gebhart/patrepeval huggingface dataset:
MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data (2013)

Many bioactive natural products are produced as "secondary metabolites" by plants, bacteria, and fungi. During the middle of the 20th century, several secondary metabolites from fungi revolutionized the pharmaceutical industry, for example, penicillin, lovastatin, and cyclosporine. They are generally biosynthesized by enzymes encoded by clusters of coordinately regulated genes, and several motif-based methods have been developed to detect secondary metabolite biosynthetic (SMB) gene clusters using the sequence information of typical SMB core genes such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). However, no detection method exists for SMB gene clusters that are functional and do not include core SMB genes at present. To advance the exploration of SMB gene clusters, especially those without known core genes, we developed MIDDAS-M, a motif-independent de novodetection algorithm for SMB gene clusters. We integrated virtual gene cluster generation in an annotated genome sequence with highly sensitive scoring of the cooperative transcriptional regulation of cluster member genes. MIDDAS-M accurately predicted 38 SMB gene clusters that have been experimentally confirmed and/or predicted by other motif-based methods in 3 fungal strains. MIDDAS-M further identified a new SMB gene cluster for ustiloxin B, which was experimentally validated. Sequence analysis of the cluster genes indicated a novel mechanism for peptide biosynthesis independent of NRPS. Because it is fully computational and independent of empirical knowledge about SMB core genes, MIDDAS-M allows a large-scale, comprehensive analysis of SMB gene clusters, including those with novel biosynthetic mechanisms that do not contain any functionally characterized genes.
Polarization-insensitive thermo-optic switch based on multimode polymeric waveguides with an ultralarge optical bandwidth (2000)

A promising polarization-insensitive thermo-optic switch based on multimode polymeric waveguides is reported. This device has a packing density of 40 channels/cm. Simulation result shows that an extinction ratio of greater than 20 dB can be achieved with the device–electrode interaction length of 30 mm. The thermo-optic switch operating at wavelengths of 632.8 nm and 1.3 μm has been demonstrated experimentally with extinction ratios of 21 and 22 dB, respectively. Such a device has an intrinsic wide optical bandwidth due to the large dynamic range of the phase-matching condition implied by the multimode waveguides. The material employed provides us with a switching speed of 100 μs.
Cytotoxic activity of nucleoside diphosphate kinase secreted from Mycobacterium tuberculosis (2003)

Pathogenicity of Mycobacterium tuberculosis is closely related to its ability to survive and replicate in the hostile environment of macrophages. For some pathogenic bacteria, secretion of ATP-utilizing enzymes into the extracellular environment aids in pathogen survival via P2Z receptor-mediated, ATP-induced death of infected macrophages. A component of these enzymes is nucleoside diphosphate kinase (Ndk). The ndk gene was cloned from M. tuberculosis H37Rv and expressed in Escherichia coli. Ndk was secreted into the culture medium by M. tuberculosis, as determined by enzymatic activity and Western blotting. Purified Ndk enhanced ATP-induced macrophage cell death, as assayed by the release of [14C]adenine. A catalytic mutant of Ndk failed to enhance ATP-induced macrophage cell death, and periodate-oxidized ATP (oATP), an irreversible inhibitor of P2Z receptor, blocked ATP/Ndk-induced cell death. Purified Ndk was also found to be autophosphorylated with broad specificity for all nucleotides. Conversion of His117-->Gln, which is part of the nucleotide-binding site, abolished autophosphorylation. Purified Ndk also showed GTPase activity. Collectively, these results indicate that secreted Ndk of M. tuberculosis acts as a cytotoxic factor for macrophages, which may help in dissemination of the bacilli and evasion of the immune system.
Effects of BAY 85-3934 administration in male Wistar rats treated with gentamicin to induce renal anemia. (2015)

