gebhart/patrepeval huggingface dataset:
Expression of human perforin in a mouse cytotoxic T lymphocyte cell line: evidence for perturbation of granule-mediated cytotoxicity (1993)

Expression of the pore-forming protein perforin is normally restricted to the cytolytic granules of cytotoxic T lymphocytes and natural killer cells. Perforin, which causes cell death by osmotic lysis, has the ability to form transmembrane channels in target cell membranes. This function makes perforin crucial in the granule-exocytosis model of T cell-mediated cytotoxicity. In the present study, variants of the mouse cytotoxic T lymphocyte cell line CTLL-R8 have been produced which express human perforin. A full-length cDNA clone (HP-10) encoding human perforin was inserted in the sense orientation into the expression plasmid pCMV5neo. The resultant construct, designated pCMV5neoHP-10, was used to transfect CTLL-R8 cells. Of eight G418-resistant clones studied, four clones expressed human perforin mRNA by Northern analysis and three of these clones also expressed human perforin protein by Western blotting. The expression of human perforin protein was associated with a pronounced (55-74%) and consistent reduction in the killing of three target cell lines, P815, YAC-1, and EL4, compared with parental CTLL-R8 cells. The reduction in target cell lysis could not be attributed to nonspecific effects of the transfection, as clones transfected with neo alone showed no reduction in killing in comparison with parental CTLL-R8 cells. Clones expressing human perforin showed very similar growth characteristics, surface phenotype, and N-alpha-benzyloxycarbonyl-l-thiobenzyl-esterase release compared with untransfected CTLL-R8 cells. The mechanism of reduction of cytolysis is unclear but may involve competition by human perforin in the handling or packaging of endogenous granule constituents (including mouse perforin) or assembly of human perforin into mouse polyperforin channels in target cell membranes. The expression of human perforin in mouse cytotoxic T cells provides a potential model for studying how cytotoxic T cells process, package, utilize, and protect themselves against the perforin molecules they produce.
Synaptotagmin restores kinetic properties of a syntaxin‐associated N‐type voltage sensitive calcium channel (1997)

The voltage sensitive N-type calcium channel interacts functionally and biochemically with synaptotagmin (p65). N-type channel interaction with p65 is demonstrated in the Xenopus oocyte expression system, where p65 alters the steady state voltage inactivation of the N-channel, and fully restores the syntaxin-modified current amplitude and inactivation kinetics in a calcium dependent manner. In agreement with the functional results, GST-p65 fusion protein binds to a cytosolic region, amino acids 710-1090 of the N-type channel (N-loop(710-1090)). The results of the combined approach provide a functional and biochemical basis for proposing that p65 interaction with the N-type channel brings p65 into a close association with a syntaxin-coupled channel. In turn, calcium entry through the liberated channel initiates fusion of the primed vesicles with the cell membrane at a short distance from the site of calcium entry.
Controlled, Copper-Catalyzed Functionalization of Polyolefins (2005)

published
Document Classification of Protein Sequences (2018)

The need for accurate, automated protein classification methods continues to increase as advances in biotechnology uncovers new proteins at a fast rate. G-protein coupled receptors (GPCRs) are a particularly difficult superfamily of proteins to classify due to the extreme diversity among its members; yet, they are an important subject in pharmacological research being the target of approximately 60% of current drugs (Muller, 2000). A comparison of BLAST, k-NN, HMM and SVM with alignment-based features by Karchin et al. (2002) has suggested that classifiers at the complexity of SVM are needed to attain high accuracy in GPCR subfamily classification. Here, analogous to document classification, we applied Decision Tree and Naïve Bayes classifiers with chi-square feature selection on n-gram counts to the GPCR family and subfamily classification task. Using the dataset and evaluation protocol from the previous study, we found the Naïve Bayes classifier surpassing the reported accuracy of SVM by 4.8% and 6.1% in level I and II subfamily classification with an accuracy of 93.2% and 92.4% respectively. The Decision Tree, while inferior to SVM, still outperforms HMM in both level I and II subfamily classification. Moreover, the n-grams selected by chi-square feature selection show evidence of biological importance. Thus, the document classification approach has resulted in a simpler, more accurate and interpretable classifier.
DISCUSSION. DESCRIPTION OF A SLIDING CAISSON AT KEYHAM DOCKYARD. (1854)

