gebhart/patrepeval huggingface dataset:
Synthesis and antiviral activity of 3'-C-cyano-3'-deoxynucleosides (1989)

A series of 3'-C-cyano-3'-deoxynucleosides have been synthesized and evaluated as antiviral agents. Reaction of 2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-erythro-pentofuranos- 3'-ulosyl derivatives of uracil, 4-N-acetylcytosine, and adenine with sodium cyanide gave a mixture of epimeric cyanohydrins, which after 3'-deoxygenation yielded the corresponding 3'-C-cyano-3'-deoxy-beta-D-xylo-pentofuranosyl derivatives 10. These compounds were epimerized to the corresponding beta-D-ribo-pentofuranosyl derivatives 11. Desilylation of 10 and 11 gave the deprotected 3'-C-cyano-3'-deoxy-beta-D-xylo- and -ribo-pentofuranosyl nucleosides. These derivatives of uridine, cytidine, and adenine, as well as the 3'-C-cyano-3'-deoxy-beta-D-xylo- and -ribo-pentofuranosyl, 3'-C-cyano-2',3'-dideoxy-beta-D-threo- and -erythro-pentofuranosyl, and 3'-C-cyano-2',3'-dideoxy-beta-D-glycero-pent-2'-enofuranosyl derivatives of thymine, were evaluated for their antiviral activity. None of the compounds proved active against the replication of retroviruses (human immunodeficiency virus, murine sarcoma virus) at concentrations that were not toxic to the host cells. However, the 3'-C-cyano-3'-deoxy-beta-D-xylo- (12e) and -ribo-pentofuranosyl (13e) derivatives of adenine showed activity against some DNA (i.e., vaccinia) and RNA (i.e., Sindbis, Semliki forest) viruses at concentrations well below the cytotoxicity threshold.
Implementation of parallel Welch power spectrum estimation based on MPI (2014)

It is well known that Welch algorithm is one of classical power spectrum estimation which is used widely. But facing a rapidly growing massive data, it will spend a plenty of time to operate Welch algorithm in the serial Matlab circumstances. Though a parallel computing toolbox is involved in Matlab in 2004, it is too expensive to be used widely. A parallel Welch algorithm, which is implemented using the Master-Slave parallel programming model with the support of Linux clusters and MPI, is proposed here depending on the theory of Welch algorithm. The experiment results show that PMWelch can achieve the same accuracy as Matlab do and can highly improve the speed.
High-Speed Distance Relaying Using a Digital Computer II-Test Results (1972)

An experimental general-purpose process-control digital- computer system described in a companion paper (I-System Description) provides high-speed phase-and ground-distance fault protection of one 230 kV transmission line. The stored program performs all of the relaying functions using the output of an analog-to- digital converter which reads the instantaneous value of the power- system currents and voltages. Model line tests described here form the basis for preliminary performance evaluation. An automatic oscillograph and diagnostic programs will allow a study of field performance.
Estimation of relatedness by DNA fingerprinting. (1988)

The recent discovery of hypervariable VNTR (variable number of tandem repeat) loci has led to much excitement among population biologists regarding the feasibility of deriving individual estimates of relatedness in field populations by DNA fingerprinting. It is shown that unbiased estimates of relatedness cannot be obtained at the individual level without knowledge of the allelic distributions in both the individuals of interest and the base population unless the proportion of shared marker alleles between unrelated individuals is essentially zero. Since the latter is usually on the order of 0.1-0.5 and since there are enormous practical difficulties in obtaining the former, only an approximate estimator for the relatedness can be given. The bias of this estimator is individual specific and inversely related to the number of marker loci and frequencies of marker alleles. Substantial sampling variance in estimates of relatedness arises from variation in identity by descent within and between loci and, with finite numbers of alleles, from variation in identity in state between genes that are not identical by descent. In the extreme case of 25 assayed loci, each with an effectively infinite number of alleles, the standard error of a relatedness estimate is no less than 14%, 20%, 35%, and 53% of the expectation for full sibs and second-, third-, and fourth-order relationships, respectively. Attempts to ascertain relatedness by means of DNA fingerprinting should proceed with caution.
Weak convergence and optimal scaling of random walk Metropolis algorithms (1997)

