gebhart/patrepeval huggingface dataset:
Oxidative susceptibility of low density lipoprotein subfractions is related to their ubiquinol-10 and alpha-tocopherol content. (1994)

The conjugated polyene fatty acid parinaric acid (PnA) undergoes a stoichiometric loss in fluorescence upon oxidation and can be used to directly monitor peroxidative stress within lipid environments. We evaluated the course of potentially atherogenic oxidative changes in low density lipoproteins (LDL) by monitoring the oxidation of PnA following its incorporation into buoyant (p = 1.026-1.032 g/ml) and dense (p = 1.040-1.054 g/ml) LDL subfractions. Copper-induced oxidation of LDL-associated PnA exhibited an initial lag phase followed by an increased rate of loss until depletion. Increased PnA oxidation occurred immediately after the antioxidants ubiquinol-10 and alpha-tocopherol were consumed but before there were marked elevations in conjugated dienes. Despite differences in sensitivity to early oxidation events, PnA oxidation and conjugated diene lag times were correlated (r = 0.582; P = 0.03), and both indicated a greater susceptibility of dense than buoyant LDL in accordance with previous reports. The greater susceptibility of PnA in dense LDL was attributed to reduced levels of ubiquinol-10 and alpha-tocopherol, which were approximately 50% lower than in buoyant LDL (mol of antioxidant/mol of LDL) and together accounted for 80% of the variation in PnA oxidation lag times. These results suggest that PnA is a useful probe of LDL oxidative susceptibility and may be superior to conjugated dienes for monitoring the initial stages of LDL lipid peroxidation. Differences in oxidative susceptibility among LDL density subfractions are detected by the PnA assay and are due in large part to differences in their antioxidant content.
Which Model to Use for Cortical Spiking Neurons? (2004)

We discuss the biological plausibility and computational efficiency of some of the most useful models of spiking and bursting neurons. We compare their applicability to large-scale simulations of cortical neural networks.
Analysis of the Change in the Carrier Concentration of SnO2 Thin Film Gas Sensor (1994)

Electrical properties and the number of unpaired electrons localized in oxygen vacancies of SnO 2 thin films were quantitatively analyzed using the van der Pauw method and ESR spectra, respectively, in order to clarify the source of carrier electrons induced on gas sensing. The concentration of carriers generated was related to the amount of unpaired electrons localized in oxygen vacancies which were produced under the flammable gas atmosphere. No adsorbed oxygen was detected by ESR. From these results it is concluded that most of the carrier electrons were supplied not from adsorbed oxygen on SnO 2 surface but from oxygen vacancies of the SnO 2 surface layer.
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems (2011)

The errors and biases we report have implications for the use and the interpretation of Illumina sequencing data. GAIIx and HiSeq data sets show slightly different error profiles. Quality filtering is essential to minimize downstream analysis artifacts. Supporting previous recommendations, the strand-specificity provides a criterion to distinguish sequencing errors from low abundance polymorphisms.
Factors affecting expression of glycolipid tumor antigens: influence of ceramide composition and coexisting glycolipid on the antigenicity of gangliotriaosylceramide in murine lymphoma cells. (1983)

