gebhart/patrepeval huggingface dataset:
Translesional synthesis on a DNA template containing a single stereoisomer of dG-(+)- or dG-(-)-anti-BPDE (7, 8-dihydroxy-anti-9, 10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (1993)

Oligodeoxynucleotides modified site-specifically with dG-(+)-trans- and dG-(+)-cis-anti-BPDE (7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene) or dG-(-)-trans- and dG-(-)-cis-anti-BPDE were used as templates in primer extension reactions catalyzed by the Klenow fragment of Escherichia coli DNA polymerase I. The primer could be extended past the dG-(-)-trans-BPDE adduct with small amounts of dAMP incorporated opposite the lesion. A small amount of base deletions was also observed while, with the dG-(-)-cis-BPDE adduct, one- and two-base deletions predominated. When templates containing dG-(+)-trans-BPDE were used, small amounts of products containing one-base deletions were observed; with dG-(+)-cis-BPDE, substitution of dAMP opposite the lesion was also detected. The frequency of nucleotide insertion for dAMP opposite dG-(-)-trans-BPDE and the frequency of extension from the primer terminus containing the dA:dG-(-)-trans-BPDE pair were much higher than those observed with the other, stereochemically different BPDE adducts. Kinetic studies were in agreement with the results of the primer extension study. When the base flanking the 5' side of dG-BPDE was changed from dC to dT, the frequency of one-base deletions increased. We conclude that the trans- or cis-addition product of dG-(-)-anti-BPDE has a higher miscoding potential than dG-(+)-anti-BPDE in our model system and that G-->T transversions and deletions predominate. These observations are consistent with the types of mutations observed in vivo.
The lattice-based screen set: a square N-color all-orders Moiré-free screen set (2011)

Periodic clustered-dot screens are widely used for electrophotographic printers due to their print stability. However, moir´e is a ubiquitous problem that arises in color printing due to the beating together of the clustered-dot, periodic halftone patterns that are used to represent different colorants. This beating or interference phenomenon introduces spurious low frequency (large period) patterns in the printed output that are very objectionable to the viewer. The traditional solution in the graphic arts and printing industry is to rotate identical square screens to angles that are maximally separated from each other. For example, the classic three-color screen set rotates three identical square screens to the angles 15&deg;, 45&deg;, and 75&deg;, respectively. However, the effectiveness of this approach is limited when printing with more than four colorants, i.e. N-color printing, where N &gt;4. Moreover, accurately achieving the angles that have maximum angular separation requires a very high resolution plate writer, as is used in commercial offset printing. In this paper, we propose a systematic way to design color screen sets for periodic, clustered-dot screens that offers more explicit control of the moir´e properties of the resulting screens when used in color printing. We find a general concept for moir´e-free screen design that is called lattice-based screen design. The basic concept behind our approach is the creation of the screen set on a 2-dimensional lattice in the frequency domain and then picking each fundamental frequency vector of the individual colorant planes in the created spectral lattice according to the desired properties. The halftone geometry of a screen set is the set of angles and frequencies in units of lines per inch (LPI) of each screen plane. The lattice-based screen design offers more flexibility in designing N-color screen sets with different halftone geometries, and all of them are guaranteed to be all-orders moir´e-free. For example, by creating a square lattice in the frequency domain, square N-color moir´e-free screen sets that consist of N rotated square screens can be achieved. The proposed approach maintains the advantage of square clustered-dot screen design and is based on low addressability of digital printing. We also propose several symmetry measures, and use them to compare the proposed 4-color square screen set and the screen sets based on a previous moir´e-free N-color non-orthogonal approach. The proposed screen set is shown to have better symmetry properties.
5‐Hydroxytryptamine‐sensitive adenylate cyclase affects phagocytosis in cockroach hemocytes (1992)