This paper considers the problem of scaling the proposal distribution of a multidimensional random walk Metropolis algorithm in order to maximize the efficiency of the algorithm. The main result is a weak convergence result as the dimension of a sequence of target densities, n, converges to $\infty$. When the proposal variance is appropriately scaled according to n, the sequence of stochastic processes formed by the first component of each Markov chain converges to the appropriate limiting Langevin diffusion process. The limiting diffusion approximation admits a straightforward efficiency maximization problem, and the resulting asymptotically optimal policy is related to the asymptotic acceptance rate of proposed moves for the algorithm. The asymptotically optimal acceptance rate is 0.234 under quite general conditions. The main result is proved in the case where the target density has a symmetric product form. Extensions of the result are discussed.
High Dynamic Range Astronomical Imaging (2007)

High dynamic range imaging methods that combine multiple exposures involve a number of processing details, such as frame alignment, motion artifact removal, and pixel data weighting. When applied to astronomical scenes, these steps require additional consideration. Specifically, motion blur artifacts must be corrected by techniques that are tolerant of saturated pixels, successive image frames need to be registered with point source precision, and the weighting of shorter exposures in the HDR compositing step are limited by signal-tonoise considerations. In addition, if there is light contributed by the foreground sky (common in light polluted regions), it needs to be offset and balanced in a blackpoint normalizing procedure. This paper identifies and describes these HDR issues specific to creating astrophotographic imagery.
The ability of Escherichia coli O157:H7 to decrease its intracellular pH and resist the toxicity of acetic acid (1997)

Batch cultures of Escherichia coli K-12 grew well in an anaerobic glucose medium at pH 5.9, but even small amounts of acetate (20 mM) inhibited growth and fermentation. E. coli O157:H7 was at least fourfold more resistant to acetate than K-12. Continuous cultures of E. coli K-12 (pH 5.9, dilution rate 0.085 h-1) did not wash out until the sodium acetate concentration in the input medium was 80 mM, whereas E. coli O157:H7 persisted until the sodium acetate concentration was 160 mM. E. coli K-12 cell accumulated as much as 500 mM acetate, but the intracellular acetate concentration of O157:H7 was never greater than 300 mM. Differences in acetate accumulation could be explained by intracellular pH and the transmembrane pH gradient (delta pH). E. coli K-12 maintained a more or less constant delta pH (intracellular pH 6.8), but E. coli O157:H7 let its delta pH decrease from 0.9 to 0.2 units as sodium acetate was added to the medium. Sodium acetate increased the rate of glucose consumption, but there was little evidence to support the idea that acetate was creating a futile cycle of protons. Increases in glucose consumption rate could be explained by increases in D-lactate production and decreases in ATP production. Intracellular acetate was initially lower than the amount predicted by delta pH, but intracellular acetate and delta pH were in equilibrium when the external acetate concentrations were high. Based on these results, the acetate tolerance of O157:H7 can be explained by fundamental differences in metabolism and intracellular pH regulation. By decreasing the intracellular pH and producing large amounts of D-lactate, O157:H7 is able to decrease delta pH and prevent toxic accumulations of intracellular acetate anion.
T-bet upregulation and subsequent interleukin 12 stimulation are essential for induction of Th1 mediated immunopathology in Crohn’s disease (2004)

T-bet induction by antigenic stimulation and subsequent stimulation by macrophage derived IL-12/IL-18 are important for establishing Th1 mediated immunopathology in CD.
Radical Cage Effects in the Photochemical Degradation of Polymers:  In-Cage Trapping of Photochemically Generated Radical Cage Pairs in Polymer Model Compounds (1999)

