gebhart/patrepeval huggingface dataset:
Toxicity studies of retroviral-mediated gene transfer for the treatment of brain tumors (1993)

Retroviral-mediated transfer of the herpes simplex virus thymidine kinase (HSVtk) gene into malignant tumors confers drug susceptibility to the antiviral drug ganciclovir. The authors have recently shown that in situ transduction of the rat 9L brain tumor following HSVtk-producer cell implantation led to tumor regression after ganciclovir administration in treated rats. A wide spectrum of potential adverse effects may, however, be associated with the application of this approach to treat brain tumors, including dissemination of the retroviral vector to nontumoral tissues within or outside the central nervous system, proliferation of the injected murine vector-producer cells at the injection site, immune-mediated responses to the implantation of xenogeneic cells, and damage to the brain from toxic by-products of the HSVtk-ganciclovir interaction. These possibilities were investigated using intracerebral and systemic injections of retroviral vector-producer cells carrying the HSVtk or the lacZ gene in mice, rats, and nonhuman primates. Using the lacZ gene as a reporter gene, no evidence of beta-galactosidase activity consistent with vector transduction was detected in any major body organ in the treated mice or rats. Similarly, the HSVtk gene transfer did not result in toxicity, with or without ganciclovir administration. In studies using rat and monkey models, no proliferation of the vector-producer cells occurred after intracerebral injection. Vector-producer cell survival was limited to 7 to 14 days. High-dose steroid therapy did not appear to extend the survival of these xenogeneic cells in rats. No significant inflammatory response was observed in the meninges or brain parenchyma. Endothelial cells were occasionally transduced in brain capillaries adjacent to the injected site of the vector-producer cells. Injection of producer cells into brain tissue elicited mild edema and reactive gliosis surrounding the injection site, which were probably the cause of a transient toxic response arising 4 to 5 days following injection of the producer cells; short-term administration of dexamethasone eliminated that response. No neurological deficits were observed in the rats or primates treated with the HSVtk vector-producer cells, with or without ganciclovir. In primates injected with producer cells, magnetic resonance imaging before, during, and after ganciclovir administration showed minimal and localized breakdown of the blood-brain barrier without significant edema or mass effect. Similarly, histological examination of the monkeys' brains showed no damage to neurons, astroglia, or myelin. Long-term clinical (> 9 months) and radiological (3 months) assessment of the primates has revealed no evidence of toxicity.(ABSTRACT TRUNCATED AT 400 WORDS)
Prediction of signs of DCT coefficients in block-based lossy image compression (2007)

A practical impossibility of prediction of signs of DCT coefficients is generally accepted. Therefore each coded sign of DCT coefficients occupies usually 1 bit of memory in compressed data. At the same time data of all coded signs of DCT coefficients occupy about 20-25% of a compressed image. In this work we propose an effective approach to predict signs of DCT coefficients in block based image compression. For that, values of pixels of already coded/decoded neighbor blocks of the image are used. The approach consist two stages. At first, values of pixels of a row and a column which both are the nearest to already coded neighbor blocks are predicted by a context-based adaptive predictor. At second stage, these row and column are used for prediction of the signs of the DCT coefficients. Depending on complexity of an image proposed method allows to compress signs of DCT coefficients to 60-85% from their original size. It corresponds to increase of compression ratio of the entire image by 3-9% (or up to 0.5 dB improvement in PSNR).
<title>Optical fractal image processor for noise-embedded targets detection</title> (1993)

A new fractal dimensionality measurement and analysis-based automatic target recognition (ATR) is presented. ATR is a multi-step procedure, such as preprocessing, interest locating, segmenting, feature extracting, and classifying. Physical Optics Corporation has developed a new ATR system, based on fractal image processing, which can perform interest locating, segmenting and feature extraction simultaneously. Experimental results of the proof-of- principle is also presented.
Biochemical studies on the reverse transcriptase and RNase H activities from human immunodeficiency virus strains resistant to 3‘-azido-3‘-deoxythymidine. (1992)

