gebhart/patrepeval huggingface dataset:
Cytokine regulation of colony-stimulating factor production in cultured human synovial fibroblasts: I. Induction of GM-CSF and G-CSF production by interleukin-1 and tumor necrosis factor (1990)

The cytokines, interleukin-1 (IL-1) and tumor necrosis factor (TNF), induce a dose-dependent production of both granulocyte-macrophage colony-stimulating factor (GM-CSF) and granulocyte CSF (G-CSF) in cultured human synovial cells, as measured by immunoassay. With IL-1, significant levels of both CSFs were first detected within 6 to 12 hours, with a maximum reached 24 to 48 hours after commencement of stimulation. A synergistic effect was detected between IL-1 and TNF in production of both CSFs in these cells. No evidence was obtained for the IL-1-induced effect to be mediated by induction of endogenous TNF nor for the TNF-induced stimulation to involve IL-1. IL-1-stimulated synovial cells were shown to secrete biologically active GM-CSF and G-CSF, which were specifically inhibited by their respective monoclonal antibodies. The transcription inhibitor, actinomycin D, and protein synthesis inhibitor, cycloheximide, inhibited the increase in GM-CSF and G-CSF production induced by IL-1 and TNF. Finally, other cytokines, IL-3, interferon gamma (IFN gamma), IL-2, platelet-derived growth factor (PDGF), epidermal growth factor (EGF) and transforming growth factor alpha (TGF alpha), failed to stimulate either GM-CSF or G-CSF production, whether alone or in the presence of IL-1. These results suggest that cytokine-stimulated synovial fibroblasts may be a major source of intraarticular CSF production in the joints of patients with inflammatory arthritis; as a result, monocyte/macrophages and granulocytes may be activated, leading to perpetuation of the inflammation and destructive events occurring in these lesions.
Virtual interface environment (1986)

A head-mounted, wide-angle, stereoscopic display system controlled by operator position, voice and gesture is under development for use as a multipurpose interface environment. Initial applications of the system are in telerobotics, data-management and human factors research. System configuration and research directions are described.
New Syntheses of E7389 C14−C35 and Halichondrin C14−C38 Building Blocks: Double-Inversion Approach (2009)

With sequential use of catalytic asymmetric Cr-mediated coupling reactions, E7389 C14-C35 and halichondrin C14-C38 building blocks have been stereoselectively synthesized. The C19-C20 bond is first formed via the catalytic asymmetric Ni/Cr-mediated coupling, i.e., 8 + 9 --> 10 (90%; dr = 22:1), in which vinyl iodide 8 is used as the limiting substrate. The C23-C24 bond is then formed via the catalytic asymmetric Co/Cr-mediated coupling, i.e., 13 + 14 --> 4 (82%; dr = 22:1), in which the alkyl-iodide bond in 14 is selectively activated over the vinyl-iodide bond. The catalytic asymmetric Ni/Cr-mediated reaction is employed to couple C14-C26 segment 19 with E7389 C27-C35 segment 20 (91%; dr = >55:1). In this synthesis, the C23-O bond is stereoselectively constructed via a double-inversion process, i.e., 21 --> 22, to furnish E7389 C14-C35 building block 22 in 84% yield. The same synthetic sequence has been employed to synthesize halichondrin C14-C38 building block 18b, i.e., 16a + 19 --> 18b.
Effect of the major DNA adduct of the antitumor drug cis-diamminedichloroplatinum (II) on the activity of a helicase essential for DNA replication, the herpes simplex virus type-1 origin-binding protein. (1994)

To determine the effect of the major DNA adduct, the intrastrand d(GpG) cross-link, produced by the antitumor drug cis-diamminedichloroplatinum(II) on the activity of a helicase known to be essential for DNA replication, we have examined its interaction with the origin-binding protein (UL9 protein) of herpes simplex virus type-1. We found that the helicase activity of the UL9 protein is inhibited only when the adduct is present on the template strand along which the protein translocates. This effect was paralleled by a comparable inhibition of the UL9 protein's DNA-dependent ATPase activity. The inhibitory effect of the lesion can be reduced by the addition of the herpes simplex virus type-1 single-stranded DNA-binding protein, ICP8. This stimulatory effect is specific for ICP8 and appears to be the result of the functional and physical interaction that is known to exist between the UL9 protein and ICP8, and not due to the preferential interaction of ICP8 with the adduct.
Networks: An Introduction (2010)