Keywords CAISSONS, SLIDING, DOCKYARDS, ENTRANCES, FLOATING, DRY, DOCKS, LOCKS, DAMS KEYHAM UK... Show All
Ferrite-Coated Nanoparticles: Synthesis and Biomedical Applications (1998)

New solid and hollow monodispersed micron-sized organic-inorganic hybrid magnetic nanoparticles have been recently prepared and characterized in our laboratory. The solid particles were formed by seeded polymerization of iron salts onto polystyrene monodispersed micron-sized (1-6 μm) particles. A further coating of these ferrite-coated particles with silica nanoparticles of significantly lower diameter (30-40 nm) was prepared by seeded polymerization of these particles with Si(OEt)4. The effect of the polystyrene surface composition on the coating of the polystyrene with ferrite and with silica is demonstrated. Hollow ferrite silica micron-sized particles were formed by burning off the polystyrene core of the former hybrid particles. Surface modification of these particles was performed by reacting these silica-coated particles with a variety of ω-alcoholic reagents or ω-alkylsilane compounds. The potential biomedical use of these ferrite-coated particles is also demonstrated and discussed.
The Expression of PDGF α-and β-Receptors in Subpopulations of PDGF-Producing Cells Implicates Autocrine Stimulatory Loops in the Control of Proliferation in Cytotrophoblasts that Have Invaded the Maternal Endometrium (1992)

AbstractIn order to explain the high proliferative potential of human placental cytotrophoblasts, we have addressed the potential involvement of platelet-derived growth factor (PDGF) ligand and receptors. Although PDGF is usually described as a mitogen for cells of mesenchymal origin, we show in this report that extra-villous term placental cytotrophoblasts express the PDGF α-and β-receptor genes, both in vivo and in vitro. In addition, cytotrophoblasts produce significant amounts of PDGF-B protein. By immunohistochemical analysis of receptor expression, we found that the PDGF a-receptors could be detected at the cell surface, while the PDGF β-receptors were only detected inrracellularly. In addition, double immunostaining analysis showed that the PDGF α-and β-receptor molecules are expressed in different subpopulations of cytotrophoblasts. The addition of PDGF-AA and PDGF-BB homodimers to cytotrophoblast primary cultures induced a significant increase in DNA synthesis. We conclude, therefore, that PDGF is a growth factor for placental cytotrophoblasts and suggest that the growth of cytotrophoblasts can partly be explained by a PDGF autostimulatory loop, limited by the number of receptor-positive cytotrophoblasts.Key Words: PDGFplatelet-derived growth factorin situ hybridizationcytotrophoblastsplacenta
On sensor management in decentralized data fusion (2005)

A probabilistic framework for decentralized data fusion and sensor management based on the notion of Bayesian information value is presented. Use is made of information as the expected utility of actions within a framework of decentralized decision-theory. Entropy is used as an information metric. Some preliminary results justifying this approach are shown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Modeling Off-line Routing and Spectrum Allocation Problem in Elastic Optical Network (2021)

The swift escalation in internet traffic due to diverse bandwidth starving applications and innovative concepts of modern technologies such as Elastic Optical Networks (EONs) and Software-defined networking (SDN) demands a dynamic and flexible optical network architecture both at the control and data plane. Characteristically, the flexibility in EONs is achieved by the emerging SDN-enabled sliceable bandwidth variable transponders (SBVTs) that support multiple optical carriers' simultaneous generation. These generated multiple optical carriers can operate different lightpaths using slice-ability or combined into a single high-rate super-channel. In this perspective, one of the major issues in EON is Routing and Spectrum Allocation (RSA). Typically, in EON, RSA is a spectrum management and Nondeterministic Polynomial-time hardness (NP-hard) problem in which network resources mainly bank on the applied ordering strategy. This article proposed a novel heuristic algorithm, Minimum Hops with Least Slot Spectrum (MHLS), to accommodate maximum traffic requests with better spectrum utilization. The proposed algorithm aims to minimize block requests, block traffic, and the total number of spectrum slots used in the network. The MHLS exploits Dijkstra-shortest-path and SDN-enabled SBVTs for RSA problem. The performance evaluation of MHLS is accomplished on the entire USA network.
Surface Pressure Dependent Fluorescence Resonance Energy Transfer in Mixed Monolayers of Amphiphilic Coumarin and Texas Red at the Air−Water Interface (1997)

