gebhart/patrepeval huggingface dataset:
PROTEOMIC ANALYSIS TO IDENTIFY BIOMARKER PROTEINS IN PANCREATIC DUCTAL ADENOCARCINOMA (2008)

Differentially expressed 25 proteins in PDAC were identified using proteomic analysis and five proteins related to carcinogenesis were validated by western blot analysis. Galectin-1 expression was highly correlated to tumour histology and stage.
Beacon-Stuffing: Wi-Fi without Associations (2007)

The design of Wi-Fi networks mimics the behavior of wired networks. For example, a Wi-Fi network interface can send and receive packets only after associating to a Wi-Fi access point (AP). In this paper, we show that the concept of association limits the capabilities of wireless networks. We present a scheme, called beacon-stuffing, that allows Wi-Fi clients to communicate without associating to any network. Beacon-stuffing enables several new applications over Wi-Fi networks, and we describe three of them in this paper: improved AP selection, delivering location-specific advertisements, and providing coupons over Wi-Fi networks without requiring the Wi-Fi client to associate to any AP.
Formation of 2-phenylethanol from styrene in the presence of zeolites and UV irradiation (1999)

2-Phenylethanol is formed via an in situ multistep reaction by irradiation of styrene in the presence of silica–alumina compounds such as zeolites in aqueous and methanolic systems; the first step is presumably an oxidation.
Poisson image editing (2003)

Using generic interpolation machinery based on solving Poisson equations, a variety of novel tools are introduced for seamless editing of image regions. The first set of tools permits the seamless importation of both opaque and transparent source image regions into a destination region. The second set is based on similar mathematical ideas and allows the user to modify the appearance of the image seamlessly, within a selected region. These changes can be arranged to affect the texture, the illumination, and the color of objects lying in the region, or to make tileable a rectangular selection.
Quantification of microRNA Expression with Next‐Generation Sequencing (2013)

Rapid advancement of next-generation sequencing technologies has made it possible to study expression profiles of microRNAs (miRNAs) comprehensively and efficiently. Multiplexing miRNA libraries by barcoding can significantly reduce sequencing cost per sample without compromising library quality. This unit provides a step-by-step protocol for isolating miRNAs and constructing multiplexed miRNA libraries. Also described is a custom computational pipeline for analyzing the multiplexed miRNA library sequencing reads generated by Illumina-based technology.
Slotted waveguide arrays for collecting near-field scattering data (2014)

We introduce a novel system for collecting near-field scattering data. The system utilizes a combination of rectangular waveguides and printed-circuit-boards, consisting of several field collection slots. Data collection is based on the modulated scattering technique. A prototype system using four waveguides was fabricated and tested in both air and water. Simulation and measurement results show that the system can detect field changes at the slot locations.
THE HEPARIN-BINDING (FIBROBLAST) GROWTH FACTOR FAMILY OF PROTEINS (1989)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries (2000)

A method is presented for the preparation and use of fluorogenic peptide substrates that allows for the configuration of general substrate libraries to rapidly identify the primary and extended specificity of proteases. The substrates contain the fluorogenic leaving group 7-amino-4-carbamoylmethylcoumarin (ACC). Substrates incorporating the ACC leaving group show kinetic profiles comparable to those with the traditionally used 7-amino-4-methylcoumarin (AMC) leaving group. The bifunctional nature of ACC allows for the efficient production of single substrates and substrate libraries by using 9-fluorenylmethoxycarbonyl (Fmoc)-based solid-phase synthesis techniques. The approximately 3-fold-increased quantum yield of ACC over AMC permits reduction in enzyme and substrate concentrations. As a consequence, a greater number of substrates can be tolerated in a single assay, thus enabling an increase in the diversity space of the library. Soluble positional protease substrate libraries of 137, 180 and 6,859 members, possessing amino acid diversity at the P4-P3-P2-P1 and P4-P3-P2 positions, respectively, were constructed. Employing this screening method, we profiled the substrate specificities of a diverse array of proteases, including the serine proteases thrombin, plasmin, factor Xa, urokinase-type plasminogen activator, tissue plasminogen activator, granzyme B, trypsin, chymotrypsin, human neutrophil elastase, and the cysteine proteases papain and cruzain. The resulting profiles create a pharmacophoric portrayal of the proteases to aid in the design of selective substrates and potent inhibitors.
Health issues with virtual reality displays (1997)

