gebhart/patrepeval huggingface dataset:
Triflavin, an antiplatelet peptide, inhibits tumor cell-extracellular matrix adhesion through an arginine-glycine-aspartic acid-dependent mechanism. (1994)

The interaction of tumor cells with extracellular matrix components such as laminin, fibronectin, and collagen has been shown to be mediated through a family of cell-surface receptors that specifically recognize an arginine-glycine-aspartic acid amino acid sequence within each protein. Triflavin, a 7.5 kDa cysteine-rich polypeptide purified from Trimeresurus flavoviridis snake venom, belongs to a family of arginine-glycine-aspartic acid-containing peptides termed disintegrins that have been isolated from the venoms of various vipers and shown to be potent inhibitors of platelet aggregation. In this study, we showed that triflavin inhibited adhesion of human hepatoma J-5 cells to extracellular matrices (fibronectin, vitronectin, fibrinogen, and collagen type I) in a dose-dependent manner. On the other hand, triflavin exerted a limited inhibitory effect on cell attachment to collagen type IV and laminin (< or = 40%). Triflavin is approximately 1000 times more potent than glycine-arginine-glycine-aspartic acid-serine at inhibiting cell adhesion. When immobilized on plate, triflavin promoted J-5 cell attachment; this attachment was inhibited by glycine-arginine-glycine-aspartic acid-serine. In addition, triflavin labeled with iodine 125 binds to J-5 cells in a saturable manner and its binding was also inhibited by glycine-arginine-glycine-aspartic acid-serine. Its Kd value was estimated to be 3.9 x 10(-7) mol/L and the number of binding sites was around 60,000 per cell. Furthermore, triflavin did not affect tritiated thymidine uptake during a 3-day incubation.(ABSTRACT TRUNCATED AT 250 WORDS)
HDR-VDP-2 (2011)

Visual metrics can play an important role in the evaluation of novel lighting, rendering, and imaging algorithms. Unfortunately, current metrics only work well for narrow intensity ranges, and do not correlate well with experimental data outside these ranges. To address these issues, we propose a visual metric for predicting visibility (discrimination) and quality (mean-opinion-score). The metric is based on a new visual model for all luminance conditions, which has been derived from new contrast sensitivity measurements. The model is calibrated and validated against several contrast discrimination data sets, and image quality databases (LIVE and TID2008). The visibility metric is shown to provide much improved predictions as compared to the original HDR-VDP and VDP metrics, especially for low luminance conditions. The image quality predictions are comparable to or better than for the MS-SSIM, which is considered one of the most successful quality metrics. The code of the proposed metric is available on-line.
Synthesis of fluorophore and quencher monomers for use in Scorpion primers and nucleic acid structural probes (2003)

We report the syntheses of monomers to incorporate fluorescein and methyl red within the sequence and at the termini of modified oligonucleotides. These monomers have been used in the solid-phase synthesis of fluorogenic oligonucleotides for genetic analysis and the study of multi-stranded nucleic acid structures.
Use of peripheral blood instead of bone marrow to monitor residual disease in children with acute lymphoblastic leukemia (2002)

In children with acute lymphoblastic leukemia (ALL), response to treatment is assessed by bone marrow aspiration. We investigated whether minimal residual disease (MRD) can be effectively monitored in peripheral blood. We used flow cytometric techniques capable of detecting 1 leukemic cell among 10 000 or more normal cells to compare MRD measurements in 718 pairs of bone marrow and peripheral blood samples collected from 226 children during treatment for newly diagnosed ALL. MRD was detected in marrow and blood in 72 pairs and in marrow but not in blood in 67 pairs; it was undetectable in the remaining 579 pairs. Remarkably, findings in marrow and blood were completely concordant in the 150 paired samples from patients with T-lineage ALL: for each of the 35 positive marrow samples, the corresponding blood sample was positive. In B-lineage ALL, however, only 37 of 104 positive marrow samples had a corresponding positive blood sample. Notably, peripheral blood MRD in these patients was associated with a very high risk for disease recurrence. The 4-year cumulative incidence of relapse in patients with B-lineage ALL was 80.0% +/- 24.9% for those who had peripheral blood MRD at the end of remission induction therapy but only 13.3% +/- 9.1% for those with MRD confined to the marrow (P =.007). These results indicate that peripheral blood may be used to monitor MRD in patients with T-lineage ALL and that peripheral blood MRD may provide strong prognostic information in patients with B-lineage ALL.
Adeno-associated virus mediated gene delivery into coronary microvessels of chronically instrumented dogs (2003)

