gebhart/patrepeval huggingface dataset:
Cloning, Expression, and Sequencing of a Cell Surface Antigen Containing a Leucine-Rich Repeat Motif from <i>Bacteroides forsythus</i> ATCC 43037 (1998)

Bacteroides forsythus is a recently recognized human periodontopathogen associated with advanced, as well as recurrent, periodontitis. However, very little is known about the mechanism of pathogenesis of this organism. The present study was undertaken to identify the surface molecules of this bacterium that may play roles in its adherence to oral tissues or triggering of a host immune response(s). The gene (bspA) encoding a cell surface-associated protein of B. forsythus with an apparent molecular mass of 98 kDa was isolated by immunoscreening of a B. forsythus gene library constructed in a lambda ZAP II vector. The encoded 98-kDa protein (BspA) contains 14 complete repeats of 23 amino acid residues that show partial homology to leucine-rich repeat motifs. A recombinant protein containing the repeat region was expressed in Escherichia coli, purified, and utilized for antibody production, as well as in vitro binding studies. The purified recombinant protein bound strongly to fibronectin and fibrinogen in a dose-dependent manner and further inhibited the binding of B. forsythus cells to these extracellular matrix (ECM) components. In addition, adult patients with B. forsythus-associated periodontitis expressed specific antibodies against the BspA protein. We report here the cloning and expression of an immunogenic cell surface-associated protein (BspA) of B. forsythus and speculate that it mediates the binding of bacteria to ECM components and clotting factors (fibronectin and fibrinogen, respectively), which may be important in the colonization of the oral cavity by this bacterium and is also a target for the host immune response.
Smectic C<sup>*</sup> Chevron Layer Structure Studied by X-Ray Diffraction (1988)

Layer structures in chiral smectic C ( S C * ) phases were studied by high-resolution X-ray diffraction. The existence of a chevron layer structure was confirmed even in thick cells such as 350 µm and even in a compound with the phase sequence of N * - S C * . Cells made by a SiO oblique-evaporation technique gave two diffraction patterns; a single peak was observed when the evaporation directions of top and bottom glasses were set in opposite directions (antiparallel), while two peaks were observed in the case of the glasses set in the same direction (parallel). Thus, the chevron structure was confirmed to exist quite generally except for in the SiO antiparallel cells.
Is there evidence for phospho-oligosaccharides as insulin mediators? (1997)

glycosylphosphatidylinositol/insulin
Performance Evaluation of a Commercial Application, Trade, in Scale-out Environments (2007)

Scale-out approach, in contrast to scale-up approach (exploring increasing performance by utilizing more powerful shared-memory servers), refers to deployment of applications on a large number of small, inexpensive, but tightly packaged and tightly interconnected servers. The purpose of this study is to understand the performance of scale-out architectures with a typical enterprise workload, IBM Trade Performance Benchmark Sample for WebSphere Application Server (a.k.a. Trade). We describe a performance evaluation methodology that gives accurate predictions of application performance and system utilization by utilizing experimental data driven model development. Through experiments and extrapolation from the derived model, we show that for such workload, WebSphere Application Server packages for distributed environments scale well while the possible bottleneck of the application deployment is the database tier.
Reassortment of Avian Influenza A/H6N6 Viruses from Live Poultry Markets in Guangdong, China (2016)

Since early 2013, H7N9-subtype avian influenza virus (AIV) has caused human infection in eastern China. To evaluate AIV contamination and the public risk of infection, we systematically implemented environmental sampling from live poultry markets in Guangdong Province. Through real-time polymerase chain reaction assays and next-generation sequencing, we generated full nucleotide sequences of all 10 H6N6 AIVs isolated during sampling. Focusing on sequence analyses of hemagglutinin genes of the 10 H6N6 AIVs revealed that the viruses were low pathogenic AIVs with the typical hemagglutinin cleavage site of P-Q-I-E-T-R-G. The hemagglutinin, neuraminidase, and nucleocapsid genes of nine AIVs were of ST2853-like (H6-subtype) lineage, ST192-like (N6-subtype) lineage, and HN573-like (H6-subtype) lineage, respectively; whereas the other five genes were of ST339-like (H6-subtype) lineage. However, the polymerase PB2 and nucleocapsid genes of one strain (HZ057) were of GS/GD-like (H5N1-subtype) and ST339-like lineages. Phylogenic analysis revealed that all eight genes of the 10 viruses belonged to Eurasian avian lineage. Altogether, the 10 AIVs were reassortants of different genetic groups of exchanges with the same virus subtype, thus illustrating the genetic diversity and complexity of H6N6-subtype AIVs in Guangdong Province.
Platform-level Support for Authorization in Cloud Services with OAuth 2 (2014)

