gebhart/patrepeval huggingface dataset:
Transcriptional regulation of the spo0F gene of Bacillus subtilis (1986)

We have cloned the early sporulation gene spo0F, which encodes an open reading frame of 124 codons. The putative Spo0F protein derived from this open reading frame, which has been shown to share homology with the Spo0A protein as well as several other regulatory proteins from Escherichia coli, Salmonella typhimurium, and Klebsiella pneumoniae, also shares homology with the E. coli EcoRI methyltransferase. We have shown by S1 nuclease mapping of in vivo transcripts that spo0F is regulated from dual promoters: RNA II was transcribed from an upstream promoter, and RNA I was initated 30 base pairs downstream from RNA II. The promoter sequences for RNA II, but not those for RNA I, conformed to the -10 region consensus sequence for sigma 43 promoters. RNA II was found in low amounts in exponentially growing cells but was not observed in stationary-phase cells, and the presence of RNA II was glucose insensitive. RNA I was found in low amounts in exponentially growing cells, increased three- to fivefold at the end of exponential growth, and remained at this higher level for at least 3 h into stationary phase. RNA I was repressed by glucose during exponential growth but not during stationary phase.
Evaluation of the topical hemostatic efficacy and safety of TISSEEL VH S/D fibrin sealant compared with currently licensed TISSEEL VH in patients undergoing cardiac surgery: a phase 3, randomized, double-blind clinical study. (2007)

TISSEEL VH S/D is safe and effective for use as an adjunct to hemostasis in patients undergoing cardiac surgery.
Electron Transfer in Self-Assembled Inorganic Polyelectrolyte/Metal Nanoparticle Heterostructures (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTElectron Transfer in Self-Assembled Inorganic Polyelectrolyte/Metal Nanoparticle HeterostructuresDaniel L. Feldheim, Katherine C. Grabar, Michael J. Natan, and Thomas E. MalloukView Author Information Department of Chemistry, Pennsylvania State University University Park, Pennsylvania 16802 Cite this: J. Am. Chem. Soc. 1996, 118, 32, 7640–7641Publication Date (Web):August 14, 1996Publication History Received10 April 1996Published online14 August 1996Published inissue 1 January 1996https://doi.org/10.1021/ja9612007Copyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views1527Altmetric-Citations283LEARN 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 InReddit Read OnlinePDF (177 KB) Get e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Gold,Layers,Metal nanoparticles,Nanoparticles,Thickness Get e-Alerts
Role of caveolin and caveolae in insulin signaling and diabetes (2003)

Caveolae are specialized membrane microdomains present within the plasma membrane of the vast majority of cell types. They have a unique composition in that they are highly enriched in cholesterol, sphingolipids, and their coat proteins the caveolins (-1, -2, and -3). In recent years it has been recognized that caveolae act as signaling platforms, serving as a concentrating point for numerous signaling molecules, as well as regulating flux through many distinct signaling cascades. Although caveolae are found in a variety of cell types, they are most abundant in adipose tissue. This fact has led to the intense study of the function of these organelles in adipocytes. It has now become apparent that effective insulin signaling in the adipocyte may be strictly dependent on localization of at least two insulin-responsive elements to caveolae (insulin receptor and GLUT4), as well as on a direct functional interaction between caveolin-1 and the insulin receptor. We present a critical discussion of these recent findings.
Cover song detection: From high scores to general classification (2010)

Existing cover song detection systems require prior knowledge of the number of cover songs in a test set in order to identify cover(s) to a reference song. We describe a system that does not require such prior knowledge. The input to the system is a reference track and test track, and the output is a binary classification of whether the inputs are either a reference and a cover or a reference and a non-cover. The system differs from state-of-the-art detectors by calculating multiple input features, performing a novel type of test song normalization in order to combat against “impostor” tracks, and performing classification using either a support vector machine (SVM) or multi-layer perceptron (MLP). On the covers80 test set, the system achieves an equal error rate of 10%, compared to 21.3% achieved by the 2007 LabROSA cover song detection system.
Practical parallax occlusion mapping with approximate soft shadows for detailed surface rendering (2006)

Article Share on Practical parallax occlusion mapping with approximate soft shadows for detailed surface rendering Author: Natalya Tatarchuk ATI Research ATI ResearchView Profile Authors Info & Claims SIGGRAPH '06: ACM SIGGRAPH 2006 CoursesJuly 2006 Pages 81–112https://doi.org/10.1145/1185657.1185830Published:30 July 2006Publication History 11citation109DownloadsMetricsTotal Citations11Total Downloads109Last 12 Months20Last 6 weeks6 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Hyaluronan Fragments Synergize with Interferon-γ to Induce the C-X-C Chemokines Mig and Interferon-inducible Protein-10 in Mouse Macrophages (1998)

