gebhart/patrepeval huggingface dataset:
Involvement of the PI 3-kinase signaling pathway in progression of colon adenocarcinoma (2003)

The phosphoinositide 3-kinase (PI 3-kinase) signaling pathway has been shown to play a pivotal role in intracellular signal transduction pathways involved in cell growth, cellular transformation and tumorigenesis. Analysis of several colon adenocarcinoma cell lines indicates that the PI 3-kinase signaling pathway is up-regulated in colon cancers. In particular, the protein levels and phosphorylation status of Akt and p70 S6 kinase are up-regulated in colon adenocarcinoma cell lines. More significantly, we have demonstrated for the first time that the phosphorylation of FKHR, a downstream target of Akt, is increased in these cell lines. Intriguingly, phosphorylation of three components of the PI 3-kinase signaling pathway, namely Akt, p70 S6 kinase and FKHR, are in direct correlation with the degree of tumorigenic potential of the colon cell lines tested. No differences in the protein levels of the two subunits of PI 3-kinase, p85 and p110alpha, and PTEN were noted. Real-time quantitative PCR indicated an increase in levels of Akt message only, and not of the other signaling pathway components. Inhibition of the PI 3-kinase with wortmannin decreased the anchorage-independent growth of colon cells in a soft agar assay. Hence, the components of the PI 3-kinase signaling pathway could serve as potential candidates for drug development in treatment of colon cancer.
Development and Evaluation of An Adaptive Transit Signal Priority System Using Connected Vehicle Technology (2014)

Transit signal priority (TSP) can be a very effective preferential treatment for transit vehicles in congested urban networks. There are two problems with the current practice of the transit signal priority. First, random bus arrival time is not sufficiently accounted for, which’ve become the major hindrance in practice for implementing active or adaptive TSP strategies when a near-side bus stop is present. Secondly, most research focuses on providing bus priority at local intersection level, but bus schedule reliability should be achieved at route level and relevant studies have been lacking.\n\nIn the first part of this research, a stochastic mixed-integer nonlinear programming (SMINP) model is developed to explicitly to account for uncertain bus arrival time. A queue delay algorithm is developed as the supporting algorithm for SMINP to capture the delays caused by the interactions between vehicle queues and buses entering and exiting near-side bus stops. A concept of using signal timing deviations to approximate the impacts of TSP operations on other traffic is proposed for the first time in this research. In the second part of the research, the deterministic version of the SMINP model is extended to the arterial setting, where a route-based TSP (R-TSP) model is develop to optimize for schedule-related bus performances on the corridor level. The R-TSP model uses the real-time data available only from the connected vehicle communications technology.\n\nBased on the connected vehicle technology, a real-time signal control system that implements the proposed TSP models is prototyped in the simulation environment. The connected vehicle technology is also used as the main detection and monitoring mechanism for the real-time control of the adaptive TSP signal system. The adaptive TSP control module is designed as a plug-in module that is envisioned to work with a modern fixed-time or adaptive signal controller with connected vehicle communications capabilities.\n\nUsing this TSP-enabled signal control system, simulation studies were carried out in both a single intersection setting and a five-intersection arterial setting. The effectiveness of the SMINP model to handle uncertain bus arrival time and the R-TSP model to achieve corridor-level bus schedule reliability were studied. Discussions, conclusions and future research on the topic of adaptive TSP models were made.
Senescent cells as a source of inflammatory factors for tumor progression (2010)

Cellular senescence, which is associated with aging, is a process by which cells enter a state of permanent cell cycle arrest, therefore constituting a potent tumor suppressive mechanism. Recent studies show that, despite the beneficial effects of cellular senescence, senescent cells can also exert harmful effects on the tissue microenvironment. The most significant of these effects is the acquisition of a senescent-associated secretory phenotype (SASP), which entails a striking increase in the secretion of pro-inflammatory cytokines. Here, we summarize our knowledge of the SASP and the impact it has on tissue microenvironments and ability to stimulate tumor progression.
New Synthetic Methods for Carbocyclic and Heterocyclic Compounds Bearing Phosphonate Moiety with Biological Significances (1993)