The OAuth 2 web authorization framework allows services to act on behalf of users when interacting with other services. It avoids sharing username and passwords across services, thus, in principle protecting users from several threats. However, it is known that the implementation of this kind of authorization protocol is tricky, and potentially leads to vulnerable web services. In this paper we present a toolkit for Java-based Cloud platforms which facilitates the deployment of the OAuth 2 authorization framework into existing web services. We developed a set of interceptors, using aspect-oriented programming techniques for SOA, to handle the main OAuth flow. Secondly, we created an Eclipse plug-in to integrate OAuth into cloud services with minimum effort.
Cell wall substrate specificity of six different lysozymes and lysozyme inhibitory activity of bacterial extracts (2006)

We have investigated the specificity of six different lysozymes for peptidoglycan substrates obtained by extraction of a number of gram-negative bacteria and Micrococcus lysodeikticus with chloroform/Tris-HCl buffer (chloroform/buffer). The lysozymes included two that are commercially available (hen egg white lysozyme or HEWL, and mutanolysin from Streptomyces globisporus or M1L), and four that were chromatographically purified (bacteriophage lambda lysozyme or LaL, bacteriophage T4 lysozyme or T4L, goose egg white lysozyme or GEWL, and cauliflower lysozyme or CFL). HEWL was much more effective on M. lysodeikticus than on any of the gram-negative cell walls, while the opposite was found for LaL. Also the gram-negative cell walls showed remarkable differences in susceptibility to the different lysozymes, even for closely related species like Escherichia coli and Salmonella Typhimurium. These differences could not be due to the presence of lysozyme inhibitors such as Ivy from E. coli in the cell wall substrates because we showed that chloroform extraction effectively removed this inhibitor. Interestingly, we found strong inhibitory activity to HEWL in the chloroform/buffer extracts of Salmonella Typhimurium, and to LaL in the extracts of Pseudomonas aeruginosa, suggesting that other lysozyme inhibitors than Ivy exist and are probably widespread in gram-negative bacteria.
Improved lysozyme assay in biological fluids. (1979)

We describe a simple, rapid, sensitive, and highly reproducible assay for lysozyme, with use of concentrated cell suspensions of Micrococcus lysodeikticus in Tris-buffered glycerol/water (40/60 by vol), pH 7.5. Stored at -20 degrees C, the cells' susceptibility to lysozyme remains unaltered over long periods. Almost identical concentration curves were obtained with different aliquots of the same preparation during eight months. Lysozyme activity was reflected in the decrease in absorbance of the reaction mixture after incubation for 15 min at 37 degrees C. Concentrations of egg-white lysozyme as low as 0.02 mg/L can be accurately assayed.
Enzymes in organic synthesis, 4. Investigation of the pancreatin‐catalyzed acylation of cis‐cyclopent‐2‐ene‐1,4‐diol with various trichloroethyl and vinyl Alkanoates (1991)

Abstract During the pancreatin‐catalyzed acetylation of the meso‐diol 1 with 2,2,2‐trichloroethyl acetate ( 2a ) in tetrahydrofuran/tri‐ethylamine, the enantiomeric monoacetates 3a and ent‐ 3a are formed at nearly equal rates. ent‐ 3a is rapidly acetylated in a second enzyme‐catalyzed step, forming 4a , whereas 3a resists further enzymatic acetylation. Thus, the monoacetate 3a can be obtained in 48% yield with an enantiomeric excess (e.e.) of more than 99%. 2,2,2‐Trichloroethyl propanoate and butanoate give the corresponding monoacylation products even in slightly better yield, whereas the octanoate affords the mono‐acylation product with a lower enantiomeric excess. 2,2,2‐Trichloroethyl monochloroacetate provides the monoacylation product in a 40% yield with an e.e. of 90%. The dichloroacetate, however, affords the diacylation product exclusively in an enzyme‐independent chemical reaction. With the 2,2,2‐trichloroethyl esters of isobutyric, phenylacetic, and benzoic acid no transesterification could be achieved within 24 hours. The application of vinyl acetate, however, represents a significant improvement in the synthesis of enantiomerically pure monoacetate 3a from meso‐diol 1 .
Reduction of uranium by cytochrome c3 of Desulfovibrio vulgaris (1993)

