gebhart/patrepeval huggingface dataset:
Protein N-myristoylation in Escherichia coli: reconstitution of a eukaryotic protein modification in bacteria. (1990)

Protein N-myristoylation refers to the covalent attachment of a myristoyl group (C14:0), via amide linkage, to the NH2-terminal glycine residue of certain cellular and viral proteins. Myristoyl-CoA:protein N-myristoyltransferase (NMT) catalyzes this cotranslational modification. We have developed a system for studying the substrate requirements and biological effects of protein N-myristoylation as well as NMT structure-activity relationships. Expression of the yeast NMT1 gene in Escherichia coli, a bacterium that has no endogenous NMT activity, results in production of the intact 53-kDa NMT polypeptide as well as a truncated polypeptide derived from proteolytic removal of its NH2-terminal 39 amino acids. Each E. coli-synthesized NMT species has fatty acid and peptide substrate specificities that are indistinguishable from those of NMT recovered from Saccharomyces cerevisiae, suggesting that the NH2-terminal domain of this enzyme is not required for its catalytic activity. By using a dual plasmid system, N-myristoylation of a mammalian protein was reconstituted in E. coli by simultaneous expression of the yeast NMT1 gene and a murine cDNA encoding the catalytic (C) subunit of cAMP-dependent protein kinase (PK-A). The fatty acid specificity of N-myristoylation was preserved in this system: [9,10(n)-3H]myristate but not [9,10(n)3H]palmitate was efficiently linked to Gly-1 of the C subunit. [13,14(n)-3H]10-Propoxydecanoic acid, a heteroatom-containing analog of myristic acid with reduced hydrophobicity but similar chain length, was an effective alternative substrate for NMT that also could be incorporated into the C subunit of PK-A. Such analogs have recently been shown to inhibit replication of certain retroviruses that depend upon linkage of a myristoyl group to their gag polyprotein precursors (e.g., the Pr55gag of human immunodeficiency virus type 1). A major advantage of the bacterial system over eukaryotic systems is the absence of endogenous NMT and substrates, providing a more straightforward way of preparing myristoylated, analog-substituted, and nonmyristoylated forms of a given protein for comparison of their structural and functional properties. The system should facilitate screening of enzyme inhibitors as well as alternative NMT fatty acid substrates for their ability to be incorporated into a specific target protein. Our experimental system may prove useful for recapitulating other eukaryotic protein modifications in E. coli so that structure-activity relationships of modifying enzymes and their substrates can be more readily assessed.
GRB990123: The Case for Saturated Comptonization (1999)

The recent simultaneous detection of optical, X-ray and gamma-ray photons from GRB990123 during the burst provides the first broadband multi-wavelength characterization of the burst spectrum and evolution. Here we show that a direct correlation exists between the time-varying gamma-ray spectral shape and the prompt optical emission. This combined with the unique signatures of the time-resolved spectra of GRB990123 convincingly supports earlier predictions of the saturated Comptonization model. Contrary to other suggestions, we find that the entire continuum from optical to gamma-rays can be generated from a single source of leptons (electrons and pairs). The optical flux only appears to lag the gamma-ray flux due to the high initial Thomson depth of the plasma. Once the plasma has completely thinned out, the late time afterglow behavior of our model is the same as in standard models based on the Blandford-McKee (1976) solution.
Dual Analysis of Triglycerides from Certain Common Lipids and Seed Extracts (2011)

A number of reference oils, two commercial oils, and several oil extracts from seeds of Nicotiana species were analyzed for the fatty acid content and also for triglyceride composition. The seed oils were obtained using an accelerated solvent extraction procedure, which was proven to be very efficient and reproducible. The fatty acids were analyzed after the hydrolysis of the oils, using trimethylsilylation and gas chromatography/mass spectrometry (GC/MS) analysis. The levels of sixteen molecular species of triglycerides in the oils were measured after GC separation using MS for identification and flame ionization detection (FID) for quantitation. The results for the fatty acids and those for triglycerides were combined to generate uniform information regarding the composition of the analyzed oils. For a number of oils, the individual triglyceride quantitation and mass spectra were reported for the first time. The study showed that in some cases, oils with similar fatty acid content do not have the same triglycerides profile. The fatty acids and triglycerides profile for selected Nicotiana species were described for the first time in the literature.
Boundary Element Methods in Acoustics (1991)