A series of biochemical investigations to compare the DNA polymerase and RNase H functions of the reverse transcriptases (RTs) corresponding to azidothymidine (AZT)-sensitive and -resistant human immunodeficiency virus (HIV) strains are described. Steady-state kinetic studies with purified recombinant enzymes utilizing several templates and three inhibitors, 3' azido-3' deoxythymidine triphosphate (AZTTP), 3-amino-thymidine 5'-triphosphate, and 2',3'-didehydro-2',3'-dideoxythymidine 5'-triphosphate, found consistent 2-4-fold differences between the enzymes from the two strains over a wide pH range. A strong pH dependence for all three inhibitors was found at pH values below 7.4 and suggested an ionizable group on the enzyme with a pK of about 7. The sensitivities of the RNase H activities of the two enzymes to AZTTP and AZTMP were also compared and found to be similar. The nucleotide incorporation fidelities of recombinant RTs corresponding to AZT-sensitive and -resistant clinical isolates were compared and the error specificities determined. No significant differences were found. Both enzymes were equally able to incorporate AZTTP into an elongating M13 DNA strand with concomitant chain termination. Purified wild-type and mutant virions from cell-culture supernatants were compared in "endogenous" DNA synthesis reactions, and the sensitivities of this activity to AZTTP were found to be similar. The contrast between the small differences found in this study and the high level of viral resistance in tissue culture presumably reflects an incomplete understanding of AZT inhibition of HIV in the cell.
Potential treatments and treatment strategies in Creutzfeldt-Jakob disease. (2003)

Creutzfeldt-Jakob disease is a rare neurodegenerative disease that follows a rapidly progressive course, leading to death, usually only a few months from onset. Over the last 30 years, many treatments have been tried for this condition, including a wide variety of antiviral agents and immunomodulating drugs. More recently, potential treatments have been devised that interfere with the pathological processes involved in the formation of the prion protein. Most of these experiments have been performed in in vitro and tissue culture models and have yet to be tried in human prion disease. As yet, no treatment has been of sustained benefit but, currently, a preliminary open-label trial of quinacrine is underway in the UK.
An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC (2004)

The proposed model is based on the measurement of the retention times of 346 tryptic peptides in the 560- to 4,000-Da mass range, derived from a mixture of 17 protein digests. These peptides were measured in HPLC-MALDI MS runs, with peptide identities confirmed by MS/MS. The model relies on summation of the retention coefficients of the individual amino acids, as in previous approaches, but additional terms are introduced that depend on the retention coefficients for amino acids at the N-terminal of the peptide. In the 17-protein mixture, optimization of two sets of coefficients, along with additional compensation for peptide length and hydrophobicity, yielded a linear dependence of retention time on hydrophobicity, with an R2 value about 0.94. The predictive capability of the model was used to distinguish peptides with close m/z values and for detailed peptide mapping of selected proteins. Its applicability was tested on columns of different sizes, from nano- to narrow-bore, and for direct sample injection, or injection via a pre-column. It can be used for accurate prediction of retention times for tryptic peptides on reversed-phase (300-A pore size) columns of different sizes with a linear water-ACN gradient and with TFA as the ion-pairing modifier.
Two-step polymerase chain reactions and restriction endonuclease analyses detect and differentiate ompA DNA of Chlamydia spp (1992)

Specific and sensitive amplification of major outer membrane protein (MOMP) gene (ompA) DNA sequences of Chlamydia species with various MOMP genotypes was achieved by a two-step polymerase chain reaction (PCR). Degenerate, inosine-containing oligonucleotide primers homologous to the 5' and 3' ends of the translated regions of all chlamydial MOMP genes were used in a PCR to amplify a DNA fragment of approximately 1,120 bp. A portion of this DNA fragment was amplified in a second genus-specific reaction that yielded a DNA fragment of approximately 930 bp. A pair of degenerate oligonucleotide primers homologous to internal sequences of the primary DNA fragment was used in this PCR. This method detected three cognate chlamydial genomes in a background of 1 microgram of unrelated DNA. MOMP genes of 13 representative chlamydial MOMP genotypes of the species C. trachomatis, C. pneumoniae, and C. psittaci were amplified. In a secondary PCR, group-specific detection was achieved by the simultaneous use of one genus-specific primer and three primers derived from different fingerprint regions of three major groups of chlamydiae. This multiplex PCR differentiated the groups by the length of the amplified DNA fragments and detected the simultaneous presence of DNA sequences of the Chlamydia spp. with different MOMP genotypes. Further differentiation as ompA restriction fragment length polymorphism types among all chlamydial strains with the various MOMP genotypes analyzed here was achieved by restriction endonuclease analysis of the secondary PCR products. DNA sequences corresponding to the ompA restriction fragment length polymorphism type B577 of C. psittaci were detected in two of seven milk samples from cases of bovine mastitis.
Single Image Haze Removal Using Dark Channel Prior (2010)

