gebhart/patrepeval huggingface dataset:
Computational Insights into the Chemical Structures and Mechanisms of the Chromogenic and Neurotoxic Effects of Aromatic γ-diketones (2003)

The chromogenic properties of various candidate structures, i.e., isoindole monomers and dimers and their derivatives, of the chromophores formed from the reactions of 1,2-diacetylbenzene (1,2-DAB), a typical representative of chromogenic and neurotoxic aromatic γ-diketones, with NH3, amino acids, and proteins, have been calculated by using density functional theory. The calculated results indicate that the isoindole monomers should not exhibit a color, whereas the isoindole derivative dimers should all be colored. Further oxidization of the isoindole derivative dimers can significantly change the colors of the dimers, and the results calculated for the oxidized isoindole derivative dimers are completely consistent with all of the experimental data for the chromogenic and neurotoxic effects of 1,2-DAB. It has been demonstrated that the violet/blue chromophores formed from the reactions of 1,2-DAB with amino acids/proteins under neutral and acidic conditions are likely to be the oxidized isoindole derivative dimer structures (like 7b) cross-linking the proteins, whereas the brown chromophores formed when pH ≥ 7.5 could be the oxidized dimer structures (like 7a) without cross-linking proteins. Our results strongly support the conclusion that the chromogenic effects of aromatic γ-diketones are closely related to their neurotoxic effects and further predict that both the chromogenic and neurotoxic effects are associated with the same chemical reaction process under the neutral and acidic conditions. Such a reaction process most likely starts from the formation of the isoindole−protein adducts followed by the dimerization and further oxidization.
A modeling approach for continuum robotic manipulators: Effects of nonlinear internal device friction (2011)

In recent years, flexible robotic catheter systems have been developed for minimally invasive cardiac surgery. These systems commonly include a passive flexible catheter, which is biocompatible, and an active servo system which provides the actuation for the flexible catheter. To relate control actuation motion of the servo system to catheter motion, models of continuous catheters have been developed. A typical approach is to assume a kinematic model in which the catheter maintains constant curvature along its length when articulated. However, this approach cannot explain the nonlinear behavior of the catheter when the effect of internal friction is considered. In this paper we present a lumped-parameter modeling approach that allows for the inclusion of nonlinear effects, including friction. The proposed approach has been used to model a prototype catheter where internal friction is modeled using a modified Dahl friction model. To evaluate the efficacy of the modeling approach, the simulation results were compared to an experimental catheter prototype. Results show that the proposed approach significantly improves simulation accuracy as compared to the case where friction is not considered. In addition, the effects of friction on catheter performance were investigated using the developed modeling approach.
A ribozyme transcribed by a ribozyme (2011)

Prominent current ideas on how life emerged on Earth include an RNA world hypothesis in which RNA performed informational as well as catalytic functions in the absence of both DNA and protein. Demonstration of a self-replicative system based on ribonucleic acid polymers as both information carriers and catalysts would lend support to such a scenario. A pivotal component of this system would be an RNA dependent RNA polymerase ribozyme capable of replicating its own RNA gene. Recent work from the Holliger group at the Laboratory for Molecular Biology in Cambridge has provided synthetic ribozymes1 that just might foreshadow the future engineering of such self-replicative systems.
Sequence specific generation of a DNA panhardle permits PCR amplication of unknown flanking DNA (1992)

We present a novel method for the PCR amplification of unknown DNA that flanks a known segment directly from human genomic DNA. PCR requires that primer annealing sites be present on each end of the DNA segment that is to be amplified. In this method, known DNA is placed on the uncharacterized side of the sequence of interest via DNA polymerase mediated generation of a PCR template that is shaped like a pan with a handle. Generation of this template permits specific amplification of the unknown sequence. Taq (DNA) polymerase was used to form the original template and to generate the PCR product. 2.2 kb of the beta-globin gene, and 657 bp of the 5' flanking region of the cystic fibrosis transmembrane conductance regulator gene, were amplified directly from human genomic DNA using primers that initially flank only one side of the region amplified. This method will provide a powerful tool for acquiring DNA sequence information.
InP Photonic Integrated Circuit with On-chip Tunable Laser Source for 2D Optical Beam Steering (2013)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text W. Guo, P. R. A. Binetti, C. Althouse, L. A. Johansson, and L. A. Coldren, "InP Photonic Integrated Circuit with On-chip Tunable Laser Source for 2D Optical Beam Steering," in Optical Fiber Communication Conference/National Fiber Optic Engineers Conference 2013, OSA Technical Digest (online) (Optica Publishing Group, 2013), paper OTh3I.7. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Simultaneous Inversion of Galvanic and Induction Logging Measurements to Improve Resolution (1994)