Abstract The effects of 5‐hydroxytryptamine (5‐HT), octopamine, and dopamine on adenylate cyclase activity were studied using fragmented hemocyte membranes of the American cockroach, Periplaneta americana . 5‐HT and octopamine increased cAMP production with maximal effects at 10 nM and 10 μM respectively. Dopamine did not affect adenylate cyclase activity. The effects of octopamine and 5‐HT are not additive, indicating that both are working through the same receptor. A pharmacological profile suggests that the receptor present on the cockroach hemocytes is more similar to a 5‐HT receptor than an octopamine receptor. Mammalian antagonists of 5‐HT‐receptors blocked the 5‐HT‐induced increase in cAMP production with the following order of potency: mianserin &gt; ketanserin &gt; spiperone &gt; ICS 205,930. In phagocytosis assays using whole hemocytes, 5‐HT increases cAMP production above control levels at 0.25, 0.75, 15, and 65 min. Addition of Bt 2 cAMP at 0.1 mM inhibits phagocytosis whereas, at 10 nM, Bt 2 cAMP enhances phagocytosis. Imidazole at 0.1 mM also enhanced phagocytosis. A 5‐HT‐mediated elevation in cAMP production may result in either an activation or inhibition of phagocytic activities. © 1992 Wiley‐Liss, Inc.
Impact of the histone deacetylase inhibitor 4-phenylbutyrate on the clearance of apoptotic pancreatic carcinoma cells by human macrophages (2011)

Histone deacetylase inhibitors have been found to have potent anticancer activities, partly induced by tumour cell apoptosis. The clearance of apoptotic tumour cells is an important mechanism of antitumour immune surveillance. The aim of this study was to assess the impact of 4-phenylbutyrate (4-PB) and its immunological effects on the macrophage clearance of apoptotic pancreatic ductal adenocarcinoma (PDAC) cells. To this end, a co-culture system of human macrophages from donors and PDAC patients, and PDAC cell lines (T3M4, PANC-1 and AsPC-1) was established to study the effect of 4-PB. Apoptosis and phagocytic activity were analysed using flow cytometry, and phagocytosis was confirmed by confocal microscopy. Further, p21 expression was quantified by immunoblot analysis. 4-PB treatment (0-10 mM) resulted in a dose-dependent induction of tumour cell apoptosis in two of the cell lines (T3M4 and PANC-1), but it also induced human macrophage apoptosis. The apoptotic effect of gemcitabine on PDAC cells was further enhanced by 4-PB. Moreover, 4-PB led to a dose-dependent overexpression of the cell cycle regulator p21 in tumour cells. In co-culture, apoptotic PDAC cells were phagocytosed by donor macrophages and phagocytosis was increased through tumour cell exposure to 4-PB and/or gemcitabine, whereas phagocytosis of PANC-1 cells was reduced using macrophages of PDAC patients treated with 4-PB. The 4-PB treatment induced human macrophage expression of the pro-angiogenic IL-8 and simultaneously inhibited inflammatory cytokine release through modulation of IL-10 and TNFα after phagocytosis of apoptotic PDAC cells. In conclusion, the 4-PB treatment activated tumour cell death in PDAC cells, resulting in tumour cell phagocytosis by macrophages. The latter were characterized by an anti-inflammatory and pro-angiogenic cytokine response demonstrating adverse, tumour-promoting effects of macrophages on tumour cells. Thus, the potential of 4-PB as an anticancer agent against PDAC cannot be reliably assessed without taking into account the complex tumour microenvironment.
A preliminary study of salt flank illumination at Vinton Dome, Louisiana: Do we need lateral wavefield continuation? (2003)

Project and study overview Vinton Dome project collaboration between AGL (U of H) and Output Exploration.Salt dome onshore Louisiana (first well drilled in 1901).Simultaneous acquisition of 3D surface seismic data and 3D, 3C VSP data (Constance et al., 1999).
Tandem repeat coupled with endonuclease cleavage (TREC): a seamless modification tool for genome engineering in yeast (2010)