In this paper, we propose a simple but effective image prior-dark channel prior to remove haze from a single input image. The dark channel prior is a kind of statistics of outdoor haze-free images. It is based on a key observation-most local patches in outdoor haze-free images contain some pixels whose intensity is very low in at least one color channel. Using this prior with the haze imaging model, we can directly estimate the thickness of the haze and recover a high-quality haze-free image. Results on a variety of hazy images demonstrate the power of the proposed prior. Moreover, a high-quality depth map can also be obtained as a byproduct of haze removal.
Quantum Confinement Effects Enable Photocatalyzed Nitrate Reduction at Neutral pH Using CdS Nanocrystals (1997)

Size-quantized CdS nanocrystals serve as photocatalysts for nitrate reduction at neutral pH under conditions that mimic illumination by sunlight with overall product quantum yields of up to 4% for ∼20 Å, amine-terminated particles. Due to the effects of quantum confinement on electron and hole redox potentials, photocatalyzed nitrate reduction rates depend strongly on the apparent particle size, and the fastest reduction rates are observed with the smallest nanocrystals which have the highest exciton energy. Using a Tafel plot and the empirical pseudopotential model to estimate electron redox potentials, the apparent electron transfer coefficient and the apparent standard rate constant are estimated at 0.23 and 4.0 × 10-12 cm/s, respectively, for amine-terminated particles. The apparent values for these constants indicate sluggish kinetics and the probable influence of adsorption and double-layer effects on the observed reaction rate. The effect of nitrate adsorption on photoreduction rates is described well by a Langmuir−Hinschelwood expression. Nitrate reduction rates are reduced 2-fold or more on negatively charged, carboxy-terminated nanocrystals that electrostatically repel nitrate. Chloride competes with nitrate for access to particle surfaces, and reduced photoreduction rates are observed for both amine- and carboxy-terminated particles with increased NaCl concentration. The rate of photocatalyzed nitrate reduction on the amine-capped particles goes through a minimum at about pH 6.5, whereas the efficiency of nitrate reduction for the carboxy-terminated system decreases monotonically with increasing pH. In the absence of an electron donor other than water, rapid photocorrosion is observed; therefore, formate is used as the sacrificial electron donor in this study.
Cytokine mRNA Degradation in Cardiomyocytes Restrains Sterile Inflammation in Pressure-Overloaded Hearts (2020)

The degradation of cytokine mRNA by Regnase-1 in cardiomyocytes plays an important role in restraining sterile inflammation in failing hearts and the Regnase-1-mediated pathway might be a therapeutic target to treat patients with heart failure.
Clonagem do cDNA e análise filogenética dos genes do hormônio de crescimento da tainha Mugil platanus (Mugilomorpha, Mugilidae) e do agulha-negra Hemiramphus brasiliensis (Atherinomorpha, Hemiramphidae) (2006)

Atherinid and mugilid fishes are currently considered sister groups. However, there are many controversies about this hypothesis. In order to evaluate the phylogenetic relationship between aterinids, mugilids and percomorphs, GH (growth hormone) cDNA sequences of the mullet Mugil platanus (Mugilomorpha) and the halfbeak Hemiramphus brasiliensis (Atherinomorpha) were obtained using the RACE protocol (Rapid Amplification of cDNA Ends). The H. brasiliensis GH cDNA contains an open reading frame of 615 nucleotides encoding a preprotein of 204 amino acid residues, while the partial M. platanus GH cDNA contains an open reading frame of 597 nucleotides encoding a preprotein of 199 amino acid residues. Both hormones exhibit typical GH features when compared to those of mature GHs from other Acanthopterygian fishes. The deduced GH amino acid sequences were used to infer a phylogenetic tree using the maximum parsimony method. The topology found has placed Atherinomorpha and Mugilomorpha within Percomorpha, indicating that mugilids are probably more related to perciforms than atherinids.
LDL particle size in relation to insulin, proinsulin, and insulin sensitivity. The Insulin Resistance Atherosclerosis Study. (1999)