The mechanism for U(VI) reduction by Desulfovibrio vulgaris (Hildenborough) was investigated. The H2-dependent U(VI) reductase activity in the soluble fraction of the cells was lost when the soluble fraction was passed over a cationic exchange column which extracted cytochrome c3. Addition of cytochrome c3 back to the soluble fraction that had been passed over the cationic exchange column restored the U(VI)-reducing capacity. Reduced cytochrome c3 was oxidized by U(VI), as was a c-type cytochrome(s) in whole-cell suspensions. When cytochrome c3 was combined with hydrogenase, its physiological electron donor, U(VI) was reduced in the presence of H2. Hydrogenase alone could not reduce U(VI). Rapid U(VI) reduction was followed by a subsequent slow precipitation of the U(IV) mineral uraninite. Cytochrome c3 reduced U(VI) in a uranium-contaminated surface water and groundwater. Cytochrome c3 provides the first enzyme model for the reduction and biomineralization of uranium in sedimentary environments. Furthermore, the finding that cytochrome c3 can catalyze the reductive precipitation of uranium may aid in the development of fixed-enzyme reactors and/or organisms with enhanced U(VI)-reducing capacity for the bioremediation of uranium-contaminated waters and waste streams.
Iron, Chelation and the Growth of Marine Phytoplankton I. Growth Kinetics and Chlorophyll Production in Cultures of the Euryhaline Flagellate <i>Dunalliela Tertiolecta</i> under Iron-Limiting Conditions (1970)

One of the major advances made in the development of media for the culture of marine phytoplankton was the introduction of chelating agents as a means of controlling the concentrations of the trace metals necessary for plant growth; an excellent historical survey of this field has been provided by Provasoli, McLaughlin and Droop (1957). Much of the discussion concerning the role of the chelating agents has centred upon the maintenance of the iron in solution at concentrations adequate for plant nutrition (Droop, 1961; Provasoli, 1963; Johnston, 1964). In the absence of chelators, the pH of the culture media would result in almost complete precipitation of the iron.
Unshackling evolution (2013)

In 1994 Karl Sims showed that computational evolution can produce interesting morphologies that resemble natural organisms. Despite nearly two decades of work since, evolved morphologies are not obviously more complex or natural, and the field seems to have hit a complexity ceiling. One hypothesis for the lack of increased complexity is that most work, including Sims', evolves morphologies composed of rigid elements, such as solid cubes and cylinders, limiting the design space. A second hypothesis is that the encodings of previous work have been overly regular, not allowing complex regularities with variation. Here we test both hypotheses by evolving soft robots with multiple materials and a powerful generative encoding called a compositional pattern-producing network (CPPN). Robots are selected for locomotion speed. We find that CPPNs evolve faster robots than a direct encoding and that the CPPN morphologies appear more natural. We also find that locomotion performance increases as more materials are added, that diversity of form and behavior can be increased with different cost functions without stifling performance, and that organisms can be evolved at different levels of resolution. These findings suggest the ability of generative soft-voxel systems to scale towards evolving a large diversity of complex, natural, multi-material creatures. Our results suggest that future work that combines the evolution of CPPN-encoded soft, multi-material robots with modern diversity-encouraging techniques could finally enable the creation of creatures far more complex and interesting than those produced by Sims nearly twenty years ago.
Dublin Radiocarbon Dates I (1961)

A C 14 -dating installation was operated in the Physics Department, Trinity College, Dublin, from early 1958 until early 1960, by I. R. McAulay. Construction and testing of the apparatus had occupied 15 months previous to this. Material for dating was selected and pretreated by W. A. Watts, who also collected and submitted the samples and carried out pollen analyses except where the contrary is stated in the text. The project was a short-term one with two main aims; to obtain a few key archaeologic dates, particularly in the Neolithic, to help orientate chronologic discussion; and to test the validity of the pollen zonation for the post-Atlantic of Mitchell (1956).
Internal Friction in Solids IV. Relation Between Cold Work and Internal Friction (1938)

