gebhart/patrepeval huggingface dataset:
Photo‐oxidation of poly(p‐phenylenevinylene) (1997)

The operating lifetime of light‐emitting devices (LEDs) based on poly( p ‐phenylenevinylene) (PPV), one of the most widely used conjugated polymers for polymer‐based LEDs, is sensitive to air exposure. The effects associated with the photo‐oxidation of PPV in air are examined. Possible photo‐induced oxidation products are proposed based on simulations using stilbene as a model compound. X‐ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy, and quantum‐chemical calculations all indicate that a series of photo‐oxidation products from on the surface of the PPV thin films.
A geminivirus replication protein is a sequence-specific DNA binding protein. (1992)

The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules designated as components A and B. The A component encodes the only viral protein, AL1, that is required for viral replication. We showed that AL1 interacts specifically with TGMV A and B DNA by using an immunoprecipitation assay for AL1:DNA complex formation. In this assay, a monoclonal antibody against AL1 precipitated AL1:TGMV DNA complexes, whereas an unrelated antibody failed to precipitate the complexes. Competition assays with homologous and heterologous DNAs established the specificity of AL1:DNA binding. AL1 produced by transgenic tobacco plants and by baculovirus-infected insect cells exhibited similar DNA binding activity. The AL1 binding site maps to 52 bp on the left side of the common region, a 235-bp region that is highly conserved between the two TGMV genome components. The AL1:DNA binding site does not include the putative hairpin structure that is conserved in the common regions or the equivalent 5' intergenic regions of all geminiviruses. These studies demonstrate that a geminivirus replication protein is a sequence-specific DNA binding protein, and the studies have important implications for the role of this protein in virus replication.
Design of 18 krpm rated speed SMPM synchronous machine for &#x201C;wobble&#x201D; laser welding (2014)

This paper presents the design concepts and the test results of a Permanent Magnet Synchronous Motor (PMSM) for an electro-mechanical actuator used in a laser-welding machine for the dynamic wobble of the beam. The motor is directly integrated with the mechanical component in a rotating architecture in order to minimize the total inertia and the actuator's size. A prototype has been manufactured using the design data of the optimization procedure. Due to mechanical considerations and the stringent envelope requirements, the proposed motor has the PMs directly glued on the surface of the rotor steel made in one piece. Test results confirm the performance of the system and prototype.
The Effects of Dividend Taxeson Equity Prices: A Re-Examination of the 1997 U.K. Tax Reform (2007)

This Working Paper should not be reported as representing the views of the IMF.The views expressed in this Working Paper are those of the author(s) and do not necessarily represent those of the IMF or IMF policy.Working Papers describe research in progress by the author(s) and are published to elicit comments and to further debate.We re-examine the extent to which personal taxes on dividends are capitalized into the equity prices of domestic firms, using data from around the time of the 1997 U.K. dividend tax reform, which removed a significant tax credit for an important group of investors: U.K. pension funds.The tax-adjusted CAPM suggests that the impact should depend on an average of dividend tax rates across all investors, and that U.K. pension funds should reduce their holdings of the previously tax-favored asset: U.K. equities.Given that U.K. pension funds are small relative to the total size of the world capital market, a small open economy-type argument implies that the main effect of the reform would be to reduce U.K. pension funds' ownership of U.K. equities, with little impact on their price.We present evidence which is consistent with these hypotheses.We discuss why previous research (Bell and Jenkinson, 2002) reached a different conclusion.
The invasive Neisseria meningitidis MenC CC103 from Brazil is characterized by an accessory gene repertoire (2017)

Neisseria meningitidis infections are a major issue for global health. The invasive MenC ST-103 clonal complex (CC103) has been the most prevalent in meningococcal outbreaks in Brazil, occurring also in several countries worldwide. Here we have analysed the population structure and accessory genome of MenC CC103 strains from a global perspective. An in-depth phylogenomic analysis revealed a lineage of N. meningitidis causing meningitis in Brazil and the United Kingdom. This lineage was also characterized as harbouring a particular accessory genome composed of CRISPR/Cas and restriction modification systems. This lineage was also characterized by a genomic island resembling an integrative and conjugative element. This island carried genes potentially associated with virulence and fitness. We propose this accessory gene repertoire could be contributing to the spatial-temporal persistence of the invasive MenC CC103 lineage.
Sequence of the structural gene (rmpM) for the class 4 outer membrane protein of Neisseria meningitidis, homology of the protein to gonococcal protein III and Escherichia coli OmpA, and construction of meningococcal strains that lack class 4 protein (1989)

