gebhart/patrepeval huggingface dataset:
Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms (2016)

The opportunistic pathogen Pseudomonas aeruginosa produces colorful redox-active metabolites called phenazines, which underpin biofilm development, virulence, and clinical outcomes. Although phenazines exist in many forms, the best studied is pyocyanin. Here, we describe pyocyanin demethylase (PodA), a hitherto uncharacterized protein that oxidizes the pyocyanin methyl group to formaldehyde and reduces the pyrazine ring via an unusual tautomerizing demethylation reaction. Treatment with PodA disrupts P. aeruginosa biofilm formation similarly to DNase, suggesting interference with the pyocyanin-dependent release of extracellular DNA into the matrix. PodA-dependent pyocyanin demethylation also restricts established biofilm aggregate populations experiencing anoxic conditions. Together, these results show that modulating extracellular redox-active metabolites can influence the fitness of a biofilm-forming microorganism.
Hand gesture recognition using Bag-of-features and multi-class Support Vector Machine (2010)

This paper discusses the use of the Scale Invariance Feature Transform (SIFT) features for bare hand gesture recognition. In the training stage, we can not use SIFT keypoints of training images directly with a multi-class Support Vector Machine (SVM) to build a training classifier model, because of the space incompatibility of the SIFT keypoints for every training image that contains the hand gesture only. Therefore, the Bag-of-features model was introduced. After extracting the keypoints for every training image using the SIFT algorithm, a vector quantization technique is used to unify them. The quantization will map keypoints extracted from every training image into a unified dimensional histogram vector (Bag-of-words) after K-means clustering. This histogram is treated as an input vector for a multi-class SVM to build the training classifier model. In the testing stage, the keypoints are extracted from every image captured from the webcam and fed into the cluster model to map them with one (Bag-of-words) vector, which is finally fed into the multi-class SVM training classifier model to recognize the hand gesture.
Anti-PD-1 antibody significantly increases therapeutic efficacy of Listeria monocytogenes (Lm)-LLO immunotherapy (2013)

Our findings demonstrate that combination of Lm-LLO-based vaccine with blocking of PD-1/PD-L1 interaction is a feasible approach with clinical translation potential that can lead to overall enhancement of the efficacy of anti-tumor immunotherapy.
Modern Synthetic Methods for Copper‐Mediated C(aryl)O, C(aryl)N, and C(aryl)S Bond Formation (2003)

The copper-mediated C(aryl)[bond]N, C(aryl)[bond]O, and C(aryl)[bond]S bond formation is an important transformation and has been developed to include a wide range of substrates. This Review highlights the recent developments in the copper-mediated (both stoichiometric and catalytic) reactions of aryl boronic acids, aryl halides, iodonium salts, siloxanes, stannanes, plumbanes, bismuthates, and trifluoroborate salts as aryl donors. In particular, the recent introduction of boronic acids as reaction partners in both O- and N-arylation has been a significant discovery and will occupy centre-stage in this review. Clear improvements can be obtained by the correct choice of copper source, base, ligands, and other additives. Mechanistic investigations should provide insight into the catalytically active species, which would aid in the development of milder, more-efficient methods.
Specific Patterns of Electrophile Adduction Trigger Keap1 Ubiquitination and Nrf2 Activation (2005)

