gebhart/patrepeval huggingface dataset:
Characterization of RarA, a Novel AraC Family Multidrug Resistance Regulator in Klebsiella pneumoniae (2012)

Transcriptional regulators, such as SoxS, RamA, MarA, and Rob, which upregulate the AcrAB efflux pump, have been shown to be associated with multidrug resistance in clinically relevant Gram-negative bacteria. In addition to the multidrug resistance phenotype, these regulators have also been shown to play a role in the cellular metabolism and possibly the virulence potential of microbial cells. As such, the increased expression of these proteins is likely to cause pleiotropic phenotypes. Klebsiella pneumoniae is a major nosocomial pathogen which can express the SoxS, MarA, Rob, and RamA proteins, and the accompanying paper shows that the increased transcription of ramA is associated with tigecycline resistance (M. Veleba and T. Schneiders, Antimicrob. Agents Chemother. 56:4466-4467, 2012). Bioinformatic analyses of the available Klebsiella genome sequences show that an additional AraC-type regulator is encoded chromosomally. In this work, we characterize this novel AraC-type regulator, hereby called RarA (Regulator of antibiotic resistance A), which is encoded in K. pneumoniae, Enterobacter sp. 638, Serratia proteamaculans 568, and Enterobacter cloacae. We show that the overexpression of rarA results in a multidrug resistance phenotype which requires a functional AcrAB efflux pump but is independent of the other AraC regulators. Quantitative real-time PCR experiments show that rarA (MGH 78578 KPN_02968) and its neighboring efflux pump operon oqxAB (KPN_02969_02970) are consistently upregulated in clinical isolates collected from various geographical locations (Chile, Turkey, and Germany). Our results suggest that rarA overexpression upregulates the oqxAB efflux pump. Additionally, it appears that oqxR, encoding a GntR-type regulator adjacent to the oqxAB operon, is able to downregulate the expression of the oqxAB efflux pump, where OqxR complementation resulted in reductions to olaquindox MICs.
On the complexity of computing the homology type of a triangulation (2002)

An algorithm for computing the homology type of a triangulation is analyzed. By triangulation is meant a finite simplicial complex; its homology type is given by its homology groups (with integer coefficients). The algorithm could be used in computer-aided design to tell whether two finite-element meshes or Bezier-spline surfaces are of the same topological type, and whether they can be embedded in R/sup 3/. Homology computation is a pure combinatorial problem of considerable intrinsic interest. While the worst-case bounds obtained for this algorithm are poor, it is argued that many triangulations (in general) and virtually all triangulations in design are very sparse in a particular sense. This sparseness measure is formalized, and a probabilistic analysis of the sparse case is performed to show that the expected running time, of the algorithm is roughly quadratic in the geometric complexity (number of simplices) and linear in the dimension.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Potentiation of Tumor Necrosis Factor α-induced Secreted Phospholipase A2 (sPLA2)-IIA Expression in Mesangial Cells by an Autocrine Loop Involving sPLA2 and Peroxisome Proliferator-activated Receptor α Activation (2003)

In rat mesangial cells, exogenously added secreted phospholipases A2 (sPLA2s) potentiate the expression of pro-inflammatory sPLA2-IIA first induced by cytokines like tumor necrosis factor-alpha (TNFalpha) and interleukin-1 beta. The transcriptional pathway mediating this effect is, however, unknown. Because products of PLA2 activity are endogenous activators of peroxisome proliferator-activated receptor alpha (PPAR alpha, we postulated that sPLA2s mediate their effects on sPLA2-IIA expression via sPLA2 activity and subsequent PPAR alpha activation. This study shows that various sPLA2s, including venom enzymes, human sPLA2-IIA, and wild-type and catalytically inactive H48Q mutant of porcine pancreatic sPLA2-IB, enhance the TNF alpha-induced sPLA2-IIA expression at the mRNA and protein levels. In cells transfected with luciferase sPLA2-IIA promoter constructs, sPLA2s are active only when the promoter contains a functional PPRE-1 site. The effect of exogenous sPLA2s is also blocked by the PPAR alpha inhibitor MK886. Interestingly, the expression of sPLA2-IIA induced by TNF alpha alone is also attenuated by MK886, by the sPLA2-IIA inhibitor LY311727, by heparinase, which prevents the binding of sPLA2-IIA to heparan sulfate proteoglycans, and by the specific cPLA2-alpha inhibitor pyrrolidine-1. Together, these data indicate that sPLA2-IIA released from mesangial cells by TNF alpha stimulates its own expression via an autocrine loop involving cPLA2 and PPAR alpha. This signaling pathway is also used by exogenously added sPLA2s including pancreatic sPLA2-IB and is distinct from that used by TNF alpha.
Application of sparse signal recovery to pilot-assisted channel estimation (2008)