During the late 1980s and early 1990s virtual reality (VR) technology enjoyed a prolonged honeymoon with the international media who presented a glossy futuristic image of the technology. It was inevitable that the media would eventually tire of this image and look for new journalistic angles, such as the negative effects of VR. Some speculation then ensued about the negative social consequences of VR in the public domain ("Social autism" and "The end of civilisation as we know it&amp;hellip;" --- Stone, 1992, BBC Horizon), although these speculations now appear unfounded.The first direct assertion, in the international media, that there might be visual safety issues with VR technology, came from the reporting of findings from Mon-Williams, Wann and Rushton in 1993 [5]. Since then a steady trickle of media features have strongly hinted at virtual problems that may arise (e.g. Business Week, July 10, 1995; New Scientist, Jan 27, 1996), each being followed by accusations of "scare-mongering" from some sectors of the VR community. Our research findings have fueled some of the negative reports, and our position has angered some VR protagonists. Also, like other research groups in this field, we are often approached by journalists in pursuit of a sensationalist story.Hence we think it is timely to examine what we know about the effects of virtual reality displays; what we don't know about virtual reality displays; and what research should be undertaken to resolve the unknown issues.
A model for the detection of motion over time (2002)

A model is proposed for the incremental estimation of visual motion fields from image sequences. The authors' model exploits three standard constraints on image motion within an optimization framework: (1) data conservation-the intensity structure of a surface patch changes gradually over time; (2) spatial coherence-neighboring points have similar motions; and (3) temporal coherence-the image velocity of a surface patch changes gradually. The authors' formulation takes into account the possibility of multiple motions at a particular location. They present an incremental scheme for the minimization of the objective function, based on simulated annealing. All computations are parallel, local, and incremental, and occlusion and disocclusion boundaries are estimated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Dysfunction of Organic Anion Transporting Polypeptide 1a1 Alters Intestinal Bacteria and Bile Acid Metabolism in Mice (2012)

Organic anion transporting polypeptide 1a1 (Oatp1a1) is predominantly expressed in liver and is able to transport bile acids (BAs) in vitro. Male Oatp1a1-null mice have increased concentrations of taurodeoxycholic acid (TDCA), a secondary BA generated by intestinal bacteria, in both serum and livers. Therefore, in the present study, BA concentrations and intestinal bacteria in wild-type (WT) and Oatp1a1-null mice were quantified to investigate whether the increase of secondary BAs in Oatp1a1-null mice is due to alterations in intestinal bacteria. The data demonstrate that Oatp1a1-null mice : (1) have similar bile flow and BA concentrations in bile as WT mice; (2) have a markedly different BA composition in the intestinal contents, with a decrease in conjugated BAs and an increase in unconjugated BAs; (3) have BAs in the feces that are more deconjugated, desulfated, 7-dehydroxylated, 3-epimerized, and oxidized, but less 7-epimerized; (4) have 10-fold more bacteria in the small intestine, and 2-fold more bacteria in the large intestine which is majorly due to a 200% increase in Bacteroides and a 30% reduction in Firmicutes; and (5) have a different urinary excretion of bacteria-related metabolites than WT mice. In conclusion, the present study for the first time established that lack of a liver transporter (Oatp1a1) markedly alters the intestinal environment in mice, namely the bacteria composition.
Continuous microcellular polystyrene foam extrusion with supercritical CO2 (2002)

Abstract The continuous production of polystyrene microcellular foams with supercritical CO 2 was achieved on a two‐stage single‐screw extruder. Simulations related to the foaming process were accomplished by modeling the phase equilibria with the Sanchez‐Lacombe equation of state and combining the equations of motion, the energy balance, and the Carreau viscosity model to characterize the flow field and pressure distribution in the die. The position of nucleation in the die was determined from the simulation results via a computational fluid dynamics code (FLUENT). Experimental parameters were selected according to the T g and phase equilibria. The effects of CO 2 concentration and die pressure are explored. Below the solubility limit, higher CO 2 concentrations lead to smaller cell size and greater cell density. With an increase of die pressure, the cell size decreases and the cell density increases.
Contributions of Individual Muscles to the Submental Surface Electromyogram During Swallowing (1999)

Submental surface electromyographic recordings are commonly used in the investigation of swallowing disorders. The measured electromyography is thought to reflect the actions of floor-of-mouth muscles. Although this is a reasonable assumption, to date there have been no investigations to delineate which muscles contribute to this surface recording. The primary goal of this experiment was to determine which muscles contribute most to the submental surface. Electromyography was recorded simultaneously from the submental surface as well as from five individual muscles: mylohyoid, anterior belly of the digastric, geniohyoid, genioglossus and platysma. Three analysis methods were performed to estimate individual muscle contributions: correlation, numeric, and analytic. For the numeric and analytic analyses, a linear model was defined and used to represent the relationship between the surface and intramuscular recordings. Muscles that received a high correlation, numeric and/or analytic value were considered to be primary contributors to the submental recording. Regardless of analysis approach, the primary contributions to the submental surface recording were the mylohyoid, anterior belly of the digastric, and the geniohyoid muscles. Contributions from the genioglossus and the platysma muscles were minimal. Contributions as a function of bolus volume and viscosity are also discussed.
ADP-ribosylation of nuclear proteins in vivo. Identification of histone H2B as a major acceptor for mono- and poly(ADP-ribose) in dimethyl sulfate-treated hepatoma AH 7974 cells. (1984)