Activation of the transcription factor Nrf2 regulates expression of phase II enzymes and other adaptive responses to electrophile and oxidant stress. Nrf2 concentrations are regulated by the thiol-rich sensor protein Keap1, which is an adaptor protein for Cul3-dependent ubiquitination and degradation of Nrf2. However, the links between site specificity of Keap1 modification by electrophiles and mechanisms of Nrf2 activation are poorly understood. We studied the actions of the prototypical Nrf2 inducer tert-butylhydroquinone (tBHQ) and two biotin-tagged, thiol-reactive electrophiles, N-iodoacetyl-N-biotinylhexylenediamine (IAB) and 1-biotinamido-4-(4'-[maleimidoethyl-cyclohexane]-carboxamido)butane (BMCC). Both IAB and tBHQ induced antioxidant response element (ARE)-directed green fluorescent protein (GFP) expression in ARE/thymidine kinase GFP HepG2 cells, and both initiated nuclear Nrf2 accumulation and induction of heme oxygenase 1 in HEK293 cells. In contrast, BMCC produced none of these effects. Liquid chromatography tandem mass spectrometry (MS-MS) analysis of human Keap1 modified by IAB or BMCC in vitro indicated that IAB adduction occurred primarily in the central linker domain, whereas BMCC modified other Keap1 domains. Treatment of FLAG-Keap1-transfected HEK293 with the Nrf2-activating compounds IAB and tBHQ generated high molecular weight Keap1 forms, which were identified as K-48-linked polyubiquitin conjugates by immunoblotting and liquid chromatography MS-MS. Keap1 polyubiquitination coincided with Nrf2 stabilization and nuclear accumulation. In contrast, BMCC did not induce Keap1 polyubiquitination. Our results suggest that Nrf2 activation is regulated through the polyubiquitination of Keap1, which in turn is triggered by specific patterns of electrophile modification of the Keap1 central linker domain. These results suggest that Keap1 adduction triggers a switching of Cul3-dependent ubiquitination from Nrf2 to Keap1, leading to Nrf2 activation.
Regulation of Ligands for the NKG2D Activating Receptor (2013)

NKG2D is an activating receptor expressed by all NK cells and subsets of T cells. It serves as a major recognition receptor for detection and elimination of transformed and infected cells and participates in the genesis of several inflammatory diseases. The ligands for NKG2D are self-proteins that are induced by pathways that are active in certain pathophysiological states. NKG2D ligands are regulated transcriptionally, at the level of mRNA and protein stability, and by cleavage from the cell surface. In some cases, ligand induction can be attributed to pathways that are activated specifically in cancer cells or infected cells. We review the numerous pathways that have been implicated in the regulation of NKG2D ligands, discuss the pathologic states in which those pathways are likely to act, and attempt to synthesize the findings into general schemes of NKG2D ligand regulation in NK cell responses to cancer and infection.
Sustained Hedgehog signaling is required for basal cell carcinoma proliferation and survival: conditional skin tumorigenesis recapitulates the hair growth cycle (2004)

Temporally and spatially constrained Hedgehog (Hh) signaling regulates cyclic growth of hair follicle epithelium while constitutive Hh signaling drives the development of basal cell carcinomas (BCCs), the most common cancers in humans. Using mice engineered to conditionally express the Hh effector Gli2, we show that continued Hh signaling is required for growth of established BCCs. Transgene inactivation led to BCC regression accompanied by reduced tumor cell proliferation and increased apoptosis, leaving behind a small subset of nonproliferative cells that could form tumors upon transgene reactivation. Nearly all BCCs arose from hair follicles, which harbor cutaneous epithelial stem cells, and reconstitution of regressing tumor cells with an inductive mesenchyme led to multilineage differentiation and hair follicle formation. Our data reveal that continued Hh signaling is required for proliferation and survival of established BCCs, provide compelling support for the concept that these tumors represent an aberrant form of follicle organogenesis, and uncover potential limitations to treating BCCs using Hh pathway inhibitors.
Region-based video coding with embedded zero-trees (1997)

Summary form only given. In this paper, we describe a region-based video coding algorithm that is currently under investigation for inclusion in the emerging MPEG4 standard. This algorithm was incorporated in a submission that scored highly in the MPEG4 subjective tests of November 1995 (Talluri et al. 1997). Good coding efficiency is achieved by combining motion segmented region-based coding with the Shapiro's embedded zero-tree wavelet (EZW) method.
Flow cytometry of mammalian sperm: progress in DNA and morphology measurement. (1979)