The structural gene (rmpM) of the class 4 outer membrane protein of Neisseria meningitidis has been cloned and sequenced. The derived amino acid sequence reveals a 218-amino-acid protein following a 22-amino-acid signal peptide. The protein shows 94.2% homology with protein III of Neisseria gonorrhoeae and shares its two potential disulfide loops. The protein also shares limited homology with Escherichia coli OmpA. N. gonorrhoeae protein III has been shown to elicit blocking antibodies that prevent the killing of serum-resistant strains by immune sera (P. A. Rice, H. E. Vayo, M. R. Tam, and M. S. Blake, J. Exp. Med. 164:1735-1748, 1986). The very close homology of meningococcal class 4 protein with gonococcal protein III suggests that meningococcal outer membrane preparations containing class 4 protein may similarly stimulate blocking antibodies. In order to investigate the role of the class 4 protein in the pathogenesis of meningococcal infection, we have used an erythromycin resistance gene in developing two meningococcal strains that lack class 4 protein.
The GC box as a silencer (1987)

A DNA control sequence GTGGGCGGGGCAAT, or the "GC" box, has been described in the promoter regions upstream of a number of eukaryotic genes transcribed by polymerase II (for review, see Dynan, W.S. and Tjian, R., Nature 316:774, 1985). The "GC" box can occur in single or multiple copies and is the binding site for a protein factor, Sp1, which activates initiation of transcription. We have observed in the rainbow trout protamine gene 3' to the TATA box, three "GC" boxes spaced at 80 bp intervals. The first is 5' to the cap site and possesses the ability to "silence" transcription from the protamine promoter in constructs linking this promoter to the bacterial chloramphenicol acetyl transferase (CAT) coding sequence following transfection to COS-1 cells. A model is proposed to account for the silencing of the protamine gene in all tissues except developing sperm cells.
Rational Modifications of HIV-1 Envelope Glycoproteins for Immunogen Design (2006)

An effective vaccine against the human immunodeficiency virus type 1 (HIV-1) will likely require the elicitation of broadly neutralizing antibodies as well as cellular responses. The HIV exterior envelope glycoprotein trimers, gp120, and the transmembrane glycoprotein, gp41, mediate entry and are the sole viral targets for neutralizing antibodies. However, as subunit immunogens the envelope glycoproteins do not efficiently elicit antibodies capable of neutralizing the extremely diverse array of viruses circulating in the human population. The preponderance of data suggest that inefficient generation of broadly neutralizing antibodies is due to naturally evolved mechanisms of immune evasion inherent in the unmodified HIV envelope glycoproteins. Because the established modes of anti-viral vaccine development, live-attenuation and virus inactivation have not yet been successful for HIV, we and others have focused on subunit vaccine design. In this review, we describe current approaches of rational modification of the envelope glycoproteins based upon structure, antigenicity, biochemistry and biophysics to alter the properties of the envelope glycoproteins such that, as subunit immunogens, they now better elicit broadly neutralizing antibodies. The application of structure-assisted, rational subunit vaccine design may be a general paradigm for future efforts to develop vaccines against emerging human pathogens.
Nonlinear Optical Properties of Semiconductor Microcrystals (2023)

The absorption edge of CdSe and CdSSe microcrystals has been observed to undergo a significant short-wavelength shift (of more than 30 meV) during excitation by light pulses at the second harmonic from a Nd:YAG laser. An optical-nonlinearity mechanism is proposed. This mechanism involves the filling of levels in the energy spectrum of a spatially bounded multiexciton system in microcrystals with a size comparable to the exciton radius.
Ketamine for rapid reduction of suicidal ideation: a randomized controlled trial (2015)

The current findings provide initial support for the safety and tolerability of ketamine as an intervention for SI in patients who are at elevated risk for suicidal behavior. Larger, well-powered studies are warranted.
Millimeter Wave-induced Vibrational Modes in DNA as a Possible Alternative to Animal Tests to Probe for Carcinogenic Mutations (1997)