Hallmarks of chronic inflammation and tissue fibrosis are increased influx of activated inflammatory cells, mediator release, and increased turnover and production of the extracellular matrix (ECM). Recent evidence has suggested that fragments of the ECM component hyaluronan play a role in chronic inflammation by inducing macrophage expression of chemokines. Interferon-gamma (IFN-gamma), an important regulator of macrophage functions, has been shown to induce the C-X-C chemokines Mig and IP-10. These chemokines affect T-cell recruitment and inhibit angiogenesis. The purpose of this investigation was to determine the effect of hyaluronan (HA) on IFN-gamma-induced Mig and IP-10 expression in mouse macrophages. We found a marked synergy between HA and IFN-gamma on Mig and IP-10 mRNA and protein expression in mouse macrophages. This was most significant with Mig, which was not induced by HA alone. The synergy was specific for HA, was not dependent on new protein synthesis, was not mediated by tumor necrosis factor-alpha, was selective for Mig and IP-10, and occurred at the level of gene transcription. These data suggest that the ECM component HA may influence chronic inflammatory states by working in concert with IFN-gamma to alter macrophage chemokine expression.
NEXT GENERATION DNA VACCINES FOR HIV-1 (2002)

We studied the effects of first generation HIV-1 plasmid vaccines in 167 individuals. The vaccines were very well tolerated and induced helper T cell responses in most vaccine recipients. However, the CTL responses were below a 20% response rate. Improvement in vaccine potency is an important goal of this technology and a central focus of our laboratory. To improve on these response rates, we used RNA optimized constructs pGag and pEnv). These vaccines express 20-100 fold better than first generation vectors. However, our studies support that additional enhancements are needed to further boost the immune response. We report that we can significantly enhance the induced CD8 effector cell response by including engineered B7 costimulatory molecules. We observed that B7.2 was more effective at driving cellular immune responses than B7.1 as a plasmid vaccine. We developed gene swaps and deletions between these two molecules. This manipulation resulted in a dramatically enhanced cellular immune response as measured by CTL, or ICC or Elispot. We have also explored the use of cytokines as plasmid vaccine adjuvants. We observed that IL-12 and IL-15 were effective as plasmid vaccine adjuvants. Interestingly, IL-15 appeared to allow T cell expansion in the absence of significant T cell help. Improvement of the immune response induced by plasmid vaccines can be engineered in multiple ways. Our studies show that both costimulation as well as cytokine signals can be harnessed for more potent vaccine development. These results have important implications for the design of vaccines for prophylaxis and therapy.
Intracellular Folding Pathway of the Cystine Knot-Containing Glycoprotein Hormone α-Subunit (2000)

Three of the five disulfide bonds in the glycoprotein hormone alpha-subunit (GPH-alpha) form a cystine knot motif that stabilizes a three-loop antiparallel structure. Previously, we described a mutant (alpha(k)) that contained only the three knot disulfide bonds and demonstrated that the cystine knot was necessary and sufficient for efficient GPH-alpha folding and secretion. In this study, we used alpha(k) as a model to study the intracellular GPH-alpha folding pathway. Cystine knot formation proceeded through a 1-disulfide intermediate that contained the 28-82 disulfide bond. Formation of disulfide bond 10-60, then disulfide bond 32-84, followed the formation of 28-82. Whether the two non-cystine knot bonds 7-31 and 59-87 could form independent of the knot was also tested. Disulfide bond 7-31 formed rapidly, whereas 59-87 did not form when all cysteine residues of the cystine knot were converted to alanine, suggesting that 7-31 forms early in the folding pathway and that 59-87 forms during or after cystine knot formation. Finally, loop 2 of GPH-alpha has been shown to be very flexible, suggesting that loop 2 does not actively drive GPH-alpha folding. To test this, we replaced residues 36-55 in the flexible loop 2 with an artificially flexible glycine chain. Consistent with our hypothesis, folding and secretion were unaffected when loop 2 was replaced with the glycine chain. Based on these findings, we describe a model for the intracellular folding pathway of GPH-alpha and discuss how these findings may provide insight into the folding mechanisms of other cystine knot-containing proteins.
Effect of Chokes on Simultaneous Simulation of Reservoir and Surface Facilities (1994)

Abstract The main purpose of this paper is to show the importance of chokes in the simulation of surface facilities and reservoirs as integrated systems. In order to predict producing rates accurately, it is necessary not only to model the fluid flow in the reservoir but also to couple the gathering system to the reservoir. The interaction between these two parts can have a great influence in the performance of the whole system and this interaction is greatly affected by the use of chokes in surface facilities. Existing choke models are evaluated and the effect of placing chokes in the surface model is studied and some results are presented. Techniques for simultaneous simulation of reservoir, well and surface facilities will be presented in a future paper.
SIGNIFICANT IMPROVEMENT OF QUALITY FOR LONG OLIGONUCLEOTIDES BY USING CONTROLLED PORE GLASS WITH LARGE PORES (2005)