The objective of this study was to assess the potential of adeno-associated virus (AAV)-mediated gene delivery into coronary microvessels in vivo in a large animal. Ten mongrel dogs were chronically instrumented and allowed to recover for 10 days. Dogs were reanesthetized, and the aorta was constricted by a hydraulic occluder, whereby left ventricular (LV) pressure increased by 30% and left circumflex coronary artery blood flow by 50%. Recombinant AAV (serotype 2, CMV enhancer/chicken beta-actin promoter) encoding for green fluorescent protein (GFP) was injected as a bolus into the left atrium during aortic constriction at total titers of 1010 or 1012 infectious units. Dogs were followed for 2 (n = 4)or4wk(n = 6). Hemodynamics or body weight did not change. In LV tissue slices, a fluorescein-labeled antibody to GFP stained endothelial and smooth muscle cells but was absent in myocytes. To quantify transduction, slices were then stained with antibodies against alpha-smooth muscle actin or von Willebrand factor. Approximately 4% of arterioles and 2% of microvessels stained positive for anti-GFP independent from viral titer or duration. By regression analyses, the percent of vessels transfected was proportional to the increase in LV systolic pressure during occlusion. AAV is a potential vector for gene transfer into the coronary microcirculation in large animals, including perhaps humans.
Use of genetically altered mice to study the role of serum amyloid P component in amyloid deposition (2003)

A precise role for serum amyloid P component (SAP), a common component of all known types of amyloid fibrils, in amyloid deposition in vivo is not known. Thus we investigated the relationship between SAP and amyloid deposition, using the transgenic mouse model of familial amyloidotic polyneuropathy (FAP). Because high serum levels of mouse endogenous or human SAP did not affect human transthyretin-derived amyloid deporsition in the transgenic mouse model of FAP, we approached this question by analyzing the induction of experimental AA amyloidosis in SAP-deficient and wild-type mice. Our experiments presented compelling evidence that, although not essential in the deposition of AA amyloid, SAP significantly accelerates the reaction. We then examined the persistence of splenic AA amyloid fibrils in SAP-deficient and wild-type mice to assess potential ways of treating individuals with amyloidosis. Our results indicated that lack of SAP in AA amyloid deposits does not enhance regression of the deposits in vivo and suggested that dissociation of bound SAP from AA amyloid deposits would not significantly accelerate regression of the deposits in vivo.
Human Cytomegalovirus and Autoimmune Disease (2014)

Human cytomegalovirus (HCMV) represents a prototypic pathogenic member of the β-subgroup of the herpesvirus family. A range of HCMV features like its lytic replication in multiple tissues, the lifelong persistence through periods of latency and intermitting reactivation, the extraordinary large proteome, and extensive manipulation of adaptive and innate immunity make HCMV a high profile candidate for involvement in autoimmune disorders. We surveyed the available literature for reports on HCMV association with onset or exacerbation of autoimmune disease. A causative linkage between HCMV and systemic lupus erythematosus (SLE), systemic sclerosis (SSc), diabetes mellitus type 1, and rheumatoid arthritis (RA) is suggested by the literature. However, a clear association of HCMV seroprevalence and disease could not be established, leaving the question open whether HCMV could play a coresponsible role for onset of disease. For convincing conclusions population-based prospective studies must be performed in the future. Specific immunopathogenic mechanisms by which HCMV could contribute to the course of autoimmune disease have been suggested, for example, molecular mimicry by UL94 in SSc and UL83/pp65 in SLE patients, as well as aggravation of joint inflammation by induction and expansion of CD4+/CD28- T-cells in RA patients. Further studies are needed to validate these findings and to lay the grounds for targeted therapeutic intervention.
A Live Attenuated West Nile Virus Strain as a Potential Veterinary Vaccine (2000)

