gebhart/patrepeval huggingface dataset:
Proton Nuclear Magnetic Resonance Spectroscopy (NMR) Methods for Determining the Purity of Reference Drug Standards and Illicit Forensic Drug Seizures (2005)

A rapid, sensitive, accurate, precise, reproducible, and versatile method for determining the purity of reference drug standards and the routine analysis of illicit drugs and adulterants using proton (1H) Nuclear Magnetic Resonance (NMR) Spectroscopy is presented. The methodology uses a weighed sample dissolved in a deuterated solvent or solvent mixture containing a high purity internal standard. The NMR experiment employs 8 scans using a 45 second delay and 90 degrees pulse. In the determination of purity of reference standards, the number of quantitative determinations available is equal to the number of peak groups that are baseline resolved. The relative standard deviation (RSD) of these signals is usually < 1% for pure standards, and the results agree well with other purity determining methods. This method can also aid in the determination of correct molecular weight for standards containing an unknown number of waters of hydration or an unknown number of acids per drug in salts. Because the molar response for the hydrogen nucleus is 1 for all compounds, and since no separation media are used, only one linearity study is required to test a probe. In the presented study, the linearity of the NMR probe was determined using methamphetamine HCl dissolved in deuterium oxide (D2O) with maleic acid as the internal standard (5 mg) for a range of concentrations from 0.033 to 69.18 mg/ml with a resulting correlation coefficient of >0.9999 for all 6 methamphetamine peak groups. The spectra of complex illicit heroin, methamphetamine, MDMA, and cocaine samples are presented, as well as an extensive list of compounds, their solubilities and the solvent(s) and internal standard used.
A Well-Defined Silica-Supported Tungsten Oxo Alkylidene Is a Highly Active Alkene Metathesis Catalyst (2013)

Grafting (ArO)2W(═O)(═CHtBu) (ArO = 2,6-mesitylphenoxide) on partially dehydroxylated silica forms mostly [(≡SiO)W(═O)(═CHtBu)(OAr)] along with minor amounts of [(≡SiO)W(═O)(CH2tBu)(OAr)2] (20%), both fully characterized by elemental analysis and IR and NMR spectroscopies. The well-defined oxo alkylidene surface complex [(≡SiO)W(═O)(═CHtBu)OAr] is among the most active heterogeneous metathesis catalysts reported to date in the self-metathesis of cis-4-nonene and ethyl oleate, in sharp contrast to the classical heterogeneous catalysts based on WO3/SiO2.
Mechanism of inhibition of human immunodeficiency virus type 1 reverse transcriptase and human DNA polymerases alpha, beta, and gamma by the 5'-triphosphates of carbovir, 3'-azido-3'-deoxythymidine, 2',3'-dideoxyguanosine and 3'-deoxythymidine. A novel RNA template for the evaluation of antiretroviral drugs (1991)

Carbovir (the carbocyclic analog of 2'-3'-didehydro-2',3'-dideoxyguanosine) is a potent inhibitor of human immunodeficiency virus type 1 (HIV-1) replication. Assays were developed to assess the mechanism of inhibition by the 5'-triphosphate of carbovir of HIV-1 reverse transcriptase using either RNA or DNA templates that contain all four natural nucleotides. Carbovir-TP was a potent inhibitor of HIV-1 reverse transcriptase using either template with Ki values similar to that observed by AZT-TP, ddGTP, and ddTTP. The kinetic constants for incorporation of these nucleotide analogs into DNA by HIV-1 reverse transcriptase using either template were similar to the values seen for their respective natural nucleotides. In addition, the incorporation of either carbovir-TP or AZT-TP in the presence of dGTP or dTTP, respectively, indicated that the mechanism of inhibition by these two nucleotide analogs was due to their incorporation into the DNA resulting in chain termination. Carbovir-TP was not a potent inhibitor of DNA polymerase alpha, beta, or gamma, or DNA primase. Given the potent activity of carbovir-TP against HIV-1 reverse transcriptase and its lack of activity against human DNA polymerases, we believe that further evaluation of this compound as a potential drug for the treatment of HIV-1 infection is warranted.
Regulation of tyrosine phosphorylation in neutrophils by the NADPH oxidase. Role of reactive oxygen intermediates (1993)

