gebhart/patrepeval huggingface dataset:
Prevalence studies of GB Virus-C infection using reverse transcriptase-polymerase chain reaction (1996)

Among the three recently described GB viruses (GBV-A, GBV-B, and GBV-C), only GBV-C has been linked to cryptogenic hepatitis in man. Because of the limited utility of currently available research tests to determine antibody response to GBV-C proteins, the prevalence of GBV-C RNA in human sera was studied using reverse transcription-polymerase chain reaction (RT-PCR). The prevalence of GBV-C is higher among volunteer blood donors with elevated serum alanine aminotransferase (ALT) levels (3.9%) than among volunteer blood donors with normal ALT levels (0.8%). Higher rates were also noted among commercial blood donors (12.9%) and intravenous drug users (16.0%). GBV-C was frequently detected in residents of West Africa, where the prevalence was > 10% in most age groups. Approximately 20% of patients diagnosed with either acute or chronic hepatitis C virus (HCV) were found to be positive for GBV-C RNA. In addition, GBV-C RNA sequences were detected in individuals diagnosed with non-A-E hepatitis, with clinical courses ranging from mild disease to fulminant hepatitis. Fourteen of sixteen subjects with or without clinically apparent hepatitis were positive for GBV-C RNA more than 1 year after the initial positive result.
Drug discovery: Past, present and future (1998)

New drug discovery from early on involved a trial-and-error approach on naturally derived materials and substances until the end of the nineteenth century. The first half of the twentieth century witnessed systematic pharmacological evaluations of both natural and synthetic compounds. However, most new drugs until the 1970s were discovered by serendipity. With the exponential development of molecular biology on one hand and computer technology on the other, it became possible from 1980 onwards to place drug discovery on a rational basis. Cloning of genes has led to the development of methodologies for specific receptor-directed and enzyme-directed drug discoveries. Advances in recombinant DNA and transgenic technologies have enabled the production of human hormonal and other endogenous biomolecules as new drugs. As we understand more about the co-ordinating and regulating powers of the cerebral cortex during the next century, especially of the frontal lobe, man may be able to use bio-feedback training to voluntarily regulate the release of neurotransmitters, hormones, and other molecules involved in the regulation of various physiological processes in health as well as in disease.
Phylogenetic analysis of influenza C virus nonstructural (NS) protein genes and identification of the NS2 protein (2000)

The nucleotide sequences of RNA segment 7 (nonstructural protein gene; NS) were compared among 34 influenza C virus strains isolated between 1947 and 1992. The results showed that all the NS genes analysed had the potential to encode NS1 and NS2 proteins of 246 and 182 amino acids, respectively. The deduced amino acid sequence of the previously unidentified NS2 was fairly well conserved, although it was more divergent than the NS1 protein sequence. Moreover, immunoprecipitation experiments with rabbit immune serum against a glutathione S-transferase fusion protein containing the C-terminal region of the 182 amino acid NS2 protein revealed synthesis of a protein with an apparent molecular mass of approximately 22 kDa in infected cells. A phylogenetic analysis showed that the 34 NS genes were split into two distinct groups, A and B. Comparison of the phylogenetic positions of the individual isolates in the NS gene tree with those in the haemagglutinin-esterase (HE) gene tree suggested that most of the influenza C viruses currently circulating in Japan, irrespective of their HE gene lineage, had acquired group B NS genes through reassortment events that presumably occurred either in the 1970s or in the early 1980s.
Representation and recovery of road geometry in YARF (2003)

YARF, like several other road following systems, models the road as features which form concentric circular arcs lying in a flat ground plane. Two approximations are made in order to use a linear estimation technique to determine the spine parameters. The paper demonstrates that errors due to these approximations are reduced substantially by estimating the spine parameters in a data-dependent coordinate system rather than in a vehicle-centered coordinate system. It discusses the problem of estimating the spine parameters in the presence of outlying data. Using standard least squares estimation can result in the vehicle drifting off the road due to errors in the parameter estimates caused by such contaminants in the data. The use of least median squares estimation to overcome these problems is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mutation Rates and Intrinsic Fidelity of Retroviral Reverse Transcriptases (2009)

