gebhart/patrepeval huggingface dataset:
Cyan-emitting and orange-emitting fluorescent proteins as a donor/acceptor pair for fluorescence resonance energy transfer (2004)

GFP (green fluorescent protein)-based FRET (fluorescence resonance energy transfer) technology has facilitated the exploration of the spatio-temporal patterns of cellular signalling. While most studies have used cyan- and yellow-emitting FPs (fluorescent proteins) as FRET donors and acceptors respectively, this pair of proteins suffers from problems of pH-sensitivity and bleeding between channels. In the present paper, we demonstrate the use of an alternative additional donor/acceptor pair. We have cloned two genes encoding FPs from stony corals. We isolated a cyan-emitting FP from Acropara sp., whose tentacles exhibit cyan coloration. Similar to GFP from Renilla reniformis, the cyan FP forms a tight dimeric complex. We also discovered an orange-emitting FP from Fungia concinna. As the orange FP exists in a complex oligomeric structure, we converted this protein into a monomeric form through the introduction of three amino acid substitutions, recently reported to be effective for converting DsRed into a monomer (Clontech). We used the cyan FP and monomeric orange FP as a donor/acceptor pair to monitor the activity of caspase 3 during apoptosis. Due to the close spectral overlap of the donor emission and acceptor absorption (a large Förster distance), substantial pH-resistance of the donor fluorescence quantum yield and the acceptor absorbance, as well as good separation of the donor and acceptor signals, the new pair can be used for more effective quantitative FRET imaging.
Safety and Feasibility of Repeated and Transient Blood–Brain Barrier Disruption by Pulsed Ultrasound in Patients with Recurrent Glioblastoma (2019)

SonoCloud-1 treatments were well tolerated and may increase the effectiveness of systemic drug therapies, such as carboplatin, in the brain without inducing neurotoxicity.<i>See related commentary by Sonabend and Stupp, p. 3750</i>.
Mild insomnia induced by environmental perturbations in the rat: a study of this new model and of its possible applications in pharmacological research. (1982)

This paper describes an experimental model for testing new products in a situation where sleep is impaired by a nonpharmacological procedure. This model consists in studying the effect of hypnogenic substances on sleep perturbations which take place when chronically implanted rats are moved to a novel individual cage, connected for the first time to their recording cable and dosed intragastrically with test products, vehicle or placebo. Continuous polygraphic recordings were taken throughout the daily treatment period (15 days) and scored for the presence of slow wave sleep (SWS), and rapid eye movement sleep (REM). The hourly vigilance stages were also computed to determine the parameters of their nycthemeral rhythms. In vehicle-treated rats, a decrease in SWS and REM values and a delay of SWS and REM phases of nycthemeral rhythms occurred on the first day as compared with the end of the recording period. Phenobarbital (5 mg/kg p.o.), mecloqualone (5 mg/kg p.o.) and a new benzodiazepine CM 7302 (7 mg/kg p.o.) led to an immediate or fast recovery, whereas no improvement was observed with placebo and with clorazepate dipotassium (9 mg/kg p.o.). This model can be considered as an attractive model for studying mild insomnia because it allows "true" hypnogenic drugs to be selected in a minimum amount of time.
Novel Immunoreactive Glycoprotein Orthologs of Ehrlichia spp. (2003)

We previously identified a strongly immunoreactive 43 kDa protein (p43) of Ehrlichia canis. As an immunodiagnostic antigen, the p43 had a 96% accuracy as compared with IFA and provided species-specific diagnosis of E. canis infections. Further investigation has revealed that the E. canis p43 represents the N-terminal portion of the largest immunoreactive protein described in Ehrlichia spp. with a predicted molecular mass of 153 kDa. Analysis of the recombinant N-terminal region (p43) of the p153 by protein gel electrophoresis demonstrated a larger than predicted molecular mass (approximately 30%), and presence of carbohydrate glycans, indicating that the p153 is a glycoprotein. A BLASTn search was performed on the E. chaffeensis genome sequence (95%), and the gene encoding the p153 ortholog was identified in E. chaffeensis. The E. canis p153 (4,263 bp) and E. chaffeensis p156 (4,389 bp) genes had similar chromosomal locations, downstream of the homologous (approximately 87%) deoxyguanosine-triphosphate triphosphohydrolase genes, and homologous (approximately 90%) intergenic sequences preceding the open reading frames. Nucleic acid sequence homology (52%) observed between the glycoprotein genes supported previous findings with regard to genetic divergence of the p43 gene fragment, and the p153 and p156 proteins had amino acid similarity of 32%. A native E. canis protein with a molecular mass of 200 kDa reacted with antisera produced against the N-terminal region (p43) of the p153, suggesting that the native protein was posttranslationally modified. Similarly, recombinant constructs of E. chaffeensis p156 migrated larger than predicted (approximately 200 kDa), and carbohydrate was detected on the recombinant proteins. The chromosomal location, amino acid homology, and biophysical properties support the conclusion that the p153 and p156 glycoproteins (designated gp200s) are species-specific immunoreactive orthologs.
Stretchability of thin metal films on elastomer substrates (2004)