Abstract New synthetic routes leading to various derivatives of cyclopropane. pyrrole, indole, and isoxazoline with phosphonate moiety are described.
T-ray tomography (1997)

We demonstrate tomographic T-ray imaging, using the timing information present in terahertz (THz) pulses in a reflection geometry. THz pulses are reflected from refractive-index discontinuities inside an object, and the time delays of these pulses are used to determine the positions of the discontinuities along the propagation direction. In this fashion a tomographic image can be constructed.
Synthesis and membrane action of polymyxin B analogues (2005)

We have designed synthetic peptides that mimic the primary and secondary structure of the cationic lipopeptide antibiotic polymyxin B (PxB) in order to determine the structural requirements for membrane action and to assess possible therapeutic potential. Two analogues with related sequences to that of PxB, but including synthetic simplifications (disulphide bridge between two cysteines in positions 4 and 10, N-terminal nonanoic acid), have been synthesized. Peptide-lipid interactions have been studied by fluorescence resonance energy transfer between pyrene and 4,4-difluoro-5-methyl-4-bora-3alpha,4alpha-diaza-s-indacene-3-dodecanoyl (BODIPY)probes covalently linked to phospholipids, and the possibility of membrane disruption or permeabilization has been assessed by light scattering and fluorescence quenching assays. The synthetic peptide sP-B, which closely mimics the primary and secondary structures of PxB, binds to vesicles of anionic 1-palmitoyl-2-oleoylglycero-sn-3-phosphoglycerol (POPG) or of lipids extracted from Escherichia coli membranes, and induces apposition of the vesicles and selective lipid exchange without permeabilization of the membrane. We conclude that sP-B forms functional vesicle-vesicle contacts that are selective, as previously described for PxB. The second analogue, sP-C, has a permutation of two amino acids that breaks the hydrophobic patch formed by D-Phe and Leu residues on the cyclic part of the sequence. sP-C lipopeptide is more effective than sP-B in inducing lipid mixing, but shows no selectivity for the lipids that exchange through the vesicle-vesicle contacts, and at high concentrations has a membrane-permeabilizing effect. The deacylated and non-antibiotic derivative PxB-nonapeptide (PxB-NP) does not induce the formation of functional intervesicle contacts in the range of concentrations studied.
Tunable Magneto-Dielectric Polymer Nanocomposites for Microwave Applications (2010)

Magneto-dielectric polymer nanocomposites are investigated as a new class of functional materials well suited for RF and microwave device applications. Magnetite ( <b xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Fe</b> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> <b xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</b> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> ) nanoparticles are homogeneously dispersed in a polymer matrix, which exhibits low losses at microwave frequencies. The monodispersion of the magnetic nanoparticles, with sub-10-nm diameters and tight size distribution, enhances the microwave properties of the engineered composite material by increasing the relative permeability and relative permittivity. Moreover, complex permeability and permittivity of the nanocomposite material can be tuned by an externally applied dc magnetic field with a strength that is achievable with commercial permanent magnets. Multilayered microstrip test fixtures and preexisting measurement techniques were conjointly implemented to extract the microwave properties of the nanocomposite material in the frequency range between 1-6 GHz. The measured data revealed tunability of 5.5% in the permittivity, 37% in the permeability, and more than <b xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">100</b> × reduction in the loss tangent at specific frequencies under externally applied magnetic fields.
Local Botulinum Toxin Type A Injections in the Treatment of Spastic Toes (2002)

Botulinum toxin type A treatment using doses based on spasticity severity seems to be safe and effective in the treatment of spastic toes, and further study is warranted.
IMPROVING VIABILITY OF FREEZE-DRIED LACTIC ACID BACTERIA USING LYOPROTECTANTS IN COMBINATION WITH OSMOTIC AND COLD ADAPTATION (2007)