Retroviruses are RNA viruses that replicate through a DNA intermediate, in a process catalyzed by the viral reverse transcriptase (RT). Although cellular polymerases and host factors contribute to retroviral mutagenesis, the RT errors play a major role in retroviral mutation. RT mutations that affect the accuracy of the viral polymerase have been identified by in vitro analysis of the fidelity of DNA synthesis, by using enzymological (gel-based) and genetic assays (e.g., M13mp2 lacZ forward mutation assays). For several amino acid substitutions, these observations have been confirmed in cell culture using viral vectors. This review provides an update on studies leading to the identification of the major components of the fidelity center in retroviral RTs.
Motility of the spirochete leptospira (1988)

Abstract Spirochetes are a group of bacteria with a unique ultrastructure and a fascinating swimming behavior. This article reviews the hydrodynamics of spirochete motility, and examines the motility of the spirochete Leptospira in detail. Models of Leptospira motility are discussed, and future experiments are proposed. The outermost structure of Leptospira is a membrane sheath, and within this sheath are a helically shaped cell cylinder and two periplasmic flagella. One periplasmic flagellum is attached subterminally at either end of the cell cylinder and extends partway down the length of the cell. In swimming cells, each end of the cell may assume either a spiral or a hook shape. Translational cells have the anterior end spiral shaped, and the posterior end hook shaped. In the model of Berg et al., the periplasmic flagella are believed to rotate between the sheath and the cell cylinder. Rotation of the anterior periplasmic flagellum causes the generation of a gyrating spiral‐shaped wave. This wave is believed sufficient to propel the cells forward in a low‐viscosity medium. The cell cylinder concomitantly rolls around the periplasmic flagella in the opposite direction—which allows the cell to literally screw through a gel‐like viscous medium without slippage. This model is presented, and it is contrasted to previous models of Leptospira motility.
Natural product isolation – how to get from biological material to pure compounds (2013)

Since the last comprehensive review by Otto Sticher on natural product isolation in NPR (O. Sticher, Nat. Prod. Rep., 2008, 25, 517), a plethora of new reports on isolation of secondary compounds from higher plants, marine organisms and microorganisms has been published. Although methods described earlier like the liquid-solid chromatographic techniques (VLC, FC, MPLC, HPLC) or partition chromatographic methods are still the major tools for isolating pure compounds, some developments like hydrophilic interaction chromatography (HILIC) have not been fully covered in previous reviews. Furthermore, examples of using different preparative solid-phase extraction (SPE) columns including molecular imprinting technology have been included. Special attention is given to chiral stationary phases in isolation of natural products. Methods for proper identification of plant material, problems of post-harvest changes in plant material, extraction methods including application of ionic liquids, de-replication procedures during natural product isolation are further issues to be discussed by the review. Selected work published between 2008 and mid-2012 is covered.
Bax interacts with the permeability transition pore to induce permeability transition and cytochromecrelease in isolated mitochondria (1998)

Cytochrome c release and the mitochondrial permeability transition (PT), including loss of the transmembrane potential (Deltapsi), play an important role in apoptosis. Using isolated mitochondria, we found that recombinant Bax and Bak, proapoptotic members of the Bcl-2 family, induced mitochondrial Deltapsi loss, swelling, and cytochrome c release. All of these changes were dependent on Ca2+ and were prevented by cyclosporin A (CsA) and bongkrekic acid, both of which close the PT pores (megachannels), indicating that Bax- and Bak-induced mitochondrial changes were mediated through the opening of these pores. Bax-induced mitochondrial changes were inhibited by recombinant Bcl-xL and transgene-derived Bcl-2, antiapoptotic members of the Bcl-2 family, as well as by oligomycin, suggesting a possible regulatory effect of F0F1-ATPase on Bax-induced mitochondrial changes. Proapoptotic Bax- and Bak-BH3 (Bcl-2 homology) peptides, but not a mutant BH3 peptide nor a mutant Bak lacking BH3, induced the mitochondrial changes, indicating an essential role of the BH3 region. A coimmunoprecipitation study revealed that Bax and Bak interacted with the voltage-dependent anion channel, which is a component of PT pores. Taken together, these findings suggest that proapoptotic Bcl-2 family proteins, including Bax and Bak, induce the mitochondrial PT and cytochrome c release by interacting with the PT pores.
A human calcium-activated potassium channel gene expressed in vascular smooth muscle (1995)

