gebhart/patrepeval huggingface dataset:
<title>Excited-state quenching of dye-linked oligonucleotides</title> (1992)

Fluorescence energy transfer (FET) can be used to obtain structural and dynamic information on duplex and branched DNA molecules suitably labeled with donor and acceptor dyes. However, dye-DNA interaction cause excited-state quenching of the dyes and complicate the analysis of FET data. We have investigated the excited-state quenching of two common FET dyes, fluorescein and tetramethyl rhodamine, covalently linked to synthetic oligonucleotides. The rate of quenching is shown to depend on the base sequence and association state of the oligonucleotide, and also the length of the linker chain. Furthermore, the dyes can adopt more than one configuration with respect to the oligonucleotide strand and the degree of quenching is different in each configuration. The implications of these findings for FET measurements in nucleic acids are discussed.
Synthesis of 2 (or 2, 5-Di)-Substituted-1, 3, 4-thiadiazole Derivatives (1965)

2-Sulfanilylamino-1, 3, 4-thiadiazoles (VII) possessing a heterocycle in the 5-position were synthesized by the condensation of N-acetylsulfanilyl chloride with 2-amino-1, 3, 4-thiadiazole with a heterocyclic substituent in the 5-position. The latter was obtained by heating the corresponding aldehyde thiosemicarbazone with ferric chloride solution. The treatment of the aldehyde 3-thio-4-(N-acetylsulfanilyl) semicarbazone with ferric chloride also afforded VII. Various kinds of 2-dialkylaminoacylamino-1, 3, 4-thiadiazoles were obtained by the application of haloacyl halide to 2-amino-1, 3, 4-thiadiazole, followed by amination. The addition of amines to 2-crotonamido-1, 3, 4-thiadiazole gave the dialkylaminobutyrylamino derivative.
Association of Prostate Cancer Risk With Genetic Polymorphisms in Vitamin D Receptor and Androgen Receptor (1997)

These results are consistent with a multigenic model of prostate cancer susceptibility. On the basis of the joint effect of several genetic loci, one might ultimately be able to construct a risk profile to predict advanced disease, so that men whose disease is unlikely to progress to an advanced stage can possibly be spared aggressive treatment.
Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs (2013)

We herewith present a novel and universal method to convert protein-ligand coordinates into a simple fingerprint of 210 integers registering the corresponding molecular interaction pattern. Each interaction (hydrophobic, aromatic, hydrogen bond, ionic bond, metal complexation) is detected on the fly and physically described by a pseudoatom centered either on the interacting ligand atom, the interacting protein atom, or the geometric center of both interacting atoms. Counting all possible triplets of interaction pseudoatoms within six distance ranges, and pruning the full integer vector to keep the most frequent triplets enables the definition of a simple (210 integers) and coordinate frame-invariant interaction pattern descriptor (TIFP) that can be applied to compare any pair of protein-ligand complexes. TIFP fingerprints have been calculated for ca. 10,000 druggable protein-ligand complexes therefore enabling a wide comparison of relationships between interaction pattern similarity and ligand or binding site pairwise similarity. We notably show that interaction pattern similarity strongly depends on binding site similarity. In addition to the TIFP fingerprint which registers intermolecular interactions between a ligand and its target protein, we developed two tools (Ishape, Grim) to align protein-ligand complexes from their interaction patterns. Ishape is based on the overlap of interaction pseudoatoms using a smooth Gaussian function, whereas Grim utilizes a standard clique detection algorithm to match interaction pattern graphs. Both tools are complementary and enable protein-ligand complex alignments capitalizing on both global and local pattern similarities. The new fingerprint and companion alignment tools have been successfully used in three scenarios: (i) interaction-biased alignment of protein-ligand complexes, (ii) postprocessing docking poses according to known interaction patterns for a particular target, and (iii) virtual screening for bioisosteric scaffolds sharing similar interaction patterns.
Do Voice Recordings Reveal whether a Person Is Intoxicated? A Case Study (1990)