ABSTRACT  Effect of lyoprotectants on survival of Lactococcus lactis and Lactobacillus sakei after freeze drying was investigated. Their survivals in 9.1% w/w of skim milk, soy milk, egg yolk, sucrose, lactose, glucose, trehalose and sorbitol were compared, and the protectants caused high viability were selected to develop formulations of mixed protectants. Compared to soy milk and sorbitol, higher viability of L. lactis was observed with lactose, skim milk and sucrose. For freeze-dried L. sakei, the survival in skim milk and soy milk was greater than that in trehalose, sucrose and lactose. Among all protectants tested, glucose and egg yolk provided the lowest protection to these bacteria. Of all lyoprotectant formulations, the highest number of L. lactis  survivors was found in mixed lyoprotectants containing 3.97 g lactose, 3.97 g sucrose, 3.97 g trehalose, 8.73 g skim milk and 79.36 g distilled water. The protectant mixture provided the highest viability of L. sakei contained 3.97 g lactose, 3.97 g sucrose, 3.97 g trehalose, 8.73 g skim milk and 79.40 g soy milk with distilled water (1:1). Compared to single protectant, the number of L. lactis and L. sakei survivors in these formulations was increased by 11.69-20.15% and 9.51-18.15%, respectively. To improve viability, osmotic adaptation alone (with 0.3 M sucrose) or in combination with cold adaptation (10°C) induced cross-protection of L. lactis and L. sakei in selected protectant mixtures after freeze drying and storage for 28 days at -80°C were studied. These adaptation treatments did not provide protection of L. lactis and L. sakei cells after freeze drying and storage.
Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain (2015)

Sequencing of a bulk polymerase chain reaction (PCR) product to identify drug resistance mutations informs antiretroviral therapy selection but has limited sensitivity for minority variants. Alternatively, deep sequencing is capable of detecting minority variants but is subject to sequencing errors and PCR resampling due to low input templates. We screened for resistance mutations among 184 HIV-1-infected, therapy-naive subjects using the 454 sequencing platform to sequence two amplicons spanning HIV-1 reverse transcriptase codons 34-245. Samples from 19 subjects were also analyzed using the MiSeq sequencing platform for comparison. Errors and PCR resampling were addressed by tagging each HIV-1 RNA template copy (i.e., cDNA) with a unique sequence tag (Primer ID), allowing a consensus sequence to be constructed for each original template from resampled sequences. In control reactions, Primer ID reduced 454 and MiSeq errors from 71 to 2.6 and from 24 to 1.2 errors/10,000 nucleotides, respectively. MiSeq also allowed accurate sequencing of codon 65, an important drug resistance position embedded in a homopolymeric run that is poorly resolved by the 454 platform. Excluding homopolymeric positions, 14% of subjects had evidence of ≥1 resistance mutation among Primer ID consensus sequences, compared to 2.7% by bulk population sequencing. When calls were restricted to mutations that appeared twice among consensus sequence populations, 6% of subjects had detectable resistance mutations. The use of Primer ID revealed 5-15% template utilization on average, limiting the depth of deep sequencing sampling and revealing sampling variation due to low template utilization. Primer ID addresses important limitations of deep sequencing and produces less biased estimates of low-level resistance mutations in the viral population.
IL-18 accounts for both TNF-alpha- and Fas ligand-mediated hepatotoxic pathways in endotoxin-induced liver injury in mice (1997)

