gebhart/patrepeval huggingface dataset:
Genetic Analysis of Glucose Tolerance in Inbred Mouse Strains: Evidence for Polygenic Control (1988)

To determine genetic factors involved in diabetes susceptibility in inbred strains of mice, we initially evaluated differences in fed plasma glucose and insulin concentrations among six strains (AKR/J, C3H/HeJ, C57BL/6J, C57L/J, DBA/2J, and SWR/J). There was considerable variation in fed plasma glucose concentration, with C3H/HeJ mice the most glucose tolerant (174 +/- 7 mg/dl) and C57BL/6J mice the least glucose tolerant (252 +/- 7 mg/dl, P less than .0001 vs. C3H/HeJ mice). Glycosylated hemoglobin of C57BL/6J mice (4.0 +/- 0.06%) was also higher than that of C3H/HeJ mice (3.52 +/- 0.06%, P less than .0001). The fed plasma insulin concentration did not differ between these two strains. Glucose tolerance was further evaluated in overnight-fasted C3H/HeJ and C57BL/6J mice by an intraperitoneal glucose tolerance test (IPGTT). Although fasting plasma glucose did not differ, the most remarkable difference in plasma glucose during IPGTT between C57BL/6J and C3H/HeJ mice was noted at 30 min (489 +/- 29 vs. 227 +/- 20 mg/dl, P less than .001). To determine the number of genes involved in the phenotypic difference in glucose tolerance, C57BL/6J males were crossed with C3H/HeJ females (F1, C3H/HeJ X C57BL/6J), and the F1 hybrid females were backcrossed with C57BL/6J males (backcrossed, F1 X C57BL/6J). Plasma glucose after 30 min on IPGTT was 219 +/- 8 (n = 21), 456 +/- 18 (n = 23), and 292 +/- 13 (n = 23) mg/dl for C3H/HeJ, C57BL/6J, and F1 mice, respectively (P less than .001 for all comparisons).(ABSTRACT TRUNCATED AT 250 WORDS)
The gag gene products of human immunodeficiency virus type 1: alignment within the gag open reading frame, identification of posttranslational modifications, and evidence for alternative gag precursors (1988)

Seven human immunodeficiency virus gag polypeptides were identified in the purified virus and in infected CD4+ lymphocytes by peptide mapping and limited amino acid sequencing of immune-purified proteins. Two gag polyproteins of 55,000 (p55) and 41,000 (p41) daltons were rapidly labeled and readily processed into the major internal gag proteins that were aligned within the gag open reading frame (ORF) as NH2-p16 (MA)-p24 (CA)-p9 (NC)-p7-COOH. The myristoylated p16 (matrix, MA) protein was processed from the myristoylated p55 gag precursor protein. The immunoreactivity of the p16 (MA) protein with region-specific gag antisera and the conservation of the N-terminal myristyl group of the p55 precursor protein in p16 (MA) confirmed its position as the N-terminal-most protein. The p9 (nucleocapsid, NC) protein was localized to residue 378 of the gag ORF, next to the C terminus of the p24/p25 (core antigen, CA) protein. The p9 protein had a repeating Cys residue containing motif which is found in the nucleic acid-binding Cys residue-containing proteins of retroviruses. The p24 (CA) protein, which was localized to residue 133 of the gag ORF, was apparently derived by C-terminal processing of an intermediate polypeptide, p25. Both the mature p24 (CA) and p16 (MA) proteins were phosphorylated at Ser residue(s). We also identified two forms of gag p41 species, one resulting from the C-terminal processing of p55 and the other originating either from N-terminal processing of p55 or from de novo synthesis.
Enoyl-Acyl Carrier Protein Reductase (fabI) Plays a Determinant Role in Completing Cycles of Fatty Acid Elongation in Escherichia coli (1995)