Variability in DNA content and head shape of mammalian sperm are potentially useful markers for flow cytometric monitoring of genetic damage in spermatogenic cells. The high refractive index and extreme flatness of the sperm heads produce an optical effect which interferes with DNA measurements in flow cytometers which have dye excitation and fluorescence light collection normal to the axis of flow. Orientation of sperm in flow controls this effect and results in coefficients of variation of 2.5% and 4.2%, respectively, for DNA measurements of mouse and human sperm. Alternatively, the optical effect can be used to generate shape-related information. Measurements on randomly oriented sperm from three mammalian species using a pair of fluorescence detectors indicate that large shape differences are detectable. Acriflavine-Feulgen stained sperm nuclei are significantly bleached during flow cytometric measurements at power levels routinely used in many flow cytometers. Dual beam studies of this phenomenon indicate it may be useful in detecting abnormally shaped sperm.
Branched‐chain amino acids improve insulin resistance in patients with hepatitis C virus‐related liver disease: report of two cases (2007)

Abstract Hepatitis C virus (HCV) infection causes insulin resistance. Because increased insulin resistance is a risk factor for development of hepatocellular carcinoma and reduced long‐term survival, insulin resistance is a therapeutic target in patients with HCV infection. Branched‐chain amino acids (BCAAs) are not only structural constituents of proteins but they are also considered as regulators of insulin signalling. We first describe two cases suggesting that administration of BCAAs improves insulin resistance associated with HCV‐related liver disease. Although there were no changes in body weight, plasma glucose concentration and haemoglobin A1c (HbA1c) value were decreased. Moreover, BCAAs caused a decrease in both fasting insulin concentration and the value of homeostasis model assessment for insulin resistance. Thus, BCAAs are a potential therapeutic agent for improving insulin resistance in patients with HCV‐related liver disease.
Brown Carbon Spheres in East Asian Outflow and Their Optical Properties (2008)

Atmospheric aerosols play a substantial role in climate change through radiative forcing. Combustion-produced carbonaceous particles are the main light-absorbing aerosols; thus, quantifying their optical properties is essential for determining the magnitude of direct forcing. By using the electron energy-loss spectrum in the transmission electron microscope, we quantified the optical properties of individual, submicrometer amorphous carbon spheres that are ubiquitous in East Asian–Pacific outflow. The data indicate that these common spheres are brown, not black, with a mean refractive index of 1.67 – 0.27 i (where i = \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\sqrt{1}\) \end{document} ) at a wavelength of 550 nanometers. The results suggest that brown carbon aerosols should be explicitly included in radiative forcing models.
Intraductal Papillary Mucinous Tumors of the Pancreas: Helical CT with Histopathologic Correlation (2000)

The main causes of poor CT-histopathologic correlation were related to evaluation of main pancreatic duct involvement and diagnosis of malignant transformation. The association between diabetes and specific CT criteria was highly suggestive of malignancy.
Identification and functional expression of a novel ligand binding subunit of the inhibitory glycine receptor. (1990)

By homology screening of a rat brain cDNA library we have identified a novel alpha subunit variant of the inhibitory glycine receptor, alpha 3. The deduced protein exhibits 82-83% amino acid identity to the previously characterized rat and human alpha 1 and alpha 2 subunit sequences. Upon heterologous expression in Xenopus laevis oocytes, the alpha 3 subunit formed functional agonist-gated chloride channels which displayed a low affinity for glycine and only small responses to taurine. Amplification of alpha 3 transcripts by polymerase chain reaction revealed high levels in spinal cord at later postnatal stages of development. These data indicate alpha subunit heterogeneity of the inhibitory glycine receptor in adult rats that may result in pharmacologically distinct receptor subtypes.
Calcium-activated endoplasmic reticulum stress as a major component of tumor cell death induced by 2,5-dimethyl-celecoxib, a non-coxib analogue of celecoxib (2007)