We examine the application of current research in sparse signal recovery to the problem of channel estimation. Specifically, using an orthogonal frequency division multiplexed (OFDM) transmission scheme with pilot symbol assisted modulation (PSAM), we consider the problem of identifying a frequency selective channel from a limited number Q out of a possible M tones of an OFDM symbol. The main observation is that if M is chosen as prime, one can identify the channel uniquely if Q ges 2T, where T is the number of nonzero taps in the frequency-selective channel. The identifiability result requires the minimization of the lo norm, leading to an intractable combinatorial search problem. Several methods have been proposed to deal with these issues, and the one we examine involves l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> norm regularization known as basis pursuit, We apply these methods specifically to the problem of estimating a frequency selective channel with PSAM. As a result, the bandwidth efficiency of the system is increased due to the sparsity of the channel.
Revealing the Immunogenic Risk of Polymers (2018)

Poly(ethylene glycol) (PEG) conjugation has been the gold standard to ameliorate the pharmacokinetic (PK) and immunological profiles of proteins. PEG polymer does become immunogenic once attached to proteins, evoking PEG-specific antibody (Ab) responses. The anti-PEG Abs could cause PEGylated biologic treatments to fail and even result in lethal adverse reactions. Thus the zwitterionic poly(carboxybetaine) (PCB) has been introduced as a PEG substitute for protein modification. Addressed herein is anti-polymer Ab induction by conjugating PEG and PCB polymers to a series of carrier proteins with escalating immunogenicity. Results indicate that titers of PEG-specific Abs were quantitatively correlated to the immunogenicity of carrier proteins, whereas the generation of PCB-specific Abs was minimal and insensitive to increased protein immunogenicity. This work provides insight into the immunological properties of PEG and PCB and has far-reaching implications for the development of polymer-protein conjugates.
Insulated-gate planar thyristors: II&#8212;Quantitative modeling (1980)

The basic modes of operation of a new planar, high-voltage thyristor which is controlled by an insulated gate are described in Part I. This paper presents models for the dc operation of the device. Low-current nonregenerative operation is described by an equivalent circuit containing MOSFET's, bipolar transistors, and resistors. These are analyzed by a general-purpose nonlinear circuit analysis program. Sophisticated transistor models, both bipolar and MOS, are required to accurately represent the component devices, and their characteristics are discussed. The high-conductivity state is modeled as a one-dimensional p-i-n diode. Determination of appropriate parameters is described and simulations are compared to measured characteristics. The resulting models are suitable for the design of devices with a wide variety of dc characteristics.
Effective reflectivity from self-imaging in a Talbot cavity and its effect on the threshold of a finite 2-D surface emitting laser array (1990)

2-D coherent arrays, self-imaging, Talbot effect, laser arrays.
A política do êxtase (1978)

Dans cet entretien, conduit par M. Tavares da Silva et L. Soczka, Georges Lapassade aborde les problèmes politiques, pédagogiques et institutionels de l'Université de Vincennes. où ce dernier est professeur; l'aítitude des courrants politiques dominantes à Vincennes face au problème de la drogue esí analysée. Les parellélismes entre l'expérience de la drogue, notamment des substances allucinogènes, et lu bioérzergie sont discutés. Georges Lapassade décodifie l'aspect idéologique du discours du Pouvoir face à la drogue, et conclut à la necessité d'une politique de l'extase.
Polymer induced phase separation in lyotropic smectics (1993)

Large water soluble macromolecules can be confined in all proportions into an electrostatically stabilized surfactant lamellar phase without change of the bilayer thickness. Upon progressive addition of salt, the sample phase separates into a polymer-rich and a surfactant-rich lamellar phase. Indeed, at some particular salt concentration, the intermembrane repulsive interaction is no longer sufficient to maintain the polymer coils squeezed into the lamellar structure. The phase separation is generally first order. But we could find a situation where it becomes second order.
Bcl-2 affects survival but not neuronal differentiation of PC12 cells (1993)