When LPS is administered to heat-killed Propionibacterium acnes-primed BALB/c nude mice, they develop endotoxin-induced liver injury. As previously reported, this liver injury can be prevented by treatment with an Ab against IL-18, a novel cytokine with the ability to induce IFN-gamma production and up-regulate functional Fas ligand (FasL) expression. To identify the pathologic role of IL-18 in this liver injury, we investigated the hepatic cytokine network and FasL induction after LPS challenge. After LPS challenge to BALB/c nude mice, their livers expressed IL-12 mRNA, followed by the induction of IFN-gamma and FasL mRNA and then by the late elevation of TNF-alpha mRNA, but stably expressed IL-18 mRNA. The TNF-alpha induction curve had two peaks. The first peak was the result of the direct reaction to LPS, and the late peak might have been induced, since P. acnes-elicited Kupffer cells showed one-peak TNF-alpha kinetics in response to LPS stimulation in vitro. LPS-activated P. acnes-elicited Kupffer cells secreted both IL-12 and IL-18, as determined by ELISA and bioassay, respectively. The in vivo administration of anti-IL-18 just before an LPS challenge suppressed not only the induction of IFN-gamma and the late TNF-alpha elevation, but also the FasL induction, resulting in the total prevention of liver injury, whereas such an anti-IL-12 treatment did not. Anti-IFN-gamma treatment reduced the late increase in TNF-alpha, but not FasL, resulting in a partial prevention of the liver injury. The administration of anti-TNF-alpha just before elevation of the late TNF-alpha peak also markedly, but incompletely, suppressed the LPS-induced liver injury. These data suggested that IL-18 activates both TNF-alpha- and FasL-mediated hepatocytotoxic pathways in endotoxin-induced liver injury.
The Lithium-Ethylenediamine System. II. Isomerization of Olefins and Dehydrogenation of Cyclic Dienes1,2 (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Lithium-Ethylenediamine System. II. Isomerization of Olefins and Dehydrogenation of Cyclic Dienes1,2LESLIE REGGEL, SIDNEY FRIEDMAN, and IRVING WENDERCite this: J. Org. Chem. 1958, 23, 8, 1136–1139Publication Date (Print):August 1, 1958Publication History Published online1 May 2002Published inissue 1 August 1958https://pubs.acs.org/doi/10.1021/jo01102a014https://doi.org/10.1021/jo01102a014research-articleACS PublicationsRequest reuse permissionsArticle Views280Altmetric-Citations43LEARN 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
Encoding Complex Wettability Patterns in Chemically Functionalized 3D Photonic Crystals (2011)

Much of modern technology--from data encryption to environmental sensors to templates for device fabrication--relies on encoding complex chemical information in a single material platform. Here we develop a technique for patterning multiple chemical functionalities throughout the inner surfaces of three-dimensional (3D) porous structures. Using a highly ordered 3D photonic crystal as a regionally functionalized porous carrier, we generate complex wettability patterns. Immersion of the sample in a particular fluid induces its localized infiltration and disappearance of the bright color in a unique spatial pattern dictated by the surface chemistry. We use this platform to illustrate multilevel message encryption, with selective decoding by specific solvents. Due to the highly symmetric geometry of inverse opal photonic crystals used as carriers, a remarkable selectivity of wetting is observed over a very broad range of fluids' surface tensions. These properties, combined with the easily detectable optical response, suggest that such a system could also find use as a colorimetric indicator for liquids based on wettability.
Antiangiogenic drugs in ovarian cancer (2009)

Phase II clinical trial data provide strong support for the suggestion that antiangiogenic agents have the potential to play a major therapeutic role in this difficult malignancy. It is reasonable to acknowledge that the pending results of several ongoing evidence-based randomized Phase III trials that directly explore the clinical utility of this strategy may substantially alter the current standard management approaches in advanced ovarian cancer.
OX40 costimulation by a chimeric antigen receptor abrogates CD28 and IL-2 induced IL-10 secretion by redirected CD4+T cells (2012)

Adoptive therapy with chimeric antigen receptor (CAR) redirected T cells recently showed remarkable anti-tumor efficacy in early phase clinical trials; self-repression of the immune response by T-cell secreted cytokines, however, is still an issue raising interest to abrogate the secretion of repressive cytokines while preserving the panel of CAR induced pro-inflammatory cytokines. We here revealed that T-cell activation by a CD28-ζ signaling CAR induced IL-10 secretion, which compromises T cell based immunity, along with the release of pro-inflammatory IFN-γ and IL-2. T cells stimulated by a ζ CAR without costimulation did not secrete IL-2 or IL-10; the latter, however, could be induced by supplementation with IL-2. Abrogation of CD28-ζ CAR induced IL-2 release by CD28 mutation did not reduce IL-10 secretion indicating that IL-10 can be induced by both a CD28 and an IL-2 mediated pathway. In contrast to the CD28-ζ CAR, a CAR with OX40 (CD134) costimulation did not induce IL-10. OX40 cosignaling by a 3rd generation CD28-ζ-OX40 CAR repressed CD28 induced IL-10 secretion but did not affect the secretion of pro-inflammatory cytokines, T-cell amplification or T-cell mediated cytolysis. IL-2 induced IL-10 was also repressed by OX40 co-signaling. OX40 moreover repressed IL-10 secretion by regulatory T cells which are strong IL-10 producers upon activation. Taken together OX40 cosignaling in CAR redirected T cell activation effectively represses IL-10 secretion which contributes to counteract self-repression and provides a rationale to explore OX40 co-signaling CARs in order to prolong a redirected T cell response.
Decreased glucocorticoid receptor activity following glucocorticoid receptor antisense RNA gene fragment transfection. (1991)