Gangliotriaosylceramide (Gg3Cer) was previously described as a tumor-associated antigen in murine L5178Y lymphoma [Young, W. W., Jr., and Hakomori, S., Science (Wash. D.C.), 211: 487-489, 1981]. This paper describes the major factors affecting the expression of Gg3Cer at the surface of various clones of L5178Y lymphoma. Of 26 sublines that were recloned, six cell lines showing different degrees of Gg3Cer expression at the cell surface were used for analysis of the glycolipid composition as related to its cell surface antigenicity. Three remarkable correlations between glycolipid composition and the antigenicity of Gg3Cer have been found: (a) high-expressor sublines were characterized by a large proportion of a unique molecular species of Gg3Cer having alpha-hydroxypalmitic acid in its ceramide moiety in striking contrast to low expressors which did not contain this molecular species; (b) low expressors contained a large quantity of ganglio-N-tetraosylceramide (Gg4Cer) and NeuAc alpha 2 leads to 3Gal beta 1 leads to 3GalNAc beta 1 leads to 4Gal beta 1 leads to 4Glc beta 1 leads to 1 Cer (GM1b) gangliosides, whereas these glycolipids were almost absent in high-expressor clones; and (c) nonexpressors, which were converted from the high expressors in vivo through immunotherapy with the monoclonal antibodies to Gg3Cer, contained a large quantity of ganglio-N-tetraosylceramide and NeuAc alpha 2 leads to 3Gal beta 1 leads to 3GalNAc beta 1 leads to 4Gal beta 1 leads to 4Glc beta 1 leads to 1Cer. The nonexpressors should have an induced enzyme system to metabolize Gg3Cer to ganglio-N-tetraosylceramide and NeuAc alpha 2 leads to 3Gal beta 1 leads to 3GalNAc beta 1 leads to 4Gal beta 1 leads to 4Glc beta 1 leads to 1Cer. Three factors, i.e., ceramide composition, coexisting glycolipids, and an antibody-dependent glycolipid change, are therefore important in determination of glycolipid antigenicity and antigen modulation by antibodies. The ceramide composition may affect glycolipid organization in membranes, and the coexisting glycolipid having a longer carbohydrate chain may mask the accessibility of antibody to the antigenic glycolipid. The antigenic modulation by the action of the antibody in vivo may be based on activation of a new glycosyltransferase.
The angiogenesis inhibitor tnp-470 effectively inhibits human neuroblastoma xenograft growth, especially in the setting of subclinical disease. (2001)

Tumor vascularity is highly correlated with disease outcome in neuroblastoma. Thus, novel therapeutics that target the vascular endothelium are candidates for incorporation into clinical trials. We therefore examined the effect of TNP-470 on human neuroblastoma growth in mouse models reflecting both clinically evident and minimal disease. Mice were inoculated s.c. or by tail vein injection with 10(7) human neuroblastoma-derived CHP-134 cells and treated with TNP-470 (100 mg/kg/dose s.c. three times a week or by continuous infusion) or saline. Treatment was given as a single agent in established xenografts, 10 days after 450 mg/kg of cyclophosphamide, or 12 h after tumor inoculation. Tumor growth rate was markedly inhibited in mice receiving TNP-470 administered alone both s.c. and by continuous infusion with a treatment to control ratio (T:C) at day 16 of 0.3 (P < 0.001) and a T:C at day 30 of 0.4 (P = 0.029) for each dosing method, respectively. TNP-470 also significantly inhibited tumor growth when administered following cyclophosphamide (T:C at day 30 = 0.2, P < 0.001) and inhibited disease establishment when given shortly after xenograft inoculation (T:C at day 30 = 0.1, P < 0.001) or tail vein injection. TNP-470 was shown to directly inhibit angiogenesis by Matrigel assay (P =.010) and to increase the apoptotic index in treated tumors. These data show that TNP-470 is a potent inhibitor of human neuroblastoma growth rate and tumorigenicity. We speculate that TNP-470 may be a useful adjuvant therapy for high-risk neuroblastoma patients, particularly when used in settings of minimal disease status.
Diagnostic and Prognostic MicroRNAs in Stage II Colon Cancer (2008)

MicroRNAs (miRNA) are a class of small noncoding RNAs with important posttranscriptional regulatory functions. Recent data suggest that miRNAs are aberrantly expressed in many human cancers and that they may play significant roles in carcinogenesis. Here, we used microarrays to profile the expression of 315 human miRNAs in 10 normal mucosa samples and 49 stage II colon cancers differing with regard to microsatellite status and recurrence of disease. Several miRNAs were differentially expressed between normal tissue and tumor microsatellite subtypes, with miR-145 showing the lowest expression in cancer relative to normal tissue. Microsatellite status for the majority of cancers could be correctly predicted based on miRNA expression profiles. Furthermore, a biomarker based on miRNA expression profiles could predict recurrence of disease with an overall performance accuracy of 81%, indicating a potential role of miRNAs in determining tumor aggressiveness. The expression levels of miR-320 and miR-498, both included in the predictive biomarker, correlated with the probability of recurrence-free survival by multivariate analysis. We successfully verified the expression of selected miRNAs using real-time reverse transcription-PCR assays for mature miRNAs, whereas in situ hybridization was used to detect the accumulation of miR-145 and miR-320 in normal epithelial cells and adenocarcinoma cells. Functional studies showed that miR-145 potently suppressed growth of three different colon carcinoma cell lines. In conclusion, our results suggest that perturbed expression of numerous miRNAs in colon cancer may have a functional effect on tumor cell behavior, and, furthermore, that some miRNAs with prognostic potential could be of clinical importance.
Improved Recombinant Retroviral Titers Utilizing Trichostatin A (2000)