This paper reports the spectroscopic characteristics of pure N-(Texas Red sulfonyl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine triethylammonium salt (TR) and 3-(2-benzothiaxolyl)-4-cyano-7-(octadecyloxy)coumarin (BCOC) at the air−water interface. Absorption and steady state fluorescence studies of these dyes at the air−water interface reveals the formation of aggregates at the air−water interface. Detailed studies revealed the formation of J-aggregates in the case of TR and both J- and H-aggregates in the case of BCOC. Polarized fluorescence studies confirmed that the dye molecules were highly oriented at the air−water interface. Surface pressure dependent fluorescence emission studies showed extensive quenching of the TR fluorescence that has been attributed to an efficient energy transfer from the monomeric species of TR to their aggregates which are nonfluorescent. In the case of BCOC, fluorescence emission occurs only from the J-aggregates of BCOC as the H-aggregates are nonfluorescent. Mixed films of BCOC and TR with DPPC show unique behavior. Even at very low concentration of TR, the BCOC fluorescence is completely quenched and the sensitized fluorescence from TR dominate, thus indicating efficient energy transfer from BCOC to the TR moieties. With an increase in the surface pressure, the same features are found to predominate and the quenching of TR fluorescence is attributed to the generation of TR aggregates caused as a result of compressing the monolayer. At higher surface pressures, the characteristics of the TR fluorescence are found to disappear and the fluorescence characteristics of BCOC dominate. One explanation of such behavior could be the deactivation of BCOC via the radiative pathway and inefficent energy transfer from the aggregates of BCOC to the aggregates of TR. This study therefore establishes that FRET can be a useful tool for studying aggregation in supramolecular LB assemblies.
Effect of Sulfur on the Sintering of Nickel Particles (2016)

Sintering behavior of fine nickel powder with various surface sulfur content have been systematically investigated. The nickel powder with 150 ppm sulfur demonstrated the greatest density of the sinters, while the nickel powder with 300 ppm sulfur showed the lower density than the others. It was found that the appropriate content of surface sulfur enhanced the densification of fine nickel powder, which is mainly attributed the existence of solid solution sulfur in the nickel crystal structure. However, the excess sulfur beyond the solubility limit in nickel posed the formation of nickel sulfides, and resulted in the lower density of nickel sinters.
Excess energetic materials as ingredients in commercial explosives (1994)

The efforts were focused on investigating the feasibility of using excess energetic materials from the Department of Defense and Aerospace Industries as ingredients in commercial explosives. The management of the excess energetic materials inventory in this country has become a serious problem facing the Department of Defense and its contractors, the Aerospace Industry and both state and federal regulatory agencies. According to the United States Department of the Interior, Bureau of Mines, the United States uses over 2 million metric tons of commercial explosives per year. The possibility of using these excess energetic materials in even a small portion of the commercial explosives which are used presents a significant outlet. A Class 1.3 Composite propellant (containing ammonium perchlorate and aluminum) and a Smokeless Powder Propellant (double based propellant) were researched. The safety and technical aspects of adding these materials to several common types of commercial explosives at the point of manufacture were investigated. Explosive characteristics such as detonation velocity, critical diameter, and energy release were also measured. It was concluded that the resulting mixtures either maintained the explosive characteristics of the standard formulations or they exhibited significantly enhanced explosive characteristics over those of the standard formulations. The use of thesemore » excess energetic materials as ingredients in commercial explosives presents a viable alternate use.« less
Monte Carlo simulation of electron velocity overshoot in DGSOI MOSFETs (2004)

Velocity overshoot is one of the most important new effects observed in very short channel metal oxide semiconductor field effect transistors (MOSFETs), as this is directly related to the increase in current drive and transconductance experimentally observed. Comprehensive study of velocity overshoot effects in double gate MOSFETs were performed. A Monte Carlo simulator coupled with a self-consistent Poisson-Schroedinger solver was used to calculate velocity overshoot effects, low field mobilities, average conduction effective mass, and wavefunction overlapping. It is shown that higher velocity overshoot effects are obtained at lower inversion charges and smaller silicon layer thicknesses.
Combination of small RNAs for skeletal muscle regeneration (2015)

