gebhart/patrepeval huggingface dataset:
Macrocycles as protein–protein interaction inhibitors (2017)

Macrocyclic compounds such as cyclic peptides have emerged as a new and exciting class of drug candidates for inhibition of intracellular protein-protein interactions, which are challenging targets for conventional drug modalities (i.e. small molecules and proteins). Over the past decade, several complementary technologies have been developed to synthesize macrocycle libraries and screen them for binding to therapeutically relevant targets. Two different approaches have also been explored to increase the membrane permeability of cyclic peptides. In this review, we discuss these methods and their applications in the discovery of macrocyclic compounds against protein-protein interactions.
All-silicon nanorod-based Dammann gratings (2015)

Established diffractive optical elements (DOEs), such as Dammann gratings, whose phase profile is controlled by etching different depths into a transparent dielectric substrate, suffer from a contradiction between the complexity of fabrication procedures and the performance of such gratings. In this Letter, we combine the concept of geometric phase and phase modulation in depth, and prove by theoretical analysis and numerical simulation that nanorod arrays etched on a silicon substrate have a characteristic of strong polarization conversion between two circularly polarized states and can act as a highly efficient half-wave plate. More importantly, only by changing the orientation angles of each nanorod can the arrays control the phase of a circularly polarized light, cell by cell. With the above principle, we report the realization of nanorod-based Dammann gratings reaching diffraction efficiencies of 50%-52% in the C-band fiber telecommunications window (1530-1565 nm). In this design, uniform 4×4 spot arrays with an extending angle of 59°×59° can be obtained in the far field. Because of these advantages of the single-step fabrication procedure, accurate phase controlling, and strong polarization conversion, nanorod-based Dammann gratings could be utilized for various practical applications in a range of fields.
Development of a Gas−Liquid Chromatographic Method for the Analysis of Fatty Acid Tryptamides in Cocoa Products (2006)

The determination of the occurrence and level of cocoa shells in cocoa products and chocolate is an important analytical issue. The recent European Union directive on cocoa and chocolate products (2000/36/EC) has not retained the former limit of a maximum amount of 5% of cocoa shells in cocoa nibs (based on fat-free dry matter), previously authorized for the elaboration of cocoa products such as cocoa mass. In the present study, we report a reliable gas-liquid chromatography procedure suitable for the determination of the occurrence of cocoa shells in cocoa products by detection of fatty acid tryptamides (FATs). The precision of the method was evaluated by analyzing nine different samples (cocoa liquors with different ranges of shells) six times (replicate repeatability). The variations of the robust coefficient of variation of the repeatability demonstrated that FAT(C22), FAT(C24), and total FATs are good markers for the detection of shells in cocoa products. The trueness of the method was evaluated by determining the FAT content in two spiked matrices (cocoa liquors and cocoa shells) at different levels (from 1 to 50 mg/100 g). A good relation was found between the results obtained and the spiking (recovery varied between 90 and 130%), and the linearity range was established between 1 and 50 mg/100 g in cocoa products. For total FAT contents of cocoa liquor containing 5% shells, the measurement uncertainty allows us to conclude that FAT is equal to 4.01 +/- 0.8 mg/100 g. This validated method is perfectly suitable to determine shell contents in cocoa products using FAT(C22), FAT(C24), and total FATs as markers. The results also confirmed that cocoa shells contain FAT(C24) and FAT(C22) in a constant ratio of nearly 2:1.
Evaluation and management of the febrile young infant in the emergency department (2019)

Among young infants presenting with fever, untreated serious bacterial infections can have severe outcomes, so a full sepsis workup is often recommended but may not be necessary. This issue reviews the use of novel diagnostic tools such as procalcitonin, C-reactive protein, and RNA biosignatures as well as new risk stratification tools such as the Step-by-Step approach and the Pediatric Emergency Care Applied Research Network prediction rule to determine which febrile young infants require a full sepsis workup and to guide the management of these patients in the emergency department. The most recent literature assessing the risk of concomitant bacterial meningitis with urinary tract infections and the role for viral testing, specifically herpes simplex virus and enterovirus, are also reviewed.
Preparation and Induction of Immune Responses by a DNA AIDS Vaccine (2000)

