gebhart/patrepeval huggingface dataset:
Modified constructs of the tRNA TPsiC domain to probe substrate conformational requirements of m1A58 and m5U54 tRNA methyltransferases (2000)

The TPsiC stem and loop (TSL) of tRNA contains highly conserved nucleoside modifications, m(5)C(49), T(54), Psi(55)and m(1)A(58). U(54)is methylated to m(5)U (T) by m(5)U(54)methyltransferase (RUMT); A(58)is methylated to m(1)A by m(1)A(58)tRNA methyltransferase (RAMT). RUMT recognizes and methylates a minimal TSL heptadecamer and RAMT has previously been reported to recognize and methylate the 3'-half of the tRNA molecule. We report that RAMT can recognize and methylate a TSL heptadecamer. To better understand the sensitivity of RAMT and RUMT to TSL conformation, we have designed and synthesized variously modified TSL constructs with altered local conformations and stabilities. TSLs were synthesized with natural modifications (T(54)and Psi(55)), naturally occurring modifications at unnatural positions (m(5)C(60)), altered sugar puckers (dU(54)and/or dU(55)) or with disrupted U-turn interactions (m(1)Psi(55)or m(1)m(3)Psi(55)). The unmodified heptadecamer TSL was a substrate of both RAMT and RUMT. The presence of T(54)increased thermal stability of the TSL and dramatically reduced RAMT activity toward the substrate. Local conformation around U(54)was found to be an important determinant for the activities of both RAMT and RUMT.
Assessment of an ultra-sensitive IFNγ immunoassay prototype for latent tuberculosis diagnosis (2018)

Worldwide there are about 1.7 billion individuals with latent tuberculosis infection (LTBI) and only 5% to 15% will develop active tuberculosis (TB). It is recommended to treat only those most at risk of developing active TB to avoid problems of drug resistance. LTBI diagnosis involves reviewing the individual's medical history, physical examination, and biological tests. Interferon gamma release assays (IGRA) can yield "undeterminate" or "uncertain" results, which makes clinical management decisions difficult. We assessed an ultra-sensitive immunoassay prototype based on single molecule array (SiMoA) technology to evaluate its overall performance, and in particular, its performance for indeterminate and uncertain positive or negative samples, as classified by the results from the current ELISA technique used for IFNγ quantification. We analyzed samples from hospitalized or consulting patients and healthcare workers from three hospitals in Paris, previously classified as negative (n = 30), positive (n = 35), uncertain negative (n = 25), uncertain positive (n = 31), or indeterminate (n = 30). We observed that with the SiMoA assay 83.3% of the indeterminate samples became interpretable and could be classified as negative, whereas 74% of uncertain positive samples were classified as positive. Most uncertain negative samples (72%) were reclassified as uncertain positive (68%) or positive (4%). The results suggest that the ultra-sensitive SiMoA IFNγ assay could represent a useful tool for the identification of true positive and negative samples among those giving indeterminate or uncertain results with the TB IGRA assay currently used.
Dopaminergic agents for the treatment of cocaine abuse (1999)

Cocaine is a major drug of abuse whose devastating effects have captured the attention of health officials and policy makers. Based upon the alarming health and crime-related costs associated with the use of this powerful reinforcing drug, immediate therapies are needed for the treatment of cocaine addiction. In this review, some of the small-molecule-based approaches that have been pursued in the search for such medications are highlighted. Because the pharmacological actions of cocaine stem laargely from its ability to block the dopamine transporter, many intervention strategies have focused on the dopaminergic pathway.
Radiation-induced Luminescence Properties of Tm-doped Bi4Ge3O12 Single Crystals (2023)

We grew 0.1, 0.5, and 1% Tm-doped Bi 4 Ge 3 O 12 single crystals by the floating zone method.Their photoluminescence and scintillation properties were investigated in the range from visible to near-IR.Luminescence spectra and decay times consistent with the transitions of Tm 3+ were confirmed.X-ray-irradiated dose rate response properties were evaluated using the prepared samples and an InGaAs photodiode.The 1% Tm-doped sample showed the widest dynamic range (0.03-60 Gy/h) among the prepared samples.
Introduction (2007)

