gebhart/patrepeval huggingface dataset:
Serum response factor is a critical requirement for VEGF signaling in endothelial cells and VEGF‐induced angiogenesis (2004)

Angiogenesis, new capillary blood vessel formation, is essential for embryonic development, wound healing, and cancer growth. Vascular endothelial growth factor (VEGF) induces angiogenesis by activating endothelial cell migration and proliferation. Serum response factor (SRF) is a transcription factor important for embryonic development and activation of immediate early gene expression. The roles of SRF in endothelial cell biology and angiogenesis have not been explored. Here we demonstrate that SRF is a downstream mediator of VEGF signaling in endothelial cells and a critical requirement for VEGF-induced angiogenesis. Knockdown of SRF protein levels in human and rat endothelial cells abolished VEGF-induced in vitro angiogenesis, impaired endothelial cell migration and proliferation, and inhibited VEGF-induced actin polymerization and immediate early gene expression. Injection of SRF antisense expression plasmid into gastric ulcers in rats significantly inhibited in vivo angiogenesis in granulation tissue. Mechanistically, this study also revealed that VEGF promotes SRF expression and nuclear translocation and increases SRF binding activity to DNA in endothelial cells through both Rho-actin and MEK-ERK dependent signaling pathways. These findings have potential therapeutic implications, e.g., local anti-SRF treatment may inhibit angiogenesis crucial for tumor growth.
Palladium-catalysed Synthesis of Pyrimidines (2005)

Satisfactory yields of 4-substituted pyrimidines and bicyclic pyrimidines are produced from α-methyl or α-methylene ketones when reacted with formamide and tetrakis(triphenylphosphine)palladium(0) or a 1:2 mixture of palladium(II) acetate and triphenylphosphine as catalysts.Under the same reaction conditions pyridines or imidazole are formed from 1,3-or 1,2-diketones.
Is Maturation Required for Langerhans Cell Migration? (2002)

Key papers in scientific literature sometimes bring a definitive resolution to a long-awaited issue. Others may be far less decisive but importantly implore us to question the fitness of prevailing models. So it is that a paper in this issue by F. Geissmann and colleagues (1), albeit subject to some variety of interpretation, nevertheless compels us to reexamine the widely accepted idea that migration of Langerhans cells in response to inflammatory stimuli is necessarily coupled to and follows from their maturation. It is well established that in the steady-state Langerhans cells turn over very slowly, but they can be mobilized en masse by inflammatory or antigenic stimuli. In vitro and in vivo, these inflammatory mediators have also been observed to promote maturation, and Langerhans cells that migrate from skin explants in culture usually display a mature phenotype. In further agreement with the idea that migration is linked with maturation is evidence that molecules associated with migration, particularly CCR7 (2), are induced during Langerhans cell maturation (3).

Dendritic cell (DC) “maturation” is defined functionally as the acquisition of potent immunogenic capacity. Among DC biologists, this term signifies a particular program of gene expression that typically includes the upregulation of CD40, CD83, CD86, MHC products, and other molecules associated with antigen presentation, along with simultaneous induction of CCR7 (4). At the same time, the ability to acquire and process antigen, a feature that characterizes immature DCs, is downregulated. Understanding the extent to which maturation and migration are coupled lies at the heart of understanding how DCs regulate T cell differentiation. If immature DCs promote naive T cells to develop a tolerogenic phenotype (5), then one is left wondering whether immature DCs traffic efficiently to lymph nodes from the periphery. If they do, then what of the belief that CCR7 is needed for DC migration to lymph nodes and that CCR7 is expressed only by mature DCs? Clearly, the fit of some pieces of the puzzle have to be reevaluated.
Differences in Binding Specificity for the Homologous γ- and β-Chain “Holes” on Fibrinogen:  Exclusive Binding of Ala-His-Arg-Pro-amide by the β-Chain Hole, (2006)