Selectively controlling the expression of the target genes through RNA interference (RNAi) has significant therapeutic potential for injuries or diseases of tissues. We used this strategy to accelerate and enhance skeletal muscle regeneration for the treatment of muscular atrophy. In this study, we used myostatin small interfering (si)RNA (siGDF-8), a major inhibitory factor in the development and postnatal regeneration of skeletal muscle and muscle-specific microRNAs (miR-1 and -206) to further accelerate muscle regeneration. This combination of 3 small RNAs significantly improved the gene expression of myogenic regulatory factors in vitro, suggesting myogenic activation. Moreover, cell proliferation and myotube formation improved without compromising each other, which indicates the myogenic potential of this combination of small RNAs. The recovery of chemically injured tibialis anterior muscles in rats was significantly accelerated, both functionally and structurally. This novel combination of siRNA and miRNAs has promising therapeutic potential to improve in situ skeletal muscle regeneration.
Detailed polarization properties comparison for three completely different species of highly birefringent fibers (2004)

We present a detailed experimental investigation for four dgerent fiber samples: a standard PANDA pber, two index-guiding nonlinear photonic crystal fibers. and an air-core photonic bandgap $her. Although all fibers exhibit large birefringence, their polarization properties are found to be quite different. Most surprisingly, the principle states of polarization strongly vary with wavelength for the photonic bandgap pber, indicating the presence of polarization mode coupling.
Gaussian windows: A tool for exploring multivariate data (1990)

Presented here is a method for interactively exploring a large set of quantitative multivariate data, in order to estimate the shape of the underlying density function. It is assumed that the density function is more or less smooth, but no other specific assumptions are made concerning its structure. The local structure of the data in a given region may be examined by viewing the data through a Gaussian window, whose location and shape are chosen by the user. A Gaussian window is defined by giving each data point a weight based on a multivariate Gaussian function. The weighted sample mean and sample covariance matrix are then computed, using the weights attached to the data points. These quantities are used to compute an estimate of the shape of the density function in the window region. The local structure of the data is described by a method similar to the method of principal components. By taking many such local views of the data, we can form an idea of the structure of the data set. The method is applicable in any number of dimensions. The method can be used to find and describe simple structural features such as peaks, valleys, and saddle points in the density function, and also extended structures in higher dimensions. With some practice, we can apply our geometrical intuition to these structural features in any number of dimensions, so that we can think about and describe the structure of the data. Since the computations involved are relatively simple, the method can easily be implemented on a small computer.
Recognition of guanosine by dissimilar tRNA methyltransferases (2012)

Guanosines are important for biological activities through their specific functional groups that are recognized for RNA or protein interactions. One example is recognition of N(1) of G37 in tRNA by S-adenosyl-methionine (AdoMet)-dependent tRNA methyltransferases to synthesize m(1)G37-tRNA, which is essential for translational fidelity in all biological domains. Synthesis of m(1)G37-tRNA is catalyzed by TrmD in bacteria and by Trm5 in eukarya and archaea, using unrelated and dissimilar structural folds. This raises the question of how dissimilar proteins recognize the same guanosine. Here we probe the mechanism of discrimination among functional groups of guanosine by TrmD and Trm5. Guanosine analogs were systematically introduced into tRNA through a combination of chemical and enzymatic synthesis. Single turnover kinetic assays and thermodynamic analysis of the effect of each analog on m(1)G37-tRNA synthesis reveal that TrmD and Trm5 discriminate functional groups differently. While both recognize N(1) and O(6) of G37, TrmD places a much stronger emphasis on these functional groups than Trm5. While the exocyclic 2-amino group of G37 is important for TrmD, it is dispensable for Trm5. In addition, while an adjacent G36 is obligatory for TrmD, it is nonessential for Trm5. These results depict a more rigid requirement of guanosine functional groups for TrmD than for Trm5. However, the sensitivity of both enzymes to analog substitutions, together with an experimental revelation of their low cellular concentrations relative to tRNA substrates, suggests a model in which these enzymes rapidly screen tRNA by direct recognition of G37 in order to monitor the global state of m(1)G37-tRNA.
Magnetic structure of GdCo2Ge2 (2005)

