gebhart/patrepeval huggingface dataset:
Automation of yeast two-hybrid screening. (1999)

We have developed an automated format for screening yeast two-hybrid libraries for protein-protein interactions. The format consists of a liquid array in which pooled library subsets of yeast, expressing up to 1000 different cDNAs, are mated to a yeast strain of the opposite mating type, expressing a protein of interest. Interactors are detected by a liquid assay for beta-galacsidase following prototrophic selection. The method is demonstrated by the detection of interactions between two encoded yeast RNA polymerase subunits in simulated libraries of varied complexity. To demonstrate its utility for large scale screening of complex cDNA libraries, two nuclear receptor ligand-binding domains were screened through two cDNA libraries arrayed in pooled subsets. Screening these libraries yielded clones which had previously been identified in traditional yeast two hybrid screens, as well as several new putative interacting proteins. The formatting of the cDNA library into pooled subsets lends itself to functional subtraction of the promiscuous positive class of interactor from the library. Also, the liquid arrayed format enables electronic handling of the data derived from interaction screening, which, together with the automated handling of samples, should promote large-scale proteome analysis.
SIP1 (Smad Interacting Protein 1) and δEF1 (δ-Crystallin Enhancer Binding Factor) are Structurally Similar Transcriptional Repressors (2001)

Background: Smad proteins are intracellular mediators of transforming growth factor-β (TGFβ) signalling that regulate gene expression by interacting with different classes of transcription factors including DNA-binding multi-zinc finger proteins. One of these, Smad interacting protein 1 (SIP1), is a novel two-handed zinc-finger protein that displays strong similarity with the transcriptional repressor δ-crystallin enhancer binding factor (δEF1). Here, we summarize what is known about the mechanism of action of both proteins and their role in vertebrate embryogenesis. Our data are discussed together with the present knowledge on other zinc-finger containing Smad interacting proteins. Methods: The activities and function of SIP1 have been analysed through documentation of expression patterns, the effect of over-expression of SIP1 on target-gene expression, and promoter studies using Xenopus embryos. Moreover, S1P1/Smad complexes and their association with target promoter DNA were analyzed in biochemical studies. Results: SIP1 is a transcriptional repressor displaying overlapping DNA binding specificities with δEF1. An in vivo target of SIP1 in Xenopus is a gene required for the formation of mesoderm, Brachyury ( X Bra). Our data indicate that SIP1 is required to confine X Bra gene expression to the mesoderm. Furthermore, the expression pattern in Xenopus invites us to speculate that SIP1 plays a role in specification/differentiation of neuroectoderm. Unlike δEF1, SIP1 can bind directly to activated receptor regulated Smads (R-Smads) and recruit them to the DNA. This indicates that Smads may modulate the activity of SIP1 as a transcriptional repressor. Conclusions: Our data point to a role of SIP1 in developmental processes regulated by members of the TGFβ family such as induction of mesoderm (mediated through activin-like signalling) and inhibition of neuroectoderm formation (mediated by bone morphogenetic proteins [BMPs]). Whereas SIP1 could act in TGFβ signal transduction by virtue of interaction with activated R-Smads, genetic studies in the mouse indicate that δEF1 may act in certain TGFβ pathways-i.e., BMPs and growth and differentiation factors (GDFs)-as well. The molecular mechanisms by which these transcriptional repressors act, as well as the function of the SIP1/Smad interaction, remain to be elucidated. Clinical Relevance: Mutations in components of the TGFβ signalling pathways have been associated with disease and congenital malformations. We anticipate that identification of Smad interacting transcription factors including SIP1 and their targets will help us to understand the molecular basis of certain pathologies.
Theoretical and experimental investigations of acoustic waves in embedded fluid-solid multi-string structures (2017)

Current acoustic measurements provide viable inspection for single cased wells, yet their interpretation for complicated multi-string wellbores where, for instance, two or more nested steel strings are deployed, is largely hampered by a lack of knowledge of the measured acoustic wave fields. This letter reports on theoretical and experimental investigations of the acoustic wave propagation in fluid-filled double string systems. Experimental measurements show excellent agreement with the theoretical predictions by a Sweeping Frequency Finite Element Method. The results lead to the identification of acoustic signatures that are crucial for an effective diagnosis of cement conditions in double-string cased wellbores.
TEMPO allegro: liquid catholyte redoxmers for nonaqueous redox flow batteries (2021)