The role of enoyl-acyl carrier protein (ACP) reductase (E.C. 1.3.1.9), the product of the fabI gene, was investigated in the type II, dissociated, fatty acid synthase system of Escherichia coli. All of the proteins required to catalyze one cycle of fatty acid synthesis from acetyl-CoA plus malonyl-CoA to butyryl-ACP in vitro were purified. These proteins were malonyl-CoA:ACP transacylase (fabD), beta-ketoacyl-ACP synthase III (fabH), beta-ketoacyl-ACP reductase (fabG), beta-hydroxydecanoyl-ACP dehydrase (fabA), and enoyl-ACP reductase (fabI). Unlike the other enzymes in the cycle, FabA did not efficiently convert its substrate beta-hydroxybutyryl-ACP to crotonyl-ACP, but rather the equilibrium favored formation of beta-hydroxybutyryl-ACP over crotonyl-ACP by a ratio of 9:1. The amount of butyryl-ACP formed depended on the amount of FabI protein added to the assay. Extracts from fabI(Ts) mutants accumulated beta-hydroxybutyryl-ACP, and the addition of FabI protein to the fabI(Ts) extract restored both butyryl-ACP and long-chain acyl-ACP synthesis. FabI was verified to be the only enoyl-ACP reductase required for the synthesis of fatty acids by demonstrating that purified FabI was required for the elongation of both long-chain saturated and unsaturated fatty acids. These results were corroborated by analysis of the intracellular ACP pool composition in fabI(Ts) mutants that showed beta-hydroxybutyryl-ACP and crotonyl-ACP accumulated at the nonpermissive temperature in the same ratio found in the fabI(Ts) extracts and in the in vitro reconstruction experiments that lacked FabI. We conclude that FabI is the only enoyl-ACP reductase involved in fatty acid synthesis in E. coli and that the activity of this enzyme plays a determinant role in completing cycles of fatty acid biosynthesis.
Immune response to Clostridium difficile infection (1996)

Clostridiurn difficile produces two toxins (A and B) which cause antibiotic-associated diarrhoea and pseudomembranous colitis. One of the most puzzling aspects of C. difficile infection is the wide spectrum of clinical presentation which ranges from asymptomatic carriage to fulminant, life-threatening colitis. This review examines the hypothesis that immune responses to C. difficile underlie these dramatic variations in disease presentation and course. Animals can be protected from C. difficile colitis by passive or active immunization against toxins A and B. Human antibody responses to these toxins are evident in approximately 60% of the general population. A number of clinical studies indicate that antitoxin responses in both serum and intestinal secretions may be protective whereas an inadequate immune response predisposes to severe or recurrent C. difficile diarrhoea. Thus there is now considerable interest in developing methods for passive and active immunization to combat this prevalent nosocomial intestinal pathogen. European Journal of Gastroenterology & Hepatology 1996 8:1048–1053
The antioxidant and radical scavenging activities of black pepper (Piper nigrum) seeds (2005)

Water and ethanol crude extracts from black pepper (Piper nigrum) were investigated for their antioxidant and radical scavenging activities in six different assay, namely, total antioxidant activity, reducing power, 1,1-Diphenyl-2-picryl-hydrazyl (DPPH) free radical scavenging, superoxide anion radical scavenging, hydrogen peroxide scavenging, and metal chelating activities. Both water extract (WEBP) and ethanol extract (EEBP) of black pepper exhibited strong total antioxidant activity. The 75 microg/ml concentration of WEBP and EEBP showed 95.5% and 93.3% inhibition on peroxidation of linoleic acid emulsion, respectively. On the other hand, at the same concentration, standard antioxidants such as butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT) and alpha-tocopherol exhibited 92.1%, 95.0%, and 70.4% inhibition on peroxidation of linoleic acid emulsion, respectively. Also, total phenolic content in both WEBP and EEBP were determined as gallic acid equivalents. The total phenolics content of water and ethanol extracts were determined by the Folin-Ciocalteu procedure and 54.3 and 42.8 microg gallic acid equivalent of phenols was detected in 1 mg WEBP and EEBP.
Na+-K+-ATPase α-subunit containing Q905-V930 of gastric H+-K+- ATPase α preferentially assembles with H+-K+-ATPase β (1997)