This special issue brings together a collection of papers that were presented in a symposium on “Fracture and Relaxations in Polymer Solids” at the 2005 American Chemical Society (ACS) Meeting in Washington DC. This special symposium was held in honor of the 60th birthday of Professor Albert Yee, truly one of the pioneers in the field of polymer science responsible for elucidating the chemistry, physics, and mechanics that govern polymer relaxation, fracture, and yield. Understanding and controlling the way that a material mechanically yields or fails is of enormous technical and economic importance. As a result, in the 70's, 80's and early 90's, yield and fracture was one of the “hot” topics in the polymer field. In the past decade or so there has been considerably less research activity in the fracture and yield of polymer-based systems, even though much remains to be learned. Meanwhile, the innovations on the materials development side have not stopped. We are now seeing a host of new and interesting polymeric compounds, composite or multiphase systems, hybrids that blur the lines between ceramic, metals, and polymers, and even an entirely new field of nanoscale materials. In addition to recent materials developments, scientists also have a host of new and improved analytical or characterization tools that can shed deeper insight in the chemistry, physics, and mechanics of yield and fracture. An equally important motivation for this special symposium, besides looking back to honor the work of the pioneers, is to renew research interests on this critical issue. As long as materials are used in real world or engineering applications, their mechanical properties will always be of major importance. This was clear from the strong participation in the special ACS symposium. Over 35 of the leading experts in the field presented both invited and contributed papers on this topic at this special symposium. This special issue contains a small subset of these papers. Christopher L. Soles
Chemical and Biological Assessments of the Essential Oils of Chrysophyllum albidum G. Don (2017)

The chemical compositions of the essential oils obtained from six tree parts of Chrysophyllum albidum (Sapotaceae) were extracted by hydrodistillation and analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). A total of 65, 33, 45, 21, 25 and 18 compounds, representing 79.49%, 100%, 90.81%, 98.43%, 96.62% and 98.37% of the total oil, were identified in the fruit bark, root bark, stem bark, seed bark, leaf and seed, respectively. The dominant compounds in the essential oils in six tree parts were m-xylene (66.7%; seed), p-xylene (21.4%; seed bark), -farnesene (38.1%; leaf), hexadecanoic acid (14.7%; stem bark), m-xylene (53.1%; root bark) and hexadecanoic acid (12.7%; fruit bark). The essential oils were evaluated for their antibacterial, antioxidant and insecticidal activities using Alamar blue assay, DPPH radical scavenging activity and contact toxicity test, respectively. The oils displayed moderate antibacterial potentials to some tested organisms and low radical scavenging activity to DPPH. Rhyzopertha dominica was susceptible to C. albidum stem bark essential oil only.
Optimization of Far-Field Radiation From Impedance-Loaded Nanoloops Accelerated by an Exact Analytical Formulation (2018)

Impedance loading is a common technique traditionally used in the RF to enhance the performance of an antenna, but its application in the optical regime is not as rigorously studied. This is mainly due to a lack of exact analytical expressions that can be used to rapidly predict the radiation properties of loaded nanoantennas. This paper will derive a set of useful analytical expressions for the far-field radiation properties of loop antennas loaded with an arbitrary number of lumped impedances that are valid from the RF-to-optical regimes. The analytical expressions will be validated with full-wave solvers and can be evaluated more than $100\times $ faster. The ability to perform such rapid evaluations enables, for the first time, large-scale single-objective and multi-objective optimizations. A series of optimizations reveal that electrically small superdirective antennas can be achieved at a variety of far-field angles through capacitive loading, paving the way for a pattern reconfigurable antenna. In addition, gains of greater than 3 dB can be achieved for electrically small antennas over a fractional bandwidth of 28%. Finally, it is shown that impedance loading can be used to achieve circularly polarized radiation from a single loop.
Advanced Color Toner for Fine Image Quality (2007)