Many flexible electronic surfaces comprise inorganic films on organic substrates. Mechanical failure of such integrated structures of stiff and compliant materials poses a significant challenge. This letter studies the stretchability of metal films on elastomer substrates. Our experiment shows that, when stretched, elastomer-supported metal films rupture at strains larger than those reported for freestanding films. We use a finite element code to simulate the rupture process of metal films. A freestanding metal film ruptures by forming a single neck. By contrast, a metal film on an elastomer substrate may develop an array of necks before rupture. While the pre-rupture necks do not change the electrical conductance appreciably, they elongate the metal film, leading to a large overall rupture strain.
A Magnetic Bead-Based Sensor for the Quantification of Multiple Prostate Cancer Biomarkers (2015)

Novel biomarker assays and upgraded analytical tools are urgently needed to accurately discriminate benign prostatic hypertrophy (BPH) from prostate cancer (CaP). To address this unmet clinical need, we report a piezeoelectric/magnetic bead-based assay to quantitate prostate specific antigen (PSA; free and total), prostatic acid phosphatase, carbonic anhydrase 1 (CA1), osteonectin, IL-6 soluble receptor (IL-6sr), and spondin-2. We used the sensor to measure these seven proteins in serum samples from 120 benign prostate hypertrophy patients and 100 Gleason score 6 and 7 CaP using serum samples previously collected and banked. The results were analyzed with receiver operator characteristic curve analysis. There were significant differences between BPH and CaP patients in the PSA, CA1, and spondin-2 assays. The highest AUC discrimination was achieved with a spondin-2 OR free/total PSA operation--the area under the curve was 0.84 with a p value below 10(-6). Some of these data seem to contradict previous reports and highlight the importance of sample selection and proper assay building in the development of biomarker measurement schemes. This bead-based system offers important advantages in assay building including low cost, high throughput, and rapid identification of an optimal matched antibody pair.
Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes (2007)

The recombinant HIV-1 Tat protein contains a small region corresponding to residues 47 YGRKKRRQRR 57 R, which is capable of translocating cargoes of different molecular sizes, such as proteins, DNA, RNA, or drugs, across the cell membrane in an apparently energy-independent manner. The pathway that these peptides follow for entry into the cell has been the subject of strong controversy for the last decade. This peptide is highly basic and hydrophilic. Therefore, a central question that any candidate mechanism has to answer is how this highly hydrophilic peptide is able to cross the hydrophobic barrier imposed by the cell membrane. We propose a mechanism for the spontaneous translocation of the Tat peptides across a lipid membrane. This mechanism involves strong interactions between the Tat peptides and the phosphate groups on both sides of the lipid bilayer, the insertion of charged side chains that nucleate the formation of a transient pore, followed by the translocation of the Tat peptides by diffusing on the pore surface. This mechanism explains how key ingredients, such as the cooperativity among the peptides, the large positive charge, and specifically the arginine amino acids, contribute to the uptake. The proposed mechanism also illustrates the importance of membrane fluctuations. Indeed, mechanisms that involve large fluctuations of the membrane structure, such as transient pores and the insertion of charged amino acid side chains, may be common and perhaps central to the functions of many membrane protein functions.
Regional left ventricular wall motion in pacing induced angina. (1988)