A series of (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO)-based high potential liquid redoxmers were developed by incorporating polyethylene glycol (PEG) chains. By using a hybrid flow cell, TEMPO-EG1 demonstrated excellent cyclability at various concentrations.
All-optical wavelength converter and switch based on electromagnetically induced transparency (2000)

We propose a method for all-optical switching and wavelength conversion using electromagnetically induced transparency (EIT). We discuss the mechanism for the transfer of information in this scheme and determine the conditions for which N×N wavelength conversion can be realized. We compare the properties and limits of an EIT-based switch to conventional wavelength converters.
Human immunodeficiency virus type 1 membrane fusion mediated by a laboratory-adapted strain and a primary isolate analyzed by resonance energy transfer (1996)

Previous studies of human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein-mediated membrane fusion have focused on laboratory-adapted T-lymphotropic strains of the virus. The goal of this study was to characterize membrane fusion mediated by a primary HIV-1 isolate in comparison with a laboratory-adapted strain. To this end, a new fusion assay was developed on the basis of the principle of resonance energy transfer, using HeLa cells stably transfected with gp120/gp41 from the T-lymphotropic isolate HIV-1LA1 or the macrophage-tropic primary isolate HIV-1JR-FL. These cells fused with CD4+ target cell lines with a tropism mirroring that of infection by the two viruses. Of particular note, HeLa cells expressing HIV-1JR-FL gp120/gp41 fused only with PM1 cells, a clonal derivative of HUT 78, and not with other T-cell or macrophage cell lines. These results demonstrate that the envelope glycoproteins of these strains play a major role in mediating viral tropism. Despite significant differences exhibited by HIV-1JR-FL and HIV-1LAI in terms of tropism and sensitivity to neutralization by CD4-based proteins, the present study found that membrane fusion mediated by the envelope glycoproteins of these viruses had remarkably similar properties. In particular, the degree and kinetics of membrane fusion were similar, fusion occurred at neutral pH and was dependent on the presence of divalent cations. Inhibition of HIV-1JR-FL envelope glycoprotein-mediated membrane fusion by soluble CD4 and CD4-IgG2 occurred at concentrations similar to those required to neutralize this virus. Interestingly, higher concentrations of these agents were required to inhibit HIV-1LAI envelope glycoprotein-mediated membrane fusion, in contrast to the greater sensitivity of HIV-1LAI virions to neutralization by soluble CD4 and CD4-IgG2. This finding suggests that the mechanisms of fusion inhibition and neutralization of HIV-1 are distinct.
Identification of the region(s) of human DNA responsible for metastasis in breast cancer (1996)

Conference Article| August 01 1996 Identification of the region(s) of human DNA responsible for metastasis in breast cancer HAI-JUAN CHEN; HAI-JUAN CHEN 1Cancer and Polio Research Fund Laboratories, Department of Biochemistry, University of Liverpool, P. O. Box 147, Liverpool, L69 3BX, U.K. Search for other works by this author on: This Site PubMed Google Scholar YOUQIANG KE; YOUQIANG KE 1Cancer and Polio Research Fund Laboratories, Department of Biochemistry, University of Liverpool, P. O. Box 147, Liverpool, L69 3BX, U.K. Search for other works by this author on: This Site PubMed Google Scholar ROGER BARRACLOUGH; ROGER BARRACLOUGH 1Cancer and Polio Research Fund Laboratories, Department of Biochemistry, University of Liverpool, P. O. Box 147, Liverpool, L69 3BX, U.K. Search for other works by this author on: This Site PubMed Google Scholar PHILIP S. RUDLAND PHILIP S. RUDLAND 1Cancer and Polio Research Fund Laboratories, Department of Biochemistry, University of Liverpool, P. O. Box 147, Liverpool, L69 3BX, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1996) 24 (3): 354S. https://doi.org/10.1042/bst024354s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share MailTo Twitter LinkedIn Cite Icon Cite Get Permissions Citation HAI-JUAN CHEN, YOUQIANG KE, ROGER BARRACLOUGH, PHILIP S. RUDLAND; Identification of the region(s) of human DNA responsible for metastasis in breast cancer. Biochem Soc Trans 1 August 1996; 24 (3): 354S. doi: https://doi.org/10.1042/bst024354s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1996 Biochemical Society1996 Article PDF first page preview Close Modal You do not currently have access to this content.
High performance 1.55 µm polarisation-insensitive semiconductor optical amplifier based on low-tensile-strained bulk GaInAsP (1997)