In this report we consider the possibility that speech analysis techniques may be used to determine whether an individual was intoxicated at the time that a voice recording was made, and discuss an analysis of the speech produced by the captain of the Exxon Valdez recorded at several points around the time of the accident at Prince William Sound, Alaska. A review of previous research on the effects of alcohol and other effects on speech production suggests that it may be possible to attribute a certain, unique pattern of changes in speech to the influence of alcohol. However, the rate of occurrence of this pattern or the reliability of a decision based on observations such as these is not known. Acoustic-phonetic analysis of a small number of tokens of Captain Hazelwood's speech recorded before, during and after the accident revealed a number of changes in speech behavior which are similar to the pattern of changes observed in previous laboratory-based research on the effects of alcohol on speech production. We conclude with a discussion of the limitations in making inferences concerning the state of the speaker upon the basis of phonetic data and then discuss several possible explanations of the pattern of change found in the recordings of Captain Hazelwood.
Comparison of rapid identification assays for Staphylococcus aureus (1984)

A total of 137 strains of Staphylococcus species were blindly tested by four rapid serological assays, and the results were compared with those of the tube coagulase assay. For the S. aureus isolates, the Sero-STAT Staph assay gave six false-negative results, four of which were for methicillin-resistant strains. The Accu -Staph, Staphylatex , and Staphyloslide assays identified all the coagulase-positive strains as Staphylococcus aureus. Among the coagulase-negative staphylococci, false-positive results were seen with strains of S. capitis. S. saprophyticus, and S. cohnii. The overall accuracy of the kits compared with the tube coagulase test ranged from 95.1 to 100%.
Positron emission tomography in non-Hodgkin's lymphoma: assessment of chemotherapy with fluorodeoxyglucose. (1998)

Positron emission tomography (PET) using F-18 fluorodeoxyglucose (FDG) was performed in non-Hodgkin's lymphoma (NHL), which is known to be highly responsive to chemotherapy, but also yields variable treatment results to answer the following questions: (1) What is the extent and time course of changes in FDG utilization in response to chemotherapy? (2) Are the changes of FDG uptake at early time points of chemotherapy predictive for therapy outcome? (3) Which quantitative FDG parameter provides the most sensitive measures of initial tumor response? Dynamic PET scans were performed in 11 patients at baseline and 1 and 6 weeks after initiation of chemotherapy. Based on attenuation corrected images acquired 30 to 60 minutes postinjection, standardized uptake values (SUV) were determined. Arterial input functions were estimated from vascular F-18 activity and the metabolic rates for FDG (MRFDG) were calculated using Patlak analysis. Before chemotherapy, high FDG uptake was found in all lesions (SUV[max] 13.3 +/- 4.2). Seven days after initiation of chemotherapy, tumor FDG uptake decreased 60% (SUV[max]). A further decrease of 42% was seen at day 42 resulting in a total decrease of 79% from baseline to day 42. During a follow-up of 16.0 +/- 4.2 months, six of the 11 patients continued to show complete remission. Seven days after initiation of chemotherapy, this group of patients displayed significantly lower mean MRFDG than the group of patients with relapse. At day 42, all parameters of FDG uptake showed a significant difference for both patient groups. The relative change of MRFDG from baseline to day 42, as well as from day 7 to day 42, was significantly larger as compared with SUV parameters. Standard chemotherapy of patients with NHL causes rapid decrease of tumor FDG uptake as early as 7 days after treatment, which continues to decline during therapy, indicating the sensitivity of metabolic signals to chemotherapeutic interventions. FDG uptake at 42 days after therapy was superior in prediction of long-term outcome over day 7 parameters. Dynamic data acquisition combined with Patlak analysis of FDG kinetics may provide superior information in therapy monitoring.
A bipolar small molecule based on indacenodithiophene and diketopyrrolopyrrole for solution processed organic solar cells (2013)