This article reviews the development of two attenuated West Nile virus (WNV) variants, WNI-25 and WNI-25A. These variants have lost the neuroinvasion trait of the parental virus. Attenuation was achieved through serial passages in mosquito cells and neutralization escape from WNV-specific monoclonal antibody. Genetic analysis reveals amino acid changes between the parental and each of the variants. The attenuated variants preserve the ability to replicate in mice and geese and to induce a protective immune response. WNI-25A was found to be a genetically stable virus. This variant was successfully used as a live vaccine to protect geese against a wild-type virulent WNV field isolate that closely resembles the WNV isolated during the 1999 New York epidemic.
Chromium Corroles in Four Oxidation States (2001)

We have isolated and characterized chromium complexes of 5,10,15-tris(pentafluorophenyl)corrole [(tpfc)H(3)] (1) in four oxidation states: [(tpfc(*))CrO][SbCl(6)] (6); [(tpfc)CrO] (2); [(tpfc)CrO][Cp(2)Co] (4); and [(tpfc)Cr(py)(2)] (3). Complex 6 was prepared both by electrochemical and chemical oxidation of 2; its formulation as a Cr(V)O ligand-radical species is based on UV-visible absorption as well as EPR measurements. Cobaltocene reduction of 2 gave 4; it was identified as a diamagnetic d(2) Cr(IV)O complex from its sharp (1)H NMR spectrum. Reaction of 2 with triphenylphosphine yielded a chromium(III) corrole, [(tpfc)Cr(OPPh(3))(2)] (5). Owing to its air sensitivity, 5 could not be isolated in the absence of excess OPPh(3). The structure of the Cr(III) bis-pyridine complex (3) was determined by X-ray crystallography (Cr-N distances: 1.926-1.952 A, pyrrole; 2.109, 2.129 A, pyridine).
Platelet Quantification and Growth Factor Analysis from Platelet-Rich Plasma: Implications for Wound Healing (2004)

Growth factors released from activated platelets initiate and modulate wound healing in both soft and hard tissues. A recent strategy to promote the wound-healing cascade is to prepare an autologous platelet concentrate suspended in plasma, also known as platelet-rich plasma, that contains growth factors and administer it to wound sites. The purpose of this study was to quantitate platelet number and growth factors released from a prepared platelet concentrate. Whole blood was drawn from 10 healthy patients undergoing cosmetic surgery and concentrated into platelet-rich plasma. Platelet counts on whole blood and platelet-rich plasma were determined using a Cell-Dyn 3200. Platelet-derived growth factor-BB, transforming growth factor-beta1, vascular endothelial growth factor, endothelial growth factor, and insulin-like growth factor-1 were measured in the platelet-rich plasma using the enzyme-linked immunosorbent assay method. In addition, platelet activation during the concentration procedure was analyzed by measuring P selectin values in blood serum. An 8-fold increase in platelet concentration was found in the platelet-rich plasma compared with that of whole blood (baseline whole blood, 197 +/- 42 x 10 platelets/microl; platelet concentrate, 1600 +/- 330 x 10 platelets/microl). The concentration of growth factors also increased with increasing platelet number. However, growth factor concentration varied from patient to patient. On average for the whole blood as compared with platelet-rich plasma, the platelet-derived growth factor-BB concentration increased from 3.3 +/- 0.9 ng/ml to 17 +/- 8 ng/ml, transforming growth factor-beta1 concentration increased from 35 +/- 8 ng/ml to 120 +/- 42 ng/ml, vascular endothelial growth factor concentration increased from 155 +/- 110 pg/ml to 955 +/- 1030 pg/ml, and endothelial growth factor concentration increased from 129 +/- 61 pg/ml to 470 +/- 320 pg/ml. No increase was found for insulin-like growth factor-1. In addition, no increase in platelet activation occurred during the concentration procedure as determined by the platelet surface receptor P selectin (45 +/- 16 pg/ml to 52 +/- 11 pg/ml, p = 0.65). In conclusion, a variety of potentially therapeutic growth factors were detected and released from the platelets in significant levels in platelet-rich plasma preparations. Sufficient concentrates and release of these growth factors through autologous platelet gels may be capable of expediting wound healing in a variety of as yet undetermined specific wound applications.
User Input Mode and Computer-Aided Instruction (1968)