Left ventricular cineangiograms (30 degrees right anterior oblique projection) and high fidelity left ventricular pressure were recorded at rest in 10 individuals with normal hearts and at rest and during an episode of angina provoked by rapid atrial pacing in 14 patients with obstructive coronary artery disease. Angiograms were digitised frame by frame. The ventricular perimeter was divided into 40 segments and regional ventricular function was examined by means of isometric and contour plots and by the construction of segmental pressure-wall displacement loops. In 10 patients 12 abnormal resting regions were identified. The commonest (11 regions) was delayed onset of inward endocardial motion during systole which was manifest by diagonal contour lines on the contour plot. Six regions (five with associated delay in onset of inward motion) showed resting hypokinesis. Angina was associated with the development of 19 new regions of abnormal wall motion in 12 patients. Fourteen of these regions of abnormality were thought to be primary events occurring as a consequence of ischaemia and five to be secondary events occurring in normally perfused regions of myocardium. Hypokinesis occurred in 12 regions, developing in a region with normal amplitude at rest in seven and as an extension of resting hypokinesis in five. In 10 out of 12 cases the region of hypokinesis developed in a region showing diagonal contour lines at rest. Asynchrony with delay in the timing of peak inward displacement relative to minimum volume occurred with angina in eight regions (in six cases concomitant with hypokinesis and in two cases in isolation). In contrast with hypokinesis the pattern of wall motion at rest did not permit regions developing asynchrony with angina to be identified. Pressure-displacement loops show that regional hypokinesis is associated with reduced segmental work and that regional asynchrony (delayed or premature timing of peak inward endocardial displacement) is associated with a loss of efficiency of energy transfer between the myocardium and the circulation. These observations illustrate the complex nature of wall motion abnormalities occurring with angina.
A Downhill Simplex Algorithm for Estimating Morphological Degradation Model Parameters (2001)

Noise models are crucial for designing image restoration algorithms, generating synthetic training data, and predicting algorithm performance. However, to accomplish any of these tasks, an estimate of the degradation model parameters is essential. In this paper we describe a parameter estimation algorithm for a morphological, binary image degradation model. The inputs to the estimation algorithm are i) the degraded image, and ii) information regarding the font type (italic, bold, serif, sans serif). We simulate degraded images and search for the optimal parameter by looking for a parameter value for which the neighborhood pattern distributions in the simulated image and the given degraded image are most similar. The parameter space is searched using the Nelder-Mead downhill simplex algorithm. We use the p-value of the Kolmogorov-Smirnov test for the measure of similarity between the two neighborhood pattern distributions. We show results of our algorithm on degraded document images. This research was funded in part by the Science Application International Corporation under Contract 4400019848, the Defense Advanced Research Projects Agency under Contract N660010028910, and the National Science Foundation under Grant IIS9987944. LAMP-TR-066 CAR-TR-963 CS-TR-4219 4400019848 N660010028910/IIS9987944 February 2001 A Downhill Simplex Algorithm for Estimating Morphological Degradation Model Parameters Tapas Kanungo and Qigong Zheng A Downhill Simplex Algorithm for Estimating Morphological Degradation Model Parameters Tapas Kanungo and Qigong Zheng Center for Automation Research University of Maryland College Park, MD 20742-3275 fkanungo,qzhengg@cfar.umd.edu Abstract Noise models are crucial for designing image restoration algorithms, generating synthetic tra...
Expression of p15ink4b gene during megakaryocytic differentiation of normal and myelodysplastic hematopoietic progenitors (2001)

In myelodysplastic syndrome (MDS), the expression of the cyclin-dependent kinase inhibitor p15(ink4B) (p15) is frequently decreased because of the aberrant methylation of the gene promoter; p15 is normally up-regulated during megakaryocytic differentiation. It was hypothesized that p15 methylation and deregulation of gene expression contribute to defective megakaryocytopoiesis in patients with MDS. Here it is shown that the increasing autocrine production of TGF-beta1 stimulates megakaryocytic differentiation in normal CD34(+) cells and that p15 mediates, at least in part, this effect. This TGF-beta1-dependent pathway is altered in MDS CD34(+) progenitors because of p15 methylation. The demethylating agent 2-deoxyAZAcytidin can restore the normal demethylated state of the p15 gene and increase its expression. Nevertheless, MDS CD34(+) cells only poorly differentiate to the megakaryocytic lineage. These findings suggest that p15 methylation occurs in a neoplastic clone with a profound defect of cell proliferation, survival, and differentiation that cannot be overcome by using a demethylating drug.
The dynamics of RUNX1-RUNX1T1 transcript levels after allogeneic hematopoietic stem cell transplantation predict relapse in patients with t(8;21) acute myeloid leukemia (2017)