This study explored the origins of the observation that the overall quantum yields for polymer photodegradation depend on the polymer chain length. The (CH3(CH2)nC(O)NHCH2CH2Cp)2Mo2(CO)6 (n = 3, 8, 13, 18) complexes (1−1−4−4) were synthesized and used as model complexes for the study. As is common for metal−metal bonded complexes of this type, irradiation of these molecules cleaved the metal−metal bonds and formed free radicals via the intermediate formation of a radical cage pair. Studies on previous model complexes showed that the quantum yields for degradation decreased as the chain length of the complex increased. The decrease in quantum efficiency was partially attributed to an increase in the radical cage effect as the chain length increased. Surprisingly, however, the overall quantum yields and cage effects for complexes 1−1−4−4 did not vary significantly with chain length. The similarity in the quantum yields and in the cage effects for these molecules is attributed to an internal trapping reaction of the metal radicals in the solvent cage by the H atom of the amide group. The resulting Mo···(H)−N agostic interaction forms a six-membered ring. The trapping reaction takes place by segmental rotation of the metal-containing end of the radical chain; the rate of this motion is independent of the chain length, and thus differences in the cage effects and the overall quantum yields will be diminished for the four molecules. The X-ray crystal structure of the (CH3(CH2)3C(O)NHCH2CH2Cp)2Mo2(CO)6 molecule is also reported.
Ligands of Macrophage Scavenger Receptor Induce Cytokine Expression via Differential Modulation of Protein Kinase Signaling Pathways (2001)

Our previous works demonstrated that ligands of macrophage scavenger receptor (MSR) induce protein kinases (PKs) including protein-tyrosine kinase (PTK) and up-regulate urokinase-type plasminogen activator expression (Hsu, H. Y., Hajjar, D. P., Khan, K. M., and Falcone, D. J. (1998) J. Biol. Chem. 273, 1240--1246). To continue to investigate MSR ligand-mediated signal transductions, we focus on ligands, oxidized low density lipoprotein (OxLDL), and fucoidan induction of the cytokines tumor necrosis factor-alpha (TNF) and interleukin 1 beta (IL-1). In brief, in murine macrophages J774A.1, OxLDL and fucoidan up-regulate TNF production; additionally, fucoidan but not OxLDL induces IL-1 secretion, prointerleukin 1 (proIL-1, precursor of IL-1) protein, and proIL-1 message. Simultaneously, fucoidan stimulates activity of interleukin 1-converting enzyme. We further investigate the molecular mechanism by which ligand binding-induced PK-mediated mitogen-activated protein kinase (MAPK) in regulation of expression of proIL-1 and IL-1. Specifically, fucoidan stimulates activity of p21-activated kinase (PAK) and of the MAPKs extracellular signal-regulated kinase (ERK), c-Jun NH(2)-terminal kinase (JNK), and p38. Combined with PK inhibitors and genetic mutants of Rac1 and JNK in PK activity assays, Western blotting analyses, and IL-1 enzyme-linked immunosorbent assay, the role of individual PKs in the regulation of proIL-1/IL-1 was extensively dissected. Moreover, tyrosine phosphorylation of pp60Src as well as association between pp60Src and Hsp90 play important roles in fucoidan-induced proIL-1 expression. We are the first to establish two fucoidan-mediated signaling pathways: PTK(Src)/Rac1/PAK/JNK and PTK(Src)/Rac1/PAK/p38, but not PTK/phospholipase C-gamma 1/PKC/MEK1/ERK, playing critical roles in proIL-1/IL-1 regulation. Our current results indicate and suggest a model for MSR ligands differentially modulating specific PK signal transduction pathways, which regulate atherogenesis-related inflammatory cytokines TNF and IL-1.
Synchronization of Networked Mechanical Systems With Communication Delays and Human Input (2013)

The problem of controlling a group of networked mechanical systems to synchronize and follow a common trajectory is studied in this paper. We first address the results for networked mechanical systems to achieve synchronization when the interagent communication graph is balanced and strongly connected with communication delays. Subsequently, a control law is developed to guarantee synchronization and trajectory tracking for networked mechanical systems communicating on regular graphs when there are constant time delays in communication and the interconnection topology is time-varying. The case when a human operator input is introduced in the closed-loop system is also considered. It is demonstrated that a bounded human operator input results in bounded tracking and synchronization errors, even when there are constant time delays in communication. The simulation and experimental results are presented by utilizing the kinematic and dynamic models of PHANToM Omni derived in this paper.
On an Instrument for the Coherent Investigation of Nitrogen-Vacancy Centres in Diamond (2013)