Nuclear mono- and poly(ADP-ribosyl) protein conjugates formed in living hepatoma AH 7974 cells in response to treatment with the alkylating agent dimethyl sulfate have been studied. They were isolated from the perchloric acid precipitate of freshly prepared nuclei in a relatively pure form and with an overall yield of more than 80%, utilizing aminophenylboronic acid-agarose chromatography. Exposure of the cells to 400 microM dimethyl sulfate led to a transient rise of ADP-ribosylated proteins. After 20 min, the level of endogenous poly(ADP-ribosyl) residues increased by a factor of 21, amounting to a final value of 772 +/- 57 pmol/mg of DNA while the mono(ADP-ribosyl) residues were raised to even higher concentrations (1864 pmol/mg of DNA), corresponding to a 12-fold stimulation as compared to untreated cells. As a result of dimethyl sulfate treatment, the amount of acceptor protein being modified by (ADP-ribose)n was elevated 15-fold, reaching a final proportion of 2.3 +/- 0.4% of total nuclear protein. The increase in (ADP-ribosyl)n-modified proteins was suppressed by benzamide, a potent inhibitor of poly(ADP-ribose) synthetase. More than half of the nuclear mono- and poly(ADP-ribosyl) residues were linked to histone H2B. The modifying residues could be removed from the major acceptor by treatment with 0.1 M NaOH, but not with neutral hydroxylamine. Minor amounts of other histones, especially of histone H4, were possibly also ADP-ribosylated under the stimulating effect of dimethyl sulfate. In addition, several nonhistone proteins with apparent molecular masses of 100-116 and 170 kDa were found to carry substantial amounts of mono- and poly(ADP-ribose).
Transforming Growth Factor β1 Decreases Cholesterol Supply to Mitochondria via Repression of Steroidogenic Acute Regulatory Protein Expression (1998)

Transforming growth factor-betas (TGF-betas) constitute a family of dimeric proteins that affect growth and differentiation of many cell types. TGF-beta1 has also been proposed to be an autocrine regulator of adrenocortical steroidogenesis, acting mainly by decreasing the expression of cytochrome P450c17. Here, we demonstrate that TGF-beta1 has a second target in bovine adrenocortical cells, namely the steroidogenic acute regulatory protein (StAR). Indeed, supplying cells with steroid precursors revealed that TGF-beta1 inhibited two steps in the steroid synthesis pathway, one prior to pregnenolone production and another corresponding to P450c17. More specifically, TGF-beta1 inhibited pregnenolone production but neither the conversion of 25-hydroxycholesterol to pregnenolone nor P450scc activity. Thus, TGF-beta1 must decrease the cholesterol supply to P450scc. We therefore examined the effect of TGF-beta1 on the expression of StAR, a mitochondrial protein implicated in intramitochondrial cholesterol transport. TGF-beta1 decreased the steady state level of StAR mRNA in a time- and concentration-dependent manner. This inhibition occurs at the level of StAR transcription and depends on RNA and protein synthesis. It is likely that the TGF-beta1-induced decrease of StAR expression that we report here may be expanded to other steroidogenic cells in which a decrease of cholesterol accessibility to P450scc by TGF-beta1 has been hypothesized.
Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction tools (2007)

A heuristic-based method of combining the results of the individual tools better facilitates the scanning of large proteomes for potential epitopes, yielding more actual high-affinity binders while reporting very few false positives.
Chemistry of heterocyclic compounds. 26. Synthesis and reactions of multiheteromacrocycles possessing 2,6-pyrazino subunits connected by carbon-oxygen and or -sulfur linkages (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry of heterocyclic compounds. 26. Synthesis and reactions of multiheteromacrocycles possessing 2,6-pyrazino subunits connected by carbon-oxygen and or -sulfur linkagesGeorge R. Newkome and Ashutosh NayakCite this: J. Org. Chem. 1978, 43, 3, 409–415Publication Date (Print):February 1, 1978Publication History Published online1 May 2002Published inissue 1 February 1978https://pubs.acs.org/doi/10.1021/jo00397a007https://doi.org/10.1021/jo00397a007research-articleACS PublicationsRequest reuse permissionsArticle Views148Altmetric-Citations9LEARN 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
Identification of a Mouse Homolog of the Human BTEB2 Transcription Factor as a β-Catenin-Independent Wnt-1-Responsive Gene (2001)