RUNX1-RUNX1T1 transcripts with a <3-log reduction from diagnosis within 12 months and/or a <4-log reduction at ≥12 months after allo-HSCT could accurately predict relapse and may prompt a timely intervention in patients with t(8;21) AML.
Intrinsic Differences in the Proliferation of Naive and Memory Human B Cells as a Mechanism for Enhanced Secondary Immune Responses (2003)

Humoral immune responses elicited after secondary exposure to immunizing Ag are characterized by robust and elevated reactivity of memory B cells that exceed those of naive B cells during the primary response. The mechanism underlying this difference in responsiveness of naive vs memory B cells remains unclear. We have quantitated the response of naive and memory human B cells after in vitro stimulation with T cell-derived stimuli. In response to stimulation with CD40 ligand alone or with IL-10, both IgM-expressing and Ig isotype-switched memory B cells entered their first division 20-30 h earlier than did naive B cells. In contrast, the time spent traversing subsequent divisions was similar. Consistent with previous studies, only memory cells differentiated to CD38(+) blasts in a manner that increased with consecutive division number. These differentiated CD38(+) B cells divided faster than did CD38(-) memory B cell blasts. Proliferation of CD40 ligand-stimulated naive B cells as well as both CD38(+) and CD38(-) cells present in cultures of memory B cells was increased by IL-10. In contrast, IL-2 enhanced proliferation of CD38(-) and CD38(+) memory B cell blasts, but not naive cells. Thus, memory B cells possess an intrinsic advantage over naive B cells in both the time to initiate a response and in the division-based rate of effector cell development. These differences help explain the accelerated Ab response exhibited by memory B cells after secondary challenge by an invading pathogen, a hallmark of immunological memory.
Advanced engineering mathematics (1988)

I. ORDINARY DIFFERENTIAL EQUATIONS. 1. Introduction to Differential Equations. 2. Equations of First Order. 3. Linear Differential Equations of Second Order and Higher. 4. Power Series Solutions. 5. Laplace Transform. 6. Quantitative Methods: Numerical Solution of Differential Equations. 7. Qualitative Methods: Phase Plane and Nonlinear Differential Equations. II. LINEAR ALGEBRA. 8. Systems of Linear Algebraic Equations Gauss Elimination. 9. Vector Space. 10. Matrices and Linear Equations. 11. The Eigenvalue Problem. 12. Extension to Complex Case (Optional). III. SCALAR and VECTOR FIELD THEORY. 13. Differential Calculus of Functions of Several Variables. 14. Vectors in 3-Space. 15.Curves, Surfaces, and Volumes. 16. Scalar and Vector Field Theory. IV. FOURIER SERIES AND PARTIAL DIFFERENTIAL EQUATIONS. 17. Fourier Series, Fourier Integral, Fourier Transform. 18. Diffusion Equation. 19. Wave Equation. 20. Laplace Equation. V. COMPLEX VARIABLE THEORY. 21. Functions of a Complex Variable. 22. Conformal Mapping. 23. The Complex Integral Calculus. 24. Taylor Series, Laurent Series, and the Residue Theorem. Appendix A: Review of Partial Fraction Expansions. Appendix B: Existence and Uniqueness of Solutions of Systems of Linear Algebraic Equations. Appendix C: Table of Laplace Transforms. Appendix D: Table of Fourier Transforms. Appendix E: Table of Fourier Cosine and Sine Transforms. Appendix F: Table of Conformal Maps.
Lymphotoxin β Receptor (LtβR): Dual Roles in Demyelination and Remyelination and Successful Therapeutic Intervention Using LtβR–Ig Protein (2007)