Depression is often characterized by increased cortisol secretion caused by hyperactivity of the hypothalamic-pituitary-adrenal axis and by nonsuppression of cortisol secretion following dexamethasone administration. This hyperactivity of the hypothalamic-pituitary-adrenal axis could result from a reduced glucocorticoid receptor (GR) activity in neurons involved in its control. To investigate the effect of reduced neuronal GR levels, we have blocked cellular GR mRNA processing and/or translation by introduction of a complementary GR antisense RNA strand. Two cell lines were transfected with a reporter plasmid carrying the chloramphenicol acetyltransferase (CAT) gene under control of the mouse mammary tumor virus long terminal repeat (a glucocorticoid-inducible promoter). This gene construction permitted assay of the sensitivity of the cells to glucocorticoid hormones. Cells were also cotransfected with a plasmid containing 1,815 bp of GR cDNA inserted in the reverse orientation downstream from either a neurofilament gene promoter element or the Rous sarcoma virus promoter element. Northern (RNA) blot analysis demonstrated formation of GR antisense RNA strands. Measurement of the sensitivity of CAT activity to exogeneous dexamethasone showed that although dexamethasone increased CAT activity by as much as 13-fold in control incubations, expression of GR antisense RNA caused a 2- to 4-fold decrease in the CAT response to dexamethasone. Stable transfectants bearing the GR antisense gene fragment construction demonstrated a 50 to 70% decrease of functional GR levels compared with normal cells, as evidenced by a ligand-binding assay with the type II glucocorticoid receptor-specific ligand [3H]RU 28362. These results validate the use of antisense RNA to GR to decrease cellular response to glucocorticoids.
Rheology and microstructure of dense suspensions of plate-shaped colloidal particles (1999)

The flow properties and microstructure of dense kaolin clay suspensions are explored for volume fractions, φ, as large as 0.39. To avoid flocculation these particles were suspended in pH 10 buffer solutions where edge–face interactions are negligible. These plate-shaped particles have an aspect ratio of 10–12 and, thus, are likely to show alignment above a critical volume fraction φ* > 0.10. At low φ, the suspensions are Newtonian but show substantial orientation with increased shear rate. As φ is increased, the suspensions develop a yielding type of behavior. In the concentrated region φ > φ*, elastic moduli are a function of the previously applied shear rate, γ̇, decreasing from a low shear rate plateau of G′(0) to a high shear rate plateau of G′(∞). We interpret the modulus behavior as being a consequence of changes in alignment of domains in the suspension. Conductivity and x-ray scattering measurements confirm that particle alignment increases with increasing shear rate. The normalized modulus value, Gnorm′=[G′(γ̇)−G′(∞)]/[G′(0)−G′(∞)], is independent of φ indicating that the characteristic alignment shear rate is independent of volume fraction. Conductivities and x-ray scattering intensities normalized in the same manner are also independent of the volume fraction, and superimpose on the modulus data. Surprisingly, these data indicate that fractional particle alignment at a given shear rate is independent of φ for 0.05 < φ < 0.39.
Highly Ordered Assemblies of Au Nanoparticles Organized on DNA (2003)

We developed a simple method for highly ordered assemblies of gold nanoparticles (AuNPs) along DNA molecules on substrates, and achieved assemblies with well-aligned and long-range order by using well-stretched DNA templates. In addition, oxidized aniline-capped AuNPs (AN−AuNPs) prepared in this study were strongly attached to DNA. Two different assembly methods were carried out, and consequently continuous depositions and necklace-like depositions of AN−AuNPs along DNA molecules were achieved.