Neutrophils possess a multicomponent NADPH-oxidase that produces large quantities of superoxide, which can in turn generate other reactive oxygen intermediates. Superoxide and its dismutation product, hydrogen peroxide, are powerful oxidants. Because the activity of certain tyrosine kinases and phosphatases can be affected by their redox state, we considered the possibility that endogenously generated reactive oxygen intermediates (ROI) may alter phosphotyrosine formation and thereby function as intra- or intercellular messengers in neutrophils. Exposure of human neutrophils to exogenous oxidants such as diamide induced marked tyrosine phosphorylation of several cellular proteins. More importantly, activation of the NADPH oxidase in permeabilized neutrophils, by direct stimulation of GTP-binding proteins, also resulted in enhanced tyrosine phosphorylation. The latter was NADPH-dependent, paralleled by production of superoxide, and was inhibited by diphenylene iodonium, an inhibitor of the flavoprotein component of the oxidase. Neutrophils, from a patient with chronic granulomatous disease, which are deficient in the production of ROI, demonstrated no such phosphotyrosine accumulation. We conclude that ROI produced by the NADPH oxidase can regulate tyrosine phosphorylation in granulocytes, possibly by effects of oxidation-sensitive tyrosine kinases and/or phosphatases.
Reduction of Thrombogenicity in Small-diameter Vascular Prostheses Seeded with Autologous Endothelial Cells (1986)

In a canine model small-diameter vascular grafts of knitted Dacron were seeded with autologous endothelial cells. Four weeks after surgery the grafts were removed. Seeded grafts showed a pseudo-intima covered by a monolayer, whereas control grafts showed a cellular lining only at the anastomoses. Graft pretreatment with either fibrin glue or autologous blood in combination with endothelial cell seeding promoted the neointima formation.
Synthetic Artificial Peptidases and Nucleases Using Macromolecular Catalytic Systems (2003)

Effective artificial enzymes have been designed by adopting macromolecular systems for catalyst-substrate complexes. Artificial active sites comprising two or more organic functional groups were built on macromolecular backbones, leading to several types of organic artificial proteases. The activity of metal centers for peptide or DNA hydrolysis was greatly enhanced by attachment to polystyrene, leading to artificial metallopeptidases with substrate selectivity as well as artificial metallonucleases with high catalytic activity for double stranded DNA. A small artificial protease selective for a macromolecular target protein was synthesized. Target-specific artificial proteases can be used as protein-cleaving catalytic drugs.
Adenoviral Vectors Coated with PAMAM Dendrimer Conjugates Allow CAR Independent Virus Uptake and Targeting to the EGF Receptor (2013)

Adenovirus type 5 (Ad) is an efficient gene vector with high gene transduction potential, but its efficiency depends on its native cell receptors coxsackie- and adenovirus receptor (CAR) for cell attachment and α(v)β(3/5) integrins for internalization. To enable transduction of CAR negative cancer cell lines, we have coated the negatively charged Ad by noncovalent charge interaction with cationic PAMAM (polyamidoamine) dendrimers. The specificity for tumor cell infection was increased by targeting the coated Ad to the epidermal growth factor receptor using the peptide ligand GE11, which was coupled to the PAMAM dendrimer via a 2 kDa PEG spacer. Particles were examined by measuring surface charge and size, the degree of coating was determined by transmission electron microscopy. The net positive charge of PAMAM coated Ad enhanced cellular binding and uptake leading to increased transduction efficiency, especially in low to medium CAR expressing cancer cell lines using enhanced green fluorescent protein or luciferase as transgene. While PAMAM coated Ad allowed for efficient internalization, coating with linear polyethylenimine induced excessive particle aggregation, elevated cellular toxicity and lowered transduction efficiency. PAMAM coating of Ad enabled successful transduction of cells in vitro even in the presence of neutralizing antibodies. Taken together, this study clearly proves noncovalent, charge-based coating of Ad vectors with ligand-equipped dendrimers as a viable strategy for efficient transduction of cells otherwise refractory to Ad infection.
Heparan Sulfate Is a Selective Attachment Factor for the Avian Coronavirus Infectious Bronchitis Virus Beaudette (2007)