Developing methods for alternative testing is increasingly important due to dwindling funding resources and increasing costs associated with animal testing and legislation. We propose to test the feasibility of a new and novel method for detecting DNA mutagenesis using millimeter wave spectroscopy. Although millimeter wave spectroscopy has been known since the 1950s, the cost was prohibitive and studies did not extend to large biological proteins such as DNA. Recent advances have made this technology feasible for developing laboratory and field equipment. We present preliminary findings for lesion-induced vibrational modes in DNA observed from 80 to 1000 gigahertz (GHz). These findings suggest that there are vibrational modes that can be used as identification resonances. These modes are associated with localized defects of the DNA polymers. They are unique for each defect/lesion, and should be easy to detect. We described a field-detecting detector based on the local modes.
Modeling of the Thermoelectric Power Factor in Quasi-One-Dimensional Organic Crystals (2006)

Thermoelectric power factor is modeled in a series of highly conducting quasi-one-dimensional organic crystals in order to investigate the role of interference of two most important electron-phonon interactions. It is shown that due to the mutual compensation of interaction mechanisms as a consequence of interference, simultaneous increase of electrical conductivity and thermopower can be achieved. Values of the thermoelectric power factor of the order of 600muW/cmK <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> are predicted
Mouse Sperm Lacking ADAM1b/ADAM2 Fertilin Can Fuse with the Egg Plasma Membrane and Effect Fertilization (2006)

Fertilin, a heterodimeric protein complex composed of alpha (ADAM1) and beta (ADAM2) subunits on the sperm surface, is believed to mediate adhesion and fusion between the sperm and egg plasma membranes. Here we have shown that mutant male mice lacking ADAM1b are fertile and that the loss of ADAM1b results in no significant defect in sperm functions such as migration from the uterus into oviduct, binding to egg zona pellucida, and fusion with zona pellucida-free eggs. ADAM1b-deficient epididymal sperm showed a severe reduction of ADAM2 on the cell surface, despite the normal presence of ADAM2 in testicular germ cells. The appearance of ADAM1b and ADAM2 on the sperm surface depended on formation and abundance of ADAM1b/ADAM2 fertilin in testicular germ cells. These results suggest that mouse ADAM1b/ADAM2 fertilin may play a crucial role not in the sperm/egg fusion but in the appearance of these two ADAMs on the sperm surface.
MEASURING PLANT INTERACTIONS: A NEW COMPARATIVE INDEX (2004)

We propose an index to measure the relative interaction intensity in plants (RII) with strong mathematical and statistical properties which overcome problems shown by other frequently used indices. RII has defined limits [−1, +1]; is symmetrical around zero, with identical absolute values for competition and facilitation; is linear; and does not have discontinuities in its range. It is therefore safe to use in statistical and mathematical operations. RII distribution is approximately normal, with means equal to the true population index and a sampling variance that can be derived. Its strong statistical properties make RII proper for use in parametric meta-analyses. It can be applied to any kind of interaction (from competitive exclusion to symbiosis) and in commonly published ranges of interaction intensity it offers the most consistent results. Because RII uses basic arithmetical operators, it can be scaled up and used to measure multispecific interactions at the community level.
Targeting of pericytes diminishes neovascularization and lymphangiogenesis in prostate cancer (2005)

Targeting of pericyte-NG2 decreases neovascularization and lymphangiogenesis in prostate cancer significantly.
Nonsense‐mediated RNA decay – a switch and dial for regulating gene expression (2015)

Nonsense-mediated RNA decay (NMD) represents an established quality control checkpoint for gene expression that protects cells from consequences of gene mutations and errors during RNA biogenesis that lead to premature termination during translation. Characterization of NMD-sensitive transcriptomes has revealed, however, that NMD targets not only aberrant transcripts but also a broad array of mRNA isoforms expressed from many endogenous genes. NMD is thus emerging as a master regulator that drives both fine and coarse adjustments in steady-state RNA levels in the cell. Importantly, while NMD activity is subject to autoregulation as a means to maintain homeostasis, modulation of the pathway by external cues provides a means to reprogram gene expression and drive important biological processes. Finally, the unanticipated observation that transcripts predicted to lack protein-coding capacity are also sensitive to this translation-dependent surveillance mechanism implicates NMD in regulating RNA function in new and diverse ways.
Analysis of the incubation periods, induction of obesity and histopathological changes in senescence-prone and senescence-resistant mice infected with various scrapie strains. (1998)