Amino acids N886-A911 of the rat Na + -K + -ATPase α 3 -subunit were replaced by the corresponding region (Q905-V930) of the rat gastric H + -K + -ATPase α-subunit. The chimera (NGH26) was expressed in yeast with the rat Na + -K + -ATPase β 1 -subunit (rβ 1 ), the rat H + -K + -ATPase β-subunit (HKβ), the chimeric β-subunit NHβ 1 (containing the carboxy-terminal ectodomain of HKβ), or the chimeric β-subunit HNβ 1 (containing the carboxy-terminal ectodomain of rβ 1 ). Increased resistance to trypsin digestion indicated that NGH26 preferentially assembled with HKβ and NHβ 1 rather than with rβ 1 or HNβ 1 Ouabain binding also indicated that more functional complexes were assembled when NGH26 was expressed with HKβ or NHβ 1 These results suggest that the sequence Q905-V930 interacts with the HKβ-subunit on the extracellular side of the cell membrane. The NGH26+HKβ complex is less stable than α 3 +HKβ when heated and also has a lower binding affinity for ouabain [dissociation constant (K d ) = 63 nM] compared with α 3 +rβ 1 or α 3 +HKβ (K d = 5-10 nM). In contrast, the NGH26+NHβ 1 complex is thermally as stable as α 3 +Rβ 1 complexes, and its ouabain binding affinity (K d = 10 nM) is the same as the wild type. These results indicate that the amino acids Q905-V930 of the rat gastric H + -K + -ATPase α-subunit preferentially associate with the extracellular domain of H + -K + -ATPase β-subunit to form functional pump complexes and that the cytoplasmic and/or transmembrane region of the β-subunit influences the stability of the αβ complexes.
On-stage selection of single round spermatids using a vital, mitochondrion-specific fluorescent probe MitoTracker™ and high resolution differential interference contrast microscopy (1999)

The selection of individual round spermatids for round spermatid injection (ROSI), a prerequisite for the successful application of this infertility treatment, has been hampered by the ambiguous definition of a round spermatid and the lack of specific vital and non-vital markers. Using cells from rhesus monkey and bull, we describe a non-invasive method for the on-stage selection of individual round spermatids for ROSI, based on the polarized patterns of mitochondria, visualized in live round spermatid cells by epifluorescence microscopy after incubation with MitoTracker(TM), a vital, mitochondrion-specific fluorescent probe. The correct identification of live round spermatid was confirmed by the presence of the acrosomal granule or acrosomal cap in parallel observations by Nomarski differential interference contrast microscopy. The existence of mitochondrial polarization was first established by the labelling of MitoTracker-tagged round spermatids with spermatid-specific antibodies against proteins of nascent sperm accessory structures combined with antibodies against a nuclear pore complex component, known to disappear at the round spermatid stage. Using an inverted microscope equipped with epifluorescence, the round spermatids can be individually selected from a heterogeneous population of testicular cells labelled with MitoTracker dyes. A major advantage of this approach is that the dyes are incorporated into the paternal mitochondria, destined for rapid elimination after fertilization. In addition, the relatively high excitation and emission wavelengths of MitoTracker dyes are less harmful to DNA after their photon excitation. Before the appropriate clinical testing is conducted, the MitoTracker-based round spermatid selection may be instrumental in the training of clinical staff.
<title>Fiber-coupling technique for high-power diode laser arrays</title> (1998)

Monolithic linear arrays of diode lasers, also known as diode laser bars, are the basic elements for most high-power laser applications such as solid-state laser pumping or material processing. Cylindrical microlenses used as fast- axis collimators for 10-mm diode bars require very high angles of aperture (up to 100 degree FW1/e2, equivalent to a numerical aperture of approx. 0.8) to capture most of the emitted laser power. For the efficient longitudinal pumping of laser rods, or the narrow focusing of the diode laser radiation (fiber coupling, material processing), high- quality microlenses with small lens aberrations are necessary to avoid power losses and beam quality degradation. A technique for coupling the output of high- power diode laser bars into one multimode fiber with high efficiency, easy alignment requirements and low manufacturing costs is demonstrated using a single fiber with core diameter down to 400 micrometers . This technique comprises two micro step-mirrors for beam shaping. The overall efficiency from one diode-laser bar to fiber is 71% with 20 W cm laser power through the fiber. Coupling of 12 diode laser bars and power of 200 W out of a fiber with core diameter of 0.8 mm and NA equals 0.2 is achievable with this technique.
Ketamine: a review of its pharmacologic properties and use in ambulatory anesthesia. (1992)

The administration of intravenous agents is the most commonly used method in Canada and the United States to produce sedation or general anesthesia for dental procedures. Ketamine, a dissociative anesthetic, has several advantageous physical, pharmacokinetic, and pharmacodynamic properties. It can be used to induce anesthesia, sedation, analgesia, and amnesia. Ketamine can maintain functional residual capacity, induce bronchodilation, and avoid cardiovascular depression. However, adverse effects have been demonstrated, such as cardiovascular stimulation and unpleasant emergence phenomena, both of which may be modulated by supplementation with benzodiazepines. An increase in the use of ketamine for ambulatory anesthesia has recently been advocated. This review of the literature supports the use of ketamine as an effective agent for selected anesthetic procedures.
Flexible synchronized control of dual inverter-fed traction drive during overmodulation (2008)