The beta-chain amino-terminal sequences of all known mammalian fibrins begin with the sequence Gly-His-Arg-Pro- (GHRP-), but the homologous sequence in chicken fibrin begins with the sequence Ala-His-Arg-Pro- (AHRP-). Nonetheless, chicken fibrinogen binds the synthetic peptide GHRPam, and a previously reported crystal structure has revealed that the binding is in exact conformance with that observed for the human GHRPam-fragment D complex. We now report that human fibrinogen, which is known not to bind APRP, binds the synthetic peptide AHRPam. Moreover, a crystal structure of AHRPam complexed with fragment D from human fibrinogen shows that AHRPam binds exclusively to the beta-chain hole and, unlike GHRPam, not at all to the homologous gamma-chain hole. The difference can be attributed to the methyl group of the alanine residue clashing with a critical carboxyl group in the gammaC hole but being accommodated in the roomier betaC hole where the equivalent carboxyl is situated more flexibly.
Phage typing of staphylococci. (1961)

Standardized methods are essential if phage typing of staphylococci is to be reliable and if the results obtained in different laboratories are to be compared. This paper, prepared on behalf of the Subcommittee on Phage Typing of Staphylococcus of the Nomenclature Committee of the International Association of Microbiological Societies, gives a detailed account of methods that have been found satisfactory for propagating the phages and defines a standard testing routine by which the stability of the phage preparations can be verified. Technical details are given of methods recommended for determining the phage type of staphylococci and the interpretation of differences between the types is discussed. The need for close collaboration between the epidemiologist and the laboratory worker in the use of phage typing is emphasized.
Development of a Microbial System for Production of Mussel Adhesive Protein (1989)

The polyphenolic adhesive protein of the mussel Mytilus edulis is an unusual protein composed mainly of repetitive decapeptide and hexapeptide sequences. In the mussel, the protein is first produced in a precursor form and is converted to an adhesive by post-translational modification. To develop an efficient renewable resource for production of the polyphenolic protein, we have used genetic engineering technology. cDNA sequences encoding portions of the polyphenolic protein were identified and expressed in the yeast Saccharomyces cerevisiae.
A fast and portable realizer for text generation systems (1997)

Article Free Access Share on A fast and portable realizer for text generation systems Authors: Benoit Lavoie CoGenTex, Inc., Ithaca, NY CoGenTex, Inc., Ithaca, NYView Profile , Owen Rambow CoGenTex, Inc., Ithaca, NY CoGenTex, Inc., Ithaca, NYView Profile Authors Info & Claims ANLC '97: Proceedings of the fifth conference on Applied natural language processingMarch 1997Pages 265–268https://doi.org/10.3115/974557.974596Published:31 March 1997Publication History 54citation680DownloadsMetricsTotal Citations54Total Downloads680Last 12 Months19Last 6 weeks3 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 SiteeReaderPDF
Membrane Permeabilization by Thrombin-Induced Platelet Microbicidal Protein 1 Is Modulated by Transmembrane Voltage Polarity and Magnitude (1999)

Thrombin-induced platelet microbicidal protein 1 (tPMP-1) is a small, cationic peptide generated from rabbit platelets when they are exposed to thrombin in vitro. It has potent microbicidal activity against a broad spectrum of bacterial and fungal pathogens, including Staphylococcus aureus. Previous in vitro studies involving whole staphylococcal cells and planar lipid bilayers (as artificial bacterial membrane models) suggested that membrane permeabilization by tPMP-1 is voltage dependent (S.-P. Koo, M. R. Yeaman, and A. S. Bayer, Infect. Immun. 64:3758-3764, 1996; M. R. Yeaman, A. S. Bayer, S. P. Koo, W. Foss, and P. M. Sullam, J. Clin. Investig. 101:178-187, 1998). Thus, the aims of the present study were to specifically characterize the electrophysiological events associated with membrane permeabilization by tPMP-1 by using artificial planar lipid bilayer membranes. We assessed the influence of transmembrane voltage polarity and magnitude on the initiation and modulation of tPMP-1 membrane permeabilization at various concentrations of tPMP-1 (range, 1 to 100 ng/ml) added to the cis side of the membranes. The incidence of membrane permeabilization induced by tPMP-1 at all of the concentrations tested was more frequent at -90 mV than at +90 mV. It is noteworthy that membrane permeabilization due to 1-ng/ml tPMP-1 was successfully initiated at -90 mV but not at +90 mV. Further, the mean onset times of induction of tPMP-1 activity were comparable under the various conditions. Modulation of ongoing membrane permeabilization was dependent on voltage and tPMP-1 concentration. Membrane permeabilization at a low tPMP-1 concentration (1 ng/ml) was directly correlated with trans-negative voltages, while a higher tPMP-1 concentration (100 ng/ml) induced conductance which was more dependent on trans-positive voltages. Collectively, these data indicate that the mechanism of tPMP-1 microbicidal activity at the bacterial cytoplasmic membrane may involve distinct induction and propagation stages of membrane permeabilization which, in turn, are modulated by transmembrane potential, as well as peptide concentration.
The IP Network Address Translator (NAT) (1994)