"The scientific study of networks, including computer networks, social networks, and biological networks, has received an enormous amount of interest in the last few years. The rise of the Internet and the wide availability of inexpensive computers have made it possible to gather and analyze network data on a large scale, and the development of a variety of new theoretical tools has allowed us to extract new knowledge from many different kinds of networks. The study of networks is broadly interdisciplinary and important developments have occurred in many fields, including mathematics, physics, computer and information sciences, biology, and the social sciences. This book brings together for the first time the most important breakthroughs in each of these fields and presents them in a coherent fashion, highlighting the strong interconnections between work in different areas. Subjects covered include the measurement and structure of networks in many branches of science, methods for analyzing network data, including methods developed in physics, statistics, and sociology, the fundamentals of graph theory, computer algorithms, and spectral methods, mathematical models of networks, including random graph models and generative models, and theories of dynamical processes taking place on networks"--. - Provided by publisher.
An Improved Approach to Prepare Human Brains for Research (1995)

We describe two protocols for preparing human brains collected for research and diagnosis. In both protocols, one half brain is processed for research and the other for neuropathological evaluation. Clinical, neuropathological and tissue mRNA retention data are used for sample categorization. In protocol 1, coronal, whole hemisphere slices cut at standardized landmarks are frozen with a cooling device at -90 degrees C, which yields discrete anatomical structures. In selected instances, small blocks of brain are frozen at -160 degrees C in liquid nitrogen vapor. Cooling device or liquid nitrogen vapor frozen samples are suitable for in situ hybridization, protein blotting or immunohistochemistry. Morphological freezing artifacts are minimal. In protocol 2, one half brain is frozen en bloc on dry ice; this tissue is suitable for regional evaluation of gene expression or neurochemistry. Morphological freezing artifacts are severe. In both protocols, the other half brain is fixed in formalin prior to sectioning and diagnostic evaluation. The standardized selection of paraffin blocks from each brain allows precise diagnoses to be established, including identification of dangerous infectious processes; moreover, it makes it possible to produce a set of uniformly selected blocks and slides for comparative studies. These protocols lead to standardized tissue preparation for research and reduce variables impairing interpretation and comparison of data.
Giant Gold−Glutathione Cluster Compounds:  Intense Optical Activity in Metal-Based Transitions (2000)

A series of giant metal-cluster compounds, each composed of a gold core and a glutathione (GSH) adsorbate layer, have been prepared from Au(I)SG polymers and separated by gel electrophoresis, using methods reported in a recent Letter [J. Phys. Chem. B 1998, 102, 10643−6]. Identification of the separated compounds by core mass is accomplished through laser desorption mass spectrometry of matrix-diluted films. Three principal compounds have core masses of ca. 4.3, 5.6, and 8.2 kDa (in the range of ∼20−40 Au atoms), and show structured optical absorption spectra with clear optical absorption onsets near 1.7, 1.3, and 1.0 eV, respectively. Each of these shows unusually strong chiroptical activity in the metal-based electronic transitions across the near-infrared, visible, and near-ultraviolet regions, whereas neither the crude (unseparated) mixture nor its higher molecular weight components possess such strong optical activity. The location and strength of the optical activity suggest a metal electronic structure that is highly sensitive to the chiral environment imposed by the glutathione adsorbate groups, if indeed the gold core is not inherently chiral. Mechanisms that could account for the observed optical activity are discussed, but the mere presence of strong chiroptical effects in this metallic-cluster system places these novel compounds in a special class of molecular substances. Previously known giant metal-cluster compounds (and nanocrystals) have not been reported to exhibit significant optical activity. With these results, there emerges a rather complete picture of the evolution of optical and electronic properties of thiol-based gold cluster compounds (or self-assembled monolayer passivated gold nanocrystals) from 20 to 1000 Au atoms (0.7−3.2 nm core diameter).
Homologous recombination between plasmids in mammalian cells can be enhanced by treatment of input DNA. (1984)