The similarity in histopathological changes seen in scrapie-infected mice and in an uninfected senescence-accelerated mouse strain led to a study in which the mouse strain that is prone to senescence (SAMP8), a strain that is resistant to senescence (SAMR1) and a progenitor strain (AKR) of these two strains were infected with three different scrapie strains, ME7, 139A and 22L. For each scrapie strain, the incubation period was shortest in AKR mice and longest in SAMR1 mice. The induction of obesity was a function of scrapie strain and not mouse strain; ME7 caused obesity in all mouse strains, whereas the average weights of mice injected with 139A and 22L did not differ significantly from mice injected with homogenates of normal mouse brain. The pattern of vacuolation seen in the brain of each mouse strain was primarily dependent on the scrapie strain injected. There were, in general, similarities to the patterns induced in other inbred strains; e.g. ME7 caused extensive forebrain vacuolation, 22L caused prominent vacuolation in the cerebellum, and the 139A strain induced characteristic white matter vacuolation. Vacuolation was also seen in the medulla and midbrain of SAMP8 mice injected with normal mouse brain, which is consistent with the occurrence of accelerated ageing changes in the brain of this strain. Further analysis of the differences among these mouse strains should provide information relating to the observed differences in scrapie incubation periods.
Analysis of Big Data Technologies and Method - Query Large Web Public RDF Datasets on Amazon Cloud Using Hadoop and Open Source Parsers (2013)

Extremely large datasets found in Big Data projects are difficult to work with using conventional databases, statistical software, and visualization tools. Massively parallel software, such as Hadoop, running on tens, hundreds, or even thousands of servers is more suitable for Big Data challenges. Additionally, in order to achieve the highest performance when querying large datasets, it is necessary to work these datasets at rest without preprocessing or moving them into a repository. Therefore, this work will analyze tools and techniques to overcome working with large datasets at rest. Parsing and querying will be done on the raw dataset - the untouched Web Data Commons RDF files. Web Data Commons comprises five billion pages of web pages crawled from the Internet. This work will analyze available tools and appropriate methods to assist the Big Data developer in working with these extremely large, semantic RDF datasets. Hadoop, open source parsers, and Amazon Cloud services will be used to data mine these files. In order to assist in further discovery, recommendations for future research will be included.
Clearance of Thrombin from Circulation in Rabbits by High-affinity Binding Sites on Endothelium (1980)

The clearance of (125)I-thrombin and diisopropylphosphoryl-(125)I-thrombin (DIP-thrombin) from the circulation in rabbits was studied. When given either intraarterially or intravenously, DIP-thrombin, which is active-site blocked, was approximately 90% cleared from the circulation by 1 min, the time of earliest sampling, indicating a large first-pass effect. DIP-thrombin given intravenously is found predominantly in the lungs, whereas DIP-thrombin injected into the aortic arch is distributed diffusely in approximate proportion to the blood supply. Renal artery, femoral artery, ear artery, left atrium, and portal vein infusions demonstrate that kidney, muscle, ear, heart, and liver, respectively, can remove DIP-thrombin from the circulation. These data imply that the clearance of DIP-thrombin is not a function of a specific organ but of the vascular bed per se. The clearance of DIP-thrombin was reversible since injection of 0.5 mg of unlabeled DIP-thrombin 10 min after the injection of a tracer dose of DIP-(125)I-thrombin resulted in the rapid reappearance of the DIP-(125)I-thrombin into the circulation. In addition, the clearance of DIP-thrombin was saturable, i.e., clearance of DIP-(125)I-thrombin was inhibited by unlabeled DIP-thrombin in a dose-dependent fashion. In vivo Scatchard analysis of the saturation of the clearance process demonstrated that DIP-thrombin can be removed by binding to high-affinity binding sites, since dissociation constants (K(D)) of 10 and 13 nM were obtained for human and bovine DIP-thrombin, respectively. In contrast to DIP-thrombin, approximately 75% of the radioactivity associated with active thrombin remained in the circulation at 1 min. By 10 min 55% of (125)I-thrombin had been removed from the circulation, and essentially all of the radioactivity can be accounted for in the liver. Sodium dodecyl sulfate-polyacrylamide gel radioelectrophoresis of plasma samples taken after injection of (125)I-thrombin demonstrated that all of the active thrombin was converted to covalent thrombin-antithrombin III complex by the time of initial sampling (30 s). The in vitro conversion of (125)I-thrombin to thrombin-antithrombin III complex was considerably slower (50+/-5% conversion at 30 s). The simultaneous injection of excess unlabeled DIP-thrombin inhibited the rate of formation of (125)I-thrombin-antithrombin III complex formation in vivo (but not in vitro), which suggests that the binding of active thrombin to the high affinity binding sites is required for the rapid inactivation of thrombin in vivo. We propose that (a) thrombin in the circulation binds to active site-independent high-affinity binding sites on the endothelial cell surface; (b) the inactivation of thrombin by antithrombin III is faster in vivo than in vitro because the high-affinity binding sites, present in a high concentration in the microcirculation, catalyze the reaction; (c) thrombin-antithrombin III complexes are selectively removed by the liver.
Tetrahydrobiopterin increases insulin sensitivity in patients with type 2 diabetes and coronary heart disease (2004)