An evaluation of on-line computer-aided instruction within a management information system compared typewriter and lightpen input modes as students learned to use the system. The following conclusions were supported: 1. Computer-aided instruction is feasible in a general-purpose management information system; 2. It is also feasible to demonstrate retention of learned material through computer-administered tests; 3. Professional typing skills are not necessary to use the typewriter input mode effectively, provided that the inputs required are short and direct; 4. In this particular setting there seemed to be evidence that the typewriter was a more effective input device than the lightpen during the instructional sequence, but this evidence is questionable in view of considerable individual differences among the students; 5. Regardless of performance, students responded favorably to their experience with computer-aided instruction.
Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment (2013)

In this work we announce and evaluate a high throughput virtual screening pipeline for in-silico screening of virtual compound databases using high performance computing (HPC). Notable features of this pipeline are an automated receptor preparation scheme with unsupervised binding site identification. The pipeline includes receptor/target preparation, ligand preparation, VinaLC docking calculation, and molecular mechanics/generalized Born surface area (MM/GBSA) rescoring using the GB model by Onufriev and co-workers [J. Chem. Theory Comput. 2007, 3, 156-169]. Furthermore, we leverage HPC resources to perform an unprecedented, comprehensive evaluation of MM/GBSA rescoring when applied to the DUD-E data set (Directory of Useful Decoys: Enhanced), in which we selected 38 protein targets and a total of ∼0.7 million actives and decoys. The computer wall time for virtual screening has been reduced drastically on HPC machines, which increases the feasibility of extremely large ligand database screening with more accurate methods. HPC resources allowed us to rescore 20 poses per compound and evaluate the optimal number of poses to rescore. We find that keeping 5-10 poses is a good compromise between accuracy and computational expense. Overall the results demonstrate that MM/GBSA rescoring has higher average receiver operating characteristic (ROC) area under curve (AUC) values and consistently better early recovery of actives than Vina docking alone. Specifically, the enrichment performance is target-dependent. MM/GBSA rescoring significantly out performs Vina docking for the folate enzymes, kinases, and several other enzymes. The more accurate energy function and solvation terms of the MM/GBSA method allow MM/GBSA to achieve better enrichment, but the rescoring is still limited by the docking method to generate the poses with the correct binding modes.
Synthetic peptides corresponding to sequences of snake venom neurotoxins and rabies virus glycoprotein bind to the nicotinic acetylcholine receptor (1987)

Peptides corresponding to portions of loop 2 of snake venom curare-mimetic neurotoxins and to a structurally similar region of rabies virus glycoprotein were synthesized. Interaction of these peptides with purified Torpedo electric organ acetylcholine receptor was tested by measuring their ability to block the binding of 125I-labeled alpha-bungarotoxin to the receptor. In addition, inhibition of alpha-bungarotoxin binding to a 32-residue synthetic peptide corresponding to positions 173-204 of the alpha-subunit was determined. Neurotoxin and glycoprotein peptides corresponding to toxin loop 2 inhibited labeled toxin binding to the receptor with IC50 values comparable to those of nicotine and the competitive antagonist d-tubocurarine and to the alpha-subunit peptides with apparent affinities between those of d-tubocurarine and alpha-cobratoxin. Substitution of neurotoxin residue Arg37, the proposed counterpart of the quaternary ammonium of acetylcholine, with a negatively charged Glu residue reduced the apparent affinity about 10-fold. Peptides containing the neurotoxin invariant residue Trp29 and 10- to 100-fold higher affinities than peptides lacking this residue. These results demonstrate that relatively short synthetic peptides retain some of the binding ability of the native protein from which they are derived, indicating that such peptides are useful in the study of protein-protein interactions. The ability of the peptides to compete alpha-bungarotoxin binding to the receptor with apparent affinities comparable to those of other cholinergic ligands indicates that loop 2 of the neurotoxins and the structurally similar segment of the rabies virus glycoprotein act as recognition sites for the acetylcholine receptor. Invariant toxin residues Arg37 and Trp29 and their viral homologs play important, although not essential, roles in binding, possibly by interaction with complementary anionic and hydrophobic subsites on the acetylcholine receptor. The alpha-subunit peptide most likely contains all of the determinants for binding of the toxin and glycoprotein peptides present on the alpha-subunit, because these peptides bind to the 32-residue alpha-subunit peptide with the same or greater affinity as to the intact subunit.
Functional analysis of human Fc gamma RII (CD32) isoforms expressed in B lymphocytes. (1994)