Resonant and nonresonant magnetic x-ray scattering studies of GdCo2Ge2 were performed to determine its magnetic structure at low temperature. This compound orders in an incommensurate antiferromagnetic AF structure characterized by a propagation wave vector = 00 z. The value of z is temperature dependent and approaches 0.930 reciprocal lattice units well below TN=33.25 K. A peak corresponding to 3z was also observed, indicating either a squaring up of the magnetic structure or the presence of a noncollinear amplitude modulated structure below TN. Fitting the angular dependence of the magnetic scattering integrated intensities to the relevant resonant and nonresonant scattering cross sections revealed that the moment direction lies primarily in the tetragonal basal plane. Scattering measurements at the Co K- edge failed to detect any resonant signal, consistent with the absence of a magnetic moment on the Co sites.
CYTIDINE DEAMINASE AND LACTOFERRIN IN INFLAMMATORY SYNOVIAL FLUIDS. INDICATORS OF LOCAL POLYMORPHONUCLEAR CELL FUNCTION? (1992)

Cytidine deaminase (CD) is a cytoplasmatic enzyme present predominantly in polymorphonuclear cells (PMNC) in inflamed joints. Lactoferrin is situated in the secondary granules of PMNC and is released by secretory/phagocytic stimuli, whereas CD is released mainly upon cell lysis. To study the release of these molecules in arthritic conditions we measured CD and lactoferrin levels in synovial fluid (SF) drawn from patients with rheumatoid arthritis (RA), crystal pyrophosphate disease (CPPD), psoriatic arthropathy, reactive arthritis, spondylarthropathy, and osteoarthrosis. CD activity was highest in SF from RA and CPPD followed by psoriatic arthropathy, reactive arthritis and spondylarthropathy. Lactoferrin concentrations were highest in CPPD followed by RA, reactive arthritis, psoriatic arthropathy, and spondylarthropathy. Both CD and lactoferrin levels were low in osteoarthrosis SF. Although SF CD activity and lactoferrin levels correlated well in all diagnostic groups, the ratio between CD and lactoferrin was higher for RA, psoriatic arthropathy, and spondylarthropathy compared to reactive arthritis and CPPD. This suggests predominant release by PMNC lysis in the more chronic arthritis groups and more degranulation in the more episodic CPPD and reactive arthritis groups. CD activity and lactoferrin levels correlated significantly with SF cell counts in the RA and psoriatic arthropathy groups.
Visible Light Photoredox Catalyzed Cascade Cyclizations of α‐Bromochalcones or α‐Bromocinnamates with Heteroarenes (2014)

Abstract Vinyl radicals were generated from α‐bromochalcones or α‐bromocinnamate ethyl ester under visible light photoredox catalyzed conditions via an oxidative quenching cycle of the iridium complex [Ir{dF(CF 3 )ppy} 2 (dtbbpy)]PF 6 and subjected to cascade cyclizations with heteroarenes entailing two consecutive CC bond formations and three CH activations. The process is amenable to furans, benzofurans, pyrroles, and indoles, giving rise to a broad variety of novel polycyclic frameworks in high yields under mild and environmentally benign reaction conditions. magnified image
Dissipation and Criticality in the Lowest Landau Level of Graphene (2008)

The lowest Landau level of graphene is studied numerically by considering a tight-binding Hamiltonian with disorder. The Hall conductance sigma_{xy} and the longitudinal conductance sigma_{xx} are computed. We demonstrate that bond disorder can produce a plateaulike feature centered at nu=0, while the longitudinal conductance is nonzero in the same region, reflecting a band of extended states between +/-E_{c}, whose magnitude depends on the disorder strength. The critical exponent corresponding to the localization length at the edges of this band is found to be 2.47+/-0.04. When both bond disorder and a finite mass term exist the localization length exponent varies continuously between approximately 1.0 and approximately 7/3.
Frequency multiplication in high-energy electron beams Semiannual progress report, 1 Oct. 1967 - 31 Mar. 1968 (1968)

Electron beam-plasma interactions, cyclotron harmonic instabilities, paramagnetic and semiconductor materials, and harmonic current generation