Recombinant retroviruses are a common vehicle to deliver an exogenous gene to a target cell, which makes them a useful tool in the field of gene therapy. A major drawback to using recombinant retroviruses is the low titer achieved, resulting in a limited number of target cells infected and subsequently poor expression of a transgene. In this study, we created an ecotropic producer cell line that contained recombinant mouse nerve growth factor (NGF) and the reporter gene LacZ. This cell line, termed psi 2/LIG/NGF, was treated with the drug trichostatin A, an inhibitor of histone deacetylase. At a concentration of 3 microM trichostatin A, the retroviral titer of this producer cell line was increased 34-fold relative to untreated control cells and 3.4-fold compared to the commonly used hyperacetylating compound sodium butyrate. Producer cells treated with trichostatin A also increased the number of primary rat marrow stromal cells infected 5.8-fold compared to untreated producer cells. These results offer a simple and effective solution for converting low titer producer cell clones to higher titer clones, which can be easily tested and applied.
Conserved structural features in eukaryotic and prokaryotic fucosyltransferases (1998)

Fucosyltransferases are the enzymes transferring fucose from GDP-Fuc to Gal in an alpha1,2-linkage and to GlcNAc in alpha1,3-, alpha1,4-, or alpha1,6-linkages. Since all fucosyltransferases utilize the same nucleotide sugar, their specificity will probably reside in the recognition of the acceptor and in the type of linkage formed. A search of nucleotide and protein databases yielded more than 30 sequences of fucosyltransferases originating from mammals, chicken, nematode, and bacteria. On the basis of protein sequence similarities, these enzymes can be classified into four distinct families: (1) the alpha-2-fucosyltransferases, (2) the alpha-3-fucosyltransferases, (3) the mammalian alpha-6-fucosyltransferases, and (4) the bacterial alpha-6-fucosyltransferases. Nevertheless, using the sensitive hydrophobic cluster analysis (HCA) method, conserved structural features as well as a consensus peptide motif have been clearly identified in the catalytic domains of all alpha-2 and alpha-6-fucosyltranferases, from prokaryotic and eukaryotic origin, that allowed the grouping of these enzymes into one superfamily. In addition, a few amino acids were found strictly conserved in this family, and two of these residues have been reported to be essential for enzyme activity for a human alpha-2-fucosyltransferase. The alpha-3-fucosyltransferases constitute a distinct family as they lack the consensus peptide, but some regions display similarities with the alpha-2 and alpha-6-fucosyltranferases. All these observations strongly suggest that the fucosyltransferases share some common structural and catalytic features.
Peptide Design Aided by Neural Networks:  Biological Activity of Artificial Signal Peptidase I Cleavage Sites (1998)

De novo designed signal peptidase I cleavage sites were tested for their biological activity in vivo in an Escherichia coli expression and secretion system. The artificial cleavage site sequences were generated by two different computer-based design techniques, a simple statistical method, and a neural network approach. In previous experiments, a neural network was used for feature extraction from a set of known signal peptidase I cleavage sites and served as the fitness function in an evolutionary design cycle leading to idealized cleavage site sequences. The cleavage sites proposed by the two algorithms were active in vivo as predicted. There seems to be an interdependence between several cleavage site features for the constitution of sequences recognized by signal peptidase. It is concluded that neural networks are useful tools for sequence-oriented peptide design.
Development of Herbicide Resistant Plant Through Plant Tissue Culture (1987)

