gebhart/patrepeval huggingface dataset:
Antibacterial and antivirulence effect of 6-<i>N</i>-hydroxylaminopurine in<i>Listeria monocytogenes</i> (2016)

The emerging development of antibiotic resistant bacteria calls for novel types of antibacterial agents. In this work we examined the putative antibacterial effect of purine analogs in Listeria monocytogenes. We show that, among several tested purine analogs, only 6-N-hydroxylaminopurine (6-N-HAP) reduces the viability of the Gram-positive pathogen Listeria monocytogenes. As in Bacillus subtilis, 6-N-HAP terminates expression at guanine riboswitches in L. monocytogenes hence preventing expression of their downstream genes. However, we show that the bacteriocidal effect of the compound was unlinked to the terminated expression at the guanine riboswitches. When further examining the antimicrobial effect, we observed that 6-N-HAP acts as a potent mutagen in L. monocytogenes, by increasing the mutation rate and inducing the SOS-response. Also, addition of 6-N-HAP decreased virulence gene expression by reducing both the levels and activity of the virulence regulator PrfA.
Frequent mutations of the β-catenin gene in mouse colon tumors induced by azoxymethane (2000)

The β-catenin gene is frequently mutated at codons 33, 41 and 45 of the glycogen synthase kinase-3β phosphorylation motif in human colon cancers in patients without APC mutations. Frequent mutations at codons 32 and 34, as well as 33 and 41, have been detected in rat colon tumors induced by azoxymethane (AOM), with the second G of CTGGA sequences being considered as a mutational hot-spot. In the present study, exon 3 of the β-catenin gene in mouse colon tumors induced by AOM was amplified by PCR and mutations were detected by the single strand conformation polymorphism method, restriction enzyme fragment length polymorphism and direct sequencing. All 10 colon tumors tested were found to have β-catenin mutations, four in codon 34, three in codon 33, two in codon 41 and one in codon 37, nine being G:C→A:T transitions. However, no mutations were found in codon 32 of the mouse β-catenin gene. On immmunostaining, β-catenin was observed in the cytoplasm and nucleus of the tumor cells. The cytoplasmic staining was homogeneous, while both homogeneous and heterogeneous patterns were noted for the nuclei. Highly frequent mutations of the β-catenin gene in AOM-induced mouse colon tumors suggest that consequent alterations in the stability and localization of the protein may play an important role in this colon carcinogenesis model.
Partitioning digitally programmable power-control for applications to ballasts (2003)

The move to full digital control of power electronic circuits has been mixed. This paper describes the procession of technology to embed digital power control in power supply circuits, with particular attention to dimmable fluorescent lighting ballasts. Partitioning of power circuits shows a near optimum match with the evolving system on chip (SoC) approach taken for microcontrollers to provide an integrated digital power control. A performance description of several approaches is given with performance bounds.
Mechanism of post‐segregational killing by the <i>hoklsok</i> system of plasmid R1: <i>sok</i> antisense RNA regulates formation of a <i>hok</i> mRNA species correlated with killing of plasmid‐free cells (1990)

The hok/sok system of plasmid R1, which mediates plasmid stabilization via killing of plasmid-free segregants, encodes two genes: hok and sok. The hok gene product is a potent cell-killing protein. The expression of hok is regulated post-transcriptionally by the sok gene-encoded repressor, an antisense RNA complementary to the hok mRNA leader region. We show here that the hok mRNA is very stable, while the sok RNA decays rapidly. We also observe a new hok mRNA species which is 70 nucleotides shorter in the 3'-end than the full-length hok transcript. The appearance of the truncated hok mRNA was found to be regulated by the sok antisense RNA. Furthermore, the presence of the truncated hok mRNA was found to be correlated with efficient expression of the Hok protein. On the basis of these findings, we propose an extended model in order to explain the killing of plasmid-free segregants by the hok/sok system.
Tumour Immunomodulation: Mucins in Resistance to Initiation and Maturation of Immune Response Against Tumours (2013)