High performance, polarisation-independent semiconductor optical amplifiers based on low-tensile-strained separate confinement heterostructures and integrated with a double core taper have been realised. Fibre-to-fibre gain as large as 29 dB, with TE-TM polarisation sensitivity as low as 0.3 dB and an output saturation power of ~9 dBm are currently achieved.
Exploiting memristance for low-energy neuromorphic computing hardware (2011)

As conventional CMOS technology approaches fundamental scaling limits novel nanotechnologies offer great promise for VLSI integration at nanometer scales. The memristor, or memory resistor, is a novel nanoelectronic device that holds great promise for continued scaling for emerging applications. Memristor behavior is very similar to that of the synapses necessary for realizing a neural network. In this research, we have considered circuits that leverage memristance in the realization of an artificial synapse that can be used to implement neuromorphic computing hardware. A novel charge sharing based neural network is described which consists of a hybrid of conventional CMOS technology and novel memristors. Simulation results are presented which demonstrate that dense CMOS-memristive neural networks can be implemented with energy consumption on the order of tens of femto-joules.
Strain-Temperature Discrimination Using a Single Fiber Bragg Grating (2010)

The out-diffusion of germanium from the core of a photosensitive fiber under elevated temperature is exploited to form a Fabry-Pe¿rot filter within a single fiber Bragg grating, by subjecting the diffused region to a single exposure using the standard phase-mask technique. A key aspect of our work is the measurement of the out-diffusion through energy dispersive X-ray analysis. Furthermore, we demonstrate the use of the above single-grating filter for discrimination and simultaneous measurement of strain and temperature. The proposed technique provides a significant advantage over other existing methods that require at least two gratings.
New substituted 4‐azatricyclo[4.3.1.1<sup>3,8</sup>]undecane derivatives (1986)

Abstract The synthesis of a series of new substituted 4‐azatricyclo[4.3.1.1 3.8 ]undecane and 4‐azatricyclo[4.3.1.1 3.8 ]‐undecan‐5‐one derivatives is described. Compounds 4f and 4g displayed antiviral activity.
Power-aware RAM mapping for FPGA embedded memory blocks (2006)

Embedded memory blocks are important resources in contemporary FPGA devices. When targeting FPGAs, application designers often specify high-level memory functions which exhibit a range of sizes and control structures. These logical memories must be mapped to FPGA embedded memory resources such that physical design objectives are met. In this work a set of power-aware logical-to-physical RAM mapping algorithms are described which convert user-defined memory specifications to on-chip FPGA memory block resources. These algorithms minimize RAM dynamic power by evaluating a range of possible embedded memory block mappings and selecting the most power-efficient choice. Our automated approach has been integrated into a commercial FPGA compiler and tested with 40 large FPGA benchmarks. Through experimentation, we show that, on average, embedded memory dynamic power can be reduced by 21% and overall core dynamic power can be reduced by 7% with a minimal loss (1%) in design performance.
Multicenter phase 3 study of the complement inhibitor eculizumab for the treatment of patients with paroxysmal nocturnal hemoglobinuria (2007)