The two most compelling problems facing the IP Internet are IP address depletion and scaling in routing. Long-term and short-term solutions to these problems are being developed. The short-term solution is CIDR (Classless InterDomain Routing). The long-term solutions consist of various proposals for new internet protocols with larger addresses.
Identification of the Species of Origin for Meat Products by Rapid Evaporative Ionization Mass Spectrometry (2016)

Increasingly abundant food fraud cases have brought food authenticity and safety into major focus. This study presents a fast and effective way to identify meat products using rapid evaporative ionization mass spectrometry (REIMS). The experimental setup was demonstrated to be able to record a mass spectrometric profile of meat specimens in a time frame of <5 s. A multivariate statistical algorithm was developed and successfully tested for the identification of animal tissue with different anatomical origin, breed, and species with 100% accuracy at species and 97% accuracy at breed level. Detection of the presence of meat originating from a different species (horse, cattle, and venison) has also been demonstrated with high accuracy using mixed patties with a 5% detection limit. REIMS technology was found to be a promising tool in food safety applications providing a reliable and simple method for the rapid characterization of food products.
Efficient production by sperm-mediated gene transfer of human decay accelerating factor (hDAF) transgenic pigs for xenotransplantation (2002)

A large number of hDAF transgenic pigs to be used for xenotransplantation research were generated by using sperm-mediated gene transfer (SMGT). The efficiency of transgenesis obtained with SMGT was much greater than with any other method. In the experiments reported, up to 80% of pigs had the transgene integrated into the genome. Most of the pigs carrying the hDAF gene transcribed it in a stable manner (64%). The great majority of pigs that transcribed the gene expressed the protein (83%). The hDAF gene was transmitted to progeny. Expression was stable and found in caveolae as it is in human cells. The expressed gene was functional based on in vitro experiments performed on peripheral blood mononuclear cells. These results show that our SMGT approach to transgenesis provides an efficient procedure for studies involving large animal models.
Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics (2015)

Spatially targeted optical microproteomics (STOMP) is a novel proteomics technique for interrogating micron-scale regions of interest (ROIs) in mammalian tissue, with no requirement for genetic manipulation. Methanol or formalin-fixed specimens are stained with fluorescent dyes or antibodies to visualize ROIs, then soaked in solutions containing the photo-tag: 4-benzoylbenzyl-glycyl-hexahistidine. Confocal imaging along with two photon excitation are used to covalently couple photo-tags to all proteins within each ROI, to a resolution of 0.67 µm in the xy-plane and 1.48 µm axially. After tissue solubilization, photo-tagged proteins are isolated and identified by mass spectrometry. As a test case, we examined amyloid plaques in an Alzheimer's disease (AD) mouse model and a post-mortem AD case, confirming known plaque constituents and discovering new ones. STOMP can be applied to various biological samples including cell lines, primary cell cultures, ex vivo specimens, biopsy samples, and fixed post-mortem tissue.
Morphology of hydrofluoric acid and ammonium fluoride-treated silicon surfaces studied by surface infrared spectroscopy (1992)

