gebhart/patrepeval huggingface dataset:
Effect of acetylated and deacetylated 2-aminofluorene adducts on in vitro DNA synthesis. (1982)

We have constructed primed phi X174 DNA templates containing either acetylated or deacetylated aminofluorene adducts at the C-8 position of guanine. T4 DNA polymerase terminates synthesis one nucleotide before the acetylated adducts but incorporates an additional nucleotide opposite the deacetylated guanylaminofluorene. These observations can be explained by the known preferred conformations of the acetylated and deacetylated guanosinylaminofluorene nucleosides--the former favoring the syn conformation (so that in DNA the guanine is displaced from the helix by the fluorene ring) and the latter preferring the anti conformation (which allows normal base pairing of the guanine with cytosine). A similar differentiation between the two adducts was found with Escherichia coli DNA polymerase I. In contrast, avian myeloblastosis virus (AMV) reverse transcriptase, which terminated with a nucleotide inserted opposite the acetylated adducts, was less able to do so at the deacetylated adducts. The nucleoside incorporated by AMV reverse transcriptase opposite the acetylated adduct was exclusively cytidine, which suggests regular base pairing with the reacted guanosine nucleoside in the anti conformation; however, synthesis was completely blocked and unable to continue beyond this point. The differences between the termination patterns of the prokaryotic enzymes and AMV reverse transcriptase indicates that specific properties of a replicating polymerase can influence the conformation of a reacted nucleoside in the DNA, thus altering its recognition and possibly its mutagenic activity.
The silent risks of blood transfusion (2008)

The benefits of blood transfusion have never been conclusively demonstrated, but evidence of transfusion-related harm continues to accumulate. Given the transfusion triggers that currently predominate in clinical practice it appears that clinical outcomes could improve significantly with more widespread adoption of restrictive transfusion strategies.
Circulating Monoclonal B Lymphocytes in Non-Hodgkin's Lymphoma (1984)

Using a sensitive flow cytometric method ("kappa-lambda analysis"), we have found monoclonal B lymphocytes in the blood of 71 of 91 patients with non-Hodgkin's lymphoma. The presence of the B lymphocytes was independent of the histologic subclassification of the patient's disease. When we performed simultaneous analysis of the surface light-chain type in tumor tissue obtained by biopsy, the apparent light-chain type of the blood monoclonal cells corresponded with that of the tumor in 21 of 23 patients (P = 0.03). There was no correlation of the presence of these cells in the blood with morphologic evidence of bone-marrow involvement by lymphoma, but there was a strong correlation with clinical staging. Studies performed during prolonged clinical remission showed that whereas 16 of 25 patients with nodular non-Hodgkin's lymphoma had persistence of monoclonal lymphocytes, none of the 14 patients with diffuse histiocytic lymphoma in remission had these findings (P less than 0.005). Our analysis for B-cell clonal excess demonstrates the persistence of circulating monoclonal lymphocytes during complete remission in patients with forms of lymphoma that have a high probability of relapse, but we did not find these cells in patients in remission from categories of lymphoma in which prolonged remission is associated with cure. It is possible that the circulating monoclonal lymphocytes in patients with lymphoma are malignant cells, and their disappearance or persistence after remission may have prognostic importance.
Control conditions in the fear-potentiated startle response paradigm (1997)

In the present study, the fear-potentiated startle response paradigm was modified in order to investigate the decrease in control startle levels often observed after administration of anxiolytic drugs. The within-animal comparison of control startle amplitudes and fear-potentiated startle amplitudes normally used was replaced by a between-animal comparison. Moreover, the experimental design was extended with an additional control group, a no-shock group. The anxiolytics diazepam and chlordiazepoxide were used as pharmacological tools. The main findings were that both benzodiazepines dose-dependently reduced control startle amplitudes and no-shock startle amplitudes equally, suggesting that shock-associated contextual cues are not responsible for the drug-induced decrease in control startle amplitudes in the fear-potentiated startle response paradigm.
Determination of the cleavage site involved in C-terminal processing of penicillin-binding protein 3 of Escherichia coli (1989)