In an effort to evaluate the feasibility of developing a safe DNA vaccine for acquired immunodeficiency syndrome (AIDS), we have prepared a plasmid-based immunogen modeled after a naturally occurring noninfectious mutant of the simian immunodeficiency virus (SIV). The mutant SIV genome produces defective virus particles that are noninfectious in vitro and nonpathogenic in vivo in rhesus macaques. Analysis of the mutant genome revealed a 1.6 kb deletion that is in frame and spans integrase, vif, vpx, and most of vpr and results in a pol/vpr gene fusion. This deletion was introduced into the parental pathogenic molecular clone and the U3 region of the 5' LTR was replaced with a cytomegalovirus promoter to produce a candidate DNA vaccine, pIV. After transfection with this plasmid, SIV gag and envelope proteins are expressed and properly processed in vitro. When injected into rabbits, pIV elicited an antibody response to SIV gp130 envelope glycoprotein with titers reaching 1:2048, and a strong lymphoproliferative response to SIV gp130 and whole SIV. The potential to produce defective virus particles in vivo without integrating into the host genome should result in both a strong humoral and cellular immune response in rhesus macaques. In addition, this approach offers a safe alternative to live attenuated vaccines and DNA vaccines that are capable of integration.
Low-Dose Inhaled Carbon Monoxide Reduces Pulmonary Vascular Resistance During Acute Hypoxemia in Adult Sheep (2001)

Carbon monoxide (CO) is produced by the action of the heme oxygenase (HO) complex through the oxidation of heme. CO, like nitric oxide (NO), is a molecular gas that among other actions stimulates guanylyl cyclase and increases cGMP levels in smooth muscle cells, regulating the vascular tone. Acute hypoxia generates pulmonary hypertension and increases the expression of inducible HO isoform (HO-1) in the vascular endothelium. Inhaled NO causes a potent pulmonary vasodilation. We hypothesized that inhaled CO might produce similar actions as NO on pulmonary vascular resistance (PVR). To test our contention, we studied the effects of inhaled CO (40 ppm) in the augmented PVR observed during hypoxemia. Five chronically instrumented German Merino sheep were submitted to a protocol consisting of 20 min of normoxemia (N), 20 min of isocapnic hypoxemia (H20), 20 min of isocapnic hypoxemia plus CO 40 ppm (H40), and 20 min of recovery (R). In the control protocol, we did not administer inhaled CO. Arterial gases and pH, percentage of carboxyhemoglobin (COHb), systemic and pulmonary arterial pressure, systemic and pulmonary vascular resistance, and cardiac output were measured during each period. During H20 period, there was a significant increase in cardiac output and PVR in sheep submitted to both protocols. The sheep treated with inhaled CO (H40 + CO) showed a modest but significant decrease (16%) in the elevated PVR. Our data indicate that inhaled CO decreases pulmonary vascular resistance associated with acute hypoxemia in adult sheep.
FXR/TGR5 Dual Agonist Prevents Progression of Nephropathy in Diabetes and Obesity (2017)

Bile acids are ligands for the nuclear hormone receptor farnesoid X receptor (FXR) and the G protein-coupled receptor TGR5. We have shown that FXR and TGR5 have renoprotective roles in diabetes- and obesity-related kidney disease. Here, we determined whether these effects are mediated through differential or synergistic signaling pathways. We administered the FXR/TGR5 dual agonist INT-767 to DBA/2J mice with streptozotocin-induced diabetes, db/db mice with type 2 diabetes, and C57BL/6J mice with high-fat diet-induced obesity. We also examined the individual effects of the selective FXR agonist obeticholic acid (OCA) and the TGR5 agonist INT-777 in diabetic mice. The FXR agonist OCA and the TGR5 agonist INT-777 modulated distinct renal signaling pathways involved in the pathogenesis and treatment of diabetic nephropathy. Treatment of diabetic DBA/2J and db/db mice with the dual FXR/TGR5 agonist INT-767 improved proteinuria and prevented podocyte injury, mesangial expansion, and tubulointerstitial fibrosis. INT-767 exerted coordinated effects on multiple pathways, including stimulation of a signaling cascade involving AMP-activated protein kinase, sirtuin 1, PGC-1<i>α</i>, sirtuin 3, estrogen-related receptor-<i>α</i>, and Nrf-1; inhibition of endoplasmic reticulum stress; and inhibition of enhanced renal fatty acid and cholesterol metabolism. Additionally, in mice with diet-induced obesity, INT-767 prevented mitochondrial dysfunction and oxidative stress determined by fluorescence lifetime imaging of NADH and kidney fibrosis determined by second harmonic imaging microscopy. These results identify the renal signaling pathways regulated by FXR and TGR5, which may be promising targets for the treatment of nephropathy in diabetes and obesity.
BST-1, a surface molecule of bone marrow stromal cell lines that facilitates pre-B-cell growth. (1994)