Abstract Improved resolution in estimating formation resistivities can provide more accurate values of residual and movable hydrocarbon saturations. Routinely, formation resistivity information derived from galvanic and induction logging measurements are interpreted independently. As a result, several models of formation resistivity can emerge that are typically not consistent. Here, we illustrate how simultaneous inversion of data from galvanic and induction tools can yield more consistent and better resolved parameters. When measuring formation resistivities, different References and illustrations at end of paper physical principles govern galvanic and induction tools. In galvanic tools, the voltage differences measured are related to the surface charges at the interfaces between adjacent media of different resistivities, whereas in induction tools, the voltage induced in a measuring coil is caused by magnetic fields of alternating currents flowing in the surrounding formation. A joint inversion of galvanic and induction data is proposed, in which a single earth model, consisting of a distribution of resistivities, is simultaneously applied to the two types of measurements. Combining measurements based on different physical principles also improves resolution. A complete concept of resolution is proposed that involves earth model, measuring device, data noise, and interpretation technique as components. A number of earth models and tool combinations (Dual Laterolog, Dual Induction, Thin Bed Resistivity Tool, Microlaterolog) are analyzed and discussed under the framework of the proposed resolution concept. The analysis clearly shows the advantages of combining data from different instruments to improve interpreted results.
Single-Molecule Patch-Clamp FRET Microscopy Studies of NMDA Receptor Ion Channel Dynamics in Living Cells: Revealing the Multiple Conformational States Associated with a Channel at Its Electrical Off State (2014)

Conformational dynamics plays a critical role in the activation, deactivation, and open-close activities of ion channels in living cells. Such conformational dynamics is often inhomogeneous and extremely difficult to be directly characterized by ensemble-averaged spectroscopic imaging or only by single channel patch-clamp electric recording methods. We have developed a new and combined technical approach, single-molecule patch-clamp FRET microscopy, to probe ion channel conformational dynamics in living cell by simultaneous and correlated measurements of real-time single-molecule FRET spectroscopic imaging with single-channel electric current recording. Our approach is particularly capable of resolving ion channel conformational change rate process when the channel is at its electrically off states and before the ion channel is activated, the so-called "silent time" when the electric current signals are at zero or background. We have probed NMDA (N-methyl-D-aspartate) receptor ion channel in live HEK-293 cell, especially, the single ion channel open-close activity and its associated protein conformational changes simultaneously. Furthermore, we have revealed that the seemingly identical electrically off states are associated with multiple conformational states. On the basis of our experimental results, we have proposed a multistate clamshell model to interpret the NMDA receptor open-close dynamics.
The tumor autocrine motility factor receptor, gp78, is a ubiquitin protein ligase implicated in degradation from the endoplasmic reticulum (2001)

gp78, also known as the tumor autocrine motility factor receptor, is a transmembrane protein whose expression is correlated with tumor metastasis. We establish that gp78 is a RING finger-dependent ubiquitin protein ligase (E3) of the endoplasmic reticulum (ER). Consistent with this, gp78 specifically recruits MmUBC7, a ubiquitin-conjugating enzyme (E2) implicated in ER-associated degradation (ERAD), through a region distinct from the RING finger. gp78 can target itself for proteasomal degradation in a RING finger- and MmUBC7-dependent manner. Importantly, gp78 can also mediate degradation of CD3-delta, a well-characterized ERAD substrate. In contrast, gp78 lacking an intact RING finger or its multiple membrane-spanning domains stabilizes CD3-delta. gp78 has thus been found to be an example of a mammalian cellular E3 intrinsic to the ER, suggesting a potential link between ubiquitylation, ERAD, and metastasis.
Genetic Susceptibility to Venous Thrombosis (2001)

