gebhart/patrepeval huggingface dataset:
Synergism between interleukin-8 and tumor necrosis factor-alpha for neutrophil-mediated platelet activation. (1995)

We previously showed that two polymorphonuclear neutrophil (PMN)-derived proteinases, namely cathepsin G (Cat. G) and elastase (HLE), acting in synergy activated nearby platelets in vitro. This cellular interaction could result in a pathology such as the adult respiratory distress syndrome (ARDS). Since elevated levels of tumor necrosis factor-alpha (TNF-alpha) and interleukin-8 (IL-8) were detected in these patients and therefore could be involved in this disease, we looked for their effects in the PMN-platelet cooperation system. Addition of IL-8 to mixed suspensions of PMN and platelets induced weak but significant platelet aggregations. Upon preincubation with TNF-alpha, aggregations triggered by IL-8 were significantly increased. The targets of these cytokines were not the platelets but the PMNs. This was shown by following beta-glucuronidase release and more interestingly by measuring the enzymatic activities of Cat. G and HLE in the supernatant. Inhibition of the platelet response upon addition of a serine proteinase inhibitor, eglin C, clearly demonstrated the involvement of these two enzymes. Taken together, these results constitute an additional argument for the role of the PMN-platelet interaction in ARDS.
Tumor necrosis factor up-regulates gamma-interferon binding in a human carcinoma cell line. (1990)

WiDR colorectal carcinoma cells are highly sensitive to the synergistic cytotoxic effects of tumor necrosis factor (TNF) and gamma-interferon (IFN-gamma). In the present study, we have investigated the effects of recombinant human (rh) TNF and IFN-gamma on the binding of both ligands in this cell line. WiDR cells exhibited high affinity binding sites for both 125I-rhTNF (Kd = 1.66 x 10(-10) M, 920 sites/cell) and 125I-rhIFN-gamma (Kd = 4.15 x 10(-10) M, 18,960 sites/cell). Preincubation of the cells with rhTNF (24 h) increased cell-associated 125I-rhIFN-gamma radioactivity by 129% when binding was carried out at 37 degrees C, as a result of an increase in both surface bound and internalized 125I-rhIFN-gamma. However, rhTNF did not alter the degradation profile of released 125I-rhIFN-gamma radioactivity. Scatchard analysis of 125I-rhIFN-gamama binding data (4 degrees C) revealed that rhTNF induced a 245% increase in 125I-rhIFN-gamma binding sites. Conversely, rhIFN-gamma caused a 68% increase in 125I-rhTNF binding sites and a 58% increase in receptor affinity. rhIFN-gamma also increased the subsequent binding of 125I-rhIFN-gamma, whereas rhTNF increased the subsequent binding of 125I-rhTNF. Furthermore, preincubation of the cells with both rhTNF and rhIFN-gamma also resulted in an increase in the binding of both ligands. Actinomycin D and cycloheximide blocked all the effects of rhTNF and rhIFN-gamma on ligand binding. However, the basal level of 125I-rhIFN-gamma binding was insensitive to either inhibitor, whereas the basal level of 125I-rhTNF binding was decreased by both inhibitors. These data indicate that in some cell types TNF and IFN-gamma may induce an increase in their own receptors (homologous up-regulation) and concomitantly increase each other's receptors (heterologous up-regulation) and that these actions are due, in part, to enhanced receptor synthesis.
Heat-shock protein peptide complex–96 vaccination for recurrent glioblastoma: a phase II, single-arm trial (2013)

The HSPPC-96 vaccine is safe and warrants further study of efficacy for the treatment of recurrent GBM. Significant pretreatment lymphopenia may impact the outcomes of immunotherapy and deserves additional investigation.
A region-based multiresolution image fusion algorithm (2003)

We propose a multiresolution fusion algorithm which combines aspects of region and pixel-based fusion. We use multiresolution decompositions to represent the input images at different scales, and introduce a multiresolution/multimodal segmentation to partition the image domain at these scales. The basic idea is to use this segmentation to guide the fusion process. A region-based multiresolution approach allows us to consider low-level as well as intermediate-level structures, and to impose data-dependent consistency constraints based on spatial, inter and intra-scale dependencies.
Increased Intestinal Permeability in Patients with Crohn's Disease and Their Relatives (1986)