The terminal complement inhibitor eculizumab was recently shown to be effective and well tolerated in patients with paroxysmal nocturnal hemoglobinuria (PNH). Here, we extended these observations with results from an open-label, non-placebo-controlled, 52-week, phase 3 clinical safety and efficacy study evaluating eculizumab in a broader PNH patient population. Eculizumab was administered by intravenous infusion at 600 mg every 7 +/- 2 days for 4 weeks; 900 mg 7 +/- 2 days later; followed by 900 mg every 14 +/- 2 days for a total treatment period of 52 weeks. Ninety-seven patients at 33 international sites were enrolled. Patients treated with eculizumab responded with an 87% reduction in hemolysis, as measured by lactate dehydrogenase levels (P < .001). Baseline fatigue scores in the FACIT-Fatigue instrument improved by 12.2 +/- 1.1 points (P < .001). Eculizumab treatment led to an improvement in anemia. The increase in hemoglobin level occurred despite a reduction in transfusion requirements from a median of 8.0 units of packed red cells per patient before treatment to 0.0 units per patient during the study (P < .001). Overall, transfusions were reduced 52% from a mean of 12.3 to 5.9 units of packed red cells per patient. Forty-nine patients (51%) achieved transfusion independence for the entire 52-week period. Improvements in hemolysis, fatigue, and transfusion requirements with eculizumab were independent of baseline levels of hemolysis and degree of thrombocytopenia. Quality of life measures were also broadly improved with eculizumab treatment. This study demonstrates that the beneficial effects of eculizumab treatment in patients with PNH are applicable to a broader population of PNH patients than previously studied. This trial is registered at http://clinicaltrials.gov as NCT00130000.
Radioreceptor Assay of Human Chorionic Gonadotropin: Detection of Early Pregnancy (1974)

A rapid, sensitive, and specific radioreceptor assay for the determination of human chorionic gonadotropin and luteinizing hormone in plasma is described. Plasma membranes of bovine corpora lutea of early pregnancy, which bind biologically active labeled human chorionic gonadotropin, have been used as receptor. Pregnancy could be detected by assaying the gonadotropin in plasma samples obtained from day 6 to 8 after conception.
Interband Cascade Photonic Integrated Circuits on Native III-V Chip (2021)

We describe how a midwave infrared photonic integrated circuit (PIC) that combines lasers, detectors, passive waveguides, and other optical elements may be constructed on the native GaSb substrate of an interband cascade laser (ICL) structure. The active and passive building blocks may be used, for example, to fabricate an on-chip chemical detection system with a passive sensing waveguide that evanescently couples to an ambient sample gas. A variety of highly compact architectures are described, some of which incorporate both the sensing waveguide and detector into a laser cavity defined by two high-reflectivity cleaved facets. We also describe an edge-emitting laser configuration that optimizes stability by minimizing parasitic feedback from external optical elements, and which can potentially operate with lower drive power than any mid-IR laser now available. While ICL-based PICs processed on GaSb serve to illustrate the various configurations, many of the proposed concepts apply equally to quantum-cascade-laser (QCL)-based PICs processed on InP, and PICs that integrate III-V lasers and detectors on silicon. With mature processing, it should become possible to mass-produce hundreds of individual PICs on the same chip which, when singulated, will realize chemical sensing by an extremely compact and inexpensive package.
Folksonomy-Based Term Extraction for Word Cloud Generation (2012)

In this work we study the task of term extraction for word cloud generation in sparsely tagged domains, in which manual tags are scarce. We present a folksonomy-based term extraction method, called tag-boost , which boosts terms that are frequently used by the public to tag content. Our experiments with tag-boost based term extraction over different domains demonstrate tremendous improvement in word cloud quality, as reflected by the agreement between manual tags of the testing items and the cloud’s terms extracted from the items’ content. Moreover, our results demonstrate the high robustness of this approach, as compared to alternative cloud generation methods that exhibit a high sensitivity to data sparseness. Additionally, we show that tag-boost can be effectively applied even in nontagged domains, by using an external rich folksonomy borrowed from a well-tagged domain.
Primary Structure and Functional Activity of a Phosphatidylinositol-Glycan-Specific Phospholipase D (1991)

A phosphatidylinositol-glycan-specific phospholipase D (PI-G PLD) that specifically hydrolyzes the inositol phosphate linkage in proteins anchored by phosphatidylinositol-glycans (PI-Gs) has recently been purified from human and bovine sera. The primary structure of bovine PI-G PLD has now been determined and the functional activity of the enzyme has been studied. Expression of PI-G PLD complementary DNA in COS cells produced a protein that specifically hydrolyzed the inositol phosphate linkage of the PI-G anchor. Cotransfection of PI-G PLD with a PI-G-anchored protein resulted in the secretion of the PI-G-anchored protein. The results suggest that the expression of PI-G PLD may influence the expression and location of PI-G-anchored proteins.
Parameterized environment maps (2001)