Past studies have shown that serum-free cultures of PC12 cells are a useful model system for studying the mechanisms of neuronal death after neurotrophic factor deprivation. These cultures, as well as NGF-deprived cultures of sympathetic neurons, manifest and endonuclease activity that leads to "apoptotic" internucleosomal DNA cleavage. Overexpression of the proto-oncogene bcl-2 blocks apoptotic death in various cell types. To study the actions of this protein in neuronal cells, we derived PC12 cell lines stably transfected with a cDNA encoding human bcl-2. It is reported here that lines expressing high levels of the exogenous bcl-2 protein are protected from both death and apoptotic DNA fragmentation caused by removal of trophic support. However, expression of high levels of exogenous bcl-2 neither mimics nor interferes with promotion of neurite outgrowth by NGF.
True three-dimensional cone-beam reconstruction (TTCR) algorithm (1989)

A true three-dimensional cone-beam reconstruction (TTCR) algorithm for direct volume image reconstruction from 2-D cone-beam projections is developed for the complete sphere geometry. The algorithm is derived from the parallel-beam true three-dimensional reconstruction (TTR) algorithm and is based on the modified filtered backprojection technique, which uses a set of 2-D space-invariant filters. The proposed algorithm proved to be superior in spatial resolution to the parallel-beam TTR algorithm and to offer better computational efficiency.
Contrast constancy: deblurring in human vision by spatial frequency channels. (1975)

The perception of contrast was measured in humans by a technique of subjective contrast-matching, and was compared with contrast sensitivity as defined by threshold measures. 2. Contrast-matching between different spatial frequencies was performed correctly (especially at frequencies above 5 c/deg) despite the attenuation by optical and neural factors which cause large differences in contrast thresholds. 3. Contrast-matching between single lines of different widths was also veridical, and was not limited by the spatial integration (Ricco's Law) present at threshold. Adaptation to gratings altered the appearance of lines, and this could be best understood in Fourier terms. 4. The generality of these results was shown by matching the contrast of pictures which had been filtered so that each contained a one octave band of spatial frequencies. 5. Within the limits imposed by threshold and resolution, contrast-matching was largely independent of luminance and position on the retina. 6. Six out of eleven astigmatic observers showed considerable suprathreshold compensation for their orientation-specific neural deficit in contrast sensitivity. 7. These results define a new property of vision: contrast constancy. It is argued that spatial frequency channels in the visual cortex are organized to compensate for earlier attenuation. This achieves a dramatic 'deblurring' of the image, and optimizes the clarity of vision.
Di- and Tetranuclear Metal Complexes with Phenoxo Bridges:  Synthesis, Structures, and Photoluminescent and Electroluminescent Properties (2006)

Dinuclear and tetranuclear copper 2,6-bis(2-hydroxyphenyl)pyridine (H(2)L) complexes Cu2(L)2(py)2 (1) and Cu4(L)4(DMF) (2) were synthesized. The complexes 1 and 2 were characterized by elemental analyses, mass spectrometry, and single-crystal X-ray diffraction analyses. 1 crystallizes in the monoclinic space group P2(1)/n with a = 13.330(2) Angstroms, b = 9.361(1) Angstroms, c = 14.676(1) Angstroms, beta = 100.94(1) degrees, V = 1798.1(3) Angstroms(3), and Z = 2. 2 crystallizes in the monoclinic space group P2(1)/n with a = 13.360(1) Angstroms, b = 14.884(1) Angstroms, c = 15.462(2) Angstroms, beta = 97.50(4) degrees, V = 3048.4(1) Angstroms(3), and Z = 2. Tetranuclear zinc complex Zn4(L)4(py)4 (3) was prepared and characterized by X-ray diffraction. 3 crystallizes in the triclinic space group P with a = 13.770(1) Angstroms, b = 15.465(1) A, c = 16.409(2) Angstroms, alpha = 88.877(9) degrees, beta = 88.035(4) degrees, gamma = 82.956(3) degrees, V = 3465.6(5) Angstroms(3), and Z = 2. The di- and tetranuclear complexes 1-3contain phenoxo bridges. 1 is a dinuclear complex with two Cu(II) centers, two py ligands, and two L ligands, and each L ligand donates its pyridyl ring and one of the phenolate groups to one metal and shares the other phenolate group between both metals, affording a Cu(2)(mu-O)(2) core. 2, in contrast, is a tetranuclear complex with four Cu(II) centers and four L ligands. Two of the L ligands have the same coordination mode as 1, and the other two L ligands donate their pyridyl rings to one metal and share both phenolate groups between four metals, resulting in three four-membered Cu2(mu-O)2 rings, which joined each other and showed great distortion from planarity. 3 is a tetranuclear complex with four Zn(II) centers, four pyridine ligands, and four L ligands, and the L ligands have the same coordination modes as those of 2. Single-crystal X-ray analysis showed that hydrogen-bonding and pi-pi stacking interactions exist in complexes 1 and 2 resulting in two- and three-dimensional molecular arrangements, and the parallel arrangement of the ligand in the crystal of complex 3 resulted in a close inter- and intramolecular pi-pi interactions. Investigation of the crystals, as well as an amorphous thin film and powder of 3, by photoluminescence (PL) allowed the effect of the molecular packing on the emission properties to be elucidated. Furthermore, the electroluminescent (EL) properties of 3 were examined by fabricating a multilayer device with structure of [ITO/NPB/(ZnL)(n)/Alq3/LiF/Al] (NPB = N,N'-bis(alpha-naphthyl)-N,N'-diphenyl-(1,1'-biphenyl)-4,4'-diamine, Alq3 = tris(8-hydroxyquinolinato)aluminum).
Audio-video array source separation for perceptual user interfaces (2001)