Large-conductance Ca(2+)-activated K+ (BK) channels are widespread and functionally heterogeneous. In other classes of K+ channels, functional heterogeneity derives from large gene families, alternative splicing, heterologous subunit composition, and functional modulation. The molecular basis of mammalian BK channel heterogeneity is unknown, since only a single gene (mSlo) has been identified. BK channels in native vascular smooth muscle have an apparent Ca2+ sensitivity approximately 10-fold greater than native brain or skeletal muscle channels, or cloned mSlo channels. Using mSlo as a low-stringency probe, we screened human arterial smooth muscle and genomic libraries extensively in search of genes or splice variants with novel properties. We isolated the human homologue of mSlo, including two novel splice variant forms, but found no other related genes. Electrophysiological characterization of the hSlo clones in Xenopus oocytes and Chinese hamster ovary cells gave BK currents that were not measurably different from mSlo currents. However, coexpression of hSlo with a recently cloned beta-subunit derived from smooth muscle dramatically increased apparent Ca2+ sensitivity. Thus alpha-subunits alone may not determine Ca2+ sensitivity of vascular smooth muscle BK channels. hSlo was mapped to human chromosome 10q23.1, and the genomic structure was analyzed. Immediately after the amino terminal, two unusual regions of trinucleotide repeating sequences are present. The first of these regions encodes polyglycine, and the second encodes polyserine. Both regions of repeated sequence are conserved between the mouse and human genome.
Identification and Expression of δ-Isoforms of the Multifunctional Ca 2+ /Calmodulin-Dependent Protein Kinase in Failing and Nonfailing Human Myocardium (1999)

Despite its importance for the regulation of heart function, little is known about the isoform expression of the multifunctional Ca2+/calmodulin-dependent protein kinase (CaMKII) in human myocardium. In this study, we investigated the spectrum of CaMKII isoforms delta2, delta3, delta4, delta8, and delta9 in human striated muscle tissue. Isoform delta3 is characteristically expressed in cardiac muscle. In skeletal muscle, specific expression of a new isoform termed delta11 is demonstrated. Complete sequencing of human delta2 cDNA, representing all common features of the investigated CaMKII subclass, revealed its high homology to the corresponding rat cDNA. Comparative semiquantitative reverse transcription-polymerase chain reaction analyses from left ventricular tissues of normal hearts and from patients suffering from dilated cardiomyopathy showed a significant increase in transcript levels of isoform delta3 relative to the expression of glyceraldehyde-3-phosphate dehydrogenase in diseased hearts (101. 6+/-11.0% versus 64.9+/-9.9% in the nonfailing group; P<0.05, n=6). Transcript levels of the other investigated cardiac CaMKII isoforms remained unchanged. At the protein level, by using a subclass-specific antibody, we observed a similar increase of a delta-CaMKII-specific signal (7.2+/-1.0 versus 3.8+/-0.7 optical density units in the nonfailing group; P<0.05, n=4 through 6). The diseased state of the failing hearts was confirmed by a significant increase in transcript levels for atrial natriuretic peptide (292. 9+/-76.4% versus 40.1+/-3.2% in the nonfailing group; P<0.05, n=3 through 6). Our data characterize for the first time the delta-CaMKII isoform expression pattern in human hearts and demonstrate changes in this expression pattern in heart failure.
Rosiglitazone but not losartan prevents Nrf-2 dependent CD36 gene expression up-regulation in an in vivo atherosclerosis model (2008)