Morphologies of Si surfaces treated with aqueous solutions of hydrofluoric acid (HF) and ammonium fluoride (NH4F) have been investigated using surface infrared spectroscopy. We confirm that HF-treated Si(111) surfaces are terminated with a monohydride (Si—H), dihydride (Si—H2), and trihydride (Si–H3), whereas NH4F-treated Si(111) surfaces are dominantly terminated with Si—H. For Si(100), treatment in NH4F produces a surface for which the dihydride mode is enhanced compared to HF treatment, suggesting that surface Si—Si bonds on Si(100) are readily cleaved in a NH4F solution to generate a dihydride Si. The effect of varying the HF concentration on the morphology of HF-treated Si(100) surfaces is investigated. It is demonstrated that 5% HF treatment produces Si(100) surfaces which have a larger density of surface Si—Si bonds than 50% HF or 0.5% HF treatment.
A 10-Gene Classifier for Distinguishing Head and Neck Squamous Cell Carcinoma and Lung Squamous Cell Carcinoma (2007)

The results suggest that penalized discriminant analysis using these 10 genes will be highly accurate in determining the origin of squamous cell carcinomas in the lungs of patients with previous head and neck malignancies.
Luminescence of Ca2+‐activated photoprotein obelin initiated by NaOCl and MnCl2 (1993)

The luminescence of obelin is initiated by NaOCl in a reaction mixture containing no calcium. The addition of Mn2+ enhances the light emission > 300-fold. Sodium azide and histidine, as singlet oxygen quenchers, inhibit NaOCl-activated obelin luminescence in the presence or absence of Mn2+. This suggests that the addition of NaOCl to the mixture causes singlet oxygen formation (stimulated by Mn2+ ions), and singlet oxygen initiates the light-emitting reaction.
The design and fabrication of thin-film CdS/Cu2S cells of 9.15-percent conversion efficiency (1980)

Thin-film polycrystalline CdS/Cu <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> S cells with energy conversion efficiencies in sunlight of up to 9.15 percent and areas of ∼1 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> have been developed. The improvement over previously achieved efficiencies is due to the development of techniques to separately measure and minimize fill factor losses. Specific design and fabrication changes based on a detailed quantitative analysis of the cell operation, were introduced to correct series resistance, shunt conductance and field effect losses. Further increases in efficiency can be expected from the development of a planar junction thin-film CdS/Cu <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> S cell.
Recording of Intracavity Potentials Through a Single Lumen, Saline Filled Cardiac Catheter (1949)

SummaryA new technic is described to obtain intracavitary cardiac potentials through the single lumen saline filled cardiac catheter without use of the usual copper wire electrode. If the exploring terminal of an electrocardiograph is connected to the open arm end of a column of blood or saline in a catheter which has been introduced into the cavity of the heart, and if the indifferent electrode is connected to a central terminal, the completed curve will represent chiefly the fluctuations of intra-cardiac potential at the tip of the catheter.
<title>Outlier detection and motion segmentation</title> (1993)

We present a new method for solving the problem of motion segmentation, identifying the objects within an image moving independently of the background. We utilize the fact that two views of a static 3D point set are linked by a 3 X 3 Fundamental Matrix (F). The Fundamental Matrix contains all the information on structure and motion from a given set of point correspondences and is derived by a least squares method under the assumption that the majority of the image is undergoing a rigid motion. Least squares is the most commonly used method of parameter estimation in computer vision algorithms. However the estimated parameters from a least squares fit can be corrupted beyond recognition in the presence of gross errors or outliers which plague any data from real imagery. Features with a motion independent of the background are those statistically inconsistent from the calculated value of (F). Well founded methods for detecting these outlying points are described.
An Autoregulatory Circuit Affecting Peptide Signaling in Bacillus subtilis (1999)