The annual incidence of venous thrombosis, one of the leading causes of mortality and morbidity, increases from 1 per 100,000 during childhood to 1 per 100 in old age.1 In this article we will discuss conditions involving a genetic predisposition to venous thrombosis. The clinical relevance of this topic has increased with new evidence of the high prevalence of mutant genes that increase susceptibility to thrombosis.Of the three mechanisms of thrombosis defined by Virchow in the 19th century — vessel-wall injury, stasis, and “changes in the composition of blood” (hypercoagulability) — the last two predominate in venous thrombosis. Hypercoagulability . . .
CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer (2019)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, metabolic dysregulation, poor memory recall and homeostatic self-renewal, and distinct transcriptional and epigenetic programs. The ability to reinvigorate Tex cells through inhibitory receptor blockade, such as αPD-1, highlights the therapeutic potential of targeting this population. Emerging insights into the mechanisms of exhaustion are informing immunotherapies for cancer and chronic infections. However, like other immune cells, Tex cells are heterogeneous and include progenitor and terminal subsets with unique characteristics and responses to checkpoint blockade. Here, we review our current understanding of Tex cell biology, including the developmental paths, transcriptional and epigenetic features, and cell intrinsic and extrinsic factors contributing to exhaustion and how this knowledge may inform therapeutic targeting of Tex cells in chronic infections, autoimmunity, and cancer.
Bluetooth Low Energy: Wireless Connectivity for Medical Monitoring (2010)

Electronic wireless sensors could cut medical costs by enabling physicians to remotely monitor vital signs such as blood pressure, blood glucose, and blood oxygenation while patients remain at home. According to the IDC report "Worldwide Bluetooth Semiconductor 2008-2012 Forecast," published November 2008, a forthcoming radio frequency communication ("wireless connectivity") standard, Bluetooth low energy, will link wireless sensors via radio signals to the 70% of cell phones and computers likely to be fitted with the next generation of Bluetooth wireless technology, leveraging a ready-built infrastructure for data transmission. Analysis of trends indicated by this data can help physicians better manage diseases such as diabetes. The technology also addresses the concerns of cost, compatibility, and interoperability that have previously stalled widespread adoption of wireless technology in medical applications.
Teichoic acids in pathogenic Staphylococcus aureus (1977)

Twenty-six strains of Staphylococcus aureus obtained from patients with endocarditis were studied for the production of alpha- and/or beta-ribitol teichoic acid (TA), using highly specific anti-TA antibodies prepared in rabbits. A counterimmunoelectrophoretic assay was used. Beta-TA was the predominant residue produced by all strains; alpha-TA was found in all strains, but in smaller amounts and with much strain-to-strain variations. Antibodies in patients' sera were found against beta-TA in higher titers and for longer periods than were anti-alpha-TA antibodies. Antibodies against one or both TA residues were present in all but one of 26 patients.
Recombinant aequorin and green fluorescent protein as valuable tools in the study of cell signalling (2001)

Luminous proteins include primary light producers, such as aequorin, and secondary photoproteins that in some organisms red-shift light emission for better penetration in space. When expressed in heterologous systems, both types of proteins may act as versatile reporters capable of monitoring phenomena as diverse as calcium homoeostasis, protein sorting, gene expression, and so on. The Ca2+-sensitive photoprotein aequorin was targeted to defined intracellular locations (organelles, such as mitochondria, endoplasmic reticulum, sarcoplasmic reticulum, Golgi apparatus and nucleus, and cytoplasmic regions, such as the bulk cytosol and the subplasmalemmal rim), and was used to analyse Ca2+ homoeostasis at the subcellular level. We will discuss this application, reviewing its advantages and disadvantages and the experimental procedure. The applications of green fluorescent protein (GFP) are even broader. Indeed, the ability to molecularly engineer and recombinantly express a strongly fluorescent probe has provided a powerful tool for investigating a wide variety of biological events in live cells (e.g. tracking of endogenous proteins, labelling of intracellular structures, analysing promoter activity etc.). More recently, the demonstration that, using appropriate mutants and/or fusion proteins, GFP fluorescence can become sensitive to physiological parameters or activities (ion concentration, protease activity, etc.) has further expanded its applications and made GFP the favourite probe of cell biologists. We will here present two applications in the field of cell signalling, i.e. the use of GFP chimaeras for studying the recruitment of protein kinase C isoforms and the activity of intracellular proteases.
DNA Inversion on Conjugative Plasmid pVT745 (2002)