The complete synthetic Mycoplasma genitalium genome ( approximately 583 kb) has been assembled and cloned as a circular plasmid in the yeast Saccharomyces cerevisiae. Attempts to engineer the cloned genome by standard genetic methods involving the URA3/5-fluoroorotic acid (5-FOA) counter-selection have shown a high background of 5-FOA resistant clones derived from spontaneous deletions of the bacterial genome maintained in yeast. Here, we report a method that can seamlessly modify the bacterial genome in yeast with high efficiency. This method requires two sequential homologous recombination events. First, the target region is replaced with a mutagenesis cassette that consists of a knock-out CORE (an18-bp I-SceI recognition site, the SCEI gene under the control of the GAL1 promoter, and the URA3 marker) and a DNA fragment homologous to the sequence upstream of the target site. The replacement generates tandem repeat sequences flanking the CORE. Second, galactose induces the expression of I-SceI, which generates a double-strand break (DSB) at the recognition site. This DSB promotes intra-molecular homologous recombination between the repeat sequences, and leads to an excision of the CORE. As a result, a seamless modification is generated. This method can be adapted for a variety of genomic modifications and may provide an important tool to modify and design natural or synthetic genomes propagated in yeast.
An Autoinhibited Structure of α-Catenin and Its Implications for Vinculin Recruitment to Adherens Junctions (2013)

α-Catenin is an actin- and vinculin-binding protein that regulates cell-cell adhesion by interacting with cadherin adhesion receptors through β-catenin, but the mechanisms by which it anchors the cadherin-catenin complex to the actin cytoskeleton at adherens junctions remain unclear. Here we determined crystal structures of αE-catenin in the autoinhibited state and the actin-binding domain of αN-catenin. Together with the small-angle x-ray scattering analysis of full-length αN-catenin, we deduced an elongated multidomain assembly of monomeric α-catenin that structurally and functionally couples the vinculin- and actin-binding mechanisms. Cellular and biochemical studies of αE- and αN-catenins show that αE-catenin recruits vinculin to adherens junctions more effectively than αN-catenin, partly because of its higher affinity for actin filaments. We propose a molecular switch mechanism involving multistate conformational changes of α-catenin. This would be driven by actomyosin-generated tension to dynamically regulate the vinculin-assisted linkage between adherens junctions and the actin cytoskeleton.
Online path optimization for unmanned aerial vehicles under steady wind (2012)

In this paper, online path optimization method for Unmanned Aerial Vehicles (UAV) by adjusting parameters of flight path is proposed. Especially, the energy efficient path for UAVs under the presence of steady wind is discussed. Although the relation between the energy consumption and the flight path parameters is hard to model explicitly in general, which induces the difficulty to adopt gradient based optimization techniques. On the other hand, actual energy consumption can be measured, e.g. by measuring fuel consumption rate, and it is natural to assume that the rate is a function of flight path. This paper proposes to perturb the flight path in order to estimate the gradient of the energy consumption rate that is used for the optimization, which is based on Simultaneous Perturbation Stochastic Approximation (SPSA) method. Numerical results are shown to evaluate the proposed approach, and the method succeeded to improve the energy efficiency.
Unsupervised Image Categorization by Hypergraph Partition (2011)

We present a framework for unsupervised image categorization in which images containing specific objects are taken as vertices in a hypergraph and the task of image clustering is formulated as the problem of hypergraph partition. First, a novel method is proposed to select the region of interest (ROI) of each image, and then hyperedges are constructed based on shape and appearance features extracted from the ROIs. Each vertex (image) and its k-nearest neighbors (based on shape or appearance descriptors) form two kinds of hyperedges. The weight of a hyperedge is computed as the sum of the pairwise affinities within the hyperedge. Through all of the hyperedges, not only the local grouping relationships among the images are described, but also the merits of the shape and appearance characteristics are integrated together to enhance the clustering performance. Finally, a generalized spectral clustering technique is used to solve the hypergraph partition problem. We compare the proposed method to several methods and its effectiveness is demonstrated by extensive experiments on three image databases.
Self‐assembly of model graft copolymers of agarose and weak polyelectrolyte‐based amphiphilic diblock copolymers: Controlled drug release and degradation (2012)

