gebhart/patrepeval huggingface dataset:
High-Affinity Interaction between Gram-Negative Flagellin and a Cell Surface Polypeptide Results in Human Monocyte Activation (2000)

Flagella from diverse gram-negative bacteria induce tumor necrosis factor alpha (TNF-alpha) and interleukin-1beta (IL-1beta) synthesis by human monocytes (F. Ciacci-Woolwine, P. F. McDermott, and S. B. Mizel, Infect. Immun. 67:5176-5185, 1999). In this study, we establish that purified flagellin (FliC or FljB), the major filament protein from Salmonella enterica serovar Enteritidis, S. enterica serovar Typhimurium, and Pseudomonas aeruginosa, is an extremely potent inducer of TNF-alpha production by human monocytes and THP-1 myelomonocytic cells. Fifty percent of maximal TNF-alpha production (EC(50)) was obtained with 1.5 x 10(-11) M flagellin (0.75 ng/ml). Mutagenesis studies revealed that the central hypervariable region of flagellin is essential for the TNF-alpha-inducing activity of the protein. Although less active than the wild-type protein, a Salmonella flagellin mutant composed of only the central hypervariable region retained substantial TNF-alpha-inducing activity at nanomolar concentrations. In contrast, the conserved amino- and carboxy-terminal regions are inactive. Mutational analysis of the hypervariable region revealed that it contains two equally active TNF-alpha-inducing domains. The ability of THP-1 cells to respond to purified flagellins is dramatically reduced by mild trypsin treatment of the cells. Taken together, our results demonstrate that the cytokine-inducing activity of flagellins from gram-negative bacteria results from the interaction of these proteins with high-affinity cell surface polypeptide receptors on monocytes.
Inhibition of Hyaluronan Synthesis Reduces Versican and Fibronectin Levels in Trabecular Meshwork Cells (2012)

Hyaluronan (HA) is a major component of the extracellular matrix (ECM) and is synthesized by three HA synthases (HAS). Similarities between the HAS2 knockout mouse and the hdf mutant mouse, which has a mutation in the versican gene, suggest that HA and versican expression may be linked. In this study, the relationship between HA synthesis and levels of versican, fibronectin and several other ECM components in trabecular meshwork cells from the anterior segment of the eye was investigated. HA synthesis was inhibited using 4-methylumbelliferone (4MU), or reduced by RNAi silencing of each individual HAS gene. Quantitative RT-PCR and immunoblotting demonstrated a reduction in mRNA and protein levels of versican and fibronectin. Hyaluronidase treatment also reduced versican and fibronectin levels. These effects could not be reversed by addition of excess glucose or glucosamine or exogenous HA to the culture medium. CD44, tenascin C and fibrillin-1 mRNA levels were reduced by 4MU treatment, but SPARC and CSPG6 mRNA levels were unaffected. Immunostaining of trabecular meshwork tissue after exposure to 4MU showed an altered localization pattern of HA-binding protein, versican and fibronectin. Reduction of versican by RNAi silencing did not affect HA concentration as assessed by ELISA. Together, these data imply that HA concentration affects synthesis of certain ECM components. Since precise regulation of the trabecular meshwork ECM composition and organization is required to maintain the aqueous humor outflow resistance and intraocular pressure homeostasis in the eye, coordinated coupling of HA levels and several of its ECM binding partners should facilitate this process.
IL-1, IL-4, and IFN-gamma differentially regulate cytokine production and cell surface molecule expression in cultured human thymic epithelial cells (1991)