Mucins are high molecular weight glycoproteins designed for cellular protection and sensing the external environment. Aberrant glycosylation and altered mucin expression seen in cancers are implicated in mucin-dependent refraction to immunosurveilance and immunosuppressive induction around the tumour. Although mucins provide molecular targets for immune system's tumour recognition, their characteristics dictate that the nature of immune response required for recognition and lyses of mucin-expressing tumours needs to follow predominantly a MHC-unrestricted αβ TCR-mediated effector cell response. Frequent loss of dendritic cells maturation and elimination of reactive lymphocytes altered adhesive and anti-adhesive properties of the mucins, promote tumour survival and escape from the immune response.
Effect of single intravenous administration of batroxobin on erythrocyte aggregability in patients with acute-stage cerebral infarction (1995)

We examined the effect of defibrinogenation with batroxobin on the erythrocyte aggregability (RBC-A) in 16 patients with cerebral infarction during the acute phase (less than 72 hours after onset). Eight patients received a single intravenous adminis
Granulocyte Colony-Stimulating Factor Is Present in Human Milk and Its Receptor Is Present in Human Fetal Intestine (2000)

Human milk contains substantial quantities of G-CSF. G-CSF-R are abundant on villus enterocytes, and specific proteins associated with G-CSF-R signaling are present in these cells.
Lipid Accumulation, Lipid Body Formation, and Acyl Coenzyme A Oxidases of the Yeast Yarrowia lipolytica (2004)

International audience
A Robust Active Queue Management Algorithm for Wireless Network (2008)

Abstract — Active Queue Management (AQM) has been extensively studied in the context of wired Internet. In this paper, we propose an AQM algorithm for a bottleneck node with wireless link. Specifically, we propose a robust controller design method that maintains the queue length close to an operating point. We treat capacity variation as an external disturbance and design the controller using H ∞ control techniques. This results in the controller being robust to changes in the design parameters of the system, while it meets the performance objectives. We also consider the effect of round trip time in our model. Our method of incorporating the delay into the discretized model simplifies controller design. I.
Estimating Compressive Strength of Concrete Using Deep Convolutional Neural Networks with Digital Microscope Images (2019)

Compressive strength is a critical indicator of concrete quality for ensuring the safety of existing concrete structures. As an alternative to existing nondestructive testing methods, image-based concrete compressive strength estimation models using three deep convolutional neural networks (DCNNs), namely AlexNet, GoogLeNet, and ResNet, were developed for this study. Images of the surfaces of specially produced specimens were obtained using a portable digital microscope, after which the samples were subjected to destructive tests to evaluate their compressive strength. The results were used to create a dataset linking the experimentally determined compressive strength with the image data recorded for each. The results of training, validation, and testing showed that DCNN models largely outperformed the recently proposed image processing–based ANN model. Overall, the ResNet-based model exhibited greater compressive strength estimation accuracy than either the AlexNet- or GoogLeNet-based models. These finding indicate that image data obtained using a portable digital microscope contain patterns that can be correlated with the concrete’s compressive strength, enabling the proposed DCNN models to use these patterns to estimate compressive strength. The results of this study demonstrate the applicability of DCNN models using microstructure images as an auxiliary method for the nondestructive evaluation of concrete compressive strength.
Fish consumption and cognitive function among older people in the UK: Baseline data from the OPAL study (2009)

Baseline data from participants randomised into the OPAL study provide support for the hypothesis that higher fish consumption is associated with better cognitive function in later life. However, although in the main associations remain after adjusting for education and psychological health, the data do not allow us to rule out the possibility of residual confounding e.g. from socioeconomic status or other health behaviours. Evidence is needed from randomised clinical trials to clarify the role of n-3 LCPs in cognitive health in later life in the normal older person population.
Effect of Cooling Rate on Microstructure and Strength Properties of Tin-Silver-Copper Solder Ball Bonding (2001)