Focusing exlusively on research and applications involving the use of Boundary Elements to solve problems in acoustics, this book gives basic finite formulations, organization of computations, symmetry considerations and new techniques for improving computational efficiency.
Simplified technetium-99m-EC clearance in adults from a single plasma sample. (1997)

This study suggests that EC clearance could be determined by a simplified single-sample method with an acceptable s.e.e.
Ancillary Approaches to Toxicokinetic Evaluations (1995)

The principal objective of toxicokinetic studies is to assess systemic exposure of the toxicity species to test compound during nonclinical toxicity studies by generation of pharmacokinetic data on the rate, extent, and duration of exposure. Toxicokinetics are normally integrated within the toxicity studies (concomitant); however, there are a number of circumstances when prospective, retrospective, or other ancillary types of toxicokinetic studies are performed in support of toxicity studies. The need for retrospective toxicokinetic studies arises when the original toxicity study was conducted with insufficient plasma concentration determinations, especially when pilot toxicity studies show lack of toxicity or unusual organ toxicities. Examples of ancillary toxicokinetic studies from the Drug Metabolism and Drug Safety departments at The R. W. Johnson Pharmaceutical Research Institute and from the scientific literature are provided that highlight the challenges associated with these alternate approaches. Each example includes a discussion of the rationale for the supportive toxicokinetic study, the specific experimental designs, the data interpretation, and the usefulness of the toxicokinetic data in decision-making. The ancillary toxicokinetic studies cited provided important information on establishing systemic exposure during long-term toxicity studies, allowing comparisons to human exposures, elucidating compound-related toxicities, and explaining lack of toxicity due to autoinduction and resulting low levels of parent compound.
Regulation of IgG antibody titers by the amount persisting of immune‐complexed antigen (1994)

Antigens normally induce an immunoglobulin (Ig)G response which stays at an elevated level for several weeks or months, constituting an important part of the immunological memory. This study investigated factors influencing the level of neutralizing IgG titers against a virus and shows that within the range tested it was independent of the number of initially available and potentially responding T helper and B cells, but was regulated by the amount of specific IgG-immune complexes forming depots of persisting antigen. These findings support the notion that the efficiency of vaccines in inducing long-lasting protective IgG is regulated predominantly by the amount of persisting (and presumably follicular dendritic cell-associated) antigen-antibody complexes.
Microfluidics with foams (2009)

Lab-on-a-chip devices can handle very tiny amounts of fluids, as small as a picolitre. Samples of gas are conveniently encapsulated and transported within bubbles. The generation of these calibrated bubbles involves specific microfluidic devices that we describe. When the bubble concentration is high enough in a channel, they come into contact, and they flow as a crystalline foam. The flow of the foams depends strongly on the arrangement of bubbles within the channel, which entails original dynamical behaviours such as super-stability of the flow, or on the contrary spontaneous oscillations.
Segmentation of intrathoracic airway trees: a fuzzy logic approach (1998)

Three-dimensional (3-D) analysis of airway trees extracted from computed tomography (CT) image data can provide objective information about lung structure and function. However, manual analysis of 3-D lung CT images is tedious, time consuming and, thus, impractical for routine clinical care. We have previously reported an automated rule-based method for extraction of airway trees from 3-D CT images using a priori knowledge about airway-tree anatomy. Although the method's sensitivity was quite good, its specificity suffered from a large number of falsely detected airways. We present a new approach to airway-tree detection based on fuzzy logic that increases the method's specificity without compromising its sensitivity. The method was validated in 32 CT image slices randomly selected from five volumetric canine electron-beam CT data sets. The fuzzy-logic method significantly outperformed the previously reported rule-based method (p < 0.002).
Leveraging off Advances in Internet Technology to Bring Data to the Expert User On-Shore (1999)