Plasmid pVT745 from Actinobacillus actinomycetemcomitans strain VT745 can be transferred to other A. actinomycetemcomitans strains at a frequency of 10(-6). Screening of transconjugants revealed that the DNA of pDMG21A, a pVT745 derivative containing a kanamycin resistance gene, displayed a structural rearrangement after transfer. A 9-kb segment on the plasmid had switched orientation. The inversion was independent of RecA and required the activity of the pVT745-encoded site-specific recombinase. This recombinase, termed Inv, was highly homologous to invertases of the Din family. Two recombination sites of 22 bp, which are arranged in opposite orientation and which function as DNA crossover sequences, were identified on pVT745. One of the sites was located adjacent to the 5' end of the invertase gene, inv. Inversion of the 9-kb segment on pVT745 derivatives has been observed in all A. actinomycetemcomitans strains tested except for the original host, VT745. This would suggest that a host factor that is either inactive or absent in VT745 is required for efficient recombination. Inactivation of the invertase in the donor strain resulted in a 1,000-fold increase in the number of transconjugants upon plasmid transfer. It is proposed that an activated invertase causes the immediate loss of the plasmid in most recipient cells after mating. No biological role has been associated with the invertase as of yet.
Transcriptional Activation Domains of Human Heat Shock Factor 1 Recruit Human SWI/SNF (2001)

Chromatin remodeling complexes such as SWI/SNF use the energy of ATP hydrolysis to remodel nucleosomal DNA and increase transcription of nucleosomal templates. Human heat shock factor one (hHSF1) is a tightly regulated activator that stimulates transcriptional initiation and elongation using different portions of its activation domains. Here we demonstrate that hHSF1 associates with BRG1, the ATPase subunit of human SWI/SNF (hSWI/SNF) at endogenous protein concentrations. We also show that hHSF1 activation domains recruit hSWI/SNF to a chromatin template in a purified system. Mutation of hHSF1 residues responsible for activation of transcriptional elongation has the most severe effect on recruitment of SWI/SNF and association of hHSF1 with BRG1, suggesting that recruitment of chromatin remodeling activity might play a role in stimulation of elongation.
Isolation and characterization of a novel receptor-type protein tyrosine kinase (hek) from a human pre-B cell line. (1992)

In this report we describe the identification and characterization of a novel tumor-associated receptor-type tyrosine kinase (hek). We produced a monoclonal antibody (III.A4) that detected a novel glycoprotein on the immunizing pre-B cell acute lymphoblastic leukemia cell line (LK63). This antigen was shown to be expressed sporadically on hemopoietic tumor cell lines and on ex vivo tumors. However, using antibody staining, the molecule was undetectable on normal tissues. Further biochemical characterization showed this molecule (hek) to be a phosphoroprotein. This observation taken together with the tumor-associated nature of hek expression suggested that hek might be a receptor-type protein tyrosine kinase. This was demonstrated by affinity purification of hek. In in vitro kinase experiments the purified hek protein was autophosphorylated on tyrosine and also mediated tyrosine phosphorylation of casein. Purified hek was subjected to N-terminal amino acid sequence analysis which showed that hek had a unique N terminus. Amino acid sequence determination of peptides from a V8 protease digest of hek yielded one 21-amino acid stretch of sequence which showed close homology with the eph subfamily of protein tyrosine kinases. These studies show hek to be a novel human tumor-associated protein tyrosine kinase, which by analogy with previously characterized protein tyrosine kinase proto-oncogenes, may have a role in tumorigenesis.
Fast parallel outlier detection for categorical datasets using MapReduce (2008)