A new linear A–D–A type low band gap small molecule (IDT-2DPP) based on 4,4,9,9-tetrakis(4-hexylphenyl)-4,9-dihydro-s-indaceno[1,2-b:5,6-b′]dithiophene (IDT) and 2,5-bis(2-ethylhexyl)-3,6-di(thiophen-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione (DPP) was designed and synthesized by Pd-catalyzed Stille coupling reaction. IDT-2DPP exhibits good solubility and good thermal stability with a decomposition temperature of 395 °C. IDT-2DPP shows strong absorption from 500 to 700 nm with a high molar extinction coefficient of 1.3 × 105 M−1 cm−1 at the absorption peak (640 nm) in chloroform solution. The HOMO and LUMO levels of IDT-2DPP were estimated to be −5.11 and −3.32 eV, respectively. Solution processed bulk-heterojunction solar cells using IDT-2DPP as a donor material blending with PC71BM as an acceptor yielded a power conversion efficiency of 2.82%, and solar cells using IDT-2DPP as an acceptor material blending with P3HT as a donor yielded a power conversion efficiency of 0.83% with a high Voc of 1.17 V.
Development of insulitis without diabetes in transgenic mice lacking perforin-dependent cytotoxicity. (1996)

It is widely accepted that T cells play an important role in the destruction of beta cells leading to autoimmune type I diabetes, but the involved effector mechanisms have remained unclear. We addressed this issue by testing the role of perforin-dependent cytotoxicity in a disease model involving transgenic mice expressing glycoprotein of lymphocytic choriomeningitis virus (LCMV-GP) in the beta cells of the endocrine pancreas. In such mice, LCMV infection leads to a potent LCMV-GP-specific T cell response resulting in rapid development of diabetes. We report here that in perforin-deficient LCMV-GP transgenic mice, LCMV infection failed to induce diabetes despite the activation of LCMV-GP-specific T cells. Deletion of nu beta 6+ T cells in Mls-1a perforin-deficient mice and the activation of LCMV-GP-specific T cells in perforin-deficient LCMV-GP transgenic mice, however, indicated that thymic tolerance induction by negative selection was not affected by the disruption of the perforin gene and that there is no fundamental difference between the T cell repertoires of normal control and perforin-deficient mice. In addition, adoptive transfer of LCMV-GP-specific TCR transgenic perforin-deficient T cells activated by LCMV-GP recombinant vaccinia virus led to marked insulitis with infiltration of CD4+ and CD8+ T cells without the development of diabetes. These findings indicate that perforin-dependent cytotoxicity is not required for the initiation of insulitis but is crucial for the destruction of beta cells in the later phase of the disease process. Other mechanisms or soluble factors present in the inflammatory islet infiltrate apparently lack the ability to efficiently induce diabetogenic beta cell damage.
Cells expressing FLT3/ITD mutations exhibit elevated repair errors generated through alternative NHEJ pathways: implications for genomic instability and therapy (2010)

The internal tandem duplication (ITD) mutations of the FMS-like tyrosine kinase-3 (FLT3) receptor found in acute myeloid leukemia patients are associated with poor prognosis. Although DNA double-strand breaks (DSBs) are mainly repaired by the DNA-PK-dependent nonhomologous end-joining (NHEJ) pathway in normal mammalian cells, an alternative and less well-defined NHEJ pathway, characterized by microhomology at the repair junctions, play a role in the generation of deletions and translocations leading to cancer progression. Here we report that in FLT3/ITD-expressing cell lines and bone marrow mononuclear cells from FLT3/ITD knock-in mice, end-joining of DSBs occurs at microhomologous sequences resulting in a high frequency of DNA deletions. Strikingly, levels of Ku proteins, key components of the main NHEJ pathway, are decreased in FLT3/ITD(+) cell lines and murine FLT3/ITD bone marrow mononuclear cells. Concomitantly, levels of DNA ligase IIIα, a component of ALT NHEJ, are increased in FLT3/ITD-expressing cells. Cells treated with a FLT3 inhibitor demonstrate decreased DNA ligase IIIα and a reduction in DNA deletions, suggesting that FLT3 signaling regulates the pathways by which DSBs are repaired. Thus, therapy to inhibit FLT3/ITD signaling and/or DNA ligase IIIα may lead to repair that reduces repair errors and genomic instability.
Benzene production from decarboxylation of benzoic acid in the presence of ascorbic acid and a transition-metal catalyst (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBenzene production from decarboxylation of benzoic acid in the presence of ascorbic acid and a transition-metal catalystLalita K. Gardner and Glen D. LawrenceCite this: J. Agric. Food Chem. 1993, 41, 5, 693–695Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/jf00029a001https://doi.org/10.1021/jf00029a001research-articleACS PublicationsRequest reuse permissionsArticle Views3118Altmetric-Citations102LEARN 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 Get e-Alerts
Double-barrier resonant tunneling structures incorporating superlattice energy filters (1992)