The PPARgamma agonist RG exerts antioxidant properties that significantly reduced Nrf-2-dependent CD-36 up-regulation in mice under HFHC diet. Because LST treatment was also associated with a preserved PPARgamma activity, our data suggests that these RG antioxidant effects are partially independent of its PPARgamma metabolizing properties.
Novel phosphonylphosphinyl (P-C-P-C-) analogs of biochemically interesting diphosphates. Syntheses and properties of P-C-P-C-, analogs of isopentenyl diphosphate and dimethylallyl diphosphate (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel phosphonylphosphinyl (P-C-P-C-) analogs of biochemically interesting diphosphates. Syntheses and properties of P-C-P-C-, analogs of isopentenyl diphosphate and dimethylallyl diphosphateRonald W. McClard, Thomas S. Fujita, Kay E. Stremler, and C. Dale PoulterCite this: J. Am. Chem. Soc. 1987, 109, 18, 5544–5545Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://pubs.acs.org/doi/10.1021/ja00252a051https://doi.org/10.1021/ja00252a051research-articleACS PublicationsRequest reuse permissionsArticle Views378Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Imaging magnetically labeled cells with magnetomotive optical coherence tomography (2005)

We introduce a novel contrast mechanism for optical coherence tomography (OCT) whereby the optical scattering of magnetically labeled cells is modified by means of an externally applied magnetic field. This modification is made through the addition of a small electromagnet to the imaging arm of a conventional OCT interferometer. We measure the magnetomotive OCT signal by differencing pairs of axial scans (A-scans) acquired with the magnetic field on and off. Magnetomotive contrast is demonstrated in bulk three-dimensional cell scaffolds containing macrophages labeled with microparticles of iron oxide, demonstrating magnetic-specific contrast over a dynamic range of 30 dB.
A method to preserve sputum for delayed examination (2003)

Examination of sputum cell counts is limited by the need to process samples within hours of expectoration. The validity and repeatability of a method to preserve sputum for delayed processing and examination were investigated in this study. Portions of selected sputum from 39 subjects were dispersed with dithiothreitol (routine method), or were fixed in a dithiothreitol-formaldehyde mixture for 48-72 h before dispersal with trypsin (preservation method). Total and differential cell counts using the two methods were compared; within-method repeatability of the preservation method was also examined. The intraclass correlation coefficient (ICC) for total cell counts and percentage of eosinophils, neutrophils and macrophages in sputum processed by the two methods was 0.89, 0.86, 0.91 and 0.90, respectively. Within-method repeatability (ICC) of the preservation method for the same cellular indices was 0.99, 0.94, 0.97 and 0.97, respectively. The interobserver repeatability for eosinophils, neutrophils and macrophages was 0.96, 0.97 and 0.97 using the preservation method, and 0.96, 0.99 and 0.99 using the routine method, respectively. This method of sputum preservation and dispersal is valid, reliable and convenient, and may be used for delayed processing and examination.
Molecular aspects of virulence of Pasteurella haemolytica. (1990)

Pasteurella haemolytica is represented by two biotypes (A and T), 15 serotypes, and numerous untypable strains. Specific biotypes and serotypes are associated with fibrinous pleuropneumonia (pneumonic pasteurellosis) in cattle, sheep, and goats, septicemic pasteurellosis in lambs, and mastitis in ewes. Four virulence factors have been associated with P. haemolytica: fimbriae, a polysaccharide capsule, endotoxin [lipopolysaccharide (LPS)], and leukotoxin (LKT). The interactions of these virulence factors with components of the pulmonary alveolus are discussed as a model for the pathogenesis of pasteurellosis. Fimbriae on P. haemolytica may enhance colonization of the upper respiratory tract. The capsule of P. haemolytica varies in composition among serotypes. It inhibits complement-mediated serum killing as well as phagocytosis and intracellular killing of P. haemolytica. The capsule enhances neutrophil directed migration and adhesion of P. haemolytica to alveolar epithelium. Pasteurella haemolytica LPS can alter bovine leukocyte functions, by dose-dependent inhibition or augmentation; it is directly toxic to bovine endothelium; it modifies cardiopulmonary hemodynamics; and it elevates circulatory prostanoids, serotonin, cAMP, and cGMP. Leukotoxin is produced by all known serotypes and many untypable strains. Leukotoxin is a poreforming cytolysin that affects ruminant leukocytes and platelets by altering function at low levels but causing lysis at high levels.
Visual localization within LIDAR maps for automated urban driving (2014)