The microstructure and the strength property of Sn–3.5 mass%Ag and Sn–2.5 mass%Ag–0.8 mass%Cu solder ball bonding formed at various cooling rates were investigated. The grain size of Sn phase and the lamellar space depended on the cooling rate Rc. The reaction layer was thinner and the grain size of Sn phase coarsened when solder balls containing Cu were used. The reaction layer formed between Sn–3.5 mass%Ag and Cu pad was composed of (Ni–Au, Ag)3Sn4, (Ni–Au, Ag)3Sn2 and (Ni–Au, Ag)3Sn precipitates. (Cu–Ni, Au, Ag)6Sn5 was formed in the bonding interface when the ball with Cu was used. The lamellar space in both balls became smaller at faster cooling rates and was proportional to Rc(−1⁄2). The micro Vickers hardness of the solder ball with Cu decreased slightly at the slower cooling rates because of the grain size and lamella coarsening. The shear strength of joint using Sn–2.5 mass%Ag–0.8 mass%Cu was a little higher than that using Sn–3.5 mass%Ag at the slower cooling rate because of the fine lamellar structure.
General relativity in electrical engineering (2007)

In electrical engineering metamaterials have been developed that offer unprecedented control over electromagnetic fields. Here we show that general relativity lends the theoretical tools for designing devices made of such versatile materials. We consider media that facilitate space-time transformations and include negative refraction. Our theory unifies the concepts operating behind the scenes of perfect invisibility devices, perfect lenses, the optical Aharonov-Bohm effect and electromagnetic analogs of the event horizon, and may lead to further applications.
Metaphase and anaphase analysis of V79 cells exposed to erionite, UICC chrysotile and UICC crocidolite (1987)

The cytogenetic effects of erionite treatment of V79 cells were compared with those of UICC crocidolite and UICC chrysotile treatment. A significant reduction in diploid cells with an accompanying increase in aneuploid and polyploid cells was observed with all three treatments. In the erionite-treated cultures, an increase in aneuploidy was observed at all dose levels ranging from 10 to 100 micrograms/ml, whereas in the crocidolite- and chrysotile-treated cultures, significant increases in aneuploidy were observed at all dose levels except the low dose, 10 micrograms/ml. Chromatid aberrations were observed in cultures treated with crocidolite and chrysotile and were especially pronounced at dose 100 micrograms/ml of chrysotile. The clastogenic effect of erionite was weaker but statistically significant at dose 100 micrograms/ml. An extrapolation of these cytogenetic changes over dose in number of fibers suggests that erionite was more reactive than the other two minerals in producing aneuploidy. The number of fibers required to produce a similar degree of cytogenetic effects was several orders of magnitude higher for chrysotile and crocidolite than erionite. These results correlate with the higher tumorigenic potency of erionite. In general, fewer cells treated with erionite entered anaphase than those treated with the other two minerals. As a result, abnormal anaphases representing chromosomal mis-segregation were observed only in the chrysotile- and crocidolite-treated cultures. To our knowledge, this is the first report on cytogenetic effects of erionite.
Securing cloud data using information dispersal (2016)

The open nature and outsourced model of cloud computing, coupled with increasing sophistication of cyber attackers and rapid advancement in quantum computing, mandates a more adaptive and flexible approach to cloud data security. In this paper, we introduce a secure cloud storage system which can be layered transparently on existing public & private cloud infrastructure. Our approach combines secret sharing and information dispersal algorithm with more flexible authentication and access-control based security measures to provide secure storage for enterprise data.
GPU packet classification using OpenCL (2009)

Packet analysis is an important aspect of network security, which typically relies on a flexible packet filtering system to extrapolate important packet information from each processed packet. Packet analysis is a computationally intensive, highly parallelisable task, and as such, classification of large packet sets, such as those collected by a network telescope, can require significant processing time. We wish to improve upon this, through parallel classification on a GPU. In this paper, we first consider the OpenCL architecture and its applicability to packet analysis. We then introduce a number of packet demultiplexing and routing algorithms, and finally present a discussion on how some of these techniques may be leveraged within a GPGPU context to improve packet classification speeds.
Broadband adaptive disturbance rejection for a deployable optical telescope testbed (2005)

Broadband adaptive disturbance rejection is demonstrated on the artificial white-light source of the deployable optical telescope (DOT) developed by the Air Force Research Laboratory (AFRL). Large deployable optical systems are envisioned as the future of space telescopes. These systems are require active control for disturbance rejection. In this paper, we consider a multi-input, multi-output discrete-time adaptive disturbance rejection algorithm. The algorithm requires knowledge of some Markov parameters of the system from the control signal inputs to the performance variables. No information about the disturbance spectrum is required. We demonstrate broadband disturbance rejection numerically on an identified model of DOT's white-light source and experimentally on the system itself.
A Multi-Camera 6-DOF Pose Tracker (2005)

