gebhart/patrepeval huggingface dataset:
The horizontally-acquired response regulator SsrB drives a Salmonella lifestyle switch by relieving biofilm silencing (2016)

A common strategy by which bacterial pathogens reside in humans is by shifting from a virulent lifestyle, (systemic infection), to a dormant carrier state. Two major serovars of Salmonella enterica, Typhi and Typhimurium, have evolved a two-component regulatory system to exist inside Salmonella-containing vacuoles in the macrophage, as well as to persist as asymptomatic biofilms in the gallbladder. Here we present evidence that SsrB, a transcriptional regulator encoded on the SPI-2 pathogenicity-island, determines the switch between these two lifestyles by controlling ancestral and horizontally-acquired genes. In the acidic macrophage vacuole, the kinase SsrA phosphorylates SsrB, and SsrB~P relieves silencing of virulence genes and activates their transcription. In the absence of SsrA, unphosphorylated SsrB directs transcription of factors required for biofilm formation specifically by activating csgD (agfD), the master biofilm regulator by disrupting the silenced, H-NS-bound promoter. Anti-silencing mechanisms thus control the switch between opposing lifestyles.
Effect of the nerve fiber path eccentricity on the single fiber action potential (2013)

The relative position of an indwelling electrode to the nerve fiber plays a critical role in the shape of the single fiber action potential (SFAP) detected by the electrode. Parameters such as electrode to fiber distance, fiber path, and position of the nodes of Ranvier can have a substantial influence on the shape and frequency content of the SFAP. This study explores the effects of these parameters on the shape of simulated SFAPs within a nerve bundle with a thin-film Longitudinal Intrafascicular Electrode (tfLIFE) longitudinally implanted at the midline of a 2.4 mm diameter nerve fascicle. The SFAPs were calculated for various distances, fiber paths and nodal offsets for a 10 μm caliber myelinated fibers. The correlation coefficient was used to quantify the changes in the SFAP shape. It was found that all parameters play a role in changing the SFAP shape. The nodal offset was found to have the greatest effect, altering the correlation coefficient nearly 0.2 from the reference SFAP. Knowing that the parameters have such an effect on the SFAP shape has lead to the conclusion that fiber distance, path and nodal offset has the potential of allowing the extraction of nerve fiber locations relative to the electrode structure.
Polarimetric dimension and nonregularity of tightly focused light beams (2020)

Polarimetric dimension and nonregularity are newly introduced concepts that characterize three-dimensional (3D) polarization states of light. We analyze the spectral polarimetric dimension and the degree of nonregularity associated with two kinds of tightly focused beams: a radially fully polarized Gaussian Schell-model (GSM) beam and a partially polarized beam composed of an incoherent superposition of two orthogonally polarized (coherent) plane-wave modes. We show that for both beams the focal field can exhibit genuine 3D and nonregular character, with even perfect nonregularity encountered for the tightly focused two-mode beam. These features originate from the partial spatial coherence and partial polarization of the incident beams, and in the limit of full coherence and polarization the three-dimensionality and nonregularity of the focal field vanish. We also find that the GSM beam can generate a nanoscale region around the focus where the field is essentially 3D unpolarized. The results demonstrate the rich polarimetric structure of focal fields and may find uses in optical particle manipulation and sensing.
Transfected cell microarrays: an efficient tool for high-throughput functional analysis (2007)

Transfected cell microarrays are considered to be a breakthrough methodology for high-throughput and high-content functional genomics. Here, recent advances in the cell microarray field are reviewed, along with its potential to increase the speed of determining gene function. These advances, combined with an increasing number and diversity of gene perturbing systems, such as RNAi and ectopic gene expression, provide tools for expanding our understanding of biology at the systems level.
The development of the Braun Oral-B Ultra Plaque Remover: an in vitro robot study. (1996)

A combination of a new brush head (EB9) with longer tufts of bristles designed to improve interdental penetration, and an increased frequency of bristle movement (63Hz, 3,800 strokes per minute - D9 handle) was associated with significantly greater removal of artificial plaque. Visual observation of typodonts suggested that this increased efficacy is related to greater removal of plaque from interdental surfaces and occlusal fissures. These results suggest that the D9/EB9 prototype electric toothbrush is suitable for further investigation and clinical evaluation.
Activation of type II calcium/calmodulin-dependent protein kinase by Ca2+/calmodulin is inhibited by autophosphorylation of threonine within the calmodulin-binding domain. (1990)