&lt;p&gt;Data are presented as means ± SEM. (A) Plasma EPO levels, and (B) kidney and (C) liver relative expression of erythropoietin (EPO) mRNA 4 h after oral administration of BAY 85-3934. Before administration, rats had been treated with vehicle or gentamicin. (&lt;i&gt;n&lt;/i&gt; = 5 animals per group). *&lt;i&gt;p&lt;/i&gt;&lt;0.05, **&lt;i&gt;p&lt;/i&gt;&lt;0.01, and ***&lt;i&gt;p&lt;/i&gt;&lt;0.001 compared with vehicle group,&lt;sup&gt; §&lt;/sup&gt;&lt;i&gt;p&lt;/i&gt;&lt;0.05 and &lt;sup&gt;§§&lt;/sup&gt;&lt;i&gt;p&lt;/i&gt;&lt;0.001 compared with control group, t-test. (D) Kidney and (E) liver mRNA expression levels of hypoxia-inducible factor target genes relative to mean of vehicle treated animals after oral administration of BAY 85-3934 (&lt;i&gt;n&lt;/i&gt; = 4 to 5 animals per group, error bars not shown for clarity of presentation). For definition of gene symbols, see &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111838#pone-0111838-t001" target="_blank"&gt;Table 1&lt;/a&gt;. (F) Time-course of changes in packed cell volume (PCV) following treatment with BAY 85-3934 or vehicle (once daily, five times per week, number of animals as indicated). (G) Hemoglobin levels 7 days after start of treatment with BAY 85-3934 or vehicle at day 22 of experiment shown in (F). *&lt;i&gt;p&lt;/i&gt;&lt;0.05, **&lt;i&gt;p&lt;/i&gt;&lt;0.01, and ***&lt;i&gt;p&lt;/i&gt;&lt;0.001 compared with vehicle group; &lt;sup&gt;#&lt;/sup&gt;&lt;i&gt;p&lt;/i&gt;&lt;0.05 compared with sham group; t-test.&lt;/p&gt;
High-power microwave gas discharge in high-Q evanescent-mode cavity resonators and its instantaneous/long-term effects (2013)

This paper presents the first experimental and theoretical investigation of high-power RF gas discharge as applied to RF front-end filters with critical air gaps in the 10s of μm. Specifically, a strongly-coupled high-Q evanescent-mode resonant cavity is utilized as a vehicle in this study. This cavity tends to concentrate the resonant electric field in a small volume between its loading post and top wall. Both experiments conducted up to 45.3 dBm at 6.5 GHz and molecular-dynamics-based modeling suggest that, as the input power is increased, gas ionization leads to increasing gas discharge inside this volume. In addition to the measured RF data, surface analysis of the cavity post and top wall lead to the same conclusion. Besides the observed instantaneous effects on the resonator's RF performance, the impact of gas discharge in its long-term performance and potential failure is analyzed.
Hydrogen/deuterium exchange mass spectrometry applied to IL-23 interaction characteristics: potential impact for therapeutics (2015)

IL-23 is an important therapeutic target for the treatment of inflammatory diseases. Adnectins are targeted protein therapeutics that are derived from domain III of human fibronectin and have a similar protein scaffold to antibodies. Adnectin 2 was found to bind to IL-23 and compete with the IL-23/IL-23R interaction, posing a potential protein therapeutic. Hydrogen/deuterium exchange mass spectrometry and computational methods were applied to probe the binding interactions between IL-23 and Adnectin 2 and to determine the correlation between the two orthogonal methods. This review summarizes the current structural knowledge about IL-23 and focuses on the applicability of hydrogen/deuterium exchange mass spectrometry to investigate the higher order structure of proteins, which plays an important role in the discovery of new and improved biotherapeutics.
Physiologic effects of intramedullary reaming. (2006)

Reaming has a significant biologic and mechanical impact on the physiology of fracture healing. A review of the thermal, pulmonary, and osteogenic effects of reaming can provide evidence-based guidelines to assist the clinician in improving patient outcomes. Thermal necrosis is a rare but commonly referenced complication of reaming. The risks of heat-induced cortical damage can be minimized by sequential reaming with sharp instruments and by reaming with instruments that are sized appropriately to fit the intramedullary canal. The use of a tourniquet while reaming does not increase the risk of thermal necrosis. Reaming results in increased intramedullary pressure and secondary embolization of marrow elements to the pulmonary system. The clinical significance of these embolic events remains controversial. Potential complications can be reduced by using reamer designs and techniques that minimize the increases in intramedullary pressure. Outcome studies consistently show that reaming potentiates the healing response with intramedullary fixation of long-bone fractures. Recent laboratory studies implicate alterations in cortical blood flow patterns and the osteogenic potential of reaming debris as critical components of this process.
A complex notch filter based approach to device the control strategy for a generalized unbalanced grid connected distributed generator (2013)