We investigated the response of purified and cloned human thymic epithelial cells (TEC) to IL-1, IL-4, and IFN-gamma stimulation in vitro. IL-1 alpha strongly up-regulated the production of granulocyte-macrophage CSF (GM-CSF), granulocyte CSF (G-CSF), IL-6, and IL-8, as measured by specific immunoenzymetric assays and by increased steady state mRNA levels. IL-4 or IFN-gamma did not induce these cytokines in TEC but in a sustained and dose-dependent manner down-regulated the IL-1-induced GM-CSF protein and mRNA levels. Only IFN-gamma, and not IL-4, suppressed the IL-1-induced G-CSF and IL-8 production, as shown at both the protein and mRNA levels. The inhibition was dose dependent, sustained for at least 96 h, and more pronounced for G-CSF than for IL-8. In contrast, both IL-4 and IFN-gamma enhanced the IL-1-induced IL-6 production. IL-4 and IFN-gamma had additive effects to increase IL-6 secretion and to more completely suppress the IL-1-induced GM-CSF. Analyses of cell surface molecules showed that intercellular adhesion molecule 1 (ICAM-1) expression on TEC was increased by IL-1 or IFN-gamma. IL-4 slightly down-regulated constitutive ICAM-1 levels but did not significantly modify the levels of expression induced by either IL-1 or IFN-gamma. MHC class II expression was induced by IFN-gamma but not by IL-1 or IL-4. The combination of IL-1 and IL-4 with IFN-gamma did not alter the levels of class II MHC Ag induced by IFN-gamma. In conclusion, TEC cytokine production and cell surface molecule expression are differentially regulated via a complex cytokine network. Our data suggest that developing T cells provide, in part, the signals controlling the function of their supporting stroma.
Implantation of a New Porous Gelatin–Siloxane Hybrid into a Brain Lesion as a Potential Scaffold for Tissue Regeneration (2006)

For brain tissue regeneration, any scaffold for migrated or transplanted stem cells with supportive angiogenesis is important once necrotic brain tissue has formed a cavity after injury such as cerebral ischemia. In this study, a new porous gelatin-siloxane hybrid derived from the integration of gelatin and 3-(glycidoxypropyl) trimethoxysilane was implanted as a three-dimensional scaffold into a defect of the cerebral cortex. The porous hybrid implanted into the lesion remained at the same site for 60 days, kept integrity of the brain shape, and attached well to the surrounding brain tissues. Marginal cavities of the scaffolds were occupied by newly formed tissue in the brain, where newly produced vascular endothelial, astroglial, and microglial cells were found with bromodeoxyuridine double positivity, and the numbers of those cells were dose-dependently increased with the addition of basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF). Extension of dendrites was also found from the surrounding cerebral cortex to the newly formed tissue, especially with the addition of bFGF and EGF. The present study showed that a new porous gelatin-siloxane hybrid had biocompatibility after implantation into a lesion of the central nervous system, and thus provided a potential scaffold for cell migration, angiogenesis and dendrite elongation with dose-dependent effects of additive bFGF and EGF.
Therapeutic Modulation of Microbiota-Host Metabolic Interactions (2012)

The complex metabolic relationships between the host and its microbiota change throughout life and vary extensively between individuals, affecting disease risk factors and therapeutic responses through drug metabolism. Elucidating the biochemical mechanisms underlying this human supraorganism symbiosis is yielding new therapeutic insights to improve human health, treat disease, and potentially modify human disease risk factors. Therapeutic options include targeting drugs to microbial genes or co-regulated host pathways and modifying the gut microbiota through diet, probiotic and prebiotic interventions, bariatric surgery, fecal transplants, or ecological engineering. The age-associated co-development of the host and its microbiota provides a series of windows for therapeutic intervention from early life through old age.
Ayahuasca in Adolescence: A Preliminary Psychiatric Assessment (2005)

Ayahuasca is believed to be harmless for those (including adolescents) drinking it within a religious setting. Nevertheless controlled studies on the mental/ psychiatric status of ritual hallucinogenic ayahuasca concoction consumers are still lacking. In this study, 40 adolescents from a Brazilian ayahuasca sect were compared with 40 controls matched on sex, age, and educational background for psychiatric symptomatology. Screening scales for depression, anxiety, alcohol consumption patterns (abuse), attentional problems, and body dysmorphic disorders were used. It was found that, compared to controls, considerable lower frequencies of positive scoring for anxiety, body dismorphism, and attentional problems were detected among ayahuasca-using adolescents despite overall similar psychopathological profiles displayed by both study groups. Low frequencies of psychiatric symptoms detected among adolescents consuming ayahuasca within a religious context may reflect a protective effect due to their religious affiliation. However further studies on the possible interference of other variables in the outcome are necessary.
Learning subjective nouns using extraction pattern bootstrapping (2003)