Chromatographic peptide mapping of lysyl endopeptidase digests of penicillin-binding protein 3 (PBP 3) of Escherichia coli revealed peptides that differed in retention time between the precursor and mature forms. The peptides were purified from a processing-defective (prc) mutant and a wild-type (prc+) strain. These peptides were identified as the C-terminal region of the precursor form and mature PBP 3 by amino acid sequencing. Each of the C-terminal peptides was cleaved into two fragments by trypsin digestion. By sequencing the resultant carboxyl-side fragment derived from the mature form, it was concluded that the C-terminal residue of mature PBP 3 was Val-577, and thus the Val-577-Ile-578 bond is the cleavage site for processing. This conclusion was consistent with the amino acid compositions of the relevant peptides, which suggested that the peptide from the cleavage site to the end of the deduced sequence (Ile-578-Ser-588) was present in the precursor but absent in the mature form. One lysyl peptide bond resisted both lysyl endopeptidase and trypsin and remained uncleaved in the peptide analyzed above.
Injection of Antisense RNA Specific for E-Cadherin Demonstrates That E-Cadherin Facilitates Compaction, the First Differentiative Step of the Mammalian Embryo (1992)

We have investigated the effect of antisense E-cadherin RNA in the preimplantation mouse embryo. Antisense RNA was injected into each cell of two-cell embryos that were cultured for 2 days until the normal time of compaction and scored for abnormalities. Embryos injected with the antisense RNA showed delayed compaction compared to the embryos injected with control, or sense, RNA. Delayed cleavage was not the cause because nuclear staining with Hoechst dye 33258 showed about the same number of nuclei in both uncompacted embryos injected with antisense RNA compared with compacted embryos injected with sense RNA at the same hours post human chorionic gonadotropin (hCG). Immunofluorescence with a monoclonal antibody to E-cadherin was markedly diminished in embryos injected with antisense RNA compared with control, injected embryos, suggesting that the observed delayed compaction is due to the inhibition of E-cadherin gene expression by antisense RNA. Embryos injected with antisense RNA eventually compacted and then expressed E-cadherin, but at lower apparent levels than controls. Injection of a single blastomere at the two-cell stage created half-embryo abnormalities.
Synthesis and structure-activity study of protease inhibitors. I. (Guanidinophenyl)propionate and guanidinocinnamate derivatives. (1984)

Guanidino-ester derivatives were synthesized and evaluated for inhibitory activities against trypsin, plasmin, kallikrein, thrombin and Cl esterase, as well as on in vitro complement-mediated hemolysis. Among the compounds synthesized, phenyl α-ethyl-p-guanidinocinnamate (IVg) and phenyl α-propyl-p-guanidinocinnamate (IVh) exhibited potent and selective Cl esterase inhibition (IC50 : 7×10-6 and 6×10-6 M, respectively) and 6-methyl-3-pyridyl α-ethyl-p-guanidinocinnamate (IVi) markedly suppressed complement-mediated hemolysis (86% inhibition at 1×10-3M).
A specific fluorogenic assay for N‐acetylgalactosamine‐4‐sulphatase activity using immunoadsorption (1990)

A method combining immune capture and enzyme detection by fluorochemistry has been developed for the diagnostic assay of N-acetylgalactosamine-4-sulphatase (4-sulphatase). The procedure uses a monoclonal antibody 4-S 4.1 to immunoadsorb 4-sulphatase specifically from complex protein samples containing other sulphatases, and 4-methylumbelliferyl sulphate to detect captured 4-sulphatase. The assay provides an accurate and simple method for the diagnosis of Maroteaux-Lamy syndrome (Mucopolysaccharidosis type VI).
Design and Creation of New Nanomaterials for Therapeutic RNAi (2007)

RNA interference is an evolutionarily conserved gene-silencing phenomenon that shows great promise for developing new therapies. However, the development of small interfering RNA (siRNA)-based therapies needs to overcome two barriers and be able to (i) identify chemically stable and effective siRNA sequences and (ii) efficiently silence target genes with siRNA doses that will be clinically feasible in humans. Here, we report the design and creation of interfering nanoparticles (iNOPs) as new systemic gene-silencing agents. iNOPs have two subunits: (i) a well-defined functionalized lipid nanoparticle as a delivery agent and (ii) a chemically modified siRNA for sustained silencing in vivo. When we injected iNOPs containing only 1-5 mg kg(-1) siRNA into mice, an endogenous gene for apolipoprotein B (apoB) was silenced in liver, plasma levels of apoB decreased, and total plasma cholesterol was lowered. iNOP treatment was nontoxic and did not induce an immune response. Our results show that these iNOPs can silence disease-related endogenous genes in clinically acceptable and therapeutically affordable doses.
Tetra-O-methyl nordihydroguaiaretic acid induces G2 arrest in mammalian cells and exhibits tumoricidal activity in vivo. (2001)