Polysaccharide-based copolymers are promising biomaterials due to their biocompatibility and biodegradability. For potential biomedical applications the copolymer as a whole and all the degraded species must be biocompatible and easily removable from the system. In this regards, new model pH-responsive seaweed agarose (Agr) grafted with weak polyelectrolyte-based well-defined amphiphilic block copolymers ca. poly[(methyl methacrylate)-b-(2-dimethylamino)ethyl methacrylate)] (PMMA-b-PDMA) were designed and synthesized to study the self-assembly, degradation, and in vitro hydrophobic/hydrophilic drug release behavior. The graft copolymer solutions display extremely low critical micelle concentration (CMC) and form pH responsive stable micelles. The degradation study of the graft copolymer reveals that the entire degraded components are well soluble/dispersible in water due to formation of mixed micelles. The micelles are also strongly adsorbed on the mica surface owing to electrostatic interaction. One application of the graft copolymer micelles is that it can entrap both hydrophilic and poorly water soluble hydrophobic drugs effectively and exhibit slow release kinetics. The release kinetics of both the hydrophilic and poorly water soluble hydrophobic drugs change with pH as well as with the composition of the graft copolymer.
Exercise induced vasodepressor syncope. (1994)

Five cases of exercise induced pure vasodepressor syncope in patients without significant structural heart disease are reported. Hypotension and symptoms of syncope or pre-syncope were induced by treadmill exercise testing and in each case limited exercise performance. Evidence of inappropriate peripheral vasodilation, probably as a consequence of ventricular mechanoreceptor stimulation, was shown in all five patients. Head up tilt testing resulted in hypotension in four patients and isoprenaline infusion in the supine position resulted in hypotension in the fifth. These patients had a new condition of exercise induced neurally mediated (vasodepressor) syncope without appreciable structural cardiac abnormalities.
tert-Butylhydroperoxide (TBHP) mediated oxidative cross-dehydrogenative coupling of quinoxalin-2(1H)-ones with 4-hydroxycoumarins, 4-hydroxy-6-methyl-2-pyrone and 2-hydroxy-1,4-naphthoquinone under metal-free conditions (2020)

Correction for 'tert-Butylhydroperoxide (TBHP) mediated oxidative cross-dehydrogenative coupling of quinoxalin-2(1H)-ones with 4-hydroxycoumarins, 4-hydroxy-6-methyl-2-pyrone and 2-hydroxy-1,4-naphthoquinone under metal-free conditions' by Suraj Sharma et al., Org. Biomol. Chem., 2020, 18, 6537-6548, DOI: .
Conditional-Replication, Integration, Excision, and Retrieval Plasmid-Host Systems for Gene Structure-Function Studies of Bacteria (2001)

We have developed a series of powerful and versatile conditional-replication, integration, and modular (CRIM) plasmids. CRIM plasmids can be replicated at medium or high copy numbers in different hosts for making gene (or mutant) libraries. They can be integrated in single copies into the chromosomes of Escherichia coli and related bacteria to study gene function under normal physiological conditions. They can be excised from the chromosome, e.g., to verify that phenotypes are caused by their presence. Furthermore, they can be retrieved singly or en masse for subsequent molecular analyses. CRIM plasmids are integrated into the chromosome by site-specific recombination at one of five different phage attachment sites. Integrants are selected as antibiotic-resistant transformations. Since CRIM plasmids encode different forms of resistance, several can be used together in the same cell for stable expression of complex metabolic or regulatory pathways from diverse sources. Following integration, integrants are stably maintained in the absence of antibiotic selection. Each CRIM plasmid has a polylinker or one of several promoters for ectopic expression of the inserted DNA. Their modular design allows easy construction of new variants with different combinations of features. We also report a series of easily curable, low-copy-number helper plasmids encoding all the requisite Int proteins alone or with the respective Xis protein. These helper plasmids facilitate integration, excision ("curing"), or retrieval of the CRIM plasmids.
Resonance frequency, damping, and differential gain in 1.5 mu m multiple quantum-well lasers (1992)

A systematic investigation is presented into the intrinsic frequency response of quantum-well lasers, using parasitic-free relative intensity noise (RIN) measurements. There is shown to be a strong dependence of the resonance frequency on the number of quantum wells in the active region, originating from variations both in internal losses and in differential gain. The differential gain is found to have values higher than in corresponding bulk lasers, but only in devices with a large number of wells. The damping is also found to vary in a manner consonant with the changes in differential gain; however, comparison with bulk lasers indicates substantially stronger gain suppression in the quantum-well lasers studied.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Compact Focusing Grating Couplers Between Optical Fibers and Silicon-on-Insulator Photonic Wire Waveguides (2007)