In this paper, a p-q theory based approach, using Complex Notch Filter, is proposed to control active and reactive power flow of a distributed generator connected to a generalized unbalanced grid. The proposed method facilitates high bandwidth grid power flow control along with maintaining sinusoidal grid currents by finding suitable inverter current references directly in the a-b-c frame. The proposed method is faster than the conventional methods because of the absence of the Phase Lock Loop and Park's transformation requirement. A novel method of extracting the phase angle of the fundamental grid voltage is proposed. A Complex Notch Filter based method for extracting positive and negative sequence components together with filtering grid voltage harmonics is also proposed to reduce the computational burden on the processor. The method is devised for a generalized three-phase system. The proposed method is validated through rigorous tests and experimental results presented depict the efficacy of the proposed method.
Design of a small-size interlocking system with high availability (1999)

An interlocking system consists of an interlocking logical unit and a power controlling unit. After this logical unit calculates the relationship among the train position, the rail shifting position, and the signal, it decides the aspect of the signal. The power controlling unit supplies electrical power to the switch motor and the signal light according to the decision of the logical unit. This paper proposes a small-sized interlocking system which uses a triplex redundant off-the-shelf controller with fail-safe checker as an interlocking logical unit. A majority voting circuit ensures the safety of parallel output from the interlocking logical unit. This circuit satisfies the condition of total self-checking (of D.A. Anderson) and also the condition of high availability. In other words, no single fault ever leads to a hazardous state and this circuit ensures safety after single fault occurrence. © 1999 Scripta Technica, Electr Eng Jpn, 128(2): 63–73, 1999
Interleukin‐1 stimulated activation of the COT catalytic subunit through the phosphorylation of Thr290 and Ser62 (2006)

The protein kinase COT/Tpl2 is activated by interleukin-1 (IL-1), TNFalpha and lipopolysaccharide, and its activation by these agonists involves the IkappaB kinase beta (IKKbeta) catalysed phosphorylation of the p105 regulatory subunit. Here, we show that COT activation also requires catalytic subunit phosphorylation, since IL-1beta induced a 5-10-fold activation of a COT mutant unable to bind p105. Activation was paralleled by the phosphorylation of Thr290 and Ser62 and unaffected by the IKKbeta inhibitor PS1145 at concentrations which prevented the degradation of IkappaBalpha. Mutagenesis experiments indicated that COT activation is initiated by Thr290 phosphorylation catalysed by an IL-1-stimulated protein kinase distinct from IKKbeta, while Ser62 phosphorylation is an autophosphorylation event required for maximal activation.
The Configurational Stability of Primary Grignard Reagents (1963)

The n.m.r. spectrum of the methylene hydrogens of 3,3-dimethylbutylmagnesium chloride in diethyl ether that the trans and gauche coupling constants, J_t and J_g, have the same respective values for each conformation (I-III), the separation of the outer lines for I should be ( J_t + J_g), while the corresponding separation for a rapidly interconverting mixture of II and III would be 1/2(J_t + 3J_g). Therefore, if the averaging of coupling constants observed in the high-temperature spectra is a consequence of changes in conformational populations, the separation of the outer lines would be expected to change appreciably with temperature.
In situ sputtern : development of an in situ sputtering chamber to study the growths of perovskite thin films in real time using synchrotron X-rays (2016)