This study was conducted to select and develop herbicide resistant plant through tissue culture. Growth response of seedlings and callis of various rice varieties with Echinochloa species was assessed under the treatment of various rates of butachlor [N-(butoxy methyl)-2-chloro-2', 6'-diethyl acetamide] and simetryne [2,4-bis(ethyl amino)-6-methyl thio-1,3,5-triazine]. Further, succinate dehydrogenase activity was determined in herbicide treated callus to characterize different response of plants to herbicide. Rice variety like Sangpung showed relative resistance in both callus and seedling states against butachlor, indicating maintenance of resistance. However, in the simetryne treatment, the similar response was not observed in callus and seedling state, although there was a great different response among plant materials against simetryne. Rice variety which exhibited resistance in callus and seedling states showed low succinate dehydrogenase inhibition index. Succinate dehydrogenase inhibition index can be used as an important marker characters to differentiate varietal response of plant to herbicide. Rice plant was differentiated from butachlor and simetryne tolerant callus treated at M is growing under the growth chamber and can be used for resistant source.
Detailed Toxicity Studies of Liposomal Gadolinium-DTPA (1991)

Acute, subacute, and delayed toxicity testing was assessed in mice for liposomal gadolinium-DTPA (Gd-DTPA), blank liposomes, and nonliposomal Gd-DTPA. In the subacute experiments mice were injected intravenously (IV) with 0.3 mmol/kg Gd-DTPA per day for 30 days in the form of either free Gd-DTPA, liposomal Gd-DTPA, or an equivalent amount of lipid in blank liposomes without Gd-DTPA. The interpolated acute LD50 of liposomal and nonliposomal Gd-DTPA, estimated as a means of identifying the approximate level, was similar (LD50 = 5.7 mmol/kg Gd-DTPA). In subacute toxicity testing, prolonged high doses of liposomal Gd-DTPA caused splenomegaly, cardiomegaly, lymphocytopenia and hypergammaglobulinemia (P less than .05). Nonliposomal Gd-DTPA caused mild cardiomegaly and altered liver enzymes (P less than .05). Blank liposomes caused relatively mild splenomegaly (P less than .05) but few other changes. Delayed testing three months after the subacute testing showed that most of the changes caused by the liposomal Gd-DTPA were reversible.
Stimulation of Dopamine Synthesis in Caudate Nucleus by Intrastriatal Enkephalins and Antagonism by Naloxone (1978)

The intraventricular injection of methionine-enkephalin (50 to 100 micrograms) or [d-Ala2]-methionine-enkephalinamide (1.5 to 12 micrograms), a synthetic enkephalin analog resistant to enzyme degradation, caused a marked dose-dependent increase in dihydroxyphenylacetic acid and homovanillic acid concentrations in the rat striatum. The [d-Ala2] analog increased the accumulation of dopa in the striatum after aromatic amino acid decarboxylase inhibition, indicating that it increased dopamine synthesis. At the highest doses used both enkephalins failed to modify brain serotonin metabolism. The monolateral microinjection of the [d-Ala2]] analog (3 to 6 micrograms) into the caudate nucleus increased the concentration of dihydroxyphenylacetic acid in the injected side, whereas bilateral injection increased the concentration of this compound in both caudate nuclei and caused catalepsy. The stimulant effect of the [d-Ala2] analog on dopamine synthesis in the striatum persisted after destruction of striatal postsynaptic dopamine receptors with kainic acid. The biochemical and behavioral effects of enkephalins were prevented by naloxone, a specific narcotic antagonist. The results indicate that enkephalins stimulate dopamine synthesis by an action on opioid receptors localized on dopaminergic nerve terminals.
Unique single‐domain antigen binding fragments derived from naturally occurring camel heavy‐chain antibodies (1999)