The cause of Crohn's disease is unknown, although alterations in intestinal permeability may play a primary role. Because we were interested in permeability changes that occur before the onset of intestinal inflammation, we took advantage of the known genetic predisposition to this disease and studied not only patients with Crohn's disease, but their clinically unaffected relatives as well. Intestinal permeability was assessed using the marker polyethylene glycol-400 ingested with a standard meal. We found that 17 normal volunteers absorbed 215 +/- 29.6 mg (mean +/- SE), whereas 11 patients with Crohn's disease absorbed 514 +/- 94.7 mg and their 32 healthy relatives absorbed 566 +/- 62.4 mg. The twofold increase in permeability of patients and their relatives (p less than 0.005 compared with controls) indicates that the intestinal defect in the ability to exclude larger sized molecules is not secondary to clinically recognized intestinal inflammation, but is a primary defect that may be an etiologic factor in this disease.
The Effect of Halogenated Hydantoins on Biofilms (1997)

Abstract The biocidal efficacy of halogenated hydantoins against laboratory-prepared biofilms was compared to the free halogen donors NaOCl and NaOBr. Higher biocide concentrations were required to control a filamentous biofilm than to control free floating planktonic bacteria. Control of a biocide-resistant S. natans biofilm was best obtained with a repeated slug+3 hour continuous treatment procedure or with conventional continuous biocide treatment. A bromine, methylethylhydantoin-containing oxidizing biocide (BrMEH) was found to be more efficacious than either free chlorine or free bromine in controlling filamentous biofilms. Previous studies indicating the inability of free chlorine to penetrate biofilms were supported as the combination of free and combined halogen was demonstrated to be more effective than free chlorine or bromine alone against attached bacteria.
Repair of deletions and double-strand gaps by homologous recombination in a mammalian in vitro system. (1991)

We have designed an in vitro system using mammalian nuclear extracts, or fractions derived from them, that can restore the sequences missing at double-strand breaks (gaps) or in deletions. The recombination substrates consist of (i) recipient DNA, pSV2neo with gaps or deletions ranging from 70 to 390 bp in the neo sequence, and (ii) donor DNAs with either complete homology to the recipient (pSV2neo) or plasmids whose homology with pSV2neo is limited to a 1.0- to 1.3-kbp neo segment spanning the gaps or deletions. Incubation of these substrates with various enzyme fractions results in repair of the recipient DNA's disrupted neo gene. The recombinational repair was monitored by transforming recA Escherichia coli to kanamycin resistance and by a new assay which measures the extent of DNA strand transfer from the donor substrate to the recipient DNA. Thus, either streptavidin- or antidigoxigenin-tagged beads are used to separate the biotinylated or digoxigeninylated recipient DNA, respectively, after incubation with the isotopically labeled donor DNA. In contrast to the transfection assay, the DNA strand transfer measurements are direct, quantitative, rapid, and easy, and they provide starting material for the characterization of the recombination products and intermediates. Accordingly, DNA bound to beads serves as a suitable template for the polymerase chain reaction. With appropriate pairs of oligonucleotide primers, we have confirmed that both gaps and deletions are fully repaired, that deletions can be transferred from the recipient DNA to the donor's intact neo sequence, and that cointegrant molecules containing donor and recipient DNA sequences are formed.
Molecular diversity and combinatorial chemistry : libraries and drug discovery (1996)