We explore the idea of creating a subjectivity classifier that uses lists of subjective nouns learned by bootstrapping algorithms. The goal of our research is to develop a system that can distinguish subjective sentences from objective sentences. First, we use two bootstrapping algorithms that exploit extraction patterns to learn sets of subjective nouns. Then we train a Naive Bayes classifier using the subjective nouns, discourse features, and subjectivity clues identified in prior research. The bootstrapping algorithms learned over 1000 subjective nouns, and the subjectivity classifier performed well, achieving 77% recall with 81% precision.
Ab initioand molecular dynamics predictions for electron and phonon transport in bismuth telluride (2008)

Phonon and electron transport in ${\mathrm{Bi}}_{2}{\mathrm{Te}}_{3}$ has been investigated using a multiscale approach, combining the first-principles calculations, molecular dynamics (MD) simulations, and Boltzmann transport equations (BTEs). Good agreements are found with the available experimental results. The MD simulations along with the Green-Kubo autocorrelation decay method are used to calculate the lattice thermal conductivity in both the in-plane and cross-plane directions, where the required classical interatomic potentials for ${\mathrm{Bi}}_{2}{\mathrm{Te}}_{3}$ are developed on the basis of first-principles calculations and experimental results. In the decomposition of the lattice thermal conductivity, the contributions from the short-range acoustic and optical phonons are found to be temperature independent and direction independent, while the long-range acoustic phonons dominate the phonon transport with a strong temperature and direction dependence (represented by a modified Slack relation). The sum of the short-range acoustic and optical phonon contribution is about $0.2\phantom{\rule{0.3em}{0ex}}\mathrm{W}∕\mathrm{m}\phantom{\rule{0.2em}{0ex}}\mathrm{K}$ and signifies the limit when the long-range transport is suppressed by nanostructure engineering. The electrical transport is calculated using the full-band structure from the linearized augmented plane-wave method, BTE, and the energy-dependent relaxation-time models with the nonparabolic Kane energy dispersion. Temperature dependence of the energy gap is found to be important for the prediction of electrical transport in the intrinsic regime. Appropriate modeling of relaxation times is also essential for the calculation of electric and thermal transport, especially in the intrinsic regime. The maximum of the Seebeck coefficient appears when the chemical potential approaches the band edge and can be estimated by a simple expression containing the band gap. The scatterings by the acoustic, optical, and polar-optical phonons dominate the electrical conductivity and electric thermal conductivity.
Shared MHC Class II–Dependent Melanoma Ribosomal Protein L8 Identified by Phage Display (2007)

Antigens recognized by T helper (Th) cells in the context of MHC class II molecules have vaccine potential against cancer and infectious agents. We have described previously a melanoma patient's HLA-DR7-restricted Th cell clone recognizing an antigen, which is shared among melanoma and glioma cells derived from various patients. Here, this antigen was cloned using a novel antigen phage display approach. The antigen was identified as the ribosomal protein L8 (RPL8). A peptide of RPL8 significantly stimulated proliferation and/or cytokine expression of the Th cell clone and lymphocytes in four of nine HLA-DR7(+) melanoma patients but not in healthy volunteers. The RPL8 antigen may represent a relevant vaccine target for patients with melanoma, glioma, and breast carcinoma whose tumors express this protein.
Breast cancer — one term, many entities? (2011)

