gebhart/patrepeval huggingface dataset:
Retention Behavior of Vitamin D and Related Compounds During High-Performance Liquid Chromatography (1995)

Abstract The retention behavior of vitamin D2-D5 and provitamin D2-D5 are examined using high-performance liquid chromatography. Inclusion chromatography using cyclodextrin as the mobile phase additive in reversed-phase high-performance liquid chromatography is also used for this purpose. Reversed-phase high-performance liquid chromatography is more effective than normal-phase high-performance liquid chromatography in separating these analogs. The addition of methyl- β - cyclodextrin to the mobile phase is effective in separating the pair of vitamin-D2 and - D3 or provitamin-D2 and -D3 The separation of the pair of stereoisomeric Cookson-type derivatives of vitamin-D2 or -D3 was also examined and found that normal-phase high-performance liquid chromatography is effective for this purpose.
The Cellular Basis of Pacing-Induced Dilated Cardiomyopathy (1995)

Myocyte cell loss and myocyte reactive hypertrophy are the major components of ventricular remodeling in pacing-induced dilated cardiomyopathy.
Wavelength performance of holographic optical elements (1985)

A comprehensive treatment is presented for the diffraction efficiencies of transmission holographic elements and cascade lenses when subject to broad spectral and field angle detunings. Experimental measurements are made in support of our theory on holographic optical elements fabricated in bleached silver-halide emulsions and in dichromated gelatin. The theory of holographic grating diffraction efficiency is studied through two approaches. A numerical treatment based on the theory of thin grating decomposition is implemented and shown to be in close agreement with other theories. Additionally, a more approximate approach is pursued in which the volume grating is treated as a phased array of scatterers. The latter approach leads to closed-form formulas in addition to a simple physical picture of volume effects. It is found that three-element cascades can exhibit spectral and field angle bandwidths essentially as broad as two-element cascades and that these bandwidths are in excess of 2300 Å and 7° respectively.
Huperzine A, a novel promising acetylcholinesterase inhibitor (1996)

The effects of huperzine A on memory impairments induced by scopolamine were evaluated using a radial maze task and inhibition of cholinesterase in vitro compared with the effects of E2020 and tacrine. Scopolamine (0.2 mg kg-1) significantly impaired spatial memory in rats. Huperzine A (0.1-0.4 mg kg-1, p.o.), E2020 (0.5-1.0 mg kg-1, p.o.) and tacrine (1.0-2.0 mg kg-1, p.o.) could reverse these scopolamine-induced memory deficits. The ratios of huperzine A, E2020 and tacrine for butyrylcholinesterase:acetylcholinesterase determined by a colourimetric method were 884.57, 489.05, and 0.80, respectively. The results demonstrated that huperzine A was the most selective acetylcholinterase inhibitor, and improved the working memory deficit induced by scopolamine significantly better than did E2020 or tacrine, suggesting it may be a promising agent for clinical therapy of cognitive impairment in patients with Alzheimer's Disease.
Affimer proteins for F-actin: novel affinity reagents that label F-actin in live and fixed cells (2018)

Imaging the actin cytoskeleton in cells uses a wide range of approaches. Typically, a fluorescent derivative of the small cyclic peptide phalloidin is used to image F-actin in fixed cells. Lifeact and F-tractin are popular for imaging the cytoskeleton in live cells. Here we characterised novel affinity reagents called Affimers that specifically bind to F-actin in vitro to determine if they are suitable alternatives as eGFP-fusion proteins, to label actin in live cells, or for labeling F-actin in fixed cells. In vitro experiments showed that 3 out of the 4 Affimers (Affimers 6, 14 and 24) tested bind tightly to purified F-actin, and appear to have overlapping binding sites. As eGFP-fusion proteins, the same 3 Affimers label F-actin in live cells. FRAP experiments suggest that eGFP-Affimer 6 behaves most similarly to F-tractin and Lifeact. However, it does not colocalise with mCherry-actin in dynamic ruffles, and may preferentially bind stable actin filaments. All 4 Affimers label F-actin in methanol fixed cells, while only Affimer 14 labels F-actin after paraformaldehyde fixation. eGFP-Affimer 6 has potential for use in selectively imaging the stable actin cytoskeleton in live cells, while all 4 Affimers are strong alternatives to phalloidin for labelling F-actin in fixed cells.
Plasmid Chemokines and Colony-Stimulating Factors Enhance the Immunogenicity of DNA Priming-Viral Vector Boosting Human Immunodeficiency Virus Type 1 Vaccines (2003)