We have used the eukaryotic-prokaryotic shuttle vector pSV2Neo to demonstrate that cultured mammalian somatic cells have the enzymatic machinery to mediate homologous recombination and that the frequency of this recombination can be enhanced by pretreatment of the input DNA. Two nonoverlapping deletion mutants of pSV2Neo were constructed, each affecting the bacterial aminoglycoside 3'-phosphorylase gene (the neo gene), which confers resistance to aminoglycoside antibiotics on bacteria and resistance to the antibiotic G418 on mammalian cells. Mammalian cells transfected with either deletion plasmid alone yield no G418 -resistant colonies. Cells cotransfected with both deletion plasmids yield G418 -resistant colonies with high frequency. We show that these resistant colonies result from recombination involving homologous crossing-over or gene conversion between the deletion plasmids by rescuing from the resistant cells both types of reciprocal recombinant, full-length plasmids, and doubly deleted plasmids. Cutting one of the input plasmids to generate a double-stranded gap in the neo gene considerably enhances the frequency of homologous recombination within the gene. This suggests that targeting exogenous DNA to specific sites in mammalian chromosomes could be facilitated by suitable pretreatment of the DNA.
Effect of Urea on Volatile Generation from Maillard Reaction of Cysteine and Ribose (2000)

Urea occurs naturally in many food products, and its presence affects food quality. However, little is known about its impact on flavor generation in food production. In this study, the urea contents in beef, pork, and chicken were determined. The effects of urea and pH on thermal flavor generation were investigated using the model system of cysteine with ribose, which was heated to the roasting temperature of 180 degrees C for 2 h at pH 5 and pH 8.5. The results revealed relatively large amounts of urea in these meats and demonstrated that pH affects aroma generation. Volatiles identified from the reaction system of ribose and cysteine showed that sulfur-containing compounds such as thiophenes, thiazoles, and thiophenethiols were the most abundant compounds. The addition of urea into the reaction mixture caused the disappearance or reduction in content of some sulfur-containing compounds but resulted in the generation of several important nitrogen-containing volatiles, like pyrazine, methylpyrazine, 2,5- (and 2,6-)dimethylpyrazine and other alkylpyrazines, which are known to elicit roasty, nutty flavor notes. A plausible explanation for this phenomenon is that ammonia can be released from urea upon heating and the formed ammonia competes with hydrogen sulfide to react with Maillard reaction precursors to produce nitrogen-containing compounds such as alkylpyrazines.
NMR 3J(C1,H3) couplings in 1‐X‐bicyclo[1.1.1]pentanes. FPT–DFT and NBO studies of hyperconjugative interactions and heavy atom substituent effects (2001)

Abstract In this work a rationalization of the very large substituent effects on 3 J(C 1 ,H 3 ) couplings in 1‐X‐bicyclo[1.1.1]pentanes is presented. The Fermi contact contribution to such couplings was calculated in a series of 13 X‐derivatives within the DFT–B3LYP framework using the finite perturbation theory. Core electrons for atoms beyond the Second Row were taken into account using effective core potentials. Calculated couplings are in very good agreement with experimental values. The role played by hyperconjugative interactions involving bonds or antibonds belonging to the coupling pathway are studied using the NBO approach. Heavy atom contribution to substituent effects on 3 J(C 1 ,H 3 ) couplings was estimated as small. This contrasts notably with trends observed in the corresponding 13 C substituent chemical shifts, SCSs. The latter were estimated comparing for X=Cl, Br, I, SnMe 3 , calculated SCSs with their experimental values. Such estimations are in line with explicit calculations of the spin‐orbit contribution reported in the literature for smaller compounds. © 2001 John Wiley &amp; Sons, Inc. J Comput Chem 22: 1615–1621, 2001
Measurement of electrical characteristics of atmospheric pressure non-thermal He plasma (2007)