Inflammation mediated by macrophages is increasingly found to play a central role in diseases and disorders that affect a myriad of organs, prominent among these are diseases of the CNS. The neurotoxicant-induced, cuprizone model of demyelination is ideally suited for the analysis of inflammatory events. Demyelination on exposure to cuprizone is accompanied by predictable microglial activation and astrogliosis, and, after cuprizone withdrawal, this activation reproducibly diminishes during remyelination. This study demonstrates enhanced expression of lymphotoxin beta receptor (Lt betaR) during the demyelination phase of this model, and Lt betaR is found in areas enriched with microglial and astroglial cells. Deletion of the Lt betaR gene (Lt betaR-/-) resulted in a significant delay in demyelination but also a slight delay in remyelination. Inhibition of Lt betaR signaling by an Lt betaR-Ig fusion decoy protein successfully delayed demyelination in wild-type mice. Unexpectedly, this Lt betaR-Ig decoy protein dramatically accelerated the rate of remyelination, even after the maximal pathological disease state had been reached. This strongly indicates the beneficial role of Lt betaR-Ig in the delay of demyelination and the acceleration of remyelination. The discrepancy between remyelination rates in these systems could be attributed to developmental abnormalities in the immune systems of Lt betaR-/- mice. These findings bode well for the use of an inhibitory Lt betaR-Ig as a candidate biological therapy in demyelinating disorders, because it is beneficial during both demyelination and remyelination.
Intratracheal Administration of Recombinant Human Factor IX (BeneFix™) Achieves Therapeutic Levels in Hemophilia B Dogs (2001)

The purpose of this paper was to establish proof of concept for administration of human recombinant F.IX (rF.IX) by inhalation for therapy of hemophilia B. The pharmacokinetics of intratracheal (IT) administration of rF.IX was studied in nine hemophilia B dogs randomized into 3 groups that received 200 IU/kg IT, 1,000 IU/kg IT, or 200 IU/kg intravenously (IV). IT rF.IX produced therapeutic levels of F.IX antigen and activity and the pharmacokinetic parameters were consistent with a slow release from a depot site within the lungs. Bioavailability compared to IV administration was 11% for 200 IU/kg IT and 4.9% for 1,000 IU/kg. The whole blood clotting time began to shorten at 2 h but F.IX bioactivity was not detected until 8 h post infusion in both IT groups. In all groups, F.IX activity was detected through 72 h post administration. These data demonstrate that biologically active rF.IX can reach the systemic circulation when given IT. Aerosolization of rF.IX may provide a needle-free therapeutic option for delivery of rF.IX to hemophilia B patients.
The modulation of Protein A-IgG(Fc) binding by the reversible addition of 2-nitrobenzyl groups (1995)

Conference Article| May 01 1995 The modulation of Protein A-IgG(Fc) binding by the reversible addition of 2-nitrobenzyl groups STEPHEN THOMPSON; STEPHEN THOMPSON 1Department of Clinical Biochemistry, The Medical School, Framlington Place, University of Newcastle, Newcastle Upon Tyne, NE2 4HH Search for other works by this author on: This Site PubMed Google Scholar MARIE-CLAUDE FAWCETT; MARIE-CLAUDE FAWCETT 1Department of Clinical Biochemistry, The Medical School, Framlington Place, University of Newcastle, Newcastle Upon Tyne, NE2 4HH Search for other works by this author on: This Site PubMed Google Scholar JULIA A. SPOORS; JULIA A. SPOORS 1Department of Clinical Biochemistry, The Medical School, Framlington Place, University of Newcastle, Newcastle Upon Tyne, NE2 4HH Search for other works by this author on: This Site PubMed Google Scholar COLIN H. SELF COLIN H. SELF 1Department of Clinical Biochemistry, The Medical School, Framlington Place, University of Newcastle, Newcastle Upon Tyne, NE2 4HH Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1995) 23 (2): 155S. https://doi.org/10.1042/bst023155s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation STEPHEN THOMPSON, MARIE-CLAUDE FAWCETT, JULIA A. SPOORS, COLIN H. SELF; The modulation of Protein A-IgG(Fc) binding by the reversible addition of 2-nitrobenzyl groups. Biochem Soc Trans 1 May 1995; 23 (2): 155S. doi: https://doi.org/10.1042/bst023155s 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. © 1995 Biochemical Society1995 Article PDF first page preview Close Modal You do not currently have access to this content.