Sputter deposition is a versatile and industrially important deposition technique for thin films. There is an increasing demand for matching the characteristics of thin film ferroelectric materials to the requirements of the semi-conductor industry. The actual film properties are largely determined by the sputtering parameters such as pressure conditions and power settings. Depending on particular applications of the ferroelectric layers, for example tunable capacitors, non-volatile random access memories, electro-optical devices or thermistors, the electrical properties of thin films have to be tailored accordingly to achieve optimal performance. Inherently, these macroscopic parameters are influenced by the microstructure and crystallographic state of the films. Therefore, in the context of miniaturization of microelectronic circuits and devices and the necessary adaption of film thickness and grain size, thedeposition process has to be studied in situ. For this purpose, a sputter deposition chamber was built in the course of this work to investigate the deposition process in real time using intense X-rays from different synchrotron radiation sources. The remarkable properties of modern synchrotron radiation source allow for performing real time studiesof a variety of reactions, processing and manufacturing procedures. In orderto enable a versatile adaptability of the in situ sputtering unit to several synchrotron radiation sources in the world, the chamber was designed to be small and light weight without affecting its performance for in situ sputtering techniques. The chamber can be equipped with different annealing stages to heat the sample from room temperature up to 1000◦ C. Furthermore, the chamberis high-vacuum compatible and can run with different gases and gas mixtures needed for plasma operation during the sputtering process. By means of various X-ray diffraction and scattering experiments, it willbe shown that the characterization of the film formation and film growth is feasible in real time, thus adding an important dimension to the fundamental understanding of the evolution of the film microstructure. Furthermore, these techniques were used to study the temperature dependence of the deposition process and the growth on different substrate materials. It is observed that temperature has a clear influence on the film structure and morphology during all stages of deposition. This correlation is discussed in the context ofan established scientific model. In contrast to the temperature, the choice of substrate material decreasingly affects the film properties with increasing layer thickness. Finally, the crystallization of the films was found to occur homo-geneously throughout the thickness of the deposited layer and to be largely termperature-dependent. A summary and an outlook concludes this work.
Improving the catalytic performance of SAPO-18 for the methanol-to-olefins (MTO) reaction by controlling the Si distribution and crystal size (2016)

The physico-chemical properties of the small pore SAPO-18 zeotype have been controlled by properly selecting the organic molecules acting as organic structure directing agents (OSDAs).
Author Correction: Removal of artificial sweeteners and their effects on microbial communities in sequencing batch reactors (2018)

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Gas breakdown and plasma generation by dielectric resonator arrays (2016)

Summary form only given. Dielectric resonators are illuminated by electromagnetic planes waves and used to ignite and sustain arrays of microwave plasmas. The resonators consist of calcium titanate cylinders (nom. 30 mm diam. × 15 mm high). The resonators were arranged in a line with separation distances between 0.5 and 5 mm. We report plasma ignition in the gaps between the resonators using the HEM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">111</sub> resonance1 at 1.1 GHz. Paschen curves of the breakdown field and breakdown voltage are measured in reduced pressure argon. The breakdown is consistent with parallel plate microwave breakdown measurements2 except if the discharge gap is 1 mm or less. Sustained argon plasmas between 0.5 Torr and 1 atm are found to alter the electromagnetic scattering, suggesting applications in plasma-reconfigurable metamaterials and photonic crystals.
Chemical Vapour Deposition of TBC: An Alternative Process for Gas Turbine Components (2000)

This paper deals with a development of a new process for the deposition of Thermal Barrier Coatings (TBC) based on Chemical Vapour Deposition (CVD). The research program started in September 1998 under a BRITE/Euram III project. The CVD process involves the evaporation of zirconium and yttrium starting from metal-organic precursors and their reaction with oxygen in a hot wall reactor in order to deposit TBC layers. The influence of different deposition parameters such as evaporation temperature, pressure and substrate temperature on structure, deposition rate and process yield are described. The characterisation of different precursors behaviour is also described. Preliminary results, obtained with optimised conditions, have shown ZrO2-Y2O3 columnar layers with deposition rates of interest from an industrial point of view.
Source-Based, Structure-Based and Traditional Names of Common Polymers (2017)