This work develops a method for determining the electrical characteristics of an atmospheric pressure non-thermal He plasma. It is applied on an original low power plasma source that has some specific properties, as follows: (1) it uses high sinusoidal voltages generated in an LRC series resonant circuit; (2) the frequency of the sinusoidal waveform that maintains the discharge (<1 MHz) is lower than those used till now (>13.56 MHz); (3) the circuit is powered with dc voltages lower than 5 V and dc currents up to 1 A; and (4) the plasma torch is made of the usual materials and has a single electrode. As a function of the power and the gas (helium) flow rate, the generated plasma has three developing stages: pointed, extended (oval ball) and jet. The developed calculation algorithm of the electrical characteristics of the plasma uses only the parameters that can be measured without disturbing the plasma. The algorithm was validated by direct measurement of the plasma current. The electrical measurements show that the plasma has a purely resistive behaviour. As a function of the absorbed power and the gas flow rate, the plasma resistance varies in the range of 104 − 105 Ω.
The Arabidopsis RGA Gene Encodes a Transcriptional Regulator Repressing the Gibberellin Signal Transduction Pathway (1998)

The recessive rga mutation is able to partially suppress phenotypic defects of the Arabidopsis gibberellin (GA) biosynthetic mutant ga1-3. Defects in stem elongation, flowering time, and leaf abaxial trichome initiation are suppressed by rga. This indicates that RGA is a negative regulator of the GA signal transduction pathway. We have identified 10 additional alleles of rga from a fast-neutron mutagenized ga1-3 population and used them to isolate the RGA gene by genomic subtraction. Our data suggest that RGA may be functioning as a transcriptional regulator. RGA was found to be a member of the VHIID regulatory family, which includes the radial root organizing gene SCARECROW and another GA signal transduction repressor, GAI. RGA and GAI proteins share a high degree of homology, but their N termini are more divergent. The presence of several structural features, including homopolymeric serine and threonine residues, a putative nuclear localization signal, leucine heptad repeats, and an LXXLL motif, indicates that the RGA protein may be a transcriptional regulator that represses the GA response. In support of the putative nuclear localization signal, we demonstrated that a transiently expressed green fluorescent protein-RGA fusion protein is localized to the nucleus in onion epidermal cells. Because the rga mutation abolished the high level of expression of the GA biosynthetic gene GA4 in the ga1-3 mutant background, we conclude that RGA may also play a role in controlling GA biosynthesis.
INDUCTION OF ALLOGRAFT NONRESPONSIVENESS AFTER INTRATHYMIC INOCULATION WITH DONOR CLASS I ALLOPEPTIDES (1997)

We have recently demonstrated that cardiac allograft rejection in the PVG.R8-to-PVG.1U rat strain combination involves the recognition of a isolated class I (RT1.Aa) molecules as peptides in the context of the recipient MHC molecules. Three synthetic peptides (P1, P2, and P3) corresponding to the α-helices of the RT1.Aa molecule served as T-cell epitopes for graft rejection. In this study, we demonstrate that two of these peptides (P2 and P3) are sufficient to induce immune nonresponsiveness(median survival time >237 days) to cardiac allografts when presented to the recipient immune system in the thymus 7 days before transplantation. This effect was time dependent, as intrathymic inoculation 60 days before transplantation did not prolong graft survival (median survival time=12 days). Previous studies have demonstrated a critical role for alloantibody responses in mediating graft rejection in this rat strain combination. We, therefore, studied the role alloantibody responses may play in the observed immune nonresponsiveness. The titers of alloantibody in serum samples harvested from graft recipients at different times after transplantation were measured. We used recipient primary aortic endothelial cells genetically manipulated to express the donor RT1.Aa molecule as targets in an enzyme-linked immunosorbent assay. High titers of anti-RT1.Aa IgM antibody were detected in unmanipulated controls at the time of graft rejection. The IgM antibody switched to high IgG titers in intrathymically inoculated rats with accelerated or delayed rejection. Graft rejection in intrathymically manipulated recipients that had achieved a transient state of immunological nonresponsiveness correlated with higher titers of the IgG2b alloantibody. In marked contrast, the long-term graft survivors expressed undetectable or low levels of the IgG2b antibody and moderate to high levels of the IgG1 and IgG2a subclasses. These data suggest that the IgG2b alloantibody may contribute to the rejection reaction, whereas IgG1 and IgG2a may be involved in active enhancement of graft survival.
Analysis of spectral clustering algorithms for community detection: the\n general bipartite setting (2018)