Secondary Structure Templated Libraries: Mimicking Nature Construct Diversity: A New Paradigm for Combinatorial Chemistry Enhancing the Drug Discovery Process by Integration of High-Throughput Chemistry and Structure-Based Drug Design Phosphorus as a Scaffold: Combinatorial Libraries of Non-nucleotide Phosphoramidates Convergent Solid-Phase Synthesis of Phosphoramidate Combinatorial Libraries Solid-Phase Synthesis, Characterization, and Screening of a 43,000-Compound Tetrahydroisoquinoline Combinatorial Library Solid-Phase and Combinatorial Synthesis of Heterocyclic Scaffolds: Dihydropyridines, Pyridines, and Pyrido [2,3-d]pyrimidines Polymer-Supported Chemistry: Synthesis of Small-Ring Heterocycles A Solution-Phase Strategy for the Parallel Synthesis of Chemical Libraries Containing Small Organic Molecules: A General Dipeptide Mimetic and a Flexible General Template Structurally Homogeneous and Heterogeneous Libraries: Scaffold-Based Libraries and Libraries Built Using Bifunctional Building Blocks Liquid-Phase Combinatorial Synthesis Libraries of Transition-Metal Catalysts: High-Throughput Screening of Catalysts for Synthetic Organic Methodology Mixtures of Molecules Versus Mixtures of Pure Compounds on Polymeric Beads Generation of Solution-Phase Libraries of Organic Molecules by Combinatorial Biocatalysis Living Libraries Using Gene Transfer: A Renaissance for Natural Products Phage Expression of a De Novo Designed Coiled Coil Stem Loop Miniprotein Scaffold for Constrained Peptide Library Display Automation of High-Throughput Synthesis: Automated Laboratory Workstations Designed to Perform and Support Combinatorial Chemistry Boosting the Productivity of Medicinal Chemistry Through Automation Tools: Novel Technological Developments Enable a Wide Range of Automated Synthetic Procedures A Modular System for Combinatorial and Automated Synthesis LiBrain: Software for Automated Design of Exploratory and Targeted Combinatorial Libraries Automation Issues at the Interface Between Combinatorial Chemistry and High-Throughput Screening Tools for Combinatorial Chemistry Magic-Angle Spinning NMR Spectroscopy of Polystyrene-Bound Organic Molecules: Monitoring a Three-Step Solid-Phase Synthesis Involving a Heck Reaction A High-Throughput Functional Assay for G-Protein-Coupled Receptors: Method for Screening Combinatorial Libraries Use of Combinatorial Libraries in the Discovery and Development of Novel Anti-infectives Application of Polymer-Supported Chemistry to the Discovery and Optimization of Lead Drug Candidates Using Pharmacophore Diversity To Select Molecules To Test from Commercial Catalogues
Stereochemical Analysis by Solid-State NMR:  Structural Predictions in Ambuic Acid (2003)

Relative stereochemistry is predicted for ambuic acid using a novel solid-state NMR approach. This NMR technique entails a comparison of measured shift tensor principal values with computed values for all diastereomers, allowing the selection of a best-fit structure. The proposed method extends previous solution NMR structural data by simultaneously modeling with high statistical probability hydrogen-bonding arrangements and molecular conformation at two positions. A dimeric structure is proposed for ambuic acid based on the initial poor fit of the carboxyl carbon tensors to a monomeric model. The dimer model, consisting of hydrogen bonding between pairs of neighboring carboxyl groups, reduces the root mean square error at the carboxy tensor by a factor of 2.7. Lattice details are thus also described by the proposed approach. The structural characterization method presented is of general applicability and may be especially useful for characterizing difficult to crystallize or hydrogen-poor materials.
A Proteomic Analysis of Arginine-methylated Protein Complexes (2003)

Arginine methylation is a post-translational modification that results in the formation of asymmetrical and symmetrical dimethylated arginines (a- and sDMA). This modification is catalyzed by type I and II protein-arginine methyltransferases (PRMT), respectively. The two major enzymes PRMT1 (type I) and PRMT5 (type II) preferentially methylate arginines located in RG-rich clusters. Arginine methylation is a common modification, but the reagents for detecting this modification have been lacking. Thus, fewer than 20 proteins have been identified in the last 40 years as containing dimethylated arginines. We have generated previously four arginine methyl-specific antibodies; ASYM24 and ASYM25 are specific for aDMA, whereas SYM10 and SYM11 recognize sDMA. All of these antibodies were generated by using peptides with aDMA or sDMA in the context of different RG-rich sequences. HeLa cell extracts were used to purify the protein complexes recognized by each of the four antibodies, and the proteins were identified by microcapillary reverse-phase liquid chromatography coupled on line with electrospray ionization tandem mass spectrometry. The analysis of two tandem mass spectra for each methyl-specific antibody resulted in the identification of over 200 new proteins that are putatively arginine-methylated. The major protein complexes that were purified include components required for pre-mRNA splicing, polyadenylation, transcription, signal transduction, and cytoskeleton and DNA repair. These findings provide a basis for the identification of the role of arginine methylation in many cellular processes.
Temporally and Spatially Coordinated Expression of Cell Cycle Regulatory Factors After Angioplasty (1997)