It is now well established that autophosphorylation of a threonine residue located next to each calmodulin-binding domain in the subunits of type II Ca2+/calmodulin-dependent protein kinase causes the kinase to remain active, although at a reduced rate, after Ca2+ is removed from the reaction. This autophosphorylated form of the kinase is still sensitive to Ca2+/calmodulin, which is required for a maximum catalytic rate. After removal of Ca2+, new sites are autophosphorylated by the partially active kinase. Autophosphorylation of these sites abolishes sensitivity of the kinase to Ca2+/calmodulin (Hashimoto, Y., Schworer, C. M., Colbran, R. J., and Soderling, T. R. (1987) J. Biol. Chem. 262, 8051-8055). We have identified two pairs of homologous residues, Thr305 and Ser314 in the alpha subunit and Thr306 and Ser315 in the beta subunit, that are autophosphorylated only after removal of Ca2+ from an autophosphorylation reaction. The sites were identified by direct sequencing of labeled tryptic phosphopeptides isolated by reverse-phase high pressure liquid chromatography. Thr305-306 is rapidly dephosphorylated by purified protein phosphatases 1 and 2A, whereas Ser314-315 is resistant to dephosphorylation. We have shown by selective dephosphorylation that the presence of phosphate on Thr305-306 blocks sensitivity of the kinase to Ca2+/calmodulin. In contrast, the presence of phosphate on Ser314-315 is associated with an increase in the Kact for Ca2+/calmodulin of only about 2-fold, producing a relatively small decrease in sensitivity to Ca2+/calmodulin.
Machine Learning and Deep Learning Methods for Intrusion Detection Systems: A Survey (2019)

Networks play important roles in modern life, and cyber security has become a vital research area. An intrusion detection system (IDS) which is an important cyber security technique, monitors the state of software and hardware running in the network. Despite decades of development, existing IDSs still face challenges in improving the detection accuracy, reducing the false alarm rate and detecting unknown attacks. To solve the above problems, many researchers have focused on developing IDSs that capitalize on machine learning methods. Machine learning methods can automatically discover the essential differences between normal data and abnormal data with high accuracy. In addition, machine learning methods have strong generalizability, so they are also able to detect unknown attacks. Deep learning is a branch of machine learning, whose performance is remarkable and has become a research hotspot. This survey proposes a taxonomy of IDS that takes data objects as the main dimension to classify and summarize machine learning-based and deep learning-based IDS literature. We believe that this type of taxonomy framework is fit for cyber security researchers. The survey first clarifies the concept and taxonomy of IDSs. Then, the machine learning algorithms frequently used in IDSs, metrics, and benchmark datasets are introduced. Next, combined with the representative literature, we take the proposed taxonomic system as a baseline and explain how to solve key IDS issues with machine learning and deep learning techniques. Finally, challenges and future developments are discussed by reviewing recent representative studies.
Acute Focal Neurological Deficits in Aneurysmal Subarachnoid Hemorrhage (2003)

In the presence of ICH, pathological microdialysis values may indicate reversible tissue damage. Extreme microdialysis values and pathological microdialysis concentrations that further deteriorate 2-fold are highly indicative of the development of cerebral infarction and permanent neurological deficits. Therefore, the analysis of relative changes of microdialysis parameters is crucial for the detection of ischemia in SAH patients.
By what means should nanoscaled materials be constructed: molecule, medium, or human? (2009)

There is great potential in nanoscale science and technology, and construction of macrosized materials and systems possessing nanoscale structural features is a crucial factor in the everyday application of nanoscience and nanotechnology. Because nanoscale substances are often constructed through self-assembly of unit molecules and nanomaterials, control of the self-assembly process is required. In order to establish general guidelines for the fabrication of materials with nanoscale structural characteristics, i.e., nanoscaled materials, we introduce here examples of recent research in related fields categorised as: (i) self-assembled structures with forms generally determined by intrinsic interactions between molecules and/or unit nanomaterials, (ii) self-assemblies influenced by their surrounding media, especially interfacial environments, (iii) modulation of self-assembly by artificial operation or external stimuli. Examples are not limited to organic molecules, which are often regarded as the archetypal species in self-assembly chemistry, and many examples of inorganic assemblies and hybrid structures are included in this review.
Marketing to children: The premium effect (2009)

