gebhart/patrepeval huggingface dataset:
Regulation of germ-line epsilon transcription and induction of epsilon switching in cloned EBV-transformed and malignant human B cell lines by cytokines and CD4+ T cells (1992)

IL-4 induces germ-line epsilon transcript synthesis in normal human B cells, but a second signal provided by CD4+ T cells is required for subsequent production of productive epsilon mRNA and IgE synthesis. In the present study we demonstrate that IL-4 specifically induces germ-line epsilon transcripts in most EBV lymphoblastoid (LCL) and EBV+ and EBV- Burkitt's lymphoma (BL) cells without inducing IgE synthesis. However, cocultivation of cloned sIgM+, sIgE- EBV-LCL or BL cells with activated CD4+ T cell clones in the presence of IL-4 resulted in IgE production in 13 to 24% of the wells. Analysis of rearranged DNA in IgE-producing cloned BL cells indicated that epsilon switching occurred through a recombination deletion event. IgE production is a stable feature of the cloned switched EBV-LCL and BL cells because these cells continued to produce relatively high levels of IgE in the absence of IL-4 and CD4+ T cells. Induction of IgE synthesis was blocked by IFN-gamma, IFN-alpha, and transforming growth factor beta (TGF-beta), but only TGF-beta inhibited IL-4-induced germ-line epsilon mRNA expression. These results suggest that the inhibitory effects of TGF-beta are mediated via inhibition of germ-line epsilon expression, whereas IFN-alpha and IFN-gamma block other steps in the regulatory processes resulting in induction of IgE synthesis by established human B cell line cells. Our results indicate that the same set of signals that induce normal B cells to switch to IgE synthesis also induce high frequency epsilon switching in cloned established EBV transformed and malignant B cell lines including classical cell lines such as JY and BL-2.
Photochemical behaviour of rhodamine 6G in Nafion membrane (1992)

Sorption of laser dye rhodamine 6G in perfluorosulphonate cation-exchange membrane (Nafion) from aqueous solution has been investigated by optical absorption and emission studies. In the H+ form, the optical absorption spectra changes with water content in the membrane and is attributed to the change in H+ ion concentration in dry and wet (with water) conditions of the membrane. The dye is present in the protonated form in the dry membrane and in the cationic form in the wet membrane. In the Na+ form, rhodamine 6G is present in the cationic form and the optical absorption spectra do not show changes in dry and water-wet conditions of the membrane. The fluorescence lifetime of rhodamine 6G is 3.97 ns and decay is single exponential. In the Na+ and H+ forms of the membrane, the fluorescence decay is biexponential. The lifetime and the relative ratio vary for the Na+ and H+ forms and also with the water content in the membrane. Owing to the large size of the dye low values for the diffusion coefficient are observed (3.2 × 10–11 and 2.0 × 10–8 cm2 s–1 for Na+ and H+ form of Nafion, respectively). As compared to aqueous solutions, rhodamine 6G in Nafion membrane is observed to be photostable.
Detection of Polyomavirus Simian Virus 40 Tumor Antigen DNA in AIDS-Related Systemic Non-Hodgkin Lymphoma (2002)

Systemic non-Hodgkin lymphoma (S-NHL) is a common malignancy during HIV infection, and it is hypothesized that infectious agents may be involved in the etiology. Epstein-Barr virus DNA is found in <40% of patients with AIDS-related S-NHL, suggesting that other oncogenic viruses, such as polyomaviruses, may play a role in pathogenesis. We analyzed AIDS-related S-NHL samples, NHL samples from HIV-negative patients, peripheral blood leukocytes from HIV-infected and -uninfected patients without NHL, and lymph nodes without tumors from HIV-infected patients. Specimens were examined by polymerase chain reaction analysis with use of primers specific for an N-terminal region of the oncoprotein large tumor antigen (T-ag) gene conserved among all three polyomaviruses (simian virus 40 [SV40], JC virus, and BK virus). Polyomavirus T-ag DNA sequences, proven to be SV40-specific, were detected more frequently in AIDS-related S-NHL samples (6 of 26) than in peripheral blood leukocytes from HIV-infected patients (6 of 26 vs. 0 of 69; p = .0001), NHL samples from HIV-negative patients (6 of 26 vs. 0 of 10; p = .09), or lymph nodes (6 of 26 vs. 0 of 7; p = .16). Sequences of C-terminal T-ag DNA from SV40 were amplified from two AIDS-related S-NHL samples. Epstein-Barr virus DNA sequences were detected in 38% (10 of 26) AIDS-related S-NHL samples, 50% (5 of 10) HIV-negative S-NHL samples, and 57% (4 of 7) lymph nodes. None of the S-NHL samples were positive for both Epstein-Barr virus DNA and SV40 DNA. Further studies of the possible role of SV40 in the pathogenesis of S-NHL are warranted.
Therapeutic and Diagnostic Antibodies to CD146: Thirty Years of Research on Its Potential for Detection and Treatment of Tumors (2017)