This paper was prepared for presentation at the 1999 SPE Annual Technical Conference and Exhibition held in Houston, Texas, 3–6 October 1999.
Chemistry and health effects of polymethoxyflavones and hydroxylated polymethoxyflavones (2008)

Polymethoxyflavones (PMFs) and hydroxylated polymethoxyflavones exist exclusively in citrus genus, especially in the citrus peels which have been used as herbal medicine for several diseases for thousands of years. In this review, the natural occurrence, isolation and separation of PMFs; synthetic scheme of hydroxylated PMF preparation, especially the reaction mechanism of preparation of 5-hydroxylated PMFs; biotransformation and metabolic fate of PMFs; the preliminary study on PMF bioavailability and the close relationship among solubility, permeability, absorption and oral bioavailability are summarized. The published bioactivity data on anti-inflammatory, anti-cancer and anti-atherogenic properties of PMFs have also been detailed along with a report of new findings of hydroxylated PMFs and their potent biological activities.
A Concise Total Synthesis of Dactylol via Ring Closing Metathesis (1996)

A straightforward total synthesis of the cyclooctenoid sesquiterpene dactylol (1) and of 3a-epi-dactylol (13) has been achieved in six synthetic operations. The unusual rearranged bicyclo[6.3.0]undecane isoprenoid skeleton of these target molecules has been formed via an initial three-component coupling triggered by 1,4-addition of a methylcopper reagent (MeLi, CuI, Bu(3)P) to cyclopentenone, followed by trapping of the enolate formed with 2,2-dimethyl-4-pentenal as the electrophile. The aldol 8 thus obtained was elaborated into the trans-disubstituted cyclopentanone derivative 10 which reacted with a methallylcerium reagent to afford a mixture of the tertiary alcohols 11a and 12a. Separation and O-silylation of these diastereoisomers, ring-closing metathesis (RCM) of the resulting dienes 11b and 12b to form the cyclooctene ring using Schrocks molybdenum carbene 5 as a precatalyst, and a final deprotection afforded the title compound and its epimer in excellent yields. This approach clearly surpasses previous ones in terms of efficiency, flexibility, accessibility of the substrates, number of steps, atom economy, and overall yield.
Studies of aggregated gamma-globulin. II. Effect in vivo. (1960)

Summary Injection of aggregated human γ-globulin into the skin of guinea pig, rat and man produced inflammatory changes. Histologically, the injection sites of guinea pigs and rats demonstrated marked polymorphonuclear and mononuclear infiltrations that were maximal at about 24 hr. Intravenous administration of aggregated human γ-globulin, which is strikingly anticomplementary in vitro , rendered the sera of recipient animals deficient in hemolytically active C′ for several hours.
Vif is crucial for human immunodeficiency virus type 1 proviral DNA synthesis in infected cells (1993)

The human immunodeficiency virus type 1 (HIV-1) vif gene encodes a 23-kDa protein of unknown function, also produced by most other known lentiviruses. Vif was found to be essential for the spread of HIV-1 in peripheral blood lymphocytes and in primary macrophages, as well as in some but not all established T-cell lines. Vif was required at the stage of viral particle formation, for cell-to-cell as well as for cell-free transmission of HIV-1. Accordingly, vif-defective viruses could be complemented by the expression of vif in the producer but not in the target cell. vif-defective virions contained wild-type amounts of Gag and Env proteins, reverse transcriptase, integrase, genomic RNA, and partial reverse transcripts. Most importantly, they could enter cells normally, and the vif defect could not be rescued through the use of HIV(MLV [murine leukemia virus]) pseudotypes. Instead, vif-mutant viruses were severely impaired in their ability to complete the synthesis of proviral DNA, once internalized in the target cell. These results suggest that Vif plays a role which is novel for a retroviral protein, in allowing the processing and/or the transport of the internalized HIV core.
Long-range structural effects of a Charcot–Marie–Tooth disease-causing mutation in human glycyl-tRNA synthetase (2007)