We found an inverse relation of proinsulin to LDL particle size in a large tri-ethnic population with varying degrees of glucose tolerance. This relation was independent of age, BMI, and triglyceride and HDL cholesterol concentrations, and was more pronounced in men than in women.
Adaptive Control of Artificial Pancreas Systems ‐ A Review (2014)

Artificial pancreas (AP) systems offer an important improvement in regulating blood glucose concentration for patients with type 1 diabetes, compared to current approaches. AP consists of sensors, control algorithms and an insulin pump. Different AP control algorithms such as proportional‐integral‐derivative, model‐predictive control, adaptive control, and fuzzy logic control have been investigated in simulation and clinical studies in the past three decades. The variability over time and complexity of the dynamics of blood glucose concentration, unsteady disturbances such as meals, time‐varying delays on measurements and insulin infusion, and noisy data from sensors create a challenging system to AP. Adaptive control is a powerful control technique that can deal with such challenges. In this paper, a review of adaptive control techniques for blood glucose regulation with an AP system is presented. The investigations and advances in technology produced impressive results, but there is still a need for a reliable AP system that is both commercially viable and appealing to patients with type 1 diabetes.
The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW‐LIKE genes (1999)

Mutations at the SCARECROW (SCR) locus in Arabidopsis thaliana result in defective radial patterning in the root and shoot. The SCR gene product contains sequences which suggest that it is a transcription factor. A number of Arabidopsis Expressed Sequence Tags (ESTs) have been identified that encode gene products bearing remarkable similarity to SCR throughout their carboxyl-termini, indicating that SCR is the prototype of a novel gene family. These ESTs have been designated SCARECROW-LIKE (SCL). The gene products of the GIBBERELLIN-INSENSITIVE (GAI) and the REPRESSOR of ga1-3 (RGA) loci show high structural and sequence similarity to SCR and the SCLs. Sequence analysis of the products of the GRAS (GAI, RGA, SCR) gene family indicates that they share a variable amino-terminus and a highly conserved carboxyl-terminus that contains five recognizable motifs. The SCLs have distinct patterns of expression, but all of those analyzed show expression in the root. One of them, SCL3, has a tissue-specific pattern of expression in the root similar to SCR. The importance of the GRAS gene family in plant biology has been established by the functional analyses of SCR, GAI and RGA.
A role for docosahexaenoic acid-derived neuroprotectin D1 in neural cell survival and Alzheimer disease (2005)

Deficiency in docosahexaenoic acid (DHA), a brain-essential omega-3 fatty acid, is associated with cognitive decline. Here we report that, in cytokine-stressed human neural cells, DHA attenuates amyloid-beta (Abeta) secretion, an effect accompanied by the formation of NPD1, a novel, DHA-derived 10,17S-docosatriene. DHA and NPD1 were reduced in Alzheimer disease (AD) hippocampal cornu ammonis region 1, but not in the thalamus or occipital lobes from the same brains. The expression of key enzymes in NPD1 biosynthesis, cytosolic phospholipase A2 and 15-lipoxygenase, was altered in AD hippocampus. NPD1 repressed Abeta42-triggered activation of proinflammatory genes while upregulating the antiapoptotic genes encoding Bcl-2, Bcl-xl, and Bfl-1(A1). Soluble amyloid precursor protein-alpha stimulated NPD1 biosynthesis from DHA. These results indicate that NPD1 promotes brain cell survival via the induction of antiapoptotic and neuroprotective gene-expression programs that suppress Abeta42-induced neurotoxicity.
Cutting Edge: Inflammatory Signaling by Borrelia burgdorferi Lipoproteins Is Mediated by Toll-Like Receptor 2 (1999)