CD146 (MCAM, MUC18, S-Endo1) is a transmembrane glycoprotein belonging to both CAM and mucin families. It exists as different splice variants and is cleaved from the membrane by metalloproteases to generate a soluble form. CD146 is expressed by numerous cancer cells as well as being one of the numerous proteins expressed by the vascular endothelium. It has also been identified on smooth muscle cells, pericytes, and some immune cells. This protein was initially described as an actor involved in tumor growth and metastatic dissemination processes. Some recent works highlighted the role of CD146 in angiogenesis. Interestingly, this knowledge allowed the development of therapeutic and diagnostic tools specifically targeting the different CD146 variants. The first anti-CD146 antibody designed to study the function of this molecule, MUC18, was described by the Pr. J.P. Jonhson in 1987. In this review, we will discuss the 30 following years of research focused on the detection, study, and blocking of this protein in physiological and pathological processes.
Performance assessment measures for univariate feedback control (1992)

Abstract A normalized performance index, η( b ), is introduced to characterize the performance of feedback control schemes. η( b ) is attractive because it provides a measure of the proximity of control to minimum variance control, which is the optimal feedback control provided that the process can be described by a linear transfer function with additive disturbance. Both time domain and spectral interpretations of this performance index are discussed. A fast, simple, on‐line method for estimating η( b ) is given, along with some of the statistical properties of the estimator. Simulation and industrial examples demonstrate the utility of η( b /)
Antitumor Immunity After Vaccination With B Lymphoma Cells Overexpressing a Triad of Costimulatory Molecules (2003)

Increasing expression of costimulatory molecules on B lymphoma cells by infection with a recombinant FP virus encoding B7-1, ICAM-1, and LFA-3 stimulates antitumor immune responses in vivo and may provide a novel strategy for treating patients with B-cell malignancies.
Novel mutatıons and diverse clinical phenotypes in recombınase-activating gene 1 deficiency (2012)

Epigenetic factors such as compound genetic defects, enviromental factors, and exposure to recurrent infections may modify phenotypical characteristics of RAG deficiencies. Inoculation of live vaccines such as BCG should be postponed until primary immunodeficiency disease is excluded with appropriate screening tests in suspected cases.
Electrical enhancement of biocide efficacy against Pseudomonas aeruginosa biofilms (1992)

When applied within a low-strength electric field (+/- 12 V/cm) with a low current density (+/- 2.1 mA/cm2), several industrial biocides exhibited enhanced killing action against Pseudomonas aeruginosa biofilms grown on stainless steel studs. Biocide concentrations lower than those necessary to kill planktonic cells of P. aeruginosa (1, 5, and 10 ppm of the active ingredients of kathon, glutaraldehyde, and quaternary ammonium compound, respectively) were bactericidal within 24 h when applied within our electrified device.
Effect of beta radiation on proliferating human Tenon's capsule fibroblasts. (1991)