Breast cancer, rather than constituting a monolithic entity, comprises heterogeneous tumors with different clinical characteristics, disease courses, and responses to specific treatments. Tumor-intrinsic features, including classical histological and immunopathological classifications as well as more recently described molecular subtypes, separate breast tumors into multiple groups. Tumor-extrinsic features, including microenvironmental configuration, also have prognostic significance and further expand the list of tumor-defining variables. A better understanding of the features underlying heterogeneity, as well as of the mechanisms and consequences of their interactions, is essential to improve targeting of existing therapies and to develop novel agents addressing specific combinations of features.
Automatic Image Annotation Using Adaptive Color Classification (1996)

We describe a system which automatically annotates images with a set of prespecified keywords, based on supervised color classification of pixels intoNprespecified classes using simple pixelwise operations. The conditional distribution of the chrominance components of pixels belonging to each class is modeled by a two-dimensional Gaussian function, where the mean vector and the covariance matrix for each class are estimated from appropriate training sets. Then, a succession of binary hypothesis tests with image-adaptive thresholds has been employed to decide whether each pixel in a given image belongs to one of the predetermined classes. To this effect, a universal decision threshold is first selected for each class based on receiver operating characteristics (ROC) curves quantifying the optimum “true positive” vs “false positive” performance on the training set. Then, a new method is introduced for adapting these thresholds to the characteristics of individual input images based on histogram cluster analysis. If a particular pixel is found to belong to more than one class, a maximuma posterioriprobability (MAP) rule is employed to resolve the ambiguity. The performance improvement obtained by the proposed adaptive hypothesis testing approach over using universal decision thresholds is demonstrated by annotating a database of 31 images.
One minute pulse operation in the TORE SUPRA tokamak (1993)

Deuterium plasmas with a current of 1 MA, having quasi-stationary conditions for one minute, were obtained in TORE SUPRA, a large superconducting tokamak. The plasma current was partially noninductively driven by a 2.5 MW, 62 s lower hybrid wave pulse, resulting in a high central electron temperature (5.5 keV) for a plasma with a central electron density of 3.5 × 1019 m-3
Chemistry of micelles series. 22. Cascade polymers: synthesis and characterization of four-directional spherical dendritic macromolecules based on adamantane (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry of micelles series. 22. Cascade polymers: synthesis and characterization of four-directional spherical dendritic macromolecules based on adamantaneGeorge R. Newkome, Ashutosh Nayak, Rajani K. Behera, Charles N. Moorefield, and Gregory R. BakerCite this: J. Org. Chem. 1992, 57, 1, 358–362Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/jo00027a061https://doi.org/10.1021/jo00027a061research-articleACS PublicationsRequest reuse permissionsArticle Views1346Altmetric-Citations129LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Conventional High Rate Well Completions: Limitations of Frac&Pack, High Rate Water Pack and Open Hole Gravel Pack Completions (1998)

Abstract New Deep Water completions in the Gulf of Mexico (GOM) are expected to produce over 20,000 bpd or more than 100 MMscf/d from reservoirs less than 200 ft thick. At these high flow rates (100 bpd/ft, 500 Mscf/d/ft) turbulence in the gravel filled perforations starts to play a significant role. This study attempts to assess which type of completion is most suited for these high rate wells. Frac&amp;Pack (F&amp;P) completions are compared with High Rate Water Packs (HRWP) and Open Hole Gravel Packs (OHGP). Both Oil wells and Gas wells are analyzed. The concept that, in cased hole gravel packed completions, the main source of damage is in the perforation tunnels (casing and cement sheath) has been used to build inflow models for each completion type. These models use standard inflow equations for radial flow in the reservoir and linear flow in the perforation tunnel. This inflow model was matched to field data for HRWP and F&amp;P completions by changing the effective number of perforations flowing as well as the average gravel permeability in these perforations. For OHGP completions no detailed field data was available and general completion assumptions were used as inputs to estimate the inflow performance. Results generated from these field calibrated models, in the predictive mode, show that for high rate gas wells (&amp;gt; 500 Mscf/d per ft of perforations), where the high pressure drops in the perforation tunnel dominates the inflow, the benefits of fracturing the formation diminishes for reservoirs with permeabilities greater than 150 mD. Above 150 mD. a HRWP become more efficient than a F&amp;P. At reservoir permeabilities above 600 mD OHGP's however may become more efficient. In high rate oil wells (&amp;gt; 100 bpd/ft perfs) the total pressure drop is not so much dominated by the perforation tunnel. Hence the benefits of fracturing the formation continue to a permeability of 900 mD before OHGP becomes more efficient. The field matches suggest that F&amp;P completions in general only have 0.7 to 2.3 shots per foot (spf) flowing with an average gravel permeability of no more than 17 Darcy. For HRWP it is found that more perforations are flowing (5 spf) and that the average gravel permeability is still high (13.6 Darcy).
Rail Component Detection, Optimization, and Assessment for Automatic Rail Track Inspection (2013)