The agent of Lyme disease, Borrelia burgdorferi, produces membrane lipoproteins possessing potent inflammatory properties linked to disease pathology. The recent association of toll-like receptors (TLR) 2 and 4 with LPS responses prompted the examination of TLR involvement in lipoprotein signaling. The ability of human cell lines to respond to lipoproteins was correlated with the expression of TLR2. Transfection of TLR2 into cell lines conferred responsiveness to lipoproteins, lipopeptides, and sonicated B. burgdorferi, as measured by nuclear translocation of NF-kappaB and cytokine production. The physiological importance of this interaction was demonstrated by the 10-fold greater sensitivity of TLR2-transfected cells to lipoproteins than LPS. Futhermore, TLR2-dependent signaling by lipoproteins was facilitated by CD14. These data indicate that TLR2 facilitates the inflammatory events associated with Lyme arthritis. In addition, the widespread expression of lipoproteins by other bacterial species suggests that this interaction may have broad implications in microbial inflammation and pathogenesis.
Impaired Ability of Bone Marrow Stromal Cells to Support B-Lymphopoiesis With Age (1998)

B-lymphopoiesis decreases with age. We studied how aging affects bone marrow stromal cells, because they provide the growth factors and cell contacts required for B-lymphopoiesis. No differences were noted in the cell-surface phenotype of young and old primary-cultured stromal cells. Fluorescence-activated cell sorter-purified stromal cells from old mice were deficient in the ability to support the proliferation of interleukin-7 (IL-7)-specific B-lymphoid cell lines. The kinetics of this response indicated that IL-7 was not immediately available from stromal cells of either age and was further delayed on aged stromal cells. The levels of IL-7 protein within stromal cells were equivalent between young and old animals, suggesting that the production of IL-7 was not altered by aging. Negligible amounts of IL-7 were found either freely secreted or in the extracellular matrix of cultures of young and old marrow. Contact between the lymphoid cells and the primary stromal cells was required for detectable proliferation, suggesting that cell contact was required for the release of IL-7. We propose that stromal cells regulate B-lymphopoiesis by limiting the amount of IL-7 available to the developing precursors. Therefore, we conclude that the age-related decrease in the function of bone marrow stromal cells is related to the impaired release of IL-7.
Functionalized single wall carbon nanotube sensor in a perturbed microwave resonant cavity based toxin/pollutant gas pressure sensor (2010)

The Vlasov and Maxwell’s equations are established and solved numerically to describe the effects of toxin/pollutant gas pressure and functionalized single wall carbon nanotube (SWCNT) sensor in a perturbed microwave resonant cavity. The dependence of the absorption coefficient on incident frequency, toxin/pollutant gas pressure, electron density, and collision frequency is presented. The numerical results illustrate that the resonant frequency shifts by a suitable amount for modest changes in toxin/pollutant gas pressure. It is also illustrated that high density and low collision of the blend of toxin/pollutant gas and SWCNT sensor in a microwave resonant cavity can be employed as broadband absorption of microwave and the detection of toxin/pollutant gas characteristics through adjustments of the amount of toxin/pollutant gas pressure and functionalized SCWNT sensor. The numerical results additionally illustrate that the microwave absorption spectra of the blend of toxin/pollutant gas and SWCNT sensor in a microwave resonant cavity are in good agreement with the available experimental data. The present method is, in principle, applicable to any kind of a single nanofiber, nanowire, silica gel, cotton fiber, and even various types of nanotubes.
Sialosyllactotetraosylceramide, a novel ganglioside antigen detected in human carcinomas by a monoclonal antibody (1985)

A novel ganglioside was detected in a small cell lung carcinoma by TLC-immunostaining of gangliosides with a monoclonal antibody, the C-50 MAb. Structural characterization showed this ganglioside to be IV3NeuAc-LcOse4Cer, a hitherto unknown ganglioside. This ganglioside has also been detected as a minor component in many different carcinomas using the C-50 MAb. The normally dominant CA-50 ganglioside antigen is IV3NeuAc, III4Fuc-LcOse4Cer. Based upon solid-phase binding to IV3NeuAc, III4-LcOse4Cer and IV3NeuAc-LcOse4Cer it is concluded that the C-50 MAb recognizes an epitope present in sialylated type I carbohydrate chains.