The effects of different doses of beta radiation from a strontium-90 source on the proliferation of human Tenon's capsule fibroblasts were studied. The cultured fibroblasts were exposed to doses of 100, 250, 500, 750, 1000, 1500, and 3000 rads, and cell numbers were counted at days 3, 7, and 14. Treatment inhibited the proliferation of the fibroblasts. At seven days the cells exposed to 3000 rads showed a decrease relative to the starting cell numbers, and at 14 days the cells exposed to 1500 and 3000 rads showed a decrease in cell numbers. The doses of radiation which inhibited cell proliferation more than 50% (at day 7 and 14) and yet did not cause a decrease in the cell population were 500, 750, and 1000 rads. beta Radiation reduces the proliferation of human Tenon's capsule fibroblasts, and at higher doses this effect may be more pronounced one and two weeks after irradiation.
Rat apolipoprotein E mRNA. Cloning and sequencing of double-stranded cDNA. (1983)

A 900-base pair clone corresponding to rat liver apolipoprotein E (apo-E) mRNA, and containing a 3'-terminal poly(A) segment, was identified from a library of rat liver cDNA clones in the plasmid pBR322 by specific hybrid selection and translation of mRNA. A restriction endonuclease DNA fragment from this recombinant plasmid was used to clone the 5'-terminal region of the apo-E mRNA by primed synthesis of cDNA. A portion of the double-stranded cDNA corresponding to the 3'-terminal region of apo-E mRNA was subcloned into the bacteriophage M13mp7 and employed as a template for the synthesis of a radioactively labeled, cDNA hybridization probe. This cDNA probe was used in a RNA-blot hybridization assay that showed the length of the apo-E mRNA to be about 1200 nucleotides. The hybridization assay also demonstrated that apo-E mRNA is present in rat intestine, but at about a 100-fold lower level than that of the rat liver. The nucleotide sequence of rat liver apo-E mRNA was determined from the cloned, double-stranded cDNAs. The amino acid sequence of rat liver apo-E was inferred from the nucleotide sequence, which showed that the mRNA codes for a precursor protein of 311 amino acids. A comparison to the NH2-terminal amino acid sequence of rat plasma apo-E indicated that the first 18 amino acids of the primary translation product are not present in the mature protein and are probably removed during co-translational processing. The coding region was flanked by a 3'-untranslated region of 109 nucleotides, which contained a characteristic AAUAAA sequence that ended 13 nucleotides from a 3'-terminal poly(A) segment. At the 5'-terminal region of the mRNA, 23 nucleotides of an untranslated region were also determined. The inferred amino acid sequence of mature rat apo-E, which contains 293 amino acids, was compared to the amino acid sequence of human apo-E, which contains 299 amino acids. Using an alignment that permitted a maximum homology of amino acids, it was found that overall, 69% of the amino acid positions are identical in both proteins. The amino acid identities are clustered in two broad domains separated by a short region of nonhomology, an NH2-terminal domain of 173 residues where 80% are identical, and a COOH-terminal domain of 84 residues where 70% are identical. These two domains may be associated with specific functional roles in the protein.
Neuroprotective role of astrocytes in cerebral ischemia: Focus on ischemic preconditioning (2005)

Following focal cerebral ischemia ("stroke") a complex and dynamic interaction of vascular cells, glial cells, and neurons determines the extent of the ensuing lesion. Traditionally, the focus has been on mechanisms of damage, while recently it has become clear that endogenous mechanisms of protection are equally important for the final outcome. Glial cells, in particular astrocytes, have always been viewed as supporters of neuronal function. Only recently a very active role for glial cells has been emerging in physiology and pathophysiology. Not surprisingly, then, specific protective pathways have been identified by which these cells can protect or even help to regenerate brain tissue after acute insults. However, as exemplified by the existence of the glial scar, which forms around lesioned brain tissue, is composed mainly of astrocytes and plays a key role in regeneration failure, it is an oversimplification to assign merely protective functions to astrocytes. The present review will discuss the role of astrocytes in ischemic brain injury with a focus on neuroprotection in general. In this context we will consider particularly the phenomenon of "ischemic tolerance," which is an experimental paradigm helpful in discriminating destructive from protective mechanisms after cerebral ischemia.
1997 construction & design survey. (1997)