The transcription inhibitor tetra-O-methyl nordihydroguaiaretic acid (M4N) was found to arrest the proliferation of C3, C33a, CEM-T4, and TC-1 cells in culture at the G2 stage of the cell cycle. Investigation into the mechanism of arrest revealed that M4N reduces mRNA levels and subsequent protein production of the cyclin-dependent kinase CDC2, resulting in the inactivation of the CDC2/cyclin B complex (maturation promoting factor). When injected intratumorally in a C3-cell induced C57bl/6 mouse tumor model system, M4N demonstrated substantial tumoricidal activity that correlated with a reduction in tumor cell CDC2 protein levels. These findings suggest that M4N may be a useful chemotherapeutic agent for the control of unregulated cellular proliferation.
New Circulin Macrocyclic Polypeptides from Chassalia parvifolia (2000)

Four new macrocyclic polypeptides were isolated and identified from an extract of the tropical tree Chassalia parvifolia. Circulins C-F are 29-30 amino acid cyclic peptides in which the entire primary amino acid chain is covalently cyclized via peptide bonds. Their structures were deduced from a combination of FABMS analyses, N-terminal Edman degradation, endoproteinase digestion, and amino acid analyses. All the peptides share a high degree of sequence homology and contain six cysteine residues forming three intramolecular disulfide bridges. Circulins C-F inhibited the cytopathic effects of in vitro HIV-1 infection with EC(50) values of 50-275 nM.
Effect of GDNF on neuroblast proliferation and photoreceptor survival: additive protection with docosahexaenoic acid. (2001)

These results show that GDNF stimulated the cell cycle progression, leading to neuroblast proliferation at early stages of development, and delayed the onset of apoptosis later on, improving differentiation and acting as a trophic factor for photoreceptors. The combination of GDNF with DHA had an additive effect both on photoreceptor survival and on opsin expression. Preservation of mitochondrial function may be involved in the antiapoptotic effect of both factors.
The impact of viewing geometry on vision through the atmosphere (2002)

An increase in the off-nadir viewing angle for an airborne visible/near-infrared through short-wave infrared (VNIR/SWIR) imaging spectrometer leads to a decrease in upward atmospheric transmittance and an increase in line-of-sight scattered path radiance. These effects combine to reduce the spectral contrast between different materials in the sensed signal. We analyze the impact of viewing angle on material discriminability for 237 materials over a wide range of conditions. Material discriminability is quantified using a statistical algorithm that employs a subspace model to represent the set of spectra for a material as conditions vary. We show that reliable material discrimination is possible over a range of conditions even for large off-nadir viewing angles. We illustrate the performance of material identification over different viewing angles using simulated forest hyperspectral images.
Alpha 2-adrenergic receptor subtypes: subtle mutation of the alpha 2A-adrenergic receptor in vivo by gene targeting strategies reveals the role of this subtype in multiple physiological settings. (1998)