A drawback of extensive coxib use for antitumor purposes is the risk of life-threatening side effects that are thought to be a class effect and probably due to the resulting imbalance of eicosanoid levels. 2,5-Dimethyl-celecoxib (DMC) is a close structural analogue of the selective cyclooxygenase-2 inhibitor celecoxib that lacks cyclooxygenase-2-inhibitory function but that nonetheless is able to potently mimic the antitumor effects of celecoxib in vitro and in vivo. To further establish the potential usefulness of DMC as an anticancer agent, we compared DMC and various coxibs and nonsteroidal anti-inflammatory drugs with regard to their ability to stimulate the endoplasmic reticulum (ER) stress response (ESR) and subsequent apoptotic cell death. We show that DMC increases intracellular free calcium levels and potently triggers the ESR in various tumor cell lines, as indicated by transient inhibition of protein synthesis, activation of ER stress-associated proteins GRP78/BiP, CHOP/GADD153, and caspase-4, and subsequent tumor cell death. Small interfering RNA-mediated knockdown of the protective chaperone GRP78 further sensitizes tumor cells to killing by DMC, whereas inhibition of caspase-4 prevents drug-induced apoptosis. In comparison, celecoxib less potently replicates these effects of DMC, whereas none of the other tested coxibs (rofecoxib and valdecoxib) or traditional nonsteroidal anti-inflammatory drugs (flurbiprofen, indomethacin, and sulindac) trigger the ESR or cause apoptosis at comparable concentrations. The effects of DMC are not restricted to in vitro conditions, as this drug also generates ER stress in xenografted tumor cells in vivo, concomitant with increased apoptosis and reduced tumor growth. We propose that it might be worthwhile to further evaluate the potential of DMC as a non-coxib alternative to celecoxib for anticancer purposes.
Human-Computer Relation and Computer Framework under Cloud Computing Environment (2012)

After the discussion of Cloud Computing including concepts,characteristics,advantages,services models and types,this paper an alyzed the Human-Computer Relation under Cloud Computing Environment,proposed the Human-centered,Computer-invisible and Aware-service marked Human-Computer Relation,the key lies in how to make computer providing services to human imperceptibly,the last part argued that in order to realize this new Human-Computer Relation,Non-Von Neumann Computer based on demand-driv en model should be design,to break through the limitations of traditional computer,the main features of this type Non-Von Neumann Computer were explored as well for further studies.
Intelligent disaster management system based on cloud-enabled vehicular networks (2011)

The importance of emergency response systems cannot be overemphasized today due to the many manmade and natural disasters in the recent years such as September 2001 and the recent Japan earthquake and tsunami disaster. The overall cost of the Japan disaster alone is estimated to have exceeded 300 billion USD. Transportation and telecommunications play a critical role in disaster response and management in order to minimize loss of human life, economic cost and disruptions. Our research is concerned with developing emergency response systems for disasters of various scales with a focus on transportation systems which exploit ICT developments. In this paper, we leverage Intelligent Transportation Systems (ITS) including VANETs (Vehicular Ad hoc Networks), mobile and Cloud computing technologies to propose an intelligent disaster management system. The system is intelligent because it is able to gather information from multiple sources and locations, including from the point of incident, and is able to make effective strategies and decisions, and propagate the information to vehicles and other nodes in real-time. The effectiveness of our system is demonstrated through modelling the impact of a disaster on a real city transport environment and comparing it with the case where our disaster management system was in place. We report great benefits derived from the adoption of our proposed system in terms of improved and balanced traffic flow and smooth evacuation.
Biological and Clinical Availability of Adipose-Derived Stem Cells for Pelvic Dead Space Repair (2012)

Adipose-derived stem cells (ADSCs) are a very attractive cell source for regenerative and reconstructive medicine. Although ADSCs have already been used in cardiovascular disease and cosmetic surgery, they have not yet been used in gastroenterological surgery. In this study, we clarified the utility of the combined application of ADSCs and resected intraperitoneal fatty tissues as a sealant for the pelvic dead space that sometimes causes severe and fatal complications in colorectal and gynecological surgeries. In pelvic dead space model mice, mouse ADSCs efficiently maintained transplanted intraperitoneal fatty tissues without any incidence of adhesion to surrounding organs. In vivo and in vitro analyses revealed that transplanted ADSCs differentiated into endothelial cells by expressing the angiogenic factors vascular endothelial growth factor and hepatocyte growth factor. Mouse and human ADSCs contained a CD45(-)CD34(+) subset possessing high colony formation and sphere formation abilities. In addition, the CD45(-)CD34(+) subset consisted of two characteristic subsets: the CD34(+)CD90(+) angiogenic subset and the CD34(+)CD90(-) adipogenic subset. Grafts of human ADSCs with fat transplanted into mice were efficiently maintained for more than 12 months without volume reductions. A comparative study of graft maintenance efficacy between cultured human ADSCs and freshly isolated ADSCs indicated that the cultivation of ADSCs decreased their graft maintenance ability. These findings suggested that the angiogenic and adipogenic subsets act in coordination with each other and are essential for efficient graft maintenance.
Ethylene profitability trends (1990)