Researchers are interested in the marketing of unhealthy food items to children, particularly as childhood obesity rates appear to be rising (Margery, Daniels and Boulton, 2001). While television advertising, fast food websites devoted to children and parental attitudes to children’s consumption of unhealthy food have been examined in depth, little research has been conducted on the effect of premiums on children’s food preferences (Pettigrew and Roberts, 2006). This paper reviews the small amount of research on premiums in the context of marketing of fast food to children, and discusses the possible implications in terms of interpretations of the Australian Association of National Advertisers’ (AANA) Code of Ethics and the Responsible Children’s Marketing Initiative by the Australian Food and Beverage Industry.
International Conference on Petroleum Phase Behavior and Fouling (1999)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTInternational Conference on Petroleum Phase Behavior and FoulingIrwin A. WieheView Author Information Conference ChairCite this: Energy Fuels 2000, 14, 1, 1Publication Date (Web):November 24, 1999Publication History Published online24 November 1999Published inissue 1 January 2000https://pubs.acs.org/doi/10.1021/ef990205xhttps://doi.org/10.1021/ef990205xeditorialACS PublicationsCopyright © 2000 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views416Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (15 KB) Get e-AlertscloseSUBJECTS:Deposition,Emulsions,Energy,Fossil fuels Get e-Alerts
Smart temperature sensors in standard CMOS (2010)

A smart temperature sensor is an integrated system consisting of a temperature sensor, its bias circuitry and an analog-to-digital converter (ADC). When manufactured in CMOS technology, such sensors have found widespread use due to their low cost, small size and ease of use. In this paper the basic operating principles of CMOS smart temperature sensors are explained and the stateof-the-art is reviewed. Two new figures of merit for smart temperature sensors are defined, which express the tradeoff between their energy/conversion and their resolution and inaccuracy, respectively. A survey of data published over the last 25 years shows that both these figures of merit usefully bound the performance of state-of-the-art smart temperature sensors.
The immunophilin FKBP52 specifically binds to tubulin and prevents microtubule formation (2007)

The FK506 binding protein FKBP52 belongs to the large family of immunophilins and is known as a steroid receptor-associated protein. Previous data suggest that FKBP52 is associated with the motor protein dynein and with the cytoskeleton during mitosis. Here we demonstrate a specific and direct interaction between FKBP52 and tubulin. The region of FKBP52 located between aa 267 and 400, which includes the tetratricopeptide repeat domain, is required for tubulin binding. We provide evidence that FKBP52 prevents tubulin polymerization and that an 84 residue sequence located in the C-terminal part of the molecule (aa 375-458) is necessary and sufficient for its microtubule depolymerization activity. In colocalization experiments in PC12 cells, FKBP52 is associated with tubulin in motile cellular compartments. Furthermore, we suggest that, by using siRNA, a decrease of FKBP52 expression in PC12 cells may lead to differentiated cell phenotype characterized by neurite extensions. Collectively, our data define an unexpected property of FKBP52 as a novel regulator of microtubule dynamics. The possible role of microtubule formation and tubulin binding of other immunophilins such as FKBP12 and FKBP51 is discussed.
A non-alkoxide sol–gel route to highly active and selective Cu–Cr catalysts for glycerol conversion (2009)

A non-alkoxide sol–gel route to highly active and selective Cu–Cr catalysts for glycerol conversion is presented. The addition of propylene oxide to ethanol solutions of Cr(NO3)3·9H2O and Cu(NO3)2·3H2O resulted in the formation of transparent Cu–Cr gels. The resulting gels were converted to the Cu–Cr catalysts by atmospheric drying and calcination. The Cu–Cr catalysts are characterized by X-ray diffraction (XRD), N2 physisorption, temperature-programmed reduction (TPR), and transmission electron microscopy (TEM). The results show that the surface area of the Cu–Cr catalyst is adjusted by the hydrolysis conditions, Cu/Cr molar ratio, and treatment conditions (such as gas atmosphere and final temperature). For the sample with Cu/Cr = 0.5, the surface area of Cu–Cr xerogel can reach 94 m2/g and decreased to only 31 m2/g after calcination at 500 °C. The catalysts show significant catalytic activity and selectivity in glycerol conversion, i.e. above 52% conversion of glycerol and above 88% selectivity to 1,2-propanediol at 210 °C and 4.15 MPa H2 pressure. CuCr2O4 supported Cu catalysts are much more active than Cr2O3 supported Cu catalysts. This indicates a strong interaction between Cu and CuCr2O4 that is significantly improving the effectiveness of the catalyst for glycerol conversion.
A new correlated double sampling (CDS) technique for low voltage design environment in advanced CMOS technology (2002)

