of the drug, and is an effective treatment modality for patients with these diseases. The high degree of penetration into the central nervous system suggests that this drug regimen may be useful as consolidation therapy for patients at high risk for central nervous system disease.