Managed care might seem to be putting a damper on healthcare construction, but in fact it's one of several industry changes creating opportunities for architectural and design firms. One example of a trend toward making surroundings as pleasant as possible is the west campus expansion at East Texas Medical Center in Tyler (left). Designed and built by Ellerbe Becket and completed in 1995, the project, including a nine-story medical office building, features artwork and rooftop gardens.
The Control of Progesterone Secretion During the Estrous Cycle and Early Pseudopregnancy in the Rat: Prolactin, Gonadotropin and Steroid Levels Associated with Rescue of the Corpus Luteum of Pseudopregnancy12 (1975)

The hormonal factors associated with converting a corpus luteum of estrous cycle into a corpus luteum of pseudopregnancy were studied by measuring LH and FSH prolactin, estradiol and progesterone levels in decapitated rats during the 4-day estrous cycle and a comparable time of pseudopregnancy (lights on 0600-0800 hr.). During the estrous cycle, prolactin, LH and FSH remained low and unchanging except on the afternoon of proestrus, when typical proestrous surges were observed. In contrast, estradiol levels began to increase on D-1, from baseline values of 7 pg/ml to approximately 15-20 pg/ml. These levels were maintained until the afternoon of D-2 when estradiol further increased to reach peak levels of 40-50 pg/ml by 0900 hr on proestrus. Estradiol then declined in relation to the increase in LH secreation and had returned to baseline by estrus. Progesterone secretion by the corpora lutea of the cycle also increased on the afternoon of D-1 and reached a maximum value of 25-30 ng/ml early on the morning of D-2. At this time, a precipitious fall in progesterone occurred, returning to baseline values of 5-1- ng/ml by 0700 on D-2 signifying the regression of the corpora lutea of the cycle. Progesterone remained low thereafter until the afternoon of proestrus when levels increased in response to the proestrus when levels increased in response to the proestrous surge of LH. Following cervical stimulation at 1900 hr on proestrus, no differences were noted, with respect to the estrous cycle, in LH, FSH or estradiol secreation through the afternoon of D-2. Surprisingly, progesterone levels did not differ in the cycle and pseudopregnancy until the early morning of D-29 instead of progesterone levels falling to baseline as they had during the cycle, the corpora lutea of pseudopregnancy were rescused, progesterone increasing dramatically to reach levels of 45-50 ng/ml by 1700 hr on that same day. The only difference in hormone secretion that was noted which could account for this marked divergence in progesterone secretion was the pattern of prolactin secretion following cervical stimulation. In contrast to the low levels seen during the estrous cycle, biphasio surges of prolactin secretion occured each day, one being nocturnal (0100-0900 hr) and the other diurnal (1500-2100 hr). The rescue of the corpus luteum occured in association with the nocturnal surge on D-2. These results suggest that nocturnal surge on D-2, PROLACTIN IS THE MAJOR Luteotropic stimulus which transforms and estrous cycle into pseudopregnancy by prolonging progesterone secretion from the corpus luteum. Moreover, if LH is important for progesterone secretion, no changes were observed in the pattern of LH secretion which can account for the rescue of the corpus luteum.
A proposed mechanism for nitrogen acquisition by grass seedlings through oxidation of symbiotic bacteria (2012)

In this paper we propose and provide evidence for a mechanism, oxidative nitrogen scavenging (ONS), whereby seedlings of some grass species may extract nitrogen from symbiotic diazotrophic bacteria through oxidation by plant-secreted reactive oxygen species (ROS). Experiments on this proposed mechanism employ tall fescue (Festuca arundinaceae) seedlings to elucidate features of the oxidative mechanism. We employed 15N(2) gas assimilation experiments to demonstrate nitrogen fixation, direct microscopic visualization of bacteria on seedling surfaces to visualize the bacterial oxidation process, reactive oxygen probes to test for the presence of H(2)O(2) and cultural experiments to assess conditions under which H(2)O(2) is secreted by seedlings. We also made surveys of the seedlings of several grass species to assess the distribution of the phenomenon of microbial oxidation in the Poaceae. Key elements of the proposed mechanism for nitrogen acquisition in seedlings include: 1) diazotrophic bacteria are vectored on or within seeds; 2) at seed germination bacteria colonize seedling roots and shoots; 3) seedling tissues secrete ROS onto bacteria; 4) bacterial cell walls, membranes, nucleic acids, proteins and other biological molecules are oxidized; 5) nitrates and/or smaller fragments of organic nitrogen-containing molecules resulting from oxidation may be absorbed by seedling tissues and larger peptide fragments may be further processed by secreted or cell wall plant proteases until they are small enough for transport into cells. Hydrogen peroxide secretion from seedling roots and bacterial oxidation was observed in several species in subfamily Pooideae where seeds possessed adherent paleas and lemmas, but was not seen in grasses that lacked this feature or long-cultivated crop species.
Imaging Artificial Caries on the Occlusal Surfaces with Polarization-Sensitive Optical Coherence Tomography (2006)