Previous investigators have found that cold working of metals has a marked effect upon internal friction, increasing it, in certain cases, by a factor of more than ten. In the present paper it is assumed that the effect of cold work upon internal friction is due to the residual internal stresses which it produces. During vibration these residual stresses give rise to fluctuations in temperature, and thus to local heat currents, which are inevitably associated with a rise in entropy, i.e., with internal friction. A formula is obtained for this internal friction in terms of the energy associated with the residual stresses, and the temperature variation of the modulus of rigidity. It gives the observed order of magnitude. According to the theory developed in this paper, the measurement of the internal friction of a cold worked specimen over a wide frequency range and for various types of vibration will give not only the mean square of the residual stresses, but also their preferred axes, if any, and the mean linear dimensions of their inhomogeneities.
Multi-input bidirectional DC-DC converter combining DC-link and magnetic-coupling for fuel cell systems (2005)

This paper presents a new multi-input bidirectional dc-dc converter which connects a fuel cell, storage and load by a combination of a dc-link and magnetic-coupling. A boost-dual-half-bridge and a bidirectional direct-connected switching cell are used. The topology is simple and only needs six power switches. The load and the sources are galvanically isolated. Furthermore, the proposed converter draws/injects smooth current from the fuel cell and the supercapacitor. The system is suitable for medium-power applications where simple topology, autonomous operation, compact packaging, and low cost are required. Different control schemes to manage power flow are proposed and compared. Simulation and experimental results that verify the effectiveness of the topology and its control scheme are presented. Moreover, it is shown that the idea of combining the dc-link and magnetic-coupling can be further developed to a general topology for multi-port bidirectional dc-dc converters.
Alzheimer’s disease, cerebral blood flow, and nitric oxide. (2010)

神経源性と考えられてきたアルツハイマー病（AD）を初めとする認知・記憶障害にも，脳循環低下による慢性的な酸素供給の減少と代謝障害が関与することを示す報告が少なからず見られる．その中で，脳血管内皮障害の占める役割に多くの注目が寄せられている．内皮障害には血管性危険因子（vascular risk factor）や加齢が強い関わりをもつ．内皮機能の主要なマーカーとしての一酸化窒素（NO）とADとの関係について最近興味ある情報が数多く見られる．β-amyloid（Aβ）沈着と脳微小血管内皮障害との間に強い相関が観察されている．NOの減少はAβ沈着を助長し，AβはNOの働きや合成を抑制して脳血流を減少する．NO合成酵素（NOS）阻害薬はAβの有害作用を増幅する．AD治療薬であるコリンエステラーゼ阻害薬の血管作用にNOが関係する可能性が示唆されている．脳における炎症反応はiNOSを介してNOの過剰産生をもたらし神経変性や神経死をひき起す．新しい視点からのAD研究が，ADの予防と治療の発展に貢献することを願っている．
Effect of Rotigotine vs Placebo on Cognitive Functions Among Patients With Mild to Moderate Alzheimer Disease (2020)

ClinicalTrials.gov Identifier: NCT03250741.
Einleitung II — Die Politische Entwicklung Japans 1850 – 1930 (1983)

Als Beginn der Modernisierung Japans und damit auch seiner “modernen” politischen Geschichte wird in den meisten Untersuchungen die Meiji-Restauration von 1868 angesehen. Zweifellos waren die damit verbundene Abschaffung des Shōgun-Amtes, das die oberste politische Instanz des Feudalsystems gewesen war, und die Rückgabe der Regierungsmacht an den Tennō ein wichtiger politischer Einschnitt. Aber viele der Entwicklungen, die zu einer Modernisierung von Politik, Wirtschaft und Gesellschaft führen sollten, hatten bereits in den vorhergehenden Jahrzehnten begonnen. Voraussetzungen für die Modernisierung entstanden sogar noch sehr viel früher, so daß im Grunde genommen die Zeit ab 1600, die Neuzeit in der japanischen Geschichte, in eine Betrachtung der modernen politischen Entwicklung mit einbezogen werden müßte.
Synchronous double C–N bond formation via C–H activation for a novel synthetic route to phenazine (2015)

A novel synthetic strategy for phenazine formation is reported following self-coupling of anilines by Pd-Ag binary nanocluster-catalysed synchronous double C-N bond formation via non-radical mode of ortho-aryl C-H activation.
Thin Layer Chromatography Coupled with Surface-Enhanced Raman Scattering as a Facile Method for On-Site Quantitative Monitoring of Chemical Reactions (2014)