The low affinity IgG receptor Fc gamma RII (CD32) represents the most widely distributed class of human Fc gamma R. To analyze the biologic functions of different Fc gamma RII isoforms, we stably transfected Fc gamma RIIb1, IIb1*, IIb2, IIa, and a IIa tail- mutant to the mouse IIA1.6 B lymphoma cell line. Of these, Fc gamma RIIb1* represents a receptor variant that is identical to IIb1 except for a single amino acid difference in the cytoplasmic tail (amino acid position 11) where a tyrosine (IIb1) is replaced by an aspartic acid (IIb1*). Evaluation of capping ability showed the Fc gamma RIIb1 molecules to cap effectively, which was even more apparent with IIb1*. None of the Fc gamma RIIa, IIa tail-, or IIb2 isoforms capped significantly. Internalization of Fc gamma R-antibody complexes proved very efficient for both the Fc gamma RIIa and IIb2 isoforms, whereas the IIb1 molecules internalized moderately compared with IIb1*, which internalized less efficiently. Notably, human IgG aggregates were internalized effectively by Fc gamma RIIa and moderately by IIb2. Neither Fc gamma RIIb1 nor IIb1* proved capable of internalizing such IgG aggregates. Cross-linking of the different Fc gamma R molecules showed Fc gamma RIIa capable of triggering increases in [Ca2+]i. Fc gamma R expressed on B cells were able to down-regulate [Ca2+]i on co-cross-linking with slgG. Notably, all three Fc gamma RIIb receptors proved active in this respect, in contrast to Fc gamma RIIa. The cell distribution of these Fc gamma RII isoforms was analyzed in a panel of human B cell lines to complement the IIA1.6 B cell model. Fc gamma RIIa was found expressed both at message and protein levels in all tested human B cell lines. In the pre-B cell lines evaluated, no Fc gamma RIIb molecules were detectable, whereas both Fc gamma RIIb1 and IIb2 molecules were found present in more mature B cell lines. These data support both a complex expression pattern of Fc gamma RII isoforms in B cell lines and functional differences between these B cell molecules.
Silole-containing σ- and π-conjugated compounds (1998)

Synthesis, properties, and application of new σ- and π-electron systems consisting of the silole rings are described. A series of 2,5- and 1,1-difunctionalized siloles have been prepared based on the intramolecular reductive cyclization of diethynylsilanes. Starting from these functionalized siloles, oligo(2,5-silole)s and oligo(1,1-silole)s have been synthesized as model compounds for poly(2,5-silole)s and poly(1,1-silole)s, respectively, which are still veiled target molecules in this field. Some silole-containing π-conjugated cooligomers and copolymers with thiophene, pyrrole, and acetylene π-electron systems have also been prepared. They all have unique photophysical properties such as long-wavelength absorption in the UV/VIS absorption spectra. Some silole-based π-conjugated compounds have also been found to work as new useful materials for organic electroluminescent devices.
HIV type 1 Gag virus-like particle budding from spheroplasts of Saccharomyces cerevisiae (2002)

Expression of retroviral Gag protein in yeast has previously shown Gag targeting to the plasma membrane but little or no production of Gag virus-like particles (VLPs). Here we show that, after removal of the cell wall, the expression of HIV type 1 Gag protein in Saccharomyces cerevisiae spheroplasts allowed simultaneous budding of VLPs from the plasma membrane. Our data show that (i) the VLPs released from yeast spheroplasts were spherical and had morphological features, such as membrane apposed electron-dense layers, characteristic of the immature form of HIV particles; (ii) the VLPs were completely enclosed in the plasma membrane derived from yeast, which is denser than that of higher eukaryotic cells; (iii) the VLP Gag shells remained intact after treatment of nonionic detergent; and (iv) the VLPs were released soon after removal of the cell wall and accumulated up to 300 microg/liter of culture. Our results also show that VLP production was abolished by amino acid substitution of the Gag N-terminal myristoylglycine and impaired when Gag C-terminal deletions were extended beyond the nucleocapsid domain. These results were consistent with those obtained previously in higher eukaryotic expression systems, suggesting that similar Gag domains were used for VLP assembly. We suggest that the system described here offers significant advantages for studying host factors required for VLP budding. The system also may be available for production of vector virus-free VLPs for practical applications such as vaccine development.