The avian coronavirus infectious bronchitis virus (IBV) strain Beaudette is an embryo-adapted virus that has extended species tropism in cell culture. In order to understand the acquired tropism of the Beaudette strain, we compared the S protein sequences of several IBV strains. The Beaudette strain was found to contain a putative heparan sulfate (HS)-binding site, indicating that the Beaudette virus may use HS as a selective receptor. To ascertain the requirements of cell-surface HS for Beaudette infectivity, we assayed for infectivity in the presence of soluble heparin as a competitor and determined infectivity in mutant cell lines with no HS or glycosaminoglycan expression. Our results indicate that HS plays a role as an attachment factor for IBV, working in concert with other factors like sialic acid to mediate virus binding to cells, and may explain in part the extended tropism of IBV Beaudette.
Activities of RPR 106972 (a new oral streptogramin), cefditoren (a new oral cephalosporin), two new oxazolidinones (U-100592 and U-100766), and other oral and parenteral agents against 203 penicillin-susceptible and -resistant pneumococci (1996)

Agar dilution was used to determine the MICs of RPR 106972 (a new oral streptogramin), cefditoren (a new oral cephalosporin), two new oxazolidinones (U-100592 and U-100766), and other oral and parenteral agents for 203 penicillin-susceptible and -resistant pneumococci. All pneumococci were inhibited by RPR 106972 at < or = 0.5 microgram/ml. Cefditoren was very active against all pneumococcal groups, with MICs of < or = 2.0 micrograms/ml. Amoxicillin with or without clavulanate was the next most active oral beta-lactam, followed by cefdinir, cefuroxime, cefpodoxime, and cefprozil. U-100592 and U-100766 were very active against all classes of pneumococci, with all MICs < or = 1.0 microgram/ml.
Compressed pattern diagnosis for scan chain failures (2006)

In scan based designs, 10%-30% defects are in scan chains. Hence scan chain fault diagnosis becomes an important process for silicon debug and yield ramp up. With embedded compression techniques getting popular, chain diagnosis on devices with the embedded compression techniques becomes a challenge. In this paper, we provide a general methodology that can be applied for performing chain diagnosis in the context of any embedded compression techniques with any existing chain diagnosis algorithms. The proposed methodology enables seamless reuse of the existing chain diagnosis infrastructure with compressed test data. Experimental results show that with compressed patterns, the chain diagnosis resolution can be enhanced up to one order of magnitude with only 25% of failure cycles collected from ATE, compared to the diagnosis results with uncompressed patterns.
An apertureless near field microscope for fluorescence imaging (2003)

Summary form only given. We demonstrate an apertureless near-field scanning microscope for fluorescence imaging with λ/20 resolution. The use of fluorescence allows artifact free imaging and provides a stringent test that the contrast mechanism is optical in origin.
Reduction of soluble adhesion molecules (sICAM-1, sVCAM-1, and sE-selectin) and vascular endothelial growth factor levels in serum of rheumatoid arthritis patients following multiple intravenous infusions of infliximab. (2004)

Our study, besides a rapid suppression of disease activity, showed that serum soluble adhesion molecules and VEGF concentrations are down-regulated following anti-TNF-alpha antibody therapy combined with MTX. Repeated doses of infliximab sustained the reductions in the soluble adhesion molecules and VEGF concentrations, although they were less effective than the first and second infusions of infliximab.
Detecting non-allelic homologous recombination from high-throughput sequencing data (2015)

Non-allelic homologous recombination (NAHR) is a common mechanism for generating genome rearrangements and is implicated in numerous genetic disorders, but its detection in high-throughput sequencing data poses a serious challenge. We present a probabilistic model of NAHR and demonstrate its ability to find NAHR in low-coverage sequencing data from 44 individuals. We identify NAHR-mediated deletions or duplications in 109 of 324 potential NAHR loci in at least one of the individuals. These calls segregate by ancestry, are more common in closely spaced repeats, often result in duplicated genes or pseudogenes, and affect highly studied genes such as GBA and CYP2E1.
Energy transfer in surface enhanced luminescence (1983)

Radiationless energy transfer from excited dye molecules to silver islands has been studied. The dye is separated from the metal surface by a thin layer of SiOx. When the spacer layer thickness is increased from d=0, an increase in the luminescence intensity is observed. For the low quantum yield dye Basic Fuchsin, a maximum luminescence enhancement of 200 is observed at dSiO≂25 Å, relative to dye on an inert substrate. With further increase in spacer thickness, the luminescence intensity drops rapidly toward the unenhanced value. The results are interpreted in terms of competition between local field enhancement and loss of excitation by energy transfer to the metal.
Recursive equations for hardwired binary adders (1989)