It is my hope that this thesis may serve as a guide for future students wishing to build a microscope from scratch. The design and construction of a scanning, confocal fluorescence microscope equipped with shaped microwave excitation is detailed. The use of the microscope is demonstrated by coherently manipulating single Nitrogen-Vacancy centres in diamond. Further the instrument is used to investigate a dual Halbach array magnet system.
Adhesion and cytokine production by monocytes on poly(2‐methacryloyloxyethyl phosphorylcholine‐<i>co</i>‐alkyl methacrylate)‐coated polymers (1995)

Human monocytes isolated from peripheral venous blood were assayed for their ability to adhere to various polymers. The culture supernatants were also assayed for the cytokines, interleukin-1 beta (IL-beta), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-alpha). The polymers evaluated for adherence and cytokine production included Pellethane, polyethylene and poly[n-butyl methacrylate (BMA)] coated with poly[2-methacryloyloxyethyl phosphorylcholine (MPC)-co-alkyl methacrylate] copolymers. In some experiments the test polymers were adsorbed with fibrinogen or IgG prior to the addition of monocytes. MPC copolymer-coated materials inhibited monocyte and macrophage adhesion after 1 and 8 days of culture relative to corresponding uncoated polymers and tissue culture polystyrene (TCPS). The degree of inhibition by coated Pellethane compared to uncoated Pellethane was the greatest, while inhibition of adhesion by coated poly(BMA) was the least compared to uncoated poly(BMA). However, adhesion was significantly decreased on both coated and uncoated poly(BMA) by day 8. While IL-1 beta, IL-6, and TNF-alpha release was variably influenced by polymer coating, release was consistently inhibited relative to TCPS on day 1. However, cytokine production was not inhibited compared to corresponding uncoated polymers on day 1. With or without protein preadsorption, IL-1 beta release was not detectable in the supernatants of any polymer on day 8, IL-6 production was diminished on day 8, and TNF-alpha production was sustained on day 8. Overall, MPC copolymer-coated and uncoated poly(BMA) were the least stimulating, while TCPS was the most stimulating.(ABSTRACT TRUNCATED AT 250 WORDS)
Performance of SOI Bragg Grating Ring Resonator for Nonlinear Sensing Applications (2014)

In this paper, a spectroscopic sensor formed by a silicon-on-insulator waveguiding Bragg grating ring resonator working in linear and non-linear regime is proposed. In linear regime, the device shows a spectral response characterized by a photonic band gap (PBG). Very close to the band gap edges, the resonant structure exhibits split modes having a splitting magnitude equal to the PBG spectral extension, whose characteristics can be exploited to obtain a RI optical sensor almost insensitive to the fabrication tolerances and environmental perturbations. When the device operates in nonlinear regime, exactly in the spectral region showing the split resonant modes, the RI sensing performance is strongly improved with respect to the linear regime. This improvement, demonstrated by taking into account all the non-linear effects excited in the integrated silicon structure (i.e., Two Photon Absorption (TPA), TPA-induced Free Carrier Absorption, plasma dispersion, Self-Phase-Modulation and Cross-Phase-Modulation effects as induced by Kerr nonlinearity) as well as the deleterious thermal and stress effects, allows enhancing the performance of the RI split mode resonant sensors, while achieving good immunity to the fabrication tolerances and environmental perturbations. The improvement in terms of sensor resolution can be at least one order of magnitude, still without using optimal parameters.
On the Efficiency of Spatial Channel Reuse in Ultra-Dense THz Networks (2015)