IUPAC recommendations on source-based nomenclature for single-strand polymers have so far addressed its application mainly to copolymers, non-linear polymers and polymer assemblies, and within generic source-based nomenclature of polymers. In this document, rules are formulated for devising a satisfactory source-based name for a polymer, whether homopolymer or copolymer, which are as clear and rigorous as possible. Thus, the source-based system for naming polymers is presented in a totality that serves as a user-friendly alternative to the structure-based system of polymer nomenclature. In addition, because of their widespread and established use, recommendations for the use of traditional names of polymers are also elaborated.
Role of Bcl-2 Family Members in Caspase-Independent Apoptosis duringChlamydiaInfection (2002)

Infection with an obligate intracellular bacterium, the Chlamydia trachomatis lymphogranuloma venereum (LGV/L2) strain or the guinea pig inclusion conjunctivitis serovar of Chlamydia psittaci, leads to apoptosis of host cells. The apoptosis is not affected by a broad-spectrum caspase inhibitor, and caspase-3 is not activated in infected cells, suggesting that apoptosis mediated by these two strains of Chlamydia is independent of known caspases. Overexpression of the proapoptotic Bcl-2 family member, Bax, was previously shown to induce caspase-independent apoptosis, and we find that Bax is activated and translocates from the cytosol to the mitochondria in C. psittaci-infected cells. C. psittaci-induced apoptosis is inhibited in host cells overexpressing Bax inhibitor-1 and is inhibited through overexpression of Bcl-2, which blocks both caspase-dependent and -independent apoptosis. As Bax and mitochondria are ideally located to sense stress-related metabolic changes emanating from the interior of an infected cell, it is likely that Bax-dependent apoptosis may also be observed in cells infected with other intracellular pathogens.
Oxidation of 1,2-bis (cyanoalkyl) hydrazines to azobisnitriles using trichloroisocyanuric acid (2004)

Azobisnitriles were synthesised in excellent yields by oxidation of the corresponding 1, 2-bis (cyanoalkyl) hydrazines using trichloroisocyanuric acid in acetonitrile medium at room temperature.
Gold nanocolloid–protein interactions and their impact on β-sheet amyloid fibril formation (2018)

The influence of the presence of small molecules and nanoparticles on the mechanism of amyloid fibril formation has attracted attention because amyloid protein fibrils are associated with degenerative diseases. Here, we studied the interaction between gold nanoparticles (AuNPs) and a model protein (lysozyme). Both the formation of amyloid fibrils in the presence of gold nanoparticles, as well as the interaction between lysozyme and the amyloid fibrils with AuNPs, were investigated to gain an understanding of the distinct behaviour of lysozyme in its fibrillar and globular form. It was observed that the presence of AuNPs delayed the unfolding of α-helixes present in the globular lysozyme and the formation of the amyloid fibrils. However, the addition of AuNPs was also associated with a larger amount of β-sheet structures in the system once equilibrium was reached. Furthermore, the results showed that the driving force of the interaction between AuNPs and lysozyme in its fibrillar and globular forms was significantly different, and that the interaction of AuNPs with the preformed lysozyme amyloid fibrils led to a structural change in the protein.
A neural network based intelligent planner for the coordinated hybrid agent framework (2006)

Recently, a coordinated hybrid agent (CHA) framework was proposed for the control of multiagent systems (MASs). In the past few years, it has been applied to both homogeneous and heterogeneous multi-agent systems. In previous studies, the coordination among agents were implemented based on the designer's knowledge of the system. For large complex systems, it would be desirable if we can plan the coordination among agents dynamically. In this study, we demonstrate that an intelligent planner can be designed for the CHA framework to automatically generate desired actions for multiple robots in a multiagent system. The proposed intelligent planner is based on the construction of a biologically inspired neural network. The dynamics of each neuron in the topologically organized neural network is characterized by a shunting neural equation. A landscape of the neural activities for all neurons of a CHA agent contains information about the agent's local goal, permanent obstacles and temporary obstacles. Each agent treats other robots as moving obstacles. The objective for building the intelligent planner is to plan actions for multiple mobile robots to coordinate with others and to achieve the global goal while each agent achieves its local goal. Simulation results show that in order to control a large complex system, an intelligent planner can be designed for the CHA framework so that coordination among agents can be achieved.