Application of full color printers has spread rapidly in the office environment, and demands on the full color printer have been also increasing; especially, high-speed printing, oilless fusing and fine image quality are strongly requested. Recently, several types of chemical toner have been launched. Because they have small and narrow particle size distributions, they have an advantage in fine image quality. However, the resin of chemical toners are usually styrene-acrylic, which is not suitable for high-speed printing and glossy images for pictorial applications because the styrene-acrylic has to be high molecular weight to make toner have sufficient durability. On the other hand, polyester has better properties for high-speed printing than styrene-acrylic because of the existence of a polar group that enhances a compatibility with the cellulose of paper. Polyester has good durability even if it has a low molecular weight and thus can provide a glossy image. Thus polyester has several advantages over styrene-acrylic. In general, it is difficult to use polyester as the binder resin of chemical toner. On the other hand, it is easy to make polyester color toner by the pulverization method, but it is difficult to make pulverized toner having small and narrow particle size distribution for fine image quality, and it is also difficult to make pulverized toner having both oilless fusing ability and sufficient durability. In this article, design of oilless fusable, pulverized color toner with small and narrow particle size distribution was investigated. This advanced color toner named "MC toner" can provide high-speed printing, oilless fusing, and also fine image quality.
HSCT high-lift technology requirements (1992)

The viewgraphs and discussion of high lift needs and related aerodynamic goals established in system studies are described. The goals are presented for the takeoff, approach, and subsonic climb and cruise modes. The status of the related high lift databases and available design and analysis methods are described. Various high lift research and technology areas for future work including innovative concepts verification, flap design, computational fluid dynamics (CFD) calibration and application, high Reynolds number testing, subsonic/transonic flap optimization, and flight testing are described.
Regulation of LFA-1 Expression by CD34 Positive Cells and Inducible Growth Factor Production by Stroma Enable Formation of Bone Marrow Compartments; Subject Heading (2000)

Leukocyte function associated antigen 1 (LFA-1) is an adhesion molecule indispensable in immune and inflammatory reactions, but its role in hematopoiesis is poorly understood. LFA-1 is considered as a marker of late stage stem cell maturation when expressed on CD34(+) bone marrow cells. We observed that CD34(+) bone marrow cells express LFA-1, that based on LFA-1 expression several subpopulations can be distinguished, and that the level of expression appeared highly variable among different donors. Unanticipated, in time course experiments we observed that CD34(+) LFA-1(-) cells expressed LFA-1 within 24 hours upon culture. These in vitro findings support the hypothesis that once contacts with bone marrow stroma are lost, LFA-1 is upregulated by default, due to the lack of negative regulating signals from stromal cells. This might also explain the widely variable expression of LFA-1 as a result of crowding of cells in the bone marrow with subsequent loss of contact with stroma and upregulation of LFA-1, thus equipping cells with adequate adhesion receptors to migrate throughout the bone marrow. Interestingly, the expression of the LFA-1 specific activation epitope L16 on these cells is low, even after culture. This demonstrated that LFA-1 is not activated, as was confirmed by low adhesion to ICAM-1. Activation of adhesion molecules is induced by several growth factors. Indeed, we show here that an osteoblastic cell line under normal conditions does hardly produce hematopoietic growth factors but these are rapidly induced after stimulation. Such rapid induction endows the bone marrow stroma with the property to modulate the adhesive strength and enabling migration through the different environments within the stroma. Prove for such compartments within the bone marrow is provided by histological data.
The Future of Drug Delivery (2023)

Drug delivery technologies have been proven to improve treatment outcomes in many ways, including enhancing therapeutic efficacy, reducing toxicity, increasing patient compliance, and enabling entirely new medical treatments.As the therapeutic landscape has evolved
Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET (2020)

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.
Reversing Endogenous Alloreactive B Cell GC Responses With Anti-CD154 or CTLA-4Ig (2013)