The humoral immune response of camels, dromedaries and llamas includes functional antibodies formed by two heavy chains and no light chains. The amino acid sequence of the variable domain of the naturally occurring heavy-chain antibodies reveals the necessary adaptations to compensate for the absence of the light chain. In contrast to the conventional antibodies, a large proportion of the heavy-chain antibodies acts as competitive enzyme inhibitors. Studies on the dromedary immunoglobulin genes start to shed light on the ontogeny of these heavy-chain antibodies. The presence of the heavy-chain antibodies and the possibility of immunizing a dromedary allows for the production of antigen binders consisting of a single domain only. These minimal antigen-binding fragments are well expressed in bacteria, bind the antigen with affinity in the nM range and are very stable. We expect that such camelid single domain antibodies will find their way into a number of biotechnological or medical applications. The structure of the camelid single domain is homologous to the human VH, however, the antigen-binding loop structures deviate fundamentally from the canonical structures described for human or mouse VHs. This has two additional advantages: (1) the camel or llama derived single domain antibodies might be an ideal scaffold for anti-idiotypic vaccinations; and (2) the development of smaller peptides or peptide mimetic drugs derived from of the antigen binding loops might be facilitated due to their less complex antigen binding site. Copyright © 1999 John Wiley & Sons, Ltd.
Noise Reduction in Image Sequences Using Motion-Compensated Temporal Filtering (1984)

Noise in television signals degrades both the image quality and the performance of image coding algorithms. This paper describes a nonlinear temporal filtering algorithm using motion compensation for reducing noise in image sequences. A specific implementation for NTSC composite television signals is described, and simulation results on several video sequences are presented. This approach is shown to be successful in improving image quality and also improving the efficiency of subsequent image coding operations.
25 years of quantum cryptography (1996)

The fates of SIGACT News and Quantum Cryptography are inseparably entangled. The exact date of Stephen Wiesner's invention of "conjugate coding" is unknown but it cannot be far from April 1969, when the premier issue of SIGACT News ---or rather SICACT News as it was known at the time---came out. Much later, it was in SIGACT News that Wiesner's paper finally appeared [74] in the wake of the first author's early collaboration with Charles H. Bennett [7]. It was also in SIGACT News that the original experimental demonstration for quantum key distribution was announced for the first time [6] and that a thorough bibliography was published [19]. Finally, it was in SIGACT News that Doug Wiedemann chose to publish his discovery when he reinvented quantum key distribution in 1987, unaware of all previous work but Wiesner's [73, 5].Most of the first decade of the history of quantum cryptography consisted of this lone unpublished paper by Wiesner. Fortunately, Bennett was among the few initiates who knew of Wiesner's ideas directly from the horse's mouth. His meeting with the first author of this column in 1979 was the beginning of a most fruitful lifelong collaboration. It took us five more years to invent quantum key distribution [4], which is still today the best-known application of quantum mechanics to cryptography. The second author joined in slightly later, followed by a few others. But until the early 1990's, no more than a handful of people were involved in quantum cryptographic research. Since then, the field has taken off with a vengeance, starting with Artur K. Ekert's proposal to use quantum nonlocality for cryptographic purposes [33].The golden age started in earnest when Ekert organized the first international workshop on quantum cryptography in Broadway, England, in 1993. Since then, many conferences have been devoted at least partly to quantum cryptography, which has become a major international topic. The purpose of the aforementioned 1993 bibliography in SIGACT News was to cite as much as possible all papers ever written on the subject, including unpublished manuscripts: there were 57 entries in total. Today, such an undertaking would be nearly impossible owing to the explosion of new research in the field.The purpose of this column is to give an overview of the current research in quantum cryptography. It is not our intention to be exhaustive and we apologize in advance to any researcher whose work we may have omitted. Note that we do not necessarily agree with the claims in every paper mentioned here: this column should not be construed as a seal of approval!
Carbon Nanotubes Filled with a Chemotherapeutic Agent: A Nanocarrier Mediates Inhibition of Tumor Cell Growth (2008)

A reversible filling-emptying process could be performed successfully within this work. This highlights the potential of CNTs for applications in the field of drug delivery.
Synthesis of Epothilones: Stereoselective Routes to Epothilone B (1998)

In connection with our studies of the total syntheses of epothilones we report our efforts on the syntheses of epothilone B using a macro-lactonization and a metathesis approach. Key reaction for the solution of the acyclic stereoselection is a stereoselective aldol reaction.