Alpha 2-adrenergic receptors (alpha 2AARs) are coupled by pertussis-toxin sensitive G proteins to various effectors, including adenylyl cyclase and ion channels. The alpha 2AARs respond to endogenous norepinephrine and epinephrine to elicit a variety of physiological responses, including inhibition of neurotransmitter release, suppression of insulin release from pancreatic beta cells, activation of platelet aggregation, and contraction of arteriolar smooth muscle. Three distinct alpha 2AR subtypes (alpha 2A, alpha 2B, alpha 2C) have been characterized by both pharmacological and molecular biological approaches; however, the lack of subtype-specific ligands has precluded an understanding of the physiological relevance of each subtype. Previous studies demonstrated that mutation of a conserved aspartate residue in the alpha 2AAR to asparagine (D79N alpha 2AAR) resulted in a receptor that retained its ability to inhibit voltage-gated Ca2+ channels and cAMP production but was unable to activate K+ currents in AtT20 cells (Surprenant et al., 1992). To explore the physiological role of the alpha 2AAR subtype and to evaluate the selectivity of alpha 2AAR effects with respect to various signal transduction pathways, we used gene targeting in embryonic stem cells to create a mouse line that expresses the mutant D79N alpha 2AAR instead of the wild-type alpha 2AAR. We established a D79N alpha 2AAR mouse line and characterized various alpha 2AAR-mediated physiological functions in these mutant mice. Because the in vivo D79N alpha 2AAR is expressed at a reduced density relative to wild-type alpha 2A and is not selectively uncoupled from a single signal transduction pathway, our findings of losses of alpha 2AAR-mediated functions in the D79N mice reflect a requirement for the alpha 2AAR subtype but do not reveal the importance of a specific signal transduction pathway. The alpha 2AAR subtype appears to mediate reduction in blood pressure following alpha 2A agonist administration as well as sedative, anesthetic-sparing, and analgesic responses to alpha 2AAR agonists. Therefore, the alpha 2AAR subtype appears to mediate a majority of the clinically relevant responses associated with alpha 2AAR agonist treatment.
Circulating Epithelial Cells in Patients with Benign Colon Diseases (2011)

These results indicate that patients with benign inflammatory colon diseases in particular can harbor viable circulating epithelial cells that are detectable with current CTC assays. This finding points to the need for further molecular characterization of circulating epithelial cells and has important implications for the use of CTC testing.
Diet-gene interactions in human lipoprotein metabolism. (1997)

Genetic variation can influence the effects of hypocholesterolemic dietary interventions on lipoproteins involved in coronary artery disease (CAD). Individuals with the E4 allelic variant of the apo E gene exhibit greater low-density lipoprotein (LDL) cholesterol reductions on low-fat, low-cholesterol diets than subjects with other alleles. Another apolipoprotein structural variant, apo A-IV-2, attenuates the response of LDL cholesterol to dietary cholesterol. Other studies have associated lipoprotein response to dietary modifications with DNA polymorphisms in the genes for apo B and the LDL receptor, and in the promoter region of the apo A-I gene. Studies in our laboratory involving variation in dietary fat and carbohydrate intake have demonstrated that alleles at the apo E gene locus are associated with changes in large, buoyant but not smaller, denser LDL subclasses. On the other hand, a low-fat diet induces a reduction in small, dense LDL in individuals with a genetically influenced metabolic profile characterized by a predominance of these particles. Moreover, reductions in LDL cholesterol and apo B in these subjects are greater than in the majority of subjects with larger LDL. Since in humans a predominance of small LDL signifies a higher risk for coronary artery disease than that associated with larger LDL, metabolic and genetic factors contributing to the small LDL trait may account for a substantial portion of the coronary risk benefit attributed to reduced-fat diets. Studies in large population groups or in suitable animal models will be necessary to determine the impact of genetic influences on dietary response affecting lipoprotein metabolism and their interactions with other environmental and hormonal factors.
Use of a concentric-arc grating as a thin-film spectrograph for guided waves (1980)

We describe a thin-film spectrograph for guided optical or surface acoustic waves which involves wave diffraction from a concentric-arc grating in a slab waveguide. In this spectrograph, diffracted waves in the waveguide form spectra of various orders which are in focus on a circle similar to the Rowland circle of an ordinary grating spectrograph. The optics described above may also be used for acousto-optic deflection, integrated optic spectrum analyzers, and other applications.
Microcellular propagation characteristics for personal communications in urban and suburban environments (1994)

New microcellular systems have been proposed to operate over short radio paths by using low-base station antennas, and transmitting at low power. In order to study radio propagation in the microcellular environments for future personal communications services (PCS), comprehensive radio propagation measurements were conducted by Telesis Technologies Laboratory (TTL) in the San Francisco Bay area using three transmitting antenna heights of 3.2, 8.7, and 13.4 m and two frequencies in the 900 and 1900 MHz bands. The paper reports the path loss measurements made in urban and suburban areas where the receiving mobile was driven along preselected line-of-sight (LOS), zig-zag, and staircase routes to gather information about direct propagation along streets, as well as diffraction over the roofs in suburban areas, and diffraction around the corners in urban areas. The results obtained for the three antenna heights are studied, and show the height gain that can be expected for microcells in different environments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The semiconductor laser linewidth due to the presence of side modes (1988)