Alloantibodies mediate acute antibody-mediated rejection as well as chronic allograft rejection in clinical transplantation. To better understand the cellular dynamics driving antibody production, we focused on the activation and differentiation of alloreactive B cells in the draining lymph nodes and spleen following sensitization to allogeneic cells or hearts. We used a modified staining approach with a single MHC Class I tetramer (K(d)) bound to two different fluorochromes to discriminate between the Class I-binding and fluorochrome-streptavidin-binding B cells with a high degree of specificity and binding efficiency. By Day 7-8 postsensitization, there was a 1.5- to 3.2-fold increase in the total numbers of K(d) -binding B cells. Within this K(d) -binding B cell population, approximately half were IgD(low) , MHC Class II(high) and CD86(+), 30-45% expressed a germinal center (Fas(+) GL7(+)) phenotype and 3-12% were IRF4(hi) plasma cells. Remarkably, blockade with anti-CD40 or CTLA-4Ig, starting on Day 7 postimmunization for 1 or 4 weeks, completely dissolved established GCs and halted further development of the alloantibody response. Thus MHC Class I tetramers can specifically track the in vivo fate of endogenous, Class I-specific B cells and was used to demonstrate the ability of delayed treatment with anti-CD154 or CTLA-4Ig to halt established allo-B cell responses.
Notch ligands potentiate IL‐7‐driven proliferation and survival of human thymocyte precursors (2009)

Notch and IL-7 are both well-characterized factors involved in T-cell development. In contrast to the mouse model, their precise requirements in the differentiation and/or proliferation of various stages of human thymic development have not been fully explored. Here, we demonstrate that IL-7 alone is sufficient to induce the differentiation of ex vivo purified CD34(+) triple negative (TN) surface (s) CD3(-) CD4(-)CD8(-) (CD3(-)CD4(-)CD8(-)), CD4 immature single positive (ISP) (sCD3(-)CD4(+)CD8(-)) and double positive (DP) (sCD3(-)CD4(+)CD8(+)) human thymic precursors to mature DP expressing sCD3 (sCD3(+)CD4(+)CD8(+)). We show that activation of Notch signaling by its ligands Delta-1 or Delta-4 potentiates IL-7-driven proliferation and survival of CD34(+) TN and to a lesser extent of CD4(+) ISP precursors. This effect of Notch is related to a sustained induction of IL-7 receptor alpha chain expression on thymocytes through a decreased methylation of its gene promoter. Thus, we show here that proliferation and differentiation of T-cell precursors are differentially modulated by IL-7 depending on the presence or absence of external signals. These results may have important implications for the clinical use of this cytokine as a strategy aimed at improving immune restoration.
Science Mandates Precision: A Plea for Accuracy in Reporting (2017)