A sum equation for the implementation of parallel hardwired binary adders is introduced. It is suggested that the proposed sum equation, when compared with Ling's high-speed sum, will result in some advantages, and that it can be used in the design of high-speed parallel adders using generally available technologies. It is shown that a 32-bit adder can be designed in three stages using 3 × 8 AND-ORs, 3 × 4 AND-OR-INVERTs and 2 × 4 OR-ANDs CMOS gates, and that a bipolar adder can be designed in four stages, with three-way NANDs and eight-way AND-dotting. In addition, it is suggested that a three-stage 32-bit adder using NANDs and AND-dotting is most likely unrealistic. The paper also describes the design of a number of adders, and discusses the speed, feasibility and complexity of their design.
RNAs containing mitochondrial ND6 and COI sequences present an abnormal structure in chemically induced rat hepatomas (1989)

We have constructed a cDNA library prepared from an hepatoma cell line (HTC cells) and isolated a clone, pHT 13, which corresponds to mRNAs present at a much higher level in rat hepatomas than in normal hepatocytes. The sequence of the pHT 13 insert has been previously published (Nucleic Acids Res. 1988, 16,10935). This clone contains mitochondrial DNA sequences with an abnormal organization, since it includes part of the NADH dehydrogenase subunit 6 (ND6) and of the cytochrome oxidase subunit I (COI) genes separated by 230 bases instead of 9 kb in mitochondrial genome from normal hepatocytes. In this work we show (1) that RNAs homologous to this clone are present in hepatoma cells but not in normal hepatocytes, (2) that a 3 kb fragment of tumor mitochondrial DNA contains both the ND6 and the COI sequences. The abnormal structure of the DNA is confirmed by Southern blot analysis which shows that distinct types of mitochondrial DNAs are present in hepatoma cells.
Effects of Age, Sex, and Ethnicity on the Association Between Apolipoprotein E Genotype and Alzheimer Disease (1997)

The APOE epsilon4 allele represents a major risk factor for AD in all ethnic groups studied, across all ages between 40 and 90 years, and in both men and women. The association between APOE epsilon4 and AD in African Americans requires clarification, and the attenuated effect of APOE epsilon4 in Hispanics should be investigated further.
Thorium(IV) Molecular Clusters with a Hexanuclear Th Core (2011)

Three polynuclear thorium(IV) molecular complexes have been synthesized under ambient conditions from reactions of an amorphous Th precipitate, obtained via hydrolysis, with carboxylate functionalized ligands. The structures of Th(6)(OH)(4)O(4)(H(2)O)(6)(HCO(2))(12)·nH(2)O (1), Th(6)(OH)(4)O(4)(H(2)O)(6)(CH(3)CO(2))(12)·nH(2)O (2), Th(6)(OH)(4)O(4)(H(2)O)(6)(ClCH(2)CO(2))(12)·4H(2)O (3) each consist of a hexanuclear Th core wherein six 9-coordinate Th(IV) cations are bridged by four μ(3)-hydroxo and four μ(3)-oxo groups. Each Th(IV) center is additionally coordinated to one bound "apical" water molecule and four oxygen atoms from bridging carboxylate functionalized organic acid units. "Decoration" of the cationic [Th(6)(μ(3)-O)(4)(μ(3)-OH)(4)](12+) cores by anionic shells of R-COO(-) ligands (R = H, CH(3), or CH(2)Cl) terminates the oligomers and results in the formation of discrete, neutral molecular clusters. Electronic structure calculations at the density functional theory level predicted that the most energetically favorable positions for the protons on the hexanuclear core result in the cluster with the highest symmetry with the protons separated as much as possible. The synthesis, structure, and characterization of the materials are reported.
Using MIC to Accelerate a Typical Data-Intensive Application: The Breadth-first Search (2013)