Steerable microphone arrays provide a flexible infrastructure for audio source separation. In order for them to be used effectively in perceptual user interfaces, there must be a mechanism in place for steering the focus of the array to the sound source. Audio-only steering techniques often perform poorly in the presence of multiple sound sources or strong reverberation. Video-only techniques can achieve high spatial precision but require that the audio and video subsystems be accurately calibrated to preserve this precision. We present an audio-video localization technique that combines the benefits of the two modalities. We implement our technique in a test environment containing multiple stereo cameras and a room-sized microphone array. Our technique achieves an 8.9 dB improvement over a single far-field microphone and a 6.7 dB improvement over source separation based on video-only localization.
Nitrate and Nitrite Ultraviolet Actinometers (1999)

Abstract We developed nitrate and nitrite actinometers to determine radiant fluxes from 290 to 410 nm. These actinometers are based on the reaction of the photochemically generated OH radical with benzoic acid to form salicylic acid (SA) and p‐hydroxybenzoic acid (pHBA). Actinom‐eter development included determination of the temperature and wavelength dependence of the quantum yield for formation of SA and pHBA from nitrate and nitrite photolysis in air‐saturated solutions. Quantum yields (at 25°C) for SA production from nitrate photolysis ranged from 0.00146 to 0.00418 between 290 and 350 nm, and from 0.00185 to 0.00633 for nitrite photolysis between 290 and 405 nm. The quantum yields for SA production were approximately 50–60% greater than quantum yields for pHBA production from nitrate and nitrite photolysis. For both actinometers, SA and pHBA formation was temperature dependent, increasing by approximately a factor of 2.2 from 0 to 35°C. Activation energies for SA formation varied with wavelength, ranging from 14.7 to 16.5 kj mol ‐ 1 between 290 and 330 nm for the nitrate actinometer and 12.3 to 17.8 kj mol‐ 1 between 310 and 390 nm for the nitrite actinometer. Activation energies for pHBA formation were 2–11% higher. Wavelength‐dependent changes in the quantum yield and activation energy for SA and pHBA formation from nitrate photolysis suggest multiple electronic transitions for nitrate from 290 to 350 nm. Quantum yields for OH radical formation from nitrate and nitrite photolyses were estimated from SA and pHBA quantum yields at 25°C. Wavelength‐dependent OH quantum yields ranged from 0.007 to 0.014 for nitrate photolysis between 290 and 330 nm and from 0.024 to 0.078 for nitrite photolysis between 298 and 390 nm. The nitrate and nitrite actinometers can maintain initial rate conditions for hours, are insensitive to laboratory lighting, easy to use and extremely sensitive; the minimum radiant energy that can be detected in our irradiation system is approximately 10 ‐9 einsteins.
Approaches to Capturing and Designing Biologically Active Small Molecules Produced by Uncultured Microbes (2010)