No AccessJournal of UrologyCommentary1 May 2018Science Mandates Precision: A Plea for Accuracy in Reporting Michael Owyong, Roshan M. Patel, Jaime Landman, and Ralph V. Clayman Michael OwyongMichael Owyong More articles by this author , Roshan M. PatelRoshan M. Patel More articles by this author , Jaime LandmanJaime Landman More articles by this author , and Ralph V. ClaymanRalph V. Clayman More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2017.10.028AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Science Mandates Precision: A Plea for Accuracy in Reporting." The Journal of Urology, 199(5), pp. 1123–1124 References 1 : Tubeless percutaneous renal surgery. J Urol1997; 157: 1578. Link, Google Scholar 2 : Percutaneous nephrostolithotomy: complications of premature nephrostomy tube removal. J Urol1986; 136: 77. Link, Google Scholar 3 : The “mini-perc” technique: a less invasive alternative to percutaneous nephrolithotomy. World J Urol1998; 16: 371. Google Scholar 4 : Single-step percutaneous nephrolithotomy (microperc): the initial clinical report. J Urol2011; 186: 140. Link, Google Scholar 5 : Extracorporeal shock wave lithotripsy: the Methodist Hospital of Indiana experience. J Urol1986; 135: 1134. Link, Google Scholar 6 : Accuracy of ultrasonography for renal stone detection and size determination: is it good enough for management decisions?. BJU Int2017; 119: 464. Google Scholar 7 : Ultra-low-dose, low-dose, and standard-dose CT of the kidney, ureters, and bladder: is there a difference? Results from a systematic review of the literature. Clin Radiol2017; 72: 11. Google Scholar 8 : Prospective evaluation of stone free rates by computed tomography after aggressive ureteroscopy. J Endourol2017; 31: A122. abstract MP8–19. Google Scholar © 2018 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetailsCited BySur R (2021) Editorial CommentJournal of Urology, VOL. 206, NO. 3, (537-537), Online publication date: 1-Sep-2021. Volume 199Issue 5May 2018Page: 1123-1124 Advertisement Copyright & Permissions© 2018 by American Urological Association Education and Research, Inc.MetricsAuthor Information Michael Owyong More articles by this author Roshan M. Patel More articles by this author Jaime Landman More articles by this author Ralph V. Clayman More articles by this author Expand All Advertisement Loading ...
Involvement of 14-3-3 Proteins in the Second Epidermal Growth Factor-induced Wave of Rac1 Activation in the Process of Cell Migration (2011)

Immense previous efforts have elucidated the core machinery in cell migration, actin remodeling regulated by Rho family small GTPases including RhoA, Cdc42, and Rac1; however, the spatiotemporal regulation of these molecules remains largely unknown. Here, we report that EGF induces biphasic Rac1 activation in the process of cell migration, and UTKO1, a cell migration inhibitor, inhibits the second EGF-induced wave of Rac1 activation but not the first wave. To address the regulation mechanism and role of the second wave of Rac1 activation, we identified 14-3-3ζ as a target protein of UTKO1 and also showed that UTKO1 abrogated the binding of 14-3-3ζ to Tiam1 that was responsible for the second wave of Rac1 activation, suggesting that the interaction of 14-3-3ζ with Tiam1 is involved in this event. To our knowledge, this is the first report to use a chemical genetic approach to demonstrate the mechanism of temporal activation of Rac1.
Non contact ultrasound stethoscope (2014)

Heartbeat and respiration are very important vital signs that indicate health and psychological states of a person. Recent technologies allow to detect both physical parameters on a human subject by using different techniques with and without contact. Noncontact systems often use electromagnetic waves for contactless measurement but approaches based on ultrasound waves, laser or video processes are also proposed. In this abstract an alternative ultrasound system for non-contact and local measurement is presented. The system works in echographic mode and ultrasound signals are processed using two methods. The experimental setup uses an elliptic mirror to focus ultrasonic waves onto the skin surface. Backscattered waves are recorded by a microphone located close to the emitting transducer. Heartbeat and respiration signals are determined from the skin displacement caused by the chest-wall motion. For comparison purpose, the cross-correlation method, which uses broadband signal, and the Doppler method, which uses narrowband signal, are applied to measure the skin displacement. Sensitivity and accuracy parameters of the two methods are compared. At least, as the measurement is local, the system can act as a noncontact stethoscope to listen the internal sounds of the human body even through the light clothes of the patient.
Extreme Values in Optical Fiber Communication Systems (2020)

Extreme value theory provides a framework to assess rare but extreme events such as network outages or cycle slips. We present the theory of extreme value statistics and its application to optical fiber communication systems. © 2020 The Author
Left atrial thrombus resolution in atrial fibrillation or flutter: Results of a prospective study with rivaroxaban (X-TRA) and a retrospective observational registry providing baseline data (CLOT-AF) (2016)

X-TRA is the first prospective, multicenter study examining LA/LAA thrombus resolution with a non-VKA oral anticoagulant in VKA-naïve patients or in patients with suboptimal VKA therapy. Rivaroxaban could be a potential option for the treatment of LA/LAA thrombi.