Data-intensive applications draw more and more attentions in the last few years. The breadth-first search (BFS), a typical data-intensive application, is so widely used that the Graph 500 benchmark uses it to rank supercomputers' performance. The Intel MIC (Many Integrated Core), which is designed for highly parallel computing, hasn't been fully evaluated for data-intensive applications. In this paper, we discuss how to use MIC to accelerate the BFS. Optimizations both for native mode and for offload mode are discussed. About native mode, we propose optimizations for thread level and data-level parallelism. We exploit the thread-level parallelism by relaxing inter-thread dependence. The optimized algorithm is proved to be more scalable. Data-level parallelism is exploited by 512-bits single instruction multiple data (SIMD) instructions. The maximum speedup we further gain is up to 3.4 times. About offload mode, we present an offload algorithm. By careful task partition and communication optimizations, it can gain speedup for large graphs which can't run natively on MIC as the limited memory size. We believe that the work is valuable for using MIC to accelerate the BFS. Meanwhile, it's a general evaluation of the MIC for data-intensive applications.
New Directions for Cultural Virtual Reality: a Global Strategy for Archiving Serving and Exhibiting 3D Computer Model of Cultural Heritage Sites (2005)

International audience
Positron emission tomography provides molecular imaging of biological processes (2000)

Diseases are biological processes, and molecular imaging with positron emission tomography (PET) is sensitive to and informative of these processes. This is illustrated by detection of biological abnormalities in neurological disorders with no computed tomography or MRI anatomic changes, as well as even before symptoms are expressed. PET whole body imaging in cancer provides the means to (i) identify early disease, (ii) differentiate benign from malignant lesions, (iii) examine all organs for metastases, and (iv) determine therapeutic effectiveness. Diagnostic accuracy of PET is 8-43% higher than conventional procedures and changes treatment in 20-40% of the patients, depending on the clinical question, in lung and colorectal cancers, melanoma, and lymphoma, with similar findings in breast, ovarian, head and neck, and renal cancers. A microPET scanner for mice, in concert with human PET systems, provides a novel technology for molecular imaging assays of metabolism and signal transduction to gene expression, from mice to patients: e.g., PET reporter gene assays are used to trace the location and temporal level of expression of therapeutic and endogenous genes. PET probes and drugs are being developed together-in low mass amounts, as molecular imaging probes to image the function of targets without disturbing them, and in mass amounts to modify the target's function as a drug. Molecular imaging by PET, optical technologies, magnetic resonance imaging, single photon emission tomography, and other technologies are assisting in moving research findings from in vitro biology to in vivo integrative mammalian biology of disease.
LC‐MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine (2012)

MAVEN is an open-source software program for interactive processing of LC-MS-based metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple reaction monitoring data or high-resolution full-scan mass spectrometry data. It automatically detects and reports peak intensities for isotope-labeled metabolites. Menu-driven, click-based navigation allows visualization of raw and analyzed data. Here we provide a User Guide for MAVEN. Step-by-step instructions are provided for data import, peak alignment across samples, identification of metabolites that differ strongly between biological conditions, quantitation and visualization of isotope-labeling patterns, and export of tables of metabolite-specific peak intensities. Together, these instructions describe a workflow that allows efficient processing of raw LC-MS data into a form ready for biological analysis.
Surface antigens of human embryonic stem cells: changes upon differentiation in culture* (2002)

We have analysed the surface antigen phenotype of a human embryonic stem (hES) cell line (H7) and the changes that occur upon differentiation induced by retinoic acid, hexamethylene bisacetamide and dimethylsulphoxide. The undifferentiated stem cells expressed Stage Specific Embryonic Antigen-3 (SSEA3), SSEA4, TRA-1-60, and TRA-1-8 but not SSEA1. In these characteristics they closely resemble human embryonal carcinoma (EC) cells derived from testicular teratocarcinomas, and are distinct from murine EC and ES cells. The undifferentiated cells also expressed the liver/bone/kidney isozyme of alkaline phosphatase detected by antibody TRA-2-54, the class 1 major histocompatability antigens, HLA-ABC, and the human Thy1 antigen. Differentiation of hES cells was induced by retinoic acid, HMBA and DMSO with the appearance of various cell types including neurons and muscle cells. The surface antigens characteristically expressed by hES cells were down-regulated following induction of differentiation and other antigens appeared, notably several ganglioside glycolipids detected by antibodies VIN-IS-56 (GD3 and GD2), VIN-2PB-22 (GD2), A2B5 (GT3) and ME311 (9-O-acetyl-GD3). Whereas the expression of HLA was slightly down-regulated upon differentiation, its expression was strongly induced by interferon-y in both the undifferentiated and the differentiated cells, although the induction in the differentiated cultures was considerably stronger than in the stem cells. In all of these features the human ES cells, and their pattern of differentiation, resembled the pluripotent human EC cell line NTERA-2 although clearly the range of cells generated by the hES cells was considerably greater.