Heterologous "prime-boost" regimens that involve priming with plasmid DNA vaccines and boosting with recombinant viral vectors have been shown to elicit potent virus-specific cytotoxic T-lymphocyte responses. Increasing evidence, however, suggests that the utility of recombinant viral vectors in human populations will be significantly limited by preexisting antivector immunity. Here we demonstrate that the coadministration of plasmid chemokines and colony-stimulating factors with plasmid DNA vaccines markedly increases the immunogenicity of DNA prime-recombinant adenovirus serotype 5 (rAd5) boost and DNA prime-recombinant vaccinia virus (rVac) boost vaccine regimens in BALB/c mice. In mice with preexisting anti-Ad5 immunity, priming with the DNA vaccine alone followed by rAd5 boosting elicited only marginal immune responses. In contrast, cytokine-augmented DNA vaccine priming followed by rAd5 vector boosting was able to generate potent immune responses in mice with preexisting anti-Ad5 immunity. These data demonstrate that plasmid cytokines can markedly improve the immunogenicity of DNA prime-viral vector boost vaccine strategies and can partially compensate for antivector immunity.
Amino Acid Substitutions in Gag Protein at Non-cleavage Sites Are Indispensable for the Development of a High Multitude of HIV-1 Resistance against Protease Inhibitors (2002)

Amino acid substitutions in human immunodeficiency virus type 1 (HIV-1) Gag cleavage sites have been identified in HIV-1 isolated from patients with AIDS failing chemotherapy containing protease inhibitors (PIs). However, a number of highly PI-resistant HIV-1 variants lack cleavage site amino acid substitutions. In this study we identified multiple novel amino acid substitutions including L75R, H219Q, V390D/V390A, R409K, and E468K in the Gag protein at non-cleavage sites in common among HIV-1 variants selected against the following four PIs: amprenavir, JE-2147, KNI-272, and UIC-94003. Analyses of replication profiles of various mutant clones including competitive HIV-1 replication assays demonstrated that these mutations were indispensable for HIV-1 replication in the presence of PIs. When some of these mutations were reverted to wild type amino acids, such HIV-1 clones failed to replicate. However, virtually the same Gag cleavage pattern was seen, indicating that the mutations affected Gag protein functions but not their cleavage sensitivity to protease. These data strongly suggest that non-cleavage site amino acid substitutions in the Gag protein recover the reduced replicative fitness of HIV-1 caused by mutations in the viral protease and may open a new avenue for designing PIs that resist the emergence of PI-resistant HIV-1.
Human inter-α-inhibitor family in inflammation: simultaneous synthesis of positive and negative acute-phase proteins (1993)

The inter-alpha-inhibitor (I alpha I) family encompasses four plasma proteins, namely free bikunin as well as I alpha I, pre-alpha-inhibitor (P alpha I) and inter-alpha-like inhibitor (I alpha LI). Each of the last three proteins is a distinct assembly of one bikunin chain with one or more unique heavy (H) chains designated H1, H2 and H3. The three H chains and the bikunin chain are encoded by four distinct mRNAs. These molecules and chains, as well as the corresponding mRNAs, were quantified in sera and liver biopsies from a series of patients with or without mild or severe acute infection. The decrease or increase observed for a given molecule or chain in the serum was in agreement with a similar change in the corresponding liver mRNA. In acute inflammation the H2 and bikunin chains are down-regulated and the relevant molecules (I alpha I, I alpha LI) behave as negative acute-phase proteins, whereas the H3 chain is up-regulated and the corresponding P alpha I molecule is a positive acute-phase protein. Also, P alpha I displays a higher-than-usual M(r); this is probably due to ligand binding. The H1 gene does not seem to be affected by the inflammatory condition. The quantitative changes in RNA levels seen in vivo were confirmed in vitro in the human hepatoma Hep3B cell line prior to or after induction with the acute-phase mediators interleukin-1 and/or -6. These results provide the first example in humans of positive and negative acute-phase proteins that are encoded by evolutionary related genes.
Antibody Microarrays: Current Status and Key Technological Advances (2006)