This paper reports on the problem of map-based visual localization in urban environments for autonomous vehicles. Self-driving cars have become a reality on roadways and are going to be a consumer product in the near future. One of the most significant road-blocks to autonomous vehicles is the prohibitive cost of the sensor suites necessary for localization. The most common sensor on these platforms, a three-dimensional (3D) light detection and ranging (LIDAR) scanner, generates dense point clouds with measures of surface reflectivity-which other state-of-the-art localization methods have shown are capable of centimeter-level accuracy. Alternatively, we seek to obtain comparable localization accuracy with significantly cheaper, commodity cameras. We propose to localize a single monocular camera within a 3D prior ground-map, generated by a survey vehicle equipped with 3D LIDAR scanners. To do so, we exploit a graphics processing unit to generate several synthetic views of our belief environment. We then seek to maximize the normalized mutual information between our real camera measurements and these synthetic views. Results are shown for two different datasets, a 3.0 km and a 1.5 km trajectory, where we also compare against the state-of-the-art in LIDAR map-based localization.
Genetics of Reproduction in Domesticated Rainbow Trout (1975)

A population consisting of parental, F1, F2 and backcrosses among two domestic strains of rainbow trout was used to estimate genetic parameters of reproductive performance for hatchery cultured stocks. Data were collected for post-spawning body weight, volume of eggs spawned, egg size, egg number and egg per 100 g body weight for a total of 1,604 2-year-old female progeny. Heritabilities estimated from full-sub comparisons were similar for all five traits and equal to about .20 ± .05 Dominance and epistatic variance was evident for all traits except number of eggs for which genetic variation appeared to be primarily additive. The coefficient of variation was lowest for egg size (18%), intermediate for body weight (23%) and egg number (25%) and highest for egg volume (28%) and eggs per unit body weight (30%). Genetic, environmental and phenotypic correlations among the traits were estimated. Generally, egg volume was highly correlated with egg number (.77 ± .07), egg size (-.55 ± .12) and body weight (.56 ± .11), however, egg volume and number were correlated arithmetically. Environmental correlations of egg volume with egg size and body weight also showed a positive relationship but were low. The correlation with egg number was equal to the genetic correlation. The genetic correlations for body weight with egg size and egg number were .46 ± .13 and .39 ± .14, respectively. Egg size was estimated by the volumetric method so negative correlation estimates indicate a positive relationship. The environmental correlation between body weight and egg size was zero. The genetic correlation between egg number and egg size was small and positive while the environmental correlation was about .20. Egg size showed a strong genetic correlation with eggs per unit body weight (.47 ± .13) while the environmental correlation was only .26. The phenotypic correlations were generally midway between estimates of the genetic and environmental correlation and the three always carried the same sign. It was suggested that selection for egg volume may be the most effective means of improving reproductive performance.
Fluorescence enhancement method for the determination of nucleic acids using cationic cyanine as a fluorescence probe (2004)

A fluorescence enhancement method with a cationic cyanine as a probe was developed for the determination of nucleic acids. Under the experimental conditions, the fluorescence enhancement of cyanine (lambda(ex)/lambda(em)= 524/591.5 nm) was observed in the presence of DNA. The calibration graphs were linear over the range of 0.01-15 microg mL(-1) for both calf thymus DNA (CT DNA) and fish sperm DNA (FS DNA). The limits of detection were 0.005 and 0.007 microg mL(-1) for CT DNA and FS DNA, respectively. The method was applied to the determination of DNA in synthetic and real samples and satisfactory results were obtained. A possible fluorescence enhancement mechanism was also studied.