Bone marrow stromal cells are essential for B-lymphocyte development. However, how stromal cells regulate B lymphopoiesis is not clear. In this paper, we report the molecular cloning of a stromal cell line-derived glycosyl-phosphatidylinositol-anchored molecule, BST-1, that facilitates pre-B-cell growth. The deduced amino acid sequence of BST-1 exhibited 33% identity with CD38. BST-1 was expressed in a wide range of tissues and in umbilical vein endothelial cells, whereas it was scarcely expressed in a variety of hematopoietic cell lines. The gene for BST-1 was assigned to chromosome 14q32.3, where immunoglobulin heavy-chain genes are clustered. BST-1 expression was enhanced in rheumatoid arthritis patient-derived bone marrow stromal cell lines that were previously shown to have an enhanced ability to support the growth of a pre-B-cell line as compared with stromal cell lines derived from healthy donors.
JIGSAW: integration of multiple sources of evidence for gene prediction (2005)

JIGSAW is available as an open source software package at http://cbcb.umd.edu/software/jigsaw.
Ensaios de combate ao cupim de monte Cornitermes cumulans (Kollar, 1832) (Isoptera, Termitidae) (1994)

Com a finalidade de combater o cupim de monte Cornitermes cumulans, importante espécie invasora, foram instalados dois campos experimentais. Experimento I: 60 ninhos foram escolhidos e medidos externamente. O ensaio constou de 6 tratamentos com 10 repetições: A) abamectina (50 cm³ CE 1,8%); B) silafluofem (200 cm³ CE 80%); C) silafluofem (400 cm³ CE 80%); D) fipronil (15g G 2%); E) fipronil (20g G 2%); F) clorpirifós (30g G 0,125%). Nos tratamentos A, B, C, as quantidades entre parênteses são da formulação comercial em 100 litros de água. Em D, E, F, são do granulado para cada ninho. Dos líquidos, usou-se um litro de calda por monte. A demolição dos montes deu-se após 103 dias da aplicação. Os melhores resultados foram obtidos com a abamectina e fipronil. Experimento II: Também neste ensaio os cupinzeiros foram 60, abrangendo 6 tratamentos com 10 repetições: A) fipronil (l0g G 2%); B) fipronil (15g G 2%); C) bendiocarbe (20g G 0,1%); D) bendiocarbe (20g G 0,5%); E) imidaclopride (0,15g G 70%); F) imidaclopride (0,30g G 70%). Em A, B, C, D, as quantidades de granulados são por ninho. Em E, F são de granulado dispersível em um litro de água, por ninho. A destruição dos cupinzeiros foi feita 148 e 149 dias após a aplicação. Os melhores resultados foram o fipronil e imidaclopride.
Computing Lower Bounds for the Quadratic Assignment Problem with an Interior Point Algorithm for Linear Programming (1995)