The Wnt/Wg signaling pathway functions during development to regulate cell fate determination and patterning in various organisms. Two pathways are reported to lie downstream of Wnt signaling in vertebrates. The canonical pathway relies on the activation of target genes through the beta-catenin-Lef/TCF complex, while the noncanonical pathway employs the activation of protein kinase C (PKC) and increases in intracellular calcium to induce target gene expression. cDNA subtractive hybridization between a cell line that overexpresses Wnt-1 (C57MG/Wnt-1) and the parental cell line (C57MG) was performed to identify downstream target genes of Wnt-1 signaling. Among the putative Wnt-1 target genes, we have identified a mouse homolog of the gene encoding human transcription factor basic transcription element binding protein 2 (mBTEB2). The mBTEB2 transcript is found at high levels in mammary tissue taken from a transgenic mouse overexpressing Wnt-1 (both tissue prior to active proliferation and tumor tissue) but is barely detectable in wild-type mouse mammary glands. The regulation of mBTEB2 by Wnt-1 signaling in tissue culture occurs through a beta-catenin-Lef/TCF-independent mechanism, as it is instead partially regulated by PKC. The Wnt-1-induced, PKC-dependent activation of mouse BTEB2 in C57MG cells, as well as the ability of Wnt-1 to stabilize beta-catenin in these cells, is consistent with the hypothesis that both the noncanonical and canonical Wnt pathways are activated concomitantly in the same cell. These results suggest that mBTEB2 is a biologically relevant target of Wnt-1 signaling that is activated through a beta-catenin-independent, PKC-sensitive pathway in response to Wnt-1.
Interfacial Electron-Transfer Kinetics of Ferrocene through Oligophenyleneethynylene Bridges Attached to Gold Electrodes as Constituents of Self-Assembled Monolayers:  Observation of a Nonmonotonic Distance Dependence (2004)

The standard heterogeneous electron-transfer rate constants (k(n)0) between substrate gold electrodes and the ferrocene redox couple attached to the electrode surface by variable lengths of substituted or unsubstituted oligophenyleneethynylene (OPE) bridges as constituents of mixed self-assembled monolayers were measured as a function of temperature. The distance dependences of the unsubstituted OPE standard rate constants and of the preexponential factors (An) obtained from an Arrhenius analysis of the unsubstituted OPE k(n)0 versus temperature data are not monotonic. This surprising result, together with the distance dependence of the substituted OPE preexponential factors, may be assessed in terms of the likely conformational variability of the OPE bridges (as a result of the low intrinsic barrier to rotation of the phenylene rings in these bridges) and the associated sensitivity of the rate of electron transfer (and, hence, the single-molecule conductance which may be estimated using An) through these bridges to the conformation of the bridge. Additionally, the measured standard rate constants were independent of the identity of the diluent component of the mixed monolayer, and using an unsaturated OPE diluent has no effect on the rate of electron transfer through a long-chain alkanethiol bridge. These observations indicate that the diluent does not participate in the electron-transfer event.
A New Approach to Linear Filtering and Prediction Problems (1960)

The classical filtering and prediction problem is re-examined using the Bode-Shannon representation of random processes and the “state-transition” method of analysis of dynamic systems. New results are: (1) The formulation and methods of solution of the problem apply without modification to stationary and nonstationary statistics and to growing-memory and infinite-memory filters. (2) A nonlinear difference (or differential) equation is derived for the covariance matrix of the optimal estimation error. From the solution of this equation the co-efficients of the difference (or differential) equation of the optimal linear filter are obtained without further calculations. (3) The filtering problem is shown to be the dual of the noise-free regulator problem. The new method developed here is applied to two well-known problems, confirming and extending earlier results. The discussion is largely self-contained and proceeds from first principles; basic concepts of the theory of random processes are reviewed in the Appendix.
<title>Markov iterated function system model of images</title> (1993)

All images have two basic characters: geometry and texture. Basing the two characters, we present Markov Iterated Function System (MIFS) model, consisting of Iterated Function System (IFS) and Markov Random Field (MRF). The fractal images have self-similarities in statistics, especially in geometric topological structure. IFS is useful for discribing the self- similarities. In the meantime, we consider a texture to be a stochastic field and usually it is anisotropic. We choose MRF as the model of the texture. It is convenient to control the geometric characters and texture through changing the parameters of MIFS model. We explored a fast iterated algorithm to realize a MIFS sample and an algorithm to estimate the parameters of MIFS.