Functional expansion of specific tRNA synthetases in higher organisms is well documented. These additional functions may explain why dominant mutations in glycyl-tRNA synthetase (GlyRS) and tyrosyl-tRNA synthetase cause Charcot-Marie-Tooth (CMT) disease, the most common heritable disease of the peripheral nervous system. At least 10 disease-causing mutant alleles of GlyRS have been annotated. These mutations scatter broadly across the primary sequence and have no apparent unifying connection. Here we report the structure of wild type and a CMT-causing mutant (G526R) of homodimeric human GlyRS. The mutation is at the site for synthesis of glycyl-adenylate, but the rest of the two structures are closely similar. Significantly, the mutant form diffracts to a higher resolution and has a greater dimer interface. The extra dimer interactions are located approximately 30 A away from the G526R mutation. Direct experiments confirm the tighter dimer interaction of the G526R protein. The results suggest the possible importance of subtle, long-range structural effects of CMT-causing mutations at the dimer interface. From analysis of a third crystal, an appended motif, found in higher eukaryote GlyRSs, seems not to have a role in these long-range effects.
Segregation analysis of idiopathic scoliosis: Demonstration of a major gene effect (1999)

Segregation analysis using a model with age and gender effects was applied to 101 pedigrees ascertained through a proband with idiopathic scoliosis. The transmission probability model was used to detect major gene effect. When we analyzed the pedigrees where affected status was assigned to persons with a Cobb's angle of more than 5 degrees we did not detect a significant major gene effect. However, when the affected status was assigned to persons with pronounced forms of disease only (a curve of at least 11 degrees) a significant contribution of a major causal gene could be established and inheritance could be described according to a dominant major gene diallele model, assuming incomplete sex and age dependent penetrance of genotypes. According to this model, the pronounced forms of idiopathic scoliosis should never occur in the absence of the mutant allele. This indicates that only the carriers of the mutant allele develop pronounced forms of the disease. At the same time, only a fraction of the carriers of the mutant gene should manifest the disease (30% of males and 50% of females).
Riemannian manifold-based support vector machine for human activity classification in images (2013)

This paper addresses the issue of classification of human activities in still images. We propose a novel method where part-based features focusing on human and object interaction are utilized for activity representation, and classification is designed on manifolds by exploiting underlying Riemannian geometry. The main contributions of the paper include: (a) represent human activity by appearance features from image patches containing hands, and by structural features formed from the distances between the torso and patch centers; (b) formulate SVM kernel function based on the geodesics on Riemannian manifolds under the log-Euclidean metric; (c) apply multi-class SVM classifier on the manifold under the one-against-all strategy. Experiments were conducted on a dataset containing 2750 images in 7 classes of activities from 10 subjects. Results have shown good performance (average classification rate of 95.83%, false positive rate of 0.71%). Comparisons with three other related classifiers provide further support to the proposed method.
Enhanced stimulated Raman scattering in optical parametric oscillators from periodically poled KTiOPO4 (2003)

Enhanced Raman scattering and concurrent Raman oscillation have been observed in nanosecond optical parametric oscillators in the near-infrared spectral region for certain periodicities of periodically poled KTiOPO4. The increased Raman activity is associated with direct excitation of the phonon overtone band by the idler wave. The decrease in efficiency of stimulated Raman scattering at crystal temperature above 80 °C is explained by higher dephasing rate of coherently driven lattice polarization due to interaction with thermally generated phonons.
Functional domains of the granulocyte colony-stimulating factor receptor. (1991)