We present compact and broadband grating couplers in silicon-on-insulator, between single-mode fiber and nanophotonic waveguides. Curved gratings allow for a very short transition between wide waveguides and photonic wires, resulting in very compact devices.
Sofosbuvir and Velpatasvir for HCV Genotype 1, 2, 4, 5, and 6 Infection (2015)

Once-daily sofosbuvir-velpatasvir for 12 weeks provided high rates of sustained virologic response among both previously treated and untreated patients infected with HCV genotype 1, 2, 4, 5, or 6, including those with compensated cirrhosis. (Funded by Gilead Sciences; ClinicalTrials.gov number, NCT02201940.).
Postoperative Pain Management in Children has been Improved, But Can be Further Optimized (1996)

The aim of this study is to evaluate the effect of the analgesic treatment currently used in children, and to identify if problems can be related to any particular routine or group of children. Analgesics administered pre-, per- and postoperatively were recorded, and intensity of pain during rest and movement and incidence and severity of side effects were measured four times postoperatively. Fifty-nine children aged 3 to 15 years undergoing miscellaneous operations participated. All children received analgesic treatment. During the study period 26 children reported at least one episode of unacceptable pain, while unacceptable pruritus, nausea or vomiting were observed in 18 children. It was not possible to relate the incidence of pain and side effects to any particular analgesic treatment or type of surgery, but groups of children that might need additional attention were identified. Even though improvements have been obtained, it is still a challenge to optimize the postoperative pain management of children, and when doing so attention should be paid not only to pain relief, but also to side effects of the administered analgesics.
Depth from rotating point spread functions (2004)

We present a method for passive ranging with incoherent light. The scheme uses a single optical channel and is particularly suitable for locating and ranging particles. Our aim is to create an optical system with increased discrimination among depth planes as compared to classical clear aperture solutions. We thus propose a criterion for evaluating a general point spread function for use in passive ranging. Then, we show that rotating point spread functions are good according to this criterion. An experimental realization of the point spread function by use of a computer-generated hologram is presented as well as a simulation of its depth discrimination.
Mechanisms of probiotic action: Implications for therapeutic applications in inflammatory bowel diseases (2008)

Probiotics are defined as nonpathogenic living microorganisms, including some commensal bacterial flora, which have beneficial effects on host health and disease prevention and/or treatment. Clinical trials have shown beneficial effects of probiotics on several human diseases, such as inflammatory bowel diseases (IBDs), which are among the most-studied diseases testing probiotics as a potential therapy. However, a significant question regarding clinical use of probiotics is the mechanism underlying the wide range of actions. Studies discussed in this review suggest 3 distinct cellular and molecular mechanisms for probiotic regulation in IBD therapy: 1) Probiotics block pathogenic bacterial effects by producing bactericidal substances and competing with pathogens and toxins for adherence to the intestinal epithelium; 2) Probiotics regulate immune responses by enhancing the innate immunity and modulating pathogen-induced inflammation via toll-like receptor-regulated signaling pathways; and 3) Probiotics regulate intestinal epithelial homeostasis by promoting intestinal epithelial cell survival, enhancing barrier function, and stimulating protective responses. Probiotics modulate host cell signaling pathways, including Akt, mitogen-activated protein kinases, and nuclear factor-kappaB to mediate these intestinal epithelial functions. It is hoped that developing a mechanistic understanding of probiotic action will provide the rationale to support the development of new hypothesis-driven studies to define the clinical efficacy in preventive, adjunctive, or alternative treatments for IBD.
Elevated β-Endorphin in Cerebrospinal Fluid After Electrical Brain Stimulation: Artifact of Contrast Infusion? (1984)

Beta-Endorphin-like immunoreactivity in cerebrospinal fluid was assayed in 11 patients receiving electrical stimulation of the brain for chronic pain. Immunoreactivity increased dramatically after contrast ventriculography prior to stimulation. No further elevations were observed after stimulation. The magnitude and time course of elevations were identical after placement of electrodes either in the thalamus or in the periventricular gray matter. These results suggest that previous findings of stimulation-induced elevation of beta-endorphin-like immunoreactivity in cerebrospinal fluid are attributable to an artifact of contrast ventriculography.