An example of the quadratic assignment problem (QAP) is the facility location problem, in which n facilities are assigned, at minimum cost, to n sites. Between each pair of facilities, there is a given amount of flow, contributing a cost equal to the product of the flow and the distance between sites to which the facilities are assigned. Proving optimality of QAPs has been limited to instances having fewer than 20 facilities, largely because known lower bounds are weak. We compute lower bounds for a wide range of QAPs using a linear programming-based lower bound studied by Z. Drezner (1995). On the majority of QAPs tested, a new best known lower bound is computed. On 87% of the instances, we produced the best known lower bound. On several instances, including some having more the 20 facilities, the lower bound is tight. The linear programs, which can be large even for small QAPs, are solved with an interior point code that uses a preconditioned conjugate gradient algorithm to compute the interior point directions. Attempts to solve these instances using the CPLEX primal simplex algorithm as well as the CPLEX barrier (primal-dual interior point) method were successful only for the smallest instances.
A pseudo-Bayesian Aloha algorithm with mixed priorities for wireless ATM (2002)

In reservation MAC protocols, before obtaining a contention free access to the channel, a mobile must wait for its request packet to be successfully sent to the base station. A pseudo-Bayesian Aloha algorithm with multiple priorities is proposed in this paper to reduce the waiting time of delay sensitive request packets in a multimedia environment. Packets are transmitted in each slot according to a transmission probability based on the channel history and a priority parameter assigned to their priority class. An adaptation of the slotted protocol to the framed environment is also described. Simulation results are presented and show that the protocol offers a significant delay improvement for high priority packet with both Poisson and self-similar traffic while low priority packets only experience slight performance degradation.
Platinum-Based Nanostructured Materials: Synthesis, Properties, and Applications (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTPlatinum-Based Nanostructured Materials: Synthesis, Properties, and ApplicationsAicheng Chen* and Peter Holt-HindleView Author Information Department of Chemistry, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada* Corresponding author. Tel: 1-807-343-8318. Fax: 1-807-3467775. E-mail: [email protected]Cite this: Chem. Rev. 2010, 110, 6, 3767–3804Publication Date (Web):February 19, 2010Publication History Received30 November 2009Published online19 February 2010Published inissue 9 June 2010https://pubs.acs.org/doi/10.1021/cr9003902https://doi.org/10.1021/cr9003902review-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views22918Altmetric-Citations1233LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Electrodes,Metal nanoparticles,Nanomaterials,Nanoparticles,Platinum Get e-Alerts
Prostate-specific kallikrein-related peptidases and their relation to prostate cancer biology and detection (2013)

Kallikreins are a family of serine proteases with a range of tissue-specific and essential proteolytic functions. Among the best studied are the prostate tissue-specific KLK2 and KLK3 genes and their secreted protease products, human kallikrein 2, hk2, and prostate-specific antigen (PSA). Members of the so-called classic kallikreins, these highly active trypsin-like serine proteases play established roles in human reproduction. Both hK2 and PSA expression is regulated by the androgen receptor which has a fundamental role in prostate tissue development and progression of disease. This feature, combined with the ability to sensitively detect different forms of these proteins in blood and biopsies, result in a crucially important biomarker for the presence and recurrence of cancer. Emerging evidence has begun to suggest a role for these kallikreins in critical vascular events. This review discusses the established and developing biological roles of hK2 and PSA, as well as the historical and advanced use of their detection to accurately and non-invasively detect and guide treatment of prostatic disease.
<i>In-situ</i> investigation of coupling between a fibre and a slab waveguide (1990)

The mode coupling between a fibre and a slab waveguide was experimentally investigated during the formation of the slab. A thin film has been deposited on a polished fibre close to the core-clad interface. By monitoring the optical transmittance of the fibre during the film deposition the coupling efficiency between the formed slab and the fibre has been studied as a function of the film thickness. Strong attenuation in the fibre output has been observed for thickness values at which the propagation constants of the optical mode in the fibre match those of the slab waveguide.
Steam and Gas Push (SAGP)-4;Recent Theoretical Developments and Laboratory Results Using Layered Models (2001)