Wireless communications in the terahertz (THz) frequency band, 0.1-10THz, promises a rapid increase of channel capacity in next- generation networks. However, the advantages of this technology depend not only on the single link performance, but also on the possibility of several THz links to coexist in the same area. Thus, the efficiency of spatial channel reuse has to be studied. Due to the presence of specific effects in the THz band, such as molecular absorption and molecular noise, existing performance evaluation techniques are not straightforwardly applicable. In this paper, the approach for network-level analysis of THz wireless communications is proposed. This approach is based on the tools of stochastic geometry and takes into account the specific signal propagation features of the THz frequency band. The presented technique is used to derive the distribution of SINR and spectral efficiency as well as to estimate the optimal distance between receiving nodes and maximize the area capacity.
Structure-activity relationships of 8-cycloalkyl-1,3-dipropylxanthines as antagonists of adenosine receptors (1990)

8-Substituted xanthines currently represent the most potent class of adenosine-receptor antagonists. A series of 8-substituted 1,3-dipropylxanthines was prepared and their potency as antagonists of A1 and A2 adenosine receptors of human platelets and rat adipocytes, respectively, were determined. No agents studied were as potent as 8-cyclopentyl-1,3-dipropylxanthine as antagonists of the A1 adenosine receptor, but 8-(2-methylcyclopropyl)-1,3-dipropylxanthine was at least 1000-fold more potent as an antagonist of A1 than of A2 adenosine receptors. While most substitutions on the 8-cycloalkyl moiety caused decreased potency to inhibit both A1 and A2 adenosine receptors, 8-[trans-4-(acetamidomethyl)cyclohexyl]-1,3-dipropylxanthine was nearly equipotent as an antagonist of the two receptors and appeared to be the most potent antagonist of A2 adenosine receptors reported to date.
Production monitoring system development and modification; pp. 567–580 (2015)

Main attention of this paper is paid to the development of a simple, but efficient concept of a real time production monitoring system. The goal is to offer an effective concept, which will help to provide an accurate overview of the shop floor activities by diverse information appearance and improve asset management, machinery utilization, and production process stability. The subtask considered includes description of the design of a visual module for the proposed production monitoring system for a certain type of micro, small and medium sized enterprises.
Sparse Coding for Object Recognition (2013)

In recent years, the application of sparse coding techniques has led to frameworks that match or set the state-of-the-art in object recognition tasks. De-spite such success, applying sparse coding to vi-sion tasks presents unique challenges and many pa-pers addressing these concerns appear in top con-ferences annually. This paper acts as an introduc-tion to the subject of sparse coding, identifies the key research areas improving its applicability to recogni-tion tasks, and surveys recent approaches to treating these challenges. 1
Analysis and Comparison of Queues with Different Levels of Delay Information (2007)

Information about delays can enhance service quality in many industries. Delay information can take many forms, with different degrees of precision. Different levels of information have different effects on customers and therefore on the overall system. To explore these effects, we consider a queue with balking under three levels of delay information: no information, partial information (the system occupancy), and full information (the exact waiting time). We assume Poisson arrivals, independent exponential service times, and a single server. Customers decide whether to stay or balk based on their expected waiting costs, conditional on the information provided. We show how to compute the key performance measures in the three systems, obtaining closed-form solutions for special cases. We then compare the three systems. We identify some important cases where more accurate delay information improves performance. In other cases, however, information can actually hurt the provider or the customers.
Alternatives to the use of fetal bovine serum: Serum-free cell culture (2003)

Serum is commonly used as a supplement to cell culture media. It provides a broad spectrum of macromolecules, carrier proteins for lipoid substances and trace elements, attachment and spreading factors, low molecular weight nutrients, and hormones and growth factors. The most widely used animal serum supplement is fetal bovine serum, FBS. Since serum in general is an ill-defined component in cell culture media, a number of chemically defined serum-free media formulations have been developed in the last two decades. Besides modern cell biological advances in cell and tissue culture and efforts towards a standardisation of cell culture protocols in Good Cell Culture Practice, in addition, considerable ethical concerns were raised recently about the harvest and collection of fetal bovine serum. Thus, in order to decrease the annual need for bovine fetuses in terms of the 3Rs through any reduction in the use or partial replacement of serum, as well as in terms of an improvement of cell and tissue culture methodology, serum-free cell culture represents a modern, valuable and scientifically well accepted alternative to the use of FBS in cell and tissue culture.