Intimal hyperplasia following angioplasty results in part from the migration and proliferation of vascular smooth muscle cells (VSMCs). However, the cell cycle regulatory networks underlying injury-induced VSMC proliferation are largely unknown. In the present study, we examined the kinetics of expression and activity of cell cycle regulatory factors after angioplasty in rat and human arteries. Cell lysates were prepared from uninjured rat carotid arteries and at different time points after balloon denudation. Marked induction of the proliferating cell nuclear antigen (PCNA), the G1/S cyclin-dependent kinase (cdk2), and its regulatory subunits (cyclin E and cyclin A) occurred between 1 and 2 days after angioplasty, was sustained up to 10 days after injury, and then declined. Induction of these factors correlated with increased cdk2-, cyclin E-, and cyclin A-dependent kinase activity, indicating the assembly of functional cdk2/cyclin E and cdk2/cyclin A holoenzymes in the injured arterial wall. Immunohistochemical analysis revealed early expression of cdk2, cyclin E, and PCNA within the media of injured carotid arteries. At later time points, expression of these markers declined to basal levels in the media but was detected within the intimal lesion. Thus, VSMC proliferation after angioplasty in the rat carotid artery is associated with a temporally and spatially coordinated expression of cdk2, cyclins E and A, and PCNA. Analysis of human arteries also revealed expression of these factors in VSMCs within restenotic lesions. Thus, cdk2 and its regulatory cyclins may be suitable targets to limit human restenosis.
CLINICAL OUTCOMES AFTER LUMBAR DISCECTOMY FOR SCIATICA (2003)

Prognostic study, Level I-1 (prospective study). See p. 2 for complete description of levels of evidence.
Protein Transport in Plant Cells: In and Out of the Golgi (2003)

In plant cells, the Golgi apparatus is the key organelle for polysaccharide and glycolipid synthesis, protein glycosylation and protein sorting towards various cellular compartments. Protein import from the endoplasmic reticulum (ER) is a highly dynamic process, and new data suggest that transport, at least of soluble proteins, occurs via bulk flow. In this Botanical Briefing, we review the latest data on ER/Golgi inter-relations and the models for transport between the two organelles. Whether vesicles are involved in this transport event or if direct ER-Golgi connections exist are questions that are open to discussion. Whereas the majority of proteins pass through the Golgi on their way to other cell destinations, either by vesicular shuttles or through maturation of cisternae from the cis- to the trans-face, a number of membrane proteins reside in the different Golgi cisternae. Experimental evidence suggests that the length of the transmembrane domain is of crucial importance for the retention of proteins within the Golgi. In non-dividing cells, protein transport out of the Golgi is either directed towards the plasma membrane/cell wall (secretion) or to the vacuolar system. The latter comprises the lytic vacuole and protein storage vacuoles. In general, transport to either of these from the Golgi depends on different sorting signals and receptors and is mediated by clathrin-coated and dense vesicles, respectively. Being at the heart of the secretory pathway, the Golgi (transiently) accommodates regulatory proteins of secretion (e.g. SNAREs and small GTPases), of which many have been cloned in plants over the last decade. In this context, we present a list of regulatory proteins, along with structural and processing proteins, that have been located to the Golgi and the 'trans-Golgi network' by microscopy.
Aβ40-Lactam(D23/K28) Models a Conformation Highly Favorable for Nucleation of Amyloid (2005)