Antibody-based microarrays are among the novel classes of rapidly evolving proteomic technologies that holds great promise in biomedicine. Miniaturized microarrays (< 1 cm2) can be printed with thousands of individual antibodies carrying the desired specificities, and with biological sample (e.g., an entire proteome) added, virtually any specifically bound analytes can be detected. While consuming only minute amounts (< microL scale) of reagents, ultra- sensitive assays (zeptomol range) can readily be performed in a highly multiplexed manner. The microarray patterns generated can then be transformed into proteomic maps, or detailed molecular fingerprints, revealing the composition of the proteome. Thus, protein expression profiling and global proteome analysis using this tool will offer new opportunities for drug target and biomarker discovery, disease diagnostics, and insights into disease biology. Adopting the antibody microarray technology platform, several biomedical applications, ranging from focused assays to proteome-scale analysis will be rapidly emerging in the coming years. This review will discuss the current status of the antibody microarray technology focusing on recent technological advances and key issues in the process of evolving the methodology into a high-performing proteomic research tool.
Identification of phosphorylated residues that affect the activity of the mitotic kinase Aurora-A (2002)

The activity of the kinase Aurora-A (Aur-A) peaks during mitosis and depends on phosphorylation by one or more unknown kinases. Mitotic phosphorylation sites were mapped by mass spec sequencing of recombinant Aur-A protein that had been activated by incubation in extracts of metaphase-arrested Xenopus eggs. Three sites were identified: serine 53 (Ser-53), threonine 295 (Thr-295), and serine 349 (Ser-349), which are equivalent to Ser-51, Thr-288, and Ser-342, respectively, in human Aur-A. To ask how phosphorylation of these residues might affect kinase activity, each was mutated to either alanine or aspartic acid, and the recombinant proteins were then tested for their ability to be activated by M phase extract. Mutation of Thr-295, which resides in the activation loop of the kinase, to either alanine or aspartic acid abolished activity. The S349A mutant had slightly reduced activity, indicating that phosphorylation is not required for activity. The S349D mutation completely blocked activation, suggesting that Ser-349 is important for either the structure or regulation of Aur-A. Finally, like human Aur-A, overexpression of Xenopus Aur-A transformed NIH 3T3 cells and led to tumors in nude mice. These results provide further evidence that Xenopus Aur-A is a functional ortholog of human Aur-A and, along with the recently described crystal structure of human Aur-A, should help in future studies of the mechanisms that regulate Aur-A activity during mitotic progression.
Transient control of interleukin-4-producing natural killer T cells in the livers of Listeria monocytogenes-infected mice by interleukin-12 (1997)

Unconstrained development of gamma interferon (IFN-gamma)-secreting natural killer (NK) cells and T helper (Th) 1 cells is central to protection against Listeria monocytogenes. In contrast, interleukin 4 (IL-4) is considered harmful. IL-12 produced by infected macrophages promotes, and IL-4 interferes with, protective antilisterial immunity. The liver NK T lymphocytes, which are a potent source of IL-4, are downregulated at an intermediate stage of listeriosis. Here we demonstrate that endogenous IL-12 participates in the control of IL-4-producing liver NK T lymphocytes during listeriosis. The effects of L. monocytogenes infection on IL-4-producing liver NK T lymphocytes were reversed by antibody neutralization of IL-12 but not of IFN-gamma or tumor necrosis factor alpha (TNF-alpha). IL-4 production by liver NK T lymphocytes was virtually unaffected by heat-killed L. monocytogenes (HKL). Viable L. monocytogenes markedly increased the numbers of IL-12 producers in livers in parallel with an increase in macrophage numbers, whereas HKL failed to do so with similar efficiency. These results indicate that in the liver endogenous IL-12 improves protective immunity against listeriosis by downregulating IL-4-producing NK T lymphocytes. Moreover, our findings that HKL have a low level of IL-12-inducing activity and fail to control IL-4-producing NK T lymphocytes in the liver are consistent with the lesser protective capacity of HKL compared to that of live listeriae.
The Davis Grapevine Virus Collection (1992)