By coupling surface-enhanced Raman spectroscopy (SERS) with thin layer chromatography (TLC), a facile and powerful method was developed for on-site monitoring the process of chemical reactions. Samples were preseparated on a TLC plate following a common TLC procedure, and then determined by SERS after fabricating a large-area, uniform SERS substrate on the TLC plate by spraying gold nanoparticles (AuNPs). Reproducible and strong SERS signals were obtained with substrates prepared by spraying 42-nm AuNPs at a density of 5.54 × 10(10) N/cm(2) on the TLC plate. The capacity of this TLC-SERS method was evaluated by monitoring a typical Suzuki coupling reaction of phenylboronic acid and 2-bromopyridine as a model. Results showed that this proposed method is able to identify reaction product that is invisible to the naked eye, and distinguish the reactant 2-bromopyridine and product 2-phenylpyridine, which showed almost the same retention factors (R(f)). Under the optimized conditions, the peak area of the characteristic Raman band (755 cm(-1)) of the product 2-phenylpyridine showed a good linear correlation with concentration in the range of 2-200 mg/L (R(2) = 0.9741), the estimated detection limit (1 mg/L 2-phenylpyridine) is much lower than the concentration of the chemicals in the common organic synthesis reaction system, and the product yield determined by the proposed TLC-SERS method agreed very well with that by UPLC-MS/MS. In addition, a new byproduct in the reaction system was found and identified through continuous Raman detection from the point of sample to the solvent front. This facile TLC-SERS method is quick, easy to handle, low-cost, sensitive, and can be exploited in on-site monitoring the processes of chemical reactions, as well as environmental and biological processes.
Dictionary of Chemistry (2014)

This Dictionary provides an explanation of the main ideas of and concepts central to chemistry. Each entry in this A-Z resource begins with a clear, one-sentence definition that explains why the term is important. These sentences are followed by a fuller explanation and, where appropriate, examples, diagrams, tables and equations. Key terms such as inorganic chemistry, organic chemistry, physical chemistry, the chemical industry, and qualitative analysis tell the user about the main features of important aspects of chemistry, with cross-references leading to related terms in each field. Other entries give a historical perspective, showing in outline how important themes of chemistry have developed.
The dopamine beta‐hydroxylase inhibitor nepicastat increases dopamine release and potentiates psychostimulant‐induced dopamine release in the prefrontal cortex (2013)

The dopamine-beta-hydroxylase inhibitor nepicastat has been shown to reproduce disulfiram ability to suppress the reinstatement of cocaine seeking after extinction in rats. To clarify its mechanism of action, we examined the effect of nepicastat, given alone or in association with cocaine or amphetamine, on catecholamine release in the medial prefrontal cortex and the nucleus accumbens, two key regions involved in the reinforcing and motivational effects of cocaine and in the reinstatement of cocaine seeking. Nepicastat effect on catecholamines was evaluated by microdialysis in freely moving rats. Nepicastat reduced noradrenaline release both in the medial prefrontal cortex and in the nucleus accumbens, and increased dopamine release in the medial prefrontal cortex but not in the nucleus accumbens. Moreover, nepicastat markedly potentiated cocaine- and amphetamine-induced extracellular dopamine accumulation in the medial prefrontal cortex but not in the nucleus accumbens. Extracellular dopamine accumulation produced by nepicastat alone or by its combination with cocaine or amphetamine was suppressed by the α2 -adrenoceptor agonist clonidine. It is suggested that nepicastat, by suppressing noradrenaline synthesis and release, eliminated the α2 -adrenoceptor mediated inhibitory mechanism that constrains dopamine release and cocaine- and amphetamine-induced dopamine release from noradrenaline or dopamine terminals in the medial prefrontal cortex.
2.45 GHz microwave-excited atmospheric pressure air microplasmas based on microstrip technology (2005)

A plasma system based on microstrip technology was developed for the generation of atmospheric pressure microplasmas. A discharge gap was placed between the striplines and the ground plane on the transverse cross section in the direction of microwave propagation. This microstrip structure permits the concentration of electric fields at the discharge gap, which is confirmed by a computer simulation using the three-dimensional simulation code based on the finite-difference time-domain method, and can produce atmospheric pressure plasmas even in air. The microplasmas were sustained in the discharge gap (width: 0.2 mm, length: 6 mm) at a microwave power of 1 W. The experimentally measured rotational temperature of nitrogen molecules was 800 K, indicating these plasmas to be nonthermal plasmas. This plasma system will provide a portable microplasma system utilizing a small semiconductor microwave source and a large-scale atmospheric pressure nonthermal plasma using the array configuration.