In this paper, we present a real-time automatic vision-based rail inspection system, which performs inspections at 16 km/h with a frame rate of 20 fps. The system robustly detects important rail components such as ties, tie plates, and anchors, with high accuracy and efficiency. To achieve this goal, we first develop a set of image and video analytics and then propose a novel global optimization framework to combine evidence from multiple cameras, Global Positioning System, and distance measurement instrument to further improve the detection performance. Moreover, as the anchor is an important type of rail fastener, we have thus advanced the effort to detect anchor exceptions, which includes assessing the anchor conditions at the tie level and identifying anchor pattern exceptions at the compliance level. Quantitative analysis performed on a large video data set captured with different track and lighting conditions, as well as on a real-time field test, has demonstrated very encouraging performance on both rail component detection and anchor exception detection. Specifically, an average of 94.67% precision and 93% recall rate has been achieved for detecting all three rail components, and a 100% detection rate is achieved for compliance-level anchor exception with three false positives per hour. To our best knowledge, our system is the first to address and solve both component and exception detection problems in this rail inspection area.
Evolution and Protein Packaging of Small-Molecule RNA Aptamers (2011)

A high-affinity RNA aptamer (K(d) = 50 nM) was efficiently identified by SELEX against a heteroaryldihydropyrimidine structure, chosen as a representative drug-like molecule with no cross reactivity with mammalian or bacterial cells. This aptamer, its weaker-binding variants, and a known aptamer against theophylline were each embedded in a longer RNA sequence that was encapsidated inside a virus-like particle by a convenient expression technique. These nucleoprotein particles were shown by backscattering interferometry to bind to the small-molecule ligands with affinities similar to those of the free (nonencapsidated) aptamers. The system therefore comprises a general approach to the production and sequestration of functional RNA molecules, characterized by a convenient label-free analytical technique.
CD28 and secretory immunoglobulin A‐dependent activation of eosinophils: inhibition of mediator release by the anti‐allergic drug, suplatast tosilate (2004)

Through inhibition of chemotaxis, IPD-1151T might limit the number of eosinophils at the inflammation site. Furthermore, it could reduce the pathological potential of eosinophils by inhibiting the release of ROS and cationic proteins, main inflammatory mediators produced by eosinophils. Moreover, the inhibition of immunoregulatory cytokines released by eosinophils could locally modify the immune response.
The sequence of 28S ribosomal RNA varies within and between human cell lines (1993)

The primary structure of 28S ribosomal RNA constitutes a conserved core which is similar among most 23S-like rRNAs and expansion segments which occur at specific positions in the sequence. The expansion segments account for most of the size difference between prokaryotic (archaeal and eubacterial) and eukaryotic rRNAs and they exhibit a sequence variation which is unique among rRNAs. We have investigated the sequence variation of one of the expansion segments, V8, by sequencing a total of 111 V8 segments from 9 different human cell lines and tissues and have found 35 different variants. The variation occur mainly at two 'hot spots' which are separated by 170 nucleotides in the primary sequence but are neighbours in the secondary structure. The sequence of V8 segments varies both within and between human cell lines and tissues. The implications for the evolution of the eukaryotic 28S rRNA are discussed together with possible functions of the expansion segments. We also present a secondary structure model for the V8 segment based on comparative sequence analysis and chemical and enzymatic foot printing.