Analysis of operation of dual inverter-fed motor drive with synchronized pulsewidth modulation (PWM) in the zone of overmodulation has been performed. This drive topology, which is perspective for traction application, includes two insulated dc sources (with equal or different voltages), feeding two standard three-phase inverters, connected with an open-end winding induction motor. Algorithms of synchronized PWM provide in the zone of overmodulation both continuous synchronization of the phase voltage of the induction motor and required sharing of the output power between two dc sources. Simulation results are given for dual inverter-fed systems with continuous and discontinuous versions of synchronized PWM.
Algorithm for Data Clustering in Pattern Recognition Problems Based on Quantum Mechanics (2001)

We propose a novel clustering method that is based on physical intuition derived from quantum mechanics. Starting with given data points, we construct a scale-space probability function. Viewing the latter as the lowest eigenstate of a Schrödinger equation, we use simple analytic operations to derive a potential function whose minima determine cluster centers. The method has one parameter, determining the scale over which cluster structures are searched. We demonstrate it on data analyzed in two dimensions (chosen from the eigenvectors of the correlation matrix). The method is applicable in higher dimensions by limiting the evaluation of the Schrödinger potential to the locations of data points.
Spectral clustering in the weighted stochastic block model. (2019)

This paper is concerned with the statistical analysis of a real-valued symmetric data matrix. We assume a weighted stochastic block model: the matrix indices, taken to represent nodes, can be partitioned into communities so that all entries corresponding to a given community pair are replicates of the same random variable. Extending results previously known only for unweighted graphs, we provide a limit theorem showing that the point cloud obtained from spectrally embedding the data matrix follows a Gaussian mixture model where each community is represented with an elliptical component. We can therefore formally evaluate how well the communities separate under different data transformations, for example, whether it is productive to take logs. We find that performance is invariant to affine transformation of the entries, but this expected and desirable feature hinges on adaptively selecting the eigenvectors according to eigenvalue magnitude and using Gaussian clustering. We present a network anomaly detection problem with cyber-security data where the matrix of log p-values, as opposed to p-values, has both theoretical and empirical advantages.
DNA/RNA Analysis of Phytoplankton by Flow Cytometry (2000)

The past 10 years or so have seen the combination of molecular and biochemical techniques within the confines of cytometry. The use of flow cytometry in microbiology is finally coming of age. This unit carefully defines the criteria for evaluation of DNA and RNA in phytoplankton. Of course not everyone works with phytoplankton, but the methods outlined are very appropriately representative for other organisms. In addition, the unit discusses the methods for evaluating cell cycle and discriminating specific taxa using fluorescent oligonucleotide probes targeted to 18S rRNA.
Effects of a Combination of Beta Carotene and Vitamin A on Lung Cancer and Cardiovascular Disease (1996)

After an average of four years of supplementation, the combination of beta carotene and vitamin A had no benefit and may have had an adverse effect on the incidence of lung cancer and on the risk of death from lung cancer, cardiovascular disease, and any cause in smokers and workers exposed to asbestos.
Quantitative Imaging Biomarkers: The Application of Advanced Image Processing and Analysis to Clinical and Preclinical Decision Making (2012)

The importance of medical imaging for clinical decision making has been steadily increasing over the last four decades. Recently, there has also been an emphasis on medical imaging for preclinical decision making, i.e., for use in pharamaceutical and medical device development. There is also a drive towards quantification of imaging findings by using quantitative imaging biomarkers, which can improve sensitivity, specificity, accuracy and reproducibility of imaged characteristics used for diagnostic and therapeutic decisions. An important component of the discovery, characterization, validation and application of quantitative imaging biomarkers is the extraction of information and meaning from images through image processing and subsequent analysis. However, many advanced image processing and analysis methods are not applied directly to questions of clinical interest, i.e., for diagnostic and therapeutic decision making, which is a consideration that should be closely linked to the development of such algorithms. This article is meant to address these concerns. First, quantitative imaging biomarkers are introduced by providing definitions and concepts. Then, potential applications of advanced image processing and analysis to areas of quantitative imaging biomarker research are described; specifically, research into osteoarthritis (OA), Alzheimer's disease (AD) and cancer is presented. Then, challenges in quantitative imaging biomarker research are discussed. Finally, a conceptual framework for integrating clinical and preclinical considerations into the development of quantitative imaging biomarkers and their computer-assisted methods of extraction is presented.
Frequency of human B cells that differentiate in response to anti-CD3 activated T cells (1991)