A key factor influencing the quality of long oligonucleotides is the choice of controlled pore glass (CPG) which is used as a solid support during oligonucleotide synthesis. We studied the influence of CPG pore size on the quality of 75-mer oligonucleotides. Using electrophoresis and HPLC, we demonstrated failure modes that can occur at certain oligo lengths with 1000A pore size, and compared yield and purity of 75-mer oligos using 1000A and larger pore size CPG. We showed that oligonucleotides with much better quality are obtained using CPG with pore sizes of 1400A and larger. We also identified the key characteristics for CPG selection that lead to the best CPG performance.
INFLUENCE OF REINFORCING BARS ON SHRINKAGE STRESSES IN CONCRETE SLABS. TECHNICAL NOTE (2000)

As a kind of structural element, continuous reinforced concrete (RC) slabs have been widely used in modern transportation engineering, such as highway and airport pavements and bridge decks. It is well known that cracking in concrete slabs significantly influences their service life. Concrete shrinkage may be the principle reason for the initial crack formation in the slabs. This paper presents an attempt to provide an analytical tool for the prediction of stress distribution in RC slabs after undergoing matrix shrinking restrained by the reinforcing bars. The model incorporates the material parameters of the reinforcing bar and the concrete matrix, and it enables prediction of the stress development in concrete with time.
Anti-Inflammatory Effects of Alkaline Phosphatase in Coronary Artery Bypass Surgery with Cardiopulmonary Bypass (2009)

Laboratory and clinical data have implicated endotoxin as an important factor in the inflammatory response to cardiopulmonary bypass. Alkaline phosphatase prevents endotoxin-induced systemic inflammation in animals and humans. We assessed the effects of the administration of bovine intestinal alkaline phosphatase on surgical complications in patients undergoing coronary artery bypass grafting. In a double blind, randomized, placebo-controlled study, a total of 63 patients undergoing coronary artery bypass grafting were enrolled. Bovine intestinal alkaline phosphatase or placebo was administered as an intravenous bolus followed by continuous infusion for 36 hours. The primary endpoint was reduction of post-surgical inflammation. No significant safety concerns were identified. The overall inflammatory response to coronary artery bypass grafting with cardiopulmonary bypass was low in both placebo and bovine intestinal alkaline phosphatase patient group. Five patients in the placebo group displayed a significant TNFalpha response followed by an increase in plasma levels of IL-6 and IL-8. Such a TNFalpha response was not observed in the bovine intestinal alkaline phosphatase group, suggesting anti-inflammatory activity of bovine intestinal alkaline phosphatase. Other variables related to systemic inflammation showed no statistically significant differences. Bovine intestinal alkaline phosphatase can be administered safely in an attempt to reduce the inflammatory response in coronary artery bypass grafting patients with a low to intermediate EuroSCORE. The anti-inflammatory effects might be more pronounced in patients developing more fulminant postoperative inflammatory responses. This will be investigated in a further trial with inclusion of patients undergoing complicated cardiac surgery, demanding extended cardiopulmonary bypass and aortic cross clamp time. In this review article some recent patents related to the field are also discussed.
Classification of Hyperspectral Breast Images for Cancer Detection (2009)

In 2009 approximately one out of eight women has breast cancer. More than 180,000 women are expected to be diagnosed with breast cancer and more than 40,000 women are expected to die from it. Most breast cancer deaths can be prevented if it is detected and treated early. The most common imaging techniques for breast cancer detection are x-ray mammography and computed tomography (CT). These two methods aim to detect any lumps or masses in breast tissues that may be cancerous. However, there is an inherent problem associated with these two methods. They are expensive and involve radiating the breast tissues which may be dangerous since even small doses of radiation can induce mutation that leads to cancer. Fourier transform infrared (FTIR) spectroscopy is a measurement technique in which the absorbance of a tissue sample for many wavelengths is captured using infrared beams. The purpose of capturing many distinct wavelengths (in our case we capture 1641 wavelengths corresponding to 720 nm to 4000 nm in 2 nm increments) is so that much more information is captured. There are three steps involved in performing FTIR: (1) identifying sample regions by manual inspection using optical microscope (2) applying an opaque mask with an aperture of controlled size to restrict infrared beam absorption to the area of interest (3) measuring the attenuation of the incident infrared beam with a detector In this paper we present a machine learning approach in hyperspectral image analysis for breast cancer detection. We consider the scenario where a band sequential image of a breast tissue specimen is collected using FTIR spectroscopy. Our goal is to determine which parts of the image correspond to cancer cells and which parts of the image correspond to non-cancer cells. We first discuss spectrum selection and principal component analysis (PCA) to reduce the dimensionality of the image. We then discuss the implementation of K-means++ clustering algorithm for data set represented as points in a high dimensional space. We finally add noise to the image and discuss the robustness of our approach.
The Delta-Eddington Approximation for Radiative Flux Transfer (1976)