The competence and sporulation factor (CSF) of Bacillus subtilis is an extracellular pentapeptide produced from the product of phrC. CSF has at least three activities: (i) at low concentrations, it stimulates expression of genes activated by the transcription factor ComA; at higher concentrations, it (ii) inhibits expression of those same genes and (iii) stimulates sporulation. Because the activities of CSF are concentration dependent, we measured the amount of extracellular CSF produced by cells. We found that by mid-exponential phase, CSF accumulated to concentrations (1 to 5 nM) that stimulate ComA-dependent gene expression. Upon entry into stationary phase, CSF reached 50 to 100 nM, concentrations that stimulate sporulation and inhibit ComA-dependent gene expression. Transcription of phrC was found to be controlled by two promoters: P1, which precedes rapC, the gene upstream of phrC; and P2, which directs transcription of phrC only. Both RapC and CSF were found to be part of autoregulatory loops that affect transcription from P1, which we show is activated by ComA approximately P. RapC negatively regulates its own expression, presumably due to its ability to inhibit accumulation of ComA approximately P. CSF positively regulates its own expression, presumably due to its ability to inhibit RapC activity. Transcription from P2, which is controlled by the alternate sigma factor sigma(H), increased as cells entered stationary phase, contributing to the increase in extracellular CSF at this time. In addition to controlling transcription of phrC, sigmaH appears to control expression of at least one other gene required for production of CSF.
Cross-reactions between Salmonella typhi and 24 other bacterial species. (1980)

Cross-reactions between antigens from S. typhi and 24 other bacterial species were studied by quantitative immunoelectrophoretic methods. A sonicated S. typhi antigen preparation and a corresponding pooled rabbit antiserum regularly presenting 86 immunoprecipitates were used as a reference system. Antigens from Enterobacteriaceae cross-reacted intensively with the S. typhi antigens. No cross-reactions between S. typhi and antigens from gram-positive bacteria were found, and only a few cross-reactions with antigens from gram-negative bacteria outside the Enterobacteriaceae. The taxonomic perspectives of the immunoelectrophoretic approach are stressed by results showing that the number of cross-reacting antigens between S. typhi and other Enterobacteriaceae was positively correlated to the number of identical reactions in a collection of 28 biochemical tests.
The Life-Cycle of Operons (2006)

Operons are a major feature of all prokaryotic genomes, but how and why operon structures vary is not well understood. To elucidate the life-cycle of operons, we compared gene order between Escherichia coli K12 and its relatives and identified the recently formed and destroyed operons in E. coli. This allowed us to determine how operons form, how they become closely spaced, and how they die. Our findings suggest that operon evolution may be driven by selection on gene expression patterns. First, both operon creation and operon destruction lead to large changes in gene expression patterns. For example, the removal of lysA and ruvA from ancestral operons that contained essential genes allowed their expression to respond to lysine levels and DNA damage, respectively. Second, some operons have undergone accelerated evolution, with multiple new genes being added during a brief period. Third, although genes within operons are usually closely spaced because of a neutral bias toward deletion and because of selection against large overlaps, genes in highly expressed operons tend to be widely spaced because of regulatory fine-tuning by intervening sequences. Although operon evolution may be adaptive, it need not be optimal: new operons often comprise functionally unrelated genes that were already in proximity before the operon formed.
Directional cell search for millimeter wave cellular systems (2014)

Millimeter wave (mmW) bands between 30 and 300 GHz are considered a promising candidate for next-generation cellular networks to relieve spectral congestion in conventional cellular frequencies. However, cellular communication at these frequencies will likely require highly directional transmissions to achieve suitable signal range. This reliance on directional beamforming complicates initial cell search since the mobile and base station must jointly search over a potentially large angular directional space to locate a suitable path to initiate communication. This paper proposes a directional cell search procedure where each base station periodically transmits synchronization signals in randomly varying directions. Detectors are derived for this synchronization signal based on a Generalized Likelihood Ratio Test (GLRT) for the case where (i) the mobile has only analog beamforming (where the mobile can “look” in only direction at a time) and (ii) digital beamforming where the mobile has access to digital samples from all antennas. Simulations under realistic parameters demonstrate that mobiles may not be able to achieve suitable detection performance with analog beamforming alone. In contrast, digital beamforming offers dramatically better performance. We argue that the additional power consumption cost of digital beamforming can be offset by using very low quantization rates with minimal performance loss, thus arguing that low-rate fully digital front-ends may be a better design choice for directional cell search.