Activation of T cells by mAb to the CD3 molecular complex induces the differentiation of many more Ig-secreting cells (ISC) from resting human B cells in bulk cultures than do other modes of polyclonal B cell activation. In the current experiments, a limiting dilution assay was used to demonstrate that this increase in ISC generation reflects an increased frequency of responding B cells. Highly purified B cells were cultured at densities of between 1000 cells and 0.5 cell per microwell with fresh, mitomycin C-treated T cells (T mito) or T cell clones stimulated by immobilized mAb to CD3. After 5 days in culture, the number of wells containing ISC was determined, and the frequency of responding B cells was calculated. The proportion of B cells responding to anti-CD3-stimulated T cells was very large (10.7 +/- 2.8%) and greatly surpassed that induced by other polyclonal activators. B cells cultured with anti-CD3-stimulated T cell clones responded better than did those cultured with T mito. The addition of exogenous IL-2 or IL-6 to cultures supported by activated T mito enhanced the frequency of responding B cells, whereas IL-4 did not increase the generation of ISC and inhibited the augmentation of B cell responses induced by IL-2. Supplementation of cultures with mitomycin C-treated B cells as accessory cells had less of an effect. The addition of both accessory cells and IL-2 markedly increased B cell responsiveness, with precursor frequencies of 60 to 80% noted. In some experiments, cultures were carried out for 7 to 14 days and supernatants were analyzed for IgM, IgG, and IgA secretion. B cells activated by anti-CD3-stimulated T cells produced all three Ig isotypes. When the classes of Ig produced by single B cells were examined, it was observed that the stimulation of individual B cell precursors led to the production of multiple Ig isotypes, suggesting that isotype switching occurs in these cultures. These results demonstrate that under optimum culture conditions, T cells stimulated with immobilized anti-CD3 can activate the majority of human peripheral blood B cells to produce Ig and induce isotype switching by many.
The increment of micronucleus frequency in cervical carcinoma during irradiation in vivo and its prognostic value for tumour radiocurability (1999)

A potential usefulness of micronucleus assay for prediction of tumour radiosensitivity has been tested in 64 patients with advanced stage (II B-IV B) cervical carcinoma treated by radiotherapy. The study of cellular radiosensitivity in vitro was conducted in parallel with the study of cellular damage after tumour irradiation in vivo. Radiosensitivity of in vitro cultured primary cells isolated from tumour biopsies taken before radiotherapy was evaluated using cytokinesis-block micronucleus assay. Frequency of micronuclei per binucleated cell (MN/BNC) at 2 Gy was used as a measure of radiosensitivity. Radiation sensitivity in vivo was expressed as per cent increment of micronucleus frequency in cells isolated from biopsy taken after 20 Gy (external irradiation, 10 x 2 Gy) over the pre-treatment spontaneous micronucleus level and was called MN20. Very low correlation (r = 0.324) was observed between micronucleus frequency in vitro and in vivo. Although micronucleus frequency at 2 Gy differed widely between tumours evaluated (mean MN/BNC was 0.224; range 0.08-0.416), no significant correlation was observed between this parameter and clinical outcome. The average increment of micronucleus frequency after 20 Gy amounted to 193% of spontaneous level (range 60-610%) and was independent of spontaneous micronucleation before radiotherapy. In contrast to in vitro results, these from in vivo assay seem to have a predictive value for radiotherapy of cervix cancer. The micronucleus increment in vivo that reached at least 117.5% of pretreatment value (first quartile for MN20 data set) correlated significantly with better tumour local control (P < 0.008) and overall survival (P < 0.045). Our results suggest that evaluation of increment of micronucleus frequency during radiotherapy (after fixed tested dose of 20 Gy) offers a potentially valuable approach to predicting individual radioresponsiveness and may be helpful for individualization of treatment strategy in advanced stage cervical cancer.