Outlier detection has received considerable attention in many applications, such as detecting network attacks or credit card fraud The massive datasets currently available for mining in some of these outlier detection applications require large parallel systems, and consequently parallelizable outlier detection methods. Most existing outlier detection methods assume that all of the attributes of a dataset are numerical, usually have a quadratic time complexity with respect to the number of points in the dataset, and quite often they require multiple dataset scans. In this paper, we propose a fast parallel outlier detection strategy based on the Attribute Value Frequency (AVF) approach, a high-speed, scalable outlier detection method for categorical data that is inherently easy to parallelize. Our proposed solution, MR-AVF, is based on the MapReduce paradigm for parallel programming, which offers load balancing and fault tolerance. MR-AVF is particularly simple to develop and it is shown to be highly scalable with respect to the number of cluster nodes.
Synthesis of chiral fused pyrimidines from (+)-3-carene- and limonene-derived isomeric β-enaminones (2000)

New heterocyclic compounds, pyrimidines annelated with modified terpenic frames, were synthesised from positional isomers of β-enaminones derived from limonene and (+)-3-carene.
Antibodies against intercellular adhesion molecule-1 and lymphocyte function-associated antigen-1 prevent glomerular injury in rat experimental crescentic glomerulonephritis (1993)

The involvement of adhesion molecules in the glomerular accumulation of inflammatory cells and subsequent glomerular injury was examined in WKY rats with nephrotoxic serum nephritis. This model is characterized by early infiltration of CD8-positive NK cells, followed by influx of monocytes/macrophages into the glomeruli. At day 1 and later, up-regulated expression of intercellular adhesion molecule-1 (ICAM-1) was observed exclusively in the glomerular endothelial cells in association with the influx of CD8-positive cells and monocytes/macrophages. These cells expressed lymphocyte function-associated Ag-1 (LFA-1). Repeated injection of mAb against rat ICAM-1 or alpha-subunit of LFA-1 (LFA-1 alpha) dose dependently prevented the development of proteinuria, the influx of these cells, and subsequent crescent formation in this nephrotoxic serum nephritis model. Furthermore, simultaneous administration of anti-ICAM-1 mAb and anti-LFA-1 alpha mAb exerted additive protective effects against urinary protein excretion and crescentic glomerulonephritis. Binding of anti-GBM antibody to the glomeruli and production of circulating anti-rabbit IgG antibody were unaffected by injection of these mAb. These results indicate that adhesion of CD8-positive cells and monocytes to glomerular endothelial cells through the LFA-1/ICAM-1 pathway is crucial for the initiation and subsequent progression of nephrotoxic serum nephritis in WKY rats.
RNA binding protein RBM14 promotes radio-resistance in glioblastoma by regulating DNA repair and cell differentiation (2014)

Glioblastoma multiforme (GBM) is the most aggressive and lethal type of brain tumor. Standard treatment for GBM patients is surgery followed by radiotherapy and/or chemotherapy, but tumors always recur. Traditional therapies seem to fail because they eliminate only the bulk of the tumors and spare a population of stem-like cells termed tumor-initiating cells. The stem-like state and preferential activation of DNA damage response in the GBM tumor-initiating cells contribute to their radio-resistance and recurrence. The molecular mechanisms underlying this efficient activation of damage response and maintenance of stem-like state remain elusive. Here we show that RBM14 controls DNA repair pathways and also prevents cell differentiation in GBM spheres, causing radio-resistance. Knockdown of RBM14 affects GBM sphere maintenance and sensitizes radio-resistant GBM cells at the cellular level. We demonstrate that RBM14 knockdown blocks GBM regrowth after irradiation in vivo. In addition, RBM14 stimulates DNA repair by controlling the DNA-PK-dependent non-homologous end-joining (NHEJ) pathway. These results reveal unexpected functions of the RNA-binding protein RBM14 in control of DNA repair and maintenance of tumor-initiating cells. Targeting the RBM14-dependent pathway may prevent recurrence of tumors and eradicate the deadly disease completely.