Article Share on Parameterized environment maps Authors: Ziyad S. Hakura Stanford Univ., Stanford, CA Stanford Univ., Stanford, CAView Profile , John M. Snyder Microsoft Research Microsoft ResearchView Profile , Jerome E. Lengyel Microsoft Research Microsoft ResearchView Profile Authors Info & Claims I3D '01: Proceedings of the 2001 symposium on Interactive 3D graphicsMarch 2001 Pages 203–208https://doi.org/10.1145/364338.364402Online:01 March 2001Publication History 20citation497DownloadsMetricsTotal Citations20Total Downloads497Last 12 Months4Last 6 weeks0 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
Model-Plant Mismatch Detection with Support Vector Machines (2017)

We propose a model-plant mismatch (MPM) detection strategy based on a novel closed-loop identification approach and one-class support vector machine (SVM) learning technique. With this scheme we can monitor MPM and noise model change separately, thus discriminating the MPM from noise model change. Another advantage of this approach is that it is applicable to routine operating data that may lack any external excitations. Theoretical derivations on the closed-loop identification method are provided in this paper, showing that it can furnish a consistent parameter estimate for the process model even in the case where a priori knowledge about the true noise model structure is not available. We build an SVM model based on process and noise model estimates from training data to predict the occurrence of MPM in the testing data. An example on paper machine control is provided to verify the proposed MPM detection framework.
Evaluating the Rate and Substrate Specificity of Laboratory Evolved XNA Polymerases (2017)

Engineered polymerases that can copy genetic information between DNA and xeno-nucleic acids (XNA) hold tremendous value as reagents in future biotechnology applications. However, current XNA polymerases function with inferior activity relative to their natural counterparts, indicating that current polymerase engineering efforts would benefit from new benchmarking assays. Here, we describe a highly parallel, low-cost method for measuring the average rate and substrate specificity of XNA polymerases in a standard qPCR instrument. Our approach, termed polymerase kinetic profiling (PKPro), involves monitoring XNA synthesis on a self-priming template using high-resolution melting (HRM) fluorescent dyes that intercalate into the growing duplex as the template strand is copied into XNA. Since changes in fluorescence are directly proportional to XNA synthesis, quantitative measurements are obtained by calibrating the fluorescent signal against chemically synthesized standards. Using PKPro, we discovered that XNA polymerases function with rates of ∼1-80 nt/min and exhibit substrate specificities of ∼0.1-5-fold for xNTP versus dNTP. Last, we show how PKPro could be used in a highly parallel screen by analyzing 288 different polymerase reaction conditions. On the basis of these results, we suggest that PKPro provides a powerful tool for evaluating the activity of XNA polymerases.
Characterization of Flavonols in Cranberry (<i>Vaccinium macrocarpon</i>) Powder (2003)

Flavonoids were extracted from cranberry powder with acetone and ethyl acetate and subsequently fractionated with Sephadex LH-20 column chromatography. The fraction eluted with a 60% methanol solution was composed primarily of phenolic constituents with maximum absorbance at 340 nm. A high-performance liquid chromatography procedure was developed, which resolved 22 distinct peaks with UV/vis and mass spectra corresponding to flavonol glycoside conjugates. Six new constituents not previously reported in cranberry or in cranberry products were determined through NMR spectroscopy to be myricetin-3-beta-xylopyranoside, quercetin-3-beta-glucoside, quercetin-3-alpha-arabinopyranoside, 3'-methoxyquercetin-3-alpha-xylopyranoside, quercetin-3-O-(6' '-p-coumaroyl)-beta-galactoside, and quercetin-3-O-(6' '-benzoyl)-beta-galactoside. Quercetin-3-O-(6' '-p-coumaroyl)-beta-galactoside and quercetin-3-O-(6' '-benzoyl)-beta-galactoside represent a new class of cranberry flavonol compounds with three conjugated components consisting of a flavonol, sugar, and carboxylic acid (benzoic or hydroxycinnamic acids). This is also the first report identifying quercetin-3-arabinoside in both furanose and pyranose forms in cranberry. Elucidation of specific flavonol glycosides in cranberry is significant since the specificity of the sugar moiety may play a role in the bioavailability of the flavonol glycosides in vivo.