Polarization-sensitive optical coherence tomography (PS-OCT) is a nondestructive imaging system that can utilize near-infrared (IR) light to produce depth-resolved images of dental enamel and has the potential to monitor early enamel occlusal caries. The objective of this study was to investigate the relationship between the magnitude of backscattered light and depolarization recorded by PS-OCT with changes in the enamel mineral volume in an artificial caries model. Artificial lesions were created on a selected region on the occlusal surfaces of sound posterior teeth (n=10) using a well-characterized 14-day pH cycling model. An all-fiber-based PS-OCT system operating at 1,310 nm was used to collect serial images at day 0 and day 14 prior to tooth sectioning. The quantitative mineral content profile and relative mineral loss, DeltaZ (%volxmicrom), of the carious enamel samples were obtained from transverse sections using high-resolution digital microradiography (DM). Line profiles of PS-OCT and DM images were used to evaluate the artificial caries severity and depth. The integrated reflectivity of the perpendicular-axis PS-OCT image, quantifying lesion severity, was correlated to the DeltaZ of the caries lesions. There was also a strong correlation between the lesion depth calculated from both imaging modalities. PS-OCT can image and quantify artificial occlusal caries by measuring the increase in backscattering and depolarization of near-IR light. This optical method has promising applications for in vivo detection and monitoring of early enamel occlusal caries.
Adaptive filtering in subbands with critical sampling: analysis, experiments, and application to acoustic echo cancellation (1992)

An exact analysis of the critically subsampled two-band modelization scheme is given, and it is demonstrated that adaptive cross-filters between the subbands are necessary for modelization with small output errors. It is shown that perfect reconstruction filter banks can yield exact modelization. These results are extended to the critically subsampled multiband schemes, and important computational savings are seen to be achieved by using good quality filter banks. The problem of adaptive identification in critically subsampled subbands is considered and an appropriate adaptation algorithm is derived. The authors give a detailed analysis of the computational complexity of all the discussed schemes, and experimentally verify the theoretical results that are obtained. The adaptive behavior of the subband schemes that were tested is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Specific recognition nucleotides and their DNA context determine the affinity of E2 protein for 17 binding sites in the BPV-1 genome. (1989)

The DNA context of nucleotides that a protein recognizes can influence the strength of the protein-DNA interaction. Moreover, in prokaryotes, understanding the quantitative differences in binding affinities that result in part from the DNA context is often important in describing regulatory mechanisms. Nevertheless, these issues have not been a major focus yet for the investigation of protein-DNA interactions in eukaryotes. In this study, we explored the binding specificity and the range of affinities that the BPV-1 E2 transcriptional activator has for DNA. Because E2 binding sites are positioned near several different BPV-1 promoters, such quantitative information may be important to understand transcriptional regulatory mechanisms in BPV-1. Gel retardation assays and DNA footprinting were used to quantitate the affinities of the E2 binding sites in the viral genome. In the process, five sites were discovered, which, on the basis of sequence, had not been predicted previously to interact with the E2 protein. Equilibrium and kinetic studies show that the range of E2 affinities of the 17 sites varied over 300-fold. The sequence elements responsible for E2 recognition of DNA were determined by missing contact analysis of several sites and a point mutation analysis of one site. The results presented show that the affinity of an E2 binding site is to a large extent determined by the availability of specific contacts, but the data also strongly suggest that DNA structure plays an important role.