Most of the work in head-pose tracking has concentrated on single-camera systems with a relatively small field of view which have limited accuracy because features are only observed in a single viewing direction. We present a multicamera pose tracker that handles an arbitrary configuration of cameras rigidly fixed to the observer's head. By using multiple cameras, we increase the robustness and accuracy by which a 6-DOF pose is tracked. However, in a multicamera rig setting, earlier methods for determining the unknown pose from three world-to-camera correspondences are no longer applicable. We present a RANSAC (M. Fischler and R. Bolles, 1981) based method that handles multicamera rigs by using a fast nonlinear minimization step in each RANSAC round.
Activation of the simian virus 40 (SV40) genome abrogates sensitivity to AVP in a rabbit collecting tubule cell line by repressing membrane expression of AVP receptors. (1991)

To analyze the role of SV40 genome in the phenotypic alterations previously observed in SV40-transformed cell lines, we infected rabbit renal cortical cells with a temperature-sensitive SV40 mutant strain (tsA58) and compared the cell phenotypes at temperatures permissive (33 degrees C) and restrictive (39.5 degrees C) for SV40 genome expression. At both temperatures, the resulting cell line (RC.SVtsA58) expresses cytokeratin and uvomorulin, but epithelial differentiation is more elaborate at 39.5 degrees C as shown by the formation of a well-organized cuboidal monolayer with numerous tight junctions and desmosomes. Functional characteristics are also markedly influenced by the culture temperature: cells grown at 33 degrees C respond only to isoproterenol (ISO, 10(-6) M) by a sevenfold increase in cAMP cell content above basal values; in contrast, when transferred to 39.5 degrees C, they exhibit increased sensitivity to ISO (ISO/basal: 19.1) and a dramatic response to 10(-7) M dDarginine vasopressin (dDAVP/basal: 18.2, apparent Ka: 5 X 10(-9) M) which peaks 48 h after the temperature shift. The latter is associated with membrane expression of V2-type AVP receptors (approximately 50 fmol/10(6) cells) which are undetectable when SV40 genome is activated (33 degrees C). Clonal analysis, additivity studies, and desensitization experiments argue for the presence of a single cell type responsive to both AVP and ISO. The characteristics of the RC. SVtsA58 cell line at 39.5 degrees C (effector-stimulated cAMP profile, lack of expression of brush-border hydrolases and Tamm-Horsfall protein) suggest that it originates from the cortical collecting tubule, and probably from principal cells.
Endophyte-host associations in grasses. XXII. Conidia formation by <i>Acremonium</i> endophytes on the phylloplanes of <i>Agrostis hiemalis</i> and <i>Poa rigidifolia</i> (1996)

(1996). Endophyte-host associations in grasses. XXII. Conidia formation by Acremonium endophytes on the phylloplanes of Agrostis hiemalis and Poa rigidifolia. Mycologia: Vol. 88, No. 2, pp. 174-178.
<scp>mapman</scp> : a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes (2004)

MAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. SCAVENGER modules assign the measured parameters to hierarchical categories (formed 'BINs', 'subBINs'). A first build of TRANSCRIPTSCAVENGER groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes. METABOLITESCAVENGER groups hundreds of metabolites into pathways or groups of structurally related compounds. An IMAGEANNOTATOR module uses these groupings to organise and display experimental data sets onto diagrams of the users' choice. A modular structure allows users to edit existing categories, add new categories and develop SCAVENGER modules for other sorts of data. MAPMAN is used to analyse two sets of 22K Affymetrix arrays that investigate the response of Arabidopsis rosettes to low sugar: one investigates the response to a 6-h extension of the night, and the other compares wild-type Columbia-0 (Col-0) and the starchless pgm mutant (plastid phosphoglucomutase) at the end of the night. There were qualitatively similar responses in both treatments. Many genes involved in photosynthesis, nutrient acquisition, amino acid, nucleotide, lipid and cell wall synthesis, cell wall modification, and RNA and protein synthesis were repressed. Many genes assigned to amino acid, nucleotide, lipid and cell wall breakdown were induced. Changed expression of genes for trehalose metabolism point to a role for trehalose-6-phosphate (Tre6P) as a starvation signal. Widespread changes in the expression of genes encoding receptor kinases, transcription factors, components of signalling pathways, proteins involved in post-translational modification and turnover, and proteins involved in the synthesis and sensing of cytokinins, abscisic acid (ABA) and ethylene revealing large-scale rewiring of the regulatory network is an early response to sugar depletion.
Miniaturized-Element Frequency Selective Surface Metamaterials: A Solution to Enhance Radiation of RFICs (2019)