Tetrahydrobiopterin (BH(4)) is an essential cofactor of nitric oxide synthase that improves endothelial function in diabetics, smokers, and patients with hypercholesterolemia. Insulin resistance has been suggested as a contributing factor in the development of endothelial dysfunction via an abnormal pteridine metabolism. We hypothesized that BH(4) would restore flow-mediated vasodilation (FMD, endothelial-dependent vasodilation), which may affect insulin resistance in type 2 diabetic patients. Thirty-two subjects (12 type 2 diabetic subjects, 10 matched nondiabetic subjects, and 10 healthy unmatched subjects) underwent infusion of BH(4) or saline in a random crossover study. Insulin sensitivity index (S(I)) was measured by hyperinsulinemic isoglycemic clamp. FMD was measured using ultrasonography. BH(4) significantly increased S(I) in the type 2 diabetics [3.6 +/- 0.6 vs. 4.9 +/- 0.7 x 10(-4) dl.kg(-1).min(-1)/(microU/ml), P < 0.05], while having no effects in nondiabetics [8.9 +/- 1.1 vs. 9.0 +/- 0.9 x 10(-4) dl.kg(-1).min(-1)/(microU/ml), P = 0.92] or in healthy subjects [17.5 +/- 1.6 vs. 18 +/- 1.8 x 10(-4) dl.kg(-1).min(-1)/(microU/ml), P = 0.87]. BH(4) did not affect the relative changes in brachial artery diameter from baseline FMD (%) in type 2 diabetic subjects (2.3 +/- 0.8 vs. 1.8 +/- 1.0%, P = 0.42), nondiabetic subjects (5.3 +/- 1.1 vs. 6.6 +/- 0.9%, P = 0.32), or healthy subjects (11.9 +/- 0.6 vs. 11.0 +/- 1.0%, P = 0.48). In conclusion, BH(4) significantly increases insulin sensitivity in type 2 diabetic patients without any discernible improvement in endothelial function.
Binding identities and attributes using digitally signed certificates (2002)

A certificate is digitally signed by a certificate authority (CA) to confirm that the information in the certificate is valid and belongs to the subject. Certificate users can verify the integrity and validity of a certificate by checking the issuing CA's digital signature in the certificate and, if necessary, chasing certificate chain and revocation lists. Usually, we use certificates to provide the integrity of identity or attribute information of the subject. Attributes must be coupled with the corresponding identities. We introduce comprehensive approaches to bind identity and attribute certificates, identifying three different techniques: monolithic, autonomic, and chained signatures. We describe each technique and analyze the relative advantages and disadvantages of each.
Highly efficient waveguide phase modulator for integrated optoelectronics (1986)

The characteristics of novel reverse-biased waveguide phase modulators are reported. These devices, which use the translation of a depletion edge, have provided the highest efficiency figure of merit (56 °/Vmm) ever reported for a reverse-biased device. Furthermore, the speed of the device is only limited by the RC time constant. The investigated devices were GaAs/AlGaAs ridge waveguide modulators, a geometry which is well suited for integrated optoelectronics.