In this paper, a new Correlated Double Sampling (CDS) Technique based on Fixed Voltage Difference (FVD) is introduced. Compared with the traditional CDS technique with voltage sampling for A/D conversion, this method has the advantage of low voltage capability, which relieves the high resolution requirement of the subsequent A/D converter as a result of the limited voltage swing in advanced deep-submicron CMOS technologies. The new technique also allows the use of reference voltages to control the dynamic range of the circuit. The FVD CDS technique has been applied to the readout circuit of a low voltage CMOS Active Pixel Sensor (APS) circuits with an array size of 128x128 fabricated by a 0.25µm CMOS process from TSMC. The circuit is proven to be functional at extremely low VDD with added dynamic range. 1.
Development of Semi-Conductor Device Cleaning by Cavitation Jet. (2001)

Cleaning method of semi-conductor device is developed applying cavitation jet which is generated through two different pressure nozzles. Its remarkable features are non-contact type, big pressure amplification ratio, wide cleaning effect area, having ultrasonic wave effect, easy introduction of functioned water in accordance with its purpose. Therefore, it is optimum cleaning for semi-conductor device which is mechanically weak and has an electrostatic charging problem. Comparison tests result in that cleaning efficiency of caviation cleaning is better than that of water jet cleaning, and cleaning time in case of cavitation jet is shorter than that in case of water jet.
Immune responses of mice to inactivated rabies vaccine administered orally: potentiation by <i>Quillaja saponin</i> (1986)

Administered orally, Quillaja saponin markedly potentiated the humoral immune responses of mice fed inactivated rabies vaccine, and significantly increased their resistance to subsequent intracerebral challenge with live rabies virus. Although mean serum neutralizing antibody titres were generally 8- to 16-fold higher when vaccine was given intraperitoneally, orally administered vaccine, with saponin, stimulated production of high protective antibody levels that were maintained for at least 6 months. The potentiating effect of saponin appeared to be mediated through several mechanisms, one of which was by increasing the permeability of the intestinal mucosa, allowing increased uptake of viral antigen. The potentiating effect was enhanced when saponin was administered in advance (up to at least 16 h) of the oral vaccine. Mice tolerated the effective saponin doses without any visible signs of distress or injury. In view of the many favourable physiological activities and low toxicity of orally delivered saponins, it is suggested that they may find more general applications in the immunopotentiation of oral vaccines.
On the Predicted Performance of Oil Lubricated Thrust Collars in Integrally Geared Compressors (2014)

Integrally geared compressors (IGCs) comprise single stage impellers installed on the ends of pinion shafts, all driven by a main bull gear (BG) and shaft system. When compared to single shaft multistage centrifugal compressors, the benefits of IGCs include better thermal efficiency, reduced footprint and simple foundation, dispensing with a high speed coupling, as well as better access for maintenance and overhauls. In IGCs, the compression of the process gas induces axial loads on the pinion shafts that are transmitted via thrust collars (TCs) to the main drive shaft and balanced by a single thrust bearing. The TCs, located on either side of pinion gears, slightly overlap with the BG outer diameter to form lentil-shaped lubricant-wetted regions. Archival literature on the design and optimization of TCs is scant, in spite of their widespread usage as they are comprised of simple geometry mechanical elements. This paper presents an analysis of the hydrodynamic film pressure generated in a lubricated TC due to the rotation of both TC and BGs and specified taper angles for both bodies. The model solves the Reynolds equation of hydrodynamic lubrication to predict the operating film thickness that generates a pressure field reacting to impellers' thrust loads, these forces being a function of the pinion speed and the process gas physical properties. The model also predicts performance parameters, such as power loss and axial stiffness, and damping force coefficients. A parametric study brings out the taper angles in the TC and BG that balance the transmitted load with a lesser friction factor and peak pressure, along with large axial stiffness and damping.
Disruption of the Cereblon Gene Enhances Hepatic AMPK Activity and Prevents High-Fat Diet–Induced Obesity and Insulin Resistance in Mice (2013)

A nonsense mutation in cereblon (CRBN) causes a mild type of mental retardation in humans. An earlier study showed that CRBN negatively regulates the functional activity of AMP-activated protein kinase (AMPK) in vitro by binding directly to the α1-subunit of the AMPK complex. However, the in vivo role of CRBN was not studied. For elucidation of the physiological functions of Crbn, a mouse strain was generated in which the Crbn gene was deleted throughout the whole body. In Crbn-deficient mice fed a normal diet, AMPK in the liver showed hyperphosphorylation, which indicated the constitutive activation of AMPK. Since Crbn-deficient mice showed significantly less weight gain when fed a high-fat diet and their insulin sensitivity was considerably improved, the functions of Crbn in the liver were primarily investigated. These results provide the first in vivo evidence that Crbn is a negative modulator of AMPK, which suggests that Crbn may be a potential target for metabolic disorders of the liver.