Abstract This paper is a continuation of earlier papers on the development of the SAGP process presented at Annual Technical Meetings of the Petroleum Society. SAGP improves the thermal efficiency of SAGD by adding non-condensible gas to the steam. Significant steam savings are achieved by lowering the average temperature in the reservoir and by reducing heat loss to the overburden. Rising gas fingers increase the pressure towards the top of the reservoir and displace oil downwards even though the temperature is below that of saturated steam. The gas hold-up in the reservoir equals the volume of the produced oil, with allowance for the effects of pressure, temperature, and partial pressure of the steam. The gas in the chamber comes from the combination of added gas, solution gas, and gas generated by chemical reactions, minus gas produced with the oil and the net gas driven to or coming from outside the depleted region by pressure difference. The gas hold-up and gas dissolved were estimated and it was found that, in general, more gas is required for higher pressures. Effects of layered sands on SAGD and SAGP performance are studied experimentally using a physical model. In SAGD, steam spreads below the low-permeability layers and oil cannot drain from above until the steam vapour can penetrate to replace it. In SAGP, gas fingers rise into the low-permeability layers and displace the oil downwards below steam temperature. Mechanisms for the enhancement of oil drainage from the low-permeability layers by gas fingers are discussed together with the experimental results. SAGP continues to show promising results and it is thought that results in the field will be better than in our experiments. Introduction Several papers(1-4) have been presented on the theoretical and laboratory studies of the Steam and Gas Push (SAGP) process since it was described first in 1997 at the 48th Annual Technical Meeting of the Petroleum Society. The process improves the thermal efficiency for SAGD by adding a small amount of noncondensible gas to the injected steam. Steam condenses and leaves concentrated gas in the upper portion of the vapour chamber. As a result, only the region near the injector and producer, where the gas concentration is low, is heated to the temperature of saturated steam. The upper part of the reservoir remains at a relatively low temperature and the heat loss is low; significant steam is saved. The gas required to achieve the SAGP effect is obtained from gas dissolved in the oil, gas generated by chemical reaction, net reservoir gas flowing into the recovery region, and gas supplied from injection. In heavy oil and bitumen reservoirs, such as those in Athabasca and Cold Lake, the operating pressure for SAGD is usually higher than the initial reservoir pressure and gas injection is required. The required gas hold-up in the vapour chamber is related to the volume of oil produced, with allowances for operating pressures and temperature. To make the injected gas more effective in the chamber, the production of gas should be minimum.
AudioCycle: Browsing Musical Loop Libraries (2009)

This paper presents AudioCycle, a prototype application for browsing through music loop libraries. AudioCycle provides the user with a graphical view where the audio extracts are visualized and organized according to their similarity in terms of musical properties, such as timbre, harmony, and rhythm. The user is able to navigate in this visual representation, and listen to individual audio extracts, searching for those of interest. AudioCycle draws from a range of technologies, including audio analysis from music information retrieval research, 3D visualization, spatial auditory rendering, audio time-scaling and pitch modification. The proposed approach extends on previously described music and audio browsers. Concepts developed here will be of interest to DJs, remixers, musicians, soundtrack composers, but also sound designers and foley artists. Possible extension to multimedia libraries are also suggested.
Stimulation of Calcium Influx in HL60 Cells by Cholesteryl-Modified Homopolymer Oligodeoxynucleotides (1992)

Cholesteryl-modified 15-mer homopolymers of cytidine and thymidine phosphodiester oligodeoxynucleotides (chol-OdC15 and chol-OdT15), but not chol-modified heteropolymeric oligos or chol-modified phosphorothioate oligos, were found to increase cytosolic free Ca2+ in HL60 cells. A flow cytometer and the calcium-sensitive dye indo-1 were used to make multiparameter measurements on the HL60 cells. Chol-OdC15 (5-10 microM) triggered a rapid increase (within 1 min) in [Ca2+]i, with a subsequent slow decline to baseline over 15 min in the continuous presence of agonist. The effect was preserved after unloading the intracellular Ca2+ stores with caffeine and ryanodine. The effect was not sensitive to membrane depolarization by KCl (60 mM) or nimodipine, a dihydropyridine calcium channel antagonist. An increase in [Ca2+]i was absent in a Ca(2+)-free solution and was inhibited by the inorganic Ca2+ channel blocker Cd2+. The results suggest that Ca2+ influx activated by the chol-oligomer is probably mediated by receptor-operated Ca2+ channels. This effect may be due to direct binding of the chol-oligo to the channel or to induced conformational changes due to modification of the local microenvironment.