Requests for specific strains of California grapevine viruses, virus and virus-like diseases as well as for specific indicator strains of cultivars are constantly received from various research laboratories over the world for use in research, comparative studies, and teaching. The old Davis virus and virus-like disease collection of own-rooted grapevines established in the 1960s had been degenerating due to phylloxera. A new expanded collection has been established as own-rooted plants and also in graft-inoculated cultivars on rootstocks. Each entry in the new collection has a designated number consisting of descriptive letters and numerals (like GFLV-100). New entries have been and will continue to be accepted. Collections of grapevines are pools of reference and source materials of standard type cultivars of viruses, virus and virus-like diseases. There are three additional collections of grapevines on the UCD campus, each of which serves a different purpose: the Department of Viticulture and Enology collection, the UCD Foundation Plant Materials Services collection of indexed and registered cultivars, and the United States Department of Agriculture - Agricultural Research Services (USDA-ARS) National Clonal Germplasm Repository collection.
Adsorption of Small Molecules in LTA Zeolites. 1. NH3, CO2, and H2O in Zeolite 4A (2004)

We have developed force fields for the calculation of adsorption of NH3, CO2, and H2O on zeolite 4A by performing Gibbs ensemble Monte Carlo simulations to fit experimental isotherms at 298 K. The calculated NH3 and CO2 isotherms are in excellent agreement with experimental data over a wide range of temperatures and several orders of magnitude in pressure. We have calculated isotherms for H2O in 4A using two different models and have found that H2O saturates zeolite 4A even at pressures as low as 0.01 kPa for the range of temperatures studied. We have studied the geometry of the adsorption sites and their dependence on loading. At low pressures, CO2 molecules adsorb with their longitudinal axis pointing toward the center of the supercage, whereas at higher pressures, the two oxygen atoms are equidistant from the Na atom in the binding site.
Candidate pathways and genes for nasopharyngeal carcinoma based on bioinformatics study. (2015)

has-miR-615-3p might take part in the pathogenetic process of NPC through regulating MCM4 which is enriched in cell cycle. The DEmiRNAs identified in the present study might serve as new biomarkers for NPC.
Amplification of bacterial genomic DNA by the polymerase chain reaction and direct sequencing after asymmetric amplification: application to the study of periplasmic permeases (1989)

The polymerase chain reaction (PCR) has been used to amplify DNA fragments by using eucaryotic genomic DNA as a template. We show that bacterial genomic DNA can be used as a template for PCR amplification. We demonstrate that DNA fragments at least as large as 4,400 base pairs can be amplified with fidelity and that the amplified DNA can be used as a substrate for most operations involving DNA. We discuss problems inherent in the direct sequencing of the amplified product, one of the important exploitations of this methodology. We have solved the problems by developing an "asymmetric amplification" method in which one of the oligonucleotide primers is used in limiting amounts, thus allowing the accumulation of single-stranded copies of only one of the DNA strands. As an illustration of the use of PCR in bacteria, we have amplified, sequenced, and subcloned several DNA fragments carrying mutations in genes of the histidine permease operon. These mutations are part of a preliminary approach to studying protein-protein interactions in transport, and their nature is discussed.
Oxidative damage in Alzheimer’s dementia, and the potential etiopathogenic role of aluminosilicates, microglia and micronutrient interactions (1992)

While evidence implicating free radical oxidative processes in the etiopathogenesis of Alzheimer's dementia is accumulating, the specific cellular and biochemical mechanisms involved remain to be identified. The potential pathogenic role of microglial cells in neurodegenerative processes is indicated by the finding that purified murine microglial cells exposed in vitro to various model aluminosilicate particles stimulate the generation of tissue-injurious free radical reactive oxygen metabolites. Analogous inorganic aluminosilicate deposits have been reported to occur in the core of the characteristic senile plaques found in the brains of Alzheimer disease subjects. The possible modulation of free radical oxidative activity by antioxidant micronutrients and pharmacological agents, provides a rational basis for further preventative and therapeutic clinical investigations.
Electrode for recording direction of activation, conduction velocity, and monophasic action potential of myocardium (1997)