The laser linewidth is evaluated by solving the rate equations for a nearly single-mode laser with two modes. The resulting linewidth contribution due to the presence of side modes is introduced by the nonlinear gain in the laser diode. For weak side modes, the linewidth contribution is proportional to the third power of the side mode intensity. A linewidth contribution of about 20 MHz for a side-mode power of 100 mu W has been found experimentally for a 1.3- mu m buried-heterostructure laser.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The chromatic eye: a new reduced-eye model of ocular chromatic aberration in humans (1992)

New measurements of the chromatic difference of focus of the human eye were obtained with a two-color, vernier-alignment technique. The results were used to redefine the variation of refractive index of the reduced eye over the visible spectrum. The reduced eye was further modified by changing the refracting surface to an aspherical shape to reduce the amount of spherical aberration. The resulting chromatic-eye model provides an improved account of both the longitudinal and transverse forms of ocular chromatic aberration.
Automating hypertext for decision support (1990)

A decision support system (DSS) shell is being constructed that can support applications in a variety of fields, e.g., engineering, manufacturing, finance. The shell provides a hypertext-style interface for 'navigating' among DSS application models, data, and reports. The traditional notion of hypertext had to be enhanced. Hypertext normally requires manually, pre-defined links. A DSS shell, however, requires that hypertext connections to be built 'on the fly'. The role of hypertext is discussed in augmenting DSS applications and the decision making process. Also discussed is how hypertext nodes, links, and link markers tailored to an arbitrary DSS application were automatically generated.
<title>Incorporation of organic dye molecules in nanoporous crystals for the development of hexagonal solid state microlasers</title> (2001)

Molecular sieves, such as nanoporous AlPO<SUB>4</SUB>-5, can host a wide variety of laser-active dyes. Slim dyes like Coumarin40 or Oxazine 1, fitting into the channel pores, as well as bulky dyes like rhodamines and Oxazine 750, being located in defect sites of the molecular sieve structure, are embedded during microwave-assisted crystallization. The fast microwave-assisted crystallization offers a new procedure for the stable and monomeric encapsulation of organic dyes into molecular sieves without any degradation of the chromophores and enables the control of the morphology of the host material. Based on this class of materials a new form of microlasers has been created. Their properties depend on size and shape of the molecular sieve crystals. The microcrystals act as hexagonal ring resonators (whispering gallery mode). In dependence on the morphology of the crystals different laser properties have been observed in agreement with theoretical predictions. Large hexagonal crystals (diameter of the hexagonal plane &gt; 7 micrometers ) revealed multiline laser emission, while smaller crystals (diameter about 5 micrometers ) oscillate on one single line. The laser threshold power density decreases with decreasing diameter of the crystals. In terms of pumping needed to reach lasing molecular sieve microlasers are comparable to quantum dot semiconductor lasers.
Nonisotopic hybridization assay for determination of relative amounts of genotypic human immunodeficiency virus type 1 zidovudine resistance (1995)

A nonisotopic hybridization assay for human immunodeficiency virus genotypic zidovudine resistance determination is described. Biotinylated PCR product was hybridized with enzyme-labeled probes for wild-type or resistant mutant sequences and detected colorimetrically or chemiluminescently in a microplate format. Changes in mutant-to-wild-type ratios allow for the monitoring of longitudinal patient samples.
Amino Acid Sequence of Copper, Zinc-Superoxide Dimutase from Spinach Leaves (1986)

The complete amino acid sequence of Cu,Zn-superoxide dismutase (SOD) from spinach leaves has been determined on the basis of peptides obtained by cyanogen bromide (BrCN) cleavage and by enzymic hydrolyses with Achromobacter lyticus lysylendopeptidase, Staphylococcus aureus V8 protease, trypsin, and thermolysin. The spinach SOD consists of a total of 154 amino acid residues with alanine as the amino(N)-terminus and valine as the carboxy(C-)terminus. The present sequence, which has been established for the enzyme from a plant, is also highly homologous to those of the enzymes from other species. Especially, the residues essential for metal binding and enzyme activity have been extensively conserved among all of the Cu,Zn-SODs hitherto analyzed.