We consider spectral clustering algorithms for community detection under a\ngeneral bipartite stochastic block model (SBM). A modern spectral clustering\nalgorithm consists of three steps: (1) regularization of an appropriate\nadjacency or Laplacian matrix (2) a form of spectral truncation and (3) a\nk-means type algorithm in the reduced spectral domain. We focus on the\nadjacency-based spectral clustering and for the first step, propose a new\ndata-driven regularization that can restore the concentration of the adjacency\nmatrix even for the sparse networks. This result is based on recent work on\nregularization of random binary matrices, but avoids using unknown population\nlevel parameters, and instead estimates the necessary quantities from the data.\nWe also propose and study a novel variation of the spectral truncation step and\nshow how this variation changes the nature of the misclassification rate in a\ngeneral SBM. We then show how the consistency results can be extended to models\nbeyond SBMs, such as inhomogeneous random graph models with approximate\nclusters, including a graphon clustering problem, as well as general\nsub-Gaussian biclustering. A theme of the paper is providing a better\nunderstanding of the analysis of spectral methods for community detection and\nestablishing consistency results, under fairly general clustering models and\nfor a wide regime of degree growths, including sparse cases where the average\nexpected degree grows arbitrarily slowly.\n
Some probabilities associated with the ordering of random variables having a dirichlet distribution (1989)

This paper considers certain probabilities associated with selecting the most and the least likely multinomial events under uncertainty. The analysis is based upon the assumption that the random multinomial parametric vector is distributed as a Dirichlet-type 1 distribution. It is shown that the probability that a given event is the most or the least likely event, posterior (prior) to sample information, can be expressed as a Dirichlet-type 2 integral. In this form, numerical values for these probabilities can be obtained from the tables of the incomplete Dirichlet-type 2 integral compiled by Sobel, Uppuluri and Frankowski (1985). It is also shown that the results of this paper are useful in the probabilistic analysis of arbitrary event trees using continuous random variables.
Modelling cancer immunomodulation using epithelial organoid cultures (2018)

Here we utilize organoid technology to study immune-cancer interactions and assess immunomodulation by colorectal cancer (CRC). Transcriptional profiling and flow cytometry revealed that organoids maintain differential expression of immunomodulatory molecules present in primary tumours. Finally, we established a method to model antigen-specific epithelial cell killing and cancer immunomodulation in vitro using CRC organoids co-cultured with cytotoxic T cells (CTLs).
Plasma carcinoembryonic antigen in the diagnosis and management of patients with hepatocellular carcinoma (1981)

The value of serial carcinoembryonic antigen (CEA) measurements as a marker of disease progression or in monitoring treatment was investigated in patients with hepatocellular carcinoma. Of 40 patients, including 16 with normal serum alpha-fetoprotein (AFP) concentrations, 29 (72.5%) had abnormal plasma CEA at presentation. Although this was more common in patients with pre-existing cirrhosis, the mean and range of plasma CEA were similar in patients with and without pre-existing hepatic disease. There was no correlation between plasma CEA and any biochemical parameter of hepatic function, although plasma CEA concentrations were significantly lower in patients with well-differentiated tumors. CEA concentrations increased in 71% of patients who had no response to cytotoxic drugs, but CEA also increased in 62.5% of those patients who did respond. Plasma CEA concentrations were elevated in 62.5% of patients with normal and 79% of patients with raised serum AFP on admission to the hospital. There was no correlation between individual AFP and CEA concentrations. Although elevated plasma CEA levels may be of diagnostic value in patients with hepatocellular carcinoma in the absence of pre-existing hepatic disease, and in those with normal serum AFP, our findings indicate that it does not behave as a true tumor marker.
Gadolinium-enhanced CT angiography of the circle of Willis and neck. (2004)

CT angiography (CTA) of the cervical and intracranial vessels is a rapid, noninvasive, and relatively inexpensive technique for the evaluation of vascular abnormalities. Contraindications to the use of contrast media, however, can preclude use of iodinated agents for CTA. We report the use of gadolinium as contrast agent for CTA of the head and neck in three patients with contraindications to iodinated contrast agents.