The granulocyte colony-stimulating factor (G-CSF) receptor has a composite structure consisting of an immunoglobulin(Ig)-like domain, a cytokine receptor-homologous (CRH) domain and three fibronectin type III (FNIII) domains in the extracellular region. Introduction of G-CSF receptor cDNA into IL-3-dependent murine myeloid cell line FDC-P1 and pro-B cell line BAF-B03, which normally do not respond to G-CSF, enabled them to proliferate in response to G-CSF. On the other hand, expression of the G-CSF receptor cDNA in the IL-2-dependent T cell line CTLL-2 did not enable it to grow in response to G-CSF, although G-CSF could transiently stimulate DNA synthesis. Mutational analyses of the G-CSF receptor in FDC-P1 cells indicated that the N-terminal half of the CRH domain was essential for the recognition of G-CSF, but the Ig-like, FNIII and cytoplasmic domains were not. The CRH domain and a portion of the cytoplasmic domain of about 100 amino acids in length were indispensable for transduction of the G-CSF-triggered growth signal.
Role of cytoplasmic vacuoles in varicella-zoster virus glycoprotein trafficking and virion envelopment (1988)

Varicella-zoster virus (VZV) encodes several glycoproteins which are present on both mature viral envelopes and the surfaces of infected cell membranes. Mechanisms of VZV glycoprotein transport and virion envelopment were investigated by both continuous radiolabeling and pulse-chase analyses with tritiated fucose in VZV-infected cells. We studied in detail the large cytoplasmic vacuoles which were present in infected cells but absent from uninfected cells. The specific activity in each subcellular compartment was defined by quantitative electron microscope autoradiography, using a cross-fire probability matrix analysis to more accurately assess the individual compartment demarcated by the silver grains. By these techniques, we documented a progression of activity originating in the Golgi apparatus and traveling through the post-Golgi region into virus-induced cytoplasmic vacuoles and finally to areas of the cellular membrane associated with the egress of viral particles. Significant amounts of radiolabel were not observed in the nucleus, and only low levels of radiolabel were associated with the cellular membrane not involved with the egress of viral particles. In addition, immunolabeling of Lowicryl-embedded VZV-infected cells demonstrated the presence of VZV glycoproteins within cytoplasmic vacuole membranes as well as on virion envelopes. These observations suggested that cytoplasmic vacuoles harbored VZV-specified glycoproteins and were also the predominant site of VZV virion envelopment within the infected cell. Neither enveloped nor unenveloped viral particles were observed within the Golgi apparatus itself.
MiR‐142‐3p as a potential prognostic biomarker for esophageal squamous cell carcinoma (2011)

The main findings suggest that miR-142-3p is involved in the progression of ESCC and is a potential prognostic biomarker for ESCC.
Fentanyl???Diazepam Anesthesia with or without N2O Does Not Attenuate Cardiopulmonary Baroreflex-Mediated Vasoconstrictor Responses to Controlled Hypovolemia in Humans (1988)

Cardiopulmonary baroreceptors located primarily on the low-pressure side of the circulation sense slight reductions in cardiac filling pressures and elicit sustained peripheral vasoconstriction. Because most inhalation and many intravenous anesthetics attenuate arterial baroreflex function, the low-pressure baroreflex may serve a major role in maintaining blood pressure during intraoperative hypovolemia. To activate the low-pressure baroreflex, progressive nonhypotensive reductions in central venous pressure were produced with graded applications of lower body negative pressure (LBNP, -5, -10, -15 mm Hg) in 18 ASA class I patients before elective surgery. This produced linear reductions in stroke volume as determined by impedance cardiography and cardiac output. Cardiopulmonary baroreflex-mediated increases in total and forearm vascular resistance assisted in maintaining stable blood pressure. After ten patients were anesthetized with fentanyl (12.5 micrograms/kg) and diazepam (0.25 mg/kg) and an additional eight received these agents plus supplemental N2O (70%), reflex vasoconstrictor responses to LBNP were not attenuated and, therefore, blood pressure continued to be well maintained despite substantial reductions in cardiac filling pressures. Thus, these anesthetic regimens preserved vasoconstrictor responses mediated by cardiopulmonary baroreflexes. This promoted cardiovascular stability that may be particularly beneficial in patients with cerebral, cardiovascular, or renal disease undergoing surgical procedures with potential for rapid blood loss.