Recent solid-state NMR data (1) demonstrate that Abeta(1)(-)(40) adopts a conformation in amyloid fibrils with two in-register, parallel beta-sheets, connected by a bend structure encompassing residues D(23)VGSNKG(29), with a close contact between the side chains of Asp23 and Lys28. We hypothesized that forming this bend structure might be rate-limiting in fibril formation, as indicated by the lag period typically observed in the kinetics of Abeta(1)(-)(40) fibrillogenesis. We synthesized Abeta(1)(-)(40)-Lactam(D23/K28), a congener Abeta(1)(-)(40) peptide that contains a lactam bridge between the side chains of Asp23 and Lys28. Abeta(1)(-)(40)-Lactam(D23/K28) forms fibrils similar to those formed by Abeta(1)(-)(40). The kinetics of fibrillogenesis, however, occur without the typical lag period, and at a rate approximately 1000-fold greater than is seen with Abeta(1)(-)(40) fibrillogenesis. The strong tendency toward self-association is also shown by size exclusion chromatography in which Abeta(1)(-)(40)-Lactam(D23/K28) forms oligomers even at concentrations of approximately 1-5 microM. Under the same conditions, Abeta(1)(-)(40) shows no detectable oligomers by size exclusion chromatography. Our data suggest that Abeta(1)(-)(40)-Lactam(D23/K28) could bypass an unfavorable folding step in fibrillogenesis, because the lactam linkage "preforms" a bendlike structure in the peptide. Consistent with this view Abeta(1)(-)(40) growth is efficiently nucleated by Abeta(1)(-)(40)-Lactam(D23/K28) fibril seeds.
Hardware Design and Implementation of SM3 Hash Algorithm for Financial IC Card (2014)

This paper focuses on the circuit design for SM3, which is the only standard hash algorithm of China. This paper presents a new VLSI architecture of SM3 for financial IC card. Since there is no such hardware implementation in literature, our work is the first one to integrate SM3 into financial IC card. In accordance with the technical specifications and based on SMIC 0.13um technology, the circuit design, behavioral simulation, gate-level simulation, power analysis, and the FPGA verification are all implemented. The results show that the SM3 IP core design is correct and feasible. Comprehensive validation results show that the design is within the area of 11000 gates and the power of 1mA @ 1.2V, suitable for financial IC card, which require small area and low power, and far below the design specifications.
Reduction of CuZn-Superoxide Dismutase Activity Exacerbates Neuronal Cell Injury and Edema Formation after Transient Focal Cerebral Ischemia (1997)

Apoptotic neuronal cell death has recently been associated with the development of infarction after cerebral ischemia. In a variety of studies, CuZn-superoxide dismutase (CuZn-SOD) has been shown to protect the brain from ischemic injury. A possible role for CuZn-SOD-related modulation of neuronal viability is suggested by the finding that CuZn-SOD inhibits apoptotic neuronal cell death in response to some forms of cellular damage. We evaluated this possibility in the model of transient focal cerebral ischemia in mice bearing a disruption of the CuZn-SOD gene (Sod1). Homozygous mutant (Sod1 -/-) mice had no detectable CuZn-SOD activity, and heterozygous mutants (Sod1 +/-) showed a 50% decrease compared with wild-type mice. Sod1 -/- mice showed a high level of blood-brain barrier disruption soon after 1 hr of middle cerebral artery occlusion and 100% mortality at 24 hr after ischemia. Sod1 +/- mice showed 30% mortality at 24 hr after ischemia, and neurological deficits were exacerbated compared with wild-type controls. The Sod1 +/- animals also had increased infarct volume and brain swelling, accompanied by increased apoptotic neuronal cell death as indicated by the in situ nick-end labeling technique to detect DNA fragmentation and morphological criteria. These results suggest that oxygen-free radicals, especially superoxide anions, are an important factor for the development of infarction by brain edema formation and apoptotic neuronal cell death after focal cerebral ischemia and reperfusion.
Computer graphics curriculum (1994)

Computer graphics is a field driven by technology. Whereas the technology has changed enormously in the past 15 years, the way most computer science faculty teach computer graphics courses has not changed. The authors believe that faculty should seriously consider changing the content and approach of their computer graphics courses, and in this paper we discuss the rationale for the change and our recomendation for a new course. Note that Maria Larrondo-Petrie organized a panel session on this topic for the SIGGRAPH '94 conference (with panelists Jack Bresenham, John Lansdown, Cary Laxer and Scott Owen).
Coordinate: probabilistic forecasting of presence and availability (2002)

We present methods employed in COORDINATE, a prototype service that supports collaboration and communication by learning predictive models that provide forecasts of users ’ presence and availability. We describe how data is collected about user activity and proximity from multiple devices, in addition to analysis of the content of users ’ calendars, the time of day, and day of week. We review applications of presence forecasting embedded in the PRIORITIES application and then present details of the COORDINATE service that was informed by the earlier efforts. 1