In this article, a technique to improve the radiation characteristics of an active CMOS circuit is presented. A miniaturized-element frequency selective surface (MEFSS) cover is utilized on top of the chip to provide gain enhancement, which is essential for many applications such as radar and communication systems. This is important due to the restrictions on the thickness of metallic layers, losses in substrate, and limitations in real estate. The MEFSS cover consists of partially reflecting surface (PRS) and high-impedance surface (HIS) creating a Fabry-Pérot-type cavity (FPC). When the MEFSS structure is used, the height of FPC can be reduced without causing any deterioration to the antenna radiation. A proximity patch antenna is embedded in the HIS layer, which is fed by a small metallic trace on the last layer of chip using the coupling mechanism. By utilizing the transverse-equivalent network (TEN) of the structure and imposing the resonance condition, the geometrical parameters of the MEFSS unit cell is calculated. For demonstration purposes, a scaled MEFSS cover for gain enhancement at the center frequency of 10 GHz is designed, fabricated, and tested. The measured results, which are in agreement with simulations, show that the proposed technique is reliable in practice and gain enhancement of 9 dB can be achieved for a single-patch antenna.
Atomic Structure of Acetylcholinesterase from <i>Torpedo californica</i> : A Prototypic Acetylcholine-Binding Protein (1991)

The three-dimensional structure of acetylcholinesterase from Torpedo californica electric organ has been determined by x-ray analysis to 2.8 angstrom resolution. The form crystallized is the glycolipid-anchored homodimer that was purified subsequent to solubilization with a bacterial phosphatidylinositol-specific phospholipase C. The enzyme monomer is an alpha/beta protein that contains 537 amino acids. It consists of a 12-stranded mixed beta sheet surrounded by 14 alpha helices and bears a striking resemblance to several hydrolase structures including dienelactone hydrolase, serine carboxypeptidase-II, three neutral lipases, and haloalkane dehalogenase. The active site is unusual because it contains Glu, not Asp, in the Ser-His-acid catalytic triad and because the relation of the triad to the rest of the protein approximates a mirror image of that seen in the serine proteases. Furthermore, the active site lies near the bottom of a deep and narrow gorge that reaches halfway into the protein. Modeling of acetylcholine binding to the enzyme suggests that the quaternary ammonium ion is bound not to a negatively charged "anionic" site, but rather to some of the 14 aromatic residues that line the gorge.
On cyclostationary analysis of WiFi signals for direction estimation (2015)

Cyclostationary analysis is a powerful tool to study the Signal-Selective Direction Estimation (SSDE) problem as different types of wireless signals have different cyclostationary patterns. Generally speaking, each type of wireless signal has unique cyclic frequencies with the frequency-selective property, which distinguishes itself from other types of signals. The cyclostationary property of a signal may be induced by its modulation method, its carrier frequency, and/or its frame structure. In this paper, we study the cyclostationary property of IEEE 802.11 (WiFi) signals induced by their underlying OFDM frame structure, which includes pilots, cyclic prefix (CP), and preambles. We first analyze the pilot-induced, CP-induced, and preamble-induced cyclostationary properties of WiFi signals, respectively. We then derive their spectral correlation function (SCF) and investigate their applicability to solving the SSDE problem. Simulation results show that the pilot-induced cyclostationary property of WiFi signals is a promising feature that can be used to solve the SSDE problem.