Bacteria are one of the most important sources of bioactive natural products for drug discovery. Yet, in most habitats only a small percentage of all existing prokaryotes is amenable to cultivation and chemical study. There is strong evidence that the uncultivated diversity represents an enormous resource of novel biosynthetic enzymes and secondary metabolites. In addition, many animal-derived drug candidates that are structurally characterized but difficult to access seem to be produced by uncultivated, symbiotic bacteria. This review provides an overview about established and emerging techniques for the investigation and exploitation of the environmental metabolome. These include metagenomic library construction and screening, heterologous expression, community sequencing, and single-cell methods. Such tools, the advantages and shortcomings of which are discussed, have just begun to reveal the full metabolic potential of free-living and symbiotic bacteria, providing exciting new avenues for natural product research and environmental microbiology.
Phase-based multidimensional volume registration (2002)

We present a method for accurate image registration and motion compensation in multidimensional signals, such as two-dimensional (2-D) X-ray images and three-dimensional (3-D) computed tomography/magnetic resonance imaging volumes. The method is based on phase from quadrature filters, which makes it robust to noise and temporal intensity variations. The method is equally applicable to signals of two, three or higher number of dimensions. We use parametric models, e.g., affine models, finite elements or local affine models with global regularization. Experimental results show high accuracy for 2-D and 3-D motion compensation.
Video Compression Artifact Reduction via Spatio-Temporal Multi-Hypothesis Prediction (2015)

Annoying compression artifacts exist in most of lossy coded videos at low bit rates, which are caused by coarse quantization of transform coefficients or motion compensation from distorted frames. In this paper, we propose a compression artifact reduction approach that utilizes both the spatial and the temporal correlation to form multi-hypothesis predictions from spatio-temporal similar blocks. For each transform block, three predictions with their reliabilities are estimated, respectively. The first prediction is constructed by inversely quantizing transform coefficients directly, and its reliability is determined by the variance of quantization noise. The second prediction is derived by representing each transform block with a temporal auto-regressive (TAR) model along its motion trajectory, and its corresponding reliability is estimated from local prediction errors of the TAR model. The last prediction infers the original coefficients from similar blocks in non-local regions, and its reliability is estimated based on the distribution of coefficients in these similar blocks. Finally, all the predictions are adaptively fused according to their reliabilities to restore high-quality videos. The experimental results show that the proposed method can efficiently reduce most of the compression artifacts and improve both subjective and objective quality of block transform coded videos.
Raman Antenna Formed by Molecule/Plasmonic Nanostructure Hybrid System (2011)

A nano-antenna composed of a particle and a polarizable surface provides control of the spatial distribution and high enhancement of Raman scattering. This structure may serve as a stable platform for single molecule detection.
Exogenous Glutathione Completes the Defense against Oxidative Stress in <i>Haemophilus influenzae</i> (2003)

Since they are equipped with several strategies by which they evade the antimicrobial defense of host macrophages, it is surprising that members of the genus Haemophilus appear to be deficient in common antioxidant systems that are well established to protect prokaryotes against oxidative stress. Among others, no genetic evidence for glutathione (gamma-Glu-Cys-Gly) (GSH) biosynthesis or for alkyl hydroperoxide reduction (e.g., the Ahp system characteristic or enteric bacteria) is apparent from the Haemophilus influenzae Rd genome sequence, suggesting that the organism relies on alternative systems to maintain redox homeostasis or to reduce small alkyl hydroperoxides. In this report we address this apparent paradox for the nontypeable H. influenzae type strain NCTC 8143. Instead of biosynthesis, we could show that this strain acquires GSH by importing the thiol tripeptide from the growth medium. Although such GSH accumulation had no effect on growth rates, the presence of cellular GSH protected against methylglyoxal, tert-butyl hydroperoxide (t-BuOOH), and S-nitrosoglutathione toxicity and regulated the activity of certain antioxidant enzymes. H. influenzae NCTC 8143 extracts were shown to contain GSH-dependent peroxidase activity with t-BuOOH as the peroxide substrate. The GSH-mediated protection against t-BuOOH stress is most probably catalyzed by the product of open reading frame HI0572 (Prx/Grx), which we isolated from a genomic DNA fragment that confers wild-type resistance to t-BuOOH toxicity in the Ahp-negative Escherichia coli strain TA4315 and that introduces GSH-dependent alkyl hydroperoxide reductase activity into naturally GSH peroxidase-negative E. coli. Finally, we demonstrated that cysteine is an essential amino acid for growth and that cystine, GSH, glutathione amide, and cysteinylglycine can be catabolized in order to complement cysteine deficiency.