The profitability of ethylene production is related mainly to plant capacity use. The world ethylene capacity squeeze in 1988 and 1989 caused net margins to soar to unprecedented levels. The rush to capture the alluring profits by increasing production via new capacity additions will cause increasing competition and a normal decline in profitability over the next few years. A period of reasonable profit stability is expected to follow. According to the author, the world petrochemical industry is now operating at the high-capacity use, high-profitability end of the spectrum.
Somatodendritic localization of 5-HT1A and preterminal axonal localization of 5-HT1B serotonin receptors in adult rat brain (2000)

The 5-HT1A and 5-HT1B receptors of serotonin play important roles as auto- and heteroreceptors controlling the release of serotonin itself and of other neurotransmitters/modulators in the central nervous system (CNS). To determine the precise localization of these receptors, we examined their respective cellular and subcellular distributions in the nucleus raphe dorsalis and hippocampal formation (5-HT1A) and in the globus pallidus and substantia nigra (5-HT1B), using light and electron microscopic immunocytochemistry with specific antibodies. Both immunogold and immunoperoxidase preembedding labelings were achieved. In the nucleus raphe dorsalis, 5-HT1A immunoreactivity was found exclusively on neuronal cell bodies and dendrites, and mostly along extrasynaptic portions of their plasma membrane. After immunogold labeling, the density of membrane-associated 5-HT1A receptors could be estimated to be at least 30-40 times that in the cytoplasm. In the hippocampal formation, the somata as well as dendrites of pyramidal and granule cells displayed 5-HT1A immunoreactivity, which was also prominent on the dendritic spines of pyramidal cells. In both substantia nigra and globus pallidus, 5-HT1B receptors were preferentially associated with the membrane of fine, unmyelinated, preterminal axons, and were not found on axon terminals. A selective localization to the cytoplasm of endothelial cells of microvessels was also observed. Because the 5-HT1A receptors are somatodendritic, they are ideally situated to mediate serotonin effects on neuronal firing, both as auto- and as heteroreceptors. The localization of 5-HT1B receptors to the membrane of preterminal axons suggests that they control transmitter release from nonserotonin as well as serotonin neurons by mediating serotonin effects on axonal conduction. The fact that these two receptor subtypes predominate at extrasynaptic and nonsynaptic sites provides further evidence for diffuse serotonin transmission in the CNS.
Some properties of silane‐grafted moisture‐crosslinked polyethylene (1985)

Abstract Silane‐grafted polyethylene materials are processed in conventional thermoplastic fabrication machines. The shaped articles are then crosslinked in water by the formation of Si‐O‐Si crosslinks. This paper represents studies on the crosslinking progress in different environments at various temperatures. Molecular orientation is shown to become permanent and mostly irrecoverable even at 150°C, in the silane‐grafted solid state crosslinked specimens (the crosslinking temperature in water is well below the polymer melting temperature). These frozen molecular orientations have a significant effect on the tensile properties of the crosslinked materials causing higher yield stresses and lower elongations at break. The thermal and tensile properties of some silane‐grafted crosslinked polyethylene samples and peroxide‐crosslinked materials are compared and analyzed.
Cloning of a Second Type of Activin Receptor and Functional Characterization in Xenopus Embryos (1992)

A complementary DNA coding for a second type of activin receptor (ActRIIB) has been cloned from Xenopus laevis that fulfills the structural criteria of a transmembrane protein serine kinase. Ectodermal explants from embryos injected with activin receptor RNA show increased sensitivity to activin, as measured by the induction of muscle actin RNA. In addition, injected embryos display developmental defects characterized by inappropriate formation of dorsal mesodermal tissue. These results demonstrate that this receptor is involved in signal transduction and are consistent with the proposed role of activin in the induction and patterning of mesoderm in Xenopus embryos.