We have studied the electrical properties of GaAs/Al0.4Ga0.6As double-barrier resonant tunneling structures incorporating finite superlattices in the contact regions. The superlattices effectively act as energy filters defining the initial and final tunneling states. We have investigated an asymmetric device with one (emitter) superlattice and a symmetric device with two (emitter and collector) superlattices. These show significantly improved J(V) properties compared to other double-barrier structures and the superlattice tunnel diode.
Novel Hydroxy- and Epoxy-cis-Jasmone and Dihydrojasmone Derivatives Affect the Foraging Activity of the Peach Potato Aphid Myzus persicae (Sulzer) (Homoptera: Aphididae) (2018)

Jasmonates show great potential in sustainable agriculture due to their various roles in natural mechanisms of plant defense, and because they are non-toxic, non-mutagenic, and easily metabolized. The aim of the study was to explore structure⁻activity relationships of dihydrojasmone, <i>cis</i>-jasmone, and their derivatives at the plant⁻aphid interface. We focused on the behavioral responses of aphids, following the exogenous application of natural jasmonates and their derivatives to the host plants. Aphid probing behavior was examined using an electrical penetration graph technique (EPG). The chemoenzymatic transformation of <i>cis</i>-jasmone and the activity of two new derivatives are described. The application of <i>cis-</i>jasmone, dihydrojasmone, the hydroxyderivatives, epoxyderivatives, and alkyl-substituted δ-lactones hindered the foraging activity of <i>Myzus persicae</i> (Sulz.) (Hemiptera: Aphididae) during early stages of probing at the level of non-phloem tissues. The application of saturated bicyclic epoxy-δ-lactone enhanced plant acceptance by <i>M. persicae</i>. Jasmonate derivatives containing a hydroxy group, especially in correlation with a lactone ring, were more active than natural compounds and other derivatives studied. Jasmonates of the present study are worth considering as elements of sustainable aphid control as components of the "push⁻pull" strategy.
Visual Resolution and Contour Interaction* (1963)

Detecting the position of the gap in a Landolt C is adversely affected by black bars placed tangential to the C and at a certain distance from it. The maximum bar separation affording interaction is proportional to the minimum angle of resolution, even in cases of amblyopia where resolution is presumably not limited by optical spread of the image. It is suggested that this contour interaction is related to the size of the receptive field (and hence to the resolving capacity) associated with the retinal region used to fixate the target.
Flight test experience with an electromechanical actuator on the F-18 Systems Research Aircraft (2002)

Development of reliable power-by-wire actuation systems for both aeronautical and space applications has been sought to eliminate hydraulic systems from aircraft and spacecraft and thus improve safety, efficiency, reliability, and maintainability. The Electrically Powered Actuation Design (EPAD) program was a joint effort between the Air Force, Navy, and NASA to develop and fly a series of actuators validating power-by-wire actuation technology on a primary flight control surface of a tactical aircraft. To achieve this goal, each of the EPAD actuators was installed in place of the standard hydraulic actuator on the left aileron of the NASA F/A-18B Systems Research Aircraft (SRA) and flown throughout the SRA flight envelope. Numerous parameters were recorded, and overall actuator performance was compared with the performance of the standard hydraulic actuator on the opposite wing. This paper discusses the integration and testing of the EPAD electromechanical actuator (EMA) on the SRA. The architecture of the EMA system is discussed, as well as its integration with the F/A-18 flight control system. The flight test program is described, and actuator performance is shown to be very close to that of the standard hydraulic actuator it replaced. Lessons learned during this program are presented and discussed, as well as suggestions for future research.
Crowdsourcing support system for disaster surveillance and response (2012)