This paper presents a rapid yet accurate method, the “delta-Eddington” approximation, for calculating monochromatic radiative fluxes in an absorbing-scattering atmosphere. By combining a Dirac delta function and a two-term approximation, it overcomes the poor accuracy of the Eddington approximation for highly asymmetric phase functions. The fraction of scattering into the truncated forward peak is taken proportional to the square of the phase function asymmetry factor, which distinguishes the delta-Eddington approximation from others of similar nature. Comparisons of delta-Eddington albedos, transnmissivities and absorptivities with more exact calculations reveal typical differences of 0–0.022 and maximum differences of 0.15 over wide ranges of optical depth, sun angle, surface albedo, single-scattering albedo and phase function asymmetry. Delta-Eddington fluxes are in error, on the average, by no more than 0.5%0, and at the maximum by no more than 2% of the incident flux. This computationally fast and accurate approximation is potentially of utility in applications such as general circulation and climate modelling.
The elimination of primer-dimer accumulation in PCR (1997)

We attempted to produce primer-dimers (PDs) from a variety of primers with differing types and extents of complementarity. Where PDs were produced they were cloned and sequenced. We were unable to produce detectable PDs either with individual primers alone or with similar sequence primers even if they had 3'complementarity. These observations led to the hypothesis that a system could be developed whereby the accumulation of PDs in a PCR may be eliminated. We demonstrate a method for the general suppression of PD formation that uses a sequence of additional nucleotides (a Tail) at the 5' ends of amplimers. Tailed amplimers are present at low concentration and only participate during early cycles of PCR. In subsequent PCR cycles, amplification is achieved using a single primer that has the same sequence as that of the Tail portion of the early cycle primers, here we refer to this as a Tag. When products are small, as with PDs, there is a high local concentration of complementary sequences derived from the Tail. This favours the annealing of the complementary ends of a single strand produced by tailed primer interactions and gives rise to 'pan-handle' structures. The formation of these outcompetes the annealing of further Tag primers thereby preventing the accumulation of non-specific PD products. This aids the design of large multiplex reactions and provides a means of detecting specific amplicons directly in the reaction vessel by using an intercalating dye.
Community study of role of viral infections in exacerbations of asthma in 9-11 year old children (1995)

This study supports the hypothesis that upper respiratory viral infections are associated with 80-85% of asthma exacerbations in school age children.
Electron-affinic Sensitization (1969)

SummaryThe bacterium Serratia marcescens has been used as a test system for demonstrating the radiosensitizing properties of a class of electron-affinic organic compounds. These include: unsaturated diesters and diketo compounds, mono-, di- and triketohydrindene (indanetrione), derivatives of pyruvic acid, quinones and several miscellaneous compounds. With few exceptions, the sensitization is restricted to anoxic systems. An electron-transfer mechanism, involving interaction of the sensitizer with a charged intermediate produced by direct energy absorption in a target molecule, is proposed as the basis of a model for radiosensitization.
Towards web information extraction using extraction ontologies and (indirectly) domain ontologies (2007)

Extraction ontologies allow to swiftly proceed from initial domain modelling to running a functional prototype of a web information extraction application. We investigate the possibility of semi-automatically deriving extraction ontologies from third-party domain ontologies.
Molecular chaperone function of mammalian Hsp70 and Hsp40-a review (2000)

Virtually all organisms respond to up-shifts in temperature (heat shock) by synthesizing a set of proteins called heat shock proteins (HSPs). The HSPs are induced not only by heat shock but also by various other environmental stresses. Induction of HSPs is regulated by the trans-acting heat shock factors (HSFs) and cis-acting heat shock element (HSE) present at the promoter region of each heat shock gene. Usually, HSPs are also expressed constitutively at normal growth temperatures and have basic and indispensable functions in the life cycle of proteins as molecular chaperones, as well as playing a role in protecting cells from the deleterious stresses. Molecular chaperones are able to inhibit the aggregation of partially denatured proteins and refold them using the energy of ATP. Recently, there are expectations for the use of molecular chaperones for the protection against and therapeutic treatment of inherited diseases caused by protein misfolding. In this review, the focus will be on the mammalian Hsp40, a homologue of bacterial DnaJ heat shock protein, and the beneficial functions of molecular chaperones.