Conduction velocity and recovery of excitability are central facets of reentry arrhythmias, and yet there are no satisfactory techniques for the simultaneous measurement of both from the same area of myocardium. We have developed an electrode arrangement that allows the simultaneous recording of conduction velocity, repolarization of the myocardium together with an index of dispersion, and direction of activation of the myocardium. Three silver/silver chloride electrodes were arranged in an equilateral triangle with a reference electrode at the center. From this arrangement three monophasic action potentials were recorded. From the time of arrival of the wavefront of activation at each electrode the direction of activation and conduction velocity were calculated in real time by a computer. There was a good correlation for the in vivo signals from the circular electrode and the new electrode both for conduction velocity (r = 0.99, P < 0.001) and for direction of activation (r = 0.99, P < 0.001). This new mathematical method and electrode design allows the simultaneous measurement of conduction velocity and direction and monophasic action potential, and this can give a beat-by-beat indication of wavelength and dispersion of action potential duration.
Detection of Listeria monocytogenes in foods by immunomagnetic separation (1990)

Immunomagnetic separation with immunomagnetic beads was used to isolate strains of Listeria monocytogenes both from pure cultures and from heterogeneous suspensions. The monoclonal antibodies used recognized all six strains of serotype 4 but only one of three strains of serotype 1. Coating procedure, incubation time, and number of immunomagnetic beads influenced the sensitivity of the isolation method. Less than 1 x 10(2) bacteria per ml in pure cultures and less than 2 x 10(2) bacteria per ml in enriched foods could be detected. The method represents a new approach to extraction and isolation of pathogenic bacteria directly from foods, after resuscitation, or from enrichment broths.
Computer immunology (1997)

Natural immune systems protect animals from dangerous foreign pathogens, including bacteria, viruses, parasites, and toxins. Their role in the body is analogous to that of computer security systems in computing. Although there are many differences between living organisms and computers, the similarities are compelling and could point the way to improved computer security. 1 Improvements can be achieved by designing computer immune systems with some of the important properties of natural immune systems, including multilayered protection; highly distributed detector, effector, and memory systems; diversity of detection ability across individuals; inexact matching strategies; and sensitivity to most new foreign patterns. Some of these properties are well known but seldom implemented successfully; other properties are less well known. The immune system provides a persuasive example of how they might be implemented in a coherent system.
A monoclonal antibody against alpha-smooth muscle actin: a new probe for smooth muscle differentiation. (1986)

A monoclonal antibody (anti-alpha sm-1) recognizing exclusively alpha-smooth muscle actin was selected and characterized after immunization of BALB/c mice with the NH2-terminal synthetic decapeptide of alpha-smooth muscle actin coupled to keyhole limpet hemocyanin. Anti-alpha sm-1 helped in distinguishing smooth muscle cells from fibroblasts in mixed cultures such as rat dermal fibroblasts and chicken embryo fibroblasts. In the aortic media, it recognized a hitherto unknown population of cells negative for alpha-smooth muscle actin and for desmin. In 5-d-old rats, this population is about half of the medial cells and becomes only 8 +/- 5% in 6-wk-old animals. In cultures of rat aortic media SMCs, there is a progressive increase of this cell population together with a progressive decrease in the number of alpha-smooth muscle actin-containing stress fibers per cell. Double immunofluorescent studies carried out with anti-alpha sm-1 and anti-desmin antibodies in several organs revealed a heterogeneity of stromal cells. Desmin-negative, alpha-smooth muscle actin-positive cells were found in the rat intestinal muscularis mucosae and in the dermis around hair follicles. Moreover, desmin-positive, alpha-smooth muscle actin-negative cells were identified in the intestinal submucosa, rat testis interstitium, and uterine stroma. alpha-Smooth muscle actin was also found in myoepithelial cells of mammary and salivary glands, which are known to express cytokeratins. Finally, alpha-smooth muscle actin is present in stromal cells of mammary carcinomas, previously considered fibroblastic in nature. Thus, anti-alpha sm-1 antibody appears to be a powerful probe in the study of smooth muscle differentiation in normal and pathological conditions.