Experiences with past major disasters tell us that people with wireless devices and social network services can be effective mobile human sensors. Eye-witness reports taken at right locations can provide invaluable information and enable a disaster surveillance system to mend blind regions in sensor coverage. In this work, we develop a system, named CROSS, that supports crowdsourcing disaster surveillance data collection by volunteers exploring threatened areas. CROSS first broadcasts a volunteer request to the crowd via social network(s), such as Facebook, Twitter and so on. It then plans exploration routes for the volunteers responded to the request based on their locations.
Two methods of control over results of alcoholism treatment (1981)

International Journal of Rehabilitation Research: September 1981 - Volume 4 - Issue 3 - p 404-406
Cyclic GMP-specific phosphodiesterase inhibition and intracarotid bradykinin infusion enhances permeability into brain tumors. (1998)

Intracarotid infusion of bradykinin selectively increases the delivery of compounds into brain tumors. This study sought to determine the role of cyclic GMP in increased permeability across the blood-tumor barrier (BTB) after infusion of bradykinin. In permeability studies, 186 Wistar rats with RG2 gliomas and C6 gliomas were used. Transport across the BTB was quantified by autoradiography and reported as a unidirectional transport, Ki, for [14C]dextran (Mr 70,000) and [14C]aminoisobutyric acid (Mr 103,000), with or without inhibition of cyclic GMP-specific phosphodiesterase or soluble guanylate cyclase. We also determined cyclic GMP levels in tumors and normal brain, with or without intracarotid bradykinin infusion, using RIA. Intracarotid infusion of bradykinin selectively increased permeability in RG2 tumors and C6 tumors for both tracers. Simultaneous infusion of bradykinin and a cyclic GMP-specific phosphodiesterase inhibitor, zaprinast (20 mg/kg), resulted in significantly increased permeability across the BTB, compared to intracarotid bradykinin infusion alone. Zaprinast also significantly prolonged the permeability effects of bradykinin. Pretreatment using i.v. infusion of the soluble guanylate cyclase inhibitor, LY-83583 (125 microg/kg), significantly attenuated the bradykinin effect of opening the BTB. Cyclic GMP levels in RG2 and C6 tumors were significantly increased after intracarotid bradykinin infusion (2.8- and 2.2-fold, respectively). Cyclic GMP levels in normal brain were not increased by bradykinin infusion. These results show that increasing cyclic GMP in tumor microvessels can increase permeability in response to bradykinin.
RANTES- and interleukin-8-induced responses in normal human eosinophils: effects of priming with interleukin-5 (1994)

We report that responses of normal human eosinophils toward the chemokines RANTES and interleukin-8 (IL-8) are modulated and upregulated by priming with IL-5. In a modified Boyden chamber assay, we studied migratory responses toward the members of the chemokine family RANTES, monocyte chemotactic protein-1 (MCP-1), and macrophage inflammatory protein-1 alpha (MIP-1 alpha) (C-C subfamily), and IL-8, platelet factor-4 (PF-4), and neutrophil-activating peptide-2 (NAP-2) (C-x-C subfamily). These chemokines were also studied in terms of actin polymerization and ([Ca2+]i)-mobilizing properties, intracellular signals that are thought to play a role during migratory responses. We found that eosinophils showed significant migratory responses toward RANTES and IL-8 at concentrations of 10(-9) to 10(-7) mol/L only after priming with IL-5 (10 pmol/L). At these concentrations, PF-4, NAP-2, MCP-1, and MIP-1 alpha induced no significant migratory responses after priming. Unprimed eosinophils only showed a significant migratory response toward RANTES (10(-6) mol/L). Changes in [Ca2+]i were found after addition of RANTES, MIP-1 alpha, and NAP-2 (10 nmol/L) to unprimed eosinophils. RANTES (10(-9) to 10(-7) mol/L) significantly induced actin polymerization both in primed and unprimed eosinophils, whereas IL-8 (10(-9) to 10(-8) mol/L) and MIP-1 alpha (10(-8) mol/L) only induced actin polymerization after priming with IL-5. NAP-2, PF-4, and MCP-1 did not affect actin polymerization. These findings are further evidence for the hypothesis that cytokines like IL-5 and locally secreted chemokines like RANTES and IL-8 are both at the basis of specific eosinophil influx into the allergic inflammatory locus.